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  ✔本篇論文使用華聯產品:Human OneArray  
 Oncoscience. doi:10.18632/oncoscience.285.
 In silico and experimental analyses predict the therapeutic value of an EZH2 inhibitor GSK343 against hepatocellular carcinoma through the induction of metallothionein genes 
 
  Abstract
There are currently no effective molecular targeted therapies for hepatocellular carcinoma (HCC), the third leading cause of cancer-related death worldwide. Enhancer of zeste homolog 2 (EZH2), a histone H3 lysine 27 (H3K27)-specific methyltransferase, has been emerged as novel anticancer target. Our previous study has demonstrated that GSK343, an S-adenosyl-L-methionine (SAM)-competitive inhibitor of EZH2, induces autophagy and enhances drug sensitivity in cancer cells including HCC. In this study, an in silico study was performed and found that EZH2 was overexpressed in cancerous tissues of HCC patients at both gene and protein levels. Microarray analysis and in vitro experiments indicated that the anti-HCC activity of GSK343 was associated with the induction of metallothionein (MT) genes. In addition, the negative association of EZH2 and MT1/MT2A genes in cancer cell lines and tissues was found in public gene expression database. Taken together, our findings suggest that EZH2 inhibitors could be a good therapeutic option for HCC, and induction of MT genes was associated with the anti-HCC activity of EZH2 inhibitors.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 International Journal of Molecular Sciences. doi:10.3390/ijms17010098.
 Optimizing a Male Reproductive Aging Mouse Model by d-Galactose Injection
 
 
 
  Abstract
The d-galactose (d-gal)-injected animal model, which is typically established by administering consecutive subcutaneous d-gal injections to animals for approximately six or eight weeks, has been frequently used for aging research. In addition, this animal model has been demonstrated to accelerate aging in the brain, kidneys, liver and blood cells. However, studies on aging in male reproductive organs that have used this animal model remain few. Therefore, the current study aimed to optimize a model of male reproductive aging by administering d-gal injections to male mice and to determine the possible mechanism expediting senescence processes during spermatogenesis. In this study, C57Bl/6 mice were randomized into five groups (each containing 8–10 mice according to the daily intraperitoneal injection of vehicle control or 100 or 200 mg/kg dosages of d-gal for a period of six or eight weeks). First, mice subjected to d-gal injections for six or eight weeks demonstrated considerably decreased superoxide dismutase activity in the serum and testis lysates compared to those in the control group. The lipid peroxidation in testis also increased in the d-gal-injected groups. Furthermore, the d-gal-injected groups exhibited a decreased ratio of testis weight/body weight and sperm count compared to the control group. The percentages of both immotile sperm and abnormal sperm increased considerably in the d-gal-injected groups compared to those of the control group. To determine the genes influenced by the d-gal injection during murine spermatogenesis, a c-DNA microarray was conducted to compare testicular RNA samples between the treated groups and the control group. The d-gal-injected groups exhibited RNA transcripts of nine spermatogenesis-related genes (Cycl2, Hk1, Pltp, Utp3, Cabyr, Zpbp2, Speer2, Csnka2ip and Katnb1) that were up- or down-regulated by at least two-fold compared to the control group. Several of these genes are critical for forming sperm-head morphologies or maintaining nuclear integration (e.g., cylicin, basic protein of sperm head cytoskeleton 2 (Cylc2), casein kinase 2, alpha prime interacting protein (Csnka2ip) and katanin p80 (WD40-containing) subunit B1 (Katnb1)). These results indicate that d-gal-injected mice are suitable for investigating male reproductive aging.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Scientific Reports . doi: 10.1038/srep19156.
 A novel cell-penetrating peptide suppresses breast tumorigenesis by inhibiting β-catenin/LEF-1 signaling
 
 
 
  Abstract
The inhibition of β-catenin/LEF-1 signaling is an emerging strategy in cancer therapy. However, clinical targeted treatment of the β-catenin/LEF-1 complex remains relatively ineffective. Therefore, development of specific molecular targets is a key approach for identifying new cancer therapeutics. Thus, we attempted to synthesize a peptide (TAT-NLS-BLBD-6) that could interfere with the interaction of β-catenin and LEF-1 at nuclei in human breast cancer cells. TAT-NLS-BLBD-6 directly interacted with β-catenin and inhibited breast cancer cell growth, invasion, migration, and colony formation as well as increased arrest of sub-G1 phase and apoptosis; it also suppressed breast tumor growth in nude mouse and zebrafish xenotransplantation models, showed no signs of toxicity, and did not affect body weight. Furthermore, the human global gene expression profiles and Ingenuity Pathway Analysis software showed that the TAT-NLS-BLBD-6 downstream target genes were associated with the HER-2 and IL-9 signaling pathways. TAT-NLS-BLBD-6 commonly down-regulated 27 candidate genes in MCF-7 and MDA-MB-231 cells, which are concurrent with Wnt downstream target genes in human breast cancer. Our study suggests that TAT-NLS-BLBD-6 is a promising drug candidate for the development of effective therapeutics specific for Wnt/β-catenin signaling inhibition.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 BMC Bioinformatics. doi: 10.1186/s12859-015-0848-x.
 Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis
 
 
 
  Abstract
Background Tuberculosis (TB) is a serious infectious disease in that 90 % of those latently infected with Mycobacterium tuberculosis present no symptoms, but possess a 10 % lifetime chance of developing active TB. To prevent the spread of the disease, early diagnosis is crucial. However, current methods of detection require improvement in sensitivity, efficiency or specificity. In the present study, we conducted a microarray experiment, comparing the gene expression profiles in the peripheral blood mononuclear cells among individuals with active TB, latent infection, and healthy conditions in a Taiwanese population. Results Bioinformatics analysis revealed that most of the differentially expressed genes belonged to immune responses, inflammation pathways, and cell cycle control. Subsequent RT-PCR validation identified four differentially expressed genes, NEMF, ASUN, DHX29, and PTPRC, as potential biomarkers for the detection of active and latent TB infections. Receiver operating characteristic analysis showed that the expression level of PTPRC may discriminate active TB patients from healthy individuals, while ASUN could differentiate between the latent state of TB infection and healthy condidtion. In contrast, DHX29 may be used to identify latently infected individuals among active TB patients or healthy individuals. To test the concept of using these biomarkers as diagnostic support, we constructed classification models using these candidate biomarkers and found the Naïve Bayes-based model built with ASUN, DHX29, and PTPRC to yield the best performance. Conclusions Our study demonstrated that gene expression profiles in the blood can be used to identify not only active TB patients, but also to differentiate latently infected patients from their healthy counterparts. Validation of the constructed computational model in a larger sample size would confirm the reliability of the biomarkers and facilitate the development of a cost-effective and sensitive molecular diagnostic platform for TB.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 BMC cancer. DOI 10.1186/s12885-015-1671-5.
 Upregulation of MicroRNA-19b predicts good prognosis in patients with hepatocellular carcinoma presenting with vascular invasion or multifocal disease
 
 
 
  Abstract
Background After surgical resection of hepatocellular carcinoma (HCC), recurrence is common, especially in patients presenting with vascular invasion or multifocal disease after curative surgery. Consequently, we examined the expression pattern and prognostic value of miR-19b in samples from these patients. Methods We performed a miRNA microarray to detect differential expression of microRNAs (miRNAs) in 5 paired samples of HCC and non-tumoral adjacent liver tissue and a quantitative real-time polymerase chain reaction (PCR) analysis to validate the results in 81 paired samples of HCC and adjacent non-tumoral liver tissues. We examined the associations of miR-19b expression with clinicopathological parameters and survival. MiR-19b was knocked down in Hep3B and an mRNA microarray was performed to detect the affected genes. Results In both the miRNA microarray and real-time PCR, miR-19b was significantly overexpressed in the HCC tumor compared with adjacent non-tumor liver tissues (P < 0.001). The expression of miR-19b was significantly higher in patients who were disease-free 2 years after surgery (P < 0.001). High miR-19b expression levels were associated with higher α-fetoprotein levels (P = 0.017). In the log-rank test, high miR-19b was associated with better disease-free survival (median survival 37.107 vs. 11.357; P = 0.022). In Cox multivariate analysis, high miR-19b predicted better disease-free survival and overall survival (hazards ratio [HR] = 0.453, 95 % confidence interval [CI] = 0.245–0.845, P = 0.013; HR = 0.318, CI = 0.120–0.846, P = 0.022, respectively). N-myc downstream regulated 1 (NDRG1) was downregulated, while epithelial cell adhesion molecule (EPCAM), hypoxia-inducible factor 1-alpha (HIF1A), high-mobility group protein B2 (HMGB2), and mitogen activated protein kinase 14 (MAPK14) were upregulated when miR-19b was knocked down in Hep3B. Conclusions The overexpression of miR-19b was significantly correlated with better disease-free and overall survival in patients with HCC presenting with vascular invasion or multifocal disease after curative surgery. MiR-19b may influence the expression of NDRG1, EPCAM, HMGB2, HIF1A, and MAPK14.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Amino Acids. doi: 10.1007/s00726-015-1956-7. Epub 2015 Mar 24..
 Homocysteine thiolactone and N-homocysteinylated protein induce pro-atherogenic changes in gene expression in human vascular endothelial cells
 
 
 
  Abstract
Genetic or nutritional deficiencies in homocysteine (Hcy) metabolism lead to hyperhomocysteinemia (HHcy) and cause endothelial dysfunction, a hallmark of atherosclerosis. In addition to Hcy, related metabolites accumulate in HHcy but their role in endothelial dysfunction is unknown. Here, we examine how Hcy-thiolactone, N-Hcy-protein, and Hcy affect gene expression and molecular pathways in human umbilical vein endothelial cells. We used microarray technology, real-time quantitative polymerase chain reaction, and bioinformatic analysis with PANTHER, DAVID, and Ingenuity Pathway Analysis (IPA) resources. We identified 47, 113, and 30 mRNAs regulated by N-Hcy-protein, Hcy-thiolactone, and Hcy, respectively, and found that each metabolite induced a unique pattern of gene expression. Top molecular pathways affected by Hcy-thiolactone were chromatin organization, one-carbon metabolism, and lipid-related processes [−log(P value) = 20–31]. Top pathways affected by N-Hcy-protein and Hcy were blood coagulation, sulfur amino acid metabolism, and lipid metabolism [−log(P value)] = 4–11; also affected by Hcy-thiolactone, [−log(P value) = 8–14]. Top disease related to Hcy-thiolactone, N-Hcy-protein, and Hcy was ‘atherosclerosis, coronary heart disease’ [−log(P value) = 9–16]. Top-scored biological networks affected by Hcy-thiolactone (score = 34–40) were cardiovascular disease and function; those affected by N-Hcy-protein (score = 24–35) were ‘small molecule biochemistry, neurological disease,’ and ‘cardiovascular system development and function’; and those affected by Hcy (score = 25–37) were ‘amino acid metabolism, lipid metabolism,’ ‘cellular movement, and cardiovascular and nervous system development and function.’ These results indicate that each Hcy metabolite uniquely modulates gene expression in pathways important for vascular homeostasis and identify new genes and pathways that are linked to HHcy-induced endothelial dysfunction and vascular disease.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 PLOS Genetics. PLOS Genetics doi:10.1371/journal.pgen.1005726.
 fMiRNA-192 and miRNA-204 Directly Suppress lncRNA HOTTIP and Interrupt GLS1-Mediated Glutaminolysis in Hepatocellular Carcinoma
 
 
 
  Abstract
Accumulated evidence demonstrated that long non-coding RNAs (lncRNAs) play a pivotal role in tumorigenesis. However, it is still largely unknown how these lncRNAs were regulated by small ncRNAs, such as microRNAs (miRNAs), at the post-transcriptional level. We here use lncRNA HOTTIP as an example to study how miRNAs impact lncRNAs expression and its biological significance in hepatocellular carcinoma (HCC). LncRNA HOTTIP is a vital oncogene in HCC, one of the deadliest cancers worldwide. In the current study, we identified miR-192 and miR-204 as two microRNAs (miRNAs) suppressing HOTTIP expression via the Argonaute 2 (AGO2)-mediated RNA interference (RNAi) pathway in HCC. Interaction between miR-192 or miR-204 and HOTTIP were further confirmed using dual luciferase reporter gene assays. Consistent with this notion, a significant negative correlation between these miRNAs and HOTTIP exists in HCC tissue specimens. Interestingly, the dysregulation of the three ncRNAs was associated with overall survival of HCC patients. In addition, the posttranscriptional silencing of HOTTIP by miR-192, miR-204 or HOTTIP siRNAs could significantly suppress viability of HCC cells. On the contrary, antagonizing endogenous miR-192 or miR-204 led to increased HOTTIP expression and stimulated cell proliferation. In vivo mouse xenograft model also support the tumor suppressor role of both miRNAs. Besides the known targets (multiple 5’ end HOX A genes, i.e. HOXA13), glutaminase (GLS1) was identified as a potential downstream target of the miR-192/-204-HOTTIP axis in HCC. Considering glutaminolysis as a crucial hallmark of cancer cells and significantly inhibited cell viability after silencingGLS1, we speculate that the miR-192/-204-HOTTIP axis may interrupt HCC glutaminolysis through GLS1 inhibition. These results elucidate that the miR-192/-204-HOTTIP axis might be an important molecular pathway during hepatic cell tumorigenesis. Our data in clinical HCC samples highlight miR-192, miR-204 and HOTTIP with prognostic and potentially therapeutic
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Genomics Data. doi:10.1016/j.gdata.2015.12.013.
 Genome wide expression after different doses of irradiation of a three-dimensional (3D) model of oral mucosal
 
 
 
  Abstract
We evaluated a three-dimensional (3D) human oral cell culture that consisted of two types of cells, oral keratinocytes and fibroblasts as a model of oral mucositis which is a debilitating adverse effect of chemotherapy and radiation treatment. The 3D cell culture model was irradiated with 12 or 2 Gy, and total RNA was collected 6 h after irradiation to compare global gene expression profiles via microarray analysis. Here we provide detailed methods and analysis on these microarray data, which have been deposited in Gene Expression Omnibus (GEO): GSE62395.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Oncotarget. doi:10.18632/oncotarget.6327 .
 Overexpression of HE4 (human epididymis protein 4) enhances proliferation, invasion and metastasis of ovarian cancer
 
 
 
  Abstract
Overexpression of Human epididymis protein 4 (HE4) related with a role in ovarian cancer tumorigenesis while little is known about the molecular mechanism alteration by HE4 up regulation. Here we reported that overexpressed HE4 promoted ovarian cancer cells proliferation, invasion and metastasis. Furthermore, human whole genome gene expression profile microarrays revealed that 231 differentially expressed genes (DEGs) were altered in response to HE4, in which MAPK signaling, ECM receptor, cell cycle, steroid biosynthesis pathways were involved. The findings suggested that overexpressed HE4 played an important role in ovarian cancer progression and metastasis and that HE4 has the potential to serve as a novel therapeutic target for ovarian cancer.
   

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 Human Immunology. doi:10.1016/j.humimm.2015.09.033. Epub 2015 Sep 30..
 Functional relevance for type 1 diabetes mellitus-associated genetic variants by using integrative analyses
 
 
 
  Abstract
Type 1 diabetes mellitus (type 1 DM) is an autoimmune disease. Although genome-wide association studies (GWAS) and meta-analyses have successfully identified numerous type 1 DM-associated susceptibility loci, the underlying mechanisms for these susceptibility loci are currently largely unclear.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Prostate. doi: 10.1002/pros.23068. Epub 2015 Aug 26..
 Hsa-miR-146a-5p modulates androgen-independent prostate cancer cells apoptosis by targeting ROCK1
 
 
 
  Abstract
Background MicroRNAs (miRNAs) have been demonstrated playing important roles in the procession of prostate cancer cells transformation from androgen-dependence to androgen-independence. Methods We conducted the miRNA microarray and realtime PCR analyses in both androgen-dependent (ADPC) and androgen-independent prostate cancer (AIPC) tissues. We also explored the role of hsa-miR-146a-5p (miR-146a) in MSKCC prostate cancer clinical database. Moreover, the impact of miR-146a on prostate cancer cells apoptosis were detected by Hoechst staining and fluorescence-activated cell sorter (FACS). Its target is predicted by DIANA LAB online database and the result was assumed by western blotting and luciferase assay. Results We demonstrated that miR-146a was down-regulated in AIPC tissues and cell lines compared to that in the ADPC tissues. In MSKCC data re-analyses, we found that miR-146a was underexpressed in metastatic prostate cancer tissues and those with Gleason score >8, moreover, low level of miR-146a represented a high biochemical relapse rate after radical prostatectomy. In the functional analyses, we transfected miR-146a mimics into CPRC cell lines and found miR-146a induced cells apoptosis. In mechanic analyses, we found that miR-146a inhibited the basal level of Rho-associated, coiled-coil containing protein kinase 1 (ROCK1) expression by targeting its 3'UTR and an inverse correlation of expression between miR-146a and ROCK1 was observed. Moreover, caspase 3 activity was stimulated by miR-146a overexpression. Conclusion miR-146a has a critical role in the process of AIPC prostate cancer cells apoptosis through regulation of ROCK/Caspase 3 pathway. Targeting this pathway may be a promising therapeutic strategy for future personalized anti-cancer treatment.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Cellular and Molecular Biology Letters. DOI: 10.1515/cmble-2015-0034.
 Mechanical Strain Affects Some Microrna Profiles in Pre-Oeteoblasts
 
 
 
  Abstract
MicroRNAs (miRNAs) are important regulators of cell proliferation, differentiation and function. Mechanical strain is an essential factor for osteoblast proliferation and differentiation. A previous study revealed that a physiological mechanical tensile strain of 2500 microstrain (με) at 0.5 Hz applied once a day for 1 h over 3 consecutive days promoted osteoblast differentiation. However, the mechanoresponsive miRNAs of these osteoblasts were not identified. In this study, we applied the same mechanical tensile strain to in vitro cultivated mouse MC3T3-E1 pre-osteoblasts and identified the mechanoresponsive miRNAs. Using miRNA microarray and qRT-PCR assays, the expression patterns of miRNAs were evaluated and 5 of them were found to be significantly different between the mechanical loading group and the control group: miR-3077-5p, 3090-5p and 3103-5p were significantly upregulated and miR-466i-3p and 466h-3p were downregulated. Bioinformatics analysis revealed possible target genes for these differentially expressed miRNAs. Some target genes correlated with osteoblast differentiation. These findings indicated that the mechanical strain changed the expression levels of these miRNAs. This might be a potential regulator of osteoblast differentiation and responses to mechanical strain.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Histochemistry and Cell Biology. doi: 10.1007/s00418-015-1348-9..
 Impact of diethylhexyl phthalate on gene expression and development of mammary glands of pregnant mouse.
 
 
 
  Abstract
The widely used diethylhexyl phthalate (DEHP) is a known endocrine disruptor that causes persistent alterations in the structure and function of female reproductive system, including ovaries, uterus and oviducts. To explore the molecular mechanism of the effect of DEHP on the development of mammary glands, we investigated the cell cycle, growth, proliferation and gene expression of mammary gland cells of pregnant mice exposed to DEHP. It was demonstrated, for the first time, that the mammary gland cells of pregnant mice treated with DEHP for 0.5–3.5 days post-coitum had increased proliferation, growth rate and number of cells in the G2/S phase. The expression of cell proliferation-related genes was significantly altered after short time and low-dose DEHP treatment of mammary gland cells in vivo and in vitro. These findings showed adverse effects of DEHP on mammary gland cells in pregnant mice.
   

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 biochemical biophysical research communications. doi:10.1016/j.bbrc.2015.07.057.
 Regulation of tumorigenesis and metastasis of hepatocellular carcinoma tumor endothelial cells by microRNA-3178 and underlying mechanism
 
 
 
  Abstract
This study explored the effects of microRNA-3178 (miR-3178) on hepatocellular carcinoma (HCC) tumor endothelial cells (TECs) and on the target mRNA. Real-time polymerase chain reaction (PCR) was performed to detect the differential expression of miR-3178 in hepatic sinusoidal endothelial cells (HSECs) and HCC TECs. Furthermore, HCC TECs were transfected with miR-3178 mimic/inhibitor or their respective negative controls. The expression of miR-3178 before and after transfection was confirmed through RT-PCR. The effects of miR-3178 on the proliferation, apoptosis, cell cycle, invasion, migration, and angiogenesis of HCC TECs were also investigated through methyl thiazol tetrazolium assay, flow cytometry, matrigel invasion assay, transwell migration assay, and tube formation assay. Early growth responsive gene 3 (EGR3), as the putative target of miR-3178, was detected through RT-PCR and Western blot. Compared with HSECs, HCC TECs had lower miR-3178 expression levels (P < 0.001). MiR-3178 mimic inhibited proliferation, arrested cell cycle in G1 phase, and increased apoptosis. The numbers of migrated and invaded cells and capillary-like structures were significantly less in the mimic group than in the other groups. MiR-3178 mimic significantly decreased the mRNA and protein expression levels of EGR3. By contrast, miR-3178 inhibitor induced opposite effects. We conclude that miR-3178 was lowly expressed in HCC TECs, and miR-3178 mimic specifically inhibited the proliferation, migration, invasion, and angiogenesis and promoted the apoptosis and G1 phase arrest of HCC TECs in vitro through the inhibition of EGR3 expression. Thus, miR-3178 might be a critical target in HCC therapy.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 BMC GENOMICS. doi: 10.1186/s12864-015-1896-3..
 Weight-reduction through a low-fat diet causes differential expression of circulating microRNAs in obese C57BL/6 mice
 
 
 
  Abstract
Background To examine the circulating microRNA (miRNA) expression profile in a mouse model of diet-induced obesity (DIO) with subsequent weight reduction achieved via low-fat diet (LFD) feeding. Results Eighteen C57BL/6NCrl male mice were divided into three subgroups: (1) control, mice were fed a standard AIN-76A (fat: 11.5 kcal %) diet for 12 weeks; (2) DIO, mice were fed a 58 kcal % high-fat diet (HFD) for 12 weeks; and (3) DIO + LFD, mice were fed a HFD for 8 weeks to induce obesity and then switched to a 10.5 kcal % LFD for 4 weeks. A switch to LFD feeding led to decreases in body weight, adiposity, and blood glucose levels in DIO mice. Microarray analysis of miRNA using The Mouse & Rat miRNA OneArray® v4 system revealed significant alterations in the expression of miRNAs in DIO and DIO + LFD mice. Notably, 23 circulating miRNAs (mmu-miR-16, mmu-let-7i, mmu-miR-26a, mmu-miR-17, mmu-miR-107, mmu-miR-195, mmu-miR-20a, mmu-miR-25, mmu-miR-15b, mmu-miR-15a, mmu-let-7b, mmu-let-7a, mmu-let-7c, mmu-miR-103, mmu-let-7f, mmu-miR-106a, mmu-miR-106b, mmu-miR-93, mmu-miR-23b, mmu-miR-21, mmu-miR-30b, mmu-miR-221, and mmu-miR-19b) were significantly downregulated in DIO mice but upregulated in DIO + LFD mice. Target prediction and function annotation of associated genes revealed that these genes were predominantly involved in metabolic, insulin signaling, and adipocytokine signaling pathways that directly link the pathophysiological changes associated with obesity and weight reduction. Conclusions These results imply that obesity-related reductions in the expression of circulating miRNAs could be reversed through changes in metabolism associated with weight reduction achieved through LFD feeding.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Nature Cell Biology. 2015, 17(3):311-21. doi: 10.1038/ncb3110.
 Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis
 
 
 Einav Shoshan, Aaron K. Mobley, Russell R. Braeuer, Takafumi Kamiya, Li Huang, Mayra E. Vasquez, Ahmad Salameh, Ho Jeong Lee, Sun Jin Kim, Cristina Ivan, Guermarie Velazquez-Torres, Ka Ming Nip, Kelsey Zhu, Denise Brooks, Steven J. M. Jones, Inanc Birol,Maribel Mosqueda, Yu-ye Wen, Agda Karina Eterovic, Anil K. Sood, Patrick Hwu, Je rey E. Gershenwald, A. Gordon Robertson, George A. Calin, GalMarkel, Isaiah J. Fidler, Menashe Bar-Eli
  Abstract
Although recent studies have shown that adenosine-to-inosine (A-to-I) RNA editing occurs in microRNAs (miRNAs), its effects on tumour growth and metastasis are not well understood. We present evidence of CREB-mediated low expression of ADAR1 in metastatic melanoma cell lines and tumour specimens. Re-expression of ADAR1 resulted in the suppression of melanoma growth and metastasis in vivo. Consequently, we identified three miRNAs undergoing A-to-I editing in the weakly metastatic melanoma but not in strongly metastatic cell lines. One of these miRNAs, miR-455-5p, has two A-to-I RNA-editing sites. The biological function of edited miR-455-5p is different from that of the unedited form, as it recognizes a different set of genes. Indeed, wild-type miR-455-5p promotes melanoma metastasis through inhibition of the tumour suppressor gene CPEB1. Moreover, wild-type miR-455 enhances melanoma growth and metastasis in vivo, whereas the edited form inhibits these features. These results demonstrate a previously unrecognized role for RNA editing in melanoma progression.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Journal of Experimental Medicine. 2015, 212(3):333-49. doi: 10.1084/jem.20141702.
 Targeting IL-17B¡VIL-17RB signaling with an anti¡VIL-17RB antibody blocks pancreatic cancer metastasis by silencing multiple chemokines
 
 
 Heng-Hsiung Wu, Wendy W. Hwang-Verslues, Wen-Hsin Lee, Chun-Kai Huang, Pei-Chi Wei, Chia-Lin Chen, Jin-Yuh Shew, Eva Y.-H.P. Lee, Yung-Ming Jeng, Yu-Wen Tien, Che Ma, Wen-Hwa Lee
  Abstract
Pancreatic cancer has an extremely high mortality rate due to its aggressive metastatic nature. Resolving the underlying mechanisms will be crucial for treatment. Here, we found that overexpression of IL-17B receptor (IL-17RB) strongly correlated with postoperative metastasis and inversely correlated with progression-free survival in pancreatic cancer patients. Consistently, results from ex vivo experiments further validated that IL-17RB and its ligand, IL-17B, plays an essential role in pancreatic cancer metastasis and malignancy. Signals from IL-17B¡VIL-17RB activated CCL20/CXCL1/IL-8/TFF1 chemokine expressions via the ERK1/2 pathway to promote cancer cell invasion, macrophage and endothelial cell recruitment at primary sites, and cancer cell survival at distant organs. Treatment with a newly derived monoclonal antibody against IL-17RB blocked tumor metastasis and promoted survival in a mouse xenograft model. These findings not only illustrate a key mechanism underlying the highly aggressive characteristics of pancreatic cancer but also provide a practical approach to tackle this disease.
   

  ✔本篇論文使用華聯產品:Data Analysis  
 Scientific Reports. 2015, 5:8886. doi: 10.1038/srep08886.
 Dietary Methionine Restriction in Mice Elicits an Adaptive Cardiovascular Response to Hyperhomocysteinemia
 
 
 Amadou Ouattara, Thomas G. Hampton, Diana Cooke, Frantz Perodin, Ines Augie, David S. Orentreich, Gene P. Ables
  Abstract
Dietary methionine restriction (MR) in rodents increased lifespan despite higher heart-to-body weight ratio (w/w) and hyperhomocysteinemia, which are symptoms associated with increased risk for cardiovascular disease. We investigated this paradoxical effect of MR on cardiac function using young, old, and apolipoprotein E-deficient (ApoE-KO) mice. Indeed, MR animals exhibited higher heart-to-body weight ratio (w/w) and hyperhomocysteinemia with a molecular pattern consistent with cardiac stress while maintaining the integrity of cardiac structure. Baseline cardiac function, which was measured by non-invasive electrocardiography (ECG), showed that young MR mice had prolonged QRS intervals compared with control-fed (CF) mice, whereas old and ApoE-KO mice showed similar results for both groups. Following £]-adrenergic challenge, responses of MR mice were either similar or attenuated compared with CF mice. Cardiac contractility, which was measured by isolated heart retrograde perfusion, was similar in both groups of old mice. Finally, the MR diet induced secretion of cardioprotective hormones, adiponectin and fibroblast growth factor 21 (FGF21), in MR mice with concomitant alterations in cardiac metabolic molecular signatures. Our findings demonstrate that MR diet does not alter cardiac function in mice despite the presence of hyperhomocysteinemia because of the adaptive responses of increased adiponectin and FGF21 levels.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 RNA Biology. 2015, 12(3):343-53. doi: 10.1080/15476286.2015.1017205.
 miR-214 promotes osteoclastogenesis by targeting Pten/PI3k/Akt pathway
 
 
 Chenyang Zhao, Weijia Sun, Pengfei Zhang, Shukuan Ling, Yuheng Li, Dingsheng Zhao, Jiang Peng, Aiyuan Wang, Qi Li, Jinping Song, Cheng Wang, Xiaolong Xu, Zi Xu, Guohui Zhong, Bingxing Han, Yan-Zhong Chang, Yingxian Li
  Abstract
microRNA is necessary for osteoclast differentiation, function and survival. It has been reported that miR-199/214 cluster plays important roles in vertebrate skeletal development and miR-214 inhibits osteoblast function by targeting ATF4. Here, we show that miR-214 is up-regulated during osteoclastogenesis from bone marrow monocytes (BMMs) with macrophage colony stimulating factor (M-CSF) and receptor activator of nuclear factor-£eB ligand (RANKL) induction, which indicates that miR-214 plays a critical role in osteoclast differentiation. Overexpression of miR-214 in BMMs promotes osteoclastogenesis, whereas inhibition of miR-214 attenuates it. We further find that miR-214 functions through PI3K/Akt pathway by targeting phosphatase and tensin homolog (Pten). In vivo, osteoclast specific miR-214 transgenic mice (OC-TG214) exhibit down-regulated Pten levels, increased osteoclast activity, and reduced bone mineral density. These results reveal a crucial role of miR-214 in the differentiation of osteoclasts, which will provide a potential therapeutic target for osteoporosis.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Histochemistry and Cell Biology. 2015 Jul 14.
 Impact of diethylhexyl phthalate on gene expression and development of mammary glands of pregnant mouse
 
 
 Lan Li, Jing‑Cai Liu, Yong Zhao, Fang‑Nong Lai, Fan Yang, Wei Ge, Cheng‑Li Dou, Xi‑Feng Zhang, Hong Chen, Wei Shen
  Abstract
The widely used diethylhexyl phthalate (DEHP) is a known endocrine disruptor that causes persistent alterations in the structure and function of female reproductive system, including ovaries, uterus and oviducts. To explore the molecular mechanism of the effect of DEHP on the development of mammary glands, we investigated the cell cycle, growth, proliferation and gene expression of mammary gland cells of pregnant mice exposed to DEHP. It was demonstrated, for the first time, that the mammary gland cells of pregnant mice treated with DEHP for 0.5-3.5 days post-coitum had increased proliferation, growth rate and number of cells in the G2/S phase. The expression of cell proliferation-related genes was significantly altered after short time and low-dose DEHP treatment of mammary gland cells in vivo and in vitro. These findings showed adverse effects of DEHP on mammary gland cells in pregnant mice.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Scientific Reports. 2015, ;5:12061. doi: 10.1038/srep12061.
 Nogo-B protects mice against lipopolysaccharide-induced acute lung injury
 
 
 Wujian Xu, Ying Zhu, Yunye Ning, Yuchao Dong, Haidong Huang, Wei Zhang, Qinying Sun, Qiang Li
  Abstract
Nogo-B, a member of the reticulon 4 protein family, plays a critical role in tissue repair and acute inflammation. Its role in acute lung injury (ALI) remains unclear. Here, we assessed the function of Nogo-B during tissue injury in a lipopolysaccharide (LPS)-induced ALI mouse model. We found that pulmonary Nogo-B was significantly repressed after LPS instillation in C57BL/6 mice. Over-expression of pulmonary Nogo-B using an adenovirus vector carrying the Nogo-B-RFP-3flag gene (Ad-Nogo-B) significantly prolonged the survival of mice challenged with a lethal dose of LPS. The Ad-Nogo-B-treated mice also had less severe lung injury, less alveolar protein exudation, and a higher number of macrophages but less neutrophil infiltration compared with Ad-RFP-treated mice. Interestingly, microarray analysis showed that the Ad-Nogo-B-treated mice had different gene expression profiles compared with the controls and the prominent expression of genes related to wound healing and the humoral immune response after LPS induction. Of the 49 differently expressed genes, we found that the expression of PTX3 was significantly up-regulated following Nogo-B over-expression as observed in lung tissues and RAW264.7 cells. In conclusion, Nogo-B plays a protective role against LPS-induced ALI, and this effect might be exerted through the modulation of alveolar macrophage recruitment and PTX3 production.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Journal Of Biological Chemistry. 2015, 290(14):9101-10. doi: 10.1074/jbc.M114.631580.
 Gefitinib-mediated ROS instigates mitochondrial dysfunction and drug resistance in lung cancer cells
 
 
 Imoh S. Okon, Kathleen A. Coughlan, Miao Zhang, Qiongxin Wang, Ming-Hui Zou
  Abstract
Therapeutic benefits offered by tyrosine kinase inhibitors (TKIs), such as gefitinib (Iressa) and erlotinib (Tarceva), are limited due to the development of resistance, which contributes to treatment failure and cancer-related mortality. The aim of this study was to elucidate mechanistic insight into cellular perturbations that accompany acquired gefitinib resistance in lung cancer cells. Several lung adenocarcinoma (LAD) cell lines were screened to characterize epidermal growth factor receptor (EGFR) expression and mutation profile. To circumvent intrinsic variations between cell lines with respect to response to drug treatments, we generated gefitinib-resistant H1650 clone by long-term, chronic culture under gefitinib selection of parental cell line. Isogenic cells were analyzed by microarray, Western blot, flow cytometry, and confocal and transmission electron microscope. We observed that although chronic gefitinib treatment provided effective action against its primary target (aberrant EGFR activity), secondary effects resulted in increased cellular reactive oxygen species (ROS). Gefitinib-mediated ROS correlated with epithelial-mesenchymal transition, as well as striking perturbation of mitochondrial morphology and function. However, gefitinib treatment in the presence of ROS scavenger provided a partial rescue of mitochondrial aberrations. Furthermore, withdrawal of gefitinib from previously resistant clones correlated with normalized expression of epithelial-mesenchymal transition genes. These findings demonstrate that chronic gefitinib treatment promotes ROS and mitochondrial dysfunction in lung cancer cells. Antioxidants may alleviate ROS-mediated resistance.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Journal of Experimental & Clinical Cancer Research. 2015, 12;34:16. doi: 10.1186/s13046-015-0132-y.
 Gene expression profile analyze the molecular mechanism of CXCR7 regulating papillary thyroid carcinoma growth and metastasi
 
 
 Hengwei Zhang, Xuyong Teng, Zhangyi Liu, Lei Zhang, Zhen Liu
  Abstract
Background: To detect genetic expression profile alterations after papillary thyroid carcinoma (PTC) cells transfected with chemokine receptor CXCR7 gene by gene microarray, and gain insights into molecular mechanisms of how CXCR7 regulating PTC growth and metastasis. Methods: The Human OneArray microarray was used for a complete genome-wide transcript profiling of CXCR7 transfected PTCs (K1-CXCR7 cells), defined as experimental group. Non CXCR7 transfected PTCs (K1 cells) were used as control group. Differential analysis for per gene was performed with a random variance model and t test, p values were adjusted to control the false discovery rate. Gene ontology (GO) on differentially expressed genes to identify the biological processes in modulating the progression of papillary thyroid carcinoma. Pathway analysis was used to evaluate the signaling pathway that differentially expressed genes were involved in. In addition, quantitative real-time polymerase chain reaction (q-PCR) and Western blot were used to verify the top differentially expression genes. Results: Comparative analysis revealed that the expression level of 1149 genes was changed in response to CXCR7 transfection. After unsupervised hierarchical clustering analysis, 270 differentially expressed genes were filtered, of them 156 genes were up-regulated whereas 114 genes were down-regulated in K1-CXCR7 cells. GO enrichment analysis revealed the differentially expressed genes were mainly involved in biopolymer metabolic process, signal transduction and protein metabolism. Pathway enrichment analysis revealed differentially expressed genes were mainly involved in ECM-receptor interaction, Focal adhesion, MAPK signaling pathway and Cytokine-cytokine receptor interaction pathway. More importantly, the expression level of genes closely associated with tumor growth and metastasis was altered significantly in K1-CXCR7 cells, including up-regulated genes FN1, COL1A1, COL4A1, PDGFRB, LTB, CXCL12, MMP-11, MT1-MMP and down-regulated genes ITGA7, and Notch-1. Conclusions: Gene expression profiling analysis of papillary thyroid carcinoma can further delineate the mechanistic insights on how CXCR7 regulating papillary thyroid carcinoma growth and metastasis. CXCR7 may regulate growth and metastasis of papillary thyroid carcinoma via the activation of PI3K/AKT pathway and its downstream NF-£eB signaling, as well as the down-regulation of Notch signaling.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Annals of Thoracic Surgery. 2015, 99(4):1149-56. doi: 10.1016/j.athoracsur.2014.08.085.
 Ex vivo four-dimensional lung cancer model mimics metastasis
 
 
 Dhruva K. Mishra, Chad J. Creighton, Yiqun Zhang, Fengju Chen, Michael J. Thrall, Min P. Kim
  Abstract
BACKGROUND: We have developed a four-dimensional (4D) lung cancer model that forms perfusable tumor nodules. We determined if the model could be modified to mimic metastasis. METHODS: We modified the 4D lung cancer model by seeding H1299, A549, or H460 cells through the trachea only to the left lobes of the acellular lung matrix. The model was modified so that the tumor cells can reach the right lobes of the acellular lung matrix only through the pulmonary artery as circulating tumor cells (CTC). We determined the gene expressions of the primary tumor, CTCs, and metastatic lesions using the Human OneArray chip. RESULTS: All cell lines formed a primary tumor in the left lobe of the ex vivo 4D lung cancer model. The CTCs were identified in the media and increased over time. All cell lines formed metastatic lesions with H460 forming significantly more metastatic lesions than H1299 and A549 cells. The CTC gene signature predicted poor survival in lung cancer patients. Unique genes were significantly expressed in CTC compared with the primary tumor and metastatic lesion. CONCLUSIONS: The 4D lung cancer model can isolate tumor cells in 3 phases of tumor progression. This 4D lung cancer model may mimic the biology of lung cancer metastasis and may be used to determine its mechanism and potential therapy in the future.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Molecular and Cellular Biology. 2015, 35(7):1223-37. doi: 10.1128/MCB.00993-14.
 p54nrb/NONO Regulates Cyclic AMP-Dependent Glucocorticoid Production by Modulating Phosphodiesterase mRNA Splicing and Degradation
 
 
 Jia Yang Lu, Marion B. Sewer
  Abstract
Glucocorticoid production in the adrenal cortex is activated in response to an increase in cyclic AMP (cAMP) signaling. The nuclear protein p54(nrb)/NONO belongs to the Drosophila behavior/human splicing (DBHS) family and has been implicated in several nuclear processes, including transcription, splicing, and RNA export. We previously identified p54(nrb)/NONO as a component of a protein complex that regulates the transcription of CYP17A1, a gene required for glucocorticoid production. Based on the multiple mechanisms by which p54(nrb)/NONO has been shown to control gene expression and the ability of the protein to be recruited to the CYP17A1 promoter, we sought to further define the molecular mechanism by which p54(nrb)/NONO confers optimal cortisol production. We show here that silencing p54(nrb)/NONO expression in H295R human adrenocortical cells decreases the ability of the cells to increase intracellular cAMP production and subsequent cortisol biosynthesis in response to adrenocorticotropin hormone (ACTH) stimulation. Interestingly, the expression of multiple phosphodiesterase (PDE) isoforms, including PDE2A, PDE3A, PDE3B, PDE4A, PDE4D, and PDE11A, was induced in p54(nrb)/NONO knockdown cells. Investigation of the mechanism by which silencing of p54(nrb)/NONO led to increased expression of select PDE isoforms revealed that p54(nrb)/NONO regulates the splicing of a subset of PDE isoforms. Importantly, we also identify a role for p54(nrb)/NONO in regulating the stability of PDE transcripts by facilitating the interaction between the exoribonuclease XRN2 and select PDE transcripts. In summary, we report that p54(nrb)/NONO modulates cAMP-dependent signaling, and ultimately cAMP-stimulated glucocorticoid biosynthesis by regulating the splicing and degradation of PDE transcripts.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Journal of Allergy and Clinical Immunology. 2015, 136(1):59-68.e14. doi: 10.1016/j.jaci.2014.11.037.
 Persistence of asthma requires multiple feedback circuits involving type 2 innate lymphoid cells and IL-33
 
 
 Christianson CA, Goplen NP, Zafar I, Irvin C, Good JT Jr, Rollins DR, Gorentla B, Liu W, Gorska MM, Chu H, Martin RJ, Rafeul Alam
  Abstract
BACKGROUND: Asthma in a mouse model spontaneously resolves after cessation of allergen exposure. We developed a mouse model in which asthma features persisted for 6 months after cessation of allergen exposure. OBJECTIVE: We sought to elucidate factors contributing to the persistence of asthma. METHODS: We used a combination of immunologic, genetic, microarray, and pharmacologic approaches to dissect the mechanism of asthma persistence. RESULTS: Elimination of T cells though antibody-mediated depletion or lethal irradiation and transplantation of recombination-activating gene (Rag1)(-/-) bone marrow in mice with chronic asthma resulted in resolution of airway inflammation but not airway hyperreactivity or remodeling. Elimination of T cells and type 2 innate lymphoid cells (ILC2s) through lethal irradiation and transplantation of Rag2(-/-)£^c(-/-) bone marrow or blockade of IL-33 resulted in resolution of airway inflammation and hyperreactivity. Persistence of asthma required multiple interconnected feedback and feed-forward circuits between ILC2s and epithelial cells. Epithelial IL-33 induced ILC2s, a rich source of IL-13. The latter directly induced epithelial IL-33, establishing a positive feedback circuit. IL-33 autoinduced, generating another feedback circuit. IL-13 upregulated IL-33 receptors and facilitated IL-33 autoinduction, thus establishing a feed-forward circuit. Elimination of any component of these circuits resulted in resolution of chronic asthma. In agreement with the foregoing, IL-33 and ILC2 levels were increased in the airways of asthmatic patients. IL-33 levels correlated with disease severity. CONCLUSIONS: We present a critical network of feedback and feed-forward interactions between epithelial cells and ILC2s involved in maintaining chronic asthma. Although T cells contributed to the severity of chronic asthma, they were redundant in maintaining airway hyperreactivity and remodeling.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Tumor Biology. 2015, 36(1):219-25. doi: 10.1007/s13277-014-2622-5.
 miR-1285-3p acts as a potential tumor suppressor miRNA via downregulating JUN expression in hepatocellular carcinoma
 
 
 Jibing Liu, Jingchen Yan, Changchun Zhou, Zhenbin Yang, Qinghua Ma, Qingyan Jin
  Abstract
In the world, hepatocellular carcinoma (HCC) is one of the most common and most lethal cancers. Currently, standard therapy for unresectable HCC is a local-regional therapy with transarterial chemoembolisation (TACE). In this study, we sought to assess whether plasma circulating microRNAs (miRNAs) can be used to predict the prognosis of HCC patients receiving the TACE treatment. Firstly, we systematically examined TACE therapeutic effectiveness-related circulating miRNAs through miRNA Profiling Chips. As a result, we identified 19 circulating miRNAs to be significantly differentially expressed between the TACE-response group and the TACE-nonresponse group. In the second stage, we performed quantitative analyses of these candidate miRNAs in additional HCC patients treated with TACE and validated two of the aforementioned 19 miRNAs (miR-1285-3p and miR-4741) as candidate biomarkers for predicting prognosis of TACE. Interestingly, we found that miR-1285-3p could directly repress JUN oncogene expression in HCC cells, indicating miR-1285-3p could act as a potential tumor suppressor. In conclusion, our data indicate that circulating miR-1285-3p and miR-4741 was predictive of response to TACE therapy in HCC.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Science Signaling. 2015, 8(375):ra41. doi: 10.1126/scisignal.2005781.
 Actin cytoskeletal remodeling with protrusion formation is essential for heart regeneration in Hippo-deficient mice
 
 
 Yuka Morikawa, Min Zhang, Todd Heallen, John Leach, Ge Tao, Yang Xiao, Yan Bai, Wei Li, James T. Willerson, James F. Martin
  Abstract
The mammalian heart regenerates poorly, and damage commonly leads to heart failure. Hippo signaling is an evolutionarily conserved kinase cascade that regulates organ size during development and prevents adult mammalian cardiomyocyte regeneration by inhibiting the transcriptional coactivator Yap, which also responds to mechanical signaling in cultured cells to promote cell proliferation. To identify Yap target genes that are activated during cardiomyocyte renewal and regeneration, we performed Yap chromatin immunoprecipitation sequencing (ChIP-Seq) and mRNA expression profiling in Hippo signaling¡Vdeficient mouse hearts. We found that Yap directly regulated genes encoding cell cycle progression proteins, as well as genes encoding proteins that promote F-actin polymerization and that link the actin cytoskeleton to the extracellular matrix. Included in the latter group were components of the dystrophin glycoprotein complex, a large molecular complex that, when defective, results in muscular dystrophy in humans. Cardiomyocytes near the scar tissue of injured Hippo signaling¡Vdeficient mouse hearts showed cellular protrusions suggestive of cytoskeletal remodeling. The hearts of mdx mutant mice, which lack functional dystrophin and are a model for muscular dystrophy, showed impaired regeneration and cytoskeleton remodeling, but normal cardiomyocyte proliferation, after injury. Our data showed that, in addition to genes encoding cell cycle progression proteins, Yap regulated genes that enhance cytoskeletal remodeling. Thus, blocking the Hippo pathway input to Yap may tip the balance so that Yap responds to mechanical changes associated with heart injury to promote repair.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 OncoImmunology. 2015 Apr 16. doi:10.1080/2162402X.2015.1040215.
 Blockade of TNF-£ signaling benefits cancer therapy by suppressing effector regulatory T cell expansion
 
 
 Li-Yuan Chang, Yung-Chang Lin, Jy-Ming Chiang, Jayashri Mahalingam, Shih-Huan Su, Ching-Tai Huang, Wei-Ting Chen, Chien-Hao Huang, Wen-Juei Jeng, Yi-Cheng Chen, Shi-Ming Lin, I-Shyan Sheen, Chun-Yen Lin
  Abstract
Effector but not naïve regulatory T cells (Treg cells) can accumulate in the peripheral blood as well as the tumor microenvironment, expand during tumor progression and be one of the main suppressors for anti-tumor immunity. However, the underlying mechanisms for effector Treg cell expansion in tumor are still unknown. We demonstrate that effector Treg cell-mediated suppression of anti-tumor CD8+ T cells is tumor non-specific. Furthermore, TNFR2 expression is increased in these Treg cells by Affymetrix chip analysis which was confirmed by monoclonal antibody staining in both hepatocellular carcinoma and colorectal cancer patients and murine models. Correspondingly, increased levels of TNF-£ in both tissue and serum were also demonstrated. Interestingly, TNF-£ could not only expand effector Treg cells through TNFR2 signaling, but also enhanced their suppressive activity against anti-tumor immunity of CD8+ T cells. Furthermore, targeting TNFR2 signaling with a TNF-£ inhibitor could selectively reduce rapid resurgence of effector Treg cells after cyclophosphamide-induced lymphodepletion and markedly inhibit the growth of established tumors. Herein, we propose a novel mechanism in which TNF-£ could promote tumor-associated effector Treg cell expansion and suggest a new cancer immunotherapy strategy using TNF-£ inhibitors to reduce effector Treg cells expansion after cyclophosphamide-induced lymphodepletion.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Oncogene. 2015, 34(10):1207-19. doi: 10.1038/onc.2014.43.
 B-cell lymphoma/leukemia 10 promotes oral cancer progression through STAT1/ATF4/S100P signaling pathway
 
 
 T-S Wu, C-T Tan, C-C Chang, B-R Lin, W-T Lai, S-T Chen, M Yen-Ping Kuo, C-L Rau, F-S Jaw, H-H Chang
  Abstract
B-cell lymphoma/leukemia 10 (BCL10) is an apoptotic regulatory protein related to advanced TNM stage and disease recurrence in oral squamous cell carcinoma (OSCC). However, the regulatory mechanism of BCL10 in OSCC progression is still unknown. Here, we showed that knockdown of endogenous BCL10 could significantly reduce cell migration and invasion abilities, retard cell proliferation by G0/G1 phase accumulation and inhibit tumorigenicity in vivo. In molecular level, we identified S100P as a crucial downstream effector of BCL10-inhibited OSCC progression by high-throughput microarray analysis. S100P messenger RNA and protein expression levels were significantly diminished in silenced-BCL10 clones, and transfected S100P expression plasmids restored migration, invasion, proliferation abilities and tumorigenicity in shBCL10 transfectants. Furthermore, we provided evidence that BCL10 regulated S100P expression through signal transducers and activators of transcription 1 (STAT1) and activating transcription factor 4 (ATF4). Knockdown of BCL10 decreased S100P promoter activity, but showed no effect in truncated STAT1/ATF4 S100P promoter. In addition, we also found that the P50/P65 signaling pathway was involved in BCL10-enhanced OSCC progression. Restored S100P in silenced-BCL10 clones could markedly reverse P65 activation via outside-in signaling. Taken together, we discovered a novel axis of BCL10-regulated OSCC progression via STAT1/ATF4/S100P/P65 signaling, which could predict the prognosis of OSCC and will be beneficial for developing therapeutic strategy against advanced OSCC.
   

  ✔本篇論文使用華聯產品:Rat OneArray  
 PLoS One. 2015, 10(5):e0127352. doi: 10.1371/journal.pone.0127352. eCollection 2015.
 S100A9: A Potential Biomarker for the Progression of Non-Alcoholic Fatty Liver Disease and the Diagnosis of Non-Alcoholic Steatohepatitis
 
 
 Xiaolin Liu, Yongfeng Wang, Yanan Ming, Yanyan Song, Jingyi Zhang, Xiaoyu Chen, Minde Zeng, Yimin Mao
  Abstract
Non-alcoholic fatty liver (NAFL) has the potential to progress to non-alcoholic steatohepatitis (NASH) or to promote type 2 diabetes mellitus (T2DM). However, NASH and T2DM do not always develop coordinately. Additionally, there are no definite noninvasive methods for NASH diagnosis currently. We established rat models of NAFL, NASH, and NAFL + T2DM to recapitulate different phenotypes associated with non-alcoholic fatty liver disease (NAFLD) and its progression. Histologic features of rat livers were scored according to criteria established by the Nonalcoholic Steatohepatitis Clinical Research Network. Microarray was performed to assess gene expression changes in rat livers. We find that gene expression of s100a9 was higher in NAFL group compared with control, and was increased in NASH groups and decreased in NAFL + T2DM group compared with NAFL. In contrast, srebf1, tbx21, and gimap4 only showed limited discriminating abilities in different groups. There is a significant positive correlation between serum levels of S100A9 and NAFLD Activity Score (NAS), the severity of hepatic steatosis, and lobular inflammation (r = 0.80, 0.64 and 0.86, P < 0.001). These findings suggest that S100A9 may be extremely useful in the diagnosis of NASH (AUROC: 0.947, CI: 0.845-1.049). Additionally, serum S100A9 levels displayed a strong correlation with ALT, AST and TBil (r = 0.81, 0.89 and 0.91, P < 0.001) but a weak correlation with FBG, HOMA-IR, TG, and TC (r = -0.41, -0.40, 0.47 and 0.49, P < 0.05). CONCLUSIONS: The results we provide here suggest that S100A9 may be useful as a biomarker for the hepatic and metabolic progression of NAFLD and the non-invasive diagnosis of NASH.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 PLoS One. 2015, 10(3):e0118832. doi: 10.1371/journal.pone.0118832. eCollection 2015.
 Behavior Training Reverses Asymmetry in Hippocampal Transcriptome of the Cav3.2 Knockout Mice
 
 
 Ni-Chun Chung, Ying-Hsueh Huang, Chuan-Hsiung Chang, James C. Liao, Chih-Hsien Yang, Chien-Chang Chen, Ingrid Y. Liu
  Abstract
.Homozygous Cav3.2 knockout mice, which are defective in the pore-forming subunit of a low voltage activated T-type calcium channel, have been documented to show impaired maintenance of late-phase long-term potentiation (L-LTP) and defective retrieval of context-associated fear memory. To investigate the role of Cav3.2 in global gene expression, we performed a microarray transcriptome study on the hippocampi of the Cav3.2-/- mice and their wild-type littermates, either naïve (untrained) or trace fear conditioned. We found a significant left-right asymmetric effect on the hippocampal transcriptome caused by the Cav3.2 knockout. Between the naive Cav3.2-/- and the naive wild-type mice, 3522 differentially expressed genes (DEGs) were found in the left hippocampus, but only 4 DEGs were found in the right hippocampus. Remarkably, the effect of Cav3.2 knockout was partially reversed by trace fear conditioning. The number of DEGs in the left hippocampus was reduced to 6 in the Cav3.2 knockout mice after trace fear conditioning, compared with the wild-type naïve mice. To our knowledge, these results demonstrate for the first time the asymmetric effects of the Cav3.2 and its partial reversal by behavior training on the hippocampal transcriptome.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Oncotarget. 2015, 6(7):4976-91.
 Novel oral histone deacetylase inhibitor, MPT0E028, displays potent growth-inhibitory activity against human B-cell lymphoma in vitro and in vivo
 
 
 Han-Li Huang, Chieh-Yu Peng, Mei-Jung Lai, Chun-Han Chen, Hsueh-Yun Lee, Jing-Chi Wang, Che-Ming Teng, Shiow-Lin Pan, Jing-Ping Liou
  Abstract
Histone deacetylase (HDAC) inhibitor has been a promising therapeutic option in cancer therapy due to its ability to induce growth arrest, differentiation, and apoptosis. In this study, we demonstrated that MPT0E028, a novel HDAC inhibitor, reduces the viability of B-cell lymphomas by inducing apoptosis and shows a more potent HDAC inhibitory effect compared to SAHA, the first HDAC inhibitor approved by the FDA. In addition to HDACs inhibition, MPT0E028 also possesses potent direct Akt targeting ability as measured by the kinome diversity screening assay. Also, MPT0E028 reduces Akt phosphorylation in B-cell lymphoma with an IC50 value lower than SAHA. Transient transfection assay revealed that both targeting HDACs and Akt contribute to the apoptosis induced by MPT0E028, with both mechanisms functioning independently. Microarray analysis also shows that MPT0E028 may regulate many oncogenes expression (e.g., TP53, MYC, STAT family). Furthermore, in vivo animal model experiments demonstrated that MPT0E028 (50-200 mg/kg, po, qd) prolongs the survival rate of mice bearing human B-cell lymphoma Ramos cells and inhibits tumor growth in BJAB xenograft model. In summary, MPT0E028 possesses strong in vitro and in vivo activity against malignant cells, representing a potential therapeutic approach for cancer therapy.
   

  ✔本篇論文使用華聯產品:Data Analysis  
 Lung. 2015, 193(4):583-92. doi: 10.1007/s00408-015-9726-6.
 Identification of Commonly Dysregulated Genes in Non-small-cell Lung Cancer by Integrated Analysis of Microarray Data and qRT-PCR Validation
 
 
 Zi-Qiang Tian, Zhen-Hua Li, Shi-Wang Wen, Yue-Feng Zhang, Yong Li, Jing-Ge Cheng, Gui-Ying Wang
  Abstract
BACKGROUND: Non-small-cell lung cancer (NSCLC), the most common lung cancer, leads to the largest number of cancer-related deaths worldwide. There are many studies to identify the differentially expressed genes (DEGs) between NSCLC and normal control (NC) tissues by means of microarray technology. Because of the inconsistency of the microarray data sets, we performed an integrated analysis to identify DEGs and analyzed their biological function. METHODS AND RESULTS: We combined 15 microarray data sets and identified 1063 DEGs between NSCLC and NC tissues; in addition, we found that the DEGs were enriched in regulation of cell proliferation process and focal adhesion signaling pathway. The protein-protein interaction network analysis for the top 20 significantly DEGs revealed that CAV1, COL1A1, and ADRB2 were the significant hub proteins. Finally, we employed qRT-PCR to validate the meta-analysis approach by determining the expression of the top 10 most significantly DEGs and found that the expression of these genes were significantly different between tumor and NC tissues, in accordance with the results of meta-analysis. CONCLUSION: qRT-PCR results indicated that the meta-analysis approach in our study was acceptable. Our data suggested that some of the DEGs, including MMP12, COL11A1, THBS2, FAP, and CAV1, may participate in the pathology of NSCLC and could be applied as potential markers or therapeutic targets for NSCLC.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Cellular physiology and biochemistry. 2015, 35(6):2169-80. doi: 10.1159/000374022.
 MiR-10b Directly Targets ZEB1 and PIK3CA to Curb Adenomyotic Epithelial Cell Invasiveness via Upregulation of E-Cadherin and Inhibition of Akt Phosphorylation
 
 
 Xiao Lang, Zhen Lu, Jianchao Wang, Ting Li, Ying Loao, Chunyan Jia, Wenxia Zhao, Huiqi Fang, Ying Guo
  Abstract
BACKGROUND/AIMS: Adenomyosis is a disease in which ectopic endometrial glands and stromal cells appear in the uterine myometrium. Despite its prevalence, the molecular mechanisms involved in the development of adenomyosis are largely unknown. The aim of this study was to investigate the role of miR-10b and its target genes ZEB1 and PIK3CA in adenomyosis. METHODS: 1387 miRNAs in human normal endometrium and ectopic endometrial lesions of adenomyosis using a microarray screen assay. The significant differential expression of 10 miRNAs was confirmed by qRT-PCR. The expression of miR-10b in endometrial epithelial cells isolated from normal endometrium and paired eutopic and ectopic endometrium of adenomyosis was measured by qRT-PCR. Subsequently, the targets of miR-10b were predicted by bioinformatics and confirmed using a luciferase assay, and the mRNA and protein expression of ZEB1 and PIK3CA were assessed in the endometrium or endometrial epithelial cells by qRT-PCR and western blotting or immunohistochemical analysis. Cell migration and cell invasion of endometrial epithelial cells with different treatments by Transwell assays. The expression of p-AKT, Akt and E-cadherin proteins was determined by Western blot analysis. RESULTS: MiR-10b expression was significantly downregulated in both adenomyotic lesions and adenomyotic epithelial cells. MiR-10b overexpression in adenomyotic epithelial cells inhibited cell migration and invasion. We then demonstrated that miR-10b directly targets the 3'-UTRs of ZEB1 and PIK3CA, and downregulates ZEB1 and PIK3CA in adenomyotic epithelial cells, leading to increased E-cadherin expression and decreased Akt phosphorylation.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Journal of Hepatology. 2015, 62(4):879-88. doi: 10.1016/j.jhep.2014.11.010.
 Endoplasmic reticulum heat shock protein gp96 maintains liver homeostasis and promotes hepatocellular carcinogenesis
 
 
 Saleh Rachidi, Shaoli Sun, Bill X. Wu, Elizabeth Jones, Richard R. Drake, Besim Ogretmen, L. Ashley Cowart, Christopher J. Clarke, Yusuf A. Hannun, Gabriela Chiosis, Bei Liu, Zihai Li
  Abstract
Background & Aims: gp96, or grp94, is an endoplasmic reticulum (ER)-localized heat shock protein 90 paralog that acts as a protein chaperone and plays an important role for example in ER homeostasis, ER stress, Wnt and integrin signaling, and calcium homeostasis, which are vital processes in oncogenesis. However, the cancer-intrinsic function of gp96 remains controversial. Methods: We studied the roles of gp96 in liver biology in mice via an Albumin promoter-driven Cre recombinase-mediated disruption of gp96 gene, hsp90b1. The impact of gp96 status on hepatic carcinogenesis in response to diethyl-nitrosoamine (DENA) was probed. The roles of gp96 on human hepatocellular carcinoma cells (HCC) were also examined pharmacologically with a targeted gp96 inhibitor. Results: We demonstrated that gp96 maintains liver development and hepatocyte function in vivo, and its loss genetically promotes adaptive accumulation of long chain ceramides, accompanied by steatotic regeneration of residual gp96+ hepatocytes. The need for compensatory expansion of gp96+ cells in the gp96− background predisposes mice to develop carcinogen-induced hepatic hyperplasia and cancer from gp96+ but not gp96− hepatocytes. We also found that genetic and pharmacological inhibition of gp96 in human HCCs perturbed multiple growth signals, and attenuated proliferation and expansion.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 International Journal of Oncology. 2015, 46(6):2639-48. doi: 10.3892/ijo.2015.2964.
 The role of WWOX tumor suppressor gene in the regulation of EMT process via regulation of CDH1-ZEB1-VIM expression in endometrial cancer
 
 
 Nowakowska M, Pospiech K, Stępień A, Wołkowicz M, Gałdyszyńska M, Popęda M, Wójcik-Krowiranda K, Bieńkiewicz A, Bednarek AK, Elżbieta Płuciennik
  Abstract
This study defines the role of WWOX in the regulation of epithelial to mesenchymal transition. A group of 164 endometrial adenocarcinoma patients was studied as well as an ECC1 well-differentiated steroid-responsive endometrial cell line, which was transducted with WWOX cDNA by a retroviral system. The relationship between WWOX gene and EMT marker (CDH1, VIM, ZEB1, SNAI1) expression on mRNA (RT-qPCR) and protein levels (western blotting) was evaluated. The EMT processes were also analysed in vitro by adhesion of cells to extracellular matrix proteins, migration through a basement membrane, anchorage-independent growth and MMP activity assay. DNA microarrays (HumanOneArray™) were used to determine WWOX-dependent pathways in an ECC1 cell line. A positive correlation was observed between WWOX and ZEB1, and a negative correlation between CDH1 and VIM. WWOX expression was found to inversely correlate with the risk of recurrence of tumors in patients. However, in the WWOX-expressing ECC1 cell line, WWOX expression was found to be inversely related with VIM and positively with CDH1. The ECC1/WWOX cell line variant demonstrated increased migratory capacity, with increased expression of metalloproteinases MMP2/MMP9. However, these cells were not able to form colonies in suspension and revealed decreased adhesion to fibronectin and fibrinogen. Microarray analysis demonstrated that WWOX has an impact on the variety of cellular pathways including the cadherin and integrin signalling pathways. Our results suggest that the WWOX gene plays a role in the regulation of EMT processes in endometrial cancer by controlling the expression of proteins associated with cell motility, thus influencing tissue remodeling, with the suppression of mesenchymal markers.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 BMC Genomics. 2015, 16:501. doi: 10.1186/s12864-015-1642-x.
 Reorganization of metastamiRs in the evolution of metastatic aggressive neuroblastoma cells
 
 
 Faizan H Khan, Vijayabaskar Pandian, Satishkumar Ramraj, Sheeja Aravindan, Terence S Herman, Natarajan Aravindan
  Abstract
Background: MetastamiRs have momentous clinical relevance and have been correlated with disease progression in many tumors. In this study, we identified neuroblastoma metastamiRs exploiting unique mouse models of favorable and high-risk metastatic human neuroblastoma. Further, we related their deregulation to the modulation of target proteins and established their association with clinical outcomes. Results: Whole genome miRNA microarray analysis identified 74 metastamiRs across the manifold of metastatic tumors. RT-qPCR on select miRNAs validated profile expression. Results from bio-informatics across the ingenuity pathway, miRCancer, and literature data-mining endorsed the expression of these miRNAs in multiple tumor systems and showed their role in metastasis, identifying them as metastamiRs. Immunoblotting and TMA-IHC analyses revealed alterations in the expression/phosphorylation of metastamiRs¡¦ targets, including ADAMTS-1, AKT1/2/3, ASK1, AURK£], Birc1, Birc2, Bric5, £]-CATENIN, CASP8, CD54, CDK4, CREB, CTGF, CXCR4, CYCLIN-D1, EGFR, ELK1, ESR1, CFOS, FOSB, FRA, GRB10, GSK3£], IL1£, JUND, kRAS, KRTAP1, MCP1, MEGF10, MMP2, MMP3, MMP9, MMP10, MTA2, MYB, cMYC, NF2, NOS3, P21, pP38, PTPN3, CLEAVED PARP, PKC, SDF-1£], SEMA3D, SELE, STAT3, TLR3, TNF£, TNFR1, and VEGF in aggressive cells ex vivo and in a manifold of metastatic tumors in vivo. miRNA mimic (hsa-miR-125b, hsa-miR-27b, hsa-miR-93, hsa-miR-20a) and inhibitor (hsa-miR-1224-3p, hsa-miR-1260) approach for select miRNAs revealed the direct influence of the altered metastamiRs in the regulation of identified protein targets. Clinical outcome association analysis with the validated metastamiRs¡¦ targets corresponded strongly with poor overall and relapse-free survival. Conclusions: For the first time, these results identified a comprehensive list of neuroblastoma metastamiRs, related their deregulation to altered expression of protein targets, and established their association with poor clinical outcomes. The identified set of distinctive neuroblastoma metastamiRs could serve as potential candidates for diagnostic markers for the switch from favorable to high-risk metastatic disease.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 BMC Genomics. 2015, 16:156. doi: 10.1186/s12864-015-1356-0.
 Deregulation of sertoli and leydig cells function in patients with klinefelter syndrome as evidenced by testis transcriptome analysis
 
 
 Marco D¡¦Aurora, Alberto Ferlin, Marta Di Nicola, Andrea Garolla, Luca De Toni, Sara Franchi, Giandomenico Palka, Carlo Foresta, Liborio Stuppia, Valentina Gatta
  Abstract
Background: Klinefelter Syndrome (KS) is the most common abnormality of sex chromosomes (47,XXY) and represents the first genetic cause of male infertility. Mechanisms leading to KS testis degeneration are still not completely defined but considered to be mainly the result of germ cells loss. In order to unravel the molecular basis of global testis dysfunction in KS patients, we performed a transcriptome analysis on testis biopsies obtained from 6 azoospermic non-mosaic KS patients and 3 control subjects. Results: The analysis found that, compared to controls, KS patients showed the differential up- and down-expression of 656 and 247 transcripts. The large majority of the deregulated transcripts were expressed by Sertoli cells (SCs) and Leydig cells (LCs). Functional analysis of the deregulated transcripts indicated changes of genes involved in cell death, inflammatory response, lipid metabolism, steroidogenesis, blood-testis-barrier formation and maintenance, as well as spermatogenesis failure. Conclusions: Taken together, present data highlight the modulation of hundreds of genes in the somatic components of KS patient testis. The increased LCs steroidogenic function together with the impairment of inflammatory pathways and BTB structure, result in increased apoptosis. These findings may represent a critical roadmap for therapeutic intervention and prevention of KS-related testis failure.
   

  ✔本篇論文使用華聯產品:  
 BMC Plant Biology. 2015, 15:156. doi: 10.1186/s12870-015-0515-4.
 The additive effects of GS3 and qGL3 on rice grain length regulation revealed by genetic and transcriptome comparisons
 
 
 Xiuying Gao, Xiaojun Zhang, Hongxia Lan, Ji Huang, Jianfei Wang, Hongsheng Zhang
  Abstract
Background: Grain length, as a critical trait for rice grain size and shape, has a great effect on grain yield and appearance quality. Although several grain size/shape genes have been cloned, the genetic interaction among these genes and the molecular mechanisms of grain size/shape architecture have not yet to be explored. Results: To investigate the genetic interaction between two major grain length loci of rice, GS3 and qGL3, we developed two near-isogenic lines (NILs), NIL-GS3 (GS3/qGL3) and NIL-qgl3 (gs3/qgl3), in the genetic background of 93¡V11 (gs3/qGL3) by conventional backcrossing and marker-assisted selection (MAS). Another NIL-GS3/qgl3 (GS3/qgl3) was developed by crossing NIL-GS3 with NIL-qgl3 and using MAS. By comparing the grain lengths of 93¡V11, NIL-GS3, NIL-qgl3 and NIL-GS3/qgl3, we investigated the effects of GS3, qGL3 and GS3 ¡Ñ qGL3 interaction on grain length based on two-way ANOVA. We found that GS3 and qGL3 had additive effects on rice grain length regulation. Comparative analysis of primary panicle transcriptomes in the four NILs revealed that the genes affected by GS3 and qGL3 partially overlapped, and both loci might be involved in brassinosteroid signaling. Conclusion: Our data provide new information to better understand the rice grain length regulation mechanism and help rice breeders improve rice yield and appearance quality by molecular design breeding.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 PLoS One. 2015, 10(3):e0121765. doi: 10.1371/journal.pone.0121765. eCollection 2015.
 Smyd1 Facilitates Heart Development by Antagonizing Oxidative and ER Stress Responses
 
 
 Tara L. Rasmussen, Yanlin Ma, Chong Yon Park, June Harriss, Stephanie A. Pierce, Joseph D. Dekker, Nicolas Valenzuela, Deepak Srivastava, Robert J. Schwartz, M. David Stewart, Haley O. Tucker
  Abstract
Smyd1/Bop is an evolutionary conserved histone methyltransferase previously shown by conventional knockout to be critical for embryonic heart development. To further explore the mechanism(s) in a cell autonomous context, we conditionally ablated Smyd1 in the first and second heart fields of mice using a knock-in (KI) Nkx2.5-cre driver. Robust deletion of floxed-Smyd1 in cardiomyocytes and the outflow tract (OFT) resulted in embryonic lethality at E9.5, truncation of the OFT and right ventricle, and additional defects consistent with impaired expansion and proliferation of the second heart field (SHF). Using a transgenic (Tg) Nkx2.5-cre driver previously shown to not delete in the SHF and OFT, early embryonic lethality was bypassed and both ventricular chambers were formed; however, reduced cardiomyocyte proliferation and other heart defects resulted in later embryonic death at E11.5-12.5. Proliferative impairment prior to both early and mid-gestational lethality was accompanied by dysregulation of transcripts critical for endoplasmic reticulum (ER) stress. Mid-gestational death was also associated with impairment of oxidative stress defense-a phenotype highly similar to the previously characterized knockout of the Smyd1-interacting transcription factor, skNAC. We describe a potential feedback mechanism in which the stress response factor Tribbles3/TRB3, when directly methylated by Smyd1, acts as a co-repressor of Smyd1-mediated transcription. Our findings suggest that Smyd1 is required for maintaining cardiomyocyte proliferation at minimally two different embryonic heart developmental stages, and its loss leads to linked stress responses that signal ensuing lethality.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Oncology Reports. 2015, 34(1):318-24. doi: 10.3892/or.2015.3953.
 Microarray analysis of the aberrant microRNA expression pattern in gliomas of different grades
 
 
 Xiao-Peng Zhu, Ke-Jie Mou, Qing-Fu Xu, Jun-Hai Tang, Guo-Hao Huang, Jian-Ping Xu, Guang-Hui Li, Si-Jin Ai, Jean-Phillippe Hugnot, Zheng Zhou, Sheng-Qing Lv
  Abstract
Previous studies have focused on miRNA expression in brain gliomas. However, both the expression pattern of miRNAs in gliomas of different grades and various miRNAs involved in malignant progression of gliomas are poorly understood. In the present study, we used miRNA microarray-based screening to investigate the miRNA expression profile in gliomas, which was further verified by qRT-PCR in selected miRNAs. In total, we found 13 differentially expressed miRNAs between gliomas and their matched surrounding tissues. Among them, 12 miRNAs were upregulated and only one (miR-4489) was downregulated compared with the control. Furthermore, the lower expression level of miR-4489 was confirmed by qRT-PCR in 26 glioma samples. Our microarray result revealed 8, 9 and 15 aberrantly expressed miRNAs in gliomas of World Health Organization (WHO) grade II-IV, respectively. Gene Ontology (GO) and Pathway analysis indicated that target genes of the 13 miRNAs were significantly enriched in central nervous system- and tumor‑related biological processes and signaling pathways. The dysregulated miRNAs identified in the present study contribute to the tumorigenesis and malignant progression of gliomas and may serve as useful markers for advanced glioma pathological grading and prognosis.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Molecular Pharmaceutics. 2015 Jul 9. DOI: 10.1021/acs.molpharmaceut.5b00329.
 Exploring microRNA expression profiles related to the mTOR signaling pathway in mouse embryonic fibroblast cells treated with polyethylenimine
 
 
 Chia-Wei Lin, Jung-Hua Steven Kuo, Ming-Shiou Jan
  Abstract
Although the toxicology of poly(ethylenimine) (PEI) in gene expression levels has been previously investigated, little is known about the effects of PEI on the expression of microRNAs (miRNAs) that regulate gene expression at the post-transcriptional level. In this study, we explored miRNA expression profiles related to cell death mechanisms in mouse embryonic fibroblast (MEF) cells treated with PEI by applying microarray analysis. Based on the analysis of the mTOR signaling pathway, three upregulated miRNAs (mmu-miR-3090-5p, mmu-miR-346-3p, and mmu-miR-494-3p) were verified in MEF cells treated with PEI at 24 h using real-time quantitative reverse transcriptase-polymerase chain reaction. We further demonstrated that these three upregulated miRNAs resulted in the decrease of gene and protein expressions of the target gene growth factor Igf1 in MEF cells treated with PEI or transfected with three upregulated miRNA mimics. However, these three upregulated miRNAs are not all cell-specific. Finally, we demonstrated that the mTOR signaling pathway is inhibited by autophagy induction and that the cell viability decreases in MEF cells treated with PEI or transfected with these three miRNA mimics. Collectively, our data suggested that PEI may affect the regulation of miRNAs in target cells.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 International forum of allergy & rhinology. 2015 Jul 3. doi: 10.1002/alr.21586.
 Dexamethasone affects mouse olfactory mucosa gene expression and attenuates genes related to neurite outgrowth
 
 
 Jun Tian, Jayant M. Pinto, Yi Xin, Henghui Zhang, Li Li, Zhifu Sun, Yongxiang Wei
  Abstract
BACKGROUND: Olfaction is one of the important senses for humans. Systemic glucocorticoids are the most commonly used medications for olfactory loss because of their strong anti-inflammatory effects. However, their effect on olfactory function is still controversial and the precise mechanism is not clear. To gain a global view of the effect of systematic glucocorticoid treatment on gene expression in the olfactory mucosa (OM), we profiled these changes in a murine model of olfaction in order to identify underlying molecular mechanisms. METHODS: C57BL/6 mice were injected daily for 2 weeks (WK2) with dexamethasone (DEX, intraperitoneally, 1 mg/kg body weight) vs 1 day of DEX (D1) vs controls, which received saline (Ctrl) (n = 9/group). Total RNA from the OM was used to analyze global gene expression. Genes showing changes in expression were compared using the Database for Annotation, Visualization and Integrated Discovery (DAVID, v6.7) and the General Olfactory Sensitivity Database (GOSdb; http://genome.weizmann.ac.il/GOSdb). RESULTS: Between the WK2 and Ctrl groups, 3351 genes were differentially expressed, of which 236 genes were related to olfactory function. Genes involved in axon guidance, cell projection, and inflammation were enriched and overlapped significantly with those in the GOSdb. CONCLUSION: Systemic glucocorticoids exert effects on transcription of a notable number of genes in the OM and appear to orchestrate changes related to axon guidance, cell projection, and inflammation. Further examination may allow targeted therapies that lack the side effects of this category of medication.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Amino Acids. 2015, 47(7):1319-39. doi: 10.1007/s00726-015-1956-7.
 Homocysteine thiolactone and N -homocysteinylated protein induce pro-atherogenic changes in gene expression in human vascular endothelial cells
 
 
 Dorota Gurda, Luiza Handschuh, Weronika Kotkowiak, Hieronim Jakubowski
  Abstract
Genetic or nutritional deficiencies in homocysteine (Hcy) metabolism lead to hyperhomocysteinemia (HHcy) and cause endothelial dysfunction, a hallmark of atherosclerosis. In addition to Hcy, related metabolites accumulate in HHcy but their role in endothelial dysfunction is unknown. Here, we examine how Hcy-thiolactone, N-Hcyprotein, and Hcy affect gene expression and molecular pathways in human umbilical vein endothelial cells. We used microarray technology, real-time quantitative polymerase chain reaction, and bioinformatic analysis with PANTHER, DAVID, and Ingenuity Pathway Analysis (IPA) resources. We identified 47, 113, and 30 mRNAs regulated by N-Hcyprotein, Hcy-thiolactone, and Hcy, respectively, and found that each metabolite induced a unique pattern of gene expression. Top molecular pathways affected by Hcy-thiolactone were chromatin organization, one-carbon metabolism, and lipid-related processes [−log(P value) = 20¡V31]. Top pathways affected by N-Hcy-protein and Hcy were blood coagulation, sulfur amino acid metabolism, and lipid metabolism [−log(P value)] = 4¡V11; also affected by Hcythiolactone, [−log(P value) = 8¡V14]. Top disease related to Hcy-thiolactone, N-Hcy-protein, and Hcy was ¡¥atherosclerosis, coronary heart disease¡¦ [−log(P value) = 9¡V16].Top-scored biological networks affected by Hcy-thiolactone (score = 34¡V40) were cardiovascular disease and function; those affected by N-Hcy-protein (score = 24¡V35) were ¡¥small molecule biochemistry, neurological disease,¡¦ and ¡¥cardiovascular system development and function¡¦; and those affected by Hcy (score = 25¡V37) were ¡¥amino acid metabolism, lipid metabolism,¡¦ ¡¥cellular movement, and cardiovascular and nervous system development and function.¡¦These results indicate that each Hcy metabolite uniquely modulates gene expression in pathways important for vascular homeostasis and identify new genes and pathways that are linked to HHcy-induced endothelial dysfunction and vascular disease.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Molecular Medicine Reports. 2015, 11(2):887-95. doi: 10.3892/mmr.2014.2823.
 Biological effect of ketamine in urothelial cell lines and global gene expression analysis in the bladders of ketamine‑injected mice
 
 
 CHENG‑HUANG SHEN, SHOU‑TSUNG WANG, YING‑RAY LEE, SHIAU‑YUAN LIU, YI‑ZHEN LI, JIANN‑DER WU, YI‑JU CHEN, Yi‑Wen Liu
  Abstract
Ketamine is used clinically for anesthesia but is also abused as a recreational drug. Previously, it has been established that ketamine‑induced bladder interstitial cystitis is a common syndrome in ketamine‑abusing individuals. As the mechanisms underlying ketamine‑induced cystitis have yet to be revealed, the present study investigated the effect of ketamine on human urothelial cell lines and utilized a ketamine‑injected mouse model to identify ketamine‑induced changes in gene expression in mice bladders. In the in vitro bladder cell line assay, ketamine induced cytotoxicity in a dose‑ and time‑dependent manner. Ketamine arrested the cells in G1 phase and increased the sub‑G1 population, and also increased the barrier permeability of these cell lines. In the ketamine‑injected mouse model, ketamine did not change the body weight and bladder histology of the animals at the dose of 30 mg/kg/day for 60 days. Global gene expression analysis of the animals' bladders following data screening identified ten upregulated genes and 36 downregulated genes induced by ketamine. A total of 52% of keratin family genes were downregulated, particularly keratin 6a, 13 and 14, which was confirmed by polymerase chain reaction analysis. Keratin 14 protein, one of the 36 ketamine‑induced downregulated genes, was also reduced in the ketamine‑treated mouse bladder, as determined by immunohistochemical analysis. This suggested that cytotoxicity and keratin gene downregulation may have a critical role in ketamine‑induced cystitis.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Clinical & Experimental Metastasis. 2015, 32(5):417-28. doi: 10.1007/s10585-015-9712-7.
 Loss of PCDH9 is associated with the differentiation of tumor cells and metastasis and predicts poor survival in gastric cancer
 
 
 Ying Chen, Honggang Xiang, Yingfan Zhang, Jiejun Wang, Guanzhen Yu
  Abstract
Microarray studies revealed down-regulation of PCDH9 mRNA level in lymph node metastasis of gastric cancer compared with the primary tumors. The expression of PCDH9 protein and its clinicopathological relevance were assessed on tissue microarrays of 1072 cases of gastric cancer. Its prognostic value was further evaluated on a small cohort of 175 gastric cancers. PCDH9 was down-regulated during the development and progression of gastric cancer. The overall rates of PCDH9 expression in normal, primary tumor, nodal and hepatic metastatic tissues were 100 % (1072/1072), 48.0 % (515/1072), 20.1 % (34/169), and 5.6 % (1/18), respectively. Positive staining of PCDH9 protein was significantly reversely correlated with tumor size, tumor differentiation, tumor invasion, lymph node metastasis, and disease progression. The Cox proportional hazards model revealed that the PCDH9 was an independent prognostic factor for gastric cancer. Therefore, decreased expression of PCDH9 is frequent in human gastric cancer metastasis and PCDH9 expression is an independent prognostic factor, suggesting that PCDH9 could be a promising biomarker of this malignanc
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Toxicology Research. 2015, 4, 365-375. doi: 10.1039/C4TX00181H.
 A gene signature for gold nanoparticle-exposed human cell lines
 
 
 Ruei-Yue Liang, Hsin-Fang Tu, Xiaotong Tan, Yu-Shan Yeh, Pin Ju Chueh, Show-Mei Chuang
  Abstract
There is currently a significant need for effective methods aimed at diagnosing and screening for nanoparticle exposure. We previously investigated the toxicity of three different particle sized gold nanoparticles (AuNPs) toward different types of mammalian cells and explored a related gene expression profile by cDNA microarray analysis of AuNP-exposed MRC-5 cells. In this study, we sought to further identify genes that could be used as biomarkers for AuNP exposure. We used cDNA microarray analysis to obtain comprehensive gene expression profiles from A549 cells exposed to three different-sized AuNPs. A total of 409 genes were commonly up-regulated by the tested AuNPs; of them, 71 had previously been analyzed to be up-regulated in MRC-5 cells. Among the top-ranked 30 of these 71 up-regulated genes, based on the magnitude of induction, nine genes were confirmed to be transcriptionally induced in A549 cells by all three tested AuNPs, as assessed by quantitative real-time polymerase chain reaction (qPCR). Among them, TSC22D3, TRIB3, PCK2 and DDIT4 were the most sensitive to the three AuNPs, and showed dose-dependent changes in several human cell lines. qPCR and immunoblotting analyses revealed that the same concentrations of micro-Au and nano-TiO2 failed to elicit up-regulation of these four genes at the mRNA and protein levels in any tested cell lines. Although the definition and practical implementation of specific biomarkers for nanoparticles is still in its infancy, our data suggest that it may be possible to define reliable biomarkers for the diagnosis of nanomaterial exposure.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Scientific Reports. 2015, 5:10106. doi: 10.1038/srep10106.
 Characterization of a Self-renewing and Multi-potent Cell Population Isolated from Human Minor Salivary Glands
 
 
 Lin Lu, Yan Li, Ming-juan Du, Chen Zhang, Xiang-yu Zhang, Hai-zhou Tong, Lei Liu, Ting-lu Han, Wan-di Li, Li Yan, Ning-bei Yin, Hai-dong Li, Zhen-min Zhao
  Abstract
Adult stem cells play an important role in maintaining tissue homeostasis. Although these cells are found in many tissues, the presence of stem cells in the human minor salivary glands is not well explored. Using the explant culture method, we isolated a population of cells with self-renewal and differentiation capacities harboring that reside in the human minor salivary glands, called human minor salivary gland mesenchymal stem cells (hMSGMSCs). These cells show embryonic stem cell and mesenchymal stem cell phenotypes. Our results demonstrate that hMSGMSCs have the potential to undergo mesodermal, ectodermal and endodermal differentiation in conditioned culture systems in vitro. Furthermore, in vivo transplantation of hMSGMSCs into SCID mice after partial hepatectomy shows that hMSGMSCs are able to survive and engraft, characterized by the survival of labeled cells and the expression of the hepatocyte markers AFP and KRT18. These data demonstrate the existence of hMSGMSCs and suggest their potential in cell therapy and regenerative medicine.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 The Journal of Immunology. 2015, 194(3):1292-303. doi: 10.4049/jimmunol.1402593.
 The Endoplasmic Reticulum Adaptor Protein ERAdP Initiates NK Cell Activation via the Ubc13-Mediated NF-£eB Pathway
 
 
 Jun Chen, Lu Hao, Chong Li, Buqing Ye, Ying Du, Honglian Zhang, Bo Long, Pingping Zhu, Benyu Liu, Liuliu Yang, Peifeng Li, Yong Tian, Zusen Fan
  Abstract
NK cells play a pivotal role in innate immune responses against pathogenic infections. However, the underlying mechanisms driving defined NK functions remain largely elusive. In this study, we identified a novel endoplasmic reticulum (ER) membrane protein, ER adaptor protein (ERAdP), which is constitutively expressed in human and mouse NK cells. ERAdP is expressed at low levels in peripheral NK cells of hepatitis B virus-associated hepatocellular carcinoma patients. We show that ERAdP initiates NK cell activation through the NF-£eB pathway. Notably, ERAdP interacts with ubiquitin-conjugating enzyme 13 (Ubc13) to potentiate its charging activity. Thus, ERAdP augments Ubc13-mediated NF-£eB essential modulator ubiquitination to trigger the Ubc13-mediated NF-£eB pathway, leading to NK cell activation. Finally, ERAdP transgenic mice display hyperactivated NK cells that are more resistant to pathogenic infections. Therefore, understanding the mechanism of ERAdP-mediated NK cell activation will provide strategies for treatment of infectious diseases.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Biomaterials. 2015, 66:29-40. doi: 10.1016/j.biomaterials.2015.06.028.
 Chitosan facilitates structure formation of the salivary gland by regulating the basement membrane components
 
 
 Ya-Chuan Hsiao, Tsung-Lin Yang
  Abstract
Tissue structure is important for inherent physiological function and should be recapitulated during tissue engineering for regenerative purposes. The salivary gland is a branched organ that is responsible for saliva secretion and regulation. The salivary glands develop from epithelial-mesenchymal interactions, and depend on the support of the basement membrane (BM). Chitosan-based biomaterials have been demonstrated to be competent in facilitating the formation of salivary gland tissue structure. However, the underlying mechanisms have remained elusive. In the developing submandibular gland (SMG), the chitosan effect was found to diminish when collagen and laminin were removed from cultured SMG explants. Chitosan increased the expression of BM components including collagen, laminin, and heparan sulfate proteoglycan, and also facilitated BM components and the corresponding receptors to be expressed in tissue-specific patterns beneficial for SMG branching. The chitosan effect decreased when either laminin components or receptors were inhibited, as well when the downstream signaling was blocked. Our results revealed that chitosan promotes salivary glands branching through the BM. By regulating BM components and receptors, chitosan efficiently stimulated downstream signaling to facilitate salivary gland branching. The present study revealed the underlying mechanism of the chitosan effect in engineering SMG structure formation.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 PLoS One. 2015, 10(2):e112716. doi: 10.1371/journal.pone.0112716. eCollection 2015.
 Inhibited Wnt Signaling Causes Age-Dependent Abnormalities in the Bone Matrix Mineralization in the Apert Syndrome FGFR2S252W/+ Mice
 
 
 Li Zhang, Peng Chen, Lin Chen, Tujun Weng, Shichang Zhang, Xia Zhou, Luchuan Liu, Bo Zhang
  Abstract
Apert syndrome (AS) is a type of autosomal dominant disease characterized by premature fusion of the cranial sutures, severe syndactyly, and other abnormalities in internal organs. Approximately 70% of AS cases are caused by a single mutation, S252W, in fibroblast growth factor receptor 2 (FGFR2). Two groups have generated FGFR2 knock-in mice Fgfr2S252W/+ that exhibit features of AS. During the present study of AS using the Fgfr2S252W/+ mouse model, an age-related phenotype of bone homeostasis was discovered. The long bone mass was lower in 2 month old mutant mice than in age-matched controls but higher in 5 month old mutant mice. This unusual phenotype suggested that bone marrow-derived mesenchymal stem cells (BMSCs), which are vital to maintain bone homeostasis, might be involved. BMSCs were isolated from Fgfr2S252W/+ mice and found that S252W mutation could impair osteogenic differentiation BMSCs but enhance mineralization of more mature osteoblasts. A microarray analysis revealed that Wnt pathway inhibitors SRFP1/2/4 were up-regulated in mutant BMSCs. This work provides evidence to show that the Wnt/£]-catenin pathway is inhibited in both mutant BMSCs and osteoblasts, and differentiation defects of these cells can be ameliorated by Wnt3a treatment. The present study suggested that the bone abnormalities caused by deregulation of Wnt pathway may underlie the symptoms of AS.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Molecular Medicine Reports. 2015, 12(3):3525-30. doi: 10.3892/mmr.2015.3835.
 Identification of a microRNA signature in endothelial cells with mechanical stretch stimulation
 
 
 Jubing Zheng, Kui Zhang, Yueli Wang, Jian Cao, Feng Zhang, Jubing Zheng, Ran Dong
  Abstract
The current study aimed to verify an miRNA signature in endothelial cells undergoing mechanical stretch stimulation. In the present study, microarray profiling was conducted in order to identify the differential expression of miRNAs in endothelial cells undergoing mechanical stimulation, compared with unstimulated endothelial cells. The microarray data was then validated by reverse transcription‑quantitative polymerase chain reaction. Genes and signaling pathways regulated by the miRNAs were investigated in silico using Gene Ontology and the Kyoto Encyclopedia of Genes or Genomes, which are ontological and network‑mapping algorithms. The microarray data collected demonstrated that 38 miRNAs exhibited significant differential expression in endothelial cells with mechanical stretch stimulation. Of these, 20 were upregulated and 18 were downregulated. The results from the in silico analysis indicated that the miRNAs identified were participants in mechanical stretch‑induced endothelial dysfunction. During the initial stage of vein graft failure, which is induced by endothelial dysfunction, a unique miRNA signature was identified. The identified miRNAs are suggested to be involved in the pathological processes of traumatic injury.
   

  ✔本篇論文使用華聯產品:  
 PLoS One. 2015, 10(7):e0131391. doi: 10.1371/journal.pone.0131391. eCollection 2015.
 Comparative Transcriptome Analysis of Shoots and Roots of TNG67 and TCN1 Rice Seedlings under Cold Stress and Following Subsequent Recovery: Insights into Metabolic Pathways, Phytohormones, and Transcription Factors
 
 
 Yun-Wei Yang, Hung-Chi Chen, Wei-Fu Jen, Li-Yu Liu, Men-Chi Chang
  Abstract
Cold stress affects rice growth, quality and yield. The investigation of genome-wide gene expression is important for understanding cold stress tolerance in rice. We performed comparative transcriptome analysis of the shoots and roots of 2 rice seedlings (TNG67, cold-tolerant; and TCN1, cold-sensitive) in response to low temperatures and restoration of normal temperatures following cold exposure. TNG67 tolerated cold stress via rapid alterations in gene expression and the re-establishment of homeostasis, whereas the opposite was observed in TCN1, especially after subsequent recovery. Gene ontology and pathway analyses revealed that cold stress substantially regulated the expression of genes involved in protein metabolism, modification, translation, stress responses, and cell death. TNG67 takes advantage of energy-saving and recycling resources to more efficiently synthesize metabolites compared with TCN1 during adjustment to cold stress. During recovery, expression of OsRR4 type-A response regulators was upregulated in TNG67 shoots, whereas that of genes involved in oxidative stress, chemical stimuli and carbohydrate metabolic processes was downregulated in TCN1. Expression of genes related to protein metabolism, modification, folding and defense responses was upregulated in TNG67 but not in TCN1 roots. In addition, abscisic acid (ABA)-, polyamine-, auxin- and jasmonic acid (JA)-related genes were preferentially regulated in TNG67 shoots and roots and were closely associated with cold stress tolerance. The TFs AP2/ERF were predominantly expressed in the shoots and roots of both TNG67 and TCN1. The TNG67-preferred TFs which express in shoot or root, such as OsIAA23, SNAC2, OsWRKY1v2, 24, 53, 71, HMGB, OsbHLH and OsMyb, may be good candidates for cold stress tolerance-related genes in rice. Our findings highlight important alterations in the expression of cold-tolerant genes, metabolic pathways, and hormone-related and TF-encoding genes in TNG67 rice during cold stress and recovery. The cross-talk of hormones may play an essential role in the ability of rice plants to cope with cold stress.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 BioMed Research International. 2015:410721. doi: 10.1155/2015/410721.
 TLR4/NF-£eB-Responsive MicroRNAs and Their Potential Target Genes: A Mouse Model of Skeletal Muscle Ischemia-Reperfusion Injury
 
 
 Johnson Chia-Shen Yang, Shao-ChunWu, Cheng-Shyuan Rau, Yi-Chun Chen, Tsu-Hsiang Lu, Yi-ChanWu, Siou-Ling Tzeng, Chia-JungWu, Ching-Hua Hsieh
  Abstract
Background. The aim of this study was to profile TLR4/NF-£eB-responsive microRNAs (miRNAs) and their potential target genes in the skeletal muscles of mice following ischemia-reperfusion injury. Methods. Thigh skeletal muscles of C57BL/6, Tlr4−/−, and NF-£eB−/− mice isolated based on femoral artery perfusion were subjected to ischemia for 2 h and reperfusion for 0 h, 4 h, 1 d, and 7 d. The muscle specimens were analyzed with miRNA arrays. Immunoprecipitation with an argonaute 2- (Ago2-) specific monoclonal antibody followed by whole genome microarray was performed to identify mRNA associated with the RNA-silencing machinery. The potential targets of each upregulated miRNA were identified by combined analysis involving the bioinformatics algorithm miRanda and whole genome expression. Results. Three TLR4/NF-£eB-responsive miRNAs (miR-15a, miR-744, and miR-1196) were significantly upregulated in the muscles following ischemia-reperfusion injury. The combined in silico and whole genome microarray approaches identified 5, 4, and 20 potential target genes for miR-15a, miR-744, and miR-1196, respectively. Among the 3 genes (Zbed4, Lrsam1, and Ddx21) regulated by at least 2 of the 3 upregulated miRNAs, Lrsam1 and Ddx21 are known to be associated with the innate immunity pathway. Conclusions. This study profiled TLR4/NF-£eB-responsive miRNAs and their potential target genes in mouse skeletal muscle subjected to ischemia-reperfusion injury.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Cancer Research. 2015, 75(10):1992-2004. doi: 10.1158/0008-5472.CAN-14-0611.
 The Endogenous Cell-Fate Factor Dachshund restrains Prostate Epithelial Cell Migration via Repression of Cytokine Secretion via a CXCL Signaling Module
 
 
 Ke Chen, Xuanmao Jiao, Liping Wang, Xiaoming Ju, Min Wang, Gabriele Di Sante, Shaohua Xu, Qiong Wang, Kevin Li, Xin Sun, Congwen Xu, Zhiping Li, Mathew C. Casimiro, Adam Ertel, Sankar Addya, Peter McCue, Michael P. Lisanti, Chenguang Wang, Richard J. Davis, Graeme Mardon, Kongming Wu, Richard G. Pestell
  Abstract
Prostate cancer is the second leading form of cancer-related death in men. In a subset of prostate cancer patients, increased chemokine signaling IL8 and IL6 correlates with castrate-resistant prostate cancer (CRPC). IL8 and IL6 are produced by prostate epithelial cells and promote prostate cancer cell invasion; however, the mechanisms restraining prostate epithelial cell cytokine secretion are poorly understood. Herein, the cell-fate determinant factor DACH1 inhibited CRPC tumor growth in mice. Using Dach1(fl/fl)/Probasin-Cre bitransgenic mice, we show IL8 and IL6 secretion was altered by approximately 1,000-fold by endogenous Dach1. Endogenous Dach1 is shown to serve as a key endogenous restraint to prostate epithelial cell growth and restrains migration via CXCL signaling. DACH1 inhibited expression, transcription, and secretion of the CXCL genes (IL8 and IL6) by binding to their promoter regulatory regions in chromatin. DACH1 is thus a newly defined determinant of benign and malignant prostate epithelium cellular growth, migration, and cytokine abundance in vivo.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Journal of Agricultural and Food Chemistry. 2015, 63(16):4148-59. doi: 10.1021/acs.jafc.5b01005.
 Up-Regulation of miR-34a Expression in Response to the Luteolin-Induced Neurite Outgrowth of PC12 Cells
 
 
 Pei-Yi Chen, Ming-Jiuan Wu, Heng-Yuan Chang, Mi-Hsueh Tai, Chi-Tang Ho, Jui-Hung Yen
  Abstract
Luteolin (3',4',5,7-tetrahydroxyflavone), a flavonoid found in several vegetables and fruits, has been reported to possess neurotrophic activities that are associated with its capacity to promote neuronal survival and differentiation. In the present study, we report for the first time a genomewide screen for microRNAs (miRNAs) regulated during the luteolin-mediated neurite outgrowth of PC12 cells. We found that after luteolin treatment, the abundance of 16 miRNAs was markedly up-regulated and that of 3 miRNAs was down-regulated in PC12 cells. The induction of miR-34a by luteolin was the most pronounced among these differentially expressed miRNAs. The correlation between miR-34a down-regulation and decreased luteolin-mediated neurite outgrowth may indicate a mechanism by which miR-34a may act as a modulator of neuronal differentiation. Furthermore, we found that luteolin enhanced the phosphorylation of p53 at Ser15, which was associated with the promotion of miR-34a transcription and neurite outgrowth. Moreover, the level of sirtuin 1 (SIRT1), a known miR-34a target, was reduced during luteolin-induced neurite outgrowth. In turn, the level of acetylated p53, a substrate of SIRT1, was correspondingly increased in luteolin-treated PC12 cells. In addition to p53 activation, we further identified that luteolin-induced miR-34a transcription and neurite outgrowth involved the activation of the JNK and p38 MAPK pathways. However, the inhibition of JNK and p38 MAPK activation did not block luteolin-induced p53 activation in PC12 cells. Our findings suggested that the activation of both p53-dependent and p53-independent miR-34a/SIRT1 pathways plays a critical role in the mechanisms underlying luteolin-induced neuritogenesis.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Phytomedicine. 2015, 22(7-8):768-77. doi: 10.1016/j.phymed.2015.05.053.
 Glycyrrhizin, silymarin, and ursodeoxycholic acid regulate a common hepatoprotective pathway in HepG2 cells
 
 
 Chien-Yun Hsiang, Li-JenLin, Shung-Te Kao, Hsin-Yi Lo, Shun-Ting Chou, Tin-YunHo
  Abstract
BACKGROUND: Glycyrrhizin, silymarin, and ursodeoxycholic acid are widely used hepatoprotectants for the treatment of liver disorders, such as hepatitis C virus infection, primary biliary cirrhosis, and hepatocellular carcinoma. PURPOSE: The gene expression profiles of HepG2 cells responsive to glycyrrhizin, silymarin, and ursodeoxycholic acid were analyzed in this study. METHODS: HepG2 cells were treated with 25 µM hepatoprotectants for 24 h. Gene expression profiles of hepatoprotectants-treated cells were analyzed by oligonucleotide microarray in triplicates. Nuclear factor-£eB (NF-£eB) activities were assessed by luciferase assay. RESULTS: Among a total of 30,968 genes, 252 genes were commonly regulated by glycyrrhizin, silymarin, and ursodeoxycholic acid. These compounds affected the expression of genes relevant various biological pathways, such as neurotransmission, and glucose and lipid metabolism. Genes involved in hepatocarcinogenesis, apoptosis, and anti-oxidative pathways were differentially regulated by all compounds. Moreover, interaction networks showed that NF-£eB might play a central role in the regulation of gene expression. Further analysis revealed that these hepatoprotectants inhibited NF-£eB activities in a dose-dependent manner. CONCLUSION: Our data suggested that glycyrrhizin, silymarin, and ursodeoxycholic acid regulated the expression of genes relevant to apoptosis and oxidative stress in HepG2 cells. Moreover, the regulation by these hepatoprotectants might be relevant to the suppression of NF-£eB activities.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Neurobiology of Aging. 2015, 36(3):1356-68. doi: 10.1016/j.neurobiolaging.2014.11.020.
 The CCAAT/enhancer-binding protein delta/miR135a/thrombospondin 1 axis mediates PGE2-induced angiogenesis in Alzheimer's disease
 
 
 Chiung-Yuan Ko, Yu-Yi Chu, Shuh Narumiya, Jhih-Ying Chi, Tomoyuki Furuyashiki, Tomohiro Aoki, Shao-Ming Wang, Wen-Chang Chang, Ju-Ming Wang
  Abstract
In Alzheimer's disease (AD), large populations of endothelial cells undergo angiogenesis due to brain hypoxia and inflammation. Substantial evidence from epidemiologic, pathologic, and clinical reports suggests that vascular factors are critical for the pathogenesis of AD. However, the precise mechanistic correlation between inflammation and angiogenesis in AD has not been well elucidated. Prostaglandin E2 (PGE2), a key factor of the inflammatory response, has been known to promote angiogenesis. In this study, we demonstrated that PGE2 acts through EP4 receptor and protein kinase A to modulate CCAAT/enhancer-binding protein delta (CEBPD) abundance in astrocytes. Attenuated vessel formation was observed in the brains of AppTg/Cebpd(-/-) mice. We showed that miR135a was responsive to the induction of CEBPD and further negatively regulated thrombospondin 1 (THBS1) transcription by directly targeting its 3'-untranslated region (3'UTR) in astrocytes. Furthermore, conditioned media from astrocytes expressing miR135a promoted Human umbilical vein endothelial cells (HUVECs) tube-like formation, which correlated with the effects of PGE2 on angiogenesis. Our results indicated that CEBPD contributes to the repression of THBS1 transcription by activating the expression of miR135a in astrocytes following PGE2 treatment. We provided new evidence that astrocytic CEBPD increases angiogenesis during AD pathogenesis. This discovery supports the negative influence of CEBPD activation in astrocytes with respect to AD pathogenesis and implies that the CEBPD/miR135a/THBS1 axis could be a therapeutic target of AD.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 PLoS One. 2015, 10(4):e0124504. doi: 10.1371/journal.pone.0124504. eCollection 2015.
 Transcriptional Modulation of Intestinal Innate Defense/Inflammation Genes by Preterm Infant Microbiota in a Humanized Gnotobiotic Mouse Model
 
 
 Lei Lu, Yueyue Yu, Yuee Guo, Yunwei Wang, Eugene B. Chang, Erika C. Claud
  Abstract
Background and Aims: It is known that postnatal functional maturation of the small intestine is facilitated by microbial colonization of the gut. Preterm infants exhibit defects in gut maturation, weak innate immunity against intestinal infection and increased susceptibility to inflammatory disorders, all of which may be related to the inappropriate microbial colonization of their immature intestines. The earliest microbes to colonize the preterm infant gut encounter a naïve, immature intestine. Thus this earliest microbiota potentially has the greatest opportunity to fundamentally influence intestinal development and immune function. The aim of this study was to characterize the effect of early microbial colonization on global gene expression in the distal small intestine during postnatal gut development. Methods: Gnotobiotic mouse models with experimental colonization by early (prior to two weeks of life) intestinal microbiota from preterm human infants were utilized. Microarray analysis was used to assess global gene expression in the intestinal epithelium. Results and Conclusion: Multiple intestinal genes involved in metabolism, cell cycle regulation, cell-cell or cell-extracellular matrix communication, and immune function are developmental- and intestinal microbiota- regulated. Using a humanized gnotobiotic mouse model, we demonstrate that certain early preterm infant microbiota from prior to 2 weeks of life specifically induce increased NF-£eB activation and a phenotype of increased inflammation whereas other preterm microbiota specifically induce decreased NF-£eB activation. These fundamental differences correlate with altered clinical outcomes and suggest the existence of optimal early microbial communities to improve health outcomes.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 The International Journal of Biochemistry & Cell Biology. 2015, 60:99-111. doi: 10.1016/j.biocel.2014.12.024.
 Identification of stage-specific markers during differentiation of hair cells from mouse inner ear stem cells or progenitor cells in vitro
 
 
 Quanwen Liu, JiarongChen, XiangliGao, JieDing, ZihuaTang, CuiZhang, Jianling Chen, Liang Li, PingChen, JinfuWang
  Abstract
The induction of inner ear hair cells from stem cells or progenitor cells in the inner ear proceeds through a committed inner ear sensory progenitor cell stage prior to hair cell differentiation. To increase the efficacy of inducing inner ear hair cell differentiation from the stem cells or progenitor cells, it is essential to identify comprehensive markers for the stem cells/progenitor cells from the inner ear, the committed inner ear sensory progenitor cells and the differentiating hair cells to optimize induction conditions. Here, we report that we efficiently isolated and expanded the stem cells or progenitor cells from postnatal mouse cochleae, and induced the generation of inner ear progenitor cells and subsequent differentiation of hair cells. We profiled the gene expression of the stem cells or progenitor cells, the inner ear progenitor cells, and hair cells using aRNA microarray analysis. The pathway and gene ontology (GO) analysis of differentially expressed genes was performed. Analysis of genes exclusively detected in one particular cellular population revealed 30, 38, and 31 genes specific for inner ear stem cells, inner ear progenitor cells, and hair cells, respectively. We further examined the expression of these genes in vivo and determined that Gdf10+Ccdc121, Tmprss9+Orm1, and Chrna9+Espnl are marker genes specific for inner ear stem cells, inner ear progenitor cells, and differentiating hair cells, respectively. The identification of these marker genes will likely help the effort to increase the efficacy of hair cell induction from the stem cells or progenitor cells.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Environmental Toxicology. 2015, 30(6):712-23. doi: 10.1002/tox.21949.
 Prenatal and neonatal exposure to perfluorooctane sulfonic acid results in aberrant changes in miRNA expression profile and levels in developing rat livers
 
 
 Fan Wang, Yihe Jin, Faqi Wang, Junsheng Ma, Wei Liu
  Abstract
Perfluorooctane sulfonate (PFOS) is an animal carcinogen. However, the underlying mechanism in cancer initiation is still largely unknown. Recently identified microRNAs (miRNAs) may play an important role in toxicant exposure and in the process of toxicant-induced tumorigenesis. We used PFOS to investigate PFOS-induced changes in miRNA expression in developing rat liver and the potential mechanism of PFOS-induced toxic action. Dams received 3.2 mg/kg PFOS in their feed from gestational day 1 (GD1) to postnatal day 7 (PND 7). Pups then had free access to treated feed until PND 7. We isolated RNAs from liver tissues on PND 1 and 7 and analyzed the expression profiles of 387 known rat miRNAs using microarray technology. PFOS exposure induced significant changes in miRNA expression profiles. Forty-six miRNAs had significant expression alterations on PND 1, nine miRNAs on PND 7. Specifically, expression of four miRNAs was up-regulated on PND 7 but down-regulated on PND1 (p < 0.05). Many aberrantly expressed miRNAs were related to various cancers. We found oncogenic and tumor-suppressing miRNAs, which included miR-19b, miR-21*, miR-17-3p, miR-125a-3p, miR-16, miR-26a, miR-1, miR-200c, and miR-451. In addition, four miRNAs were simultaneous significantly expressed on both PND 1 and 7. Functional Annotation analysis of the predicted transcript targets revealed that PFOS exposure potentially alters pathways associated with different cancers (cancer, melanoma, pancreatic cancer, colorectal cancer, and glioma), biological processes which include positive regulation of apoptosis and cell proliferation. Results showed PFOS exposure altered the expression of a suite of miRNAs.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Evidence-Based Complementary and Alternative Medicine. 2015:425760. doi: 10.1155/2015/425760.
 Molecular Signatures in the Prevention of Radiation Damage by the Synergistic Effect of N-Acetyl Cysteine and Qingre Liyan Decoction, a Traditional Chinese Medicine, Using a 3-Dimensional Cell Culture Model of Oral Mucositis
 
 
 Lavanya Kondapalli, Cyrus Parsa, Hari Chandana Mulamalla, Robert Orlando, Doreen Pon, Ying Huang, Moses S. S. Chow, Maria P. Lambros
  Abstract
Qingre Liyan decoction (QYD), a Traditional Chinese medicine, and N-acetyl cysteine (NAC) have been used to prevent radiation induced mucositis. This work evaluates the protective mechanisms of QYD, NAC, and their combination (NAC-QYD) at the cellular and transcriptional level. A validated organotypic model of oral mucosal consisting of a three-dimensional (3D) cell tissue-culture of primary human keratinocytes exposed to X-ray irradiation was used. Six hours after the irradiation, the tissues were evaluated by hematoxylin and eosin (H and E) and a TUNEL assay to assess histopathology and apoptosis, respectively. Total RNA was extracted and used for microarray gene expression profiling. The tissue-cultures treated with NAC-QYD preserved their integrity and showed no apoptosis. Microarray results revealed that the NAC-QYD caused the upregulation of genes encoding metallothioneins, HMOX1, and other components of the Nrf2 pathway, which protects against oxidative stress. DNA repair genes (XCP, GADD45G, RAD9, and XRCC1), protective genes (EGFR and PPARD), and genes of the NF£eB pathway were upregulated. Finally, tissue-cultures treated prophylactically with NAC-QYD showed significant downregulation of apoptosis, cytokines and chemokines genes, and constrained damage-associated molecular patterns (DAMPs). NAC-QYD treatment involves the protective effect of Nrf2, NF£eB, and DNA repair factors.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Oncogene. 2014 Dec 22. doi: 10.1038/onc.2014.409.
 NCOA3-mediated upregulation of mucin expression via transcriptional and post-translational changes during the development of pancreatic cancer
 
 
 S Kumar, S Das, S Rachagani, S Kaur, S Joshi, SL Johansson, MP Ponnusamy, M Jain, SK Batra
  Abstract
Pancreatic cancer (PC) is characterized by aberrant overexpression of mucins that contribute to its pathogenesis. Although the inflammatory cytokines contribute to mucin overexpression, the mucin profile of PC is markedly distinct from that of normal or inflamed pancreas. We postulated that de novo expression of various mucins in PC involves chromatin modifications. Analysis of chromatin modifying enzymes by PCR array identified differential expression of NCOA3 in MUC4-expressing PC cell lines. Immunohistochemistry analysis in tumor tissues from patients and spontaneous mouse models, and microarray analysis following the knockdown of NCOA3 were performed to elucidate its role in mucin regulation and overall impact on PC. Silencing of NCOA3 in PC cell lines resulted in significant downregulation of two most differentially expressed mucins in PC, MUC4 and MUC1 (P<0.01). Immunohistochemistry analysis in PC tissues and metastatic lesions established an association between NCOA3 and mucin (MUC1 and MUC4) expression. Spontaneous mouse model of PC (K-rasG12D; Pdx-1cre) showed early expression of Ncoa3 during pre-neoplastic lesions. Mechanistically, NCOA3 knockdown abrogated retinoic acid-mediated MUC4 upregulation by restricting MUC4 promoter accessibility as demonstrated by micrococcus nuclease digestion (P<0.05) and chromatin immuno-precipitation analysis. NCOA3 also created pro-inflammatory conditions by upregulating chemokines like CXCL1, 2, 5 and CCL20 (P<0.001). AKT, ubiquitin C, ERK1/2 and NF-£eB occupied dominant nodes in the networks significantly modulated after NCOA3 silencing. In addition, NCOA3 stabilized mucins post translationally through fucosylation by FUT8, as the knockdown of FUT8 resulted in the downregulation of MUC4 and MUC1 at protein levels.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Oncotarget. 2014, 5(20):9838-50.
 A novel action mechanism for MPT0G013, a derivative of arylsulfonamide, inhibits tumor angiogenesis through upregulation of TIMP3 expression
 
 
 Chih-Ya Wang, Jing-Ping Liou, An-Chi Tsai, Mei-Jung Lai, Yi-Min Liu, Hsueh-Yun Lee, Jing-Chi Wang, Che-Ming Teng, Shiow-Lin Pan
  Abstract
Tissue inhibitors of metalloproteinases 3 (TIMP3) were originally characterized as inhibitors of matrix metalloproteinases (MMPs), acting as potent antiangiogenic proteins. In this study, we demonstrated that the arylsulfonamide derivative MPT0G013 has potent antiangiogenic activities in vitro and in vivo viainducing TIMP3 expression. Treatments with MPT0G013 significantly inhibited endothelial cell functions, such as cell proliferation, migration, and tube formation, as well as induced p21 and cell cycle arrest at the G0/G1 phase. Subsequent microarray analysis showed significant induction of TIMP3 gene expression by MPT0G013, and siRNA-mediated blockage of TIMP3 up-regulation abrogated the antiangiogenic activities of MPT0G013 and prevented inhibition of p-AKT and p-ERK proteins. Importantly, MPT0G013 exhibited antiangiogenic activities in in vivo Matrigel plug assays, inhibited tumor growth and up-regulated TIMP3 and p21 proteins in HCT116 mouse xenograft models. These data suggest potential therapeutic application of MPT0G013 for angiogenesis-related diseases such as cancer.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 International Journal of Clinical and Experimental Medicine. 2014, 7(12): 5226¡V5234.
 Aberrant expression of microRNAs in serum may identify individuals with pancreatic cancer
 
 
 Wei-Chang Chen, Heng-Jun Gao, Hai-Hui Sheng, Mao-Song Lin, Jun-Xing Huang
  Abstract
Pancreatic cancer (PC) has the poorest survival rate among all types of human cancer due to the lack of sensitive and non-invasive diagnostic screen methods for PC screening. Our aim was to identify novel serum microRNA (miRNA) biomarkers for the early detection of PC. We used microarray to screen differential expression of miRNAs in two pooled serum samples (6 PC patients and 6 healthy controls). A panel of miRNAs (22 over-expression and 23 decreased) were deregulated in serum of PC patients in comparison to controls. The expressions of 8 selected miRNAs were further evaluated in sera from 49 PC patients and 27 controls using quantitative reverse transcription-polymerase chain reaction. The levels of serum miR-492 and miR-663a were significantly decreased in PC patients compared with controls (P < 0.05). ROC curve analysis showed that serum miR-492 and miR-663a yield an AUC of 0.787 with 75.5% sensitivity and 70.0% specificity and 0.870 with 85.7% sensitivity and 80.0% specificity, respectively, for discriminating between PC patients and healthy controls. In addition, the level of miR-663a was significantly and inversely associated with TNM stage (P = 0.027). These results suggested that serum miR-492 and miR-663a could have strong potential as novel non-invasive biomarkers for the early detection of PC.
   

  ✔本篇論文使用華聯產品:Rat OneArray  
 Transactions of Tianjin University. 2014, 20: 451-457. doi: 10.1007/s12209-014-2294-7.
 Transcriptomic Analysis of Aflatoxin B1-Regulated Genes in Rat Hepatic Epithelial Cells
 
 
 Liu Yang, Guanghui Li, Junwen Li, Zhaoli Chen, Jing Ji, Haiyong Wang
  Abstract
Aflatoxins are the most popular hepatotoxicants. Chronic exposure to aflatoxins leads to a wide variety of liver diseases, such as hepatocellular carcinoma. In this study, we analyzed the genome wide expression profiles of aflatoxin B1-induced rat hepatic epithelial cells. The expression of 325, 184 and 199 special genes was altered when exposed to 0.03, 0.1 and 0.2 £gmol/L aflatoxin B1 respectively, and 239 genes were commonly expressed. After the functional analysis on these dose-special genes, we determined several key pathways related to hepatotoxicity, such as TGF-beta signaling pathway, tight junction, adherens junction, the regulation of actin cytoskeleton, ErbB signaling pathway, p53 signaling pathway, pathways in cancer and axon guidance. Common genes were mainly associated with focal adhesion, ECM-receptor interaction, and cell adhesion molecules. Gene ontology annotations showed a good concordance with these pathways. The quantitative real-time polymerase chain reaction(PCR) analysis of selected genes showed similar patterns in microarrays. The toxicogenomic study provides a better understanding of molecular mechanisms of aflatoxins.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 PLoS One. 2014 December 1. doi: 10.1371/journal.pone.0113649.
 Nifedipine Promotes the Proliferation and Migration of Breast Cancer Cells
 
 
 Dong-Qing Guo, Hao Zhang, Sheng-Jiang Tan, Yu-Chun Gu
  Abstract
Nifedipine is widely used as a calcium channel blocker (CCB) to treat angina and hypertension,but it is controversial with respect the risk of stimulation of cancers. In this study, we demonstrated that nifedipine promoted the proliferation and migration of breast cancer cells both invivo and invitro. However, verapamil, another calcium channel blocker, didn¡¦t exert the similar effects. Nifedipine and high concentration KCl failed to alter the [Ca2+]i in MDA-MB-231 cells, suggesting that such nifedipine effect was not related with calcium channel. Moreover, nifedipine decreased miRNA-524-5p, resulting in the up-regulation of brain protein I3 (BRI3). Erk pathway was consequently activated and led to the proliferation and migration of breast cancer cells. Silencing BRI3 reversed the promoting effect of nifedipine on the breast cancer. In a summary, nifedipine stimulated the proliferation and migration of breast cancer cells via the axis of miRNA-524-5p-BRI3¡VErk pathway independently of its calcium channel-blocking activity. Our findings highlight that nifedipine but not verapamil is conducive for breast cancer growth and metastasis, urging that the caution should be taken in clinic to prescribe nifedipine to women who suffering both hypertension and breast cancer, and hypertension with a tendency in breast cancers.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 PLoS One. 2014 December 5. doi: 10.1371/journal.pone.0114781.
 Functional Study of One Nucleotide Mutation in Pri-MiR-125a Coding Region which Related to Recurrent Pregnancy Loss
 
 
 Yi Hu, Zheng-Hao Huo, Chun-Mei Liu, Shi-Guo Liu, Ning Zhang, Kun-Lun Yin, Xu Ma, Hong-Fei Xia
  Abstract
MicroRNAs (miRNAs) are short non-coding RNAs which modulate gene expression by binding to complementary segments present in the 3¡¬UTR of the mRNAs of protein coding genes. MiRNAs play very important roles in maintaining normal human body physiology conditions, meanwhile, abnormal miRNA expressions have been found related to many human diseases spanning from psychiatric disorders to malignant cancers. Recently, emerging reports have indicated that disturbed miRNAs expression contributed to the pathogenesis of recurrent pregnancy loss (RPL). In this study, we identified a new mutation site (+29A>G, position relative to pre-miR-125a) by scanning pri-miR-125a coding region in 389 Chinese Han RPL patients. This site was co-existed with two polymorphisms (rs12976445 and rs41275794) in patients heterogeneously and changed the predicted secondary structures of pri-miR-125a. Subsequent in vitro analysis indicated that the A>G mutation reduced mature miR-125a expression, and further led to less efficient inhibition of verified target genes. Functional analysis showed that mutant pri-mir-125a can enhance endometrial stromal cells (ESCs) invasive capacity and increase the sensitivity of ESCs cells to mifepristone. Moreover, we further analyzed the possible molecular mechanism by RIP-chip assay and found that mutant pri-mir-125a disturbed the expression of miR-125a targetome, the functions of which includes embryonic development, cell proliferation, migration and invasion. These data suggest that A>G mutation in pri-miR-125a coding region contributes to the genetic predisposition to RPL by disordering the production of miR-125a, which consequently meddled in gene regulatory network between mir-125a and mRNA.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Northeast Bioengineering Conference (NEBEC). 2014 April 25-27.
 FGF2 and oxygen: Regulators of intergrin alpha-11 and extracellular matrix molecules
 
 
 Alexandra Grella, Denis Kole, Tanja Dominko
  Abstract
Recently, derivation and maintenance of pluripotent stem cells has been focused on environmental cues, with emphasis on the role of extracellular matrix (ECM) and adhesion molecules (AM). We have developed a novel approach that allows for induction of stem cell gene expression in human dermal fibroblasts (hDF) without the use of transgenes. By culturing cells in low oxygen (5% O2) with addition of exogenous FGF2 we have shown that hDF in defined culture conditions express stem cell genes and show translation and nuclear translocation of stem cell transcription factors. We have demonstrated that this shift is coupled with an FGF2-dependent down-regulation of the majority of AM and ECM targets; specifically induction of a significant down-regulation of integrin alpha 11 (Itga11) transcript and results in Itga11 loss from focal adhesions. Investigation of the mechanism by which FGF2 may be involved in regulation of Itga11 is being investigated by studying the molecular pathway downstream of FGF2 ligand that may be involved in the loss of Itga11 and associated collagen I attachment. Dissecting the molecular mechanisms involved in regulation through modulation of extracellular environment and its effect on plasticity may provide insight into the acquisition into the mechanisms involved in reprogramming of differentiated cells.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Oncotarget. 2014 Nov 17.
 Transcriptomic profiling of taxol-resistant ovarian cancer cells identifies FKBP5 and the androgen receptor as critical markers of chemotherapeutic response
 
 
 Nian-Kang Sun, Shang-Lang Huang, Pu-Yuan Chang, Hsing-Pang Lu, Chuck C.-K. Chao
  Abstract
Taxol is a mitotoxin widely used to treat human cancers, including of the breast and ovary. However, taxol resistance (txr) limits treatment efficacy in human patients. To study chemoresistance in ovarian cancer, we established txr ovarian carcinoma cells derived from the SKOV3 cell lineage. The cells obtained were cross-resistant to other mitotoxins such as vincristine while they showed no resistance to the genotoxin cisplatin. Transcriptomic analysis identified 112 highly up-regulated genes in txr cells. Surprisingly, FK506-binding protein 5 (FKBP5) was transiently up-regulated 100-fold in txr cells but showed decreased expression in prolonged culture. Silencing of FKBP5 sensitized txr cells to taxol, whereas ectopic expression of FKBP5 increased resistance to the drug. Modulation of FKBP5 expression produced similar effects in response to vincristine but not to cisplatin. We observed that a panel of newly identified txr genes was trancriptionally regulated by FKBP5 and silencing of these genes sensitized cells to taxol. Notably, immunoprecipitation experiments revealed that FKBP5 forms a protein complex with the androgen receptor (AR), and this complex regulates the transcriptional activity of both proteins. Furthermore, we found that the Akt kinase pathway is regulated by FKBP5. These results indicate that the FKBP5/AR complex may affect cancer cell sensitivity to taxol by regulating expression of txr genes. Our findings suggest that mitotoxin-based treatment against ovarian cancer should be avoided when the Akt/FKBP5/AR axis is activated.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 BioMed Research International. 2014 Oct 13.
 TLR4/NF-𝜅B-Responsive MicroRNAs and Their Potential Target Genes: A Mouse Model of Skeletal Muscle Ischemia-Reperfusion Injury
 
 
 Johnson Chia-Shen Yang, Shao-Chun Wu, Cheng-Shyuan Rau, Yi-Chun Chen, Tsu-Hsiang Lu, Yi-Chan Wu, Siou-Ling Tzeng, Chia-Jung Wu, Ching-Hua Hsieh
  Abstract
Background. The aim of this study was to profile TLR4/NF-£eB-responsive microRNAs (miRNAs) and their potential target genes in the skeletal muscles of mice following ischemia-reperfusion injury. Methods. Thigh skeletal muscles of C57BL/6, Tlr4−/−, and NF-£eB−/− mice isolated based on femoral artery perfusion were subjected to ischemia for 2 h and reperfusion for 0 h, 4 h, 1 d, and 7 d. The muscle specimens were analyzed with miRNA arrays. Immunoprecipitation with an argonaute 2- (Ago2-) specific monoclonal antibody followed by whole genome microarray was performed to identify mRNA associated with the RNA-silencing machinery. The potential targets of each upregulated miRNA were identified by combined analysis involving the bioinformatics algorithm miRanda and whole genome expression. Results. Three TLR4/NF-£eB-responsive miRNAs (miR-15a, miR-744, and miR-1196) were significantly upregulated in the muscles following ischemia-reperfusion injury. The combined in silico and whole genome microarray approaches identified 5, 4, and 20 potential target genes for miR-15a, miR-744, and miR-1196, respectively. Among the 3 genes (Zbed4, Lrsam1, and Ddx21) regulated by at least 2 of the 3 upregulated miRNAs, Lrsam1 and Ddx21 are known to be associated with the innate immunity pathway. Conclusions. This study profiled TLR4/NF-£eB-responsive miRNAs and their potential target genes in mouse skeletal muscle subjected to ischemia-reperfusion injury.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 PLoS One. 2014 Oct 14. doi: 10.1371/journal.pone.0109198.
 Cellular Intrinsic Mechanism Affecting the Outcome of AML Treated with Ara-C in a Syngeneic Mouse Model
 
 
 Bin Yin, Wenjun Zhao, Lirong Wei, Dongming Tan, Guangsong Su, Yanwen Zheng, Chao He, Zhengwei J. Mao, Timothy P. Singleton
  Abstract
The mechanisms underlying acute myeloid leukemia (AML) treatment failure are not clear. Here, we established a mouse model of AML by syngeneictransplantation of BXH-2 derived myeloid leukemic cells and developed an efficacious Ara-C-based regimen for treatment of these mice. We proved that leukemic cell load was correlated with survival. We also demonstrated that the susceptibility of leukemia cells to Ara-C could significantly affect the survival. To examine the molecular alterations in cells with different sensitivity, genome-wide expression of the leukemic cells was profiled, revealing that overall 366 and 212 genes became upregulated or downregulated, respectively, in the resistant cells. Many of these genes are involved in the regulation of cell cycle, cellular proliferation, and apoptosis. Some of them were further validated by quantitative PCR. Interestingly, the Ara-Cresistant cells retained the sensitivity to ABT-737, an inhibitor of anti-apoptosis proteins, and treatment with ABT-737 prolonged the life span of mice engrafted with resistant cells. These results suggest that leukemic load and intrinsic cellular resistance can affect the outcome of AML treated withAra-C. Incorporation of apoptosis inhibitors, such as ABT-737, into traditional cytotoxic regimens merits consideration for the treatment of AML in a subset of patients with resistance to Ara-C. This work provided direct in vivo evidence that leukemic load and intrinsic cellular resistance can affect theoutcome of AML treated with Ara-C, suggesting that incorporation of apoptosis inhibitors into traditional cytotoxic regimens merits consideration for the treatment of AML in a subset of patients with resistance to Ara-C.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Medical Journal of Chinese People's Liberation Army. 2014 Oct 1. doi: 10.11855/j.issn.0577-7402.2014.10.08.
 Identification of the difference in gene expression between glioma stem cells and neural stem cells by oligonucleotide microarray
 
 
 Shuang LIU, Feng YIN, Jian-ning ZHANG, Ming-ming ZHAO, Chun-hui ZHOU, Shu-wei WANG, Xin-ru GUO
  Abstract
Objective¡@To identify the differential expressed genes of human glioma stem cells (GSCs) and human neural stem cells (NSCs) by gene chip technology. Methods¡@Human HOA5.1 OneArray microarray (including 29 186 genes) was adopted and hybridized with probes which were prepared from the total RNAs of GSCs and NSCs. Differential expressed genes between the GSCs and NSCs were assayed after scanning oligonucleotide microarray with ScanArray 4000, and some of these genes such as DCX, PTGS2, SCGN, GAD2, OTX2, PEG10 and NRXN3 were verified by real-time-Q-PCR method. Results¡@Compared with the genes in normal NSCs, 1372 down-regulated and 1501 up-regulated genes in GSCs were revealed by means of microarray, and these genes were associated with axon guidance, cell cycle, cell adhesion, immune-inflammatory responses and cancer-related signal pathways. The results of qRT-PCR were consistent with that of microarray. Conclusions¡@Multiple genes play important roles in development of glioma. This study may provide new clues for the targeted therapy of malignant glioma.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Molecular Medicine Reports. 2014 Oct 30. doi: 10.3892/mmr.2014.2823.
 Biological effect of ketamine in urothelial cell lines and global gene expression analysis in the bladders of ketamine‑injected mice
 
 
 YI‑WEN LIU, CHENG‑HUANG SHEN, SHOU‑TSUNG WANG, YING‑RAY LEE, SHIAU‑YUAN LIU, YI‑ZHEN LI, JIANN‑DER WU, YI‑JU CHEN
  Abstract
Ketamine is used clinically for anesthesia but is also abused as a recreational drug. Previously, it has been established that ketamine‑inducedbladder interstitial cystitis is a common syndrome in ketamine‑abusing individuals. As the mechanisms underlying ketamine‑induced cystitis have yet to be revealed, the present study investigated the effect of ketamine on human urothelial cell lines and utilized a ketamine‑injected mouse model to identify ketamine‑induced changes in gene expression in mice bladders. In the in vitro bladder cell line assay, ketamine induced cytotoxicity in a dose‑ and time‑dependent manner. Ketamine arrested the cells in G1 phase and increased the sub‑G1 population, and also increased the barrier permeability of these cell lines. In the ketamine‑injected mouse model, ketamine did not change the body weight and bladder histology of the animals at the dose of 30 mg/kg/day for 60 days. Global gene expression analysis of the animals' bladders following data screening identified ten upregulated genes and 36 downregulated genes induced by ketamine. A total of 52% of keratin family genes were downregulated, particularly keratin 6a, 13 and 14, which was confirmed by polymerase chain reaction analysis. Keratin 14 protein, one of the 36 ketamine‑induced downregulated genes, was also reduced in the ketamine‑treated mouse bladder, as determined by immunohistochemical analysis. This suggested that cytotoxicity and keratin genedownregulation may have a critical role in ketamine‑induced cystitis.
   

  ✔本篇論文使用華聯產品:Array technology and applications  
 Pediatrics & Neonatology. 2014 Nov 4. doi:10.1016/j.pedneo.2014.08.001.
 Genetic Evaluation of Children with Global Developmental Delay¡XCurrent Status of Network Systems in Taiwan
 
 
 Shio-Jean Lin, Yong-Lin Foo, Julie Chi Chow, Ming-Chi Lai, Wen-Hui Tsai, Li-Chen Tung, Mei-Chin Kuo
  Abstract
This review article aims to introduce the screening and referral network of genetic evaluation for children with developmental delay in Taiwan. For these children, integrated systems provide services from the medical, educational, and social welfare sectors. All cities and counties in Taiwan have established a network for screening, detection, referral, evaluation, and intervention services. Increased awareness improves early detection and intervention. There remains a gap between supply and demand, especially with regard to financial resources and professional manpower. Genetic etiology has a major role in prenatal causes of developmental delay. A summary of reports on some related genetic disorders in the Taiwanese population is included in this review. Genetic diagnosis allows counseling with regard to recurrence risk and prevention. Networking with neonatal screening, laboratory diagnosis, genetic counseling, and orphan drugs logistics systems can provide effective treatment for patients. In Taiwan, several laboratories provide genetic tests for clinical diagnosis. Accessibility to advanced expensive tests such as gene chips or whole exome sequencing is limited because of funding problems; however, the service system in Taiwan can still operate in a relatively cost-effective manner. This experience in Taiwan may serve as a reference for other countries.
   

  ✔本篇論文使用華聯產品:Array technology and applications  
 Advances in Clinical Chemistry. 2014 Nov 4. doi:10.1016/bs.acc.2014.09.007.
 Circulating microRNAs as Promising Tumor Biomarkers
 
 
 Qing H. Meng, Meng Chen, George A. Calin
  Abstract
microRNAs (miRNAs) are small, nonprotein-coding RNAs that function as posttranscriptional regulators of target genes. miRNAs are involved in multiple cell differentiation, proliferation, and apoptosis processes that are closely related to tumorigenesis. Circulating miRNAs are promising cancer biomarkers under development with great translational potential in personalized medicine. Here, we describe the origin and function of circulating miRNAs and compare the current new high-throughput technology applied to miRNA quantitation. The latest publications on circulating miRNAs were summarized, indicating that miRNAs are potential biomarkers of diagnosis, prognosis, and treatment response of major cancer types including prostate, breast, lung, colorectal, and hematological cancers. We addressed the strengths and limitations of applying circulating miRNAs in clinical laboratory and several issues associated with the accurate measurement of circulating miRNAs.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Molecular and Cellular Endocrinology. 2014, 382(2):804-13. doi: 10.1016/j.mce.2013.10.031.
 Knockdown of TrkA in cumulus oocyte complexes (COCs) inhibits EGF-induced cumulus expansion by down-regulation of IL-6
 
 
 Sun F, Wang Y, Liang N, Yao G, Tian H, Zhai Y, Yin Y
  Abstract
Tyrosine kinase receptor A (TrkA), the high-affinity receptor of nerve growth factor (NGF), is known to play key roles in ovarian follicular development, such as assembly of early follicles and follicular ovulation. However, little is known about the roles of TrkA in cumulus oocyte complex (COC)expansion. In this study, we found that TrkA was abundant in large antral follicles and knockdown of TrkA in COCs attenuated epidermal growth factor (EGF)-induced COC expansion and further decreased the ovulation rate. The effect of TrkA on COC expansion was not mediated through downstream EGF effectors, phosphorylation of extracellular regulated protein kinases 1/2 (ERK1/2) or drosophila mothers against decapentaplegic protein (SMAD), or through up-regulation of COC expansion-related transcripts such as prostaglandin-endoperoxide synthase 2 (Ptgs2), hyaluronan synthase 2 (Has2), TNF-induced protein 6 (Tnfaip6) or pentraxin 3 (Ptx3). However, pharmacological blockade of TrkA transducing activity (K252£) in COCsdecreased the mRNA expression and protein secretion of interleukin-6 (IL-6), identified from mRNA microarray of K252£-treated COCs. Meanwhile,knockdown of IL-6 attenuated EGF-induced COC expansion. In addition, IL-6 rescued the inhibitory effect of K252£ on EGF-induced cumulusexpansion. Therefore, IL-6 may act as a new potential cumulus expansion-related transcript, which may be involved in the integration of TrkA and EGF signaling in affecting COC expansion. Here, we provide mechanistic insights into the roles of TrkA in EGF-induced cumulus expansion. Understanding potential cross-points between TrkA and EGF affecting cumulus expansion will help in the discovery of new therapeutic targets in ovulation-related diseases.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Oncogene. 2014 Jun 23. doi: 10.1038/onc.2014.177.
 HSF1 regulation of £]-catenin in mammary cancer cells through control of HuR/elavL1 expression
 
 
 SK Calderwood, S-D Chou, A Murshid, T Eguchi, J Gong
  Abstract
There is now compelling evidence to indicate a place for heat shock factor 1 (HSF1) in mammary carcinogenesis, tumour progression and metastasis. Here we have investigated a role for HSF1 in regulating the expression of the stem cell renewal factor £]-catenin in immortalized humanmammary epithelial and carcinoma cells. We found HSF1 to be involved in regulating the translation of £]-catenin, by investigating effects of gain and loss of HSF1 on this protein. Interestingly, although HSF1 is a potent transcription factor, it was not directly involved in regulating levels of £]-catenin mRNA. Instead, our data suggest a complex role in translational regulation. HSF1 was shown to regulate levels of the RNA-binding protein HuR that controlled £]-catenin translation. An extra complexity was added to this scenario when it was shown that the long non-coding RNA molecule lincRNA-p21, known to be involved in £]-catenin mRNA (CTNNB1) translational regulation, was controlled by HSF1 repression. We have shown previously thatHSF1 was positively regulated through phosphorylation by mammalian target of rapamycin (mTOR) kinase on a key residue, serine 326, essential for transcriptional activity. In this study, we found that mTOR knockdown not only decreased HSF1-S326 phosphorylation in mammary cells, but also decreased £]-catenin expression through a mechanism requiring HuR. Our data point to a complex role for HSF1 in the regulation of HuR and £]-catenin expression that may be significant in mammary carcinogenesis.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Scientific Reports. 2014 Oct 6;4:6527. doi: 10.1038/srep06527.
 Reduced miR-3127-5p expression promotes NSCLC proliferation/invasion and contributes to dasatinib sensitivity via the c-Abl/Ras/ERK pathway
 
 
 Bo Su, Wen Gao, Yifeng Sun, Chang Chen, Peng Zhang, Huikang Xie, Likun Hou, Zheng Hui, Yongjie Xu, Qiaoling Du, Xiao Zhou
  Abstract
miR-3127-5p is a primate-specific miRNA which is down-regulated in recurrent NSCLC tissue vs. matched primary tumor tissue (N = 15) and in tumor tissue vs. normal lung tissue (N = 177). Reduced miR-3127-5p expression is associated with a higher Ki-67 proliferation index and unfavorable prognosis in NSCLC. Overexpression of miR-3127-5p significantly reduced NSCLC cells proliferation, migration, and motility in vitro and in vivo. The oncogene ABL1 was a direct miR-3127-5p target, and miR-3127-5p regulated the activation of the Abl/Ras/ERK pathway and transactivated downstream proliferation/metastasis-associated molecules. Overexpression of miR-3127-5p in A549 or H292 cells resulted in enhanced resistance todasatinib, an Abl/src tyrosine kinase inhibitor. miR-3127-5p expression levels were correlated with dasatinib sensitivity in NSCLC cell lines without K-Ras G12 mutation. In conclusion, miR-3127-5p acts as a tumor suppressor gene and is a potential biomarker for dasatinib sensitivity in the non-mutated Ras subset of NSCLC.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Frontiers in Genetics. 2014, 5:246. doi: 10.3389/fgene.2014.00246.
 An investigation into anti-proliferative effects of microRNAs encoded by the miR-106a-363 cluster on human carcinoma cells and keratinocytes using microarray profiling of miRNA transcriptomes
 
 
 Cuong Khuu, Anne-MartheJevnaker, MagneBryne, HaraldOsmundsen
  Abstract
Transfection of human oral squamous carcinoma cells (clone E10) with mimics for unexpressed miR-20b or miR-363-5p, encoded by the miR-106a-363 cluster (miR-20b, miR-106a, miR-363-3p, or miR-363-5p), caused 40-50% decrease in proliferation. Transfection with mimics for miR-18a or miR-92a, encoded by the miR-17-92 cluster (all members being expressed in E10 cells), had no effect on proliferation. In contrast, mimic for the siblingmiRNA-19a yielded about 20% inhibition of proliferation. To investigate miRNA involvement profiling of miRNA transcriptomes were carried out using deoxyoligonucleotide microarrays. In transfectants for miR-19a, or miR-20b or miR-363-5p most differentially expressed miRNAs exhibited decreased expression, including some miRNAs encoded in paralogous miR-17-92-or miR-106b-25 cluster. Only in cells transfected with miR-19a mimic significantly increased expression of miR-20b observed-about 50-fold as judged by qRT-PCR. Further studies using qRT-PCR showed that transfection of E10 cells with mimic for miRNAs encoded by miR-17-92 - or miR-106a-363 - or the miR-106b-25 cluster confirmed selective effect on expression on sibling miRNAs. We conclude that high levels of miRNAs encoded by the miR-106a-363 cluster may contribute to inhibition of proliferation by decreasing expression of several sibling miRNAs encoded by miR-17-92 or by the miR-106b-25 cluster. The inhibition of proliferation observed in miR-19a-mimic transfectants is likely caused by the miR-19a-dependent increase in the levels of miR-20b and miR-106a. Bioinformatic analysis of differentially expressed miRNAs from miR-106a, miR-20b and miR-363-5p transfectants, but not miR-92a transfectants, yielded significant associations to "Cellular Growth and Proliferation" and "Cell Cycle." Western blotting results showed that levels of affected proteins to differ between transfectants, suggesting that different anti-proliferative mechanisms may operate in these transfectants.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Molecular Carcinogenesis. 2014 Sep 22. doi: 10.1002/mc.22221.
 MicroRNA-191, by promoting the EMT and increasing CSC-like properties, is involved in neoplastic and metastatic properties of transformed human bronchial epithelial cells
 
 
 Qizhan Liu, Wenchao Xu, Jie Ji, Yuan Xu, Yawei Liu, Le Shi, Yi Liu, Xiaolin Lu, Yue Zhao, Fei Luo, Bairu Wang, Rongrong Jiang, Jianping Zhang
  Abstract
Lung cancer is the leading cause of cancer mortality worldwide. A common interest in lung cancer research is the identification of biomarkers for early diagnosis and accurate prognosis. There is increasing evidence that microRNAs (miRNAs) are involved in lung cancer. To explore new biomarkers of chemical exposure in risk assessment of chemical carcinogenesis and lung cancer, we analyzed miRNA expression profiles of human bronchialepithelial (HBE) cells malignantly transformed by arsenite. High-throughput microarray analysis showed that 51 miRNAs were differentially expressed in transformed HBE cells relative to normal HBE cells. In particular, miR-191 was up-regulated in transformed cells. In HBE cells, arsenite induced increases of miR-191 and WT1 levels, decreased BASP1 expression, and activated the Wnt/£]-catenin pathway, effects that were blocked by miR-191 knockdown. In addition, a luciferase reporter assay indicated that BASP1 is a direct target of miR-191. By inhibiting the expression of BASP1, miR-191 increased the expression of WT1 to promote activation of Wnt/£]-catenin pathway. In transformed cells, inhibition of miR-191 expression blocked the epithelial-mesenchymal transition (EMT) and cancer stem cell (CSC)-like properties of cells and decreased their migratory capacity andneoplastic properties. Thus, these results demonstrate that miR-191 modulates the EMT and the CSC-like properties of transformed cells and indicate that it is an onco-miR involved in the neoplastic and metastatic properties of transformed cells. 
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Archives of Toxicology. 2014 Oct 2.
 Di-(2-ethylhexyl) phthalate accelerates atherosclerosis in apolipoprotein E-deficient mice
 
 
 Jin‑Feng Zhao, Sheng‑Huang Hsiao, Ming‑Hua Hsu, Kuan‑Chuan Pao, Yu Ru Kou, Song‑Kun Shyue, Tzong‑Shyuan Lee
  Abstract
Di-(2-ethylhexyl) phthalate (DEHP) is associated with atherosclerosis-related cardiovascular disease complications, but we lack direct evidence of its unfavorable effect on atherogenesis. In this study, we aimed to clarify in vivo and in vitro the contribution of DEHP to the development ofatherosclerosis and its underlying mechanisms. Apolipoprotein E-deficient (apoE-/-) mice chronically treated with DEHP for 4 weeks showed exacerbated hyperlipidemia, systemic inflammation, and atherosclerosis. In addition, DEHP promoted low-density lipoprotein (LDL) oxidation, which led to inflammation in endothelial cells as evidenced by increased protein expression of pro-inflammatory mediators. Furthermore, chronic DEHP treatment increased hepatic cholesterol accumulation by downregulating the protein expression of key regulators in cholesterol clearance including LDL receptor, cholesterol 7£-hydrolase, ATP-binding cassette transporter G5 and G8, and liver X receptor £. Moreover, the adiposity and inflammation of white adipose tissues were promoted in DEHP-treated apoE-/- mice. In conclusion, DEHP may disturb cholesterol homeostasis and deregulate the inflammatory response, thus leading to accelerated atherosclerosis.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Journal of Agricultural and Food Chemistry. 2014, 62(36):8952-61. doi: 10.1021/jf5002099.
 A Novel Insulin Receptor-Binding Protein from Momordica charantia Enhances Glucose Uptake and Glucose Clearance in Vitro and in Vivo through Triggering Insulin Receptor Signaling Pathway
 
 
 Chien-Yun Hsiang, Hsin-Yi Lo, Tin-Yun Ho, Chia-Cheng Li, Jaw-Chyun Chen, Jau-Jin Liu
  Abstract
Diabetes, a common metabolic disorder, is characterized by hyperglycemia. Insulin is the principal mediator of glucose homeostasis. In a previous study, we identified a trypsin inhibitor, named Momordica charantia insulin receptor (IR)-binding protein (mcIRBP) in this study, that might interact with IR. The physical and functional interactions between mcIRBP and IR were clearly analyzed in the present study. Photo-cross-linking coupled with mass spectrometry showed that three regions (17-21, 34-40, and 59-66 residues) located on mcIRBP physically interacted with leucine-rich repeat domain and cysteine-rich region of IR. IR-binding assay showed that the binding behavior of mcIRBP and insulin displayed a cooperative manner. After binding to IR, mcIRBP activated the kinase activity of IR by (5.87 ¡Ó 0.45)-fold, increased the amount of phospho-IR protein by (1.31 ¡Ó 0.03)-fold, affected phosphoinositide-3-kinase/Akt pathways, and consequently stimulated the uptake of glucose in 3T3-L1 cells by (1.36 ¡Ó 0.12)-fold. Intraperitoneal injection of 2.5 nmol/kg mcIRBP significantly decreased the blood glucose levels by 20.9 ¡Ó 3.2% and 10.8 ¡Ó 3.6% in normal and diabetic mice, respectively. Microarray analysis showed that mcIRBP affected genes involved in insulin signaling transduction pathway in mice. In conclusion, our findings suggest that mcIRBP is a novel IRBP that binds to sites different from the insulin-binding sites on IR and stimulates both theglucose uptake in cells and the glucose clearance in mice.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Tumor Biology. 2014 Sep 18.
 miR-1285-3p acts as a potential tumor suppressor miRNA via downregulating JUN expression in hepatocellular carcinoma
 
 
 Jibing Liu, Jingchen Yan, Changchun Zhou, Qinghua Ma, Qingyan Jin, Zhenbin Yang
  Abstract
In the world, hepatocellular carcinoma (HCC) is one of the most common and most lethal cancers. Currently, standard therapy for unresectable HCC is a local-regional therapy with transarterial chemoembolisation (TACE). In this study, we sought to assess whether plasma circulating microRNAs (miRNAs) can be used to predict the prognosis of HCC patients receiving the TACE treatment. Firstly, we systematically examined TACE therapeutic effectiveness-related circulating miRNAs through miRNA Profiling Chips. As a result, we identified 19 circulating miRNAs to be significantly differentially expressed between the TACE-response group and the TACE-nonresponse group. In the second stage, we performed quantitative analyses of these candidate miRNAs in additional HCC patients treated with TACE and validated two of the aforementioned 19 miRNAs (miR-1285-3pand miR-4741) as candidate biomarkers for predicting prognosis of TACE. Interestingly, we found that miR-1285-3p could directly repress JUNoncogene expression in HCC cells, indicating miR-1285-3p could act as a potential tumor suppressor. In conclusion, our data indicate that circulatingmiR-1285-3p and miR-4741 was predictive of response to TACE therapy in HCC.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 International Journal of Clinical and Experimental Medicine (IJCEM). 2014, 7(9):2541-2549.
 Response gene to complement 32 (RGC-32) in endothelial cells is induced by glucose and helpful to maintain glucose homeostasis
 
 
 Shuzhen Guo, Melissa J Philbrick, Xiaojing An, Ming Xu, Jiaping Wu
  Abstract
Endothelium dysfunction has been understood primarily in terms of abnormal vasomotor function, which plays an important role in the pathogenesis of diabetes and chronic diabetic complications. However, it has not been fully studied that the endothelium may regulate metabolism itself. Theresponse gene to complement 32 (RGC-32) has be considered as an angiogenic inhibitor in the context of endothelial cells. We found that RGC-32was induced by high fat diet in vivo and by glucose or insulin in endothelial cells, and then we set out to investigate the role of endothelial RGC-32 in metabolism. DNA array analysis and qPCR results showed that glutamine-fructose-6-phosphate aminotransferase [isomerizing] 1 (GFPT1), solute carrier family 2 (facilitated glucose transporter), member 12 (SLC2A12, GLUT12) and glucagon-like peptide 2 receptor (GLP2R) may be among possible glucose metabolism related downstream genes of RGC-32. Additionally, in the mice with endothelial specific over-expressed RGC-32, the disposal of carbohydrate was improved without changing insulin sensitivity when mice were faced with high fat diet challenges. Taken together, our findings suggest that RGC-32 in the endothelial cells regulates glucose metabolism related genes and subsequent helps to maintain the homeostasisof blood glucose.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Cell Death & Disease. 2014 Oct 2. doi: 10.1038/cddis.2014.407.
 MicroRNA-207 enhances radiation-induced apoptosis by directly targeting Akt3 in cochlea hair cells
 
 
 Y-w Yuan, P-x Tan, S-s Du, C Ren, Q-w Yao, R Zheng, R Li
  Abstract
MicroRNAs (miRNAs) have important roles in various types of cellular biological processes. Our study aimed to determine whether miRNAs function in the regulation of ionizing radiation (IR)-induced cell death in auditory cells and to determine how they affect the cellular response to IR. Microarray and qRT-PCR were performed to identify and confirm the differential expression of miRNAs in the cochlea hair cell line HEI-OC1 and in vivo after IR. Upregulation or downregulation of miRNAs using miRNA mimics or inhibitor were detected to characterize the biological effects of the indicated miRNAs. Bioinformatic analyses, luciferase reporter assays and mRNA knockdown were performed to identify a miRNA target gene. We determined that miR-207 was significantly upregulated after IR. MiR-207 enhances IR-induced apoptosis and DNA damage in HEI-OC1 cells. Furthermore, Akt3 was confirmed to be a direct target of miR-207. Downregulation of Akt3 mimics the effects of miR-207. MiR-207 enhances IR-induced apoptosis by directly targeting Akt3 and anti-miR-207 may have a potential role in protecting cochlea hair cells from IR.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 BioMed Research International. 2014 Sep 8.
 Gene Expression Profiling of Biological Pathway Alterations by Radiation Exposure
 
 
 Kuei-Fang Lee, Julia Tzu-Ya Weng, Paul Wei-Che Hsu, Yu-Hsiang Chi, Ching-Kai Chen, Ingrid Y. Liu, Yi-Cheng Chen, Lawrence Shih-Hsin Wu
  Abstract
Though damage caused by radiation has been the focus of rigorous research, the mechanisms through which radiation exerts harmful effects on cells are complex and not well-understood. In particular, the influence of low dose radiation exposure on the regulation of genes and pathways remains unclear. In an attempt to investigate the molecular alterations induced by varying doses of radiation, a genome-wide expression analysis was conducted. Peripheral blood mononuclear cells were collected from five participants and each sample was subjected to 0.5 Gy, 1 Gy, 2.5 Gy, and 5 Gy of cobalt 60 radiation, followed by array-based expression profiling. Gene set enrichment analysis indicated that the immune system and cancer development pathways appeared to be the major affected targets by radiation exposure. Therefore, 1 Gy radioactive exposure seemed to be a critical threshold dosage. In fact, after 1 Gy radiation exposure, expression levels of several genes including FADD, TNFRSF10B, TNFRSF8, TNFRSF10A, TNFSF10, TNFSF8, CASP1, and CASP4 that are associated with carcinogenesis and metabolic disorders showed significant alterations. Our results suggest that exposure to low-dose radiation may elicit changes in metabolic and immune pathways, potentially increasing the risk of immune dysfunctions and metabolic disorders.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 BioMed Research International. 2014 Sep 16.
 MicroRNA Expression Profiling Altered by Variant Dosage of Radiation Exposure
 
 
 Kuei-Fang Lee, Yi-Cheng Chen, Paul Wei-Che Hsu, Ingrid Y. Liu, Lawrence Shih-Hsin Wu
  Abstract
Various biological effects are associated with radiation exposure. Irradiated cells may elevate the risk for genetic instability, mutation, and cancer under low levels of radiation exposure, in addition to being able to extend the postradiation side effects in normal tissues. Radiation-induced bystander effect (RIBE) is the focus of rigorous research as it may promote the development of cancer even at low radiation doses. Alterations in the DNA sequence could not explain these biological effects of radiation and it is thought that epigenetics factors may be involved. Indeed, some microRNAs (or miRNAs) have been found to correlate radiation-induced damages and may be potential biomarkers for the various biological effects caused by different levels of radiation exposure. However, the regulatory role that miRNA plays in this aspect remains elusive. In this study, we profiled the expression changes in miRNA under fractionated radiation exposure in human peripheral blood mononuclear cells. By utilizing publicly available microRNA knowledge bases and performing cross validations with our previous gene expression profiling under the same radiation condition, we identified various miRNA-gene interactions specific to different doses of radiation treatment, providing new insights for the molecular underpinnings of radiation injury.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 PLoS One. 2014 Aug 18. doi: 10.1371/journal.pone.0104650.
 A Novel Glycated Hemoglobin A1c-Lowering Traditional Chinese Medicinal Formula, Identified by Translational Medicine Study
 
 
 Hsin-Yi Lo, Chien-Yun Hsiang, Tsai-Chung Li, Chia-Cheng Li, Hui-Chi Huang, Jaw-Chyun Chen, Tin-Yun Ho
  Abstract
Diabetes is a chronic metabolic disorder that has a significant impact on the health care system. The reduction of glycated hemoglobin A1c is highly associated with the improvements of glycemic control and diabetic complications. In this study, we identified a traditional Chinese medicinal formula with a HbA1c-lowering potential from clinical evidences. By surveying 9,973 diabetic patients enrolled in Taiwan Diabetic Care Management Program, we found that Chu-Yeh-Shih-Kao-Tang (CYSKT) significantly reduced HbA1c values in diabetic patients. CYSKT reduced the levels of HbA1c and fasting blood glucose, and stimulated the blood glucose clearance in type 2 diabetic mice. CYSKT affected the expressions of genes associated with insulin signaling pathway, increased the amount of phosphorylated insulin receptor in cells and tissues, and stimulated the translocation of glucose transporter 4. Moreover, CYSKT affected the expressions of genes related to diabetic complications, improved the levels of renal function indexes, and increased the survival rate of diabetic mice. In conclusion, this was a translational medicine study that applied a ¡§bedside-to-bench¡¨ approach to identify a novel HbA1c-lowering formula. Our findings suggested that oral administration of CYSKT affected insulin signaling pathway, decreased HbA1c and blood glucose levels, and consequently reduced mortality rate in type 2 diabetic mice.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Tumor Biology. 2014 Jul 16.
 MiR-7-5p is frequently downregulated in glioblastoma microvasculature and inhibits vascular endothelial cell proliferation by targeting RAF1
 
 
 Zhiguo Liu, Yuguang Liu, Lianling Li, Zhenkuan Xu, Baibin Bi, Jian Yi Li, Yunyan Wang
  Abstract
The aberrant expression of microRNAs (miRNAs) is always associated with tumor development and progression. Microvascular proliferation is one of the unique pathologic features of glioblastoma (GBM) . In this study, the microvasculature from GBM or normal brain tissue derived from neurosurgeries was purified and total RNA was isolated from purified microvasculature. The difference of miRNA expression profiles betweenglioblastoma microvasculature and normal brain capillaries was investigated. It was found that miR-7-5p in GBM microvessels was significantly reduced compared with that in normal brain capillaries. In the in vitro experiments, overexpression of miR-7-5p significantly inhibited human umbilical vein endothelial cell proliferation. Forced expression of miR-7-5p in human umbilical vein endothelial cells in vitro significantly reduced the protein level of RAF1 and repressed the activity of the luciferase, a reporter vector carrying the 3'-untranslated region of RAF1. These findings indicate that RAF1 is one of the miR-7-5p target genes. Furthermore, a significant inverse correlation between miR-7-5p expression and RAF1 protein level in GBMmicrovasculature was found. These data suggest that miR-7-5p functions as a tumor suppressor gene to regulate GBM microvascular endothelial cellproliferation potentially by targeting the RAF1 oncogene, implicating an important role for miR-7-5p in the pathogenesis of GBM. It may serve as a guide for the antitumor angiogenesis drug development.
   

  ✔本篇論文使用華聯產品:Rat OneArray  
 Journal of Ethnopharmacology. 2014 Jul 19. doi: 10.1016/j.jep.2014.07.022.
 Comparative pharmacokinetics of rhein in normal and loperamide-induced constipated rats and microarray analysis of drug-metabolizing genes
 
 
 Mei-Ling Hou, Li-WenChang, Chi-HungLin, Lie-ChwenLin, Tung-HuTsai
  Abstract
ETHNOPHARMACOLOGICAL RELEVANCE: Rhein is a pharmacological active component found in Rheum palmatum L. that is the major herb of the San-Huang-Xie-Xin-Tang (SHXXT), a medicinal herbal product used as a remedy for constipation. Here we have investigated the comparativepharmacokinetics of rhein in normal and constipated rats. Microarray analysis was used to explore whether drug-metabolizing genes will be altered after SHXXT treatment. MATERIALS AND METHODS: The comparative pharmacokinetics of rhein in normal and loperamide-induced constipated rats was studied by liquid chromatography with electrospray ionization tandem mass spectrometry (LC-MS/MS). Gene expression profiling in drug-metabolizing genes after SHXXT treatment was investigated by microarray analysis and real-time polymerase chain reaction (RT-PCR). Results: A validated LC-MS/MS method was applied to investigate the comparative pharmacokinetics of rhein in normal and loperamind-induced constipated rats. The pharmacokinetic results demonstrate that the loperamind-induced constipation reduced the absorption of rhein. Cmax significant reduced by 2.5-fold, the AUC decreased by 27.8%; however, the elimination half-life (t1/2) was prolonged by 1.6-fold. Tmax and mean residence time (MRT) were significantly prolonged by 2.8-fold, and 1.7-fold, respectively. The volume of distribution (Vss) increased by 2.2-fold. The data of microarray analysis on gene expression indicate that five drug-metabolizing genes, including Cyp7a1, Cyp2c6, Ces2e, Atp1b1, and Slc7a2 were significantly altered by the SHXXT (0.5 g/kg) treatment. Conclusion: The loperamide-induced constipation reduced the absorption of rhein. Since among the 25,338 genes analyzed, there were five genessignificantly altered by SHXXT treatment. Thus, information on minor drug-metabolizing genes altered by SHXXT treatment indicates that SHXXT is relatively safe for clinical application.
   

  ✔本篇論文使用華聯產品:Rat OneArray  
 Journal of Neurosurgery Spine. 2014 Jul 25.
 Nerve growth factor promotes expression of novel genes in intervertebral disc cells that regulate tissue degradation
 
 
 Ting-Hsien Kao, Yi-Jen Peng, Hsi-Kai Tsou, Donald M. Salter, Herng-Sheng Lee
  Abstract
Object: Increased neurotrophin activity in degenerative intervertebral discs (IVDs) is one potential cause of chronic low-back pain (LBP). The aim of the study was to assess if nerve growth factor (NGF) might alter gene expression of IVD cells and contribute to disc degeneration by enhancingexpression or activity of factors that cause breakdown of IVD matrix. Methods: Rat-tail IVD cells were stimulated by NGF and subjected to microarray analysis. Real-time polymerase chain reaction, Western blotting, and immunocytochemistry of rat and human IVD cells and tissues treated with NGF in vitro in the absence or presence of the NGF inhibitor Ro 08-2750 were used to confirm findings of the microarray studies. Phosphorylation of mitogen-activated protein kinase (MAPK) was used to identify cell signaling pathways involved in NGF stimulation in the absence or presence of Ro 08-2750. Results: Microarray analysis demonstrated increased expression of chitinase 3-like 1 (Chi3l1), lipocalin 2 (Lcn2), and matrix metalloproteinase-3 (Mmp3) following NGF stimulation of rat IVD cells in vitro. Increased gene expression was confirmed by real-time polymerase chain reaction with a relative increase in the Mmp/Timp ratio. Increased expression of Chi3l1, Lcn2, and Mmp3 following NGF stimulation was also demonstrated in rat cells and human tissue in vitro. Effects of NGF on protein expression were blocked by an NGF inhibitor and appear to function through the extracellular-regulation kinase 1/2 (ERK1/2) MAPK pathway. Conclusions Nerve growth factor has potential effects on matrix turnover activity and influences the catabolic/anabolic balance of IVD cells in an adverse way that may potentiate IVD degeneration. Anti-NGF treatment might be beneficial to ameliorate progressive tissue breakdown in IVD degeneration and may lead to pain relief.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Oncology Reports. 2014 Jul 17. doi: 10.3892/or.2014.3335.
 WWOX modulates the gene expression profile in the T98G glioblastoma cell line rendering its phenotype less malignant
 
 
 KATARZYNA KOŚLA, MAGDALENA NOWAKOWSKA, KAROLINA POSPIECH, ANDRZEJ K. BEDNAREK
  Abstract
The aim of the present study was to assess the influence of WWOX gene upregulation on the transcriptome and phenotype of the T98G glioblastomacell line. The cells with high WWOX expression demonstrated a significantly different transcription profile for approximately 3,000 genes. The main cellular pathways affected were Wnt, TGF£], Notch and Hedgehog. Moreover, the WWOX-transfected cells proliferated at less than half the rate, exhibited greatly lowered adhesion to ECM, increased apoptosis and impaired 3D culture formation. They also demonstrated an increased ability for crossing the basement membrane. Our results indicate that WWOX, apart from its tumor-suppressor function, appears to be a key regulator of the main cellular functions of the cell cycle and apoptosis. Furthermore, our results showed that WWOX may be involved in controlling metabolism, cytoskeletal structure and differentiation.
   

  ✔本篇論文使用華聯產品:Array technology and applications  
 American Journal of Epidemiology. 2014, 180(2):140-52. doi: 10.1093/aje/kwu135..
 Design and Analysis for Studying microRNAs in Human Disease: A Primer on -Omic Technologies
 
 
 Viswam S. Nair, Colin C. Pritchard, Muneesh Tewari, John P. A. Ioannidis
  Abstract
microRNAs (miRNAs) are fundamental to cellular biology. Although only approximately 22 bases long, miRNAs regulate complex processes in health and disease, including human cancer. Because miRNAs are highly stable in circulation when compared with several other classes of nucleic acids, they have generated intense interest as clinical biomarkers in diverse epidemiologic studies. As with other molecular biomarker fields, however, miRNA research has become beleaguered by pitfalls related to terminology and classification; procedural, assay, and study cohort heterogeneity; and methodological inconsistencies. Together, these issues have led to both false-positive and potentially false-negative miRNA associations. In this review, we summarize the biological rationale for studying miRNAs in human disease with a specific focus on circulating miRNAs, which highlight some of the most challenging topics in the field to date. Examples from lung cancer are used to illustrate the potential utility and some of the pitfalls in contemporary miRNA research. Although the field is in its infancy, several important lessons have been learned relating to cohort development, sample preparation, and statistical analysis that should be considered for future studies. The goal of this primer is to equip epidemiologists and clinical researchers with sound principles of study design and analysis when using miRNAs.
   

  ✔本篇論文使用華聯產品:  
 Plant Molecular Biology. 2014 Jul 8.
 Expression of a gene encoding a rice RING zinc-finger protein, OsRZFP34, enhances stomata opening
 
 
 Kuo‑Hsuan Hsu, Chia‑Chin Liu, Shaw‑Jye Wu, Ying‑Yu Kuo, Chung‑An Lu, Ching‑Rong Wu, Pei‑Jyun Lian, Chwan‑Yang Hong, Yi‑Ting Ke, Juin‑Hua Huang, Ching‑Hui Yeh
  Abstract
By oligo microarray expression profiling, we identified a rice RING zinc-finger protein (RZFP), OsRZFP34, whose gene expression increased with high temperature or abscisic acid (ABA) treatment. As compared with the wild type, rice and Arabidopsis with OsRZFP34 overexpression showed increased relative stomata opening even with ABA treatment. Furthermore, loss-of-function mutation of OsRZFP34 and AtRZFP34 (At5g22920), anOsRZFP34 homolog in Arabidopsis, decreased relative stomata aperture under nonstress control conditions. Expressing OsRZFP34 in atrzfp34 reverted the mutant phenotype to normal, which indicates a conserved molecular function between OsRZFP34 and AtRZFP34. Analysis of water loss and leaf temperature under stress conditions revealed a higher evaporation rate and cooling effect in OsRZFP34-overexpressing Arabidopsis and ricethan the wild type, atrzfp34 and osrzfp34. Thus, stomata opening, enhanced leaf cooling, and ABA insensitivity was conserved with OsRZFP34 expression. Transcription profiling of transgenic rice overexpressing OsRZFP34 revealed many genes involved in OsRZFP34-mediated stomatal movement. Several genes upregulated or downregulated in OsRZFP34-overexpressing plants were previously implicated in Ca2+ sensing, K+ regulator, and ABA response. We suggest that OsRZFP34 may modulate these genes to control stomata opening.
   

  ✔本篇論文使用華聯產品:Human OneArray,Human miRNA OneArray  
 BioMed Research International. 2014 July 1.
 Systematic expression profiling analysis identifies specific microRNA-gene interactions that may differentiate between active and latent tuberculosis infection
 
 
 Lawrence Shih-Hsin Wu, Shih-Wei Lee, Kai-Yao Huang, Tzong-Yi Lee, Paul Wei-Che Hsu, Julia Tzu-Ya Weng
  Abstract
Tuberculosis (TB) is the second most common cause of death from infectious diseases. About 90% of those infected are asymptomatic¡Xthe so-called latent TB infections (LTBI), with a 10% lifetime chance of progressing to active TB. In attempt to further understand the molecular pathogenesis of TB and develop efficient diagnostic biomarkers, several molecular studies have attempted to compare the gene and microRNA expression profiles between healthy controls versus active TB or LTBI patients. However, the results vary due to diverse genetic background, study designs, and the inherent complexity of the disease process. Thus, developing a sensitive and efficient method for the detection of LTBI is both crucial and challenging. For the present study, we performed a systematic analysis of the gene and microRNA profiles of healthy individuals versus those affected with TB or LTBI. Combined with a series of in silico analysis utilizing publicly available microRNA knowledge bases and published literature data, we have uncovered several microRNA-gene interactions that specifically target both the blood and lungs, presenting to be useful molecular signatures to help enhance the understanding of TB pathogenesis. Furthermore, some of these molecular interactions are novel, and may serve as potential biomarkers of TB and LTBI, facilitating the development for a more sensitive, efficient, and cost-effective diagnostic assay for TB and LTBI for the Taiwanese population.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Tumor Biology. 2014 Jun 19.
 Diverse effect of WWOX overexpression in HT29 and SW480 colon cancer cell lines
 
 
 Karolina Pospiech, Urszula Lewandowska, Agnieszka W, Piastowska-Ciesielska, Andrzej Kazimierz Bednarek, Magdalena Nowakowska
  Abstract
WW-domain-containing oxidoreductase (WWOX) is the tumour suppressor gene from the common fragile site FRA16D, whose altered expression has been observed in tumours of various origins. Its suppressive role and influence on basic cellular processes such as proliferation and apoptosis have been confirmed in many in vitro and in vivo studies. Moreover, its protein is thought to take part in the regulation of tissue morphogenesis and cell differentiation. However, its role in colon cancer formation remains unclear. The aim of this study was to characterize the influence of WWOX on the process of colon cancerogenesis, the basic features of the cancer cell and its expression profiles. Multiple biological tests, microarray experiments and quantitative reverse transcriptase (RT)-PCR were performed on two colon cancer cell lines, HT29 and SW480, which differ in morphology, expression of differentiation markers, migratory characteristics and metastasis potential and which represent negative (HT29) and low (SW480) WWOX expression levels. The cell lines were subjected to retroviral transfection, inducting WWOX overexpression. WWOX was found to have diverse effects on proliferation, apoptosis and the adhesion potential of modified cell lines. Our observations suggest that in the HT29 colon cancer cell line, increased expression of WWOX may result in the transition of cancer cells into a more normal colon epithelium phenotype, while in SW480, WWOX demonstrated well-known tumour suppressor properties. Our results also suggest that WWOX does not behave as classical tumour suppressor gene, and its influence on cell functioning is more global and complicated.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 BBA Molecular Cell Research. 2014 May 21. doi: 10.1016/j.bbamcr.2014.05.006..
 The protein phosphatase 2A regulatory subunit B55£ is a modulator of signaling and microRNA expression in acute myeloid leukemia cells
 
 
 Vivian R. Ruvolo, Rodrigo Jacamo, JaredK.Burks, Zhihong Zheng, Seshagiri R. Duvvuri, Liran Zhou, Yihua Qiu, Kevin R. Coombes, Nianxiang Zhang, Suk Y. Yoo, Rongqing Pan, NumsenHail Jr., Marina Konopleva, George Calin, Steven M. Kornblau, Michael Andreeff, Peter P. Ruvolo
  Abstract
We recently discovered that the protein phosphatase 2A (PP2A) B55£ subunit (PPP2R2A) is under-expressed in primary blast cells and is unfavorable for remission duration in AML patients. In this study, reverse phase protein analysis (RPPA) of 230 proteins in 511 AML patient samples revealed a strong correlation of B55£ with a number of proteins including MYC, PKC £, and SRC. B55£ suppression in OCI-AML3 cells by shRNA demonstrated that the B subunit is a PKC£ phosphatase. B55£ does not target SRC, but rather the kinase suppresses protein expression of the Bsubunit. Finally, the correlation between B55£ and MYC levels reflected a complex stoichiometric competition between B subunits. Loss of B55£ in OCI-AML3 cells did not change global PP2A activity and the only isoform that is induced is the one containing B56£. In cells containing B55£ shRNA, MYC was suppressed with concomitant induction of the competing B subunit B56£ (PPP2R5A). A recent study determined that FTY-720, a drug whose action involves the activation of PP2A, resulted in the induction of B55£ In AML cells, and a reduction of the B subunit rendered thesecells resistant to FTY-720. Finally, reduction of the B subunit resulted in an increase in the expression of miR-191-5p and a suppression of miR-142-3p. B55£ regulation of these miRs was intriguing as high levels of miR-191 portend poor survival in AML, and miR-142-3p is mutated in 2% of AML patient samples. In summary, the suppression of B55£ activates signaling pathways that could support leukemia cell survival.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 IEEE International Symposium on Bioelectronics and Bioinformatics. 2014 April 11. doi: 10.1109/ISBB.2014.6820927.
 Systematic Pipeline for the analysis of microRNA gene interactions in active and latent TB infection
 
 
 Julia Tzu-Ya Weng, Kai-Yao Huang, Shih-Wei Lee, Lawrence Shih-Hsin Wu, Yi-Cheng Chen, Tzong-Yi Lee
  Abstract
Tuberculosis (TB) is the second most common cause of death from infectious diseases. About 90% of those infected are asymptomatic¡Xthe so-called latent TB infections (LTBI), with a 10% lifetime chance of progressing to active TB. Several gene expression studies have compared healthy controls versus active TB or LTBI patients. The results vary due to diverse genetic background, study designs, and the inherent complexity of the disease process. Thus, developing a sensitive and efficient method for the detection of LTBI is both crucial and challenging. Our objective was to establish an efficient and cost-effective pipeline for gene and microRNA expression profiling in TB and LTBI. We attempted to investigate the interaction between these two types of molecular signatures as biomarkers for a more sensitive and specific differentiation among active TB, LTBI, and healthy individuals. Following our systematic pipeline, we have uncovered novel differences specific to the Taiwanese population. Differentially expressed microRNAs and their interactions with the corresponding target genes will serve as potential molecular signatures to enhance our understanding of the underlying mechanisms of TB and facilitate the development for a more sensitive diagnostic assay for LTBI.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Journal Of Lipid Research. 2014, 55(6):1098-1110. doi: 10.1194/jlr.M045807.
 Linalool is a PPAR£ ligand that reduces plasma TG levels and rewires the hepatic transcriptome and plasma metabolome
 
 
 Hee-jin Jun, Ji Hae Lee, Jiyoung Kim, Yaoyao Jia, Kyoung Heon Kim, Kwang Yeon Hwang, Eun Ju Yun, Kyoung-Rok Do, Sung-Joon Lee
  Abstract
We investigated the hypotriglyceridemic mechanism of action of linalool, an aromatic monoterpene present in teas and fragrant herbs. Reporter gene and time-resolved fluorescence resonance energy transfer assays demonstrated that linalool is a direct ligand of PPAR£. Linalool stimulation reduced cellular lipid accumulation regulating PPAR£-responsive genes and significantly induced FA oxidation, and its effects were markedly attenuated by silencing PPAR£ expression. In mice, the oral administration of linalool for 3 weeks reduced plasma TG concentrations in Western-diet-fed C57BL/6J mice (31%, P < 0.05) and human apo E2 mice (50%, P < 0.05) and regulated hepatic PPAR£ target genes. However, no such effects were seen in PPAR£-deficient mice. Transcriptome profiling revealed that linalool stimulation rewired global gene expression in lipid-loaded hepatocytes and that the effects of 1 mM linalool were comparable to those of 0.1 mM fenofibrate. Metabolomic analysis of the mouse plasma revealed that the global metabolite profiles were significantly distinguishable between linalool-fed mice and controls. Notably, the concentrations of saturated FAs were significantly reduced in linalool-fed mice. These findings suggest that the appropriate intake of a natural aromatic compound could exert beneficial metabolic effects by regulating a cellular nutrient sensor.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Molecular Nutrition & Food Research. 2014 May 19. doi: 10.1002/mnfr.201300729.
 Interspecies communication between plant and mouse gut host cells through edible plant derived exosome-like nanoparticles
 
 
 Jingyao Mu, Xiaoying Zhuang, Qilong Wang, Hong Jiang, Zhong-Bin Deng, BaomeiWang, Lifeng Zhang, Sham Kakar, Yan Jun, Donald Miller, Huang-Ge Zhang
  Abstract
SCOPE: Exosomes, small vesicles participating in intercellular communication, have been extensively studied recently; however, the role of edibleplant derived exosomes in interspecies communication has not been investigated. Here, we investigate the biological effects of edible plant derivedexosome-like nanoparticles (EPDENs) on mammalian cells. METHODS AND RESULTS: In this study, exosome-like nanoparticles from four edible plants were isolated and characterized. We show that these EPDENs contain proteins, lipids, and microRNA. EPDENs are taken up by intestinal macrophages and stem cells. The results generated from EPDEN-transfected macrophages indicate that ginger EPDENs preferentially induce the expression of the antioxidation gene, heme oxygenase-1 and the anti-inflammatory cytokine, IL-10; whereas grapefruit, ginger, and carrot EPDENs promote activation of nuclear factor like (erythroid-derived 2). Furthermore, analysis of the intestines of canonical Wnt-reporter mice, i.e. B6.Cg-Tg(BAT-lacZ)3Picc/J mice, revealed that the numbers of £]-galactosidase+ (£]-Gal) intestinal crypts are increased, suggesting that EPDEN treatment of mice leads to Wnt-mediated activation of the TCF4 transcription machinery in the crypts. CONCLUSION: The data suggest a role for EPDEN-mediated interspecies communication by inducing expression of genes for anti-inflammation cytokines, antioxidation, and activation of Wnt signaling, which are crucial for maintaining intestinal homeostasis.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 European Journal of Neuroscience. 2014 Jun 5. doi: 10.1111/ejn.12602.
 Human cellular differences in cAMP-CREB signaling correlate with light-dependent melatonin suppression and bipolar disorder
 
 
 Ludmila Gaspar, Maan van de Werken, Anne-Sophie Johansson, Ermanno Moriggi, Bjorn Owe-Larsson, Janwillem W. H. Kocks, Gabriella B. Lundkvist, Marijke C. M. Gordijn, Steven A. Brown
  Abstract
Various lines of evidence suggest a mechanistic role for altered cAMP-CREB (cAMP response element - binding protein) signaling in depressive and affective disorders. However, the establishment and validation of human inter-individual differences in this and other major signaling pathways has proven difficult. Here, we describe a novel lentiviral methodology to investigate signaling variation over long periods of time directly in human primary fibroblasts. On a cellular level, this method showed surprisingly large inter-individual differences in three major signaling pathways in human subjects that nevertheless correlated with cellular measures of genome-wide transcription and drug toxicity. We next validated this method by establishing a likely role for cAMP-mediated signaling in a human neuroendocrine response to light - the light-dependent suppression of the circadian hormonemelatonin - that shows wide inter-individual differences of unknown origin in vivo. Finally, we show an overall greater magnitude of cellular CREBsignaling in individuals with bipolar disorder, suggesting a possible role for this signaling pathway in susceptibility to mental disease. Overall, our results suggest that genetic differences in major signaling pathways can be reliably detected with sensitive viral-based reporter profiling, and that these differences can be conserved across tissues and be predictive of physiology and disease susceptibility.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Evidence-Based Complementary and Alternative Medicine. 2014 June 9.
 Electroacupuncture Improves Trinitrobenzene Sulfonic Acid-Induced Colitis, Evaluated by Transcriptomic Study
 
 
 Tin-Yun Ho, Hsin-Yi Lo, De-Cheng Chao, Chia-Cheng Li, Jau-Jin Liu, Chingju Lin, Chien-Yun Hsiang
  Abstract
Inflammatory bowel disease is a chronic colonic inflammation that displays symptoms like diarrhea and weight loss. Acupuncture has been widely accepted by Western countries for the treatment of pain. Here, we analyzed efficacy and mechanism of electroacupuncture (EA) on trinitrobenzene sulfonic acid- (TNBS-) induced colitis in mice. Mice were intrarectally administered with 250 mg/kg TNBS and electroacupunctured at Quze (PC3) and Neiguan (PC6) acupoints, which have been applied for gastrointestinal disorders. Gene expression profiles in colons and spleens were analyzed by microarray for the elucidation of mechanism of EA. Our data showed that EA at PC3 and PC6 improved macroscopic and microscopic features of colitis and the improvement displayed a frequency-dependent manner. Administration of TNBS upregulated the expression of most cytokine genes in colons, while EA downregulated the expression of TNBS-induced cytokine genes. Pathway analysis showed that EA significantly affected inflammatory pathways in colons and immunity-associated pathway in spleens. Immunohistochemical staining further showed that EA decreased the expression of interleukin-1£] and nuclear factor-£eB. In conclusion, this is the first study reporting the global gene expression profiles of EA on TNBS-induced colitis. Our findings suggested that inflammatory and immunity pathways were involved in the anti-inflammatory mechanism of EA on colitis induced by TNBS.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Asia Pacific Journal of Clinical Nutrition. 2014, 23(2):331-7. doi: 10.6133/apjcn.2014.23.2.20.
 MicroRNA-125a-3p expression in abdominal adipose tissues is associated with insulin signalling gene expressions in morbid obesity: observations in Taiwanese
 
 
 Chiu-Li Yeh, I-Chi Cheng, Yu-Chen Hou, Weu Wang, Sung-Ling Yeh
  Abstract
Background: Micro (mi) RNAs have been found to play an important role in the regulation of adipogenesis and insulin sensitivity. However, associations between miRNA and insulin signalling-related gene expressions in abdominal adipose tissues in obese subjects remain unclear. Methods: We used a microarray platform to screen miRNA expressions in abdominal adipose tissues between genders in severely obese subjects and found that the top-ranking miRNA in abdominal omental adipose tissues was miRNA-125a-3p. MicroR-125a-3p and insulin signalling-related gene expressions in abdominal omental adipose tissues of all subjects (11 men and 10 women) were subsequently quantified by a real-time PCR. Also, associations of miR-125a-3p with insulin signallingrelated gene expression and biochemical markers in obese subjects were analyzed by a linear regression analysis. Results: miR-125a-3p expressed by abdominal omental adipose tissues was much higher in obese men than women. No gender difference was observed in abdominal subcutaneous adipose tissues. Concomitant with high miR-125a-3p, c-Jun N-terminal kinase gene expression was also higher, whereas insulin receptor was lower in men than women. There were negative associations of miR-125a-3p with the insulin receptor and phosphatidylinositol 3-kinase expressions. Fasting plasma glucose and cholesterol levels were positively associated with miR-125a-3p expression. These associations were obvious in obese men but not women. Conclusion: Our results support the involvement of miR-125a-3p in regulating the insulin signalling pathway and imply that increased miR-125a-3p expression in omental adipose tissues may be a characteristic feature of insulin resistance in obese men.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Molecular and Cellular Biology. 2014 Apr 14.
 KSRP and MiR-145 Are Negative Regulators of Lipolysis in White Adipose Tissue
 
 
 Yi-Yu Lin, Chu-Fang Chou, Matteo Giovarelli, Paola Briata, Roberto Gherzi, Ching-Yi Chen
  Abstract
White adipose tissue (WAT) releases fatty acids from stored triacylglycerol (TAG) for energy source. Here, we report that targeted deletion of KH-type splicing regulatory protein (KSRP), an RNA-binding protein that regulates gene expression at multiple levels, enhances lipolysis in epididymal WAT (eWAT) due to up-regulation of genes promoting lipolytic activity. Expression of miR-145 is decreased due to impaired pri-miR-145 processing inKsrp-/- eWAT. We show that miR-145 directly targets and represses Foxo1 and Cgi58, activators of lipolytic activity, and forced expression of miR-145 attenuates lipolysis. This study reveals a novel in vivo function of KSRP in controlling adipose lipolysis through post-transcriptional regulation ofmiR-145 expression.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Leukemia. 2014 Apr 15. doi: 10.1038/leu.2014.135.
 piRNA-823 contributes to tumorigenesis by regulating de novo DNA methylation and angiogenesis in multiple myeloma
 
 
 H Yan, Q-L Wu, C-Y Sun, L-S Ai, J Deng, L Zhang, L Chen, Z-B Chu, B Tang, K Wang, X-F Wu, J Xu, Y Hu
  Abstract
Aberrant DNA hypermethylation contributes to myelomagenesis by silencing tumor-suppressor genes. Recently, a few reports have suggested that a novel class of small non-coding RNAs, called Piwi-interacting RNAs (piRNAs), may be involved in the epigenetic regulation of cancer. In this study, for the first time we provided evidence that the expression of piRNA-823 was upregulated in multiple myeloma (MM) patients and cell lines, and positively correlated with clinical stage. Silencing piRNA-823 in MM cells induced deregulation of cell cycle regulators and apoptosis-related proteins expression, accompanied by inhibition of tumorigenicity in vitro and in vivo. Moreover, piRNA-823 was directly relevant to de novo DNAmethyltransferases, DNMT3A and 3B, in primary CD138+ MM cells. The inhibited expression of piRNA-823 in MM cells resulted in marked reduction of DNMT3A and 3B at both mRNA and protein levels, which in turn led to decrease in global DNA methylation and reexpression of methylation-silenced tumor suppressor, p16INK4A. In addition, piRNA-823 abrogation in MM cells induced reduction of vascular endothelial growth factor secretion, with consequent decreased proangiogenic activity. Altogether, these data support an oncogenic role of piRNA-823 in the biology of MM, providing a rational for the development of piRNA-targeted therapeutic strategies in MM.
   

  ✔本篇論文使用華聯產品:Rat OneArray  
 Journal of Pharmaceutical and Biomedical Analysis. 2014, 96C:231-240. doi: 10.1016/j.jpba.2014.04.001.
 Development of a microdialysis system to monitor lamivudine in blood and liver for the pharmacokinetic application in herbal drug interaction and the gene expression in rats
 
 
 Chia-Ming Lu, Mei-Ling Hou, Lie-Chwen Lin, Tung-Hu Tsai
  Abstract
The aim of study is to develop a novel multiple microdialysis technique coupled to a validated chromatographic system for the measurement of protein-unbound form lamivudine and investigation of its herb-drug interaction in rat blood and liver. Furthermore, gene expression changes of drugmetabolizing enzymes in rat were evaluated by microarray analysis after being treated with a traditional Chinese herbal formulation, Long-Dan-Xie-Gan-Tang (LDXGT). The analyte was separated by a reverse-phase C18 column using the mobile phase comprising methanol and 10mM KH2PO4(15:85, v/v, adjusted to pH 6.0 with NaOH) with the flow rate of 0.8mL/min, and the UV wavelength was set at 270nm. The processes of method validation followed Food and Drug Administration (FDA) guidelines. The pharmacokinetic data demonstrated that the area under the concentration-time curve (AUC) of the lamivudine alone and the LDXGT pretreated group were 532¡Ó37.6 and 550¡Ó44.2min£gg/mL in rat blood after lamivudineadministration (10mg/kg, i.v.) and 682¡Ó196 and 642¡Ó153min£gg/mL in rat liver, respectively. The herb-drug pharmacokinetic interaction showed that with either lamivudine alone or in combination with pretreated with LDXGT, the pharmacokinetic parameters were not significantly changed except the apparent volume of distribution (Vd) at a high dose of lamivudine (30mg/kg). In addition, microarray analysis showed that among 70 altered genes (selection criteria: |Fold change|¡Ù2 and p<0.05), only 11 genes were involved in drug metabolism and indicated that a relatively small portion of drugmetabolizing genes in liver were altered at the genome level after the therapeutic dose of LDXGT treatment. In conclusion, these studies provide constructive information to interpret the herb-drug interactions between lamivudine and a popular Chinese herbal formulation.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Journal of Lipid Research. 2014 Apr 20.
 Aromatic terpenoid linalool is an agonistic ligand for PPAR£ that reduces plasma triglyceride levels and rewires the hepatic transcriptome and plasma metabolome
 
 
 Hee-jin Jun, Ji-hae Lee, Jinyoung Kim, Yaoyao Jia, Kyoung Heon Kim, Kwang Yeon Hwang, Eun Ju Yun, Kyoung Rok Do, Sung-Joon Lee
  Abstract
We investigated the hypotriglyceridemic mechanism of action of linalool, an aromatic monoterpene present in teas and fragrant herbs. Reporter gene and time-resolved fluorescence resonance energy transfer assays demonstrated that linalool is a direct ligand of peroxisome proliferator-activated receptor-£ (PPAR£). Linalool stimulation reduced cellular lipid accumulation regulating PPAR£-responsive genes and significantly induced fatty acid oxidation, and its effects were markedly attenuated by silencing PPAR£ expression. In mice, the oral administration of linalool for 3 weeks reducedplasma triglyceride concentrations in Western diet-fed C57BL/6J mice (31%, P < 0.05) and human apolipoprotein E2 mice (50%, P < 0.05) and regulated hepatic PPAR£ target genes. However, no such effects were seen in PPAR£-deficient mice. Transcriptome profiling revealed that linaloolstimulation rewired global gene expression in lipid-loaded hepatocytes and that the effects of 1 mM linalool were comparable to those of 0.1 mM fenofibrate. Metabolomic analysis of the mouse plasma revealed that the global metabolite profiles were significantly distinguishable between linalool-fed mice and controls. Notably, the concentrations of saturated fatty acids were significantly reduced in linalool-fed mice. These findings suggest that the appropriate intake of a natural aromatic compound could exert beneficial metabolic effects by regulating a cellular nutrient sensor.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Oncogene. 2014 Mar 31;0. doi: 10.1038/onc.2014.43.
 B-cell lymphoma/leukemia 10 promotes oral cancer progression through STAT1/ATF4/S100P signaling pathway
 
 
 Wu TS, Tan CT, Chang CC, Lin BR, Lai WT, Chen ST, Yen-Ping Kuo M, Rau CL, Jaw FS, H-H Chang
  Abstract
B-cell lymphoma/leukemia 10 (BCL10) is an apoptotic regulatory protein related to advanced TNM stage and disease recurrence in oral squamous cell carcinoma (OSCC). However, the regulatory mechanism of BCL10 in OSCC progression is still unknown. Here, we showed that knockdown of endogenous BCL10 could significantly reduce cell migration and invasion abilities, retard cell proliferation by G0/G1 phase accumulation and inhibit tumorigenicity in vivo. In molecular level, we identified S100P as a crucial downstream effector of BCL10-inhibited OSCC progression by high-throughput microarray analysis. S100P messenger RNA and protein expression levels were significantly diminished in silenced-BCL10 clones, and transfected S100P expression plasmids restored migration, invasion, proliferation abilities and tumorigenicity in shBCL10 transfectants. Furthermore, we provided evidence that BCL10 regulated S100P expression through signal transducers and activators of transcription 1 (STAT1) and activating transcription factor 4 (ATF4). Knockdown of BCL10 decreased S100P promoter activity, but showed no effect in truncated STAT1/ATF4 S100Ppromoter.  In addition, we also found that the P50/P65 signaling pathway was involved in BCL10-enhanced OSCC progression. Restored S100P in silenced-BCL10 clones could markedly reverse P65 activation via outside-in signaling. Taken together, we discovered a novel axis of BCL10-regulated OSCC progression via STAT1/ATF4/S100P/P65 signaling, which could predict the prognosis of OSCC and will be beneficial for developing therapeutic strategy against advanced OSCC.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 BMC Genomics. 2014, 15:P48. doi:10.1186/1471-2164-15-S2-P48.
 Analysis of correlations between zona pellucida birefringence and molecular markers of oocyte developmental competence
 
 
 Markus Montag, Marc-André Sirard, Mourad Assidi
  Abstract
Human infertility is the incapacity of a couple to conceive after one year of unprotected sexual intercourse. Selection of the best gametes for subsequent steps of fertilization and embryo transfer was shown to be the crucial step in infertility treatment procedure. Oocyte selection using morphological criteria has been the gold standard method in assisted reproductive technologies (ART) clinics. Zona Pellucida (ZP) , a filamentous matrix of glycosylated glycoproteins surrounding the oocyte, is one of these morphological criteria of oocyte selection. In fact, ZP thickness and birefringence was reported to be positively correlated with higher ability of the oocyte to achieve successful pregnancy, but this selection approach has limitations in terms of accuracy, objectivity and constancy. Recent studies using OMICs approaches have identified key molecular markers in somatic cells (cumulus and/or granulosa cells) and follicular fluid that quantitatively and non-invasively predict the oocyte quality for better selection, higher pregnancy rates and efficient infertility treatment. These biomarkers could be a valuable reinforcement of the morphological selection criteria widely used in IVF clinics. In this context, this study was designed to study the relationship between some molecular predictors of oocyte quality found by our group and the conventional morphological parameters of oocyte quality. We expect to find a positive correlation between the ZP birefringence and molecular markers of oocyte competence. Such integrative strategy should lead to a powerful combined approach that will precisely predict the oocyte developmental potential, allowing therefore efficient infertility treatment and elective single embryo transfer (eSET).
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Nanomedicine. 2014 Feb 22. doi: 10.1016/j.nano.2014.02.006.
 A steroid-mimicking nanomaterial that mediates inhibition of human lung mast cell responses
 
 
 Anthony L. Dellinger, Zhiguo Zhou, Christopher L. Kepley
  Abstract
Water-soluble fullerenes can be engineered to regulate activation of mast cells (MC) and control MC-driven diseases in vivo. To further understand their anti-inflammatory mechanisms a C70-based fullerene conjugated to four myo-inositol molecules (C70-I) was examined in vitro for its effects on the signaling pathways leading to mediator release from human lung MC. The C70-I fullerene stabilizes MC and acts synergistically with long-acting £]2-adrenergic receptor agonists (LABA) to enhance inhibition of MC mediator release through Fc£`RI-simulation. The inhibition was paralleled by the upregulation of dual-specificity phosphatase one (DUSP1) gene and protein levels. Concomitantly, increases in MAPK were blunted in C70-I treated cells. The increase in DUSP1 expression was due to the ability of C70-I to prevent the ubiquitination and degradation of DUSP1. These findings identify a mechanism of how fullerenes inhibit inflammatory mediator release from MC and suggest they could potentially be an alternative therapy for steroid resistant asthmatics.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 International journal of clinical and experimental medicineis. 2014, 7(3):607-615.
 RNAi targeting GPR4 influences HMEC-1 gene expression by microarray analysis
 
 
 Yuelang Zhang, Hui Cai, Hongbing Ma, Dongli Zhao, Xiaozhi Zhang, Zongfang Li, Shufeng Wang, Jiangsheng Wang, Rui Liu, Yi Li, Jiansheng Qian, Hongxia Wei, Liying Niu, Yan Liu, Lisha Xiao, Muyang Ding, Shiwen Jiang, Juan Ren
  Abstract
G-protein coupled receptor 4 (GPR4) belongs to a protein family comprised of 3 closely related G protein-coupled receptors. Recent studies have shown that GPR4 plays important roles in angiogenesis, proton sensing, and regulating tumor cells as an oncogenic gene. How GPR4 conducts its functions? Rare has been known. In order to detect the genes related to GPR4, microarray technology was employed. GPR4 is highly expressed in human vascular endothelial cell HMEC-1. Small interfering RNA against GPR4 was used to knockdown GPR4 expression in HMEC-1. Then RNA from the GPR4 knockdown cells and control cells were analyzed through genome microarray. Microarray results shown that among the whole genes and expressed sequence tags, 447 differentially expressed genes were identified, containing 318 up-regulated genes and 129 down-regulated genes. These genes whose expression dramatically changed may be involved in the GPR4 functions. These genes were related to cell apoptosis, cytoskeleton and signal transduction, cell proliferation, differentiation and cell-cycle regulation, gene transcription and translation and cell material and energy metabolism.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Biochemical Journal. 2014 Mar 4.
 Calreticulin activates £]1-integrin through fucosylation modification by fucosyltransferase-1 in J82 human bladder cancer cells
 
 
 Yi-Chien Lu, Chiung-Nien Chen, Chia-Ying Chu, JenHer Lu, Bo-Jeng Wang, Chia-Hua Chen, Min-Chuan Huang, Tsui-Hwa Lin, Chin-Chen Pan, Swey-Shen Alex Chen, Wen-Ming Hsu, Yung-Feng Liao, Pei-Yi Wu, Hsin-Yi Hsia, Cheng-Chi Chang, Hsinyu Lee
  Abstract
Fucosylation regulates various pathological events in cells. We previously reported that different levels of calreticulin (CRT) affect cell adhesion and metastasis of bladder cancer. However, the precise mechanism of tumor metastasis regulated by CRT remains unclear. Using DNA array, we identifiedfucosyltransferase-1 (FUT1) as a gene regulated by CRT expression levels. CRT regulated cell adhesion through £1,2-linked fucosylation on £]1-integrin and this modification was catalyzed by FUT1. To clarify FUT1 roles in bladder cancer, we transfected the human FUT1 gene into CRT-RNAi stable cell lines. FUT1 overexpression in CRT-RNAi cells resulted in increased levels of £]1-integrin fucosylation and rescued cell adhesion to type-I collagen. Treatment with Ulex europaeus agglutinin I (UEA-1), a lectin recognizes FUT1-modified glycosylation structures, did not affect cell adhesion. In contrast, a FUT1-specific fucosidase diminished the activation of £]1-integrin. These results indicated that £1,2-fucosylation on £]1-integrin were not involved in the integrin-collagen interaction but promoted £]1-integrin activation. Moreover, we demonstrated that CRT regulated FUT1 mRNA degradation in 3'-untranslated region (3'-UTR). In conclusion, our findings suggested that CRT stabilized FUT1 mRNA, thereby leading to increase in fucosylation of £]1-integrin. Furthermore, increasedfucosylation levels activate £]1-integrin rather than directly modifying the integrin binding sites.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Journal of Cellular Biochemistry. 2014 Feb 12. doi: 10.1002/jcb.24786.
 Regulatory Roles of miRNA in the Human Neural Stem Cell Transformation to Glioma Stem Cells
 
 
 Shuang Liu, Jianning Zhang, Max S. Wicha, Alfred E. Chang, Wenhong Fan, Ling Chen, Ming Fan, Qiao Li, Feng Yin
  Abstract
To investigate the expressional alternation of microRNAs (miRNA) during the malignant transformation and development of human glioma, we measuredmiRNA expression profile as well as mRNA expression profile in normal human neural stem cells (hNSCs) and human glioma stem cells (hGSCs). We found 116 miRNA up-regulated and 62 miRNA down-regulated in GSCs. On the other hand, we identified 1,372 mRNA down-regulated, and 1,501 mRNA up-regulated in GSCs compared to those in NSCs. We then analyzed the pathways and the predicted target genes of the miRNAs which differ significantly in expression between GSCs and NSCs using the statistical enrichment methods. These target mRNAs are involved in many cancer-related signaling pathways, such as cell cycle, axon guidance, glioma development, adhesion junction, MAPK and Wnt signaling. Furthermore, we obtained the differently expressed miRNA-target relationships according to the £c value which is used to calculate the regulation extent of miRNA-target and using the databases of miRanda, Targetscans and Pictar. Among the top 10 miRNA-target relationships, hsa-miR-198 and its potential targeted gene DCX and NNAT were selected for validation, and NNAT was found to be the direct target of miR-198. Finally, the functional roles of miR-155-5p and miR-124-3p whose expressions altered significantly between GSCs and NSCs were addressed. Our results provide new clues for the potential mechanisms involved in the origin and development of glioma. Clinically, the altered miRNAs may serve as potential targets and diagnostic tools for novel therapeutic strategies of glioblastoma.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Biochemical and Biophysical Research Communications. 2014 Feb 28. doi: 10.1016/j.bbrc.2014.02.073.
 miR-138-5p reverses gefitinib resistance in non-small cell lung cancer cells via negatively regulating G protein-coupled receptor 124
 
 
 Yi Gao, XiaoWu Fan, WeiNa Li, Wei Ping, Yu Deng, XiangNing Fu
  Abstract
Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR TKIs) such as gefitinib are clinically effective treatments for non-small cell lung cancer(NSCLC) patients with EGFR activating mutations. However, therapeutic effect is ultimately limited by the development of acquired TKI resistance. MicroRNAs (miRNAs) represent a category of small non-coding RNAs commonly deregulated in human malignancies. The aim of this study was to investigate the role of miRNAs in gefitinib resistance. We established a gefitinib-resistant cell model (PC9GR) by continually exposing PC9 NSCLC cells togefitinib for 6months. MiRNA microarray screening revealed miR-138-5p showed the greatest downregulation in PC9GR cells. Re-expression of miR-138-5pwas sufficient to sensitize PC9GR cells and another gefitinib-resistant NSCLC cell line, H1975, to gefitinib. Bioinformatics analysis and luciferase reporter assay showed that G protein-coupled receptor124 (GPR124) was a direct target of miR-138-5p. Experimental validation demonstrated that expression of GPR124 was suppressed by miR-138-5p on protein and mRNA levels in NSCLC cells. Furthermore, we observed an inverse correlation between the expression of miR-138-5p and GPR124 in lung adenocarcinoma specimens. Knockdown of GPR124 mimicked the effects of miR-138-5p on the sensitivity to gefitinib. Collectively, our results suggest that downregulation of miR-138-5p contributes to gefitinib resistance and that restoration of miR-138-5p or inhibition GPR124 might serve as potential therapeutic approach for overcoming NSCLC gefitinib resistance.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Nature Cell Biology. 2014 Feb 23;16(3):268-280. doi: 10.1038/ncb2910.
 MicroRNA-146a directs the symmetric division of Snail-dominant colorectal cancer stem cells
 
 
 Wei-Lun Hwang, Jeng-Kae Jiang, Shung-Haur Yang, Tse-Shun Huang, Hsin-Yi Lan, Hao-Wei Teng, Chih-Yung Yang, Ya-Ping Tsai, Chi-Hung Lin, Hsei-WeiWang, Muh-Hwa Yang
  Abstract
Asymmetrical cell division (ACD) maintains the proper number of stem cells to ensure self-renewal. In cancer cells, the deregulation of ACD disrupts the homeostasis of the stem cell pool and promotes tumour growth. However, this mechanism is unclear. Here, we show a reduction of ACD in spheroid-derived colorectal cancer stem cells (CRCSCs) compared with differentiated cancer cells. The epithelial-mesenchymal transition (EMT) inducer Snail is responsible for the ACD-to-symmetrical cell division (SCD) switch in CRCSCs. Mechanistically, Snail induces the expression of microRNA-146a (miR-146a) through the £]-catenin-TCF4 complex. miR-146a targets Numb to stabilize £]-catenin, which forms a feedback circuit to maintain Wnt activity and directs SCD. Interference with the Snail-miR-146a-£]-catenin loop by inhibiting the MEK or Wnt activity reduces the symmetrical division of CRCSCs and attenuates tumorigenicity. In colorectal cancer patients, the SnailHighNumbLow profile is correlated with cetuximab resistance and a poorer prognosis. This study elucidates a unique mechanism of EMT-induced CRCSC expansion.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Evidence-Based Complementary and Alternative Medicine. 2014 February 20.
 Deer Antler Extract Improves Fatigue Effect through Altering the Expression of Genes Related to Muscle Strength in Skeletal Muscle of Mice
 
 
 Jaw-Chyun Chen, Chien-Yun Hsiang, Yung-Chang Lin, Tin-Yun Ho
  Abstract
Deer antler is a well-known traditional Chinese medicine used in Asian countries for the tonic and the improvement of aging symptoms. The present study was designed to investigate the antifatigue effect and mechanism of Formosan sambar deer tip antler extract (FSDTAE). The swimming times to exhaustion of mice administered FSDTAE (8.2 mg/day) for 28 days were apparently longer than those of the vehicle-treated mice in forced swim test. However, the indicators of fatigue, such as the reduction in glucose level and the increases in blood urea nitrogen and lactic acid levels, were not significantly inhibited by FSDTAE. Therefore, microarray analysis was further used to examine the anti-fatigue mechanism of FSDTAE. We selected genes with fold changes >2 or <−2 in skeletal muscle for pathway analysis. FSDTAE-affected genes were involved in 9 different signaling pathways, such as GnRH signaling pathway and insulin signaling pathway. All of the significantly expressed genes were classified into 8 different categories by their functions. The most enriched category was muscular system, and 6 upregulated genes, such as troponin I, troponin T1, cysteine and glycine-rich protein 2, myosin heavy polypeptide 7, tropomyosin 2, and myomesin family member 3, were responsible for the development and contraction of muscle. Real-time PCR analysis indicated that FSDTAE increased troponins mRNA expression in skeletal muscle. In conclusion, our findings suggested that FSDTAE might increase the muscle strength through the upregulation of genes responsible for muscle contraction and consequently exhibited the anti-fatigue effect in mice.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Molecular BioSystems. 2014 Jan 14. doi: 10.1039/C3MB70564A .
 An increased ratio of serum miR-21 to miR-181a levels is associated with the early pathogenic process of chronic obstructive pulmonary disease in asymptomatic heavy smokers
 
 
 Lihua Xie, Minghua Wu, Hua Lin, Chun Liu, Honghui Yang, Juan Zhan, Shenghua Sun
  Abstract
Heavy smoking is associated with the development of chronic obstructive pulmonary disease (COPD). However, there is no valuable biomarker for evaluating COPD development in heavy smokers because they are usually asymptomatic. This study is aimed at evaluating whether the levels of serum miRNAs can serve as biomarkers for predicting the occurrence of COPD. A rat model of emphysema was induced by enforced smoking, and the dynamic miRNAs expression profile at different stages of emphysema with varying periods of smoking were analyzed by microarray and quantitative real-time polymerase chain reaction (qRT-PCR). The differentially expressing miRNAs were analyzed using Gene Ontology and the KEGG PATHWAY database. The levels of three serum candidate miRNAs were measured by qRT-PCR in 41 healthy controls (HC), 40 asymptomatic heavy smokers, and 49 COPD patients. Following smoking for varying periods, different severities of lung emphysema were observed in different groups of rats, accompanied by altered levels of some serum miRNAs associated with regulating some pathways. Furthermore, the levels of miR-21 were significantly higher in the COPD patients and asymptomatic heavy smokers than in the HC (P < 0.001), while the levels of miR-181a were significantly lower in the COPD patients and asymptomatic heavy smokers than in the HC (P < 0.001). Accordingly, the levels of serum miR-21 and miR-181a as well as their ratios had a high sensitivity (0.854) and specificity (0.850) for evaluating the development of COPD. Our data suggest that the levels of serum miR-21 and miR-181a may be valuable for evaluating the development of COPD in heavy smokers.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Environmental Toxicology. 2014 Jan 13. doi: 10.1002/tox.21949.
 Prenatal and neonatal exposure to perfluorooctane sulfonic acid results in aberrant changes in miRNA expression profile and levels in developing rat livers
 
 
 Fan Wang, Yihe Jin, Faqi Wang, Junsheng Ma, Wei Liu
  Abstract
Perfluorooctane sulfonate (PFOS) is an animal carcinogen. However, the underlying mechanism in cancer initiation is still largely unknown. Recently identified microRNAs (miRNAs) may play an important role in toxicant exposure and in the process of toxicant-induced tumorigenesis. We used PFOS to investigate PFOS-induced changes in miRNA expression in developing rat liver and the potential mechanism of PFOS-induced toxic action. Dams received 3.2 mg/kg PFOS in their feed from gestational day 1 (GD1) to postnatal day 7 (PND 7). Pups then had free access to treated feed until PND 7. We isolated RNAs from liver tissues on PND 1 and 7 and analyzed the expression profiles of 387 known rat miRNAs using microarray technology. PFOS exposure induced significant changes in miRNA expression profiles. Forty-six miRNAs had significant expression alterations on PND 1, nine miRNAs on PND 7. Specifically, expression of four miRNAs was up-regulated on PND 7 but down-regulated on PND1 (p < 0.05). Many aberrantly expressed miRNAs were related to various cancers. We found oncogenic and tumor-suppressing miRNAs, which included miR-19b, miR-21*, miR-17-3p, miR-125a-3p, miR-16, miR-26a, miR-1, miR-200c, and miR-451. In addition, four miRNAs were simultaneous significantly expressed on both PND 1 and 7. Functional Annotation analysis of the predicted transcript targets revealed that PFOS exposure potentially alters pathways associated with different cancers (cancer, melanoma, pancreatic cancer, colorectal cancer, and glioma), biological processes which include positive regulation of apoptosis and cell proliferation. Results showed PFOS exposure altered the expression of a suite of miRNAs.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 American Journal of Hypertension. 2014 Jan 11. doi:10.1093/ajh/hpt239.
 A Three-Stage Genome-Wide Association Study Combining Multilocus Test and Gene Expression Analysis for Young-Onset Hypertension in Taiwan Han Chinese
 
 
 Kuang-Mao Chiang, Hsin-Chou Yang, Yu-Jen Liang, Jaw-Wen Chen, Shiaw-Min Hwang, Hung-Yun Ho, Chih-Tai Ting, Tsung-Hsien Lin, Sheng-Hsiung Sheu, Wei-Chuan Tsai, Jyh-Hong Chen, Hsin-Bang Leu, Wei-Hsian Yin, Ting-Yu Chiu, Chin-Iuan Chen, Shing-Jong Lin, G. Neil Thomas, Brian Tomlinson, Youling Guo, Hong-Sheng Gui, Pak Chung Sham, Tai-Hing Lam, Wen-Harn Pan
  Abstract
BACKGROUND: Although many large-scale genome-wide association studies (GWASs) have been performed, only a few studies have successfully identified replicable, large-impact hypertension loci; even fewer studies have been done on Chinese subjects. Young-onset hypertension (YOH) is considered to be a more promising target disorder to investigate than late-onset hypertension because of its stronger genetic component. METHODS: To map YOH genetic variants, we performed a 3-stage study combining 1st-stage multilocus GWASs, 2nd-stage gene expression analysis, and 3rd-stage multilocus confirmatory study. RESULTS: In the 1st stage, Illumina550K data from 400 case-control pairs were used, and 22 genes flanked by 14 single nucleotide polymorphism (SNP) septets (P values adjusted for false discovery rate (pFDR) < 3.16¡Ñ10-7) were identified. In the 2nd stage, differential gene expression analysis was carried out for these genes, and 5 genes were selected (pFDR < 0.05). In the 3rd stage, we re-examined the finding with an independent set of 592 case-control pairs and with the joint samples (n = 992 case-control pairs). A total of 6 SNP septets flanking C1orf135, GSN, LARS, and ACTN4 remained significant in all 3 stages. Among them, the same septet flanking ACTN4 was also associated with blood pressure traits in the Hong Kong Hypertension Study (HKHS) and in the Wellcome Trust Case-Control Consortium Hypertension Study (WTCCCHS). LARS was detected in the HKHS, but not in the WTCCCHS. GSN may be specific to Taiwanese individuals because it was not found by either the HKHS or the WTCCCHS. CONCLUSIONS: Our study identified 4 previously unknown YOH loci in Han Chinese. Identification of these genes enriches the hypertension susceptibility gene list, thereby shedding light on the etiology of hypertension in Han Chinese.
   

  ✔本篇論文使用華聯產品:Yeast OneArray  
 Journal of Integrative Plant Biology. 2014 Jan 14. doi: 10.1111/jipb.12169.
 Identification of a novel pathway involving a GATA transcription factor in yeast and possibly plant Zn uptake and homeostasis
 
 
 Matthew J. Milner, Nicole S. Pence, Jiping Liu, Leon V.Kochian
  Abstract
To gain a better understanding of the regulation of Zn homeostasis in plants and the degree of conservation of Zn homeostasis between plants and yeast, a cDNA library from the Zn/Cd hyperaccumulating plant species, Noccaea caerulescens, was screened for its ability to restore growth under Zn limiting conditions in the yeast mutant zap1▵. ZAP1 is a transcription factor that activates the Zn dependent transcription of genes involved in Zn uptake, including ZRT1, the yeast high affinity Zn transporter. From this screen two members of the E2F family of transcription factors were found to activate ZRT1 expression in a Zn independent manner. The activation of ZRT1 by the plant E2F proteins involves E2F-mediated activation of a yeast GATA transcription factor which in turn activates ZRT1 expression. A ZRT1 promoter region necessary for activation by E2F and GATA proteins is upstream of two zinc responsive elements previously shown to bind ZAP1 in ZRT1. This activation may not involve direct binding of E2F to the ZRT1 promoter. The expression of E2F genes in yeast does not replace function of ZAP1; instead it appears to activate a novel GATA regulatory pathway involved in Zn uptake and homeostasis that is not Zn responsive.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 International Journal of Cosmetic Science. 2014 Jan 25. doi: 10.1111/ics.12117.
 Bakuchiol: A Retinol-Like Functional Compound Revealed by Gene Expression Profiling & Clinically Proven to have Anti-Aging Effects
 
 
 Krzysztof Bojanowski, Ratan K Chaudhuri
  Abstract
OBJECTIVE: The study was undertaken to compare the skin care related activities of retinol and bakuchiol, a potential alternative to retinoids. Retinol is a pivotal regulator of differentiation and growth of developing as well as adult skin. Retinoic acid is the major physiologically active metabolite of retinol regulating gene expression through retinoic acid receptor - dependant and independent pathways. METHODS: Comparative gene expression profiling of both substances in the EpiDerm FT full thickness skin substitute model was undertaken. Type I, III and IV collagen and aquaporin 3 synthesis in normal human dermal fibroblasts and in were analysed by ELISA and/or histochemistry in EpiDerm FT full thickness skin model were determined. RESULTS: Bakuchiol is a meroterpene phenol abundant in seeds and leaves of the plant Psoralea corylifolia. We present evidence that bakuchiol, having no structural resemblance to retinoids, can function as a functional analogue of retinol. Volcano plots show the great similarity of retinol and bakuchiol gene expression. Retinol-like functionality was further confirmed for the upregulation of types I, and IV collagen in DNA microarray study and also show stimulation of type III collagen in the mature fibroblast model. Bakuchiol was also formulated into a finished skin care product and was tested in clinical case study by twice-a-day facial application. The results showed that, after twelve weeks treatment, significant improvement in lines and wrinkles, pigmentation, elasticity, firmness and overall reduction in photo-damage was observed, without usual retinol therapy-associated undesirable effects. CONCLUSION: Based on these data, we propose that bakuchiol can function as an anti-aging compound through retinol-like regulation of gene expression.
   

  ✔本篇論文使用華聯產品:Array technology and applications  
 Molecular Nutrition & Food Research. 2014 Jan 21. doi: 10.1002/mnfr.201300559.
 Nutritional aspects of metabolic inflammation in relation to health-insights from transcriptomic biomarkers in PBMC of fatty acids and polyphenols
 
 
 Lydia Afman, Dragan Milenkovic, Helen M. Roche
  Abstract
Recent research has highlighted potential important interaction between metabolism and inflammation, within the context of metabolic health and nutrition, with a view to preventing diet-related disease. In addition to this, there is a paucity of evidence in relation to accurate biomarkers that are capable of reflecting this important biological interplay or relationship between metabolism and inflammation, particularly in relation to diet and health. Therefore the objective of this review is to highlight the potential role of transcriptomic approaches as a tool to capture the mechanistic basis of metabolic inflammation. Within this context, this review has focused on the potential of peripheral blood mononuclear cells transcriptomic biomarkers, because they are an accessible tissue that may reflect metabolism and subacute chronic inflammation. Also these pathways are often dysregulated in the common diet-related diseases obesity, type 2 diabetes, and cardiovascular disease, thus may be used as markers of systemic health. The review focuses on fatty acids and polyphenols, two classes of nutrients/nonnutrient food components that modulate metabolism/inflammation, which we have used as an example of a proof-of-concept with a view to understanding the extent to which transcriptomic biomarkers are related to nutritional status and/or sensitive to dietary interventions. We show that both nutritional components modulate inflammatory markers at the transcriptomic level with the capability of profiling pro- and anti-inflammatory mechanisms in a bidirectional fashion; to this end transcriptomic biomarkers may have potential within the context of metabolic inflammation. This transcriptomic biomarker approach may be a sensitive indicator of nutritional status and metabolic health.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 The Journal of Biological Chemistry. 2014 Jan 23.
 Retinoic acid receptor gamma (Rarg) and nuclear receptor subfamily 5, group A, member 2 (Nr5a2) promote conversion of fibroblasts to functional neurons
 
 
 Zixiao Shi, Tianjin Shen, Yanli Liu, Yuanyuan Huang, Jianwei Jiao
  Abstract
Somatic cells can be reprogrammed to neurons and various other cell types with retrovirus or lentivirus. The limitation of this technology is that these genome-integration viruses may increase the risk of gene mutation and cause insertional mutagenesis. We recently found that non-integration adenovirus carrying neuronal transcription factors can induce fibroblasts to neurons. However, the conversion efficiency by the adenovirus is lower than that of the retrovirus or lentivirus. Therefore, it is crucial to identify other factors or chemical compounds to obtain neurons with high efficiency. In this study, we show that the combination of Rarg (RAR-£^) and Nr5a2 (also known as Lrh-1, liver receptor homologue 1) rapidly promote the iN cells maturation within one week and greatly facilitate the conversion with neuronal purities of approximately 50% and yields of more than 130%. They also improve neuronal pattern formation, electrophysiological characteristics and functional integration in vivo. Moreover, the chemical compound agonists to Rarg and Nr5a2 function effectively as well. This approach may be used for the generation and application of iN cells in regenerative medicine.
   

  ✔本篇論文使用華聯產品:  
 BMC Research Notes. Development of a microarray for two rice subspecies: characterization and validation of gene expression in rice tissues.
 2014, 7(1):15. doi: 10.1186/1756-0500-7-15
 
 
 Jia-Shing Chen, Shang-Chi Lin, Chia-Ying Chen, Yen-Ting Hsieh, Ping-Hui Pai, Long-Kung Chen, Shengwan Lee
  Abstract
BACKGROUND: Rice is one of the major crop species in the world helping to sustain approximately half of the global population's diet especially in Asia. However, due to the impact of extreme climate change and global warming, rice crop production and yields may be adversely affected resulting in a world food crisis. Researchers have been keen to understand the effects of drought, temperature and other environmental stress factors on rice plant growth and development. Gene expression microarray technology represents a key strategy for the identification of genes and their associated expression patterns in response to stress. Here, we report on the development of the rice OneArray® microarray platform which is suitable for two major rice subspecies, japonica and indica. RESULTS: The rice OneArray® 60-mer, oligonucleotide microarray consists of a total of 21,179 probes covering 20,806 genes of japonica and 13,683 genes of indica. Through a validation study, total RNA isolated from rice shoots and roots were used for comparison of gene expression profiles via microarray examination. The results were submitted to NCBI's Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE50844 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50844). A list of significantly differentially expressed genes was generated; 438 shoot-specific genes were identified among 3,138 up-regulated genes, and 463 root-specific genes were found among 3,845 down-regulated genes. GO enrichment analysis demonstrates these results are in agreement with the known physiological processes of the different organs/tissues. Furthermore, qRT-PCR validation was performed on 66 genes, and found to significantly correlate with the microarray results (R = 0.95, p < 0.001***). CONCLUSION: The rice OneArray® 22 K microarray, the first rice microarray, covering both japonica and indica subspecies was designed and validated in a comprehensive study of gene expression in rice tissues. The rice OneArray® microarray platform revealed high specificity and sensitivity. Additional information for the rice OneArray® microarray can be found at http://www.phalanx.com.tw/index.php.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Evidence-Based Complementary and Alternative Medicine. 2014 Jan 8.
 Gene Expression Profiles Underlying Selective T-Cell-Mediated Immunity Activity of a Chinese Medicine Granule on Mice Infected with Influenza Virus H1N1
 
 
 Na-na Lu, Qi Liu, Shi-jie Ge, JunWu, Qiu Ze-ji, Ze-ji Qiu, Hong-chun Zhang, En-xiang Chao, and Zhuo-nan Yu, Li-gang Gu
  Abstract
A Chinese medicine granule, Shu-Feng-Xuan-Fei (SFXF), is critical for viral clearance in early phase of influenza virus infection. In this study, 72 ICR mice were randomly divided into six groups: normal control group, virus control group, Oseltamivir group, low-dose SFXF, medium-dose SFXF, and high-dose SFXF. Mice were anesthetized and inoculated with 4LD50 of influenza virus A (H1N1) except normal control group. Oseltamivir group received 11.375 mg¡Pkg−1¡Pd−1 Oseltamivir Phosphate. SFXF 3.76, 1.88 and 0.94 g¡Pkg−1¡Pd−1 were administrated to mice in all SFXF groups. Each group was in equal dose of 0.2ml daily for 4 consecutive days. Mice were sacrificed and then total RNA was extracted in lung tissue. Some genes involved in T-cell-mediated immunity were selected by DNA microarray. These candidate genes were verified by Real-Time PCR and western immunoblotting. Compared with virus control group, in Toll-like receptor signaling pathway, 12 virus-altered genes were significantly reduced following medium-dose SFXF treatment. Eighteen antigen processing presentation-associated genes were upregulated by medium-dose SFXF. In the process of T cell receptor signaling pathway, 19 genes were downregulated by medium-dose SFXF treatment. On exploration into effector T cells activation and cytokines, all of altered genes in virus control group were reversed by medium-dose SFXF. Real-time PCR and western immunoblotting showed that the regulation of medium-dose SFXF in IL-4, IFN-, TNF-, IL-1, TLR7, MyD88, p38, and JNK was superior to Oseltamivir and high-dose SFXF group. Therefore, SFXF granules could reduce influenza infected cells and activation of T cells.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 International Journal of Molecular Medicine. 2013, 32(3):557-67. doi: 10.3892/ijmm.2013.1424.
 Serum microRNA expression levels can predict lymph node metastasis in patients with early-stage cervical squamous cell carcinoma
 
 
 DESHENG YAO, JUNYING CHEN, YUE LI, HONG CHEN, CHANJUAN HE, NAN DING, YAN LU, TINGYU OU, SHAN ZHAO, LI LI, FENGYI LONG
  Abstract
Circulating microRNA expression levels can serve as diagnostic/prognostic biomarkers in several types of malignant tumors; however, to our knowledge, there have been reports describing their value in cervical squamous cell carcinoma (SCC). In this study, we used hybridization arrays to compare the microRNA expression profiles in cervical squamous cell carcinomas (SCC) samples among patients with lymph node metastasis (LNM) or without LNM; 89 microRNAs were found to fit our inclusion criteria. Using quantitative PCR (qPCR), we examined the expression levels of these microRNAs in cervical cancer tissue, as well as in serum from patients and healthy women. We compared the expression levels between patients with LNM (n=40) and those without LNM (n=40) and healthy controls (n=20). Using regression analysis, we generated a comprehensive set of marker microRNAs and drew the fitted binormal receiver operating characteristic (ROC) curves to access the predictive value. We identified 6 serum microRNAs that can predict LNM in cervical SCC patients; these microRNAs were miR-1246, miR-20a, miR-2392, miR-3147, miR-3162-5p and miR-4484. The area under the curve (AUC) of the comprehensive set of serum microRNAs predicting LNM was 0.932 (sensitivity, 0.856; specificity, 0.850). The predictive value of the serum microRNAs was inferior to that in tissue (AUC 0.992; sensitivity, 0.967; specificity, 0.950; P=0.018). We compared the LNM predictive value of serum microRNAs and SCC antigen (SCC-Ag) by drawing fitted binormal ROC curves However, serum microRNA analysis is by far superior to serum SCC‑Ag analysis (AUC 0.713; sensitivity, 0.612; specificity, 0.700; P<0.0001). Serum microRNAs are a good predictor of LNM with clinical value in early-stage cervical SCC.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Journal of Diabetes Research. 2013:589451. doi: 10.1155/2013/589451.
 The effect of diabetes-associated autoantigens on cell processes in human PBMCs and their relevance to autoimmune diabetes development.
 
 
 Radek Blatny, Zbynek Halbhuber, Michal Kolar, Ales Neuwirth, Lenka Petruzelkova, Tereza Ulmannova, Stanislava Kolouskova, Zdenek Sumnik, Pavlina Pithova, Maria Krivjanska, Dominik Filipp, Katerina Stechova, Jana Vcelakova
  Abstract
Type 1 Diabetes (T1D) is considered to be a T-helper- (Th-) 1 autoimmune disease; however, T1D pathogenesis likely involves many factors, and sufficient tools for autoreactive T cell detection for the study of this disease are currently lacking. In this study, using gene expression microarrays, we analysed the effect of diabetes-associated autoantigens on peripheral blood mononuclear cells (PBMCs) with the purpose of identifying (pre)diabetes-associated cell processes. Twelve patients with recent onset T1D, 18 first-degree relatives of the TD1 patients (DRL; 9/18 autoantibody positive), and 13 healthy controls (DV) were tested. PBMCs from these individuals were stimulated with a cocktail of diabetes-associated autoantigens (proinsulin, IA-2, and GAD65-derived peptides). After 72 hours, gene expression was evaluated by high-density gene microarray. The greatest number of functional differences was observed between relatives and controls (69 pathways), from which 15% of the pathways belonged to ¡§immune response-related¡¨ processes. In the T1D versus controls comparison, more pathways (24%) were classified as ¡§immune response-related.¡¨ Important pathways that were identified using data from the T1D versus controls comparison were pathways involving antigen presentation by MHCII, the activation of Th17 and Th22 responses, and cytoskeleton rearrangement-related processes. Genes involved in Th17 and TGF-beta cascades may represent novel, promising (pre)diabetes biomarkers.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 BBA Molecular and Cell Biology of Lipids. 2013 Dec 22. doi: 10.1016/j.bbalip.2013.12.005.
 Silencing diacylglycerol kinase-theta expression reduces steroid hormone biosynthesis and cholesterol metabolism in human adrenocortical cells
 
 
 Kai Cai, Natasha C. Lucki, Marion B. Sewer
  Abstract
Diacylglycerol kinase theta (DGK£c) plays a pivotal role in regulating adrenocortical steroidogenesis by synthesizing the ligand for the nuclear receptor steroidogenic factor 1 (SF1). In response to activation of the cAMP signaling cascade nuclear DGK activity is rapidly increased, facilitating PA-mediated, SF1-dependent transcription of genes required for cortisol and dehydroepiandrosterone (DHEA) biosynthesis. Based on our previous work identifying DGK£c as the enzyme that produces the agonist for SF1, we generated a tetracycline-inducible H295R stable cell line to express a short hairpin RNA (shRNA) against DGK£c and characterized the effect of silencing DGK£c on adrenocortical gene expression. Genome-wide DNA microarray analysis revealed that silencing DGK£c expression alters the expression of multiple genes, including steroidogenic genes, nuclear receptors and genes involved in sphingolipid, phospholipid and cholesterol metabolism. Interestingly, the expression of sterol regulatory element binding proteins (SREBPs) was also suppressed. Consistent with the suppression of SREBPs, we observed a down-regulation of multiple SREBP target genes, including 3-hydroxy-3-methylglutary coenzyme A reductase (HMG-CoA red) and CYP51, concomitant with a decrease in cellular cholesterol. DGK£c knockdown cells exhibited a reduced capacity to metabolize PA, with a down-regulation of lipin and phospholipase D (PLD) isoforms. In contrast, suppression of DGK£c increased the expression of several genes in the sphingolipid metabolic pathway, including acid ceramidase (ASAH1) and sphingosine kinases (SPHK). In summary, these data demonstrate that DGK£c plays an important role in steroid hormone production in human adrenocortical cells.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Journal of Biological Chemistry . 2013 Dec 23.
 Anthrax Lethal Toxin Inhibits Translation of Hypoxia Inducible Factor 1£ and Causes Decreased Tolerance to Hypoxic Stress
 
 
 Weiming Ouyang, Chikako Torigoe, Hui Fang, Tao Xie, David M. Frucht
  Abstract
Hypoxia is considered to be a contributor to the pathology associated with administration of anthrax lethal toxin (LT). However, we herein report that serum lactate levels in LT-treated mice are reduced, a finding inconsistent with the anaerobic metabolism expected to occur during hypoxia. Reduced lactate levels are also observed in the culture supernatants of LT-treated cells. LT inhibits the accumulation of hypoxia inducible factor (HIF)-1£, a subunit of HIF-1, the master regulator directing cellular responses to hypoxia. The toxin has no effect on the transcription or protein turnover of HIF-1£, but instead acts to inhibit HIF-1£ translation. LT treatment diminishes phosphorylation of eIF4B, eIF4E, and rpS6, critical components of the intracellular machinery required for HIF-1£ translation. Moreover, blockade of MKK1/2-Erk1/2, but not p38 or JNK signaling lowers HIF-1£ protein levels in both normoxic and hypoxic conditions, consistent with a role for MKK1 and MKK2 as the major targets of LT responsible for the inhibition of HIF-1£ translation. The physiological importance of the LT-induced translation blockade is demonstrated by the finding that LT treatment decreases the survival of hepatocyte cell lines grown in hypoxic conditions, an effect that is overcome by pre-induction of HIF-1£. Taken together, these data support a role for LT in dysregulating HIF-1£ and thereby disrupting homeostatic responses to hypoxia, an environmental characteristic of certain tissues at baseline and/or during disseminated infection with Bacillus anthracis.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Fertility and Sterility. 2013, 99(7):2000-8.e1. doi: 10.1016/j.fertnstert.2013.01.150.
 Gene expression profiles of cumulus cells obtained from women treated with recombinant human luteinizing hormone + recombinant human follicle-stimulating hormone or highly purified human menopausal gonadotropin versus recombinant human follicle-stimulating hormone alone
 
 
 Tatone C, Ciriminna R, Vento M, Franchi S, d'Aurora M, Sperduti S, Cela V, Borzì P, Palermo R, Stuppia L, Artini PG, Valentina Gatta
  Abstract
OBJECTIVE: To evaluate cumulus cell (CC) expression profile modulation after different stimulation protocols. DESIGN: CCs transcriptome variations were evaluated by microarray in patients undergoing different treatments for ovarian stimulation, namely, r-hLH + r-hFSH and hp-hMG, compared with a control group treated with r-hFSH. SETTING: Healthy patients undergoing assisted reproduction protocols. PATIENT(S): Sixteen healthy women with regular cycles and tubal disease or unexplained infertility. INTERVENTION(S): Four patients received hp-hMG, four received r-hFSH + r-hLH, and eight received r-hFSH daily. Aspiration of the oocytes was performed 36 hours after hCG administration. Only samples derived from cumulus-oocyte complexes containing mature oocytes showing polar body were processed. MAIN OUTCOME MEASURE(S): Comparison of genes differentially expressed in both treatment groups with the use of a hierarchic clustering analysis. RESULT(S): Data clustering analysis allowed detection of four clusters containing genes differentially expressed in both treatment groups compared with control. Functional analysis of the affected transcripts revealed genes involved in oocyte development and maturation. CONCLUSION(S): r-hLH and hCG, though acting on the same receptor, produce a differential activation of intracellular pathways. It can be hypothesized that this effect depends on their different structures and specific binding affinity for the receptor.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Cancer Research. 2013 Dec 9.
 Immune chaperone gp96 drives the contributions of macrophages to inflammatory colon tumorigenesis
 
 
 Crystal Morales, Saleh Rachidi, Feng Hong, Shaoli Sun, Xinshou Ouyang, Caroline Wallace, Yongliang Zhang, Elizabeth Garret-Mayer, Jennifer Wu, Bei Liu, Zihai Li
  Abstract
Macrophages are important drivers in the development of inflammation-associated colon cancers, but the mechanistic underpinnings for their contributions are not fully understood. Further, Toll-like receptors (TLR) have been implicated in colon cancer, but their relevant cellular sites of action are obscure. In this study, we show that the endoplasmic reticulum chaperone gp96 is essential in tumor-associated macrophages (TAM) to license their contributions to inflammatory colon tumorigenesis. Mice where gp96 was genetically deleted in a macrophage-specific manner exhibited reduced colitis and inflammation-associated colon tumorigenesis. Attenuation of colon cancer in these mice correlated strikingly with reduced mutation rates of £]-catenin, increased efficiency of the DNA repair machinery and reduced expression of pro-inflammatory cytokines, including IL-17 and IL-23 in the tumor microenvironment. The genotoxic nature of TAM-associated inflammation was evident by increased expression of genes in the DNA repair pathway. Our work deepens understanding of how TAM promote oncogenesis by altering the molecular oncogenic program within epithelial cells, and it identifies gp96 as a lynchpin chaperone needed in TAM to license their function and impact on expression of critical inflammatory cytokines in colon tumorigenesis.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Biochemical and Biophysical Research Communications. 2013 Dec 2. doi: 10.1016/j.bbrc.2013.11.108.
 Transgenic mice expressing mutant Pinin exhibit muscular dystrophy, nebulin deficiency and elevated expression of slow-type muscle fiber genes
 
 
 Hsu-Pin Wu, Shu-Yuan Hsu, Wen-Ai Wu, Ji-Wei Hu, Pin Ouyang
  Abstract
Pinin (Pnn) is a nuclear speckle-associated SR-like protein. The N-terminal region of the Pnn protein sequence is highly conserved from mammals to insects, but the C-terminal RS domain-containing region is absent in lower species. The N-terminal coiled-coil domain (CCD) is, therefore, of interest not only from a functional point of view, but also from an evolutionarily standpoint. To explore the biological role of the Pnn CCD in a physiological context, we generated transgenic mice overexpressing Pnn mutant in skeletal muscle. We found that overexpression of the CCD reduces endogenous Pnn expression in cultured cell lines as well as in transgenic skeletal muscle fibers. Pnn mutant mice exhibited reduced body mass and impaired muscle function during development. Mutant skeletal muscles show dystrophic histological features with muscle fibers heavily loaded with centrally located myonuclei. Expression profiling and pathway analysis identified over-representation of genes in gene categories associated with muscle contraction, specifically those related to slow type fiber. In addition nebulin (NEB) expression level is repressed in Pnn mutant skeletal muscle. We conclude that Pnn downregulation in skeletal muscle causes a muscular dystrophic phenotype associated with NEB deficiency and the CCD domain is incapable of replacing full length Pnn in terms of functional capacity.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 European Journal of Neuroscience. 2013 Dec 5. doi: 10.1111/ejn.12444.
 Widespread microRNA dysregulation in multiple system atrophy ¡V disease-related alteration in miR-96
 
 
 Kiren Ubhi, Edward Rockenstein, Christine Kragh, Chandra Inglis, Brian Spencer, Sarah Michael, Michael Mante, Anthony Adame, Douglas Galasko, Eliezer Masliah
  Abstract
MicroRNA (miRNA) are short sequences of RNA that function as post-transcriptional regulators by binding to target mRNA transcripts resulting in translational repression. A number of recent studies have identified miRNA as being involved in neurodegenerative disorders including Alzheimer's disease, Parkinson's disease and Huntington's disease. However, the role of miRNA in multiple system atrophy (MSA), a progressive neurodegenerative disorder characterized by oligodendroglial accumulation of alpha-synuclein remains unexamined. In this context, this study examined miRNA profiles in MSA cases compared with controls and in transgenic (tg) models of MSA compared with non-tg mice. The results demonstrate a widespread dysregulation of miRNA in MSA cases, which is recapitulated in the murine models. The study employed a cross-disease, cross-species approach to identify miRNA that were either specifically dysregulated in MSA or were commonly dysregulated in neurodegenerative conditions such as Alzheimer's disease, dementia with Lewy bodies, progressive supranuclear palsy and corticobasal degeneration or the tg mouse model equivalents of these disorders. Using this approach we identified a number of miRNA that were commonly dysregulated between disorders and those that were disease-specific. Moreover, we identified miR-96 as being up-regulated in MSA. Consistent with the up-regulation of miR-96, mRNA and protein levels of members of the solute carrier protein family SLC1A1 and SLC6A6, miR-96 target genes, were down-regulated in MSA cases and a tg model of MSA. These results suggest that miR-96 dysregulation may play a role in MSA and its target genes may be involved in the pathogenesis of MSA.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Journal of Hazardous Materials. 2013 Nov 20;264C:303-312. doi: 10.1016/j.jhazmat.2013.11.031.
 Differential cytotoxic effects of gold nanoparticles in different mammalian cell lines
 
 
 linesPin Ju Chueh, Ruei-Yue Liang, Yi-Hui Lee, Zih-Ming Zeng, Show-Mei Chuang
  Abstract
Gold nanoparticles (AuNPs) possess unique properties that have been exploited in several medical applications. However, a more comprehensive understanding of the environmental safety of AuNPs is imperative for use of these nanomaterials. Here, we describe the impacts of AuNPs in various mammalian cell models using an automatic and dye-free method for continuous monitoring of cell growth based on the measurement of cell impedance. Several well-established cytotoxicity assays were also used for comparison. AuNPs induced a concentration-dependent decrease in cell growth. This inhibitory effect was associated with apoptosis induction in Vero cells but not in MRC-5 or NIH3T3 cells. Interestingly, cDNA microarray analyses in MRC-5 cells supported the involvement of DNA damage and repair responses, cell-cycle regulation, and oxidative stress in AuNP-induced cytotoxicity and genotoxicity. Moreover, autophagy appeared to play a role in AuNPs-induced attenuation of cell growth in NIH3T3 cells. In this study, we present a comprehensive overview of AuNP-induced cytotoxicity in a variety of mammalian cell lines, comparing several cytotoxicity assays. Collectively, these assays offer convincing evidence of the cytotoxicity of AuNPs and support the value of a systematic approach for analyzing the toxicology of nanoparticles.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 PLOS Genetics. 2013, 11:e1003940. doi: 10.1371/journal.pgen.1003940.
 Crosstalk between NSL Histone Acetyltransferase and MLL/SET Complexes: NSL Complex Functions in Promoting Histone H3K4 Di-Methylation Activity by MLL/SET Complexes
 
 
 Xiaoming Zhao, Jiaming Su, Fei Wang, Da Liu, Jian Ding, Yang Yang, Joan W. Conaway, Ronald C. Conaway, Lingling Cao, Donglu Wu, Min Wu, Yong Cai, Jingji Jin
  Abstract
hMOF (MYST1), a histone acetyltransferase (HAT), forms at least two distinct multiprotein complexes in human cells. The male specific lethal (MSL) HAT complex plays a key role in dosage compensation in Drosophila and is responsible for histone H4K16ac in vivo. We and others previously described a second hMOF-containing HAT complex, the non-specific lethal (NSL) HAT complex. The NSL complex has a broader substrate specificity, can acetylate H4 on K16, K5, and K8. The WD (tryptophan-aspartate) repeat domain 5 (WDR5) and host cell factor 1 (HCF1) are shared among members of the MLL/SET (mixed-lineage leukemia/set-domain containing) family of histone H3K4 methyltransferase complexes. The presence of these shared subunits raises the possibility that there are functional links between these complexes and the histone modifications they catalyze; however, the degree to which NSL and MLL/SET influence one another's activities remains unclear. Here, we present evidence from biochemical assays and knockdown/overexpression approaches arguing that the NSL HAT promotes histone H3K4me2 by MLL/SET complexes by an acetylation-dependent mechanism. In genomic experiments, we identified a set of genes including ANKRD2, that are affected by knockdown of both NSL and MLL/SET subunits, suggested they are co-regulated by NSL and MLL/SET complexes. In ChIP assays, we observe that depletion of the NSL subunits hMOF or NSL1 resulted in a significant reduction of both H4K16ac and H3K4me2 in the vicinity of the ANKRD2 transcriptional start site proximal region. However, depletion of RbBP5 (a core component of MLL/SET complexes) only reduced H3K4me2 marks, but not H4K16ac in the same region of ANKRD2, consistent with the idea that NSL acts upstream of MLL/SET to regulate H3K4me2 at certain promoters, suggesting coordination between NSL and MLL/SET complexes is involved in transcriptional regulation of certain genes. Taken together, our results suggest a crosstalk between the NSL and MLL/SET complexes in cells.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Evidence-Based Complementary and Alternative Medicine. 2013 Nov 18.
 Gene Expression Profiles Underlying Selective T Cell-mediated Immunity Activity of a Chinese Medicine Granule on Mice Infected with Influenza Virus H1N1
 
 
 Lu Na-na, Liu Qi, Ge Shi-jie, Wu Jun, Qiu Ze-ji, Zhang Hong-chun, Zhao En-xiang, Zhang Yi, Yu Zhuo-nan, Gu Li-gang
  Abstract
Background.Efficacy of a Chinese medicine granule, Shu-Feng-Xuan-Fei (SFXF) has been demonstrated in reducing the duration of fever among patients with influenza. SFXF has also been found efficacious in reducing lung index and pathological lesion and regulating natural killer (NK) cell mediated cytotoxicity in pneumonia mice infected with influenza virus. Yet the effects of SFXF on viral infection in T cell-mediated immunity at the gene transcriptional level have never been reported.Objective.To elucidatethe effectsof SFXF on the major pathways and genes involved in T-cell mediated immunity in the lung of mice subjected toinfluenza virus H1N1 infection. Methods.Seventy-two ICR mice were randomly divided into six groups (n=12): normal control group (N), virus control group (M), Oseltamivirgroup, low-dose SFXF(SL), medium-dose SFXF(SM) and high-dose SFXF(SH). Mice were anesthetized with 2, 2, 2-tribromoethanol in tert-amyl alcohol and inoculated (i.n.) with 4LD50 of virus except normal control group. Oseltamivir groupreceived 11.375 mg•kg-1•d-1Oseltamivir Phosphate. SFXF 3.76, 1.88 and 0.94 g•kg-1•d-1were administrated to mice in all SFXF groups by gastric perfusion. Each group was in equal dose of 0.2ml daily for 4 consecutive days. Mice were sacrificed and then total RNA were extracted in lung tissue. Some genes involved in T cell-mediated immunity were selected by DNA microarray. These candidate genes were verified by Real-Time PCR and western immunoblotting. Results. Compared with virus control group, in Toll-like receptor signaling pathway, 12 virus-altered genes were significantly reduced following the medium-dose SFXF treatment. Eighteen antigen processing presentation-associated genes were up-regulated by medium-dose SFXF, among which 13 genes and 5 genes belong to MHC-I and MHC-II family respectively. In the process of T cell receptor signaling pathway, 19 genes were down-regulated by the medium-dose SFXF treatment. Exploration into effector T cells activation and cytokines, all of altered genes in virus control group were reversed by the medium-dose SFXF. Real-time PCR and western immunoblotting showed the regulation of the medium-dose SFXF in IL-4, IFN-, TNF-, IL-1, TLR7, MyD88, p38 and JNKwas superior to Oseltamivir and high-dose SFXF group. As expected, real-time PCR and western immunoblotting data were consistent with the results of microarray assay. Conclusion. Viral replication was found to have been prevented and the viral infection was eliminated with exposure to SFXF granules. The mechanism could be through the reduction of influenzainfected cells and activationof T cells. This immunomodulation effects could be realized by regulating gene expressions of T cells activation. Thus, SFXF could help to restore a balance of the host immune system, which may be critical for viral clearance in early phase of influenza virus infection.
   

  ✔本篇論文使用華聯產品:  
 Oncology Reports. 2013 Nov 28. doi: 10.3892/or.2013.2877.
 Bioinformatic analysis of the membrane cofactor protein CD46 and microRNA expression in hepatocellular carcinoma
 
 
 ZEJUN LU, CHUANFU ZHANG, JIAJUN CUI, QI SONG, LIGUI WANG, JINGBO KANG, PENG LI, XIAOFENG HU, HONGBIN SONG, JINLIANG YANG, YANSONG SUN
  Abstract
The therapeutic potential of membrane complement regulatory protein (mCRP)-neutralizing antibodies is unsatisfactory, which perhaps lies in the complex role of mCRPs in tumor occurrence and development. As a member of the mCRPs, CD46 is a transmembrane protein with a cytoplasmic domain and is implicated more in the control of the alternative complement pathway than of the classical complement pathway. Growing evidence has revealed that both the CD46 signaling pathway and microRNAs (miRNAs) play an important role in the development and progression of hepatocellular carcinoma (HCC). In the present study, we analyzed mCRP expression in different tumor tissues by employing western blotting and qPCR. To address the potential role of miRNAs in CD46 signaling, we set out to profile miRNA expression in CD46-overexpressed and -silenced HepG2 cell lines. Furthermore, bioinformatic analysis was performed to identify downstream targets of CD46 signaling. We found that the levels of CD46 expression in HCC tissues were significantly higher compared to that in the adjacent normal tissues. After complement-related gene expression profiling and unsupervised hierarchical clustering analysis of 10 HCC tissues, a total of 37 miRNAs showed significantly different expression levels before and after CD46 expression change. By bioinformatic analysis, we identified let-7b and miR-17 as downstream targets of CD46 signaling, and that the expression levels of let-7b and miR-17 were negatively correlated with that of CD46 in HepG2 cells. The present study suggests that CD46 plays an important role in HCC carcinogenesis by regulating let-7b and miR-17.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Journal of Biological Chemistry. 2013 Nov 29..
 The A2A adenosine receptor is a dual-coding gene: a novel mechanism of gene usage and signal transduction.
 
 
 Chien-fei Lee, Hsin-Lin Lai, Yi-Chao Lee, Chen-Li Chien, Yijuang Chern
  Abstract
The A2A adenosine receptor (A2AR) is a G protein-coupled receptor and a major target of caffeine. The A2AR gene encodes alternative transcripts that are initiated from at least two independent promoters. The different transcripts of the A2AR gene contain the same coding region and 3'-untranslated region and different 5'-untranslated regions that are highly conserved among species. We report here that in addition to the production of the A2AR protein, translation from an upstream, out-of-frame AUG of the rat A2AR gene produces a 134-amino acid protein (designated uORF5). An anti-uORF5 antibody recognized a protein of the predicted size of uORF5 in PC12 cells and rat brains. Upregulation of A2AR transcripts by hypoxia led to increased levels of both the A2AR and uORF5 proteins. Moreover, stimulation of A2AR increased the level of the uORF5 protein via post-transcriptional regulation. Expression of the uORF5 protein suppressed the AP1-mediated transcription promoted by nerve growth factor, and modulated the expression of several proteins that were implicated in the mitogen-activated protein (MAP) kinase pathway. Taken together, our results show that the rat A2AR gene encodes two distinct proteins (A2AR and uORF5) in an A2AR-dependent manner. Our study reveals a new example of the complexity of the mammalian genome and provides novel insights into the function of A2AR.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 The Scientific World Journal. 2013 Nov 25..
 Identification of Biomarkers for Esophageal Squamous Cell Carcinoma Using Feature Selection and Decision Tree Methods
 
 
 Chun-Wei Tung, Ming-Tsang Wu, Yu-Kuei Chen, Chun-Chieh Wu, Wei-Chung Chen, Hsien-Pin Li, Shah-Hwa Chou, Deng-ChyangWu, I-ChenWu
  Abstract
Esophageal squamous cell cancer (ESCC) is one of the most common fatal human cancers. The identification of biomarkers for early detection could be a promising strategy to decrease mortality. Previous studies utilized microarray techniques to identify more than one hundred genes; however, it is desirable to identify a small set of biomarkers for clinical use. This study proposes a sequential forward feature selection algorithm to design decision tree models for discriminating ESCC from normal tissues. Two potential biomarkers of RUVBL1 and CNIH were identified and validated based on two public available microarray datasets. To test the discrimination ability of the two biomarkers, 17 pairs of expression profiles of ESCC and normal tissues from Taiwanese male patients were measured by using microarray techniques. The classification accuracies of the two biomarkers in all three datasets were higher than 90%. Interpretable decision tree models were constructed to analyze expression patterns of the two biomarkers. RUVBL1 was consistently overexpressed in all three datasets, although we found inconsistent CNIH expression possibly affected by the diverse major risk factors for ESCC across different areas.
   

  ✔本篇論文使用華聯產品:Array technology and applications  
 Scientometrics. 2013 July 22. doi: 10.1007/s11192-013-1158-6.
 The dynamic effect of knowledge capitals in the public research institute: insights from patenting analysis of ITRI (Taiwan) and ETRI (Korea)
 
 
 Chan-Yuan Wong, Jyh-Wen Shiu, Mei-Chih Hu
  Abstract
This study aims what knowledge capital accumulated by the public research institutes (PRIs) of South Korea and Taiwan to facilitate process configurations of new industrial structure. The patenting trends of two PRIs, ETRI of South Korea and ITRI of Taiwan, are assessed to highlight the established knowledge structures for emergence of multi-agent structure since 1990s. To examine their dynamics and variations of knowledge capital, the data series are separated into two phases (catching-up phase from 1970s to 1990s, and post catching-up phase since the 2000s) in accordance to (1) number of patents, (2) number of sole owned and co-owned patents, (3) backward and forward citations, (4) science-linked patents, and (5) fields of patent. When the role of PRIs in the latecomer country is evolving from a facilitator in the catching-up phase to become a mediator in the post catching-up phase, this study demonstrated their influence and dynamic effect in reinforcing industrial strategies and national approaches to attain endogenous structural change in the national innovation system. Our results signal telecommunications is the promising technology targeted by Korea¡¦s chaebols while Taiwan¡¦s small-medium size enterprises are utilizing the aggregate knowledge capital accumulated and derived from semiconductor technologies to develop their niches onto a diverse range of product innovations.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Experimental Eye Research. 2013 Nov 1. doi: 10.1016/j.exer.2013.10.018.
 Lens specific RLIP76 transgenic mice show a phenotype similar to microphthalmia
 
 
 Sahu M, Sharma R, Yadav S, Wakamiya M, Chaudhary P, Awasthi S, Yogesh C. Awasthi
  Abstract
RALBP1/RLIP76 is a ubiquitously expressed protein, involved in promotion and regulation of functions initiated by Ral and R-Ras small GTPases. Presence of multiple domains in its structure enables RLIP76 to be involved in a number of physiological processes such as endocytosis, exocytosis, mitochondrial fission, actin cytoskeleton remodeling, and transport of exogenous and endogenous toxicants. Previously, we have established that RLIP76 provides protection to ocular tissues against oxidative stress by transporting the glutathione-conjugates of the toxic, electrophilic products of lipid peroxidation generated during oxidative stress. Therefore, we developed lens specific RLIP76 transgenic mice (lensRLIP76 Tg) to elucidate the role of RLIP76 in protection against oxidative stress, but these transgenic mice showed impaired lens development and a phenotype with small eyes similar to that observed in microphthalmia. These findings prompted us to investigate the mechanisms via which RLIP76 affects lens and eye development. In the present study, we report engineering of lensRLIP76 Tg mice, characterization of the associated phenotype, and the possible molecular mechanisms that lead to the impaired development of eye and lens in these mice. The results of microarray array analysis indicate that the genes involved in pathways for G-Protein signaling, actin cytoskeleton reorganization, endocytosis, and apoptosis are affected in these transgenic mice. The expression of transcription factors, Pax6, Hsf1, and Hsf4b known to be involved in lens development is down regulated in the lens of these Tg mice. However, the expression of heat shock proteins (Hsps), the downstream targets of Hsfs, is differentially affected in the lens showing down regulation of Hsp27, Hsp40, up regulation of Hsp60, and no effect on Hsp70 and Hsp90 expression. The disruption in the organization of actin cytoskeleton of these Tg mice was associated with the inhibition of the activation of Cdc42 and down regulation of cofilin phosphorylation. These mice may provide useful animal model for elucidating the mechanisms of lens development, and etiology of microphthalmia.
   

  ✔本篇論文使用華聯產品:Array technology and applications  
 Technology Management in the IT-Driven Services. 2013 July 28.
 Fostering Innovation Commercialization at Research Institute and University: Strategy and Policy Implications
 
 
 Cheng-Mei Tung, Ta-Yu Tseng, Wan-Chang Yen
  Abstract
Global economic development is moving towards a new era with knowledge as its foundation. Enterprises will be able to succeed in the competitive markets only if they can apply the knowledge and technology quickly in the innovation of the industries and the commercialization of products. Research institutions and universities are important sources of innovation and development, and they are also charged with the important mission of providing support for economic development. However, the development of the commercialization of research results and formation of new startup companies have not been as active and market oriented in Taiwan. The purpose of this study is to explore the current status and issues of technology development activities among the industrial, academic and governmental sectors to promote the research results commercialization (or start-ups) in Taiwan. This study evaluates the policy implication of the results commercialization including National Science Council and Small and Medium Business Agency in Taiwan. The results found the commercialization development is not active because of less market oriented in the early-stage of R&D. Besides, the technology is weak correlated with industry development needs. The suggestions of this study are 1) using the industry information map to be the base of technology R&D investment. 2) Enhancing the early stage germination activities to make the R&D project success.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 PLOS ONE. 2013, 8(10): e76265. doi:10.1371/journal.pone.0076265.
 Modeling the Neurovascular Niche: Unbiased Transcriptome Analysis of the Murine Subventricular Zone in Response to Hypoxic Insult
 
 
 Qi Li, Sandra Canosa, Kelly Flynn, Michael Michaud, Michael Krauthammer, Joseph A. Madri
  Abstract
Premature infants often experience chronic hypoxia, resulting in cognitive & motor neurodevelopmental handicaps. These sometimes devastating handicaps are thought to be caused by compromised neural precursor cell (NPC) repair/recovery resulting in variable central nervous system (CNS) repair/recovery. We have identified differential responses of two mouse strains (C57BL/6 & CD1) to chronic hypoxia that span the range of responsiveness noted in the premature human population. We previously correlated several CNS tissue and cellular behaviors with the different behavioral parameters manifested by these two strains. In this report, we use unbiased array technology to interrogate the transcriptome of the subventricular zone (SVZ) in these strains. Our results illustrate differences in mRNA expression in the SVZ of both C57BL/6 and CD1 mice following hypoxia as well as differences between C57BL/6 and CD1 SVZ under both normoxic and hypoxic conditions. Differences in expression were found in gene sets associated with Sox10-mediated neural functions that explain, in part, the differential cognitive and motor responsiveness to hypoxic insult. This may shed additional light on our understanding of the variable responses noted in the human premature infant population and facilitate early intervention approaches. Further interrogation of the differentially expressed gene sets will provide a more complete understanding of the differential responses to, and recovery from, hypoxic insult allowing for more informed modeling of the ranges of disease severity observed in the very premature human population.
   

  ✔本篇論文使用華聯產品:Array technology and applications  
 BioProcess International. 2013, 11(9).
 Cellular Communications: How Cultures and Tissues React to Their Environments
 
 
 Cheryl Scott
  Abstract
The report describe the cell signaling and cellular communication.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Cell Death & Disease. 2013, 4:e883. doi: 10.1038/cddis.2013.419.
 Implication of transcriptional repression in compound C-induced apoptosis in cancer cells
 
 
 Dai RY, Zhao XF, Li JJ, Chen R, Luo ZL, Yu LX, Chen SK, Zhang CY, Duan CY, Liu YP, Feng CH, Xia XM, Li H, HY Wang, J Fu
  Abstract
Compound C, a well-known inhibitor of AMP-activated protein kinase (AMPK), has been reported to induce apoptosis in some types of cells. However, the underlying mechanisms remain largely unclear. Using a DNA microarray analysis, we found that the expression of many genes was downregulated upon treatment with compound C. Importantly, compound C caused transcriptional repression with the induction of p53, a well-known marker of transcriptional stress response, in several cancer cell lines. Compound C did not induce the phosphorylation of p53 but dramatically increased the protein level of p53 similar to some other transcriptional inhibitors, including 5,6-dichloro-1-£]-D-ribobenzimidazole (DRB). Consistent with previous reports, we found that compound C initiated apoptotic death of cancer cells in an AMPK-independent manner. Similar to DRB and actinomycin D (ActD), two classic transcription inhibitors, compound C not only resulted in the loss of Bcl-2 and Bcl-xl protein but also induced the phosphorylation of eukaryotic initiation factor-alpha (eIF2£) on Ser51. Hence, the phosphorylation of eIF2£ might be a novel marker of transcriptional inhibition. It is noteworthy that compound C-mediated apoptosis of cancer cells is correlated with decreased expression of Bcl-2 and Bcl-xl and the phosphorylation of eIF2£ on Ser51. Remarkably, compound C exhibits potent anticancer activities in vivo. Taken together, our data suggest that compound C may be an attractive candidate for anticancer drug development.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Molecular Cancer. 2013, 12(1):129. doi:10.1186/1476-4598-12-129.
 Small molecule antagonist of the bone morphogenetic protein type I receptors suppresses growth and expression of Id1 and Id3 in lung cancer cells expressing Oct4 or nestin
 
 
 Langenfeld E, Deen M, Zachariah E, John Langenfeld
  Abstract
BACKGROUND: Bone morphogenetic proteins (BMP) are embryonic morphogens that are aberrantly expressed in lung cancer. BMPs mediate cell fate decisions and self-renewal of stem cells, through transcription regulation of inhibitor of differentiation protein/DNA binding proteins (Id1-3). Inhibition of BMP signaling decreases growth and induces cell death of lung cancer cells lines by downregulating the expression of Id proteins. It is not known whether the BMP signaling cascade regulates growth and the expression of Id proteins of lung cancer cells expressing the stem cell markers Oct4 and/or nestin. RESULTS: Our studies suggest that lung cancer cells expressing Oct4 or nestin are different cell populations. Microarray and quantitative RT-PCR demonstrated that the expression of specific stem cell markers were different between isolated Oct4 and nestin cells. Both the Oct4 and nestin populations were more tumorigenic than controls but histologically they were quite different. The isolated Oct4 and nestin cells also responded differently to inhibition of BMP signaling. Blockade of BMP signaling with the BMP receptor antagonist DMH2 caused significant growth inhibition of both the Oct4 and nestin cell populations but only increased cell death in the nestin population. DMH2 also induced the expression of nestin in the Oct4 population but not in the nestin cells. We also show that BMP signaling is an important regulator of Id1 and Id3 in both the Oct4 and nestin cell populations. Furthermore, we show that NeuN is frequently expressed in NSCLC and provide evidence suggesting that Oct4 cells give rise to cancer cells expressing nestin and/or NeuN. CONCLUSION: These studies show that although biologically different, BMP signaling is growth promoting in cancer cells expressing Oct4 or nestin. Inhibition of BMP signaling decreases expression of Id proteins and suppresses growth of cancer cells expressing Oct4 or Nestin. Small molecule antagonists of the BMP type I receptors represent potential novel drugs to target the population of cancer cells expressing stem cell markers.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 PLOS ONE. 2013, 8(10): e77936. doi:10.1371/journal.pone.0077936.
 Profiling Circulating MicroRNA Expression in Experimental Sepsis Using Cecal Ligation and Puncture
 
 
 Shao-Chun Wu, Johnson Chia-Shen Yang, Cheng-Shyuan Rau, Yi-Chun Chen, Tsu-Hsiang Lu, Ming-Wei Lin, Siou-Ling Tzeng, Yi-Chan Wu, Chia-Jung Wu, Ching-Hua Hsieh
  Abstract
The levels of circulating microRNAs (miRNAs) in mice with experimental sepsis induced by cecal ligation and puncture (CLP) were determined using whole blood samples obtained from C57BL/6 mice at 4, 8, and 24 h after CLP; miRNA expression analysis was performed in these samples using an miRNA array. Microarray analysis revealed upregulation of 10 miRNA targets (miR-16, miR-17, miR-20a, miR-20b, miR-26a, miR-26b, miR-106a, miR-106b, miR-195, and miR-451). The expression of these miRNA targets in the whole blood, serum, and white blood cells (WBCs) of CLP mice was quantified using quantitative real-time PCR; these values were compared to those in sham-operated C57BL/6 mice, and the results indicated that these miRNA targets were significantly up-regulated in the whole blood and serum but not in the WBCs. In addition, the levels of these 10 miRNA targets in the serum of Tlr2−/−, Tlr4−/−, and NF-£eB−/− mice at 8 h after CLP did not decrease significantly., which indicated that the transcription of these miRNAs was not directly mediated by the TLR2/NF-£eB or TLR4/NF-£eB pathway, and pathways induced by exposure to the gram-positive or gram-negative bacteria. Immunoprecipitation with the Argonaute 2 ribonucleoprotein complex revealed significantly increased expression of the 10 miRNA targets in the serum of mice after CLP, and the levels of 6 (miR-16, miR-17, miR-20a, miR-20b, miR-26a, and miR-26b) of these 10 miRNA targets increased significantly in exosomes isolated using ExoQuick precipitation solution. In this study, we identified circulating miRNAs that were up-regulated after CLP and determined the increase in the levels of these miRNAs, and our results suggest that circulating Ago2 complexes and exosomes may be responsible for the stability of miRNAs in the serum.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Infection, Genetics and Evolution. 2013, 20C:257-269. doi: 10.1016/j.meegid.2013.09.016.
 Global gene expression changes in BV2 microglial cell line during rabies virus infection
 
 
 Zhao P, Yang Y, Feng H, Zhao L, Qin J, Zhang T, Wang H, Yang S, Xia X
  Abstract
Microglia plays a crucial role during virus pathogenesis in the central nervous system (CNS). Infection by rabies virus (RABV) causes a fatal infectionin the CNS of all warm-blooded animals. However, the microglial responses to RABV infection have been scarcely reported. To better understand microglia-RABV interactions at the transcriptional level, a genome wide gene expression profile in mouse microglial cells line BV2 was performed using microarray analysis. The global messenger RNA changes in murine microglial cell line BV2 after 12, 24 and 48h of infection with rabies virusCVS-11 strain were investigated using DNA Microarray and quantitative real-time PCR. Infection of CVS-11 at different time points induced differentgene expression signatures in BV2 cells. The expression patterns of differentially expressed genes are shown by K-means clustering in four clusters in RABV- or mock-infected microglia at 12, 24 and 48h post infection (hpi). Gene ontology and network analysis of the differentially expressed genes in responses to RABV were performed by the Ingenuity Pathway Analysis system (IPA, Ingenuity® Systems, http://www.ingenuity.com). The results revealed that 28 genes were significantly up-regulated (P<0.01) and 1 gene was significantly down-regulated (P<0.01) in microglial cells at 12hpi, 72 genes were significantly up-regulated (P<0.01) and 24 genes were significantly down-regulated (P<0.01) at 24hpi, and 671 genes were significantly up-regulated (P<0.01) and 190 genes were significantly down-regulated (P<0.01) at 48hpi. Genes in BV2 were significantly regulated (P<0.01) in response to RABV infection and they were found to be interferon stimulated genes (Isg15, Isg20, Oasl1, Oasl2, Ifit2, Irf7 and Ifi203), chemokine genes (Ccl5, Cxcl10 and Ccrl2) and the proinflammatory factor gene (Interleukin 6). The results indicated that the differentially expressed genes frommicroglial cells after RABV infection were mainly involved in innate immune responses, inflammatory responses and host antiviral responses.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Human & Experimental Toxicology. 2013 Sep 24. doi: 10.1177/0960327113485257.
 Molecular characterization of photosensitizer-mediated photodynamic therapy by gene expression profiling
 
 
 Liu KH, Wang CP, Chang MF, Chung YW, Lou PJ, Lin JH
  Abstract
Photodynamic therapy (PDT) is a novel cancer treatment based on the tumor-specific accumulation of a photosensitizer followed by irradiation with visible light, which induces selective tumor cell death via production of reactive oxygen species. To elucidate the underlying mechanisms, microarray analysis was used to analyze the changes in gene expression patterns during PDT induced by various photosensitizers. Cancer cells were subjected to four different photosensitizer-mediated PDT and the resulting gene expression profiles were compared. We identified many differentially expressed genes reported previously as well as new genes for which the functionfunctions in PDT are still unclear. Our current results not only advance the general understanding of PDT but also suggest that distinct molecular mechanisms are involved in different photosensitizer-mediated PDT. Elucidating the signaling mechanisms in PDT will provide information to modulate the antitumor effectiveness of PDT using various photosensitizers.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Surgery. 2013, 154(4):739-47. doi: 10.1016/j.surg.2013.06.041.
 EZH2-shRNA-mediated upregulation of p21(waf1/cip1) and its transcriptional enhancers with concomitant downmodulation of mutant p53 in pancreatic ductal denocarcinoma
 
 
 Qazi AM, Gruzdyn OV, Semaan A, Seward SM, Chamala S, Dhulipala VB, Bouwman DL, Weaver DW, Gruber SA, Batchu RB
  Abstract
PURPOSE: Enhancer of zeste homologue 2 (EZH2), a component of the chromatin modification protein complex, is upregulated in pancreatic ductaladenocarcinoma (PDAC), whereas loss of p53 and its downstream target, p21(waf1/cip1), is also observed frequently. We sought to investigate the role of the p53-p21(waf1/cip1) pathway in relation to EZH2-mediated inhibition of PDAC. METHODS: The PANC-1 cell line was utilized in chromatin immunoprecipitation, gene profiling, Western blot, cell invasion, cell proliferation, and tumor xenograft assays. RESULTS: Western blot analysis with antibodies that recognize both wild-type and mutant p53 did not show any alterations in band intensity; however, antibody that detects only mutant p53 showed a band of significantly lesser intensity with EZH2 knockdown. Western blot analysis further revealed a significant upregulation of p21(waf1/cip1). Gene expression profile analysis indicated significantly enhanced transcripts of transcriptionalinducers of p21(waf1/cip1), with downregulation of mutant p53 transcript, corroborating the Western blot analysis. PANC-1 cells expressing EZH2-short hairpin RNA displayed markedly attenuated growth in SCID mice. CONCLUSION: Downregulation of mutant p53 with concomitant enhanced expression of p21(waf1/cip1) and its transcriptional trans-activators may contribute toward EZH2-mediated suppression of PDAC.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 BMC Genomics. 2013, 14(1):656. doi:10.1186/1471-2164-14-656.
 FGF2-induced effects on transcriptome associated with regeneration competence in adult human fibroblasts
 
 
 Olga Kashpur, David LaPointe, Sakthikumar Ambady, Elizabeth F Ryder, Tanja Dominko
  Abstract
BACKGROUND: Adult human fibroblasts grown in low oxygen and with FGF2 supplementation have the capacity to tip the healing outcome of skeletal muscle injury -- by favoring regeneration response in vivo over scar formation. Here, we compare the transcriptomes of control adult humandermal fibroblasts and induced regeneration-competent (iRC) fibroblasts to identify transcriptional changes that may be related to their regenerationcompetence. RESULTS: We identified a unique gene-expression profile that characterizes FGF2-induced iRC fibroblast phenotype. Significantly differentially expressed genes due to FGF2 treatment were identified and analyzed to determine overrepresented Gene Ontology terms. Genes belonging to extracellular matrix components, adhesion molecules, matrix remodelling, cytoskeleton, and cytokines were determined to be affected by FGF2 treatment. CONCLUSIONS: Transcriptome analysis comparing control adult human fibroblasts with FGF2-treated fibroblasts identified functional groups of genes that reflect transcriptional changes potentially contributing to their regeneration competence. This comparative transcriptome analysis should contribute new insights into genes that characterize cells with greater regenerative potential.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Cellular Microbiology. 2013 Sep 17. doi: 10.1111/cmi.12216.
 Streptococcal co-infection augments Candida pathogenicity by amplifying the mucosal inflammatory response
 
 
 Xu H, Sobue T, Thompson A, Xie Z, Poon K, Ricker A, Cervantes J, Diaz PI, Dongari-Bagtzoglou A
  Abstract
Mitis-group streptococci are ubiquitous oral commensals that can promote polybacterial biofilm virulence. Using a novel murine oral mucosal co-infection model we sought to determine for the first time whether these organisms promote the virulence of C. albicans mucosal biofilms in oropharyngeal infection and explored mechanisms of pathogenic synergy. We found that Streptococcus oralis colonization of the oral and gastrointestinal tract was augmented in the presence of C. albicans. S. oralis and C. albicans co-infection significantly augmented the frequency and size of oral thrush lesions. Importantly, S. oralis promoted deep organ dissemination of C. albicans. Whole mouse genome tongue microarray analysis showed that when compared with animals infected with one organism, the doubly infected animals had genes in the major categories of neutrophilic response/chemotaxis/inflammation significantly upregulated, indicative of an exaggerated inflammatory response. This response was dependent on TLR2 signalling since oral lesions, transcription of pro-inflammatory genes and neutrophil infiltration, were attenuated in TLR2-/- animals. Furthermore, S. oralis activated neutrophils in a TLR2-dependent manner in vitro. In summary, this study identifies a previously unrecognized pathogenic synergy between oral commensal bacteriaand C. albicans. This is the first report of the ability of mucosal commensal bacteria to modify the virulence of an opportunistic fungal pathogen.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Asian Journal of Andrology. 2013 Aug 26. doi: 10.1038/aja.2013.80.
 miR-205 is frequently downregulated in prostate cancer and acts as a tumor suppressor by inhibiting tumor growth
 
 
 Wang N, Li Q, Feng NH, Cheng G, Guan ZL, Wang Y, Qin C, Yin CJ, Hua LX
  Abstract
The purpose of this study was to elucidate the molecular mechanisms of microRNA-205 (miR-205) as a tumor suppressor in prostate cancer (PCa). In the present study, microRNA microarray analysis suggested that the expression of miR-205 was significantly decreased in advanced PCa compared with early PCa. Real-time PCR analysis also indicated that miR-205 expression was significantly decreased in PCa tissues compared with non-cancerous tissues. Moreover, the expression of miR-205 has been demonstrated to be associated with the clinicopathological stage and total/free prostate-specific antigen (PSA) level of PCa. Functional analyses showed that both the overexpression of miR-205 and the knockdown of c-SRC in PCa cell lines could inhibit cell growth, colony formation, migration, invasion and the cell cycle as well as induce cell apoptosis in vitro. Furthermore, over-expressing miR-205 reduced tumorigenicity in vivo. Through a luciferase activity assay and Western blotting, c-SRC was identified as a target of miR-205 in cells. The overexpression of miR-205 suppressed c-SRC and its downstream signaling molecules, including FAK, p-FAK, ERK1/2 and p-ERK1/2, and attenuated cell proliferation, invasion and tumor growth.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 International Journal of Cancer. 2013 Aug 12. doi: 10.1002/ijc.28428.
 Gene expression profile of A549 cells from tissue of 4D model predicts poor prognosis in lung cancer patients
 
 
 Dhruva K. Mishra, Chad J. Creighton, Yiqun Zhang, Don L. Gibbons, Jonathan M. Kurie, Min P. Kim
  Abstract
The tumor microenvironment plays an important role in regulating cell growth and metastasis. Recently, we developed an ex vivo lung cancer model (four dimensional, 4D) that forms perfusable tumor nodules on a lung matrix that mimics human lung cancer histopathology and protease secretion pattern. We compared the gene expression profile (Human OneArray v5 chip) of A549 cells, a human lung cancer cell line, grown in a petri dish (two-dimensional, 2D), and of the same cells grown in the matrix of our ex vivo model (4D). Furthermore, we obtained gene expression data of A549 cells grown in a petri dish (2D) and matrigel (three-dimensional, 3D) from a previous study and compared the 3D expression profile with that of 4D. Expression array analysis showed 2,954 genes differentially expressed between 2D and 4D. Gene ontology (GO) analysis showed upregulation of several genes associated with extracellular matrix, polarity and cell fate and development. Moreover, expression array analysis of 2D vs. 3D showed 1,006 genes that were most differentially expressed, with only 36 genes (4%) having similar expression patterns as observed between 2D and 4D. Finally, the differential gene expression signature of 4D cells (vs. 2D) correlated significantly with poor survival in patients with lung cancer (n 5 1,492), while the expression signature of 3D vs. 2D correlated with better survival in lung cancer patients with lung cancer. As patients with larger tumors have a worse rate of survival, the ex vivo 4D model may be a good mimic of natural progression of tumor growth in lung cancer patients.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 The Journal of Infectious Diseases. 2013 Sep 16.
 IL-22 inhibits intracellular growth of Mycobacterium tuberculosis by enhancing calgranulin A expression
 
 
 Rohan Dhiman, Sambasivan Venkatasubramanian, Padmaja Paidipally, Peter F. Barnes, Amy Tvinnereim, Ramakrishna Vankayalapati
  Abstract
Previously, we found that IL-22 inhibits intracellular growth of Mycobacterium tuberculosis (M. tb) in human monocyte-derived macrophages (MDMs). In the current study we determined the mechanisms underlying these effects. We found W7, a phagolysosomal fusion inhibitor abrogates IL-22-dependent M. tb growth inhibition in MDMs, suggesting that IL-22 acts through enhanced phagolysosomal fusion. Our microarray analysis indicated that rIL-22 enhances the expression of an intracellular signaling molecule calgranulin A. This was confirmed by real time PCR, western blot and by confocal microscopy. Calgranulin A siRNA abrogated rIL-22-dependent growth inhibition of M. tb in MDMs. IL-22 enhanced Rab7 expression and down regulated Rab14 expression of M. tb-infected MDMs, and these effects were reversed by calgranulin A siRNA. These results suggest that M. tb growth inhibition by IL-22 depends on calgranulin A and enhanced phagolysosomal fusion, which is associated with increased Rab7 and reduced Rab14 expression.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Journal of Biomedical Science. 2013, 20(1):64.
 Profiling circulating microRNA expression in a mouse model of nerve allotransplantation
 
 
 Cheng-Shyuan Rau, Johnson Chia-Shen Yang, Shao-Chun Wu, Yi-Chun Chen, Tsu-Hsiang Lu, Ming-Wei Lin, Yi-Chan Wu, Siou-Ling Tzeng, Chia-Jung Wu, Ching-Hua Hsieh
  Abstract
Background: The lack of noninvasive biomarkers of rejection remains a challenge in the accurate monitoring of deeply buried nerve allografts and precludes optimization of therapeutic intervention. This study aimed to establish the expression profile of circulating microRNAs (miRNAs) during nerve allotransplantation with or without immunosuppression. Results: Balb/c mice were randomized into 3 experimental groups, that is, (1) untreated isograft (Balb/c¡÷Balb/c), (2) untreated allograft (C57BL/6¡÷Balb/c), and (3) allograft (C57BL/6¡÷Balb/c) with FK506 immunosuppression. A 1-cm Balb/c or C57BL/6 donor sciatic nerve graft was transplanted into sciatic nerve gaps created in recipient mice. At 1, 3, 7, 10, and 14 d after nerve transplantation, nerve grafts, whole blood, and sera were obtained for miRNA expression analysis with an miRNA array and subsequent validation with quantitative real-time PCR (qRT-PCR). Three circulating miRNAs (miR-320, miR-762, and miR-423-5p) were identified in the whole blood and serum of the mice receiving an allograft with FK506 immunosuppression, within 2 weeks after nerve allotransplantation. However, these 3 circulating miRNAs were not expressed in the nerve grafts. The expression of all these 3 upregulated circulating miRNAs significantly decreased at 2, 4, and 6 d after discontinuation of FK506 immunosuppression. In the nerve graft, miR-125-3b and miR-672 were significantly upregulated in the mice that received an allograft with FK506 only at 7 d after nerve allotransplantation. Conclusions: We identified the circulating miR-320, miR-762, and miR-423-5p as potential biomarkers for monitoring the immunosuppression status of the nerve allograft. However, further research is required to investigate the mechanism behind the dysregulation of these markers and to evaluate their prognostic value in nerve allotransplantation.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Molecular Carcinogenesis. 2013 Jul 17. doi: 10.1002/mc.22064.
 Inhibitions of Epithelial to Mesenchymal Transition and Cancer Stem Cells‐Like Properties Are Involved in miR‐148a‐Mediated Anti‐Metastasis of Hepatocellular Carcinoma
 
 
 Han Yan, Xiaogang Dong, Xiaoqin Zhong, Jing Ye, Yun Zhou, Xiaojun Yang, Jian Shen, Jianping Zhang
  Abstract
The epithelial¡Vmesenchymal transition (EMT) and acquisition of cancer stem cells (CSCs)-like properties are essential steps in the metastasis and postsurgical recurrence of hepatocellular carcinomas (HCCs). The molecular mechanisms involved, however, remain obscure. As determined by an miRNA microarray analysis, there was lower expression of miR-148a in poorly differentiated HCC tissues relative to well-differentiated HCC tissues. MHCC97H and MHCC97L (HCC cells with migratory capacity) and HCC tissues with various differentiation status were selected for further investigation. The results showed that miR-148a levels inversely correlated with the differentiation status of HCC tissues. In MHCC97H and MHCC97L cells, over-expression of miR-148a blocked the EMT process, attenuated the expression of CD90 and CD44 (biomarkers for liver cancer stem cells), and inhibited their migratory capacity. Via TargetScan and microRNA.org algorithms, miR-148a was predicted to bind to the Wnt1 mRNA 3'-UTR. Wnt1 was confirmed as a target gene of miR-148a in HCC cells, and the Wnt signal pathway was determined to be involved in the miR-148a-mediated inhibition of EMT and CSCs-like properties of MHCC97H cells. Moreover, the expression of miR-148a in nonmetastatic HCC tissues was higher than that in metastatic HCC tissues. The results suggest that miR-148a inhibits the metastasis of HCCs by blocking EMT and CSCs-like properties through effects on the Wnt signaling pathway.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Science. 2013, 341(6146): 651-654. doi: 10.1126/science.1239278.
 Pluripotent Stem Cells Induced from Mouse Somatic Cells by Small-Molecule Compounds
 
 
 Pingping Hou, Yanqin Li, Xu Zhang, Chun Liu, Jingyang Guan, Honggang Li, Ting Zhao, Junqing Ye, Weifeng Yang, Kang Liu, Jian Ge, Jun Xu, Qiang Zhang, Yang Zhao, Hongkui Deng
  Abstract
Pluripotent stem cells can be induced from somatic cells, providing an unlimited cell resource, with potential for studying disease and use in regenerative medicine. However, genetic manipulation and technically challenging strategies such as nuclear transfer used in reprogramming limit their clinical applications. Here, we show that pluripotent stem cells can be generated from mouse somatic cells at a frequency up to 0.2% using a combination of seven small-molecule compounds. The chemically induced pluripotent stem cells (CiPSCs) resemble embryonic stem cells (ESCs) in terms of their gene expression profiles, epigenetic status, and potential for differentiation and germline transmission. By using small molecules, exogenous ¡§master genes¡¨ are dispensable for cell fate reprogramming. This chemical reprogramming strategy has potential use in generating functional desirable cell types for clinical applications.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Cancer Research. 2013 June 2. doi: 10.1158/0008-5472.
 A sequence polymorphism in miRNA-608 predicts recurrence after radiotherapy of nasopharyngeal carcinoma
 
 
 Jian Zheng, Jieqiong Deng, Mang Xiao, Lei Yang, Liyuan Zhang, Yonghe You, Min Hu, Na Li, Hongchun Wu, Wei Li, Jiachun Lu, Yifeng Zhou
  Abstract
Nasopharyngeal carcinoma (NPC) is treated with radiotherapy and other modalities, but there is little information on individual genetic factors to help predict and improve patient outcomes. Single nucleotide polymorphisms (SNPs) in mature microRNA (miRNA) sequences have the potential to exert broad impact since miRNAs target many mRNAs. The aim of this study was to evaluate the effects of SNPs in mature miRNA sequences on clinical outcome in NPC patients receiving radiotherapy. In particular, we analyzed associations between seven SNPs and NPC locoregional recurrence (LRR) in 837 patients from eastern China, validating the findings in an additional 828 patients from southern China. We found that miRNA-608 rs4919510C>G exhibited a consistent association with LRR in the discovery set (hazard ratio [HR]=2.05; 95% confidence interval [CI]=1.35-3.21), the validation set (HR=2.24; 95%CI=1.45-3.38), and the combined data set (HR=2.08; 95%CI=1.41-3.26). Biochemical investigations demonstrated that rs4919510C>G affects expression of miRNA-608 target genes along with NPC cell growth after irradiation in vivo and in vitro. Notably, X-ray radiation induced more chromatid breaks in lymphocyte cells from rs4919510CC carriers than in those from subjects with other genotypes (P=0.0024). Our findings reveal rs4919510C>G in miRNA-608 as a simple marker to predict locoregional recurrence in radiotherapy-treated NPC patients.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 The American Journal of Human Genetics. 2013 Jun 26. doi: 10.1016/j.ajhg.2013.05.025.
 miR-196a Ameliorates Phenotypes of Huntington Disease in Cell, Transgenic Mouse, and Induced Pluripotent Stem Cell Models
 
 
 Pei-Hsun Cheng, Chia-Ling Li, Yu-Fan Chang, Shaw-Jeng Tsai, Yen-Yu Lai, Anthony W.S. Chan, Chuan-Mu Chen, Shang-Hsun Yang
  Abstract
Huntington disease (HD) is a dominantly inherited neurodegenerative disorder characterized by dysregulation of various genes. Recently, microRNAs (miRNAs) have been reported to be involved in this dysregulation, suggesting that manipulation of appropriate miRNA regulation may have a therapeutic benefit. Here, we report the beneficial effects of miR-196a (miR196a) on HD in cell, transgenic mouse models, and human induced pluripotent stem cells derived from one individual with HD (HD-iPSCs). In the in vitro results, a reduction of mutant HTT and pathological aggregates, accompanying the overexpression of miR-196a, was observed in HD models of human embryonic kidney cells and mouse neuroblastoma cells. In the in vivo model, HD transgenic mice overexpressing miR-196a revealed the suppression of mutant HTT in the brain and also showed improvements in neuropathological progression, such as decreases of nuclear, intranuclear, and neuropil aggregates and late-stage behavioral phenotypes. Most importantly, miR-196a also decreased HTT expression and pathological aggregates when HD-iPSCs were differentiated into the neuronal stage. Mechanisms of miR-196a in HD might be through the alteration of ubiquitin-proteasome systems, gliosis, cAMP response element-binding protein pathway, and several neuronal regulatory pathways in vivo. Taken together, these results show that manipulating miR-196a provides beneficial effects in HD, suggesting the potential therapeutical role of miR-196a in HD.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Biochimica et Biophysica Acta-General Subjects. 2013 Jun 27. doi: 10.1016/j.bbagen.2013.06.025.
 Extensive evaluations of the cytotoxic effects of gold nanoparticles
 
 
 Show-Mei Chuang, Yi-Hui Lee, Ruei-Yue Liang, Gwo-Dong Roam, Zih-Ming Zeng, Hsin-Fang Tu, Shi-Kwun Wang, Pin Ju Chueh
  Abstract
Background: Many in vitro studies have revealed that the interference of dye molecules in traditional nanoparticle cytotoxicity assays results in controversial conclusions. The aim of this study is to establish an extensive and systematic method for evaluating biological effects of gold nanoparticles in mammalian cell lines. Methods: We establish the cell-impedance measurement system, a label-free, real-time cell monitoring platform that measures electrical impedance, displaying results as cell index values, in a variety of mammalian cell lines. Cytotoxic effects of gold nanoparticles are also evaluated with traditional in vitro assays. Results: Among the six cell lines, gold nanoparticles induce a dose-dependent suppression of cell growth with different levels of severity and the suppressive effect of gold nanoparticles was indirectly associated with their sizes and cellular uptake. Mechanistic studies revealed that the action of gold nanoparticles is mediated by apoptosis induction or cell cycle delay, depending on cell type and cellular context. Although redox signaling is often linked to the toxicity of nanoparticles, in this study, we found that gold nanoparticle-mediated reactive oxygen species generation was not sustained to notably modulate proteins involved in antioxidative defense system. Conclusion: The cell-impedancemeasurement system, a dye-free, real-time screening platform, provides a reliable analysis for monitoring gold nanoparticle cytotoxicity in a variety of mammalian cell lines. Furthermore, gold nanoparticles induce cellular signaling and several sets of gene expression tomodulate cellular physical processes. General significance: The systematic approach, such as cell-impedance measurement, analyzing the toxicology of nanomaterials offers convincing evidence of the cytotoxicity of gold nanomaterials.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Cell Reports. 2013, 3(6):2100-12. doi: 10.1016/j.celrep.2013.05.038.
 DNA-Damage-Induced Nuclear Export of Precursor MicroRNAs Is Regulated by the ATM-AKT Pathway
 
 
 Guohui Wan, Xinna Zhang, Robert R. Langley, Yunhua Liu, Xiaoxiao Hu, Cecil Han, Guang Peng, Lee M. Ellis, Stephen N. Jones, Xiongbin Lu
  Abstract
Expression of microRNAs (miRNAs) involves transcription of miRNA genes and maturation of the primary transcripts. Recent studies have shown that posttranscriptional processing of primary and precursor miRNAs is induced after DNA damage through regulatory RNA-binding proteins in the Drosha and Dicer complexes, such as DDX5 and KSRP. However, little is known about the regulation of nuclear export of pre-miRNAs in the DNA-damage response, a critical step in miRNA maturation. Here, we show that nuclear export of pre-miRNAs is accelerated after DNA damage in an ATM-dependent manner. The ATM-activated AKT kinase phosphorylates Nup153, a key component of the nucleopore, leading to enhanced interaction between Nup153 and Exportin-5 (XPO5) and increased nuclear export of pre-miRNAs. These findings define an important role of DNA-damage signaling in miRNA transport and maturation.
   

  ✔本篇論文使用華聯產品:Yeast OneArray  
 Journal of Agricultural and Food Chemistry. 2013 Jun 10. doi: 10.1021/jf401831e.
 Tangeretin sensitizes SGS1 deficient cells by inducing DNA damage
 
 
 Shin Yen Chong, Meng-Ying Wu, Yi-Chen Lo
  Abstract
Tangeretin, a polymethoxyflavone found in citrus peel, has been shown to have anti-atherogenic, anti-inflammatory, and anti-carcinogenic properties. However, the underlying target pathways are not fully characterized. We investigated the tangeretin sensitivity of yeast (Saccharomyces cerevisiae) mutants for DNA damage response or repair pathways. We found that tangeretin treatment significantly reduced (p < 0.05) survival rate, induced preferential G1 phase accumulation, and elevated the DNA double-strand break (DSB) signal £^H2A in DNA repair-defective sgs1£G cells, but had no obvious effects on wild-type cells or mutants of the DNA damage checkpoint (including tel1∆, sml1∆ mec1∆, sml1∆ mec1∆ tel1∆, and rad9∆ mutants). Additionally, microarray data indicated that tangeretin treatment up-regulates genes involved in nutritional processing and down-regulates genes related to RNA processing in sgs1∆ mutants. These results suggest tangeretin may sensitize SGS1 deficient cells by increasing a marker of DNA damage, and by inducing G1 arrest and possibly metabolic stress. Thus, tangeretin may be suitable for chemosensitization of cancer cells lacking DSB-repair ability.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Carcinogenesis. 2013 May 13..
 MiR-146a enhances angiogenic activity of endothelial cells in hepatocellular carcinoma by promoting PDGFRA expression
 
 
 Zhu K, Pan Q, Zhang X, Kong LQ, Fan J, Dai Z, Wang L, Yang XR, Hu J, Wan JL, Zhao YM, Tao ZH, Chai ZT, Zeng HY, Tang ZY, Zhou J, Hui-Chuan Sun
  Abstract
Endothelial cells are critical for angiogenesis, and microRNA play important roles in this process. We investigated the regulatory role of microRNAs in endothelial cells of hepatocellular carcinoma (HCC) by examining the microRNA expression profile of human umbilical vein endothelial cells (HUVECs) in the absence or presence of human HCC cells, and identified miR-146a as the most highly up-regulated microRNA. Furthermore, we revealed that miR-146a promoted the expression of platelet-derived growth factor receptor £ (PDGFRA) in HUVECs, and this process was mediated by BRCA1. Overexpression of PDGFRA in the ECs of HCC tissues was associated with microvascular invasion, and predicted a poorer prognosis. These results suggest that MiR-146a plays a key role in regulating the angiogenic activity of ECs in HCC through miR-146a-BRCA1-PDGFRA pathway. MiR-146a may emerge as a potential anti-angiogenic target on ECs for HCC therapy.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 European Journal of Oral Sciences. 2013, 1¡V10. doi: 10.1111/eos.12056.
 Expression of Clu and Tgfb1 during murine tooth development: effects of in-vivo transfection with anti-miR-214
 
 
 Amer Sehic, Cuong Khuu, Steinar Risnes, Harald Osmundsen, Qalb-E-Saleem Khan
  Abstract
Expression of clusterin (Clu) in the murine first molar tooth germ was markedly increased at postnatal developmental stages. The time-course of expression of this gene paralleled those of other genes encoding proteins involved during the secretory phase of odontogenesis, as described previously. Immunohistochemical studies of clusterin in murine molar tooth germs suggested this protein to be located in outer enamel epithelium, regressing enamel organ, secretory ameloblasts, and the dental epithelium connecting the tooth to the oral epithelium at an early eruptive stage. Immunolabelling of transforming growth factor beta-1 (TGF-b1) revealed it to be located close to clusterin. The levels of expression of Clu and Tgfb1 were markedly decreased following in-vivo transfection with anti-miR-214. In contrast, the expression of several genes associated with regulation of growth and development were increased by this treatment. We suggest that clusterin has functions during secretory odontogenesis and the early eruptive phase. Bioinformatic analysis after treatment with anti-miR-214 suggested that, whilst cellular activities associated with tooth mineralization and eruption were inhibited, activities associated with an alternative developmental activity (i.e. biosynthesis of contractile proteins) appeared to be stimulated. These changes probably occur through regulation mediated by a common cluster of transcription factors and support suggestions that microRNAs (miRNAs) are highly significant as regulators of differentiation during odontogenesis.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 The American Journal of Pathology. 2013 April 8. doi: 10.1016/j.ajpath.2013.04.022.
 Activated PAR-2 Regulates Pancreatic Cancer Progression through ILK/HIF-aeInduced TGF-a Expression and MEK/VEGF-AeMediated Angiogenesis
 
 
 Li-Hsun Chang, Shiow-Lin Pan, Chin-Yu Lai, An-Chi Tsai, Che-Ming Teng
  Abstract
Tissue factor initiates the process of thrombosis and activates cell signaling through protease-activated receptor-2 (PAR-2). The aim of this study was to investigate the pathological role of PAR-2 signaling in pancreatic cancer. We first demonstrated that activated PAR-2 up-regulated the protein expression of both hypoxia-inducible factor-1a (HIF-1a) and HIF-2a, resulting in enhanced transcription of transforming growth factor-a (TGF-a). Down-regulation of HIFs-a by siRNA or YC-1, an HIF inhibitor, resulted in depleted levels of TGF-a protein. Furthermore, PAR-2, through integrin-linked kinase (ILK) signaling, including the p-AKT, promoted HIF protein expression. Diminishing ILK by siRNA decreased the levels of PAR-2einduced p-AKT, HIFs-a, and TGF-a; our results suggest that ILK is involved in the PAR-2e mediated TGF-a via an HIF-aedependent pathway. Furthermore, the culture medium from PAR-2e treated pancreatic cancer cells enhanced human umbilical vein endothelial cell proliferation and tube formation, which was blocked by the MEK inhibitor, PD98059. We also found that activated PAR-2 Q4 enhanced tumor angiogenesis through the release of vascular endothelial growth factor-A (VEGF-A) from cancer cells, independent of the ILK/HIFs-a pathways. Consistent with microarray analysis, activated PAR-2 induced TGF-A and VEGF-A gene expression. In conclusion, the activation of PAR-2 signaling induced human pancreatic cancer progression through the induction of TGF-a expression by ILK/HIFs-a, as well as through MEK/VEGF-Aemediated angiogenesis, and it plays a role in the interaction between cancer progression and cancer-related thrombosis.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Evidence-Based Complementary and Alternative Medicine. 2013 May 8. doi:10.1155/2013/262796.
 The Phytochemical Shikonin Stimulates Epithelial-Mesenchymal Transition (EMT) in Skin Wound Healing
 
 
 Shu-Yi Yin, An-Ping Peng, Li-Ting Huang, Ya-TingWang, Chun-Wen Lan, Ning-Sun Yang
  Abstract
Although various pharmacological activities of the shikonins have been documented, understanding the hierarchical regulation of these diverse bioactivities at the genome level is unsubstantiated. In this study, through cross examination between transcriptome and microRNA array analyses, we predicted that topical treatment of shikonin in vivo affects epithelial-mesenchymal transition (EMT) and the expression of related microRNAs, including 200a, 200b, 200c, 141, 205, and 429 microRNAs, in mouse skin tissues. In situ immunohistological analyses further demonstrated that specificEMTregulatorymolecules are enhanced in shikonin-treated epidermal tissues. RT-PCR analyses subsequently confirmed that shikonin treatment downregulated expression of microRNA-205 and other members of the 200 family microRNAs. Further, expression of two RNA targets of the 200 family microRNAs in EMT regulation, Sip1 (Zeb2) and Tcf8 (Zeb1), was consistently upregulated by shikonin treatment. Enhancement of these EMT activities was also detected in shikonin-treated wounds, which repaired faster than controls. These results suggest that topical treatment with shikonin can confer a potent stimulatory effect on EMT and suppress the expression of the associated microRNAs in skin wound healing. Collectively, these cellular and molecular data provide further evidence in support of our previous findings on the specific pharmacological effects of shikonin in wound healing and immune modulation.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Journal of Diabetes Research. 2013 May 20. doi:10.1155/2013/589451.
 The Effect of Diabetes-Associated Autoantigens on Cell Processes in Human PBMCs and Their Relevance to Autoimmune Diabetes Development
 
 
 Radek Blatny, Zbynek Halbhuber, Michal Kolar, Ales Neuwirth, Lenka Petruzelkova, Tereza Ulmannova, Stanislava Kolouskova, Zdenek Sumnik, Pavlina Pithova, Maria Krivjanska, Dominik Filipp, Katerina Stechova, Jana Vcelakova
  Abstract
Type 1 Diabetes (T1D) is considered to be a T-helper- (Th-) 1 autoimmune disease; however, T1D pathogenesis likely involves many factors, and sufficient tools for autoreactive T cell detection for the study of this disease are currently lacking. In this study, using gene expression microarrays, we analysed the effect of diabetes-associated autoantigens on peripheral blood mononuclear cells (PBMCs) with the purpose of identifying (pre)diabetes-associated cell processes. Twelve patients with recent onset T1D, 18 firstdegree relatives of the TD1 patients (DRL; 9/18 autoantibody positive), and 13 healthy controls (DV) were tested. PBMCs fromthese individuals were stimulated with a cocktail of diabetes-associated autoantigens (proinsulin, IA-2, and GAD65-derived peptides). After 72 hours, gene expression was evaluated by high-density gene microarray. The greatest number of functional differences was observed between relatives and controls (69 pathways), from which 15% of the pathways belonged to ¡§immune response-related¡¨ processes. In the T1D versus controls comparison, more pathways (24%) were classified as ¡§immune response-related.¡¨ Important pathways that were identified using data from the T1D versus controls comparison were pathways involving antigen presentation by MHCII, the activation ofTh17 andTh22 responses, and cytoskeleton rearrangement-related processes. Genes involved in Th17 and TGF-beta cascades may represent novel, promising (pre)diabetes biomarkers.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 World Journal of Gastroenterology. 2013, 19(21): 3339-3346. doi:10.3748/wjg.v19.i21.3339.
 Gene expression profiles in peripheral blood mononuclear cells of ulcerative colitis patients
 
 
 Yu-Liang Xiao, Yan Du, Li-Ping Duan, Ying-Lei Miao
  Abstract
To identify peripheral blood mononuclear cell (PBMC ) gene expression profiles of ulcerative colitis (UC) patients, using oligonucleotide microarrays, to gain insights into UC molecular mechanisms.
   

  ✔本篇論文使用華聯產品:Experimental Accessories  
 PLOS ONE. 2013; 8(6): e65489. doi: 10.1371/journal.pone.0065489.
 BAK and NOXA Are Critical Determinants of Mitochondrial Apoptosis Induced by Bortezomib in Mesothelioma
 
 
 Sara Busacca, Alex D. Chacko, Astero Klabatsa, Kenneth Arthur, Michael Sheaff,Vignesh K. Gunasekharan, Julia J. Gorski, Mohamed El-Tanani, V. Courtney Broaddus, Giovanni Gaudino, Dean A. Fennell
  Abstract
Based on promising preclinical efficacy associated with the 20S proteasome inhibitor bortezomib in malignant pleural mesothelioma (MPM), two phase II clinical trials have been initiated (EORTC 08052 and ICORG 05¡V10). However, the potential mechanisms underlying resistance to this targeted drug in MPM are still unknown. Functional genetic analyses were conducted to determine the key mitochondrial apoptotic regulators required for bortezomib sensitivity and to establish how their dysregulation may confer resistance. The multidomain proapoptotic protein BAK, but not its orthologue BAX, was found to be essential for bortezomib-induced apoptosis in MPM cell lines. Immunohistochemistry was performed on tissues from the ICORG-05 phase II trial and a TMA of archived mesotheliomas. Loss of BAK was found in 39% of specimens and loss of both BAX/BAK in 37% of samples. However, MPM tissues from patients who failed to respond to bortezomib and MPM cell lines selected for resistance to bortezomib conserved BAK expression. In contrast, c-Myc dependent transactivation of NOXA was abrogated in the resistant cell lines. In summary, the block of mitochondrial apoptosis is a limiting factor for achieving efficacy of bortezomib in MPM, and the observed loss of BAK expression or NOXA transactivation may be relevant mechanisms of resistance in the clinic.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Oncology Letters . 2013 May 23. doi:10.3892/ol.2013.1380.
 A potential diagnostic marker for ovarian cancer: Involvement of the histone acetyltransferase, human males absent on the first
 
 
 NING LIU, RUI ZHANG, XIAOMING ZHAO, JIAMING SU, XIAOLEI BIAN, JINSONG NI, YONG CAI, YING YUE, JINGJI JIN
  Abstract
Human males absent on the first (hMOF), a human ortholog of the Drosophila MOF protein, is responsible for histone H4 lysine 16 (H4K16) acetylation in human cells. The depletion of hMOF leads to a global reduction in histone H4K16 acetylation in human cells, genomic instability, cell cycle defects, reduced transcription of certain genes, defective DNA damage repair and early embryonic lethality. Studies have shown that abnormal hMOF gene expression is involved in a number of primary cancers. The present study examined the involvement of hMOF expression and histone H4K16 acetylation in clinically diagnosed primary ovarian cancer tissues. Clinically diagnosed frozen primary ovarian cancer tissues were used for polymerase chain reaction (PCR), quantitative PCR (qPCR), western blotting and immunohistochemical staining approaches. A PCR analysis of mRNA expression in 47 samples revealed a downregulation of hMOF mRNA in 81% of patients, whereas only 13% of patients demonstrated upregulation. qPCR was used to validate the frequent downregulation of hMOF expression in the primary ovarian cancer tissues. As expected, the analysis of hMOF expression in 57 samples revealed that hMOF mRNA expression was significantly downregulated (>2‑fold decrease) in 65% of patients, while a <2‑fold reduction of hMOF was observed in 10.5% of patients. Furthermore, the expression of hMOF‑regulated human leukocyte antigen (HLA) complex 5, (HCP5), was also found to be downregulated in >87% of patients with a decrease in hMOF. hMOF and its regulated gene, HCP5, are frequently downregulated in human ovarian cancer, suggesting that hMOF may be involved in the pathogenesis of the disease.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Cell. 2013, 153(5): 963-975. doi: 10.1016/j.cell.2013.05.001.
 Induction of Pluripotency in Mouse Somatic Cells with Lineage Specifiers
 
 
 Jian Shu, Chen Wu, Yetao Wu, Zhiyuan Li, Sida Shao, Wenhui Zhao, Xing Tang, Huan Yang, Lijun Shen, Xiaohan Zuo, Weifeng Yang, Yan Shi, Xiaochun Chi, Hongquan Zhang, Ge Gao, Youmin Shu, Kehu Yuan, Weiwu He, Yang Zhao, Chao Tang, Hongkui Deng
  Abstract
The reprogramming factors that induce pluripotency have been identified primarily from embryonic stem cell (ESC)-enriched, pluripotency-associated factors. Here, we report that, during mouse somatic cell reprogramming, pluripotency can be induced with lineage specifiers that are pluripotency rivals to suppress ESC identity, most of which are not enriched in ESCs. We found that OCT4 and SOX2, the core regulators of pluripotency, can be replaced by lineage specifiers that are involved in mesendodermal (ME) specification and in ectodermal (ECT) specification, respectively. OCT4 and its substitutes attenuated the elevated expression of a group of ECT genes, whereas SOX2 and its substitutes curtailed a group of ME genes during reprogramming. Surprisingly, the two counteracting lineage specifiers can synergistically induce pluripotency in the absence of both OCT4 and SOX2. Our study suggests a ¡¥¡¥seesaw model¡¦¡¦ in which a balance that is established using pluripotency factors and/or counteracting lineage specifiers can facilitate reprogramming.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Liver International. 2013 Apr 14.
 MicroRNA-491 is Involved in Metastasis of Hepatocellular Carcinoma by Inhibitions of Matrix Metalloproteinase and Epithelial to Mesenchymal Transition
 
 
 Yun Zhou, Yuan Li, Jing Ye, Rongrong Jiang, Han Yan, Xiaojun Yang, Qizhan Liu b, Jianping Zhang
  Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related mortality worldwide. The prognosis of HCC patient remains poor due to intrahepatic and extrahepatic metastasis and post-surgical recurrence, however, the mechanisms underlying metastasis and recurrence remain obscure. Here, by employing an miRNAs microarray analysis, we found that miR-491 level was one of the most significant down-regulation in poorly differentiated HCC tissue compared to well differentiated HCC tissue. We then selected HepG2 (very low migratory capacity), MHCC97L (low migratory capacity), and MHCC97H (high migratory capacity) as well as HCC tissues with different status to further investigate the effects of miR-491 on the metastasis of HCC. Our data showed that miR-491 levels were inversely correlated with different status of differentiation in HCC tissues and with migratory potential in HCC cell lines. In HepG2 cells, inhibition of miR-491 increased the expression of matrix metalloproteinase 2/9 (MMP-2/9) and the migratory potential; however, in MHCC97H cells, overexpression of miR-491 level decreased the expression of MMP-2/9 and the migratory capacity. Moreover, miR-491 had a positive relationship with E-cadherin level; however, it had a negative relationship with vimentin level both in cell lines and tissue samples of HCC. MiR-491 levels of non-metastasis HCC tissue are higher than that of metastasis HCC tissue. Our results suggest that miR-491 is involved in metastasis of HCC by blocking EMT and decreasing MMP-9 levels, which may provide a new clue for preventing tumor metastasis of HCC.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Cancer Research. 2013 May 1.
 miR-124 inhibits STAT3 signaling to enhance T cell-mediated immune clearance of glioma
 
 
 Jun Wei, Fei Wang, Ling-Yuan Kong, Shuo Xu, Tiffany Doucette, Sherise D. Ferguson, Yuhui Yang, Kayla McEnery, Krishan Jethwa, Olsi Gjyshi, Wei Qiao, Nicholas B. Levine, Frederick F. Lang, Ganesh Rao, Gregory N. Fuller, George A. Calin, Amy B. Heimberger
  Abstract
MicroRNAs (miRs) have been shown to modulate critical gene transcripts involved in tumorigenesis, but their role in tumor-mediated immune suppression is largely unknown. On the basis of miRNA gene expression in gliomas using tissue microarrays, in situ hybridization, and molecular modeling, miR-124 was identified as a lead candidate for modulating signal transducer and activator of transcription 3 (STAT3) signaling, a key pathway mediating immune suppression in the tumor microenvironment. miR-124 is absent in all grades and pathological types of gliomas. Upon up regulating miR-124 in glioma cancer stem cells (gCSCs), the STAT3 pathway was inhibited, and miR-124 reversed gCSC-mediated immune suppression of T-cell proliferation and induction of Foxp3+ regulatory T-cells (Tregs). Treatment of T-cells from immunosuppressed glioblastoma patients with miR-124 induced marked effector response including up regulation of IL-2, IFN-£^, and tumor necrosis factor (TNF)-£. Both systemic administration of miR-124 or adoptive miR-124-transfected T-cell transfers exerted potent antiglioma therapeutic effects in clonotypic and genetically engineered murine models of glioblastoma and enhanced effector responses in the local tumor microenvironment. These therapeutic effects were ablated in both CD4+ and CD8+ depleted mice and nude mouse systems, indicating that the therapeutic effect of miR-124 depends on the presence of a T-cellmediated antitumor immune response. Our findings highlight the potential application of miR- 124 as a novel immunotherapeutic agent for neoplasms and serve as a model for identifying miRNAs that can be exploited as immune therapeutics.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Carcinogenesis. 2013 Apr 30.
 Depletion of 4E-BP1 and regulation of autophagy lead to YXM110-induced anti-cancer effects
 
 
 Chin-Yu Lai, Shiow-Lin Pan, Xiao-Ming Yang, Li-Hsun Chang, Ya-Ling Chang, Pan-Chyr Yang, Kuo-Hsiung Lee, Che-Ming Teng
  Abstract
Natural products have always been a profuse database for developing new chemotherapeutics. YXM110 is a newly synthesized phenanthroquinolizidines that exhibits excellent anti-cancer activity in numerous cancer cells. Here, we examined the anti-cancer mechanisms of YXM110 both in vitro and in vivo. Protein level of 4E-binding protein 1 (4E-BP1), which is crucial in cap-independent translation, was decreased significantly after YXM110 treatment via c-Jun N-terminal kinases (JNK)-mediated proteasomal degradation. Moreover, the effects of YXM110 were associated with several characteristics of autophagy, including accumulation of autophagic vacuoles, elevation of Atg12-Atg5 and LC3-II, and levels of GFP-LC3 puncta. The results suggested that depletion of Mcl-1 contributes to YXM110-triggered autophagy, whereas downregulation of lysosomal-related genes could cause autophagy impairment. Furthermore, YXM110-induced cell death were prevented by autophagy inhibitor 3-methyladenine (3-MA) and Atg5 silencing, indicating that YXM110-mediated autophagy impairment lead to cancer cell death. These data reveal key mechanisms that support the further development of YXM110 as a promising anti-cancer agent.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Evidence-Based Complementary and Alternative Medicine. 2013 May 8.
 Phytochemical shikonin stimulates epithelial¡Vmesenchymal transition (EMT) in skin wound-healing
 
 
 Shu-Yi Yin, An-Ping Peng, Li-Ting Huang, Ya-Ting Wang, Chun-Wen Lan, Ning-Sun Yang
  Abstract
Although various pharmacological activities of the shikonins have been documented, understanding of the hierarchical regulation of these diverse bio-activities at the genome level is unsubstantiated. In this study, through cross-examination between transcriptome and microRNA array analyses, we predicted that topical treatment of shikonin in vivo affects epithelial¡Vmesenchymal transition (EMT) and the expression of related microRNAs, including 200a, 200b, 200c, 141, 205 and 429 microRNAs, in mouse skin tissues. In situ immunohistological analyses further demonstrated that specific EMT regulatory molecules are enhanced in shikonin-treated epidermal tissues. RT-PCR analyses subsequently confirmed that shikonin treatment downregulated expression of microRNA-205 and other members of the 200 family microRNAs. Further, expression of two RNA targets of the 200 family microRNAs in EMT regulation, Sip1 (Zeb2) and Tcf8 (Zeb1), were consistently upregulated by shikonin treatment. Enhancement of these EMT activities was also detected in shikonin-treated wounds, which repaired faster than controls. These results suggest that topical treatment with shikonin can confer a potent stimulatory effect on EMT and suppress the expression of the associated microRNAs in skin wound-healing. These cellular and molecular evidences support our previous findings on the specific pharmacological effects of shikonin in wound-healing and immune-modulation.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Cell Cycle. 2013, 12(10): 1510-1520. doi: 10.4161/cc.24497.
 Caveolin-1 is a negative regulator of tumor growth in glioblastoma and modulates chemosensitivity to temozolomide
 
 
 Kevin Quann, Donna M. Gonzales, Isabelle Mercier, Chenguang Wang, Federica Sotgia, Richard G. Pestell, Michael P. Lisanti, Jean-François Jasmin
  Abstract
Caveolin-1 (Cav-1) is a critical regulator of tumor progression in a variety of cancers where it has been shown to act as either a tumor suppressor or tumor promoter. In glioblastoma multiforme, it has been previously demonstrated to function as a putative tumor suppressor. Our studies here, using the human glioblastoma-derived cell line U-87MG, further support the role of Cav-1 as a negative regulator of tumor growth. Using a lentiviral transduction approach, we were able to stably overexpress Cav-1 in U-87MG cells. Gene expression microarray analyses demonstrated significant enrichment in gene signatures corresponding to downregulation of MAPK, PI3K/AKT and mTO R signaling, as well as activation of apoptotic pathways in Cav-1-overexpressing U-87MG cells. These same gene signatures were later confirmed at the protein level in vitro. To explore the ability of Cav-1 to regulate tumor growth in vivo, we further show that Cav-1-overexpressing U-87MG cells display reduced tumorigenicity in an ectopic xenograft mouse model, with marked hypoactivation of MAPK and PI3K/mTO R pathways. Finally, we demonstrate that Cav-1 overexpression confers sensitivity to the most commonly used chemotherapy for glioblastoma, temozolomide. In conclusion, Cav-1 negatively regulates key cell growth and survival pathways and may be an effective biomarker for predicting response to chemotherapy in glioblastoma.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Current Molecular Medicine. 2013, 13(1): 205-219. doi: 10.2174/1566524011307010205.
 Rock1 & 2 Perform Overlapping and Unique Roles in Angiogenesis and Angiosarcoma Tumor Progression
 
 
 J Montalvo, C Spencer, A Hackathorn, K Masterjohn, A Perkins, C Doty, A Arumugam, PP Ongusaha, R Lakshmanaswamy, JK Liao, DC Mitchell, BA Bryan
  Abstract
The serine/threonine protein kinase paralogs ROCK1 & 2 have been implicated as essential modulators of angiogenesis; however their paralog-specific roles in endothelial function are unknown. shRNA knockdown of ROCK1 or 2 in endothelial cells resulted in a significant disruption of in vitro capillary network formation, cell polarization, and cell migration compared to cells harboring non-targeting control shRNA plasmids. Knockdowns led to alterations in cytoskeletal dynamics due to ROCK1 & 2-mediated reductions in actin isoform expression, and ROCK2-specific reduction in myosin phosphatase and cofilin phosphorylation. Knockdowns enhanced cell survival and led to ROCK1 & 2-mediated reduction in caspase 6 and 9 cleavage, and a ROCK2-specific reduction in caspase 3 cleavage. Microarray analysis of ROCK knockdown lines revealed overlapping and unique control of global transcription by the paralogs, and a reduction in the transcriptional regulation of just under 50% of VEGF responsive genes. Finally, paralog knockdown in xenograft angiosarcoma tumors resulted in a significant reduction in tumor formation. Our data reveals that ROCK1 & 2 exhibit overlapping and unique roles in normal and dysfunctional endothelial cells, that alterations in cytoskeletal dynamics are capable of overriding mitogen activated transcription, and that therapeutic targeting of ROCK signaling may have profound impacts for targeting angiogenesis.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 EMBO Molecular Medicine. 2013, 5(4):531-47. doi: 10.1002/emmm.201201783.
 Smurf2-mediated degradation of EZH2 enhances neuron differentiation and improves functional recovery after ischaemic stroke
 
 
 Chou RH, Shyu WC, Hsieh SC, Wu CS, Chiang SY, Chang WJ, Chen JN, Tseng YJ, Lin YH, Lee W, Yeh SP, Hsu JL, Yang CC, Hung SC, Yu YL, Hung MC
  Abstract
EZH2 plays an important role in stem cell renewal and maintenance by inducing gene silencing via its histone methyltransferase activity. Previously, we showed that EZH2 downregulation enhances neuron differentiation of human mesenchymal stem cells (hMSCs); however, the underlying mechanisms of EZH2- regulated neuron differentiation are still unclear. Here, we identify Smurf2 as the E3 ubiquitin ligase responsible for the polyubiquitination and proteasomemediated degradation of EZH2, which is required for neuron differentiation. A ChIP-on-chip screen combined with gene microarray analysis revealed that PPARg was the only gene involved in neuron differentiation with significant changes in both its modification and expression status during differentiation. Moreover, knocking down PPARg prevented cells from undergoing efficient neuron differentiation. In animal model, rats implanted with intracerebral EZH2-knocked-down hMSCs or hMSCs plus treatment with PPARg agonist (rosiglitazone) showed better improvement than those without EZH2 knockdown or rosiglitazone treatment after a stroke. Together, our results support Smurf2 as a regulator of EZH2 turnover to facilitate PPARg expression, which is specifically required for neuron differentiation, providing a molecular mechanism for clinical applications in the neurodegenerative diseases.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Cancer Letters. 2013 Apr 18. doi: 10.1016/j.canlet.2013.04.012.
 EZH2 blockade by RNA interference inhibits growth of ovarian cancer by facilitating re-expression of p21waf1/cip1 and by inhibiting mutant p53
 
 
 Seward S, Semaan A, Qazi AM, Gruzdyn OV, Chamala S, Bryant CC, Kumar S, Cameron D, Sethi S, Ali-Fehmi R, Morris R, Bouwman DL, Munkarah AR, Weaver DW, Gruber SA, Batchu RB
  Abstract
The enhancer of zeste homolog 2 (EZH2) methyltransferase, which plays a key role in transcriptional gene repression, is abnormally elevated in epithelial ovarian cancer (EOC) patients and positively correlated with increasing stage of disease. We demonstrated that EZH2 depletion by RNA interference efficiently inhibited cell proliferation, colony formation, cell invasion, activated the apoptotic pathway, and enhanced chemosensitivity. Silencing of EZH2 resulted in re-expression of p21waf1/cip1 on chromatin immunoprecipitation assay and concomitant down-regulation of trimethylated H3K27 and mutant p53 protein, contributing to attenuated EOC growth in SCID mice. Our findings suggest that EZH2-shRNA holds promise as a potential therapeutic modality for EOC.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 American journal of physiology-gastrointestinal and liver physiology. 2013, 304(1):G72-86. doi: 10.1152/ajpgi.00328.2012.
 Nordihydroguaiaretic acid improves metabolic dysregulation and aberrant hepatic lipid metabolism in mice by both PPAR£-dependent and -independent pathways
 
 
 Haiyan Zhang, Wen-Jun Shen, Yuan Cortez, Fredric B. Kraemer, Salman Azhar
  Abstract
Creosote bush-derived nordihydroguaiaretic acid (NDGA), a lipoxygenase inhibitor, possesses antioxidant properties and functions as a potent antihyperlipidemic agent in rodent models. Here, we examined the effect of chronic NDGA treatment of ob/ob mice on plasma dyslipidemia, hepatic steatosis, and changes in hepatic gene expression. Feeding ob/ob mice a chow diet supplemented with either low (0.83 g/kg diet) or high-dose (2.5 g/kg diet) NDGA for 16 wk significantly improved plasma triglyceride (TG), inflammatory chemokine levels, hyperinsulinemia, insulin sensitivity, and glucose intolerance. NDGA treatment caused a marked reduction in liver weight and TG content, while enhancing rates of fatty acid oxidation. Microarray analysis of hepatic gene expression demonstrated that NDGA treatment altered genes for lipid metabolism, with genes involved in fatty acid catabolism most significantly increased. NDGA upregulated the mRNA and nuclear protein levels of peroxisome proliferator-activated receptor (PPAR), and the activated (phosphorylated) form of AMPactivated kinase. NDGA increased PPAR promoter activity in AML12 hepatocytes and also prevented the fatty acid suppression of PPAR expression. In contrast, PPAR siRNA abrogated the stimulatory effect of NDGA on fatty acid catabolism. Likewise, no stimulatory effect of NDGA on hepatic fatty acid oxidation was observed in the livers of PPAR-deficient mice, but the ability of NDGA to reverse fatty liver conditions was unaffected. In conclusion, the beneficial actions of NDGA on dyslipidemia and hepatic steatosis in ob/ob mice are exerted primarily through enhanced fatty acid oxidation via PPAR-dependent pathways. However, PPAR-independent pathways also contribute to NDGA¡¦s action to ameliorate hepatic steatosis.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Molecular vision. 2013, 19:775-88.
 Profiling of genes associated with the murine model of oxygen-induced retinopathy
 
 
 Xia Yang, Xiaoguang Dong, Changkai Jia, Yiqiang Wang
  Abstract
Purpose: To compare the clinical features and gene expression patterns of the physiologic development of retinal vessels and oxygen-induced retinopathy (OIR) in a mouse model, with the aim of identifying differential regulators of physiologic and pathological angiogenesis in the retina. Results: The sequential orders and patterns of vasculature development in normal mice and the OIR models were significantly different. In brief, in the early days (P1 to P7) for normal mice, retinal vessels grew from the optic disc into the non-vascularized retina in a radial fashion. In the hyperoxic stage of the OIR model, the main central retina became devoid of a vascular network, and when the mice returned to the normoxic room, the vessels grew from peripheral perfused areas toward the center of the retina, but the development of intermediate and deep layers of vasculature was significantly delayed. Gene profiling at three critical time points (P8, P12, and P13) showed that 162 probes were upregulated to ≥1.5-fold or downregulated to ≤0.67-fold at one or more time points in the OIR model compared to the controls. In the 45 upregulated genes for the P8-O/P8-N group, enriched genes were mainly related to cytoskeleton formation, whereas the 62 upregulated genes for P13-O/P13-N participated in various pathological processes. In the physiologic conditions on P9, however, 135 genes were upregulated compared with P30; the gap junction and Fc gamma R-mediated phagocytosis were the two main enriched pathways for these genes. Fifty-three probes, including vascular endothelium growth factor A, annexin A2, and endothelin 2, changed at P13-O but not at P9-N, and these changed genes might reflect the modulation of pathological neovascularization. Conclusions: Angiogenesis in physiologic and pathological conditions is characterized by the differential presentation of vasculature and gene expression patterns. Investigation of those genes unique to the OIR model may help develop new strategies and therapies for intervening in retinal neovascularization.
   

  ✔本篇論文使用華聯產品:Human OneArray,Human miRNA OneArray  
 Evidence-Based Complementary and Alternative Medicine. 2013 March 29.
 A Systems Biology Approach to Characterize Biomarkers for Blood Stasis Syndrome of Unstable Angina Patients by Integrating MicroRNA and Messenger RNA Expression Profiling
 
 
 Jie Wang, Gui Yu
  Abstract
Blood stasis syndrome (BSS) in Traditional Chinese medicine (TCM) was considered to the major type of syndrome in unstable angina (UA) patients, which was proven by the epidemiological investigation. This paper identified the systems biology-based microRNA (miRNA) and mRNA expression biomarkers for BSS of UA. The aim of this study was to compare miRNAs and mRNAs profiles of peripheral blood mononuclear cells (PBMCs) from BSS of UA patients and healthy controls through a systems biology approach. We identified 1081 mRNAs and 25 miRNAs differentially expressed between BSS of UA patients and healthy controls by microarrays. We used DAVID, miRTrail and the protein-protein interactions (PPI) method to explore the related pathways and networks of differentially expressed miRNAs and mRNAs. By combining the results of pathways and networks, we found that the upregulation of miR-146b-5p may induce the downregulation of CALR to attenuate inflammation and the upregulation of miR-199a-5p may induce the downregulation of TP53 to inhibit apoptosis in BSS of UA patients. The expression patterns of miR-146b-5p, miR-199a-5p, CALR and TP53 were confirmed by real-time quantitative polymerase chain reaction (qRT-PCR) in an independent validation cohort including BBS of UA, non-BBS of UA and healthy control. miR-146b-5p, miR-199a-5p, CALR and TP53 could be the biomarkers of BSS of UA patients. The systems biology-based miRNA and mRNA expression biomarkers for the BSS of UA may be helpful for the further stratification of UA patients when deciding on interventions or clinical trials.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Journal of Ethnopharmacology. 2013, April 1. doi:10.1016/j.jep.2013.03.020.
 Screening and evaluation of traditional Chinese medicine by microarray expression analysis
 
 
 Guixiang Ren, Qionglin Liang, Yiming Wang, Xuemei Fan, Guoan Luo
  Abstract
ETHNOPHARMACOLOGICAL RELEVANCE: Salvia miltiorrhiza is a Chinese medicinal herb, which is widely used for the treatment of cardiovascular disorders. In this article, we investigated the effects of Salvia miltiorrhiza and its hydrophilic and lipophilic components (HCS and LCS) on human umbilical vein endothelial cells (HUVECs), and the molecular mechanism was explored by microarray gene expression profiling. MATERIALS AND METHODS: Cell proliferation and migration were used to evaluate the angiogenic effects of HCS, LCS and total extract of Salvia miltiorrhiza (TES). Microarray technology was applied to detect the gene expression of HUVECs treated with TES, HCS and LCS. Besides, quantitative real-time PCR was used to verify the microarray results. RESULTS: Our results showed that LCS inhibited the proliferation and migration of HUVECs, HCS promoted the proliferation and migration of HUVECs, and TES did not affect the viability of HUVECs at the concentration of 5µg/mL. From the result of principle component analysis (PCA) of microarray data, the effect of LCS on HUVECs was significantly different from the other components. Moreover, there were more differentially expression genes in LCS group than in the other groups, which meant LCS had a strong influence on HUVECs. Compared with untreated cells, 511 significantly changed genes had been detected in LCS treated cells and 236 (approximately 46%) of them were up-regulated. The mRNA expression of IL-6 was found to be increased significantly in LCS group. CONCLUSIONS: In Salvia miltiorrhiza, HCS and LCS had opposite effects on HUVECs. LCS showed significantly inhibitory action on HUVECs proliferation and migration. It was proposed that LCS could apply in the diseases caused by vascular anomaly hyperplasia. In the mechanism of action of LCS on HUVECs, the pathways of ErbB, MAPK, p53, oxidative phosphorylation and inflammatory response were involved.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Cellular Immunology. 2013 April 10. doi: 10.1016/j.cellimm.2013.04.001.
 MicroRNA-155 regulates T cell proliferation through targeting GSK3£] in cardiac allograft rejection in a murine transplantation model
 
 
 Zhiyu Feng, Yu Xia, Mingjie Zhang, Jinghao Zheng
  Abstract
Here we investigated the activity and regulation of miR-155 during cardiac allograft rejection (AR), and to examine the feasibility of using miR-155 as a biomarker of graft status. Expression of miR-155 in graft-infiltrating lymphocytes (GIL), T cells isolated from spleen (TFS), and lymphocytes separated from blood (LFB) was significantly increased during cardiac AR while GSK3£] was downregulated in GIL and TFS. Inhibition of miR-155 impaired lymphocyte proliferation and enhanced the expression of GSK3£]. Moreover, pharmacological inactivation of GSK3£] resulted in rescue of the proliferative capability of T cells pretreated with a miR-155 inhibitor. Luciferase reporter assay confirmed that miR-155 interacted with the 3¡¬-untranslated region (UTR) of GSK3£] directly. In particular, the miR-155 in LFB can distinguish recipients with AR from syngeneic controls from POD 3 and later. The present study provides a better understanding of the pathophysiological process underlying cardiac AR progression.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 PLoS One. 2013, 8(3): e58929. doi:10.1371/journal.pone.0058929.
 Genistein Up-Regulates Tumor Suppressor MicroRNA-574-3p in Prostate Cancer
 
 
 Takeshi Chiyomaru, Soichiro Yamamura, Shinichiro Fukuhara, Hideo Hidaka, Shahana Majid, Sharanjot Saini, Sumit Arora, Guoren Deng, Varahram Shahryari, Inik Chang, Yuichiro Tanaka, Z., Rajvir Dahiya
  Abstract
Genistein has been shown to inhibit cancers both in vitro and in vivo, by altering the expression of several microRNAs (miRNAs). In this study, we focused on tumor suppressor miRNAs regulated by genistein and investigated their function in prostate cancer (PCa) and target pathways. Using miRNA microarray analysis and real-time RT-PCR we observed that miR- 574-3p was significantly up-regulated in PCa cells treated with genistein compared with vehicle control. The expression of miR-574-3p was significantly lower in PCa cell lines and clinical PCa tissues compared with normal prostate cells (RWPE-1) and adjacent normal tissues. Low expression level of miR-574-3p was correlated with advanced tumor stage and higher Gleason score in PCa specimens. Re-expression of miR-574-3p in PCa cells significantly inhibited cell proliferation, migration and invasion in vitro and in vivo. miR-574-3p restoration induced apoptosis through reducing Bcl-xL and activating caspase- 9 and caspase-3. Using GeneCodis software analysis, several pathways affected by miR-574-3p were identified, such as ¡¥Pathways in cancer¡¦, ¡¥Jak-STAT signaling pathway¡¦, and ¡¥Wnt signaling pathway¡¦. Luciferase reporter assays demonstrated that miR-574-3p directly binds to the 39 UTR of several target genes (such as RAC1, EGFR and EP300) that are components of ¡¥Pathways in cancer¡¦. Quantitative real-time PCR and Western analysis showed that the mRNA and protein expression levels of the three target genes in PCa cells were markedly down-regulated with miR-574-3p. Loss-of-function studies demonstrated that the three target genes significantly affect cell proliferation, migration and invasion in PCa cell lines. Our results show that genistein up-regulates tumor suppressor miR-574-3p expression targeting several cell signaling pathways. These findings enhance understanding of how genistein regulates with miRNA in Pca.
   

  ✔本篇論文使用華聯產品:Array technology and applications  
 Current Opinion in Genetics & Development . 2013 Mar 1. doi: 10.1016/j.gde.2013.01.004..
 miRNA profiling of cancer
 
 
 Gianpiero Di Leva, Carlo M Croce
  Abstract
A steadily growing number of studies have shown that microRNAs have key roles in the regulation of cellular processes and that their dysregulation is essential to keep the malignant phenotype of cancer cells. The distorted and unique expression profile of microRNAs in different types and subsets of tumor coupled with their presence in biological fluids make of microRNAs an attractive source of sensitive biomarkers. Here, we will discuss how microRNA profiles are altered in cancer, highlighting their potential as sensitive biomarkers for cancer risk stratification, outcome prediction and classification of histological subtypes. We will also evaluate the current knowledge on the use of microRNAs as circulating biomarkers, hoping that further studies will lead to the application of microRNA signature in prognostic and predictive markers that can improve patient health.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Cell Cycle. 2013, 12(6):987-99. .
 Tumor-suppressive effects of CDK8 in endometrial cancer cells
 
 
 Weiting Gu,Chenguang Wang, Weihua Li, Fu-Ning Hsu, Lifeng Tian, Jie Zhou, Cunzhong Yuan, Xiao-Jun Xie, Tao Jiang, Sankar Addya, Yanhong Tai, Beihua Kong, Jun-Yuan Ji
  Abstract
CDK8 is either amplified or mutated in a variety of human cancers, and CDK8 functions as an oncoprotein in melanoma and colorectal cancers. Previously, we reported that loss or reduction of CDK8 results in aberrant fat accumulation in Drosophila and mammals, suggesting that CDK8 plays an important role in inhibiting lipogenesis. Epidemiological studies have identified obesity and overweight as the major risk factors of endometrial cancer, thus we examined whether CDK8 regulates endometrial cancer cell growth by using several endometrial cancer cell lines, including KLE, which express low levels of CDK8, as well as AN3 CA and HEC-1A cells, which have high levels of endogenous CDK8. We observed that ectopic expression of CDK8 in KLE cells inhibited cell proliferation and potently blocked tumor growth in an in vivo mouse model. In addition, gain of CDK8 in KLE cells blocked cell migration and invasion in transwell, wound healing and persistence of migratory directionality assays. Conversely, we observed the opposite effects in all of the aforementioned assays when CDK8 was depleted in AN3 CA cells. Similar to AN3 CA cells, depletion of CDK8 in HEC-1A cells strongly enhanced cell migration in transwell assays, while overexpression of CDK8 in HEC-1A cells blocked cell migration. Furthermore, gene profiling of KLE cells overexpressing CDK8 revealed genes whose protein products are involved in lipid metabolism, cell cycle and cell movement pathways. Finally, depletion of CDK8 increased the expression of lipogenic genes in endometrial cancer cells. Taken together, these results show a reverse correlation between CDK8 levels and several key features of the endometrial cancer cells, including cell proliferation, migration and invasion as well as tumor formation in vivo. Therefore, in contrast to the oncogenic effects of CDK8 in melanoma and colorectal cancers, our results suggest that CDK8 plays a tumor-suppressive role in endometrial cancers.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Atherosclerosis. 2013 Mar 15. doi: 10.1016/j.atherosclerosis.2013.01.036 .
 A functional polymorphism of PON1 interferes with microRNA binding to increase the risk of ischemic stroke and carotid atherosclerosis
 
 
 Mu-En Liu, Yi-Chu Liao, Ruey-Tay Lin, Yung-Song Wang, Edward His, Hsiu-Fen Lin, Ku-Chung Chen, Suh-Hang Hank Juo
  Abstract
Objective: Single nucleotide polymorphisms (SNPs) located at microRNA (miRNA) binding sites (miRSNPs) can affect the expression of genes. This study aimed to identify the miR-SNPs associated with atherosclerosis and stroke.

Methods: Patients with ischemic stroke (n =657) and stroke- and myocardial infarction-free volunteers (n =1571) were enrolled. The carotid intima-media thickness (IMT) was measured in the control participants. Seventy-nine stroke susceptibility genes were initially selected and 13 genes were predicted to have miR-SNPs at their 3'untranslated regions (3¡¦UTR). The miRNA arrays were used to further identify potential miR-SNPs. The miR-SNP rs3735590 at the paraoxonase 1 (PON1) gene was finally selected and its associations with stroke and carotid IMT were evaluated. The 3¡¦UTR reporter and SNP functional assays were then performed to validate the results.

Results: Compared with CC genotype, patients with CT or TT genotype at rs3735590 had lower risk of ischemic stroke (OR =0.72, p =0.036; OR =0.83, p =0.077, respectively). Among the healthy participants, the CT or TT genotype was associated with thinner IMT in the internal carotid arteries in comparison with CC genotype (£]=-0.76, p =0.003; £]=- 0.022, p =0.452, respectively). Our findings suggested that the minor allele T had a protective effect on atherosclerosis. Results from 3¡¦UTR reporter assays showed that PON1 is a direct target gene of miR-616. In plasmid constructs carrying the risk allele C at rs3735590, miR-616 inhibited the genetic expression of PON1. However, substitution of C by T at rs3735590 reduced the miR-616 binding affinity, leading to overexpression of the PON1 gene.

Conclusion: Our study is the first to show that the miR-SNP at PON1 could affect genetic expression and is associated with an elevated risk for ischemic stroke and subclinical atherosclerosis.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Fertility and Sterility. 2013 Mar 5. doi: 10.1016/j.fertnstert.2013.01.150.
 Gene expression profiles of cumulus cells obtained from women treated with r-hLH D r-hFSH or hp-hMG versus r-hFSH alone
 
 
 Carla Tatone, Rosanna Ciriminna, Marilena Vento, Sara Franchi, Marco d'Aurora, Samantha Sperduti, Vito Cela, Placido Borz, Roberto Palermo, Liborio Stuppia, Paolo Giovanni Artini, Valentina Gatta
  Abstract
OBJECTIVE: To evaluate cumulus cell (CC) expression profile modulation after different stimulation protocols.

DESIGN: CCs transcriptome variations were evaluated by microarray in patients undergoing different treatments for ovarian stimulation, namely, r-hLH + r-hFSH and hp-hMG, compared with a control group treated with r-hFSH.

INTERVENTION(S): Four patients received hp-hMG, four received r-hFSH + r-hLH, and eight received r-hFSH daily. Aspiration of the oocytes was performed 36 hours after hCG administration. Only samples derived from cumulus-oocyte complexes containing mature oocytes showing polar body were processed.

RESULT(S): Data clustering analysis allowed detection of four clusters containing genes differentially expressed in both treatment groups compared with control. Functional analysis of the affected transcripts revealed genes involved in oocyte development and maturation.

CONCLUSION(S): r-hLH and hCG, though acting on the same receptor, produce a differential activation of intracellular pathways. It can be hypothesized that this effect depends on their different structures and specific binding affinity for the receptor.
   

  ✔本篇論文使用華聯產品:OEM Array  
 Applied Mechanics and Materials . 2013 Jan. doi: 10.4028/www.scientific.net/AMM.284-287.315.
 Investigation of Hybridization Efficiency of a Sequence-Orientated Coaxial DNA Probe Microarryed on Biochips Using Atomic Force Microscope
 
 
 Dan-Kai Yang, Yane-Shu Lin, Jun-Yi Chen, Jui-Chuang Wu
  Abstract
Two sequence-inversed probes were microarrayed on glass slides to study the hybridization efficiency with their DNA targets. The sequences of two targets were designed to be fully complementary to their shared DNA probe in a coaxial stacking configuration. The enhancement of the hybridization efficiency was investigated through the comparison between the stacking and individual hybridization configurations. AFM was used to measure the depths of two probes at different steps of hybridization. The results indicated that the depths increased as the hybridization proceeded. Probe#1, pre-hybridizing close to the chip surface, obtained a thicker depth than the other probe pre-hybridizing away from the chip surface, Probe#2. A hypothesis was proposed to explain how the depth variation was associated with the observed hybridization efficiency.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray, Human OneArray  
 Biochimica et Biophysica Acta. 2013 Feb 8. doi: 10.1016/j.bbagrm.2013.01.011.
 Transfection of siRNAs can alter miRNA levels and trigger non-specific protein degradation in mammalian cells
 
 
 Christopher E. Hart, Stanley T. Crooke, Xue-hai Liang
  Abstract
Sequence-non-specific effects of siRNAs that alter the expression of non-targeted genes have been reported, including competition of siRNAs with endogenous RISC components. However, the detailed mechanisms and subsequent effects of such competition are not well documented. Here we analyze the competition of miRNAs in mammalian cells with low concentrations of siRNAs, and found that: 1) transfection of different siRNAs in the low nanomolar range used to deplete target RNAs can reduce the levels of miRNAs in different cell types, 2) siRNA transfection results in rapid reduction of Ago2-associated miRNAs concurrent with accumulation of Ago2-bound siRNAs and a significant change in the expression levels of many miRNAs, 3) competition largely depends on Ago2 and not Dicer, 4) microarray analysis showed that the majority of highly expressed miRNAs are reduced, in a siRNA concentration dependent manner, and low abundant miRNAs may be unchanged or repressed and a fewmiRNAs appear to have increased levels, and 5) consistent with previous studies, the expres-sion levels ofmRNAs that are targeted by highly repressedmiRNAs are preferentially increased. As a consequence of such competition, we observed that £-tubulin, a substrate of two up-regulated proteases, granzyme B and granzyme M, was rapidly degraded at the protein level upon siRNA transfection. Our results support a model in which transfection of siRNAs can change the levels of many miRNAs by competition for Ago2, leading to altered expression of many miRNA target genes, which can in turn affect downstream gene expression even at the protein level.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 PLoS One. 2013, 8(2):e54455. doi: 10.1371/journal.pone.0054455.
 MUC4 Overexpression Augments Cell Migration and Metastasis through EGFR Family Proteins in Triple Negative Breast Cancer Cells
 
 
 Partha Mukhopadhyay, Imayavaramban Lakshmanan, Moorthy P. Ponnusamy, Subhankar Chakraborty, Maneesh Jain, Priya Pai, Lynette M. Smith, Subodh M. Lele, Surinder K. Batra
  Abstract
Introduction Current studies indicate that triple negative breast cancer (TNBC), an aggressive breast cancer subtype, is associated with poor prognosis and an early pattern of metastasis. Emerging evidence suggests that MUC4 mucin is associated with metastasis of various cancers, including breast cancer. However, the functional role of MUC4 remains unclear in breast cancers, especially in TNBCs. Results MUC4 promotes proliferation, anchorage-dependent and-independent growth of TNBC cells, augments TNBC cell migratory and invasive potential in vitro, and enhances tumorigenicity and metastasis in vivo. In addition, our studies demonstrated that MUC4 up-regulates the EGFR family of proteins, and augments downstream Erk1/2, PKC-£^, and FAK mediated oncogenic signaling. Moreover, our studies also showed that knockdown of MUC4 in TNBC cells induced molecular changes suggestive of mesenchymal to epithelial transition. We also demonstrated in this study, for the first time, that knockdown of MUC4 was associated with reduced expression of EGFR and ErbB3 (EGFR family proteins) in TNBC cells, suggesting that MUC4 uses an alternative to ErbB2 mechanism to promote aggressiveness. We further demonstrate that MUC4 is differentially over-expressed in invasive TNBC tissues compared to normal breast tissue. Conclusions MUC4 mucin expression is associated with TNBC pathobiology, and its knockdown reduced aggressiveness in vitro, and tumorigenesis and metastasis in vivo. Overall, our findings suggest that MUC4 mucin promotes invasive activities of TNBC cells by altering the expression of EGFR, ErbB2, and ErbB3 molecules and their downstream signaling.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 International Immunology. 2013 Feb 14. doi: 10.1093/intimm/dxs154.
 Transcriptome signature in young children with acute otitis media due to non-typeable Haemophilus influenzae
 
 
 Keyi Liu, Linlin Chen, Ravinder Kaur, Michael E. Pichichero
  Abstract
Non-typeable Haemophilus influenzae (NTHi) causes acute otitis media (AOM) in young children. In our recent paper in Microbes and Infection we described the transcriptome signature elicited from PBMCs at onset of AOM caused by Streptococcus pneumoniae. In the current study we found very different results with NTHi AOM infections; 5.1% of 29 187 genes were differentially regulated by more than 2-fold at the onset of AOM compared with the pre-infection healthy state in the same children. Among the 1487 transcripts, 100 genes associated with the immune defense response were specifically analyzed. About half of the differentially regulated genes associated with antibacterial activity and the cell-mediated immune response were activated and half were suppressed. The important signatures for NTHi in children suggested that the balance of the immune response was toward suppression. Moreover, 90% of the genes associated with a pro-inflammatory cytokine response were down-regulated. The genes associated with the classic complement pathway were down-regulated, although the alternative complement pathway genes were up-regulated. These results provide the first human transcriptome data identifying gene expression in the immune response to be predominantly down-regulated at the onset of AOM due to NTHi.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Journal of Agricultural and Food Chemistry. 2013 Feb 15. doi: 10.1021/jf3042402.
 Momordica charantia and Its Novel Polypeptide Regulate the Glucose Homeostasis in Mice via Binding to Insulin Receptor
 
 
 Hsin-Yi Lo, Tin-Yun Ho, Chingju Lin, Chia-Cheng Li, Chien-Yun Hsiang
  Abstract
Momordica charantia (MC) has been used as an alternative therapy for diabetes mellitus. Herein we analyzed and elucidated therapeutic targets contributing to the hypoglycemic effect of aqueous extract of MC seeds (MCSE) by transcriptomic analysis. Protein ingredients aimed at the hypoglycemic target were further identified by proteomic, docking, and receptor-binding assays. Our data showed that MSCE (1 g/kg) significantly lowered the blood glucose level in normal and diabetic mice. Moreover, MCSE primarily regulated the insulin signaling pathway in muscles and adipose tissues, suggesting that MCSE might target to insulin receptor (IR), stimulate the IR-downstream pathway, and subsequently display the hypoglycemic activity in mice. We further identified that inhibitor against trypsin (TI) of MC directly docked into IR and activated the kinase activity of IR in a dose-dependent manner. In conclusion, our findings suggested that MCSE regulated glucose metabolism mainly via insulin signaling pathway. Moreover, we newly identified that TI was a novel IR-binding protein of MC that triggered the insulin signaling pathway via binding to IR.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 PLoS One. 2013, 8(1):e53795. doi: 10.1371/journal.pone.0053795.
 In Vivo Targeting of ADAM9 Gene Expression Using Lentivirus-Delivered shRNA Suppresses Prostate Cancer Growth by Regulating REG4 Dependent Cell Cycle Progression
 
 
 Che-Ming Liu, Chia-Ling Hsieh, Yun-Chi He, Sen-Jei Lo, Ji-An Liang, Teng-Fu Hsieh, Sajni Josson, Leland W. K. Chung, Mien-Chie Hung, Shian-Ying Sung
  Abstract
Cancer cells respond to stress by activating a variety of survival signaling pathways. A disintegrin and metalloproteinase (ADAM) 9 is upregulated during cancer progression and hormone therapy, functioning in part through an increase in reactive oxygen species. Here, we present in vitro and in vivo evidence that therapeutic targeting of ADAM9 gene expression by lentivirus-delivered small hairpin RNA (shRNA) significantly inhibited proliferation of human prostate cancer cell lines and blocked tumor growth in a murine model of prostate cancer bone metastasis. Cell cycle studies confirmed an increase in the G1-phase and decrease in the S-phase population of cancer cells under starvation stress conditions, which correlated with elevated intracellular superoxide levels. Microarray data showed significantly decreased levels of regenerating islet-derived family member 4 (REG4) expression in prostate cancer cells with knockdown of ADAM9 gene expression. This REG4 downregulation also resulted in induction of expression of p21Cip1/WAF1, which negatively regulates cyclin D1 and blocks the G1/S transition. Our data reveal a novel molecular mechanism of ADAM9 in the regulation of prostate cancer cell proliferation, and suggests a combined modality of ADAM9 shRNA gene therapy and cytotoxic agents for hormone refractory and bone metastatic prostate cancer.  
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Genetic Testing and Molecular Biomarkers. 2013, 17(1):40-6. doi: 10.1089/gtmb.2012.0231.
 Gender, Body Mass Index, and PPAR£^ Polymorphism Are Good Indicators in Hyperuricemia Prediction for Han Chinese
 
 
 Ming-Fen Lee, Tsan-Hon Liou, Weu Wang, Wen-Harn Pan, Wei-Jei Lee, Chung-Tan Hsu, Suh-Fen Wu, Hsin-Hung Chen
  Abstract
Hyperuricemia is closely associated with obesity and metabolic abnormalities, which is also an independent risk factor for cardiovascular diseases. The PPAR£^ gene, which is linked to obesity and metabolic abnormalities in Han Chinese, might be considered a top candidate gene that is involved in hyperuricemia. This study recruited 457 participants, aged 20-40 years old, to investigate the associations of the PPAR£^ gene and metabolic parameters with hyperuricemia. Three tag-single nucleotide polymorphisms, rs2292101, rs4684846, and rs1822825, of the PPAR£^ gene were selected to explore their association with hyperuricemia. Risk genotypes on rs1822825 of the PPAR£^ gene exhibited statistical significance with hyperuricemia (odds ratio: 1.9; 95% confidence interval: 1.05-3.57). Although gender, body mass index (BMI), serum total cholesterol concentration, or protein intake per day were statistically associated with hyperuricemia, the combination of BMI, gender, and rs1822825, rather than that of age, serum lipid profile, blood pressure, and protein intake per day, satisfied the predictability for hyperuricemia (sensitivity: 69.3%; specificity: 83.7%) in Taiwan-born obese Han Chinese. BMI, gender, and the rs1822825 polymorphism in the PPAR£^ gene appeared good biomarkers in hyperuricemia; therefore, these powerful indicators may be included in the prediction of hyperuricemia to increase the accuracy of the analysis.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Journal of Biomedical Science. 2013, 20(1):2. doi:10.1186/1423-0127-20-2.
 Circulating microRNA signatures in mice exposed to lipoteichoic acid
 
 
 Ching-Hua Hsieh, Johnson Chia-Shen Yang, Jonathan Chris Jeng, Yi-Chun Chen, Tsu-Hsiang Lu, Siou-Ling Tzeng, Yi-Chan Wu, Chia-Jung Wu, Cheng-Shyuan Rau
  Abstract
BACKGROUND: Previously, we had identified a specific whole blood¡Vderived microRNAs (miRNAs) signature in mice following in vivo injection of lipopolysaccharide (LPS) originated from Gram-negative bacteria. This study was designed to profile the circulating miRNAs expression in mice exposed to lipoteichoic acid (LTA) which is a major component of the wall of Gram-positive bacteria. RESULTS: C57BL/6 mice received intraperitoneal injections of 100 £gg of LTA originated from Bacillus subtilis, Streptococcus faecalis, and Staphylococcus aureus were killed 6 h and the whole blood samples were obtained for miRNA expression analysis using a miRNA array (Phalanx miRNA OneArray 1.0). Up-regulated expression of miRNA targets in the whole blood, serum and white blood cells (WBCs) of C57BL/6 and Tlr2−/− mice upon LTA treatment in 10, 100, or 1000 ug concentrations was quantified at indicated time (2, 6, 24, and 72 h) using real-time RT-PCR and compared with that in the serum of C57BL/6 mice injected with 100 ug of LPS. A significant increase of 4 miRNAs (miR-451, miR-668, miR-1902, and miR-1904) was observed in the whole blood and the serum in a dose- and time-dependent fashion following LTA injection. Induction of miRNA occurred in the serum after 2 h and persisted for at least 6 h. No increased expression of these 4 miRNAs was found in the WBCs. Higher but not significant expression level of these 4 miRNAs were observed following LTA treatment in the serum of Tlr2−/−against that of C57BL6 mice. In contrast, LPS exposure induced moderate expression of miR-451 but not of the other 3 miRNA targets. CONCLUSIONS: We identified a specific circulating miRNA signature in mice exposed to LTA. That expression profile is different from those of mice exposed to LPS. Those circulating miRNAs induced by LTA or LPS treatment may serve as promising biomarkers for the differentiation between exposures to Gram-positive or Gram-negative bacteria.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Oncology Reports. 2012, 28(6):2115-24. doi: 10.3892/or.2012.2054.
 miRNA expression profile of colon cancer stem cells compared to non-stem cells using the SW1116 cell line
 
 
 ZONGYOU CHEN, YANTIAN FANG, JIANBIN XIANG, XIAODONG GU, ZHENGYANG LI, FENG TANG, ZHONGWEN ZHOU
  Abstract
Colorectal cancer (CRC) is one of the major causes of cancer-related mortality worldwide. Recent studies revealed that there is a relationship between CRC occurrence and microRNA (miRNA) function. Stem cells are a type of cells that have the ability to self-renew and to proliferate extensively while maintaining the undifferentiated state. Cancer stem cells (CSCs) are closely linked to tumor recurrence and metastasis. To this end, we evaluated themiRNA expression differences between colon CSCs and non-stem cells using the SW1116 cell line, to determine the relationship between tumorstem cells and tumor biological behavior. We isolated populations of colon CSCs with the CD133+/CD44+ and CD133-/CD44- surface phenotype from a human SW1116 colon adenocarcinoma cell line using flow cytometry. The expression of miRNA and mRNA of both sets of cells was examined withmiRNA and mRNA arrays. Bioinformatic methods were used to analyze microarray results. We completed gene ontology analysis, pathway analysis,miRNA target gene prediction with databases. We identified a colon stem cell miRNA expression profile comprising 31 upregulated and 31 downregulated miRNAs, such as miR29a, miR29b, miR449b and miR4524. Some of these differentially expressed miRNAs may be involved in the regulation of stem cell differentiation. Gene ontology and pathway analyses showed that the differences are closely related to the function of the cellcycle, cell differentiation, signaling pathway, cytoskeletal proteins and cell-matrix adhesion in colon cancer stem cells. We found that miRNAs play an important role in regulating the expression of colon CSC characteristics. By regulating the expression of CSC signaling pathways, cytoskeleton and membrane proteins, miRNAs give tumor stem cells the macrobiological behavior of recurrence and metastasis. This study provides a new perspective on CRC metastasis and recurrence.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Molecular Cancer Therapeutics. 2012, 11(1):244-53. doi: 10.1158/1535-7163.MCT-11-0592.
 Tumor Suppressor MicroRNA-493 Decreases Cell Motility and Migration Ability in Human Bladder Cancer Cells by Downregulating RhoC and FZD4
 
 
 Koji Ueno, Hiroshi Hirata, Shahana Majid, Soichiro Yamamura, Varahram Shahryari, Z. Laura Tabatabai, Yuji Hinoda, Rajvir Dahiya
  Abstract
The purpose of this study was to identify new tumor suppressor microRNAs (miRNA; miR) in bladder cancer, conduct functional analysis of their suppressive role, and identify their specific target genes. To explore tumor suppressor miRs in bladder cancer, miR microarray was conducted using SV-HUC-1, T24, J82, and TCCSUP cells. Expression of miR-493 in bladder cancer (T24, J82, and TCCSUP) cells was downregulated compared with normal SV-HUC-1cells. Also, the expression of miR-493 was significantly lower in bladder cancer tissues than in their corresponding noncancerous tissues. Transfection of miR-493 into T24 or J82 cells decreased their cell growth and migration abilities. On the basis of this result, to identify potential miR-493 target genes, we used target scan algorithms to identify target oncogenes related to invasion and migration. miR-493 decreased 3'-untranslated region luciferase activity and protein expression of FZD4 and RhoC. miR-493 also decreased binding of RhoC and Rock-1. miR-493 is a new tumor suppressor miRNA in bladder cancer and inhibits cell motility through downregulation of RhoC and FZD4.
   

  ✔本篇論文使用華聯產品:Array technology and applications  
 Nature Reviews Genetics. 2012, 13: 358-369. doi:10.1038/nrg3198.
 MicroRNA profiling: approaches and considerations
 
 
 Colin C. Pritchard, Heather H. Cheng, Muneesh Tewari
  Abstract
MicroRNAs (miRNAs) are small RNAs that post-transcriptionally regulate the expression of thousands of genes in a broad range of organisms in both normal physiological contexts and in disease contexts. miRNA expression profiling is gaining popularity because miRNAs, as key regulators in gene expression networks, can influence many biological processes and also show promise as biomarkers for disease. Technological advances have spawned a multitude of platforms for miRNA profiling, and an understanding of the strengths and pitfalls of different approaches can aid in their effective use. Here, we review the major considerations for carrying out and interpreting results of miRNA-profiling studies.
   

  ✔本篇論文使用華聯產品:Experimental Accessories  
 Journal of Virology. 2012, 86(15):8041-9. doi: 10.1128/JVI.00808-12.
 Defective Antiviral Responses of Induced Pluripotent Stem Cells to Baculoviral Vector Transduction
 
 
 Chen GY, Hwang SM, Su HJ, Kuo CY, Luo WY, Lo KW, Huang CC, Chen CL, Yu SH, Yu-Chen Hu
  Abstract
Genetic engineering of induced pluripotent stem cells (iPSCs) is important for their clinical applications, and baculovirus (BV) holds promise as a gene delivery vector. To explore the feasibility of using BV for iPSCs transduction, in this study we first examined how iPSCs responded to BV. We determined that BV transduced iPSCs efficiently, without inducing appreciable negative effects on cell proliferation, apoptosis, pluripotency, and differentiation. BV transduction slightly perturbed the transcription of 12 genes involved in the Toll-like receptor (TLR) signaling pathway, but at the protein level BV elicited no well-known cytokines (e.g., interleukin-6 [IL-6], tumor necrosis factor alpha [TNF-], and beta interferon [IFN-]) except for IP-10. Molecular analyses revealed that iPSCs expressed no TLR1, -6, -8, or -9 and expressed merely low levels of TLR2, -3, and -4. In spite of evident expression of such RNA/DNA sensors as RIG-I and AIM2, iPSCs barely expressed MDA5 and DAI (DNA-dependent activator of IFN regulatory factor [IRF]). Importantly, BV transduction of iPSCs stimulated none of the aforementioned sensors or their downstream signaling mediators (IRF3 and NF-B). These data together confirmed that iPSCs responded poorly to BV due to the impaired sensing and signaling system, thereby justifying the transduction of iPSCs with the baculoviral vector.
   

  ✔本篇論文使用華聯產品:Experimental Accessories  
 PLOS ONE. 2012, 7(8):e43304. doi: 10.1371/journal.pone.0043304.
 Luteolin Induces microRNA-132 Expression and Modulates Neurite Outgrowth in PC12 Cells
 
 
 Lian-Fang Lin, Szu-Ping Chiu, Ming-Jiuan Wu, Pei-Yi Chen, Jui-Hung Yen
  Abstract
Luteolin, a food-derived flavonoid, has been reported to exert neurotrophic properties that are associated with its capacity to promote neuronal survival and neurite outgrowth. In this study, we report for the first time that luteolin induces the persistent expression of microRNA-132 (miR-132) in PC12 cells. The correlation between miR- 132 knockdown and a decrease in luteolin-mediated neurite outgrowth may indicate a mechanistic link by which miR-132 functions as a mediator for neuritogenesis. Furthermore, we find that luteolin led to the phosphorylation and activation of cAMP response element binding protein (CREB), which is associated with the up-regulation of miR-132 and neurite outgrowth. Moreover, luteolin-induced CREB activation, miR-132 expression and neurite outgrowth were inhibited by adenylate cyclase, protein kinase A (PKA) and MAPK/ERK kinase 1/2 (MEK1/2) inhibitors but not by protein kinase C (PKC) or calcium/calmodulin-dependent protein kinase II (CaMK II) inhibitors. Consistently, we find that luteolin treatment increases ERK phosphorylation and PKA activity in PC12 cells. These results show that luteolin induces the up-regulation of miR-132, which serves as an important regulator for neurotrophic actions, mainly acting through the activation of cAMP/PKA- and ERK-dependent CREB signaling pathways in PC12 cells.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 PLOS ONE. 2012, 7(3): e32907. doi:10.1371/journal.pone.0032907.
 Identification of IGF1, SLC4A4, WWOX, and SFMBT1 as Hypertension Susceptibility Genes in Han Chinese with a Genome-Wide Gene-Based Association Study
 
 
 Hsin-Chou Yang, Yu-Jen Liang, Jaw-Wen Chen, Kuang-Mao Chiang, Chia-Min Chung, Hung-Yun Ho, Chih-Tai Ting, Tsung-Hsien Lin,Sheng-Hsiung Sheu, Wei-Chuan Tsai, Jyh-Hong Chen, Hsin-Bang Leu, Wei-Hsian Yin, Ting-Yu Chiu, Ching-Iuan Chern, Shing-Jong Lin, Brian Tomlinson,Youling Guo, Pak C. Sham, Stacey S. Cherny, Tai Hing Lam, G. Neil Thomas, Wen-Harn Pan
  Abstract
Hypertension is a complex disorder with high prevalence rates all over the world. We conducted the first genome-wide gene-based association scan for hypertension in a Han Chinese population. By analyzing genome-wide single-nucleotidepolymorphism data of 400 matched pairs of young-onset hypertensive patients and normotensive controls genotyped with the Illumina HumanHap550-Duo BeadChip, 100 susceptibility genes for hypertension were identified and also validated with permutation tests. Seventeen of the 100 genes exhibited differential allelic and expression distributions between patient and control groups. These genes provided a good molecular signature for classifying hypertensive patients and normotensive controls. Among the 17 genes, IGF1, SLC4A4, WWOX, and SFMBT1 were not only identified by our gene-based association scan and gene expression analysis but were also replicated by a gene-based association analysis of the Hong Kong Hypertension Study. Moreover, cis-acting expression quantitative trait loci associated with the differentially expressed genes were found and linked to hypertension. IGF1, which encodes insulin-like growth factor 1, is associated with cardiovascular disorders, metabolic syndrome, decreased body weight/size, and changes of insulin levels in mice. SLC4A4, which encodes the electrogenic sodium bicarbonate cotransporter 1, is associated with decreased body weight/size and abnormal ion homeostasis in mice. WWOX, which encodes the WW domain-containing protein, is related to hypoglycemia and hyperphosphatemia. SFMBT1, which encodes the scm-like with four MBT domains protein 1, is a novel hypertension gene. GRB14, TMEM56 and KIAA1797 exhibited highly significant differential allelic and expressed distributions between hypertensive patients and normotensive controls. GRB14 was also found relevant to blood pressure in a previous genetic association study in East Asian populations. TMEM56 and KIAA1797 may be specific to Taiwanese populations, because they were not validated by the two replication studies. Identification of these genes enriches the collection of hypertension susceptibility genes, thereby shedding light on the etiology of hypertension in Han Chinese populations.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Clinical Cancer Research. 2012, 18(22):6188-98. doi: 10.1158/1078-0432.CCR-12-1789.
 Overexpression of ecdysoneless in pancreatic cancer and its role in oncogenesis by regulating glycolysis
 
 
 Parama Dey, Satyanarayana Rachagani, Subhankar Chakraborty, Pankaj K. Singh, Xiangshan Zhao, Channabasavaiah Basavaraju Gurumurthy, Judy M. Anderson, Subodh Lele, Michael A. Hollingsworth, Vimla Band, Surinder K. Batra
  Abstract
Purpose: To study the expression and function of a novel cell-cycle regulatory protein, human ecdysoneless (Ecd), during pancreatic cancer pathogenesis. Experimental Design: Immunohistochemical expression profiling of Ecd was done in nonneoplastic normal pancreatic tissues and pancreatic ductal adenocarcinoma lesions (from tissue microarray and Rapid Autopsy program) as well as precancerous PanIN lesions and metastatic organs. To analyze the biological significance of Ecd in pancreatic cancer progression, Ecd was stably knocked down in pancreatic cancer cell line followed by in vitro and in vivo functional assays. Results: Normal pancreatic ducts showed very weak to no Ecd expression compared to significant positive expression in pancreatic cancer tissues as well as in PanIN precursor lesions with a progressive increase in Ecd expression with increasing dysplasia (PanIN-1¡VPanIN-3). Analysis of matched primary tumors and metastases from patients with pancreatic cancer revealed that Ecd is highly expressed in both primary pancreatic tumor and in distant metastatic sites. Furthermore, knockdown of Ecd suppressed cell proliferation in vitro and tumorigenicity of pancreatic cancer cells in mice orthotopic tumors. Microarray study revealed that Ecd regulates expression of glucose transporter GLUT4 in pancreatic cancer cells and was subsequently shown to modulate glucose uptake, lactate production, and ATP generation by pancreatic cancer cells. Finally, knockdown of Ecd also reduced level of pAkt, key signaling molecule known to regulate aerobic glycolysis in cancer cells. Conclusion: Ecd is a novel tumor-promoting factor that is differentially expressed in pancreatic cancer and potentially regulates glucose metabolism within cancer cells.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Molecular Pharmacology. 2012, 82(6):1115-28. doi: 10.1124/mol.112.078485.
 Betulinic Acid Decreases Specificity Protein 1 (Sp1) Level via Increasing the Sumoylation of Sp1 to Inhibit Lung Cancer Growth
 
 
 Tsung-I. Hsu, Mei-Chun Wang, Szu-Yu Chen, Shih-Ting Huang, Yu-Min Yeh, Wu-Chou Su, Wen-Chang Chang, Jan-Jong Hung
  Abstract
Previous studies have shown that the inhibitory effect of betulinic acid (BA) on specificity protein 1 (Sp1) expression is involved in the prevention of cancer progression, but the mechanism of this effect remains to be delineated. In this study, we determined that BA treatment in HeLa cells increased the sumoylation of Sp1 by inhibiting sentrin-specific protease 1 expression. The subsequent recruitment of E3 ubiquitin-protein ligase RING finger protein 4 resulted in ubiquitin-mediated degradation in a 26S-proteosome-dependent pathway. In addition, both BA treatment and mithramycin A (MMA) treatment inhibited lung tumor growth and down-regulated Sp1 protein expression in KrasG12D-induced lung cancers of bitransgenic mice. In gene expression profiles of KrasG12D-induced lung cancers in bitransgenic mice with and without Sp1 inhibition, 542 genes were affected by MMA treatment. One of the gene products, cyclin A2, which was involved in the S and G2/M phase transition during cell cycle progression, was investigated in detail because its expression was regulated by Sp1. The down-regulation of cyclin A2 by BA treatment resulted in decreased retinoblastoma protein phosphorylation and cell cycle G2/M arrest. The BA-mediated cellular Sp1 degradation and antitumor effect were also confirmed in a xenograft mouse model by using H1299 cells. The knockdown of Sp1 in lung cancer cells attenuated the tumor-suppressive effect of BA. Taken together, the results of this study clarify the mechanism of BA-mediated Sp1 degradation and identify a pivotal role for Sp1 in the BA-induced repression of lung cancer growth.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Scandinavian Journal of Immunology. 2011 Sep 16. doi: 10.1111/j.1365-3083.2011.02637.x.
 Healthy First-Degree Relatives of Patients with Type 1 Diabetes Exhibit Significant Differences in Basal Gene Expression Pattern of Immunocompetent Cells Compared to Controls: Expression Pattern as Predeterminant of Autoimmune Diabetes
 
 
 M. Kolar, R. Blatny, Z. Halbhuber, J. Vcelakova, M. Hubackova, L. Petruzelkova, Z. Sumnik, B. Obermannova, P. Pithova, V. Stavikova, M. Krivjanska, A. Neuwirth, S. Kolouskova, D. Filipp, K. Stechova
  Abstract
Expression features of genetic landscape which predispose an individual to the type 1 diabetes are poorly understood. We addressed this question by comparing gene expression profile of freshly isolated peripheral blood mononuclear cells isolated from either patients with type 1 diabetes (T1D), or their firstdegree relatives or healthy controls. Our aim was to establish whether a distinct type of ¡¥prodiabetogenic¡¦ gene expression pattern in the group of relatives of patients with T1D could be identified. Whole-genome expression profile of nine patients with T1D, their ten first-degree relatives and ten healthy controls was analysed using the human high-density expression microarray chip. Functional aspects of candidate genes were assessed using the MetaCore software. The highest number of differentially expressed genes (547) was found between the autoantibody-negative healthy relatives and the healthy controls. Some of them represent genes critically involved in the regulation of innate immune responses such as TLR signalling and CCR3 signalling in eosinophiles, humoral immune reactions such as BCR pathway, costimulation and cytokine responses mediated by CD137, CD40 and CD28 signalling and IL-1 proinflammatory pathway. Our data demonstrate that expression profile of healthy relatives of patients with T1D is clearly distinct from the pattern found in the healthy controls. That especially concerns differential activation status of genes and signalling pathways involved in proinflammatory processes and those of innate immunity and humoral reactivity. Thus, we posit that the study of the healthy relative¡¦s gene expression pattern is instrumental for the identification of novel markers associated with the development of diabetes.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 European journal of dermatology. 2012, 22(1): 58-67. doi: 10.1684/ejd.2011.1599.
 Angelica sinensis isolate SBD.4: composition, gene expression profiling, mechanism of action and effect on wounds, in rats and humans
 
 
 Hui Zhao, Joel Deneau, Ginny O.L. Che, Shang Li, Frederic Vagnini, Parastoo Azadi, Roberto Sonon, Ravi Ramjit, Simon M.Y. Lee, Krzysztof Bojanowski
  Abstract
This report characterizes an aqueous isolate (SBD.4) of one of the most broadly used Chinese medicinal herbs, Angelica sinensis, from the perspective of its application in skin and wound care. SBD.4 has been chemically defined and was found to increase the strength of healed wounds in retired breeder (older) rats. Furthermore, the mechanism of action of this Angelica sinensis isolate was tested in the zebrafish angiogenesis model, and in human skin substitutes by DNA microarray, revealing a bioactivity profile consistent with skin repair and regeneration. When combined with several types of wound dressings, SBD.4 increased type I collagen production in human dermal fibroblasts, and when formulated in nanosilver hydrocolloid dressing, it was found effective in chronic ulcer management in humans, demonstrating that botanical high-tech wound dressings can be successfully developed to improve the treatment of chronic lesions in humans.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 BioMedicine. 2012, 2(1):10-16. doi: 10.1016/j.biomed.2012.02.002.
 DNA microarray analysis as a tool to investigate the therapeutic mechanisms and drug development of Chinese medicinal herbs
 
 
 Chia-Cheng Li, Hsin-Yi Lo, Chien-Yun Hsiang, Tin-Yun Ho
  Abstract
Chinese herbal medicines have been used for the treatment of various diseases for centuries. Although several herbal formulas and herbal components have shown therapeutic potential, the active components and the molecular mechanisms mediating the effects of said formulas remain to be discovered. Microarray analysis has become a widely used tool for the generation of gene expression data on a genome-wide scale. This paper discusses the application of whole genome expression profiling as a tool to investigate the molecular mechanisms governing the therapeutic effects of traditional Chinese medicine. This review also highlights how data derived from DNA microarray analysis can be used to screen for drug targets of various herbal drugs, to predict the therapeutic potential of herbal drugs, to analyze the safety of drugs in the preclinical stage of drug development, and to establish a modern definition of traditional Chinese medicine.
   

  ✔本篇論文使用華聯產品:Array technology and applications  
 Journal of Laboratory Automation. 2012, 17(6):405-407. doi: 10.1177/2211068212463689.
 Lab Automation Services
 
 
 Stephen Hughes
  Abstract

   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Methods in Molecular Biology. 2012, 887:95-110. doi: 10.1007/978-1-61779-860-3_10.
 Deoxyoligonucleotide Microarrays for Gene Expression Profiling in Murine Tooth Germs
 
 
 Anne-Marthe Jevnaker, Maria A. Landin, Harald Osmundsen
  Abstract
The use of deoxyoligonucleotide microarrays facilitates rapid expression profiling of gene expression using samples of about 1 £gg of total RNA. Here are described practical aspects of the procedures involved, including essential reagents. Analysis of results is discussed from a practical, experimental, point of view together with software required to carry out the required statistical analysis to isolate populations of differentially expressed genes.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Biology of Reproduction. 2012, 86(5):1-10. doi: 10.1095/biolreprod.111.097295.
 Mono-(2-Ethylhexyl) Phthalate (MEHP) Promotes Invasion and Migration of Human Testicular Embryonal Carcinoma Cells
 
 
 Yi-Chen Lin, Pei-Li Yao, John H. Richburg
  Abstract
Testicular dysgenesis syndrome refers to a collection of diseases in men, including testicular cancer, that arise as a result of abnormal testicular development. Phthalates are a class of chemicals used widely in the production of plastic products and other consumer goods. Unfortunately, phthalate exposure has been linked to reproductive dysfunction and has been shown to adversely affect normal germ cell development. In this study, we show that mono-(2-ethylhexyl) phthalate (MEHP) induces matrix metalloproteinase 2 (MMP2) expression in testicular embryonal carcinoma NT2/D1 cells but has no significant effect on MMP9 expression. NT2/D1 cells also have higher levels of MYC expression following MEHP treatment. It is widely recognized that activation of MMP2 and MYC is tightly associated with tumor metastasis and tumor progression. Gelatin zymographic analysis indicates that MEHP strongly activates MMP2 in NT2/D1 cells. Addition of the MMP2-specific inhibitor SB-3CT inhibited MEHP-enhanced cell invasion and migration, demonstrating that MMP2 plays a functional role in promoting testicular embryonal carcinoma progression in response to MEHP exposure. Furthermore, we investigated genome-wide gene expression profiles of NT2/D1 cells following MEHP exposure at 0, 3, and 24 h. Microarray analysis and semiquantitative RT-PCR revealed that MEHP exposure primarily influenced genes in cell adhesion and transcription in NT2/D1 cells. Gap junction protein-alpha 1, vinculin, and inhibitor of DNAbinding protein-1 were significantly down-regulated by MEHP treatment, while claudin-6 and beta 1-catenin expression levels were up-regulated. This study provides insight into mechanisms that may account for modulating testicular cancer progression following phthalate exposure.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Journal of Molecular Neuroscience. 2012, 47(3):604-618. doi: 10.1007/s12031-011-9690-4.
 The Effects of Unilateral Naris Occlusion on Gene Expression Profiles in Mouse Olfactory Mucosa
 
 
 Christopher T. Waggener, David M. Coppola
  Abstract
Unilateral naris occlusion has been the method of choice for effecting stimulus deprivation in studies of olfactory plasticity. Early experiments emphasized the deleterious effects of this technique on the developing olfactory system while more recent studies have pointed to several apparently ¡§compensatory¡¨ responses. However, the evidence for deprivation-induced compensatory processes in olfaction remains fragmentary. High-throughput methods such as microarray analysis can help fill the deficits in our understanding of naris occlusion as a mode of stimulus deprivation. Here we report for young adult mice the effects of early postnatal naris occlusion on the olfactory mucosal transcriptome using microarray analysis with RT¡VPCR confirmation. The transcripts of key genes involved in olfactory reception, transduction, and transmission were up-regulated in deprived-side olfactory mucosa, with opposite effects in non-deprived-side mucosa, compared to controls. Results support the hypothesis that odor environment triggers a previously unknown homeostatic control mechanism in olfactory receptor neurons designed to maximize information transfer.
   

  ✔本篇論文使用華聯產品:  
 Journal of Experimental Botany. 2013, 64(1):303-15. doi: 10.1093/jxb/ers333.
 Identification and profiling of arsenic stress-induced microRNAs in Brassica juncea
 
 
 Ashish Kumar Srivastava, S.F. D¡¦Souza, Sudhakar Srivastava, Penna Suprasanna
  Abstract
MicroRNAs (miRNAs) constitute a novel mechanism of gene regulation affecting plant development, growth, and stress response. To study the role of miRNAs in arsenic (As) stress, microarray profiling of miRNAs was performed in Brassica juncea using a custom Phalanx Plant OneArray containing 381 unique miRNA probes representing 618 miRNAs from 22 plant species. miRNA microarray hybridization of roots exposed to As for 1 h and 4 h revealed that a total of 69 miRNAs belonging to 18 plant miRNA families had significantly altered expression. The As-responsive miRNAs also exhibited a time- and organ-dependent change in their expression. Putative target prediction for the miRNAs suggested that they regulate various developmental processes (e.g. miR156, miR169, and miR172), sulphur uptake, transport, and assimilation (miR395, miR838, and miR854), and hormonal biosynthesis and/or function (e.g. miR319, miR167, miR164, and miR159). Notable changes were observed in the level of auxins [indole-3-acetic acid (IAA), indole-3- butyric acid, and naphthalene acetic acid], jasmonates [jasmonic acid (JA) and methyl jasmonate], and abscisic acid. The exogenous supply of JA and IAA improved growth of plants under As stress and altered expression of miR167, miR319, and miR854, suggesting interplay of hormones and miRNAs in the regulation of As response. In conclusion, the present work demonstrates the role of miRNAs and associated mechanisms in the plant¡¦s response towards As stress.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 PLOS ONE. 2012, 7(9):e45378. doi: 10.1371/journal.pone.0045378.
 Role of Macrophage CCAAT/Enhancer Binding Protein Delta in the Pathogenesis of Rheumatoid Arthritis in Collagen-Induced Arthritic Mice
 
 
 Ling-Hua Chang, Huei-Sheng Huang, Po-Ting Wu, I-Ming Jou, Min-Hsiung Pan, Wen-Chang Chang, Dennis Ding Hwa Wang, Ju-Ming Wang
  Abstract
BACKGROUND: The up-regulation of CCAAT/enhancer binding protein delta (CEBPD) has frequently been observed in macrophages in age-associated disorders, including rheumatoid arthritis (RA). However, the role of macrophage CEBPD in the pathogenesis of RA is unclear.METHODS: Differentially expressed genes were detected after four hours, one week and twelve weeks of supplementation with either fish oil (FO) or corn oil in normo- and dyslipidemic men using whole genome microarrays.Methodology and Principal Findings: We found that the collagen-induced arthritis (CIA) score and the number of affected paws in Cebpd-/- mice were significantly decreased compared with the wild-type (WT) mice. The histological analysis revealed an attenuated CIA in Cebpd-/- mice, as shown by reduced pannus formation and greater integrity of joint architecture in affected paws of Cebpd-/- mice compared with WT mice. In addition, immunohistochemistry analysis revealed decreased pannus proliferation and angiogenesis in Cebpd-/- mice compared with WT mice. CEBPD activated in macrophages played a functional role in promoting the tube formation of endothelial cells and the migration and proliferation of synoviocytes. In vivo DNA binding assays and reporter assays showed that CEBPD up-regulated CCL20, CXCL1, IL23A and TNFAIP6 transcripts through direct binding to their promoter regions. CCL20, IL23A, CXCL1 and TNFAIP6 contributed to the migration and proliferation of synoviocytes, and the latter two proteins were involved in tube formation of endothelial cells. Finally, two anti-inflammatory chemicals, inotilone and rosmanol, reduced the expression of CEBPD and its downstream targets and mitigated the above phenomena. CONCLUSIONS: Collectively, our findings suggest that CEBPD and its downstream effectors could be biomarkers for the diagnosis of RA and potentially serve as therapeutic targets for RA therapy.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Carcinogenesis. 2012 Nov 26. [Epub ahead of print].
 MicroRNA-320 suppresses the stem cell-like characteristics of prostate cancer cells by down-regulating the Wnt/beta-catenin signaling pathway
 
 
 I-Shan Hsieh, Kung-Chao Chang, Yao-Tsung Tsai, Jhen-Yu Ke, Pei-Jung Lu, Kuen-Haur Lee, Shauh-Der Yeh, Yuh-Ling Chen, Tse-Ming Hong
  Abstract
Prostate cancer (PCa) is a leading cause of mortality and morbidity in men worldwide, and emerging evidence suggests that the CD44(high) prostate cancer initiating cells (TICs) are associated with its poor prognosis. Although microRNAs are frequently dysregulated in human cancers, the influence of microRNAs on PCa malignancy and whether targeting TIC-associated microRNAs inhibit PCa progression remain unclear. Here, we found that miR-320 is significantly downregulated in PCa. Overexpression of miR-320 in PCa cells decreases PCa tumorigenesis in vitro and in vivo. Global gene expression profiling of miR-320-overexpressing PCa cells reveals that downstream target genes of Wnt/£]-catenin pathway and cancer stem cell markers are significantly decreased. MicroRNA-320 inhibits £]-catenin expression by targeting the 3'-untranslated region of £]-catenin mRNA. The reduction of miR-320 associated with increased £]-catenin was also found in CD44(high) sub-population of prostate cancer cells and clinical PCa specimens. Interestingly, knockdown of miR-320 significantly increases the cancer stem-like properties, such as tumorsphere formation, chemoresistance, and tumorigenic abilities, while enriching the population of stem-like TICs among PCa cells. Furthermore, increased miR-320 expression in prostate stem-like TICs significantly suppresses stem cell-like properties of PCa cells. These results support that miR-320 is a key negative regulator in prostate TICs, and suggest developing miR-320 as a novel therapeutic agent may offer benefits for PCa treatment.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Biochemical Pharmacology. 2013, 85(2):234-44. doi: 10.1016/j.bcp.2012.10.026.
 Mesalamine modulates intercellular adhesion through inhibition of p-21 activated kinase-1
 
 
 Vineeta Khare, Alex Lyakhovich, Kyle Dammann, Michaela Lang, Melanie Borgmann, Boris Tichy, Sarka Pospisilova, Gloria Luciani, Christoph Campregher, Rayko Evstatiev, Maren Pflueger, Harald Hundsberger, Christoph Gasche
  Abstract
Mesalamine (5-ASA) is widely used for the treatment of ulcerative colitis, a remitting condition characterized by chronic inflammation of the colon. Knowledge about the molecular and cellular targets of 5-ASA is limited and a clear understanding of its activity in intestinal homeostasis and interference with neoplastic progression is lacking. We sought to identify molecular pathways interfered by 5-ASA, using CRC cell lines with different genetic background. Microarray was performed for gene expression profile of 5-ASA-treated and untreated cells (HCT116 and HT29). Filtering and analysis of data identified three oncogenic pathways interfered by 5-ASA: MAPK/ERK pathway, cell adhesion and b-catenin/Wnt signaling. PAK1 emerged as a consensus target of 5-ASA, orchestrating these pathways. We further investigated the effect of 5-ASA on cell adhesion. 5-ASA increased cell adhesion which was measured by cell adhesion assay and transcellular-resistance measurement. Moreover, 5-ASA treatment restored membranous expression of adhesion molecules E-cadherin and b-catenin. Role of PAK1 as a mediator of mesalamine activity was validated in vitro and in vivo. Inhibition of PAK1 by RNA interference also increased cell adhesion. PAK1 expression was elevated in APCmin polyps and 5-ASA treatment reduced its expression. Our data demonstrates novel pharmacological mechanism of mesalamine in modulation of cell adhesion and role of PAK1 in APCmin polyposis. We propose that inhibition of PAK1 expression by 5-ASA can impede with neoplastic progression in colorectal carcinogenesis. The mechanism of PAK1 inhibition and induction of membranous translocation of adhesion proteins by 5-ASA might be independent of its known anti-inflammatory action.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Onkologie. 2012, 35(11):651-6. doi: 10.1159/000343637.
 Overexpression of MMP-1 and VEGF-C is Associated with a Less Favorable Prognosis in Esophageal Squamous Cell Carcinoma
 
 
 Yi-Sheng Tao, Xin-Yi Ma, Da-Min Chai, Li Ma, Zhen-Zhong Feng, Ze-Nong Cheng, Mao-De Lai
  Abstract
BACKGROUND: This study addresses the association of matrix metalloproteinase-1 (MMP-1) and vascular endothelial growth factor-C (VEGF-C) expression in esophageal squamous cell carcinoma (SCC) with clinicopathologic characteristics in the patients. METHODS: We profiled the expression of MMP-1 and VEGF-C by cDNA microarray in 4 cases and by reverse transcription-polymerase chain reaction (RT-PCR) in 14 cases of esophageal SCC. Another 90 cases were reviewed by immunohistochemical examination of paraffin-embedded sections. RESULTS: Expression of MMP-1 and VEGF-C mRNA in normal esophageal tissue and tumor tissue was compared. Data were fully consistent with the results of RT-PCR. Immunohistochemistry showed that compared to the normal mucosa MMP-1 and VEGF-C protein expression was upregulated in both esophageal atypical hyperplasia (n = 16) and esophageal SCC. Depth of tumor invasion, lymph node metastasis, and clinical stage were directly associated with prognosis in all cases. Furthermore, median overall survival and disease-free survival were significantly shorter in patients with a higher expression of MMP-1 and VEGF-C than in patients with lower expression levels. CONCLUSIONS: We demonstrated that the expression of both MMP-1 and VEGF-C mRNA and protein was upregulated in esophageal SCC tissues. Protein expression was associated with progressive tumor stage and poor prognosis in patients with esophageal SCC.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 BioChip Journal. 2012, 6(3):254-261. doi: 10.1007/s13206-012-6308-z.
 Gene expression profile analysis in cultured human neuronal cells after static magnetic stimulation
 
 
 Wooseok Im, Soon-Tae Lee, Seung Chan Kim
  Abstract
Although the magnetic force has been used in various human environments and medicines, their influence on the nervous system has not been fully elucidated. In this study, we investigated mRNA expressions profiles of neuronal cells after the application of static magnetic fields. Two perpetual magnets were applied to the cultured SH-SY5Y human neuronal cell, and the gene expression profiles were evaluated by using human mRNA microarray targeting 30968 genes. Results showed that the expressions of 827-known genes were altered in response to the magnetic force. Among them, 112 genes showed significant changes (>2-fold changes); 44 genes were up-regulated and 68 genes were down-regulated. Among the upregulated genes, we further confirmed the increased expressions of synapsin III and chloride channel-2 by using RT-PCR and immunocytochemistry. These results suggest that static magnetic fields influence neuronal-and biological-related gene expression profiles in human neuronal cells.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Journal of Natural Products. 2012, 75(10):1706-11. doi: 10.1021/np300250m.
 Dual Inhibition of £^-Oryzanol on Cellular Melanogenesis: Inhibition of Tyrosinase Activity and Reduction of Melanogenic Gene Expression by a Protein Kinase A-Dependent Mechanism
 
 
 Hee-jin Jun, Ji Hae Lee, Bo-Ram Cho, Woo-Duck Seo, Hang-Won Kang, Dong-Woo Kim, Kang-Jin Cho, Sung-Joon Lee
  Abstract
The in vitro effects on melanogenesis of £^-oryzanol (1), a rice bran-derived phytosterol, were investigated. The melanin content in B16F1 cells was significantly and dose-dependently reduced (?13% and ?28% at 3 and 30 £gM, respectively). Tyrosinase enzyme activity was inhibited by 1 both in a cell-free assay and when analyzed based on the measurement of cellular tyrosinase activity. Transcriptome analysis was performed to investigate the biological pathways altered by 1, and it was found that gene expression involving protein kinase A (PKA) signaling was markedly altered. Subsequent analyses revealed that 1 stimulation in B16 cells reduced cytosolic cAMP concentrations, PKA activity (?13% for cAMP levels and ?40% for PKA activity), and phosphorylation of the cAMP-response element binding protein (?57%), which, in turn, downregulated the expression of microphthalmia-associated transcription factor (MITF; ?59% for mRNA and ?64% for protein), a key melanogenic gene transcription factor. Accordingly, tyrosinase-related protein 1 (TRP-1; ?69% for mRNA and ?82% for protein) and dopachrome tautomerase (?51% for mRNA and ?92% for protein) in 1-stimulated B16F1 cells were also downregulated. These results suggest that 1 has dual inhibitory activities for cellular melanogenesis by inhibiting tyrosinase enzyme activity and reducing MITF and target genes in the PKA-dependent pathway.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Clinical Cancer Research. 2012, 18(22):6188-98. doi: 10.1158/1078-0432.CCR-12-1789.
 Overexpression of Ecdysoneless (Ecd) in Pancreatic Cancer and its Role in Oncogenesis by Regulating Glycolysis.
 
 
 Parama Dey, Satyanarayana Rachagani, Subhankar Chakraborty, Pankaj K. Singh, Xiangshan Zhao, Channabasavaiah Basavaraju Gurumurthy, Judy M. Anderson, Subodh Lele, Michael A. Hollingsworth, Vimla Band, and Surinder K. Batra
  Abstract
Immunohistochemical expression profiling of Ecd was done in nonneoplastic normal pancreatic tissues and pancreatic ductal adenocarcinoma lesions (from tissue microarray and Rapid Autopsy program) as well as precancerous PanIN lesions and metastatic organs. To analyze the biological significance of Ecd in pancreatic cancer progression, Ecd was stably knocked down in pancreatic cancer cell line followed by in vitro and in vivo functional assays. Normal pancreatic ducts showed very weak to no Ecd expression compared to significant positive expression in pancreatic cancer tissues (mean ¡Ó SE composite score: 0.3 ¡Ó 0.2 and 3.8 ¡Ó 0.2 respectively, P < 0.0001) as well as in PanIN precursor lesions with a progressive increase in Ecd expression with increasing dysplasia (PanIN-1-PanIN-3). Analysis of matched primary tumors and metastases from patients with pancreatic cancer revealed that Ecd is highly expressed in both primary pancreatic tumor and in distant metastatic sites. Furthermore, knockdown of Ecd suppressed cell proliferation in vitro and tumorigenicity of pancreatic cancer cells in mice orthotopic tumors. Microarray study revealed that Ecd regulates expression of glucose transporter GLUT4 in pancreatic cancer cells and was subsequently shown to modulate glucose uptake, lactate production, and ATP generation by pancreatic cancer cells. Finally, knockdown of Ecd also reduced level of pAkt, key signaling molecule known to regulate aerobic glycolysis in cancer cells. Ecd is a novel tumor-promoting factor that is differentially expressed in pancreatic cancer and potentially regulates glucose metabolism within cancer cells.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Lipids in Health and Disease. 2011, 65(5):339-44. doi: 10.1016/j.biopha.2011.04.013.
 Different gene expression profiles in normo- and dyslipidemic men after fish oil supplementation: results from a randomized controlled trial
 
 
 Simone Schmidt, Frank Stahl, Kai-Oliver Mutz, Thomas Scheper, Andreas Hahn, and Jan Philipp Schuchardt
  Abstract
Epidemiological studies have suggested the benefits of omega-3 polyunsaturated fatty acids (n-3 PUFAs) on cardiovascular health, but only limited data are available describing n-3 PUFA regulated pathways in humans. The aim of this study was to investigate the effects of n-3 PUFA administration on whole genome expression profiles in the blood of normo- and dyslipidemic subjects. Differentially expressed genes were detected after four hours, one week and twelve weeks of supplementation with either fish oil (FO) or corn oil in normo- and dyslipidemic men using whole genome microarrays. Independent of the oil, a significantly higher number of genes was regulated in dyslipidemic subjects compared to normolipidemic subjects. Pathway analyses discovered metabolisms dominantly affected by FO after twelve weeks of supplementation, including the lipid metabolism, immune system and cardiovascular diseases. Several pro-inflammatory genes, in particular, were down-regulated in dyslipidemic subjects, indicating the immune-modulatory and anti-inflammatory capability of FO and its bioactive FAs, eicosapentaenoic acid and docosahexaenoic acid. This is the first study showing significant differences in gene expression profiles between normo- and dyslipidemic men after FO supplementation. Further studies need to clarify the exact role of n-3 PUFAs in pathways and metabolisms which were identified as being regulated after FO supplementation in this study.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Surgery. 2012, 152(4):704-11. doi: 10.1016/j.surg.2012.07.020.
 Restoration of E-cadherin expression in pancreatic ductal adenocarcinoma treated with microRNA-101
 
 
 Aamer M. Qazi, Oksana Gruzdyn, Assaad Semaan, Shelly Seward, Sreedhar Chamala, Vasu Dhulipala, Seema Sethi, Rouba Ali-Fehmi, Philip A. Philip, David L. Bouwman, Donald W. Weaver, Scott A. Gruber, Ramesh B. Batchu
  Abstract
To investigate the possibility of inhibiting the progression of pancreatic ductal adenocarcinoma (PDAC) by facilitating the expression of E-cadherin through the enforced expression of microRNA-101 (miR-101). In situ hybridization was conducted with archival tissue using a double digoxigenin-labeled probe. Chromatin immunoprecipitation (ChIP) assay was conducted with EZ-Magna ChIPTM A. Gene profile analysis, Western blot, and immunoprecipitation assays were performed using standard protocols. We found that decreased miR-101 expression observed in archival patient tissues was significantly associated with poor prognosis indicated by low-intensity staining in high-grade tumors. ChIP assays using anti-enhancer of zeste homolog 2 (EZH2) antibodies indicated not only the interaction of EZH2 to the CDH1 (E-cadherin) promoter, but also that this interaction was significantly diminished in cells transfected with pre-miR-101. We observed a global downregulation of trimethylated lysine 27 of H3 histone (H3K27me3) along with upregulation of the enzymes histone deacetylase -1 and -2 with the re-expression of miR-101. Further, we observed lesser levels of transcriptional factors that inhibit the CDH1 promoter with pre-miR-101 treatment. Western blot analysis confirmed the enhanced E-cadherin expression. PANC-1 cells transduced with pre-miR-101 displayed markedly attenuated growth in SCID mice. These results suggest the potential therapeutic use of miR-101-enforced expression for inhibition of PDAC.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 BMC Cancer. 2012, 12:382. doi: 10.1186/1471-2407-12-382.
 Simultaneous copy number gains of NUPR1 and ERBB2 predicting poor prognosis in early-stage breast cancer
 
 
 Seung-Hyun Jung, Ahwon Lee, Seon-Hee Yim, Hae-Jin Hu, Chungyoul Choi, and Yeun-Jun Chung
  Abstract
The full extent of chromosomal alterations and their biological implications in early breast carcinogenesis has not been well examined. In this study, we aimed to identify chromosomal alterations associated with poor prognosis in early-stage breast cancers (EBC). A total of 145 EBCs (stage I and II) were examined in this study. We analyzed copy number alterations in a discovery set of 48 EBCs using oligoarray-comparative genomic hybridization. In addition, the recurrently altered regions (RARs) associated with poor prognosis were validated using an independent set of 97 EBCs. A total of 23 RARs were defined in the discovery set. Six were commonly detected in both stage I and II groups (> 50%), suggesting their connection with early breast tumorigenesis. There were gains on 1q21.2-q21.3, 8q24.13, 8q24.13-21, 8q24.3, and 8q24.3 and a loss on 8p23.1-p22. Among the 23 RARs, copy number gains on 16p11.2 (NUPR1) and 17q12 (ERBB2) showed a significant association with poor survival (P = 0.0186 and P = 0.0186, respectively). The patients simultaneously positive for both gains had a significantly worse prognosis (P = 0.0001). In the independent replication, the patients who were double-positive for NUPR1-ERBB2 gains also had a significantly poorer prognosis on multivariate analysis (HR = 7.31, 95% CI 2.65-20.15, P = 0.0001). The simultaneous gain of NUPR1 and ERBB2 can be a significant predictor of poor prognosis in EBC. Our study will help to elucidate the molecular mechanisms underlying early-stage breast cancer tumorigenesis. This study also highlights the potential for using combinations of copy number alterations as prognosis predictors for EBC.
   

  ✔本篇論文使用華聯產品:Mouse OneArray,Rat OneArray  
 Inflammation Research. 2012, 61(12):1395-404. doi: 10.1007/s00011-012-0542-7.
 Mammalian target of rapamycin complex 2 regulates inflammatory response to stress
 
 
 Desmond Mascarenhas, Sheri Routt, Baljit K. Singh
  Abstract
To explore the role of mammalian target of rapamycin 2 (mTORC2) in the activation of inflammatory and oxidative responses in rodent models of acute injury and metabolic stress. The impact of nephrilin, an inhibitor of mTORC2 complex, was assessed in three CD-1 mouse models of acute xenobiotic stress and in a hypertensive Dahl rat model of metabolic stress. Animals received daily subcutaneous bolus injections of saline or 4 mg/kg nephrilin. Tissues were assayed by ELISA, gene arrays and immunohistochemical staining.Nephrilin significantly inhibited elevations in plasma tumor necrosis factor-alpha, kidney substance P, and CX3CR1, and urinary lipocalin-2 [urinary neutrophil gelatinase-associated lipocalin (uNGAL)] in models of acute xenobiotic stress. UCHL1 gene expression levels dropped and plasma HMGB1 levels rose in the rhabdomyolysis model. Both effects were reversed by nephrilin. The inhibitor also blocked diet-induced elevations of uNGAL and albumin-creatinine ratio (UACR) as well as kidney tissue phosphorylation of PKC-beta-2-T641 and p66shc-S36, and reduced dark ring-like staining of nuclei by anti-phos-p66shc-S36 antibody in frozen sections of diseased kidneys from hypertensive Dahl rats fed an 8 % NaCl diet for 4 weeks. Taken together, our results suggest a role for mTORC2 in the inflammatory-oxidative responses to stress.
   

  ✔本篇論文使用華聯產品:Yeast OneArray  
 Metabolic Engineering. 2012, 14(6):611-22. doi: 10.1016/j.ymben.2012.07.011.
 Xylose isomerase overexpression along with engineering of the pentose phosphate pathway and evolutionary engineering enable rapid xylose utilization and ethanol production by Saccharomyces cerevisiae
 
 
 Hang Zhou, Jing-sheng Cheng, Benjamin Wang, Gerald R. Fink, Gregory Stephanopoulos
  Abstract
Xylose is the main pentose and second most abundant sugar in lignocellulosic feedstocks. To improve xylose utilization, necessary for the cost-effective bioconversion of lignocellulose, several metabolic engineering approaches have been employed in the yeast Saccharomyces cerevisiae. In this study, we describe the rational metabolic engineering of a S. cerevisiae strain, including overexpression of the Piromyces xylose isomerase gene (XYLA), Pichia stipitis xylulose kinase (XYL3) and genes of the non-oxidative pentose phosphate pathway (PPP). This engineered strain (H131-A3) was used to initialize a three-stage process of evolutionary engineering, through first aerobic and anaerobic sequential batch cultivation followed by growth in a xylose-limited chemostat. The evolved strain H131-A3-ALCS displayed significantly increased anaerobic growth rate (0.203¡Ó0.006 h?1) and xylose consumption rate (1.866 g g?1 h?1) along with high ethanol conversion yield (0.41 g/g). These figures exceed by a significant margin any other performance metrics on xylose utilization and ethanol production by S. cerevisiae reported to-date. Further inverse metabolic engineering based on functional complementation suggested that efficient xylose assimilation is attributed, in part, to the elevated expression level of xylose isomerase, which was accomplished through the multiple-copy integration of XYLA in the chromosome of the evolved strain.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Food Chemistry. 2013, 136(2):426-34. doi: 10.1016/j.foodchem.2012.08.009.
 Toona sinensis and its major bioactive compound gallic acid inhibit LPS-induced inflammation in nuclear factor-£eB transgenic mice as evaluated by in vivo bioluminescence imaging
 
 
 Chien-Yun Hsiang, You-Cheng Hseu, Yi-Chih Chang, K.J. Senthil Kumar, Tin-Yun Ho, Hsin-Ling Yang
  Abstract
In the present study, we investigated the anti-inflammatory effects of a nutritious vegetable Toona sinensis (leaf extracts, TS) and its major bioactive compound gallic acid (GA) by analysing LPS-induced NF-£eB activation in transgenic mice, using bioluminescence imaging. Mice were challenged intraperitoneally with LPS (1 mg/kg) and treated orally with TS or GA (100 or 5 mg/kg, respectively). In vivo and ex vivo imaging showed that LPS increased NF-£eB luminescence in the abdominal region, which was significantly inhibited by TS or GA. Immunohistochemical and ELISA analyses confirmed that TS and GA inhibited LPS-induced NF-£eB, interleukin-1£], and tumour necrosis factor-£ expression. Microarray analysis revealed that biological pathways associated with metabolism and the immune responses were affected by TS or GA. Particularly, LPS-induced thioredoxin-like 4B (TXNL4B) 2 expression in the small intestine, and TXNL4B, iNOS, and COX-2 expression in RAW 264.7 cells were significantly inhibited by TS or GA. Thus, the anti-inflammatory potential of TS was mediated by the downregulation of NF-£eB pathway.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Cardiovascular Research. 2012, 95(4):517-26. doi: 10.1093/cvr/cvs223.
 MicroRNA-195 regulates vascular smooth muscle cell phenotype and prevents neointimal formation
 
 
 Yung-SongWang, Hay-Yan J.Wang, Yi-Chu Liao, Pei-ChienTsai, Ku-ChungChen, Hsin-Yun Cheng, Ruey-Tay Lin, Suh-Hang Hank Juo
  Abstract
Proliferation and migration of vascular smooth muscle cells (VSMCs) can cause atherosclerosis and neointimal formation. MicroRNAs have been shown to regulate cell proliferation and phenotype transformation. We discovered abundant expression of microRNA-195 in VSMCs and conducted a series of studies to identify its function in the cardiovascular system. MicroRNA-195 expression was initially found to be altered when VSMCs were treated with oxidized low-density lipoprotein (oxLDL) in a non-replicated microRNA array experiment. Using cellular studies, we found that microRNA-195 reduced VSMC proliferation, migration, and synthesis of IL-1£], IL-6, and IL-8. Using bioinformatics prediction and experimental studies, we showed that microRNA-195 could repress the expression of Cdc42, CCND1, and FGF1 genes. Using a rat model, we found that the microRNA-195 gene, introduced by adenovirus, substantially reduced neointimal formation in a balloon-injured carotid artery. In situ hybridization confirmed the presence of microRNA-195 in the treated arteries but not in control arteries. Immunohistochemistry experiments showed abundant Cdc42 in the neointima of treated arteries. We showed that microRNA-195 plays a role in the cardiovascular system by inhibiting VSMC proliferation, migration, and proinflammatory biomarkers. MicroRNA-195 may have the potential to reduce neointimal formation in patients receiving stenting or angioplasty.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Food Chemistry. 2013, 136(1):170-7. doi: 10.1016/j.foodchem.2012.07.124.
 Ginger extract and zingerone ameliorated trinitrobenzene sulfonic acid-induced colitis in mice via modulation of nuclear factor-£eB activity and interleukin-1£] signaling pathway
 
 
 Chien-Yun Hsiang, Hsin-Yi Lo, Hui-Chi Huang, Chia-Cheng Li, Shih-Lu Wu, Tin-Yun Ho
  Abstract
Ginger is a commonly used spice with anti-inflammatory potential. Colitis is the common pathological lesion of inflammatory bowel diseases. In this study, we investigated the therapeutic effects of ginger and its component zingerone in mice with 2,4,6-trinitrobenzene sulphonic acid (TNBS)-induced colitis. Ginger and zingerone ameliorated TNBS-induced colonic injury in a dose-dependent manner. Pathway analysis of ginger- and zingerone-regulated gene expression profiles showed that ginger and zingerone significantly regulated cytokine-related pathways. Network analysis showed that nuclear factor-£eB (NF-£eB) and interleukin-1£] (IL-1£]) were key molecules involved in the expression of ginger- and zingerone-affected genes. Ex vivo imaging and immunohistochemical staining further verified that ginger and zingerone suppressed TNBS-induced NF-£eB activation and IL-1£] protein level in the colon. In conclusion, ginger improved TNBS-induced colitis via modulation of NF-£eB activity and IL-1£] signalling pathway. Moreover, zingerone might be the active component of ginger responsible for the amelioration of colitis induced by TNBS.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Virology Journal. 2012, 9:159. doi: 10.1186/1743-422X-9-159.
 Infection with street strain rabies virus induces modulation of the microRNA profile of the mouse brain
 
 
 Pingsen Zhao, Lili Zhao, Kun Zhang, Hao Feng, Hualei Wang, Tiecheng Wang, Tao Xu, Na Feng, Chengyu Wang, Yuwei Gao, Geng Huang, Chuan Qin, Songtao Yang, Xianzhu Xia
  Abstract
Rabies virus (RABV) causes a fatal infection of the central nervous systems (CNS) of warm-blooded animals. Once the clinical symptoms develop, rabies is almost invariably fatal. The mechanism of RABV pathogenesis remains poorly understood. Recent studies have shown that microRNA (miRNA) plays an important role in the pathogenesis of viral infections. Our recent findings have revealed that infection with laboratory-fixed rabies virus strain can induce modulation of the microRNA profile of mouse brains. However, no previous report has evaluated the miRNA expression profile of mouse brains infected with RABV street strain. The results of microarray analysis show that miRNA expression becomes modulated in the brains of mice infected with street RABV. Quantitative real-time PCR assay of the differentially expressed miRNAs confirmed the results of microarray assay. Functional analysis showed the differentially expressed miRNAs to be involved in many immune-related signaling pathways, such as the Jak-STAT signaling pathway, the MAPK signaling pathway, cytokine-cytokine receptor interactions, and Fc gamma R-mediated phagocytosis. The predicted expression levels of the target genes of these modulated miRNAs were found to be correlated with gene expression as measured by DNA microarray and qRT-PCR. RABV causes significant changes in the miRNA expression profiles of infected mouse brains. Predicted target genes of the differentially expression miRNAs are associated with host immune response, which may provide important information for investigation of RABV pathogenesis and therapeutic method.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Environmental Toxicology. 2012 Jul 30. DOI: 10.1002/tox.21795.
 Modulation of microRNA expression by volatile organic compounds in mouse lung
 
 
 Fan Wang, Chonglei Li, Wei Liu, Yihe Jin
  Abstract
Volatile organic compounds (VOCs) are one of main pollutants indoors. Exposure to VOCs is associated with cancer, asthma disease, and multiple chemical allergies. Despite the adverse health effects of VOCs, the molecular mechanisms underlying VOCs-induced disease remain largely unknown. MicroRNAs (miRNAs), as key post-transcriptional regulators of gene expression, may influence cellular disease state. To investigate whether lung miRNA expression profiles in mice are modified by VOCs mixture exposure, 44 male Kunming mice were exposed in 4 similar static chambers, 0 (control) and 3 different doses of VOCs mixture (groups 1¡V3). The concentrations of VOCs mixture were as follows: formaldehyde, benzene, toluene, and xylene 3.0 + 3.3 + 6.0 + 6.0 mg/m3, 5.0 + 5.5 + 10.0 + 10.0 mg/m3, 10.0 + 11.0 + 20.0 + 20.0 mg/m3, respectively, which corresponded to 30, 50, and 100 times of indoor air quality standard in China, after exposure to 2 weeks (2 h/day, 5 days/week). Small RNAs in lung and protein isolated from bronchoalveolar lavage fluid (BALF) were collected and analyzed for miRNA expression using microarray analysis and for interleukin-8 (IL-8) protein levels by enzyme-linked immunosorbent assay, respectively. VOCs exposure altered the miRNA expression profiles in lung in mice. Specifically, 69 miRNAs were significantly differentially expressed in VOCs-exposed samples versus controls. Functional annotation analysis of the predicted miRNA transcript targets revealed that VOCs exposure potentially alters signaling pathways associated with cancer, chemokine signaling, Wnt signaling, neuroactive ligand-receptor interaction, and cell adhesion molecules. IL-8 isolated from BALF and nitric oxide synthase of lung increased significantly, whereas GSH of lung decreased significantly in mice exposed to VOCs. These results indicate that inhalation of VOCs alters miRNA patterns that regulate gene expression, potentially leading to the initiation of cancer and inflammatory diseases.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 BMC Systems Biology. 2012, 6:105. doi: 10.1186/1752-0509-6-105.
 Chemoattraction of macrophages by secretory molecules derived from cells expressing the signal peptide of eosinophil cationic protein
 
 
 Yu-Shu Liu, Pei-Wen Tsai, Yong Wang, Tan-chi Fan, Chia-Hung Hsieh, Margaret Dah-Tsyr Chang, Tun-Wen Pai, Chien-Fu Huang, Chung-Yu Lan, Hao-Teng Chang
  Abstract
Eosinophil cationic protein is a clinical asthma biomarker that would be released into blood, especially gathered in bronchia. The signal peptide of eosinophil cationic protein (ECPsp) plays an important role in translocating ECP to the extracellular space. We previously reported that ECPsp inhibits microbial growth and regulates the expression of mammalian genes encoding tumor growth factor-£ (TGF-£) and epidermal growth factor receptor (EGFR). In the present study, we first generated a DNA microarray dataset, which showed that ECPsp upregulated proinflammatory molecules, including chemokines, interferon-induced molecules, and Toll-like receptors. The levels of mRNAs encoding CCL5, CXCL10, CXCL11, CXCL16, STAT1, and STAT2 were increased in the presence of ECPsp by 2.07-, 4.21-, 7.52-, 2.6-, 3.58-, and 1.67-fold, respectively. We then constructed a functional linkage network by integrating the microarray dataset with the pathway database of Kyoto Encyclopedia of Genes and Genomes (KEGG). Follow-up analysis revealed that STAT1 and STAT2, important transcriptional factors that regulate cytokine expression and release, served as hubs to connect the pathways of cytokine stimulation (TGF-£ and EGFR pathways) and inflammatory responses. Furthermore, integrating TGF-£ and EGFR with the functional linkage network indicated that STAT1 and STAT2 served as hubs that connect two functional clusters, including (1) cell proliferation and survival, and (2) inflammation. Finally, we found that conditioned medium in which cells that express ECPsp had been cultured could chemoattract macrophages. Experimentally, we also demonstrated that the migration of macrophage could be inhibited by the individual treatment of siRNAs of STAT1 or STAT2. Therefore, we hypothesize that ECPsp may function as a regulator for enhancing the migration of macrophages through the upregualtion of the transcriptional factors STAT1 and STAT2. The increased expression and release of various cytokines triggered by ECPsp may attract macrophages to bronchia to purge damaged cells. Our approach, involving experimental and computational systems biology, predicts pathways and potential biological functions for further characterization of this novel function of ECPsp under inflammatory conditions.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Journal of Biomedical Science. 2012, 19:69. doi: 10.1186/1423-0127-19-69.
 Whole blood-derived microRNA signatures in mice exposed to lipopolysaccharides
 
 
 Ching-Hua Hsieh, Cheng-Shyuan Rau, Jonathan Chris Jeng, Yi-Chun Chen, Tsu-Hsiang Lu, Chia-Jung Wu, Yi-Chan Wu, Siou-Ling Tzeng, Johnson Chia-Shen Yang
  Abstract
Lipopolysaccharide (LPS) is recognized as the most potent microbial mediator presaging the threat of invasion of Gram-negative bacteria that implicated in the pathogenesis of sepsis and septic shock. This study was designed to examine the microRNA (miRNA) expression in whole blood from mice injected with intraperitoneal LPS. C57BL/6 mice received intraperitoneal injections of varying concentrations (range, 10¡V1000 £gg) of LPS from different bacteria, including Escherichia coli, Klebsiella pneumonia, Pseudomonas aeruginosa, Salmonella enterica, and Serratia marcescens and were killed 2, 6, 24, and 72 h after LPS injection. Whole blood samples were obtained and tissues, including lung, brain, liver, and spleen, were harvested for miRNA expression analysis using an miRNA array (Phalanx miRNA OneArrayR 1.0). Upregulated expression of miRNA targets in the whole blood of C57BL/6 and Tlr4?/? mice injected with LPS was quantified using real-time RT-PCR and compared with that in the whole blood of C57BL/6 mice injected with lipoteichoic acid (LTA) from Staphylococcus aureus. Following LPS injection, a significant increase of 15 miRNAs was observed in the whole blood. Among them, only 3 miRNAs showed up-regulated expression in the lung, but no miRNAs showed a high expression level in the other examined tissues. Upregulated expression of the miRNA targets (let-7d, miR-15b, miR-16, miR-25, miR-92a, miR-103, miR-107 and miR-451) following LPS injection on real-time RT-PCR was dose- and time-dependent. miRNA induction occurred after 2 h and persisted for at least 6 h. Exposure to LPS from different bacteria did not induce significantly different expression of these miRNA targets. Additionally, significantly lower expression levels of let-7d, miR-25, miR-92a, miR-103, and miR-107 were observed in whole blood of Tlr4?/? mice. In contrast, LTA exposure induced moderate expression of miR-451 but not of the other 7 miRNA targets. We identified a specific whole blood¡Vderived miRNA signature in mice exposed to LPS, but not to LTA, from different gram-negative bacteria. These whole blood-derived miRNAs are promising as biomarkers for LPS exposure.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 The Tohoku Journal of Experimental Medicine. 2012, 226(4):301-11.
 Identification of Distinct Gene Expression Profiles between Esophageal Squamous Cell Carcinoma and Adjacent Normal Epithelial Tissues
 
 
 Yisheng Tao, Damin Chai , Li Ma, Ting Zhang, Zhenzhong Feng, Zenong Cheng, Shiwu Wu, Yanzi Qin, Maode Lai
  Abstract
Esophageal squamous cell carcinoma (ESCC) is a predominant type of esophageal cancer, which is a malignant tumor originating from the esophageal mucosa or gland and is aggressive with poor prognosis. Identification of new gene expression patterns would be helpful for providing new targets for the early detection and treatment of ESCC patients. In the present study, we employed cDNA array technology to compare gene expression profiles between ESCC tissues and adjacent normal epithelial tissues from ESCC patients. There was at least a 4-fold change in the expression levels of 72 genes that were significantly increased and 107 genes that were decreased in ESCC compared with normal esophageal epithelium. Among them, genes known to be involved in ESCC were found, including matrix metalloproteinases, transcription factors SOX-4 and SOX-17, the Wingless-type MMTV integration site family member 2, and cell cycle regulators. Moreover, we have newly identified the two genes that are down-regulated in ESCC: monoamine oxidase A, an enzyme that catalyzes monoamines oxidation and 15-hydroxyprostaglandin dehydrogenase [NAD+], a prostaglandin-synthesizing enzyme that physiologically antagonizes COX-2. Likewise, we found the three genes that are up-regulated in ESCC: CD7, a cell surface glycoprotein member of the immunoglobulin superfamily, LIM-domain kinase 1, a small subfamily with an unique combination of two N-terminal LIM motifs and a C-terminal protein kinase domain, and TTK protein kinase, a previously unidentified member of the kinase family. These newly identified genes may be involved in the progression of the tumor and/or represent properties specific to ESCC.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Experimental Hematology. 2012, 40(11):899-905.e5. doi: 10.1016/j.exphem.2012.06.011.
 Gene Expression Profiling of Acute Graft-Versus-Host Disease after Hematopoietic Stem Cell Transplantation
 
 
 Jan Verner, Jitka Kabathova, Alexandra Tomancova, Sarka Pavlova, Boris Tichy, Marek Mraz, Yvona Brychtova, Marta Krejci, Zbynek Zdrahal, Martin Trbusek, Jana Volejnikova, Petr Sedlacek, Michael Doubek, Jiri Mayer, Sarka Pospisilova
  Abstract
Acute graft-vs-host disease (aGVHD) is a frequent, life-threatening complication after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Despite that, there are no reliable molecular markers reflecting the onset or clinical course of aGVHD. We performed a pilot study on gene expression profiling in peripheral blood mononuclear cells taken from 15 patients with hematological malignancies who underwent allo-HSCT and developed aGVHD. Based on survival rates after aGVHD, patients were divided into two groups-favorable (all patients alive; median follow-up 40 months) vs unfavorable group (all patients died; median survival 2 months). Two-hundred and eighty genes differentially expressed between these two groups were identified; among them, genes responsible for cytokine signaling, inflammatory response, and regulation of cell cycle were over-represented; interleukin-8, G0S2, ANXA3, and NR4A2 were upregulated in the unfavorable group, CDKN1C was downregulated in the same group. Interestingly, the same genes were also described as overexpressed in connection with autoimmune diseases. This indicates an involvement of similar immune regulatory pathways also in aGVHD. Our data support use of gene expression profiling at aGVHD onset for a prediction of its outcomes.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Food and Chemical Toxicology. 2012, 50(9):2978-86. doi: 10.1016/j.fct.2012.05.054.
 Genipin inhibits lipopolysaccharide-induced acute systemic inflammation in mice as evidenced by nuclear factor-£eB bioluminescent imaging-guided transcriptomic analysis
 
 
 Chia-Cheng Li, Chien-Yun Hsiang, Hsin-Yi Lo, Fu-Tzu Pai, Shih-Lu Wu, Tin-Yun Ho
  Abstract
Genipin is a natural blue colorant in food industry. Inflammation is correlated with human disorders, and nuclear factor-£eB (NF-£eB) is the critical molecule involved in inflammation. In this study, the anti-inflammatory effect of genipin on the lipopolysaccharide (LPS)-induced acute systemic inflammation in mice was evaluated by NF-£eB bioluminescence-guided transcriptomic analysis. Transgenic mice carrying the NF-£eB-driven luciferase genes were administered intraperitoneally with LPS and various amounts of genipin. Bioluminescent imaging showed that genipin significantly suppressed LPS-induced NF-£eB-dependent luminescence in vivo. The suppression of LPS-induced acute inflammation by genipin was further evidenced by the reductions of cytokine levels in sera and organs. Microarray analysis of these organs showed that the transcripts of 79 genes were differentially expressed in both LPS and LPS/genipin groups, and one third of these genes belonged to chemokine ligand, chemokine receptor, and interferon (IFN)-induced protein genes. Moreover, network analysis showed that NF-£eB played a critical role in the regulation of genipin-affected gene expression. In conclusion, we newly identified that genipin exhibited anti-inflammatory effects in a model of LPS-induced acute systemic inflammation via downregulation of chemokine ligand, chemokine receptor, and IFN-induced protein productions.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Mol Nutr Food Res. 2012, 56(6):878-88. doi: 10.1002/mnfr.201100798.
 The natural carotenoid astaxanthin, a PPAR-£ agonist and PPAR-£^ antagonist, reduces hepatic lipid accumulation by rewiring the transcriptome in lipid-loaded hepatocytes
 
 
 Yaoyao Jia, Jin-Young Kim, Hee-Jin Jun, Sun-Joong Kim, Ji-Hae Lee, Minh Hien Hoang, Kwang-Yeon Hwang, Soo-Jong Um, Hyo Ihl Chang, Sung-Joon Lee
  Abstract
A natural carotenoid abundant in seafood, astaxanthin (AX), has hypolipidemic activity, but its underlying mechanisms of action and protein targets are unknown. We investigated the molecular mechanism of action of AX in hepatic hyperlipidemia by measuring peroxisome proliferator-activated receptors (PPAR) activity. We examined the binding of AX to PPAR subtypes and its effects on hepatic lipid metabolism. AX binding activated PPAR-£, but inhibited PPAR-£^ transactivation activity in reporter gene assay and time-resolved fluorescence energy transfer analyses. AX had no effect on PPAR£_/£] transactivation. AX bound directly to PPAR-£ and PPAR-£^ with moderate affinity, as assessed by surface plasmon resonance experiments. The differential effects of AX on PPARs were confirmed by measuring the expression of unique responsive genes for each PPAR subtype. AX significantly reduced cellular lipid accumulation in lipid-loaded hepatocytes. Transcriptome analysis revealed that the net effects of stimulation with AX (100 £gM) on lipid metabolic pathways were similar to those elicited by fenofibrate and lovastatin (10 £gM each), with AX rewiring the expression of genes involved in lipid metabolic pathways. AX is a PPAR-£ agonist and PPAR-£^ antagonist, reduces hepatic lipid accumulation by rewiring the transcriptome in lipid-loaded hepatocytes.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Environmental Science & Technology. 2012, 46(12):6822-9. doi: 10.1021/es3008547.
 Prenatal and Neonatal Exposure to Perfluorooctane Sulfonic Acid Results in Changes in miRNA Expression Profiles and Synapse Associated Proteins in Developing Rat Brains
 
 
 Faqi Wang, Wei Liu, Junsheng Ma, Mingxi Yu, Jiayin Dai, Yihe Jin
  Abstract
We previously identified a number of perfluorooctane sulfonic acid (PFOS)-responsive transcripts in developing rat brains using microarray analysis. However, the underlying mechanisms and functional consequences remain unclear. We hypothesized that microRNAs (miRNAs), which have emerged as powerful negative regulators of mRNA and protein levels, might be responsible for PFOS-induced mRNA changes and consequent neural dysfunctions. We used eight miRNA arrays to profile the expression of brain miRNAs in neonatal rats on postnatal days (PND) 1 and 7 with maternal treatment of 0 (Control) and 3.2 mg/kg of PFOS feed from gestational day 1 to PND 7, and subsequently examined six potentially altered synapse-associated proteins to evaluate presumptive PFOS-responsive functions. Twenty-four brain miRNAs on PND 1 and 17 on PND 7 were significantly altered with PFOS exposure (P < 0.05), with miR-466b, -672, and -297, which are critical in neurodevelopment and synapse transmission, showing a more than 5-fold reduction. Levels of three synapse-involved proteins, NGFR, TrkC, and VGLUT2, were significantly decreased with no protein up-regulated on PND 1 or 7. Perfluorooctane sulfonic acid might affect calcium actions during synapse transmission in the nervous system by interfering with SYNJ1, ITPR1, and CALM1 via their targeting miRNAs. Our results indicated that miRNA had little direct regulatory effect on the expression of mRNAs and synapse-associated proteins tested in the developing rat brain exposed to PFOS, and it seems that the PFOS-induced synaptic dysfunctions and changes in transcripts resulted from a combinatory action of biological controllers and processes, rather than directed by one single factor.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 GENES & DEVELOPMENT. 2012, 26(12):1364-75. doi: 10.1101/gad.186056.111.
 The histone H3 Lys 27 demethylase JMJD3 regulates gene expression by impacting transcriptional elongation
 
 
 Shuzhen Chen, Jian Ma, Feizhen Wu, Li-jun Xiong, Honghui Ma, Wenqi Xu, Ruitu Lv, Xiaodong Li, Judit Villen, Steven P. Gygi, Xiaole Shirley Liu, Yang Shi
  Abstract
The histone H3 Lys 27 (H3K27) demethylase JMJD3 has been shown to play important roles in transcriptional regulation and cell differentiation. However, the mechanism underlying JMJD3-mediated transcriptional regulation remains incompletely understood. Here we show that JMJD3 is associated with KIAA1718, whose substrates include dimethylated H3K27 (H3K27me2), and proteins involved in transcriptional elongation. JMJD3 and KIAA1718 directly bind to and regulate the expression of a plethora of common target genes in both a demethylase activity-dependent and -independent manner in the human promyelocytic leukemia cell line HL-60. We found that JMJD3 and KIAA1718 collaborate to demethylate trimethylated H3K27 (H3K27me3) on a subset of their target genes, some of which are bivalently marked by H3K4me3 and H3K27me3 and associated with promoter-proximal, paused RNA polymerase II (Pol II) before activation. Reduction of either JMJD3 or KIAA1718 diminishes Pol II traveling along the gene bodies of the affected genes while having no effect on the promoter-proximal Pol II. Furthermore, JMJD3 and KIAA1718 also play a role in localizing elongation factors SPT6 and SPT16 to the target genes. Our results support the model whereby JMJD3 activates bivalent gene transcription by demethylating H3K27me3 and promoting transcriptional elongation. Taken together, these findings provide new insight into the mechanisms by which JMJD3 regulates gene expression.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Nutrition & Metabolism. 2012, 9(1):45. doi: 10.1186/1743-7075-9-45.
 Transcriptome-based identification of antioxidative gene expression after fish oil supplementation in normo- and dyslipidemic men
 
 
 Simone Schmidt, Frank Stahl, Kai-Oliver Mutz, Thomas Scheper, Andreas Hahn, Jan Philipp Schuchardt
  Abstract
The beneficial effects of omega-3 polyunsaturated fatty acids (n-3 PUFAs), especially in dyslipidemic subjects with a high risk of cardiovascular disease, are widely described in the literature. A lot of effects of n-3 PUFAs and their oxidized metabolites are triggered by regulating the expression of genes. Currently, it is uncertain if the administration of n-3 PUFAs results in different expression changes of genes related to antioxidative mechanisms in normo- and dyslipidemic subjects, which may partly explain their cardioprotective effects. The aim of this study was to investigate the effects of n-3 PUFA supplementation on expression changes of genes involved in oxidative processes. Ten normo- and ten dyslipidemic men were supplemented for twelve weeks with fish oil capsules, providing 1.14?g docosahexaenoic acid and 1.56?g eicosapentaenoic acid. Gene expression levels were determined by whole genome microarray analysis and quantitative real-time polymerase chain reaction (qRT-PCR). Using microarrays, we discovered an increased expression of antioxidative enzymes and a decreased expression of pro-oxidative and tissue enzymes, such as cytochrome P450 enzymes and matrix metalloproteinases, in both normo- and dyslipidemic men. An up-regulation of catalase and heme oxigenase 2 in both normo- and dyslipidemic subjects and an up-regulation of cytochrome P450 enzyme 1A2 only in dyslipidemic subjects could be observed by qRT-PCR analysis. Supplementation of normo- and dyslipidemic subjects with n-3 PUFAs changed the expression of genes related to oxidative processes, which may suggest antioxidative and potential cardioprotective effects of n-3 PUFAs. Further studies combining genetic and metabolic endpoints are needed to verify the regulative effects of n-3 PUFAs in antioxidative gene expression to better understand their beneficial effects in health and disease prevention.
   

  ✔本篇論文使用華聯產品:Experimental Accessories  
 BMC Microbiology. 2012, 12:87. doi: 10.1186/1471-2180-12-87.
 Gene expression profiling of Mycobacterium avium subsp. paratuberculosis in simulated multi-stress conditions and within THP-1 cells reveals a new kind of interactive intramacrophage behaviour
 
 
 Leonardo A Sechi, Stefania Zanetti, Valentina Rosu, Andrea Cossu
  Abstract
Recent studies have identified in Mycobacterium avium subsp. paratuberculosis (MAP), already known as a pathogen in ruminants, a potential zoonotic agent of some autoimmune diseases in humans. Therefore, considering the possible risk for public health, it is necessary a thorough understanding of MAP's gene expression during infection of human host as well as the identification of its immunogenic and/or virulence factors for the development of appropriate diagnostic and therapeutic tools. In order to characterize MAP's transcriptome during macrophage infection, we analyzed for the first time the whole gene expression of a human derived strain of MAP in simulated intraphagosomal conditions and after intracellular infection of the human macrophage cell line THP-1 by using the DNA-microarray technology. Results showed that MAP shifts its transcriptome to an adaptive metabolism for an anoxic environment and nutrient starvation. It up-regulates several response factors to oxidative stress or intracellular conditions and allows, in terms of transcription, a passive surface peptidoglycan spoliation within the macrophage along with an intensification of the anabolic activity for lipidic membrane structures. These results indicate a possible interactive system between MAP and its host cell based on the internal mimicry unlike other intracellular pathogens, bringing new hypothesis in the virulence and pathogenicity of MAP and its importance in human health.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 PLoS ONE. 2012, 7(6):e38659. doi: 10.1371/journal.pone.0038659.
 An Artificial miRNA against HPSE Suppresses Melanoma Invasion Properties, Correlating with a Down-Regulation of Chemokines and MAPK Phosphorylation
 
 
 Xiaoyan Liu, Hongchao Chen, Xiaoling Jiang, Deren Fang, Yan Wang, Dingxian Zhu, Hong Fang
  Abstract
Ribonucleic acid interference (RNAi) based on microRNA (miRNA) context may provide an efficient and safe therapeutic knockdown effect and can be driven by ribonucleic acid polymerase II (RNAP II). In this study, we designed and synthesized miR155-based artificial miRNAs against heparanase (HPSE) constructed with BLOCK-iT? Pol II miR RNAi Expression Vector Kit. The expression levels of HPSE declined significantly in both the mRNA and protein levels in HPSE-miRNA transfected melanoma cells that exhibited reduction of adhesion, migration, and invasion ability in vitro and in vivo. We also observed that HPSE miRNA could inhibit the expressions of chemokines of interleukin-8 (IL8) and chemokine (C-X-C motif) ligand 1 (CXCL1), at both the transcriptional and translational levels. Further study on its probable mechanism declared that down-regulation of IL8 and CXCL1 by HPSE-miRNA may be correlated with reduced growth-factor simulated mitogen-activated kinase (MAPK) phosphorylation including p38 MAPK, c-Jun N-terminal kinase (JNK) and extracellular-signal-regulated kinase (ERK) 1 and 2, which could be rescued by miRNA incompatible mutated HPSE cDNA. In conclusion, we demonstrated that artificial miRNAs against HPSE might serve as an alterative mean of therapy to low HPSE expression and to block the adhesion, invasion, and metastasis of melanoma cells. Furthermore, miRNA-based RNAi was also a powerful tool for gene function study.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Leukemia & Lymphoma. 2012, 53(11):2269-78. doi: 10.3109/10428194.2012.691481.
 Establishment and Characterization of Therapy-Resistant Mantle Cell lymphoma Cell Lines Derived from Different Tissue Sites
 
 
 Adam K. Ahrens, Nagendra K. Chaturvedi, Tara M. Nordgren, Bhavana J. Dave, Shantaram S. Joshi
  Abstract
Mantle cell lymphoma (MCL) is a rare but aggressive form of B cell non-Hodgkin lymphoma in which therapy resistance is common. New therapeutic options have extended survival in refractory MCL but have not provided durable remission. Tools are needed to assess the molecular and genetic changes associated with therapy resistance. Therefore, therapy-resistant MCL cell lines were established from the liver, kidney and lungs of human Granta 519-bearing NOD-SCID (non-obese diabetic-severe combined immunodeficiency) mice following treatment with CHOP (cyclophosphamide, doxorubicin, vincristine, prednisone) chemotherapy in combination with bortezomib. The cytomorphologies, immunophenotypes, growth patterns in semi-solid agar, cytogenetic profiles and gene expression differences between these cell lines were characterized to identify major changes associated with therapy resistance. Therapy-resistant cell lines exhibit more aggressive growth patterns and markedly different gene expression profiles compared to parental Granta 519 cells. Thus, these stable therapy-resistant cell lines are useful models to further study the molecular basis of drug resistance and to identify clinically relevant molecular targets in MCL.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Circulation Research. 2012, 111(2):180-90. doi: 10.1161/CIRCRESAHA.112.270462.
 Enhanced Angiogenic and Cardiomyocyte Differentiation Capacity of Epigenetically Reprogrammed Mouse and Human Endothelial Progenitor Cells Augments Their Efficacy for Ischemic Myocardial Repair
 
 
 Melissa A. Thal, Prasanna Krishnamurthy, Alexander R. Mackie, Eneda Hoxha, Erin Lambers, Suresh Verma, Veronica Ramirez, Gangjian Qin, Douglas W. Losordo, Raj Kishore
  Abstract
Although bone marrow endothelial progenitor cell (EPC)-based therapies improve the symptoms in patients with ischemic heart disease, their limited plasticity and decreased function in patients with existing heart disease limit the full benefit of EPC therapy for cardiac regenerative medicine. We hypothesized that reprogramming mouse or human EPCs, or both, using small molecules targeting key epigenetic repressive marks would lead to a global increase in active gene transcription, induce their cardiomyogenic potential, and enhance their inherent angiogenic potential. Mouse Lin-Sca1(+)CD31(+) EPCs and human CD34(+) cells were treated with inhibitors of DNA methyltransferases (5-Azacytidine), histone deacetylases (valproic acid), and G9a histone dimethyltransferase. A 48-hour treatment led to global increase in active transcriptome, including the reactivation of pluripotency-associated and cardiomyocyte-specific mRNA expression, whereas endothelial cell-specific genes were significantly upregulated. When cultured under appropriate differentiation conditions, reprogrammed EPCs showed efficient differentiation into cardiomyocytes. Treatment with epigenetic-modifying agents show marked increase in histone acetylation on cardiomyocyte and pluripotent cell-specific gene promoters. Intramyocardial transplantation of reprogrammed mouse and human EPCs in an acute myocardial infarction mouse model showed significant improvement in ventricular functions, which was histologically supported by their de novo cardiomyocyte differentiation and increased capillary density and reduced fibrosis. Importantly, cell transplantation was safe and did not form teratomas. Taken together, our results suggest that epigenetically reprogrammed EPCs display a safe, more plastic phenotype and improve postinfarct cardiac repair by both neocardiomyogenesis and neovascularization.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Vascular and Endovascular Surgery. 2012, 46(4):300-9. doi: 10.1177/1538574412443315.
 Gene Expression Profiling in Acute Stanford Type B Aortic Dissection
 
 
 Lixin Wang, Lei Yao, Daqiao Guo, Chunsheng Wang, Bo Wan, Guoqing Ji, Cheng Yang, Jing Zhang, Zaozhuo Sheng, Weiguo Fu, Yuqi Wang
  Abstract
To compare the gene expression profiles of the aorta specimens between patients with Stanford type B aortic dissection (AD) and controls. Samples of descending aorta were collected from patients with type B AD (n = 12) and from multiorgan donors as controls (n = 12). Phalanx whole genome microarray was used to analyze differential gene expression. Of the 6375 probes validated, 623 genes were found to be differentially expressed between patients with type B AD and controls (fold change ?2). Gene ontology analysis identified significantly enriched gene groups pertaining to cell-cell adhesion, extracellular matrix, cell-matrix adhesion, cytoskeleton, immune and inflammatory response, and apoptosis. Genes encoding components related to integrity and strength of the aortic wall were downregulated, whereas those related to inflammatory response were upregulated in type B AD. The altered patterns of gene expression indicate preexisting structural defects that are probably a consequence of insufficient remodeling of the aortic wall.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Mol Cell Toxicol. 2012, 8(1):9-18.
 Genome-wide microarray investigation of molecular targets and signaling networks in response to high-LET neutron in in vivo-mimic spheroid of human carcinoma
 
 
 Jee Young Kwon, Jung Min Kim, Young Hoon Ji, Young Rok Seo
  Abstract
Although conventional clinical treatment with low LET (linear energy transfer) including gamma-ray and X-ray has been widely used for radiotherapy in various cancers, however, ineffective outcomes occur due to radioresistance caused by p53 mutation. High LET has become alternative since it is able to induce apoptosis regardless of p53 status. Indeed, the molecular mechanisms toward high LET have been suggested. Nevertheless, most studies have been done in monolayer culture system which cannot promptly represent solid tumor microenvironment. Here we applied in vivo mimic 3D spheroid to conduct microarray-based genomic expression and molecular signaling pathway analyses under neutron irradiation. As a result, 3D spheroid system was achieved using thermorevesible gel system. An effective apoptosis-inducible dose of neutron was determined by Acridine Orange (AO) staining in 3D spheroid. Differentially expressed genes in both unique and common responses to neutron were identified in the 3D spheroid compared to the monolayer cells. Total 95 and 169 genes were notably altered at transcription level toward neutron in monolayer and 3D spheroid system, respectively. Based on microarray data, putative apoptosis signaling was depicted using Pathway Studio software. In 3D-in vivo mimic model, the molecular networks interacted with ITGB1, MAP4K4, PAPPA, and SGK1 might be suggested as plausible molecular pathways. In conclusion, we demonstrate novel molecular signaling and corresponding targets of in vitro solid tumor following high LET exposure. This result might provide critical clues for clarification of neutron-induced apoptosis mechanism.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 PLoS ONE. 2012, 7(3):e31127. doi: 10.1371/journal.pone.0031127.
 ROR1 Is Expressed in Human Breast Cancer and Associated with Enhanced Tumor-Cell Growth
 
 
 Suping Zhang, Liguang Chen, Bing Cui, Han-Yu Chuang, Jianqiang Yu, Jessica Wang-Rodriguez, Li Tang, George Chen, Grzegorz W. Basak, Thomas J. Kipps
  Abstract
Receptor-tyrosine-kinase-like orphan receptor 1 (ROR1) is expressed during embryogenesis and by certain leukemias, but not by normal adult tissues. Here we show that the neoplastic cells of many human breast cancers express the ROR1 protein and high-level expression of ROR1 in breast adenocarcinoma was associated with aggressive disease. Silencing expression of ROR1 in human breast cancer cell lines found to express this protein impaired their growth in vitro and also in immune-deficient mice. We found that ROR1 could interact with casein kinase 1 epsilon (CK1£`) to activate phosphoinositide 3-kinase-mediated AKT phosphorylation and cAMP-response-element-binding protein (CREB), which was associated with enhanced tumor-cell growth. Wnt5a, a ligand of ROR1, could induce ROR1-dependent signaling and enhance cell growth. This study demonstrates that ROR1 is expressed in human breast cancers and has biological and clinical significance, indicating that it may be a potential target for breast cancer therapy.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Journal of Cellular Physiology. 2012, 227(12):3820-7. doi: 10.1002/jcp.24093.
 MED28 Regulates MEK1-dependent Cellular Migration in Human Breast Cancer Cells
 
 
 Chun-Yin Huang, Yu-Hsuan Chou, Nien-Tsu Hsieh, Hsin-Hung Chen, Ming-Fen Lee
  Abstract
MED28, a mammalian Mediator subunit, exhibits several cellular roles, including a merlin, Grb2, and cytoskeleton-associated protein (magicin), a repressor of smooth muscle cell differentiation, and an endothelial-derived gene (EG-1). Overexpression of MED28 may stimulate cell proliferation which presumably results from the transcriptional activation of the Mediator function. Additionally, several tumors, including breast cancer, highly express MED28. We have found recently that MED28 potentiated epidermal growth factor (EGF)-induced migration in human breast cancer cells. Therefore, the objective of this study is to identify the role of MED28 in the aspect of cellular migration and invasion in human breast cancer cells. Suppression of MED28 blocked cellular migration and invasion with concomitant reduced expression levels of matrix metalloproteinase-2 (MMP2) and mitogen-activated protein kinase kinase 1 (MAP2K1; MEK1); overexpression of MED28 enhanced cellular migration and upregulated MMP2 and MEK1 expression. Moreover, suppression of MEK1, by dominant-negative, kinase-dead MEK1 cDNA construct or MEK1-specific small interfering RNA (siRNA) as well as MEK1 inhibitors, blocked MED28-induced MMP2 activation, cellular migration, and invasion in breast cancer cells. Furthermore, ectopic expression of MEK1 rescued the inhibitory effect of MED28 knockdown on invasion, and exogenous MMP2 recombinant protein recovered the suppression on invasion upon MED28 or MEK1 knockdown. Our data indicate that MED28 regulates cellular migration in a MEK1-dependent manner in human breast cancer cells, reinforcing the important cellular roles of MED28.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 JOURNAL OF PROTEOMICS. 2012, 75(9):2685-96. doi: 10.1016/j.jprot.2012.03.023.
 Identification of a potential biomarker panel for the intake of the common dietary trans fat elaidic acid (trans£G9-C18:1)
 
 
 Toke Peter Krogager, Lone Vendel Nielsen, Steffen Bak, Clifford Young, Carla Ferreri, Ole Nrregaard Jensen, Peter Hjrup, Vladimiros Thoma, Ida B. Thgersen, Jan J. Enghild
  Abstract
Trans fatty acid intake has been correlated to an unfavorable plasma lipoprotein profile and an increased cardiovascular disease risk. The present study aimed to identify a plasma protein biomarker panel related to human intake of elaidic acid. The human liver cell line HepG2-SF was used as a model system, and the cells were maintained for seven days in serum-free medium containing 100 £gM elaidic acid (trans?9-C18:1), oleic acid (cis?9-C18:1) or stearic acid (C18:0). The secretomes were analyzed by stable isotope labeling of amino acids in cell culture (SILAC), difference in gel electrophoresis (DIGE) and gene expression microarray analysis. Twelve proteins were found to be differentially regulated based on SILAC data (>1.3 fold change, P-value<0.05), 13 proteins were found to be differentially regulated based on DIGE analysis (>1.3 fold change, P-value<0.05), and 17 mRNA transcripts encoding extracellular proteins were determined to be affected (>1.3 fold change, P-value<0.01) following the addition of elaidic acid compared to oleic acid or stearic acid. The results revealed that 37 proteins were regulated specifically in response to elaidic acid exposure, and nine of these proteins were confirmed to be regulated in this manner by using selected reaction monitoring mass spectrometry.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 PLoS ONE. 2012, 7(4):e34969. doi: 10.1371/journal.pone.0034969.
 Assessment of Chitosan-Affected Metabolic Response by Peroxisome Proliferator-Activated Receptor Bioluminescent Imaging-Guided Transcriptomic Analysis
 
 
 Chia-Hung Kao, Chien-Yun Hsiang, Tin-Yun Ho
  Abstract
Chitosan has been widely used in food industry as a weight-loss aid and a cholesterol-lowering agent. Previous studies have shown that chitosan affects metabolic responses and contributes to anti-diabetic, hypocholesteremic, and blood glucose-lowering effects; however, the in vivo targeting sites and mechanisms of chitosan remain to be clarified. In this study, we constructed transgenic mice, which carried the luciferase genes driven by peroxisome proliferator-activated receptor (PPAR), a key regulator of fatty acid and glucose metabolism. Bioluminescent imaging of PPAR transgenic mice was applied to report the organs that chitosan acted on, and gene expression profiles of chitosan-targeted organs were further analyzed to elucidate the mechanisms of chitosan. Bioluminescent imaging showed that constitutive PPAR activities were detected in brain and gastrointestinal tract. Administration of chitosan significantly activated the PPAR activities in brain and stomach. Microarray analysis of brain and stomach showed that several pathways involved in lipid and glucose metabolism were regulated by chitosan. Moreover, the expression levels of metabolism-associated genes like apolipoprotein B (apoB) and ghrelin genes were down-regulated by chitosan. In conclusion, these findings suggested the feasibility of PPAR bioluminescent imaging-guided transcriptomic analysis on the evaluation of chitosan-affected metabolic responses in vivo. Moreover, we newly identified that downregulated expression of apoB and ghrelin genes were novel mechanisms for chitosan-affected metabolic responses in vivo.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 PLoS ONE. 2012, 7(3):e31808. doi: 10.1371/journal.pone.0031808.
 5-Fluorouracil Induced Intestinal Mucositis via Nuclear Factor-£eB Activation by Transcriptomic Analysis and In Vivo Bioluminescence Imaging
 
 
 Chung-Ta Chang, Tin-Yun Ho, Ho Lin, Ji-An Liang, Hui-Chi Huang, Chia-Cheng Li, Hsin-Yi Lo, Shih-Lu Wu, Yi-Fang Huang, Chien-Yun Hsiang
  Abstract
5-Fluorouracil (5-FU) is a commonly used drug for the treatment of malignant cancers. However, approximately 80% of patients undergoing 5-FU treatment suffer from gastrointestinal mucositis. The aim of this report was to identify the drug target for the 5-FU-induced intestinal mucositis. 5-FU-induced intestinal mucositis was established by intraperitoneally administering mice with 100 mg/kg 5-FU. Network analysis of gene expression profile and bioluminescent imaging were applied to identify the critical molecule associated with 5-FU-induced mucositis. Our data showed that 5-FU induced inflammation in the small intestine, characterized by the increased intestinal wall thickness and crypt length, the decreased villus height, and the increased myeloperoxidase activity in tissues and proinflammatory cytokine production in sera. Network analysis of 5-FU-affected genes by transcriptomic tool showed that the expression of genes was regulated by nuclear factor-£eB (NF-£eB), and NF-£eB was the central molecule in the 5-FU-regulated biological network. NF-£eB activity was activated by 5-FU in the intestine, which was judged by in vivo bioluminescence imaging and immunohistochemical staining. However, 5-aminosalicylic acid (5-ASA) inhibited 5-FU-induced NF-£eB activation and proinflammatory cytokine production. Moreover, 5-FU-induced histological changes were improved by 5-ASA. In conclusion, our findings suggested that NF-£eB was the critical molecule associated with the pathogenesis of 5-FU-induced mucositis, and inhibition of NF-£eB activity ameliorated the mucosal damage caused by 5-FU.
   

  ✔本篇論文使用華聯產品:Mouse OneArray, Mouse&Rat miRNA OneArray  
 Neuron. 2012, 73(4):774-88. doi: 10.1016/j.neuron.2012.02.003.
 EPAC Null Mutation Impairs Learning and Social Interactions via Aberrant Regulation of miR-124 and Zif268 Translation
 
 
 Ying Yang, Xiaogang Shu, Dan Liu, You Shang, Yan Wu, Lei Pei, Xin Xu, Qing Tian, Jian Zhang, Kun Qian, Ya-Xian Wang, Ronald S. Petralia, Weihong Tu, Ling-Qiang Zhu, Jian-Zhi Wang, Youming Lu
  Abstract
EPAC proteins are the guanine nucleotide exchange factors that act as the intracellular receptors for cyclic AMP. Two variants of EPAC genes including EPAC1 and EPAC2 are cloned and are widely expressed throughout the brain. But, their functions in the brain remain unknown. Here, we genetically delete EPAC1 (EPAC1(-/-)), EPAC2 (EPAC2(-/-)), or both EPAC1 and EPAC2 genes (EPAC(-/-)) in the forebrain of mice. We show that EPAC null mutation impairs long-term potentiation (LTP) and that this impairment is paralleled with the severe deficits in spatial learning and social interactions and is mediated in a direct manner by miR-124 transcription and Zif268 translation. Knockdown of miR-124 restores Zif268 and hence reverses all aspects of the EPAC(-/-) phenotypes, whereas expression of miR-124 or knockdown of Zif268 reproduces the effects of EPAC null mutation. Thus, EPAC proteins control miR-124 transcription in the brain for processing spatial learning and social interactions.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 PLoS ONE. 2012, 7(2):e31005. doi: 10.1371/journal.pone.0031005.
 Conditional Ablation of Ezh2 in Murine Hearts Reveals Its Essential Roles in Endocardial Cushion Formation, Cardiomyocyte Proliferation and Survival
 
 
 Li Chen, Yanlin Ma, Eun Young Kim, Wei Yu, Robert J. Schwartz, Ling Qian, Jun Wang
  Abstract
Ezh2 is a histone trimethyltransferase that silences genes mainly via catalyzing trimethylation of histone 3 lysine 27 (H3K27Me3). The role of Ezh2 as a regulator of gene silencing and cell proliferation in cancer development has been extensively investigated; however, its function in heart development during embryonic cardiogenesis has not been well studied. In the present study, we used a genetically modified mouse system in which Ezh2 was specifically ablated in the mouse heart. We identified a wide spectrum of cardiovascular malformations in the Ezh2 mutant mice, which collectively led to perinatal death. In the Ezh2 mutant heart, the endocardial cushions (ECs) were hypoplastic and the endothelial-to-mesenchymal transition (EMT) process was impaired. The hearts of Ezh2 mutant mice also exhibited decreased cardiomyocyte proliferation and increased apoptosis. We further identified that the Hey2 gene, which is important for cardiomyocyte proliferation and cardiac morphogenesis, is a downstream target of Ezh2. The regulation of Hey2 expression by Ezh2 may be independent of Notch signaling activity. Our work defines an indispensible role of the chromatin remodeling factor Ezh2 in normal cardiovascular development.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 PLoS ONE. 2012, 7(1):e30635. doi: 10.1371/journal.pone.0030635 .
 microRNA-152 Mediates DNMT1-Regulated DNA Methylation in the Estrogen Receptor £ Gene
 
 
 Yung-Song Wang, Wen-Wen Chou, Ku-Chung Chen, Hsin-Yun Cheng, Ruey-Tay Lin, Suh-Hang Hank Juo
  Abstract
"Estrogen receptor a (ERa) has been shown to protect against atherosclerosis. Methylation of the ERa gene can reduce ERa expression leading to a higher risk for cardiovascular disease. Recently, microRNAs have been found to regulate DNA methyltransferases (DNMTs) and thus control methylation status in several genes. We first searched for microRNAs involved in DNMT-associated DNA methylation in the ERa gene. We also tested whether statin and a traditional Chinese medicine (San-Huang-Xie-Xin-Tang, SHXXT) could exert a therapeutic effect on microRNA, DNMT and ERa methylation. The ERa expression was decreased and ERa methylation was increased in LPS-treated human aortic smooth muscle cells (HASMCs) and the aorta from rats under a high-fat diet. microRNA-152 was found to be down regulated in the LPS-treated HASMCs. We validated that microRNA-152 can knock down DNMT1 in HASMCs leading to hypermethylation of the ERa gene. Statin had no effect on microRNA-152, DNMT1 or ERa expression. On the contrary, SHXXT could restore microRNA-152, decrease DNMT1 and increase ERa expression in both cellular and animal studies. The present study showed that microRNA-152 decreases under the pro-atherosclerotic conditions. The reduced microRNA-152 can lose an inhibitory effect on DNA methyltransferase, which leads to hypermethylation of the ERa gene and a decrease of ERa level. Although statin can not reverse these cascade proatherosclerotic changes, the SHXXT shows a promising effect to inhibit this unwanted signaling pathway."
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Mol Endocrinol. 2012, 26(2):228-43. doi: 10.1210/me.2011-1150.
 Acid Ceramidase (ASAH1) Is a Global Regulator of Steroidogenic Capacity and Adrenocortical Gene Expression
 
 
 Natasha C. Lucki, Sibali Bandyopadhyay, Elaine Wang, Alfred H. Merrill, Marion B. Sewer
  Abstract
In H295R human adrenocortical cells, ACTH rapidly activates ceramide (Cer) and sphingosine (SPH) turnover with a concomitant increase in SPH-1-phosphate secretion. These bioactive lipids modulate adrenocortical steroidogenesis, primarily by acting as second messengers in the protein kinase A/cAMP-dependent pathway. Acid ceramidase (ASAH1) directly regulates the intracellular balance of Cer, SPH, and SPH-1-phosphate by catalyzing the hydrolysis of Cer into SPH. ACTH/cAMP signaling stimulates ASAH1 transcription and activity, supporting a role for this enzyme in glucocorticoid production. Here, the role of ASAH1 in regulating steroidogenic capacity was examined using a tetracycline-inducible ASAH1 short hairpin RNA H295R human adrenocortical stable cell line. We show that ASAH1 suppression increases the transcription of multiple steroidogenic genes, including Cytochrome P450 monooxygenase (CYP)17A1, CYP11B1/2, CYP21A2, steroidogenic acute regulatory protein, hormone-sensitive lipase, 18-kDa translocator protein, and the melanocortin-2 receptor. Induced gene expression positively correlated with enhanced histone H3 acetylation at target promoters. Repression of ASAH1 expression also induced the expression of members of the nuclear receptor nuclear receptor subfamily 4 (NR4A) family while concomitantly suppressing the expression of dosage-sensitive sex reversal, adrenal hypoplasia critical region, on chromosome X, gene 1. ASAH1 knockdown altered the expression of genes involved in sphingolipid metabolism and changed the cellular amounts of distinct sphingolipid species. Finally, ASAH1 silencing increased basal and cAMP-dependent cortisol and dehydroepiandrosterone secretion, establishing ASAH1 as a pivotal regulator of steroidogenic capacity in the human adrenal cortex.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Development. 2012, 139(4):709-19. doi: 10.1242/dev.073197.
 Bmp signaling regulates a dose-dependent transcriptional program to control facial skeletal development
 
 
 Margarita Bonilla-Claudio, Jun Wang, Yan Bai, Elzbieta Klysik, Jennifer Selever, James F. Martin
  Abstract
We performed an in depth analysis of Bmp4, a critical regulator of development, disease, and evolution, in cranial neural crest (CNC). Conditional Bmp4 overexpression, using a tetracycline-regulated Bmp4 gain-of-function allele, resulted in facial skeletal changes that were most dramatic after an E10.5 Bmp4 induction. Expression profiling uncovered a signature of Bmp4-induced genes (BIG) composed predominantly of transcriptional regulators that control self-renewal, osteoblast differentiation and negative Bmp autoregulation. The complimentary experiment, CNC inactivation of Bmp2, Bmp4 and Bmp7, resulted in complete or partial loss of multiple CNC-derived skeletal elements, revealing a crucial requirement for Bmp signaling in membranous bone and cartilage development. Importantly, the BIG signature was reduced in Bmp loss-of-function mutants, indicating Bmp-regulated target genes are modulated by Bmp dose. Chromatin immunoprecipitation (ChIP) revealed a subset of the BIG signature, including Satb2, Smad6, Hand1, Gadd45£^ and Gata3, that was bound by Smad1/5 in the developing mandible, revealing direct Smad-mediated regulation. These data support the hypothesis that Bmp signaling regulates craniofacial skeletal development by balancing self-renewal and differentiation pathways in CNC progenitors.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Microbes and Infection. 2012, 14(7-8):600-9. doi: 10.1016/j.micinf.2012.01.006.
 Transcriptome signature in young children with acute otitis media due to Streptococcus pneumoniae
 
 
 Keyi Liu, Linlin Chen, Ravinder Kaur, Michael Pichichero
  Abstract
Streptococcus pneumoniae (Spn) is the predominant causative organism of acute otitis media in children. To better understand the genes that are regulated at the onset of AOM caused by Spn infection in the middle ear, the transcriptome profile of peripheral blood mononuclear cells isolated from children prior to and during an AOM event was evaluated by microarray. We found that 1903 (6.2%) of 29,187 genes were differentially regulated greater than 2-fold at the onset of AOM compared to the pre-infection stage of the same children. The ontology of differentially regulated genes was dominated by those involved with the immune response. At onset of infection, genes associated with bacterial defenses were significantly up-regulated, including beta-defensin123, S100 protein A12, Toll-like receptor 5, IL-10, and those involved in the classical and alternative complement pathways. Genes associated with inhibition of bacterial entry through clathrin-dependent endocytosis were also up-regulated. In contrast, genes associated with cell-mediated immune responses were broadly down-regulated. The results provide the first human transcriptome data identifying genes differentially regulated at the onset of AOM in children.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 European Journal of Pharmaceutical Sciences. 2012, 45(3):367-378.
 Microarray analysis revealed dysregulation of multiple genes associated with chemoresistance to As2O3 and increased tumor aggressiveness in a newly established arsenic-resistant ovarian cancer cell line, OVCAR-3/AsR
 
 
 Pei-Shi Ong, Sui-Yung Chan, Paul C. Ho
  Abstract
The potential of arsenic trioxide (As(2)O(3)) for use as a novel therapy for ovarian cancer treatment has been increasingly recognized. In this study, we developed an arsenic-resistant OVCAR-3 subline (OVCAR-3/AsR) and aimed to identify the molecular mechanisms and signaling pathways contributing to the development of acquired arsenic chemoresistance in ovarian cancer. OVCAR-3/AsR cells were obtained following continual exposure of parental OVCAR-3 cells to low dose As(2)O(3) for 12months. Cytotoxicity of OVCAR-3/AsR cells to As(2)O(3), paclitaxel and cisplatin was investigated. Cell apoptosis and cell cycle distribution following As(2)O(3) treatment of OVCAR-3/AsR cells was also analyzed using flow cytometry. Subsequently, cDNA microarray analysis was performed from the RNA samples of OVCAR-3 and OVCAR-3/AsR cells in duplicate experiments. Microarray data were analyzed using GenespringR and Pathway StudioR Softwares. OVCAR-3/AsR cells showed 9-fold greater resistance to As(2)O(3) and lack of collateral resistance to cisplatin and paclitaxel. Compared with parental OVCAR-3 cells, OVCAR-3/AsR had significantly lower apoptotic rates following As(2)O(3) treatment. These cells were also arrested at both the S phase and G(2)/M phase of the cell cycle after exposure to high concentrations of As(2)O(3). Gene expression profiling revealed significant differences in expression levels of 397 genes between OVCAR-3/AsR and OVCAR-3 cells. The differentially regulated transcripts genes have functional ontologies related to continued cancer cell growth, cell survival, tumor metastasis and tumor aggressiveness. Additionally, numerous gene targets of the nuclear factor erythroid 2-related factor 2 (NRF2) transcription factor showed elevated expression in OVCAR-3/AsR cells. Subsequent pathway analysis further revealed a gene network involving interleukin 1-alpha (IL1A) in mediating the arsenic-resistant phenotype. These results showed that changes in multiple genes and an increased in tumor aggressiveness occurred during the development of acquired chemoresistance to As(2)O(3) in ovarian cancer cells. The functional relevance of these genetic changes should be validated in future studies.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Biotechnol Lett. 2012, 34(5):805-12. doi: 10.1007/s10529-011-0838-7.
 Momilactione B inhibits protein kinase A signaling and reduces tyrosinase-related proteins 1 and 2 expression in melanocytes
 
 
 Ji Hae Lee, Boram Cho, Hee-jin Jun, Woo-Duck Seo, Dong-Woo Kim, Kang-Jin Cho, Sung-Joon Lee
  Abstract
Momilactone B (MB) is a terpenoid phytoalexin present in rice bran that exhibits several biological activities. MB reduced the melanin content in B16 melanocytes melanin content and inhibited tyrosinase activities. Using transcriptome analysis, the genes involved in protein kinase A (PKA) signaling were found to be markedly altered. B16 cells stimulated with MB had decreased concentrations of cAMP protein kinase A activity, and cAMP-response element-binding protein which is a key transcription factor for microphthalmia-associated transcription factor (MITF) expression. Accordingly, the expression of MITF and its target genes, which are essential for melanogenesis, were reduced. MB thus exhibits anti-melanogenic effects by repressing tyrosinase enzyme activity and inhibiting the PKA signaling pathway which, in turn, decreases melanogenic gene expression.
   

  ✔本篇論文使用華聯產品:Model Plant miRNA OneArray  
 Journal of Experimental Botany. doi:10.1093/jxb/ers333.
 Identification and profiling of arsenic stress-induced microRNAs in Brassica juncea
 
 
 Ashish Kumar Srivastava, S.F. D¡¦Souza
  Abstract

   

  ✔本篇論文使用華聯產品:Human OneArray  
 PLoS One. 2011, 6(2):e17014. doi: 10.1371/journal.pone.0017014.
 Transcriptional profiling of peripheral blood mononuclear cells in pancreatic cancer patients identifies novel genes with potential diagnostic utility
 
 
 Michael J. Baine, Subhankar Chakraborty, Lynette M. Smith, Kavita Mallya, Aaron R. Sasson, Randall E. Brand, Surinder K. Batra
  Abstract
BACKGROUND: It is well known that many malignancies, including pancreatic cancer (PC), possess the ability to evade the immune system by indirectly downregulating the mononuclear cell machinery necessary to launch an effective immune response. This knowledge, in conjunction with the fact that the trancriptome of peripheral blood mononuclear cells has been shown to be altered in the context of many diseases, including renal cell carcinoma, lead us to study if any such alteration in gene expression exists in PC as it may have diagnostic utility. METHODS AND FINDINGS: PBMC samples from 26 PC patients and 33 matched healthy controls were analyzed by whole genome cDNA microarray. Three hundred eighty-three genes were found to be significantly different between PC and healthy controls, with 65 having at least a 1.5 fold change in expression. Pathway analysis revealed that many of these genes fell into pathways responsible for hematopoietic differentiation, cytokine signaling, and natural killer (NK) cell and CD8+ T-cell cytotoxic response. Unsupervised hierarchical clustering analysis identified an eight-gene predictor set, consisting of SSBP2, Ube2b-rs1, CA5B, F5, TBC1D8, ANXA3, ARG1, and ADAMTS20, that could distinguish PC patients from healthy controls with an accuracy of 79% in a blinded subset of samples from treatment naïve patients, giving a sensitivity of 83% and a specificity of 75%. CONCLUSIONS: In summary, we report the first in-depth comparison of global gene expression profiles of PBMCs between PC patients and healthy controls. We have also identified a gene predictor set that can potentially be developed further for use in diagnostic algorithms in PC. Future directions of this research should include analysis of PBMC expression profiles in patients with chronic pancreatitis as well as increasing the number of early-stage patients to assess the utility of PBMCs in the early diagnosis of PC.
   

  ✔本篇論文使用華聯產品:Array technology and applications  
 Neurology Today. 2011, 11(19): 24-27. doi: 10.1097/01.NT.0000407216.70062.aa.
 Evidence Report: Genetic, Metabolic Screening Useful in children with Intellectual Development Deficits
 
 
 KURT SAMSON
  Abstract
Although there are challenges yet to be overcome in the diagnostic evaluation of children with unexplained global developmental delay or intellectual disability (GDD/ID), genetic and metabolic screening tests are increasingly useful, according to a review by the AAN Quality Standards Subcommittee and the Practice Committee of the Child Neurology Society. The review was published in the Sept. 28 online edition of Neurology. In an interview with Neurology Today, AAN subcommittee panelist David J. Michelson, MD, assistant professor of neurology and pediatrics at the Loma Linda University School of Medicine in California, discussed the fi ndings and their implications for clinicians.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Journal of Inflammation Research. 2011, 4: 127-138. doi: 10.2147/JIR.S19461.
 Inflammatory cytokines regulate endothelial cell survival and tissue repair functions via NF-£eB signaling
 
 
 Nobuhiro Kanaji, Tadashi Sato, Amy Nelson, Xingqi Wang, YingJi Li, Miok Kim, Masanori Nakanishi, Hesham Basma, Joel Michalski, Maha Farid, Michael Chandler, William Pease, Amol Patil, Stephen I Rennard, Xiangde Liu
  Abstract
Inflammation contributes to the development of fibrotic and malignant diseases. We assessed the ability of inflammatory cytokines to modulate endothelial cell survival and functions related to tissue repair/remodeling. Treatment with interleukin (IL)-1£] or tumor necrosis factor (TNF)-£ (2 ng/mL) led to human pulmonary artery endothelial cells becoming spindle-shaped fibroblast-like cells. However, immunoblot and DNA microarray showed no change in most endothelial and mesenchymal markers. In the presence of IL-1£] or TNF-£, cells were resistant to apoptosis induced by deprivation of serum and growth factor, and were more migratory. In addition, cells treated with IL-1£] or TNF-£ contracted collagen gels more robustly. In contrast, transforming growth factor-£]1 did not induce these responses. RNA interference targeting nuclear factor (NF)-£eB p65 blocked the effects of IL-1£] or TNF-£ on cell morphologic change, survival, migration, and collagen gel contraction. These results suggest that endothelial cells may contribute to tissue repair/remodeling via the NF-£eB signaling in a milieu of airway inflammation.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Eur J Dermatol. 2012, 22(1):58-67. doi: 10.1684/ejd.2011.1599.
 Angelica sinensis isolate SBD.4: composition, gene expression profiling, mechanism of action and effect on wounds, in rats and humans
 
 
 Hui ZHAO, Joel DENEAU, Ginny O.L. CHE, Shang LI, Frederic VAGNINI, Parastoo AZADI, Roberto SONON, Ravi RAMJIT, Simon M.Y. LEE, Krzysztof BOJANOWSKI
  Abstract
This report characterizes an aqueous isolate (SBD.4) of one of the most broadly used Chinese medicinal herbs, Angelica sinensis, from the perspective of its application in skin and wound care. SBD.4 has been chemically defined and was found to increase the strength of healed wounds in retired breeder (older) rats. Furthermore, the mechanism of action of this Angelica sinensis isolate was tested in the zebrafish angiogenesis model, and in human skin substitutes by DNA microarray, revealing a bioactivity profile consistent with skin repair and regeneration. When combined with several types of wound dressings, SBD.4 increased type I collagen production in human dermal fibroblasts, and when formulated in nanosilver hydrocolloid dressing, it was found effective in chronic ulcer management in humans, demonstrating that botanical high-tech wound dressings can be successfully developed to improve the treatment of chronic lesions in humans.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 ACS Nano. 2011, 5(12):9354-69. doi: 10.1021/nn2027775.
 Identification of the Nanogold Particle-Induced Endoplasmic Reticulum Stress by Omic Techniques and Systems Biology Analysis
 
 
 Yen-Yin Tsai, Yi-HueiHuang, Ya-Li Chao, Kuang-Yu Hu, Li-Te Chin, Shiu-Huey Chou, Ai-Ling Hour, Yeong-DerYao, Chi-Shun Tu, Yao-Jen Liang, Cheng-YuhTsai, Hao-Yu Wu, Shan-WenTan, Han-Min Chen
  Abstract
Growth inhibition and apoptotic/necrotic phenotype was observed in nanogold particle (AuNP)-treated human chronic myelogenous leukemia cells. To elucidate the underlying cellular mechanisms, proteomic techniques including two-dimensional electrophoresis/mass spectrometry and protein microarrays were utilized to study the differentially expressed proteome and phosphoproteome, respectively. Systems biology analysis of the proteomic data revealed that unfolded protein-associated endoplasmic reticulum (ER) stress response was the predominant event. Concomitant with transcriptomic analysis using mRNA expression, microarrays show ER stress response in the AuNP-treated cells. The ER stress protein markers' expression assay unveiled AuNPs as an efficient cellular ER stress elicitor. Upon ER stress, cellular responses, including reactive oxygen species increase, mitochondrial cytochrome c release, and mitochondria damage, chronologically occurred in the AuNP-treated cells. Conclusively, this study demonstrates that AuNPs cause cell death through induction of unmanageable ER stress.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Journal of Molecular and Cellular Cardiology. 2012, 52(3):638-49. doi: 10.1016/j.yjmcc.2011.11.011.
 Enhanced desumoylation in murine hearts by overexpressed SENP2 leads to congenital heart defects and cardiac dysfunction
 
 
 EunYoungKim, LiChen, YanlinMa, WeiYu, JiangChang, Ivan P.Moskowitz, JunWang
  Abstract
Sumoylation is a posttranslational modification implicated in a variety of cellular activities, and its role in a number of human pathogeneses such as cleft lip/palate has been well documented. However, the importance of the SUMO conjugation pathway in cardiac development and functional disorders is newly emerging. We previously reported that knockout of SUMO-1 in mice led to congenital heart diseases (CHDs). To further investigate the effects of imbalanced SUMO conjugation on heart development and function and its underlying mechanisms, we generated transgenic (Tg) mice with cardiac-specific expression of SENP2, a SUMO-specific protease that deconjugates sumoylated proteins, to evaluate the impact of desumoylation on heart development and function. Overexpression of SENP2 resulted in premature death of mice with CHDs-atrial septal defects (ASDs) and/or ventricular septal defects (VSDs). Immunobiochemistry revealed diminished cardiomyocyte proliferation in SENP2-Tg mouse hearts compared with that in wild type (WT) hearts. Surviving SENP2-Tg mice showed growth retardation, and developed cardiomyopathy with impaired cardiac function with aging. Cardiac-specific overexpression of the SUMO-1 transgene reduced the incidence of cardiac structural phenotypes in the sumoylation defective mice. Moreover, cardiac overexpression of SENP2 in the mice with Nkx2.5 haploinsufficiency promoted embryonic lethality and severity of CHDs, indicating the functional interaction between SENP2 and Nkx2.5 in vivo. Our findings indicate the indispensability of a balanced SUMO pathway for proper cardiac development and function. This article is part of a Special Issue entitled 'Post-translational Modification SI'.
   

  ✔本篇論文使用華聯產品:Data Analysis  
 PLoS ONE. 2011, 6(4):e18628. doi: 10.1371/journal.pone.0018628.
 MicroRNAs Dynamically Remodel Gastrointestinal Smooth Muscle Cells
 
 
 Chanjae Park, Wei Yan, Sean M. Ward, Sung Jin Hwang, Qiuxia Wu, William J. Hatton, Jong Kun Park, Kenton M. Sanders, Seungil Ro
  Abstract
Smooth muscle cells (SMCs) express a unique set of microRNAs (miRNAs) which regulate and maintain the differentiation state of SMCs. The goal of this study was to investigate the role of miRNAs during the development of gastrointestinal (GI) SMCs in a transgenic animal model. We generated SMC-specific Dicer null animals that express the reporter, green fluorescence protein, in a SMC-specific manner. SMC-specific knockout of Dicer prevented SMC miRNA biogenesis, causing dramatic changes in phenotype, function, and global gene expression in SMCs: the mutant mice developed severe dilation of the intestinal tract associated with the thinning and destruction of the smooth muscle (SM) layers; contractile motility in the mutant intestine was dramatically decreased; and SM contractile genes and transcriptional regulators were extensively down-regulated in the mutant SMCs. Profiling and bioinformatic analyses showed that SMC phenotype is regulated by a complex network of positive and negative feedback by SMC miRNAs, serum response factor (SRF), and other transcriptional factors. Taken together, our data suggest that SMC miRNAs are required for the development and survival of SMCs in the GI tract.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 CLINICAL IMMUNOLOGY. 2011 Sep 16. doi: 10.1111/j.1365-3083.2011.02637.x.
 Healthy first degree relatives of patients with type 1 diabetes exhibit significant differences in basal gene expression pattern of immunocompetent cells compared to controls: expression pattern as predeterminant of autoimmune diabetes
 
 
 Michal Kolar, Radek Blatny, Zbynek Halbhuber, Jana Vcelakova, Miluse Hubackova, Lenka Petruzelkova, Zdenek Sumnik, Barbora Obermannova, Pavlina Pithova, Vendula Stavikova, Maria Krivjanska, Ales Neuwirth, Stanislava Kolouskova, Dominik Filipp, Katerina Stechova
  Abstract
Introduction:? Expression features of genetic landscape which predispose an individual to the type 1 diabetes are poorly understood. We addressed this question by comparing gene expression profile of freshly isolated peripheral blood mononuclear cells isolated from either patients with type 1 diabetes, or their first degree relatives or healthy controls. Our aim was to establish whether a distinct type of "prodiabetogenic" gene expression pattern in the group of relatives of T1D patients could be identified. Methods:? Whole-genome expression profile of nine T1D patients, their ten first-degree relatives and ten healthy controls were analyzed using the human high density expression microarray chip. Functional aspects of candidate genes were assessed using the MetaCore software. Results:? The highest number of differentially expressed genes (547) was found between the autoantibody negative healthy relatives and the healthy controls. Some of them represent genes critically involved in the regulation of innate immune responses such as TLR signalling and CCR3 signalling in eosinophiles, humoral immune reactions such as BCR pathway, costimulation and cytokine responses mediated by CD137, CD40 and CD28 signalling and IL-1 proinflammatory pathway. Conclusion:? Our data demonstrate that expression profile of healthy relatives of patients with T1D is clearly distinct from the pattern found in the healthy controls. That especially concerns differential activation status of genes and signalling pathways involved in proinflammatory processes and those of innate immunity and humoral reactivity. Thus, we posit that the study of the healthy relative's gene expression pattern is instrumental for identification of novel markers associated with the development of diabetes.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Transgenic Res. 2011, 20(5):1073-86. doi: 10.1007/s11248-010-9478-2.
 Epithelial cell-targeted transgene expression enables isolation of cyan fluorescent protein (CFP)-expressing prostate stem/progenitor cells
 
 
 Weidan Peng, Yunhua Bao, Janet A. Sawicki
  Abstract
To establish a method for efficient and relatively easy isolation of a cell population containing epithelial prostate stem cells, we developed two transgenic mouse models, K5/CFP and K18/RFP. In these models, promoters of the cytokeratin 5 (Krt5) and the cytokeratin 18 (Krt18) genes regulate cyan and red fluorescent proteins (CFP and RFP), respectively. CFP and RFP reporter protein fluorescence allows for visualization of K5(+) and K18(+) epithelial cells within the cellular spatial context of the prostate gland and for their direct isolation by FACS. Using these models, it is possible to test directly the stem cell properties of prostate epithelial cell populations that are positively selected based on expression of cytoplasmic proteins, K5 and K18. After validating appropriate expression of the K5/CFP and K18/RFP transgenes in the developing and adult prostate, we demonstrate that a subset of CFP-expressing prostate cells exhibits stem cell proliferation potential and differentiation capabilities. Then, using prostate cells sorted from double transgenic mice (K5/CFP + K18/RFP), we compare RNA microarrays of sorted K5(+)K18(+) basal and K5(-)K18(+) luminal epithelial cells, and identify genes that are differentially expressed. Several genes that are over-expressed in K5(+) cells have previously been identified as potential stem cell markers. These results suggest that FACS isolation of prostate cells from these mice based on combining reporter gene fluorescence with expression of potential stem cell surface marker proteins will yield populations of cells enriched for stem cells to a degree that has not been attained by using cell surface markers alone.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Comparative Immunology, Microbiology and Infectious Diseases. 2011, 34(6):503-12. doi: 10.1016/j.cimid.2011.09.003.
 Innate immune response gene expression profiles in central nervous system of mice infected with rabies virus
 
 
 Pingsen Zhao, Lili Zhao, Tao Zhang, Yinglin Qi, Tiecheng Wang, Kejian Liu, Hualei Wang, Hao Feng, Hongli Jin, Chuan Qin, Songtao Yang, Xianzhu Xia
  Abstract
The present study was focused on the modulation of innate immune response genes in CNS of mouse in response to rabies virus (RABV) infection. The global gene expression changes in brains of RABV- or mock-infected mice were investigated using DNA microarray analysis and quantitative real-time PCR. Then functional enrichment of the differentially expressed mRNAs was performed. Microarray analysis showed that 390 genes in brain were significantly (P<0.01) regulated in response to RABV infection, with obviously up-regulated genes like interferon (IFN) stimulated genes (ISGs), IFN inducible transcription factors, cytokines and complement, etc. The significant pathways of differentially expressed genes are mainly involved in JAK-STAT signaling pathway, antigen processing and presentation, ubiquitin mediated proteolysis and complement cascades. The results suggest that the modulated genes in infected CNS were possibly involved in pathogenesis of rabies. Conversely, they may have protective effects.
   

  ✔本篇論文使用華聯產品:Rat OneArray  
 Hum Gene Ther. 2012, 23(3):255-61. doi: 10.1089/hum.2011.094.
 Improved Function of the Failing Rat Heart by Regulated Expression of Insulin-like Growth Factor-I via Intramuscular Gene Transfer
 
 
 N. Chin Lai, Tong Tang, Mei Hua Gao, Miho Sato, Atsushi Miyanohara, H. Kirk Hammond
  Abstract
Current methods of gene transfer for heart disease include injection into heart muscle or intracoronary coronary delivery, approaches that typically provide limited expression and are cumbersome to apply. To circumvent these problems, we selected a transgene, insulin-like growth factor-I (IGF-I), which may, in theory, have favorable effects on heart function when secreted from a remote site. We examined the feasibility and efficacy of skeletal muscle injection of adeno-associated virus 5 encoding IGF-I under Tet regulation (AAV5.IGFI-tet) to treat heart failure. Myocardial infarction (MI) was induced in rats by coronary occlusion; 1 week later, rats with impaired left ventricular (LV) function received 2¡Ñ10(12) genome copies (GC) of AAV5.IGFI-tet in the anterior tibialis muscle, and 4 weeks later, were randomly assigned to receive doxycycline in drinking water to activate IGF-I expression (IGF-On; n=10), or not to receive doxycycline (IGF-Off; n=10). Ten weeks after MI (5 weeks after activation of IGF-I expression), LV size and function were assessed by echocardiography and physiological studies. IGF-On rats showed reduced LV end-systolic dimension (p=0.03) and increased LV ejection fraction (p=0.02). In addition, IGF-On rats showed, before and during dobutamine infusion, increases in cardiac output (p=0.02), stroke work (p=0.0001), LV + dP/dt (p<0.0001), LV relaxation (LV - dP/dt; p=0.03), and systolic arterial blood pressure (p=0.0003). Mean arterial pressure and systemic vascular resistance were unchanged. Activation of IGF-I expression reduced cardiac fibrosis (p=0.048), apoptosis (p<0.0001), and caspase-3/7 activity (p=0.04). Serum IGF-I was increased 5 weeks after transgene activation (p=0.008). These data indicate that skeletal muscle injection of AAV5.IGFI-tet enables tetracycline-activated expression, increases serum IGF-I levels, and improves function of the failing heart.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 J Cell Physiol. 2012, 227(6):2595-604. doi: 10.1002/jcp.22999.
 Human myxomatous mitral valve prolapse: Role of bone morphogenetic protein 4 in valvular interstitial cell activation
 
 
 Rachana Sainger, Juan B. Grau, Emanuela Branchetti, Paolo Poggio, William F. Seefried, Benjamin C. Field, Michael A. Acker, Robert C. Gorman, Joseph H. Gorman III, Clark W. Hargrove III, Joseph E. Bavaria, Giovanni Ferrari
  Abstract
Myxomatous mitral valve prolapse (MVP) is the most common cardiac valvular abnormality in industrialized countries and a leading cause of mitral valve surgery for isolated mitral regurgitation. The key role of valvular interstitial cells (VICs) during mitral valve development and homeostasis has been recently suggested, however little is known about the molecular pathways leading to MVP. We aim to characterize bone morphogenetic protein 4 (BMP4) as a cellular regulator of mitral VIC activation towards a pathologic synthetic phenotype and to analyze the cellular phenotypic changes and extracellular matrix (ECM) reorganization associated with the development of myxomatous MVP. Microarray analysis showed significant up regulation of BMP4-mediated signaling molecules in myxomatous MVP when compared to controls. Histological analysis and cellular characterization suggest that during myxomatous MVP development, healthy quiescent mitral VICs undergo a phenotypic activation via up regulation of BMP4-mediated pathway. In vitro hBMP4 treatment of isolated human mitral VICs mimics the cellular activation and ECM remodeling as seen in MVP tissues. The present study characterizes the cell biology of mitral VICs in physiological and pathological conditions and provides insights into the molecular and cellular mechanisms mediated by BMP4 during MVP. The ability to test and control the plasticity of VICs using different molecules may help in developing new diagnostic and therapeutic strategies for myxomatous MVP.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Cell. 2011, 147(2):436-46. doi: 10.1016/j.cell.2011.09.022.
 Activation of STAT6 by STING Is Critical for Antiviral Innate Immunity
 
 
 Huihui Chen, Hui Sun, Fuping You, Wenxiang Sun, Xiang Zhou, Lu Chen, Jing Yang, Yutao Wang, Hong Tang, Yukun Guan, Weiwei Xia, Jun Gu, Hiroki Ishikawa, Delia Gutman, Glen Barber, Zhihai Qin, Zhengfan Jiang
  Abstract
STAT6 plays a prominent role in adaptive immunity by transducing signals from extracellular cytokines. We now show that STAT6 is required for innate immune signaling in response to virus infection. Viruses or cytoplasmic nucleic acids trigger STING (also named MITA/ERIS) to recruit STAT6 to the endoplasmic reticulum, leading to STAT6 phosphorylation on Ser(407) by TBK1 and Tyr(641), independent of JAKs. Phosphorylated STAT6 then dimerizes and translocates to the nucleus to induce specific target genes responsible for immune cell homing. Virus-induced STAT6 activation is detected in all cell-types tested, in contrast to the cell-type specific role of STAT6 in cytokine signaling, and Stat6(-/-) mice are susceptible to virus infection. Thus, STAT6 mediates immune signaling in response to both cytokines at the plasma membrane, and virus infection at the endoplasmic reticulum.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Cancer Letters. 2012, 314(2):155-65. doi: 10.1016/j.canlet.2011.09.027.
 Estrogen receptor-regulated microRNAs contribute to the BCL2/BAX imbalance in endometrial adenocarcinoma and precancerous lesions
 
 
 Xueli Zhang, Baolin Xing, Youhua Sheng, Huan Lu, Zhenhong Wei, Rong Zhang, Yifeng He
  Abstract
Uncontrolled estrogen exposure can induce an imbalance in BCL2/BAX expression in endometrial cells, leading to precancerous lesions and type I endometrial adenocarcinoma. This study aimed to explore the mechanism underlying this phenomenon. We show that the activated estrogen receptor can suppress the expression of BAX by upregulating a group of microRNAs including hsa-let-7 family members and hsa-miR-27a, thereby promoting an increased BCL2/BAX ratio as well as enhanced survival and proliferation in the affected cells. These ER-regulated hsa-let-7 microRNAs can be detected in most hyperplastic endometria, suggesting their potential utility as indicators of estrogen over-exposure.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Microbial Pathogenesis. 2012, 52(1):47-54. doi: 10.1016/j.micpath.2011.10.001.
 Changes in microRNA expression induced by rabies virus infection in mouse brains
 
 
 Pingsen Zhao, Lili Zhao, Tao Zhang, Hualei Wang, Chuan Qin, Songtao Yang, Xianzhu Xia
  Abstract
MicroRNAs (miRNAs) are small RNA (? 22 nt) molecules expressed endogenously in cells. They are involved in the regulation of gene expression. Recently, evidence has shown that cellular miRNAs have key regulatory roles in virus-host interactions. The rabies virus (RABV) causes a fatal infection of the central nervous systems (CNS) of warm-blooded animals, yet its pathogenesis remains poorly understood. To gain more insight into the pathogenesis of RABV, a miRNA microarray was performed as part of an investigation of changes in host miRNA expression in the brains of mice infected with RABV. The results showed that RABV infection induced modulation of the expression of sixteen miRNA molecules. These data were verified by real-time PCR. Functional analysis showed the differentially expressed miRNAs to be involved in many immune-related signaling pathways, such as the RIG-I-like receptor signaling pathway, JAK-STAT signaling pathway, chemokine signaling pathway, T-cell receptor signaling pathway, MAPK signaling pathway, leukocyte transendothelial migration, and natural killer cell mediated cytotoxicity. The predicted expression levels of the target genes of these modulated miRNAs correlated with measurements of gene expression measured by DNA microarray and qRT-PCR.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 BMC Research Notes. 2011 Oct 5;4:381.
 Microarray profiling reveals the integrated stress response is activated by halofuginone in mammary epithelial cells
 
 
 Yana G Kamberov , Jihoon Kim , Ralph Mazitschek , Winston P Kuo, Malcolm Whitman
  Abstract
The small molecule Halofuginone (HF) is a potent regulator of extracellular matrix (ECM ) gene expression and is unique in its therapeutic potential. While the basis for HF effects is unknown, inhibition of TGF£] signaling and activation of the amino acid restriction response (AAR) have been linked to HF transcriptional control of a number of ECM components and amelioration of fibrosis and alleviation of autoimmune disease by regulation of Th17 cell differentiation, respectively. The aim of this study was to generate a global expression profile of HF targets in epithelial cells to identify potential mediators of HF function in this cell type. We report that HF modulation of the expression of the ECM remodeling protein Mmp13 in epithelial cells is separable from previously reported effects of HF on TGF£] signal inhibition, and use microarray expression analysis to correlate this with transcriptional responses characteristic of the Integrated Stress Response (ISR). Our findings suggest activation of the ISR may be a common mechanism underlying HF biological effects.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 OMICS. 2011, 15(10):673-82. doi: 10.1089/omi.2011.0064.
 Grade-Specific Expression Profiles of miRNAs/mRNAs and Docking Study in Human Grade I-III Astrocytomas
 
 
 Pan Chen, Xia-Yu Li, Li-Yang Zhang, Wei Xiong, Ming Zhou, Lan Xiao, Fang Zeng, Xiao-Ling Li, Ming-Hua Wu, Gui-Yuan Li
  Abstract
Although several miRNAs have been identified to be involved in glioblastoma tumorigenesis, little is known about the global expression profiles of miRNAs and their functional targets in astrocytomas at earlier stages of malignancy. In this study the global expression of miRNAs and mRNAs in normal brain tissue samples and grade I-III astrocytomas were analyzed parallelly using microarrays, and the grade-specific expression profiles of them were obtained by unsupervised hierarchical clustering. It was also confirmed that miR-107, miR-124, miR-138, and miR-149 were downregulated significantly in grade I-IV astrocytomas, and overexpression of miR-124 and miR-149 inhibited glioblastoma cell proliferation and migration. Furthermore, grade-specific changes were discovered in the central biological processes, regulatory networks, and signaling pathways associated with dysregulated genes, and a regulatory network of putative functional miRNA-mRNA pairs was defined. In conclusion, our results may contribute to a better understanding of the molecular mechanisms involved in astrocytoma tumorigenesis and malignant progression.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Addiction Biology. 2011 Oct 13. doi: 10.1111/j.1369-1600.2011.00390.x.
 Comparative gene expression profiling analysis of lymphoblastoid cells reveals neuron-specific enolase gene (ENO2) as a susceptibility gene of heroin dependence
 
 
 Ding-Lieh Liao, Min-Chih Cheng, Chih-Hao Lai, Hui-Ju Tsai, Chia-Hsiang Chen
  Abstract
Heroin dependence is a complex mental disorder resulting from interactions between genetic and environmental factors. Identifying the susceptibility genes of heroin dependence is the basis for understanding the pathogenesis of heroin dependence. Using a total gene expression microarray, we detected 924 differentially expressed gene transcripts in lymphoblastoid cell lines (LCLs) between 19 male heroin-dependent individuals and 20 male control subjects, including 279 upregulated and 645 downregulated gene transcripts in heroin-dependent individuals. We verified the reduced expression of the neuron-specific enolase gene (ENO2) in heroin-dependent individuals using real-time quantitative polymerase chain reaction and Western blot analysis. We further compared the allele and genotype frequencies of three single nucleotide polymorphisms (SNPs, rs11064464, rs3213433 and rs10849541) of the ENO2 gene between 532 male heroin-dependent individuals and 369 male controls. No significant differences in the allele or genotype frequencies of these three SNPs were detected between these two groups. Nevertheless, we identified a haplotype (T-C-G) derived from these three SNPs significantly underrepresented in heroin-dependent individuals compared with the control group (72.7% versus 75.9%, P?
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 The Journal of Immunology. 2011, 187(9):4426-30. doi: 10.4049/jimmunol.1101034.
 Cutting edge: IRF8 regulates Bax transcription in vivo in primary myeloid cells
 
 
 Jine Yang, Xiaolin Hu, Mary Zimmerman, Christina M. Torres, Dafeng Yang, Sylvia B. Smith, Kebin Liu
  Abstract
A prominent phenotype of IRF8 knockout (KO) mice is the uncontrolled expansion of immature myeloid cells. The molecular mechanism underlying this myeloproliferative syndrome is still elusive. In this study, we observed that Bax expression level is low in bone marrow preginitor cells and increases dramatically in primary myeloid cells in wt mice. In contrast, Bax expression level remained at a low level in primarymyeloid cells in IRF8 KO mice. However, in vitro IRF8 KO bone marrow-differentiated myeloid cells expressed Bax at a level as high as that in wild type myeloid cells. Furthermore, we demonstrated that IRF8 specifically binds to the Bax promoter region in primary myeloid cells. Functional analysis indicated that IRF8 deficiency results in increased resistance of the primary myeloid cells to Fas-mediated apoptosis. Our findings show that IRF8 directly regulates Bax transcription in vivo, but not in vitro during myeloid cell lineage differentiation.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Chemical Research in Toxicology. 2011, 24(10):1636-43. doi: 10.1021/tx200181q.
 Whole Genome Expression in Peripheral-Blood Samples of Workers Professionally Exposed to Polycyclic Aromatic Hydrocarbons.
 
 
 Wu MT, Lee TC, Wu IC, Su HJ, Huang JL, Peng CY, Wang W, Chou TY, Lin MY, Lin WY, Huang CT, Pan CH, Ho CK.
  Abstract
This study aims to examine global gene expression profiles before and after the work-shift among coke-oven workers (COWs). COWs work six consecutive days and then take two days off. Two blood and urine samples in each worker were collected before starting to work after two days off and end-of-shift in the sixth day of work in 2009. Altered gene expressions (ratio of gene expression levels between end-of-shift and preshift work) were performed by a Human OneArray expression system which probes ~30,000-transcription expression profiling of human genes. Sixteen workers, all men, were enrolled in this study. Median urinary 1-hydroxypyrene (1OHP) levels (£gmol/mol creatinine) in end-of-shift work were significantly higher than those in preshift work (2.58 vs 0.29, p = 0.0002). Among the 20,341 genes which passed experimental quality control, 26 gene expression changes, 7 positive and 19 negative, were highly correlated with across-the-shift urinary 1OHP levels (end-of-shift-preshift 1OHP) (p-value <0.001). The high and low exposure groups of across-the-shift urinary 1OHP levels dichotomized in ~2.00 £gmol/mol creatinine were able to be distinguished by these 26 genes. Some of them are known to be involved in apoptosis, chromosome stability/DNA repair, cell cycle control/tumor suppressor, cell adhesion, development/spermatogenesis, immune function, and neuronal cell function. These findings in COWs will be an ideal model to study the relationship of PAH exposure with acute changes of gene expressions.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 The Journal of Biological Chemistry. 2011, 286(25):22211-8. doi: 10.1074/jbc.M110.180224.
 Inhibitors of histone deacetylases: correlation between isoform specificity and reactivation of HIV type 1 (HIV-1) from latently infected cells.
 
 
 Huber K, Doyon G, Plaks J, Fyne E, Mellors JW, Sluis-Cremer N.
  Abstract
Deacetylation of histone proteins at the HIV type 1 (HIV-1) long terminal repeat (LTR) by histone deactylases (HDACs) can promote transcriptional repression and virus latency. As such, HDAC inhibitors (HDACI) could be used to deplete reservoirs of persistent, quiescent HIV-1 proviral infection. However, the development of HDACI to purge latent HIV-1 requires knowledge of the HDAC isoforms contributing to viral latency and the development of inhibitors specific to these isoforms. In this study, we identify the HDACs responsible for HIV-1 latency in Jurkat J89GFP cells using a chemical approach that correlates HDACI isoform specificity with their ability to reactivate latent HIV-1 expression. We demonstrate that potent inhibition or knockdown of HDAC1, an HDAC isoform reported to drive HIV-1 into latency, was not sufficient to de-repress the viral LTR. Instead, we found that inhibition of HDAC3 was necessary to activate latent HIV-1. Consistent with this finding, we identified HDAC3 at the HIV-1 LTR by chromatin immunoprecipitation. Interestingly, we show that valproic acid is a weak inhibitor of HDAC3 (IC(50) = 5.5 mm) relative to HDAC1 (IC(50) = 170 £gm). Because the total therapeutic concentration of valproic acid ranges from 275 to 700 £gm in adults, these data may explain why this inhibitor has no effect on the decay of latent HIV reservoirs in patients. Taken together, our study suggests an important role for HDAC3 in HIV-1 latency and, importantly, describes a chemical approach that can readily be used to identify the HDAC isoforms that contribute to HIV-1 latency in other cell types.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Molecular Carcinogenesis. 2012, 51(3):280-9. doi: 10.1002/mc.20844.
 Green tea catechin extract in intervention of chronic breast cell carcinogenesis induced by environmental carcinogens
 
 
 Kusum Rathore, Hwa-Chain Robert Wang.
  Abstract
Sporadic breast cancers are mainly attributable to long-term exposure to environmental factors, via a multi-year, multi-step, and multi-path process of tumorigenesis involving cumulative genetic and epigenetic alterations in the chronic carcinogenesis of breast cells from a non-cancerous stage to precancerous and cancerous stages. Epidemiologic and experimental studies have suggested that green tea components may be used as preventive agents for breast cancer control. In our research, we have developed a cellular model that mimics breast cell carcinogenesis chronically induced by cumulative exposures to low doses of environmental carcinogens. In this study, we used our chronic carcinogenesis model as a target system to investigate the activity of green tea catechin extract (GTC) at non-cytotoxic levels in intervention of cellular carcinogenesis induced by cumulative exposures to pico-molar 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and benzo[a]pyrene (B[a]P). We identified that GTC, at a non-cytotoxic, physiologically achievable concentration of 2.5 £gg/mL, was effective in suppressing NNK- and B[a]P-induced cellular carcinogenesis, as measured by reduction of the acquired cancer-associated properties of reduced dependence on growth factors, anchorage-independent growth, increased cell mobility, and acinar-conformational disruption. We also detected that intervention of carcinogen-induced elevation of reactive oxygen species (ROS), increase of cell proliferation, activation of the ERK pathway, DNA damage, and changes in gene expression may account for the mechanisms of GTC's preventive activity. Thus, GTC may be used in dietary and chemoprevention of breast cell carcinogenesis associated with long-term exposure to low doses of environmental carcinogens.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Cancer Research. 2011, 71(19):6208-19. doi: 10.1158/0008-5472.CAN-11-0073.
 MicroRNA-708 induces apoptosis and suppresses tumorigenicity in renal cancer cells
 
 
 Saini S, Yamamura S, Majid S, Shahryari V, Hirata H, Tanaka Y, Dahiya R.
  Abstract
Cancer pathogenesis is restricted by stresses that compromise cell division and survival. In this study, we identify miR-708, a little studied member of a set of microRNAs that have been implicated in stress control, as an important tumor suppressor in renal cell carcinoma (RCC). miR-708 expression was attenuated widely in human RCC specimens. Restoration of miR-708 expression in RCC cell lines decreased cell growth, clonability, invasion, and migration and elicited a dramatic increase in apoptosis. Moreover, intratumoral delivery of miR-708 was sufficient to trigger in vivo regression of established tumors in murine xenograft models of human RCC. Investigation of the targets of miR-708 identified the inhibitor of apoptosis protein survivin as important. siRNA-mediated knockdown of survivin partially phenocopied miR-708 overexpression suggesting that the proapoptotic role of miR-708 may be mediated primarily through survivin regulation. Additionally, we identified the E-cadherin regulators ZEB2 and BMI1 as likely miR-708 targets. Taken together, our findings define a major tumor suppressive role for miR-708, which may offer an attractive new target for prognostic and therapeutic intervention in RCC.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 PLoS One. 2011, 6(8):e23682. doi: 10.1371/journal.pone.0023682.
 Comprehensive Assessment of Host Responses to Ionizing Radiation by Nuclear Factor-£eB Bioluminescence Imaging-Guided Transcriptomic Analysis
 
 
 Q Chang CT, Lin H, Ho TY, Li CC, Lo HY, Wu SL, Huang YF, Liang JA, Hsiang CY.
  Abstract
The aim of this study was to analyze the host responses to ionizing radiation by nuclear factor-£eB (NF-£eB) bioluminescence imaging-guided transcriptomic tool. Transgenic mice carrying the NF-£eB-driven luciferase gene were exposed to a single dose of 8.5 Gy total-body irradiation. In vivo imaging showed that a maximal NF-£eB-dependent bioluminescent intensity was observed at 3 h after irradiation and ex vivo imaging showed that liver, intestine, and brain displayed strong NF-£eB activations. Microarray analysis of these organs showed that irradiation altered gene expression signatures in an organ-specific manner and several pathways associated with metabolism and immune system were significantly altered. Additionally, the upregulation of fatty acid binding protein 4, serum amyloid A2, and serum amyloid A3 genes, which participate in both inflammation and lipid metabolism, suggested that irradiation might affect the cross pathways of metabolism and inflammation. Moreover, the alteration of chemokine (CC-motif) ligand 5, chemokine (CC-motif) ligand 20, and Jagged 1 genes, which are involved in the inflammation and enterocyte proliferation, suggested that these genes might be involved in the radiation enteropathy. In conclusion, this report describes the comprehensive evaluation of host responses to ionizing radiation. Our findings provide the fundamental information about the in vivo NF-£eB activity and transcriptomic pattern after irradiation. Moreover, novel targets involved in radiation injury are also suggested.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Acta Histochem. 2012, 114(4):379-85. doi: 10.1016/j.acthis.2011.07.008.
 Expression of insulin-like growth factor binding protein-4 (IGFBP-4) in acute pancreatitis induced by l-arginine in mice
 
 
 Jia Qing Shen, Jie Shen, Xing Peng Wang.
  Abstract
The mechanisms of injury and regeneration after acute pancreatitis are still incompletely understood. Insulin-like growth factor binding proteins (IGFBPs) have been reported to play roles in various pancreatic diseases, but the involvement of insulin-like growth factor binding protein-4 (IGFBP-4) in acute pancreatitis is unknown. The aim of the study was to examine the expression of IGFBP-4 in mice with acute pancreatitis induced by two doses of L-arginine. IGFBP-4 expression was assayed by microarray test, real-time RT-PCR, Western blotting, ELISA and by an immunohistochemical assay. Microarray test of pancreatic mRNA showed that IGFBP-4 mRNA increased significantly after L-arginine treatment and the increase was confirmed by real-time RT-PCR. Western blotting and ELISA assay showed similar patterns of increase of IGFBP-4 in pancreatic tissues and serum. In the control pancreas, IGFBP-4 was mainly immunolocalized in the pancreatic islets. In the pancreatic tissues of mice with pancreatitis induced by L-arginine, the immunolocalization of IGFBP-4 was detected in both acinar cells and pancreatic islets. In conclusion, our results suggest that IGFBP-4 may play a potential role in pancreatic injury and regeneration in a murine model of acute pancreatitis induced by L-arginine.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Cancer Genomics Proteomics. 2011 Mar-Apr; 8(2):77-85..
 Small Molecule Inhibition of Cytoskeletal Dynamics in Melanoma Tumors Results in Altered Transcriptional Expression Patterns of Key Genes Involved in Tumor Initiation and Progression
 
 
 Spencer C, Montalvo J, McLaughlin SR, Bryan BA.
  Abstract
Rho kinase signaling plays an important role in the oncogenic process largely through its regulation of F-actin dynamics, and inhibition of this pathway results in reduction in tumor volume and metastasis across a number of tumor types. While the cytoskeletal-regulatory role of Rho kinase has been a topic of in-depth study, the mechanisms linking Rho kinase to altered geneexpression are largely unknown. Global gene expression analysis was performed on melanoma tumors treated with sham or the small molecule inhibitor Y27632. Inhibition of Rho kinase activity in melanoma tumors results in a statistically significant change in gene transcription of 94 genes, many of which are critically involved in tumor initiation and progression. In addition to regulating tumorigenesis through modulation of the phosphoproteome, Rho kinase signaling also contributes to the regulation of the tumor transcriptome.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Biomed Pharmacother.. 2011, 65(8):547-54. doi: 10.1016/j.biopha.2011.03.008.
 CXCL9 attenuated chemotherapy-induced intestinal mucositis by inhibiting proliferation and reducing apoptosis.
 
 
 Han X, Wu Z, Di J, Pan Y, Zhang H, Du Y, Cheng Z, Jin Z, Wang Z, Zheng Q, Zhang P, Wang Y.
  Abstract
Mucositis arising from cancer chemotherapy is a common problem for which there is no definitive treatment. 5-fluorouracil (5-FU) is a common cytotoxic agent used to treat solid tumors. A global gene expression array was performed to identify genetic signals involved in the pathogenesis of mucositis. The chemokine (C-X-C motif) ligand 9 (CXCL9) was one of the candidates identified that presented a characteristic gene expression profile; its temporal expression pattern was correlated with the damage and regeneration phases of the small intestine upon 5-FU chemotherapy. We found that prophylactic CXCL9 administration was able to attenuate the severity of mucositis, weight loss and diarrhea caused by chemotherapy. CXCL9 also increased the tolerance of the mice to lethal-dose chemotherapy. Moreover, we demonstrated that CXCL9 was able to promote the proliferation and regeneration of intestinal cells by inhibiting the proliferation of normal intestinal mucosal cells prior to chemotherapy and by reducing the 5-FU-induced apoptosis in intestinal crypts. Thus, pretreatment with CXCL9 is a new and promising strategy for the alleviation of chemotherapy-induced intestinal mucositis in clinical settings.
   

  ✔本篇論文使用華聯產品:Yeast OneArray  
 PLoS One.. 2011, 6(7):e22209. doi: 10.1371/journal.pone.0022209.
 The C-Terminus of Histone H2B Is Involved in Chromatin Compaction Specifically at Telomeres, Independently of Its Monoubiquitylation at Lysine 123
 
 
 Wang CY, Hua CY, Hsu HE, Hsu CL, Tseng HY, Wright DE, Hsu PH, Jen CH, Lin CY, Wu MY, Tsai MD, Kao CF.
  Abstract
Telomeric heterochromatin assembly in budding yeast propagates through the association of Silent Information Regulator (SIR) proteins with nucleosomes, and the nucleosome array has been assumed to fold into a compacted structure. It is believed that the level of compaction and gene repression within heterochromatic regions can be modulated by histone modifications, such as acetylation of H3 lysine 56 and H4 lysine 16, and monoubiquitylation of H2B lysine 123. However, it remains unclear as to whether or not gene silencing is a direct consequence of the compaction of chromatin. Here, by investigating the role of the carboxy-terminus of histone H2B in heterochromatin formation, we identify that the disorderly compaction of chromatin induced by a mutation at H2B T122 specifically hinders telomeric heterochromatin formation. H2B T122 is positioned within the highly conserved AVTKY motif of the £C helix of H2B. Heterochromatin containing the T122E substitution in H2B remains inaccessible to ectopic dam methylase with dramatically increased mobility in sucrose gradients, indicating a compacted chromatin structure. Genetic studies indicate that this unique phenotype is independent of H2B K123 ubiquitylation and Sir4. In addition, using ChIP analysis, we demonstrate that telomere structure in the mutant is further disrupted by a defect in Sir2/Sir3 binding and the resulting invasion of euchromatic histone marks. Thus, we have revealed that the compaction of chromatin per se is not sufficient for heterochromatin formation. Instead, these results suggest that an appropriately arrayed chromatin mediated by H2B C-terminus is required for SIR binding and the subsequent formation of telomeric chromatin in yeast, thereby identifying an intrinsic property of the nucleosome that is required for the establishment of telomeric heterochromatin. This requirement is also likely to exist in higher eukaryotes, as the AVTKY motif of H2B is evolutionarily conserved.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Oncogene. 2011, 30(23):2610-21. doi: 10.1038/onc.2010.637.
 £-Catulin knockdown induces senescence in cancer cells.
 
 
 Fan LC, Chiang WF, Liang CH, Tsai YT, Wong TY, Chen KC, Hong TM, Chen YL.
  Abstract
Cellular senescence functions as a tumor suppressor that protects against cancer progression. £-Catulin, an £-catenin-related protein, is reported to have tumorigenic potential because it regulates the nuclear factor-£eB (NF-£eB) pathway, but little is known about its clinical relevance and the mechanism through which it regulates cancer progression. Here, we found that £-catulin mRNA levels were significantly upregulated in cancer cell lines and clinical oral squamous cell carcinomas, which positively correlated with tumor size (P=0.001) and American Joint Committee on Cancer (AJCC) stage (P=0.004). £-Catulin knockdown in the OC2 and A549 cancer cell lines dramatically decreased cell proliferation and contributed to cellular senescence, and inhibited OC2 xenograft growth. Mechanistic dissection showed that £-catulin depletion strongly induced the DNA-damage response (DDR) in both cell lines, via a p53/p21-dependent pathway in A549 cells, but a p53/p21-independent pathway in OC2 cells carrying mutant p53. Global gene expression analysis revealed that £-catulin knockdown altered cell-cycle regulation and DDR pathways at the presenescent stage as well as significantly downregulate several crucial genes related to mitotic chromosome condensation, DDR and DNA repair systems, which suggests that its depletion-induced cellular senescence might be caused by chromosome condensation failures, severe DNA damage and impaired DNA repair ability. Our study provides evidence that £-catulin promotes tumor growth by preventing cellular senescence and suggests that downregulating £-catulin may be a promising therapeutic approach for cancer treatment.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 J. Virol. 2011, 85(18):9268-75. doi: 10.1128/JVI.00772-11.
 GFP Reporter System with Transcriptional Sequence Heterogeneity for Monitoring Interferon Response
 
 
 Mahmoud L, Al-Saif M, Amer HM, Sheikh M, Almajhdi FN, Khabar KS.
  Abstract
The interferon (IFN) response is initiated by a variety of triggers, including viruses and foreign RNA, and involves several receptors and intracellular mediators. Although there are common cis-acting consensus sequences in the promoters of many genes stimulated during the IFN response, they exhibit core and context heterogeneity that may lead to differential transcriptional activity. We have developed and validated a live cell-based enhanced green fluorescent protein (EGFP) reporter system employing more than a hundred constructs containing multiple viruses and IFN response elements derived from a variety of promoters involved in immunity to viruses. Common and distinct response patterns were observed due to promoter heterogeneity in response to different stimuli, including IFN-£, TLR3-agonist double-stranded RNA, and several viruses. This information should serve as a resource in selecting specific reporters for sensing nonself ligands.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 J Mol Biol. 2011, 410(1):118-30. doi: 10.1016/j.jmb.2011.04.064.
 Proteomic Analysis of Ribosomes: Translational Control of mRNA Populations by Glycogen Synthase GYS1
 
 
 Fuchs G, Diges C, Kohlstaedt LA, Wehner KA, Sarnow P.
  Abstract
Ribosomes exist as a heterogenous pool of macromolecular complexes composed of ribosomal RNA molecules, ribosomal proteins, and numerous associated "nonribosomal" proteins. To identify nonribosomal proteins that may modulate ribosome activity, we examined the composition of translationally active and inactive ribosomes using a proteomic multidimensional protein identification technology. Notably, the phosphorylated isoform of glycogen synthase, glycogen synthase 1 (GYS1), was preferentially associated with elongating ribosomes. Depletion of GYS1 affected the translation of a subset of cellular mRNAs, some of which encode proteins that modulate protein biosynthesis. These findings argue that GYS1 abundance, by virtue of its ribosomal association, provides a feedback loop between the energy state of the cells and the translation machinery.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Cancer Res. 2011, 71(2):349-59. doi: 10.1158/0008-5472.CAN-10-2550.
 HMGA2 overexpression-induced ovarian surface epithelial transformation is mediated through regulation of EMT genes
 
 
 Wu J, Liu Z, Shao C, Gong Y, Hernando E, Lee P, Narita M, Muller W, Liu J, Wei JJ.
  Abstract
The AT-hook transcription factor HMGA2 is an oncogene involved in the tumorigenesis of many malignant neoplasms. HMGA2 overexpression is common in both early and late-stage high-grade ovarian serous papillary carcinoma. To test whether HMGA2 participates in the initiation of ovarian cancer and promotion of aggressive tumor growth, we examined the oncogenic properties of HMGA2 in ovarian surface epithelial (OSE) cell lines. We found that introduction of HMGA2 overexpression was sufficient to induce OSE transformation in vitro. HMGA2-mediated OSE transformation resulted in tumor formation in the xenografts of nude mice. By silencing HMGA2 in HMGA2-overexpressing OSE and ovarian cancer cell lines, the aggressiveness of tumor cell growth behaviors was partially suppressed. Global gene profiling analyses revealed that HMGA2-mediated tumorigenesis was associated with expression changes of target genes and microRNAs that are involved in epithelial-to-mesenchymal transition (EMT). Lumican, a tumor suppressor that inhibits EMT, was found to be transcriptionally repressed by HMGA2 and was frequently lost in human high-grade serous papillary carcinoma. Our findings show that HMGA2 overexpression confers a powerful oncogenic signal in ovarian cancers through the modulation of EMT genes.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 J Clin Invest. 2011, 121(1):212-25. doi: 10.1172/JCI43144.
 Thioredoxin-like 2 regulates human cancer cell growth and metastasis via redox homeostasis and NF-£eB signaling
 
 
 Qu Y, Wang J, Ray PS, Guo H, Huang J, Shin-Sim M, Bukoye BA, Liu B, Lee AV, Lin X, Huang P, Martens JW, Giuliano AE, Zhang N, Cheng NH, Cui X.
  Abstract
Cancer cells have an efficient antioxidant system to counteract their increased generation of ROS. However, whether this ability to survive high levels of ROS has an important role in the growth and metastasis of tumors is not well understood. Here, we demonstrate that the redox protein thioredoxin-like 2 (TXNL2) regulates the growth and metastasis of human breast cancer cells through a redox signaling mechanism. TXNL2 was found to be overexpressed in human cancers, including breast cancers. Knockdown of TXNL2 in human breast cancer cell lines increased ROS levels and reduced NF-£eB activity, resulting in inhibition of in vitro proliferation, survival, and invasion. In addition, TXNL2 knockdown inhibited tumorigenesis and metastasis of these cells upon transplantation into immunodeficient mice. Furthermore, analysis of primary breast cancer samples demonstrated that enhanced TXNL2 expression correlated with metastasis to the lung and brain and with decreased overall patient survival. Our studies provided insight into redox-based mechanisms underlying tumor growth and metastasis and suggest that TXNL2 could be a target for treatment of breast cancer.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 J Pathol. 2011, 224(3):377-88. doi: 10.1002/path.2871.
 FMNL2 is a positive regulator of cell motility and metastasis in colorectal carcinoma
 
 
 Zhu XL, Zeng YF, Guan J, Li YF, Deng YJ, Bian XW, Ding YQ, Liang L.
  Abstract
FMNL2 is a member of diaphanous-related formins which act as effectors of Rho family GTPases and control the actin-dependent processes such as cell motility or invasion. We previously found that FMNL2 overexpression in metastatic cell lines and tissues of colorectal carcinoma is associated with more aggressive tumour behaviour. Here we used gain-of-function and loss-of-function approaches to investigate the effects of FMNL2 on colorectal carcinoma in vitro and in vivo. Forced expression of FMNL2 caused a significant increase in tumour cell proliferation, motility, invasion in vitro, and metastasis in vivo, whereas FMNL2 depletion showed opposite effects. We examined gene expression profiles following knockdown of FMNL2 in SW480/M5 cells. Expression of 323 genes was up-regulated by more than two-fold, whereas 222 genes were down-regulated by more than two-fold in FMNL2-depleting SW480/M5 cells. Gene ontology analysis showed that most of genes belong to functional categories such as cell cycle, cytoskeleton, transcription factor, and G-protein modulator. Pathway analysis revealed that cytoskeletal regulation by the Rho GTPase pathway, the Wnt pathway, the G-protein pathway, and the P53 pathway were affected by FMNL2. Many of these genes are in functional networks associated with cell proliferation, metastasis, Wnt or the Rho signalling pathway involved in the regulation of FMNL2. The expression of five differentially expressed genes including CXXC4, CD200, VAV1, CSF1, and EPHA2 was validated by real-time PCR and western blot analysis. Thus, FMNL2 is a positive regulator of cell motility, invasion, and metastasis of colorectal carcinoma.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Birth Defects Res A Clin Mol Teratol. 2011, 91(6):468-76. doi: 10.1002/bdra.20816.
 Defective sumoylation pathway directs congenital heart disease
 
 
 Wang J, Chen L, Wen S, Zhu H, Yu W, Moskowitz IP, Shaw GM, Finnell RH, Schwartz RJ.
  Abstract
Congenital heart defects (CHDs) are the most common of all birth defects, yet molecular mechanism(s) underlying highly prevalent atrial septal defects (ASDs) and ventricular septal defects (VSDs) have remained elusive. We demonstrate the indispensability of "balanced" posttranslational small ubiquitin-like modifier (SUMO) conjugation-deconjugation pathway for normal cardiac development. Both hetero- and homozygous SUMO-1 knockout mice exhibited ASDs and VSDs with high mortality rates, which were rescued by cardiac reexpression of the SUMO-1 transgene. Because SUMO-1 was also involved in cleft lip/palate in human patients, the previous findings provided a powerful rationale to question whether SUMO-1 was mutated in infants born with cleft palates and ASDs. Sequence analysis of DNA from newborn screening blood spots revealed a single 16 bp substitution in the SUMO-1 regulatory promoter of a patient displaying both oral-facial clefts and ASDs. Diminished sumoylation activity whether by genetics, environmental toxins, and/or pharmaceuticals may significantly contribute to susceptibility to the induction of congenital heart disease worldwide.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 J Immunology. 2011, 186(3):1638-45. doi: 10.4049/jimmunol.1003146.
 c-Maf-dependent growth of Mycobacterium tuberculosis in a CD14(hi) subpopulation of monocyte-derived macrophages
 
 
 Dhiman R, Bandaru A, Barnes PF, Saha S, Tvinnereim A, Nayak RC, Paidipally P, Valluri VL, Rao LV, Vankayalapati R.
  Abstract
Macrophages are a major component of the innate immune response, comprising the first line of defense against various intracellular pathogens, including Mycobacterium tuberculosis. In this report, we studied the factors that regulate growth of M. tuberculosis H37Rv in subpopulations of human monocyte-derived macrophages (MDMs). In healthy donors, M. tuberculosis H37Rv grew 5.6-fold more rapidly in CD14(hi) MDMs compared with that in CD14(lo)CD16(+) MDMs. Compared with CD14(lo)CD16(+) cells, M. tuberculosis H37Rv-stimulated CD14(hi) monocytes produced more IL-10 and had increased mRNA expression for c-Maf, a transcription factor that upregulates IL-10 gene expression. c-Maf small interfering RNA (siRNA) inhibited IL-10 production and growth of M. tuberculosis in CD14(hi) cells. Compared with CD14(lo)CD16(+) monocytes, M. tuberculosis H37Rv-stimulated CD14(hi) cells had increased expression of 22 genes whose promoters contained a c-Maf binding site, including hyaluronan synthase 1 (HAS1). c-Maf siRNA inhibited HAS1 expression in M. tuberculosis-stimulated CD14(hi) monocytes, and HAS1 siRNA inhibited growth of M. tuberculosis in CD14(hi) MDMs. M. tuberculosis H37Rv upregulated expression of HAS1 protein and its product, hyaluronan, in CD14(hi) MDMs. We conclude that M. tuberculosis grows more rapidly in CD14(hi) than in CD14(lo)CD16(+) MDMs because CD14(hi) cells have increased expression of c-Maf, which increases production of two key factors (hyaluronan and IL-10) that promote growth of M. tuberculosis.
   

  ✔本篇論文使用華聯產品:Mouse OneArray, Mouse&Rat miRNA OneArray  
 Physiol Genomics. 2011, 43(9):488-98. doi: 10.1152/physiolgenomics.00248.2010.
 Effects of in vivo transfection with anti-miR-214 on gene expression in murine molar tooth germ
 
 
 Sehic A, Risnes S, Khuu C, Khan QE, Osmundsen H.
  Abstract
MicroRNAs (miRNAs) are an abundant class of noncoding RNAs that are believed to be important in many biological processes through regulation of gene expression. Little is known of their function in tooth morphogenesis and differentiation. MicroRNA-214 (miR-214), encoded by the polycistronic Dnm30os gene, is highly expressed during development of molar tooth germ and was selected as a target for silencing with anti-miR-214. Mandibular injection of 1-100 pmol of anti-miR-214 close to the developing first molar in newborn mice resulted in significant decrease in expression of miR-214, miR-466h, and miR-574-5p in the tooth germ. Furthermore, levels of miR-199a-3p, miR-199a-5p, miR-690, miR-720, and miR-1224 were significantly increased. Additionally, the expression of 863 genes was significantly increased and the expression of 305 genes was significantly decreased. Among the genes with increased expression was Twist-1 and Ezh2, suggested to regulate expression of miR-214. Microarray results were validated using real-time RT-PCR and Western blotting. Among genes with decreased expression were Amelx, Calb1, Enam, and Prnp; these changes also being reflected in levels of corresponding encoded proteins in the tooth germ. In the anti-miR-214-treated molars the enamel exhibited evidence of hypomineralization with remnants of organic material and reduced surface roughness after acid etching, possibly due to the transiently decreased expression of Amelx and Enam. In contrast, several genes encoding contractile proteins exhibited significantly increased expression. mRNAs involved in amelogenesis (Ambn, Amelx, Enam) were not found among targets of miRNAs that were differentially expressed following treatment with anti-miR-214. It is therefore suggested that effects of miR-214 on amelogenesis are indirect, perhaps mediated by the observed miR-214-dependent changes in levels of expression of numerous transcription factors.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Pathol Oncol Res. 2011, 17(2):357-67. doi: 10.1007/s12253-010-9334-y.
 The Effect of SYT-SSX and Extracellular Signal-Regulated Kinase (ERK) on Cell Proliferation in Synovial Sarcoma
 
 
 Cai W, Sun Y, Wang W, Han C, Ouchida M, Xia W, Zhao X, Sun B.
  Abstract
The character of Synovial sarcoma is the chromosomal translocation t(X; 18)(p11.2;q11.2), which results in the fusion of the SYT gene with a SSX gene. There is little study that could fully elucidate the mechanism of pathogenesis of this fusion transcript. This study is designed to gain more insight into the function of this fusion gene. We evaluated the whole genome expression in SYO-1 cells inhibited as a result of specific small interfering RNA for SYT-SSX. Cell proliferation and apoptosis were analyzed by flow cytometer and MTT. The proteins correlated with proliferation were also detected using western blot. TUNEL and Immunohistochemical stain assessment were also carried out on TMA of SS tissues. The mRNA level reduced over 90% caused by SYT-SSX specific siRNA. Five pathways were employed, that ERK1/2 pathway was differential significantly (p = 0.043218). Meanwhile, down-regulation of SYT-SSX fusion gene expression would inhibit the proliferation of SS cell and the survival rate decreased (34.1%), while apoptotic rate increased (10.92%). After transfected with SYT-SSX-specific siRNA it caused a block in G1/G0 phase (31.99%) of SYO-1 cells compared with control cells. The protein level of ERK1/2, p-ERK, and cyclin D1 altered in same trend with expression of SYT-SSX. In TMA stain assessment, SYT-SSX positive group with high ki-67 LI expressed more cyclin D1and CDK4 than the SYT-SSX negative group. High ki-67 LI was detected in cases with p-ERK expression. Meanwhile, cyclin D1 and CDK4 were shown to be more expressed in tumor cells with p-ERK expression. Our results suggest that the fusion gene SYT-SSX should be considered to play important role on SS cell growth via ERK pathway. This study may be valuable for understanding the pathogenic role and molecular mechanism of the fusion gene SYT-SSX in synovial sarcoma through the proposed genome-wide approach. Furthermore, the research would open up the possibility of using SYT-SSX and ERK as a therapeutic target.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Libertas Academica. 2011, 6:7-16.
 Aberrantly Expressed Genes in HaCaT Keratinocytes Chronically Exposed to Arsenic Trioxide
 
 
 Udensi K. Udensi, Hari H.P. Cohly, Barbara E. Graham-Evans, Kenneth Ndebele, Nat?lia Garcia-Reyero, Bindu Nanduri, Paul B. Tchounwou, Raphael D. Isokpehi.
  Abstract
Inorganic arsenic is a known environmental toxicant and carcinogen of global public health concern. Arsenic is genotoxic and cytotoxic to human keratinocytes. However, the biological pathways perturbed in keratinocytes by low chronic dose inorganic arsenic are not completely understood. The objective of the investigation was to discover the mechanism of arsenic carcinogenicity in human epidermal keratinocytes. We hypothesize that a combined strategy of DNA microarray, qRT-PCR and gene function annotation will identify aberrantly expressed genes in HaCaT keratinocyte cell line after chronic treatment with arsenic trioxide. Microarray data analysis identified 14 up-regulated genes and 21 down-regulated genes in response to arsenic trioxide. The expression of 4 up-regulated genes and 1 down-regulated gene were confirmed by qRT-PCR. The up-regulated genes were AKR1C3 (Aldo-Keto Reductase family 1, member C3), IGFL1 (Insulin Growth Factor-Like family member 1), IL1R2 (Interleukin 1 Receptor, type 2), and TNFSF18 (Tumor Necrosis Factor [ligand] SuperFamily, member 18) and down-regulated gene was RGS2 (Regulator of G-protein Signaling 2). The observed over expression of TNFSF18 (167 fold) coupled with moderate expression of IGFL1 (3.1 fold), IL1R2 (5.9 fold) and AKR1C3 (9.2 fold) with a decreased RGS2 (2.0 fold) suggests that chronic arsenic exposure could produce sustained levels of TNF with modulation by an IL-1 analogue resulting in chronic immunologic insult. A concomitant decrease in growth inhibiting gene (RGS2) and increase in AKR1C3 may contribute to chronic inflammation leading to metaplasia, which may eventually lead to carcinogenicity in the skin keratinocytes. Also, increased expression of IGFL1 may trigger cancer development and progression in HaCaT keratinocytes.
   

  ✔本篇論文使用華聯產品:Mouse&Rat miRNA OneArray  
 Molecular Cell. 2011, 41(4):371-83. doi: 10.1016/j.molcel.2011.01.020.
 The ATM Kinase Induces MicroRNA Biogenesis in the DNA Damage Response
 
 
 Xinna Zhang, Guohui Wan, Franklin G. Berger, Xiaoming He, Xiongbin Lu.
  Abstract
The DNA damage response involves a complex network of processes that detect and repair DNA damage. Here we show that miRNA biogenesis is globally induced upon DNA damage in an ATM-dependent manner. About one-fourth of miRNAs are significantly upregulated after DNA damage, while loss of ATM abolishes their induction. KH-type splicing regulatory protein (KSRP) is a key player that translates DNA damage signaling to miRNA biogenesis. The ATM kinase directly binds to and phosphorylates KSRP, leading to enhanced interaction between KSRP and pri-miRNAs and increased KSRP activity in miRNA processing. Mutations of the ATM phosphorylation sites of KSRP impaired its activity in regulating miRNAs. These findings reveal a mechanism by which DNA damage signaling is linked to miRNA biogenesis.
   

  ✔本篇論文使用華聯產品:Human OneArray,Human miRNA OneArray  
 J Matern Fetal Neonatal Med. 2011, 24(8):1002-12. doi: 10.3109/14767058.2010.538454.
 Global maternal early pregnancy peripheral blood mRNA and miRNA expression profiles according to plasma 25-hydroxyvitamin D concentrations
 
 
 Enquobahrie DA, Williams MA, Qiu C, Siscovick DS, Sorensen TK.
  Abstract
We investigated associations of early pregnancy maternal vitamin D concentrations with differential gene expression and post-transcription regulation. Plasma 25-hydroxyvitamin D (25[OH]D) was measured among participants of a nested case-control study. Participants with low (<25.5 ng/ml) and high (?31.7 ng/ml) 25[OH]D were identified among controls. Peripheral blood messenger RNA (mRNA) (N?=?21) and microRNA (miRNA) (N?=?13) expression studies were conducted among participants with low and high 25[OH]D concentrations. Differential expression between low/high groups were evaluated using Student's t-test, fold change, and SAM comparisons. We further investigated functions and functional relationships of differentially expressed mRNAs and targets of differentially expressed miRNAs. Three hundred and five genes (299 upregulated and 6 downregulated) and 11 miRNAs (10 downregulated and 1 upregulated) were differentially expressed among participants with low 25[OH]D compared with those who had high 25[OH]D. Genes that participate in a wide range of cellular functions, including organ and system development (e.g. angiogenesis), inflammation and metabolic processes (e.g. carbohydrate/lipid metabolism), as well as miRNAs that target these genes were differentially expressed among women with low 25[OH]D compared with those with high 25[OH]D. Early pregnancy plasma 25[OH]D concentrations are associated with maternal peripheral blood gene expression and post-transcription regulation.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Biochemical and Biophysical Research Communications. 2011, 405(1):102-6. doi: 10.1016/j.bbrc.2010.12.135.
 Identifying cell and molecular stress after radiation in a three-dimensional (3-D) model of oral mucositis
 
 
 Parsa C, Mulamalla H, Orlando R, Lau B, Huang Y, Pon D, Chow M, Lambros MP
  Abstract
Mucositis is a debilitating adverse effect of chemotherapy and radiation treatment. It is important to develop a simple and reliable in vitro model, which can routinely be used to screen new drugs for prevention and treatment of mucositis. Furthermore, identifying cell and molecular stresses especially in the initiation phase of mucositis in this model will help towards this end. We evaluated a three-dimensional (3-D) human oral cell culture that consisted of oral keratinocytes and fibroblasts as a model of oral mucositis. The 3-D cell culture model was irradiated with 12 or 2 Gy. Six hours after the irradiation we evaluated microscopic sections of the cell culture for evidence of morphologic changes including apoptosis. We used microarrays to compare the expression of several genes from the irradiated tissue with identical genes from tissue that was not irradiated. We found that irradiation with 12 Gy induced significant histopathologic effects including cellular apoptosis. Irradiation significantly affected the expression of several genes of the NF-kB pathway and several inflammatory cytokines, such as IL-1B, 1L-8, NF-kB1, and FOS compared to tissue that was not irradiated. We identified significant upregulation of several genes that belong to damage-associated molecular patterns (DAMPs) such as HMB1, S100A13, SA10014, and SA10016 in the 3-D tissues that received 12 Gy but not in tissues that received 2 Gy. In conclusion, this model quantifies radiation damage and this is an important first step towards the development 3-D tissue as a screening tool.
   

  ✔本篇論文使用華聯產品:Array technology and applications  
 Nature Methods. 2010, 7:181-186. doi:10.1038/nmeth0310-181.
 Epigenome: mapping in motion
 
 
 Monya Baker
  Abstract
As high-throughput techniques accelerate mapping of epigenetic marks, researchers are racing to find the biological meaning of these marks.
   

  ✔本篇論文使用華聯產品:Array technology and applications  
 Nature methods. 2010, 7(9):687-92. doi: 10.1038/nmeth0910-687.
 MicroRNA profiling: separating signal from noise
 
 
 Monya Baker
  Abstract
MicroRNAs may be small, but these noncoding RNAs that regulate gene expression are creating a big stir. Finding differences in the expression of microRNAs between, say, healthy and diseased cells could potentially be used to diagnose diseases or to assess treatment effects. If researchers can understand how they work, microRNAs could provide tools for manipulating genes, not to mention help to untangle how genes are regulated.At first glance, studying microRNAs seems more manageable than studying the menagerie of other types of RNA. Typical expression profiling experiments for protein-coding genes examine thousands of molecules; those for microRNAs examine hundreds. But researchers are still figuring out the most reliable ways to measure these important molecules. The most common techniques for profiling microRNAs are deep sequencing, microarrays and quantitative real-time PCR (qPCR). All are supported by several commercial offerings. Though specific products and techniques vary, researchers generally agree on the relative strengths and weaknesses of the platforms. The best choice depends on the application, says Muneesh Tewari, who studies microRNAs at the Fred Hutchinson Cancer Research Center. ¡§It's a balance of cost, precision, accuracy and sample quantity,¡¨ he says. ¡§If the purpose is to screen a bunch of samples to find a few microRNAs that change and you can tolerate a false negative, then the microarray may be the best platform. If the purpose is to detect microRNAs where the sample amount is limiting, then qPCR has better sensitivity, and if you are trying to see different isoforms or very similar microRNAs, then sequencing is going to be the best approach.
   

  ✔本篇論文使用華聯產品:Array technology and applications  
 Journal of the Chinese Medical Association. 2010, 73(3):139-143. doi: 10.1016/S1726-4901(10)70028-9.
 Good Mortality Prediction by Glasgow Coma Scale for Neurosurgical Patients
 
 
 Hsien-Wei Ting, Ming-Shung Chen, Yueh-Chun Hsieh, Chien-Lung Chan
  Abstract
Background: How to effectively use the finite resources of an intensive care unit (ICU) for neurosurgical patients is a critical decision-making process. Mortality prediction models are effective tools for allocating facilities. This study intended to distinguish the prediction power of the Acute Physiology and Chronic Health Evaluation II (APACHE II), the Simplified Acute Physiology Score II (SAPS II), and the Glasgow Coma Scale (GCS) for neurosurgical patients. Methods: According to the definitions of the APACHE II, this study recorded both APACHE II and SAPS II scores of 154 neurosurgical patients in the ICU of a 600-bed general hospital. Linear regression models of GCS (GCS-mr) were constructed. The t test, receiver operating characteristic (ROC) curve and Wilcoxon signed rank test were used as the statistical evaluation methods. Results: There were 50 (32.5%) females and 104 (67.5%) males in this study. Among them, 108 patients survived and 46 patients died. The areas under the ROC curves (AUC) of SAPS II and APACHE II were 0.872 and 0.846, respectively. The AUC of GCS-mr was 0.866, and the R2 was 0.389. The evaluation powers of SAPS II, GCS-mr and APACHE II were the same (p > 0.05). Patients with GCS ≤ 5 or motor component of GCS (GCS-M) ≤ 3 had a higher probability of mortality than patients with GCS > 5 or GCS-M > 3 (p < 0.01). Conclusion: The predictive powers of SAPS II, APACHE II and GCS-mr were the same. The GCS-mr is more convenient for predicting mortality in neurosurgical patients. Both GCS ≤ 5 and GCS-M ≤ 3 are good indicators of mortality in these patients.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 FEBS Letters. 2010, 584(14):3198-202. doi: 10.1016/j.febslet.2010.06.012.
 A strategy to rapidly identify the functional targets of microRNAs by combining bioinformatics and mRNA cytoplasmic/nucleic ratios in culture cells
 
 
 Jie Li, Wei Xia, Baochun Huang, Liucun Chen, Xueting Su, Shaohua Li, Fang Wang, Hongmei Ding, Ningsheng Shao
  Abstract
MicroRNAs are approximately 22nt non-coding RNAs that are present in a broad range of multicellular organisms. MicroRNAs play important roles in many biological or pathological processes by regulating the expression of their target genes. The fast and accurate identification of miRNA targets is a bottleneck in the clarification of the function of miRNAs. Here, we established a rapid and accurate strategy to identify miRNA functional target genes by combination of bioinformatic prediction with Cytoplasmic/Nuclear (C/N) ratios of mRNAs. The strategy comprises three steps: bioinformatic prediction, determination of mRNA C/N ratios, and confirmation by Western blotting, and might be suitable to most miRNAs. Our method will make a significant contribution to the study of the biological functions of miRNAs.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Nanotechnology. 2010, 21(23):235103. doi: 10.1088/0957-4484/21/23/235103.
 Homologous RBC-derived vesicles as ultrasmall carriers of iron oxide for magnetic resonance imaging of stem cells
 
 
 Microsugar Chang, Jong-Kai Hsiao, Ming Yao, Li-Ying Chien, Szu-Chun Hsu, Bor-Sheng Ko, Shin-Tai Chen, Hon-Man Liu, Yao-Chang Chen, Chung-Shi Yang, Dong-Ming Huang
  Abstract
Ultrasmall superparamagnetic iron oxide (USPIO) particles are very useful for cellular magnetic resonance imaging (MRI), which plays a key role in developing successful stem cell therapies. However, their low intracellular labeling efficiency, and biosafety concerns associated with their use, have limited their potential usage. In this study we develop a novel system composed of RBC-derived vesicles (RDVs) for efficient delivery of USPIO particles into human bone marrow mesenchymal stem cells (MSCs) for cellular MRI in vitro and in vivo. RDVs are highly biosafe to their autologous MSCs as manifested by cell viability, differentiation, and gene microarray assays. The data demonstrate the potential of RDVs as intracellular delivery vehicles for biomedical applications.
   

  ✔本篇論文使用華聯產品:Experimental Accessories  
 Mol Endocrinol. 2010, 24(3):540-51. doi: 10.1210/me.2009-0432.
 MicroRNA-224 Is Involved in Transforming Growth Factor-£]-Mediated Mouse Granulosa Cell Proliferation and Granulosa Cell Function by Targeting Smad4
 
 
 Guidong Yao, Mianmian Yin, Jie Lian, Hui Tian, Lin Liu, Xin Li, Fei Sun
  Abstract
"Many members of the TGF- superfamily are indicated to play important roles in ovarian follicular development, such as affecting granulosa cell function and oocyte maturation. Abnormalities associated with TGF- 1 signaling transduction could result in female infertility. MicroRNAs (miRNAs), as small noncoding RNAs, were recently found to regulate gene expression at posttranscriptional levels. However, little is known about the role of miRNAs in TGF- -mediated granulosa cell proliferation and granulosa cell function. In this study, the miRNA expression profiling was identified from TGF- 1-treated mouse preantral granulosa cells (GCs), and three miRNAs were found to be significantly up-regulated and 13 miRNAs were down-regulated. Among up-regulated miRNAs, miR-224 was the second most significantly elevated miRNA. This up-regulation was attenuated by treatment of GCs with SB431542 (an inhibitor of TGF superfamily type I receptors, thus blocking phosphorylation of the downstream effectors Smad2/3), indicating that miR-224 expression was regulated by TGF- 1/Smads pathway. The ectopic expression of miR-224 can enhance TGF- 1-induced GC proliferation through targeting Smad4. Inhibition of endogenous miR- 224 partially suppressed GC proliferation induced by TGF- 1. In addition, both miR-224 and TGF- 1 can promote estradiol release from GC, at least in part, through increasing CYP19A1 mRNA levels. This is the first demonstration that miRNAs can control reproductive functions resulting in promoting TGF- 1-induced GC proliferation and ovarian estrogen release. Such miRNA-mediated effects could be potentially used for regulation of reproductive processes or for treatment of reproductive disorders."
   

  ✔本篇論文使用華聯產品:Human OneArray, Mouse OneArray  
 Methods Mol Biol. 2009;590:165-76.
 Methylated DNA Immunoprecipitation and Microarray-Based Analysis: Detection of DNA Methylation in Breast Cancer Cell Lines
 
 
 Tim H. M. Huang, and Pearlly S. Yan, Yu-I Weng
  Abstract
The methylated DNA immunoprecipitation microarray (MeDIP-chip) is a genome-wide, high-resolution approach to detect DNA methylation in whole genome or CpG (cytosine base followed by a guanine base) islands. The method utilizes anti-methylcytosine antibody to immunoprecipitate DNA that contains highly methylated CpG sites. Enriched methylated DNA can be interrogated using DNA microarrays or by massive parallel sequencing techniques. This combined approach allows researchers to rapidly identify methylated regions in a genome-wide manner, and compare DNA methylation patterns between two samples with diversely different DNA methylation status. MeDIP-chip has been applied successfully for analyses of methylated DNA in the different targets including animal and plant tissues. Here we present a MeDIP-chip protocol that is routinely used in our laboratory, illustrated with specific examples from MeDIP-chip analysis of breast cancer cell lines. Potential technical pitfalls and solutions are also provided to serve as workflow guidelines.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Clin Transl Sci. 2010, 3(4):158-69. doi: 10.1111/j.1752-8062.2010.00212.x.
 A New Class of Human Mast Cell and Peripheral Blood Basophil Stabilizers that Differentially Control Allergic Mediator Release
 
 
 Sarah K. Norton, Anthony Dellinger, Zhiguo Zhou, Robert Lenk, Darren MacFarland, Becky Vonakis, Daniel Conrad, Christopher L. Kepley
  Abstract
Treatments for allergic disease block the effects of mediators released from activated mast cells and blood basophils. A panel of fullerene derivatives was synthesized and tested for their ability to preempt the release of allergic mediators in vitro and in vivo. The fullerene C(70)-tetraglycolic acid significantly inhibited degranulation and cytokine production from mast cells and basophils, while C(70)-tetrainositol blocked only cytokine production in mast cells and degranulation and cytokine production in basophils. The early phase of FcepsilonRI inhibition was dependent on the blunted release of intracellular calcium stores, elevations in reactive oxygen species, and several signaling molecules. Gene microarray studies further showed the two fullerene derivatives inhibited late phase responses in very different ways. C(70)-tetraglycolic acid was able to block mast cell-driven anaphylaxis in vivo, while C(70)-tetrainositol did not. No toxicity was observed with either compound. These findings demonstrate the biological effects of fullerenes critically depends on the moieties added to the carbon cage and suggest they act on different FcepsilonRI-specific molecules in mast cells and basophils. These next generation fullerene derivatives represent a new class of compounds that interfere with FcepsilonRI signaling pathways to stabilize mast cells and basophils. Thus, fullerene-based therapies may be a new approach for treating allergic diseases.
   

  ✔本篇論文使用華聯產品:Experimental Accessories  
 Journal of the Taiwan Institute of Chemical Engineers. 2011, 42(1):5-12.
 Effect of co-axially hybridized gene targets on hybridization efficiency of microarrayed DNA probes
 
 
 Kai Ren Jiang, Jie-Len Huang, Chia-Chun Chen, Hung-Ju Su, Jui-Chuang Wu
  Abstract
The effect of relative size of two co-axially hybridized gene targets on the hybridization efficiency was studied for two DNA probe configurations and various probe concentrations. Each of two sets of microarrayed probes contained a pair of DNA probes and a pair of their complementary samples labeled with two distinct fluorescent dyes. The sequence of each probe is especially designed so that two targets are simultaneously complementary to two adjacent sections of the probe. The molecular steric effect on the hybridization efficiency is investigated by comparing the dye signals between configurations of one-target and two-target hybridization scenarios. The results show that a low probe concentration gives better hybridization efficiency and the first-hybridization conducted by a shorter-size DNA target improves the hybridization efficiency of the second target coupling onto the same probe.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 CLINICAL ANDVACCINE IMMUNOLOGY. 2010, 17(12):1909-16. doi: 10.1128/CVI.00194-10.
 Serum Intercellular Adhesion Molecule 1 Variations in Young Children with Acute Otitis Media
 
 
 Keyi Liu, Janet Casey, and Michael Pichichero
  Abstract
Acute otitis media (AOM) is an inflammatory reaction in the middle ear, most often occurring in young children. Streptococcus pneumoniae, nontypeable Haemophilus influenzae, and Moraxella catarrhalis are the most common bacteria isolated. Intercellular adhesion molecule 1 (ICAM-1) is involved in the innate immune response to infection by microorganisms, in effective antigen presentation, and in subsequent T-cell activation. Here we prospectively studied levels of serum soluble ICAM-1 (sICAM-1) before, at the time of, and after antimicrobial treatment of AOM in a group of 138 children ages 6 to 30 months. Middle ear fluids were collected by tympanocentesis to identify otopathogens. We found that (i) serum levels of sICAM-1 were significantly higher in S. pneumoniae-, nontypeable H. influenzae-, and M. catarrhalis-infected children than in well children (P < 0.001), confirming that a systemic inflammatory response occurs during AOM; (ii) sICAM-1 levels varied from no elevation (110 ng/ml) to elevation to high levels (maximum, 1,470 ng/ml) among children with AOM; (iii) in paired samples, sICAM-1 levels increased 4- to 20-fold when children developed AOM compared to their sICAM-1 levels before infection; and (iv) the level of sICAM-1 returned to the pre-AOM level at the convalescent stage of AOM after successful antimicrobial therapy. We conclude that AOM often causes a systemic inflammatory reaction, as measured by elevation of the serum sICAM-1 level, and that a high variability in sICAM-1 responses occurs with the presence of otopathogens during AOM.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 J Infect Dis. 2010, 202(2):282-90. doi: 10.1086/653484.
 Transcriptional profiling of Clostridium difficile and Caco-2 cells during infection
 
 
 Janvilisri T, Scaria J, Chang YF.
  Abstract
Clostridium difficile is well recognized as the most common infectious cause of nosocomial diarrhea. The incidence and severity of C. difficile infection (CDI) is increasing worldwide. Here, we evaluated simultaneously the transcriptional changes in the human colorectal epithelial Caco-2 cells and in C. difficile after infection. A total of 271 transcripts in Caco-2 cells and 207 transcripts in C. difficile were significantly differentially expressed at 1 time point during CDI. We used the gene ontology annotations and protein-protein network interactions to underline a framework of target molecules that could potentially play a key role during CDI. These genes included those associated with cellular metabolism, transcription, transport, cell communication, and signal transduction. Our data identified certain key factors that have previously been reported to be involved in CDI, as well as novel determinants that may participate in a complex mechanism underlying the host response to infection, bacterial adaptation, and pathogenesis.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Acta Pharmacol Sin. 2010, 31(2):227-36. doi: 10.1038/aps.2009.197.
 Microarray analysis reveals the inhibition of nuclear factor-kappa B signaling by aristolochic acid in normal human kidney (HK-2) cells
 
 
 Chen YY, Chiang SY, Wu HC, Kao ST, Hsiang CY, Ho TY, Lin JG.
  Abstract
To study the molecular mechanism underlying the effect of aristolochic acid (AA), a major active component of plants from the Aristolochiaceae family using microarray analysis. Human kidney (HK-2) cells were treated with AA (0, 10, 30, and 90 micromol/L) for 24 h, and the cell viability was measured by a 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyltetrazolium bromide assay. Complementary DNA microarrays were used to investigate the gene expression pattern of HK-2 cells exposed to AA in triplicate. A quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assay was used to verify the microarray data for selected nuclear factor kappa B (NF-kappaB)-regulated genes. Furthermore, the subcellular localization of NF-kappaB p65 was visualized by immunofluorescence confocal microscopy in HK-2 cells. The NF-kappaB activity was examined by a luciferase reporter assay in HK-2/NF-kappaB transgenic cells. AA exhibited a dose-dependent cytotoxic effect in HK-2 cells and induced alterations in the gene expression profiles related to the DNA damage response, DNA repair, macromolecule metabolic process, carbohydrate metabolic process, DNA metabolic process, apoptosis, cell cycle, and transcription. In addition, 9 biological pathways associated with immunomodulatory functions were down-regulated in AA-treated HK-2 cells. A network analysis revealed that NF-kappaB played a central role in the network topology. Among NF-kappaB-regulated genes, 8 differentially expressed genes were verified by qRT-PCR. The inhibition of NF-kappaB activity by AA was further confirmed by immunofluorescence confocal microscopy and by NF-kappaB luciferase reporter assay. Our data revealed that AA could suppress NF-kappaB activity in normal human cells, perhaps partially accounting for the reported anti-inflammatory effects of some plants from the genus Aristolochia.
   

  ✔本篇論文使用華聯產品:Human miRNA OneArray  
 Mutat Res. 2011, 707(1-2):42-52. doi: 10.1016/j.mrfmmm.2010.12.009.
 Antroquinonol inhibits NSCLC proliferation by altering PI3K/mTOR proteins and miRNA expression profiles
 
 
 Kumar VB, Yuan TC, Liou JW, Yang CJ, Sung PJ, Weng CF.
  Abstract
Antroquinonol a derivative of Antrodia camphorata h