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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: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 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  
 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.
   

  ✔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 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.
   

  ✔本篇論文使用華聯產品:  
 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: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: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  
 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  
 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: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  
 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: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:  
 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: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: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  
 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: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: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: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  
 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: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  
 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: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: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  
 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: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  
 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  
 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: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  
 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: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: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: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  
 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  
 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: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  
 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: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: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: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: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: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: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: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: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: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 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: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: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 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  
 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  
 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  
 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: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  
 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: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  
 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  
 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: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: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  
 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: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: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  
 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  
 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: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: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  
 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: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  
 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:Mouse OneArray  
 Invest Ophthalmol Vis Sci. 2011, 25;52(1):527-40. doi: 10.1167/iovs.10-5731.
 Sigma receptor 1 modulates ER stress in retinal neurons.
 
 
 Yonju Ha, Ying Dun, Muthusamy Thangaraju, Jennifer N Duplantier, Zheng Dong, Kebin Liu, Vadivel Ganapathy, Sylvia B Smith
  Abstract
To investigate the mechanism of £m receptor 1 (£mR1) neuroprotection in retinal neurons. Oxidative stress, which is implicated in diabetic retinopathy, was induced in mouse primary ganglion cells (GCs) and RGC-5 cells, and the effect of the £mR1 ligand (+)-pentazocine on pro- and anti-apoptotic and endoplasmic reticulum (ER) stress gene expression was examined. Binding of £mR1 to BiP, an ER chaperone protein, and £mR1 phosphorylation status were examined by immunoprecipitation. Retinas were harvested from Ins2Akita/+ diabetic mice treated with (+)-pentazocine, and the expression of ER stress genes and of the retinal transcriptome was evaluated. Oxidative stress induced the death of primary GCs and RGC-5 cells. The effect was decreased by the application of (+)-pentazocine. Stress increased £mR1 binding to BiP and enhanced £mR1 phosphorylation in RGC-5 cells. BiP binding was prevented, and £mR1 phosphorylation decreased in the presence of (+)-pentazocine. The ER stress proteins PERK, ATF4, ATF6, IRE1£, and CHOP were upregulated in RGC-5 cells during oxidative stress, but decreased in the presence of (+)-pentazocine. A similar phenomenon was observed in retinas of Ins2Akita/+ diabetic mice. Retinal transcriptome analysis of Ins2Akita/+ mice compared with wild-type revealed differential expression of the genes critically involved in oxidative stress, differentiation, and cell death. The expression profile of those genes was reversed when the Ins2Akita/+ mice were treated with (+)-pentazocine. In retinal neurons, the molecular chaperone £mR1 binds BiP under stressful conditions; (+)-pentazocine may exert its effects by dissociating £mR1 from BiP. As stress in retinal cells increases, phosphorylation of £mR1 is increased, which is attenuated when agonists bind to the receptor.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Int. J. Biol. Sci. 2010, 6(5):428-42.
 Increased invasiveness and aggressiveness in breast epithelia with cytoplasmic p63 expression.
 
 
 Hsiao YH, Su YA, Tsai HD, Mason JT, Chou MC, Man YG.
  Abstract
Our previous studies revealed that pregnancy associated breast cancer (PABC) had significantly reduced nuclear p63 expression in myoepithelia, while intense cytoplasmic p63 expression in associated epithelia. Our current study assessed these epithelia using immunohistochemistry with a panel of aggressiveness and invasiveness related markers and comparative genomic hybridization (array-CGH) with over 30,000 DNA probes. These epithelia showed several unique alterations, including (1) immunohistochemical and morphological resemblance to invasive cancer, (2) significant gain in copy numbers of DNA coding genes for morphogenesis, angiogenesis, and metastasis, and (3) significant loss in copy numbers of DNA coding genes for tumor suppressors, cell adhesion, and macromolecular complex assembly or intra-cellular trafficking. Detected array-CGH alterations correlated well with in vivo expression of a number of corresponding proteins tested. These findings suggest that aberrant sub-cellular localization of p63 expression in normal or hyperplastic appearing epithelial cells may significant contribute to increased invasiveness and aggressiveness of these cells.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 BMC Cell Biol. 2010, 7;11:23. doi: 10.1186/1471-2121-11-23.
 CC3/TIP30 affects DNA damage repair.
 
 
 Fong S, King F, Shtivelman E.
  Abstract
The pro-apoptotic protein CC3/TIP30 has an unusual cellular function as an inhibitor of nucleocytoplasmic transport. This function is likely to be activated under conditions of stress. A number of studies support the notion that CC3 acts as a tumor and metastasis suppressor in various types of cancer. The yeast homolog of CC3 is likely to be involved in responses to DNA damage. Here we examined the potential role of CC3 in regulation of cellular responses to genotoxic stress. We found that forced expression of CC3 in CC3-negative cells strongly delays the repair of UV-induced DNA damage. Exogenously introduced CC3 negatively affects expression levels of DDB2/XPE and p21CIP1, and inhibits induction of c-FOS after UV exposure. In addition, exogenous CC3 prevents the nuclear accumulation of P21CIP in response to UV. These changes in the levels/localization of relevant proteins resulting from the enforced expression of CC3 are likely to contribute to the observed delay in DNA damage repair. Silencing of CC3 in CC3-positive cells has a modest delaying effect on repair of the UV induced damage, but has a much more significant negative affect on the translesion DNA synthesis after UV exposure. This could be related to the higher expression levels and increased nuclear localization of p21CIP1 in cells where expression of CC3 is silenced. Expression of CC3 also inhibits repair of oxidative DNA damage and leads to a decrease in levels of nucleoredoxin, that could contribute to the reduced viability of CC3 expressing cells after oxidative insult. Manipulation of the cellular levels of CC3 alters expression levels and/or subcellular localization of proteins that exhibit nucleocytoplasmic shuttling. This results in altered responses to genotoxic stress and adversely affects DNA damage repair by affecting the recruitment of adequate amounts of required proteins to proper cellular compartments. Excess of cellular CC3 has a significant negative effect on DNA repair after UV and oxidant exposure, while silencing of endogenous CC3 slightly delays repair of UV-induced damage.
   

  ✔本篇論文使用華聯產品:Mouse OneArray  
 Biomaterials. 2009, 30(17):3042-3049. doi: 10.1016/j.biomaterials.2009.02.016.
 Nuclear factor-£eB bioluminescence imaging-guided transcriptomic analysis for the assessment of host¡Vbiomaterial interaction in vivo
 
 
 Chien-Yun Hsiang, Yueh-Sheng Chen, Tin-Yun Ho
  Abstract
Establishment of a comprehensive platform for the assessment of host¡Vbiomaterial interaction in vivo is an important issue. Nuclear factor-kB (NF-kB) is an inducible transcription factor that is activated by numerous stimuli. Therefore, NF-kB-dependent luminescent signal in transgenic mice carrying the luciferase genes was used as the guide to monitor the biomaterials-affected organs, and transcriptomic analysis was further applied to evaluate the complex host responses in affected organs in this study. In vivo imaging showed that genipin-cross-linked gelatin conduit (GGC) implantation evoked the strong NF-kB activity at 6 h in the implanted region, and transcriptomic analysis showed that the expressions of interleukin-6 (IL-6), IL-24, and IL-1 family were up-regulated. A strong luminescent signal was observed in spleen on 14 d, suggesting that GGC implantation might elicit the biological events in spleen. Transcriptomic analysis of spleen showed that 13 Kyoto Encyclopedia of Genes and Genomes pathways belonging to cell cycles, immune responses, and metabolism were significantly altered by GGC implants. Connectivity Map analysis suggested that the gene signatures of GGC were similar to those of compounds that affect lipid or glucose metabolism. GeneSetTest analysis further showed that host responses to GGC implants might be related to diseases states, especially the metabolic and cardiovascular diseases. In conclusion, our data provided a concept of molecular imaging-guided transcriptomic platform for the evaluation and the prediction of host¡Vbiomaterial interaction in vivo.
   

  ✔本篇論文使用華聯產品:Human OneArray  
 Reprod Fertil Dev. 2009, 21(1):22-30.
 Embryonic gene expression profiling using microarray analysis
 
 
 Daniel Le Bourhis, Xavier Vignon, Yvan Heyman, Robin E. Everts, Sandra L. Rodriguez-Zas, Harris A. Lewin, Jean-Paul Renard, Xiangzhong Yang, X. Cindy Tian, Sadie L. Marjani
  Abstract
Microarray technology enables the interrogation of thousands of genes at one time and therefore a systems level of analysis. Recent advances in the amplification of RNA, genome sequencing and annotation, and the lower cost of developing microarrays or purchasing them commercially, have facilitated the analysis of single preimplantation embryos. The present review discusses the components of embryonic expression profiling and examines current research that has used microarrays to study the effects of in vitro production and nuclear transfer.