產品資訊 > 人類表達譜晶片 Human OneArray® v7

 
  human microarray for gene expression   人類表達譜晶片 v7 延續 "One Gene-One Probe" 的設計原理,以 IMPORT 專利技術針對 protein-coding 基因設計高專一性探針,並以自主的高速佈放技術進行晶片生產。v7 版晶片於 201511 月上市,根據 RefSeq 70Ensembl 80 資料庫進行探針的更新,以提供更高基因覆蓋率的表達譜晶片。
 
 
 
人類表達譜晶片 v7 探針內容
探針種類 探針數
  基因探針設計資料庫: 28,264
          - RefSeq release 70
          - Ensembl release 80
  控制探針數 940
  總探針數 29,204
  

基 因 探 針
 
人類表達譜晶片 v7 版本的更新是參考國際公認之 RefSeqEnsembl 序列資料庫, 設計長鏈 60 個鹼基寡核酸 (sense-strand) 的人類表達譜基因探針, 內容以蛋白質編碼基因 (protein-coding gene) 為主,相較於 v7 版本, 除了提高整體的基因覆蓋率外,更完整的覆蓋與生理途徑反應相關的基因, 並且每一個探針對其來源資料庫的目標基因皆具高度專一性,避免非目標基因的雜交影響。

此外,華聯專業團隊建構 ”華聯探針註解搜尋引擎”(PASS) 網站,方便使用者查詢各探針相對應於 NCBIEnsembl 資料庫的詳細註解。
 
   
    

控 制 探 針
 
 
為確保晶片數據品質,華聯技術團隊經過一連串的測試及驗證,設計一系列的品質控制探針, 以監控完整的晶片實驗步驟,包含樣本 RNA 完整性、樣本 RNA 放大流程、螢光標記效率、晶片雜交、晶片掃描等。
 
 
 

使用HOA文獻 ( 184 )

 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.
   

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

 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.
   

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

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

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

 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.
   

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

 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.
   

 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.
   

 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.
   

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

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

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

 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.
   

 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
   

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

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

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

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

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

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

 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.
   

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

 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.
   

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

 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.
   

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

 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.
   

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

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

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

 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.
   

 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.
   

 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.
   

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

 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.
   

 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.
   

 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.
   

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

 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.
   

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

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

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

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

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

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

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

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

 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.  
   

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

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

 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.
   

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

 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.
   

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

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

 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.
   

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

 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.
   

 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.
   

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

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

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

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

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

 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.
   

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

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

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

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

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

 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.
   

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

 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.
   

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

 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.
   

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

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

 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.
   

 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.
   

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

 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.
   

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

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

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

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

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

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

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

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

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

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

 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.
   

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

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

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

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

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

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

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

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

 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.
   

 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.
   

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

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

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

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

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

 Cancer Genet Cytogenet. 2010, 203(2):215-21. doi: 10.1016/j.cancergencyto.2010.08.022.
 GSTT1 copy number gain is a poor predictive marker for escalated-dose imatinib treatment in chronic myeloid leukemia: genetic predictive marker found using array comparative genomic hybridization.
 
 
 Koh Y, Kim DY, Park SH, Jung SH, Park E, Kim HJ, Sohn SK, Joo YD, Kim SJ, Shin HJ, Kim SH, Song HS, Chung J, Kim I, Yoon SS, Kim BK, Shin SH, Chung YJ, Park S.
  Abstract
In a study population of 45 patients who were previously enrolled in an imatinib dose escalation trial, genome-wide screening for regions of genetic gains and losses was performed using array comparative genomic hybridization (aCGH). Early molecular response (EMR), defined as >50% reduction in the ratio of BCR-ABL1 to ABL1 within 6 months after dose escalation, was a major endpoint for analysis. After aCGH analysis, copy number change of four genes was investigated in 52 patients as a validation. Copy number gain in 16p11.2 was more frequently observed in patients with EMR than in patients who failed to achieve EMR (P = 0.034). A tendency for increased copy number in 22q11.23 in patients without EMR and for decreased copy number in 17q12 in patients with EMR was observed (P = 0.072 and P = 0.070, respectively). For GSTT1, in 22q11.23, copy number gain was observed in patients without EMR (P = 0.035). GSTT1 copy number gain was related to short time to treatment failure (TTFx) in patients without BCR-ABL1 mutations (P = 0.007). In multivariate analysis, GSTT1 copy number gain was an independent predictive factor for short TTFx (P = 0.020). We conclude that chromosome regions 16p11.2, 22q11.23, and 17q12 are potential locations related to response in imatinib dose escalation therapy for CML. GSTT1 copy number gain is a genetic change affecting outcome in this setting.
   

 Chinese Medical Sciences Journal. 2010, 25(2):100-104.
 Nectin-like molecule 1 inhibits the migration and invasion of U251 glioma cells by regulating the expression of an extracellular matrix protein osteopontin.
 
 
 Yin B, Li KH, An T, Chen T, Peng XZ.
  Abstract
To investigate the molecular mechanism of nectin-like molecule 1 (NECL1) inhibiting the migration and invasion of U251 glioma cells. We infected U251 glioma cells with adeno-nectin-like molecule 1 (Ad-NECL1) or empty adenovirus (Ad). Transwell and wound healing assays were performed to observe the migration of U251 cells incubated with the cell supernatant from Ad-NECL1 or Ad infected U251 cells. DNA microarray was applied to screen the gene expression profile after the restoration of NECL1 in U251 glioma cell lines. The differential expression of osteopontin (OPN), a gene related to migration and invasion, was further analyzed with semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR), Western blot, and immunohistochemistry. The restoration of NECL1 inhibited migration of U251 cells significantly (P<0.05). Altogether 195 genes were found differentially expressed by microarray, in which 175 were up-regulated and 20 down-regulated, including 9 extracellular matrix proteins involved in the migration of cells. Both mRNA and protein expressions of OPN, the most markedly reduced extracellular matrix protein, were found decreased in U251 cells after restoration of NECL1. Immunohistochemical assay also detected an increase of OPN in glioma tissues,related with the progressing of malignant grade. A link might exist between NECL1 and the extracellular matrix protein OPN in inhibiting the migration and invasion of U251 glioma cells.
   

 J Assist Reprod Genet. 2011, 28(2):173-88. doi: 10.1007/s10815-010-9491-7.
 Biomarkers of human oocyte developmental competence expressed in cumulus cells before ICSI: a preliminary study.
 
 
 Assidi M, Montag M, Van Der Ven K, Sirard MA.
  Abstract
To identify reliable genomic biomarkers expressed in cumulus cells that accurately and non-invasively predict the oocyte developmental competence and reinforce the already used morphological criteria. Eight consenting patients were selected for ovarian stimulation and ICSI procedures. Cumulus-oocyte complexes were transvaginally punctured and individually selected based on both good morphological criteria and high zona pellucida birefringence. Following ICSI, two 3-day embryos per patient were transferred. Pregnancy outcome was recorded and proven implantation was thereafter confirmed. Differential gene expression was assessed using two microarray platforms. Further real-time PCR validation, Ingenuity pathways analysis and intra-patient analysis were performed on 17 selected candidates. Seven genes were differentially (p???0.05) associated to successful pregnancy and implantation. These biomarkers could be used to predict the oocyte developmental competence. These genomic markers are a powerful reinforcement of morphological approaches of oocyte selection. Their large-scale validation could increase pregnancy outcome and single embryo transfer efficiency.
   

 Lung Cancer. 2010, 70(2):152-7. doi: 10.1016/j.lungcan.2010.01.019.
 Copy number alterations and expression profiles of candidate genes in a pulmonary inflammatory myofibroblastic tumor.
 
 
 Seung-Hyun Jungab, Seon-Hee Yimac, Hae-Jin Huab, Chan-Kwon Jungc, Sug-Hyung Leed, Dong Hoon Kime, Yeun-Jun Chung.
  Abstract
Inflammatory myofibroblastic tumor (IMT) is a soft tissue neoplasm composed of myofibroblastic spindle cells accompanied by the inflammatory infiltrate. In addition to its phenotypic ambiguity, pathogenic mechanisms of the IMT also remain elusive. Although several chromosomal aberrations have been identified by karyotyping, detailed characteristics and extent of copy number alterations in IMT are unknown. Copy number alterations of an IMT case were examined using 30K whole-genome oligoarray-comparative genomic hybridization. RNA expression of putative cancer-related genes located in the chromosomal altered regions was assessed by qRT-PCR. We identified seven copy number gained regions, seven lost regions, nine amplifications and six homozygous deletions, which covers 2.5% of total genome. In homozygously deleted regions, RNA levels of putative tumor suppressors, SEMA3B, SEMA3F and SULT2A1, were significantly repressed being consistent with copy number status. In high-level amplification regions, RNA expression of four potential cancer-related genes was examined; GSTT1, ESR1, EVI1 and MITF. Among them, GSTT1 and ESR1 were significantly up-regulated, but EVI1 and MITF showed insignificant elevation of RNA expression. To our knowledge, this is the first genome-wide analysis of copy number alterations in IMT. Most of the putative cancer-related genes identified in this study are supposedly novel in IMT. Taken together, our results will help to elucidate the pathogenic mechanisms of IMT.
   

 Systems Biology in Reproductive Medicine. 2010, 56(4):318-26. doi: 10.3109/19396361003646109.
 Expression Profiling of Protein Tyrosine Kinases and Their Ligand Activators in Leiomyoma Uteri.
 
 
 Yong Jiang, Guangli Suo, Anil Sadarangani, Bryan Cowan, Jean Y. J. Wang.
  Abstract
The aim of this study is to compare the expression patterns of tyrosine kinases and their ligand activators between matched myometrium and leiomyoma tissues. Total RNA extracted from 42 pairs of matched leiomyomal and adjacent myometrial tissues were hybridized to a set of 840 customized oligonucleotide microarrays to compare the expression profiles of 244 selected human genes including 90 tyrosine kinases and 103 ligands. Among the 244 genes surveyed, 38 were found to exhibit differential expression between pairs of myometrium and leiomyoma tissues. Clustering analysis of the expression ratios of these 38 genes from 42 pairs of samples led to the subdivision of fibroid samples into three groups, based in principle on the expression ratios of two peptide ligands, CYR61 and EFNA4. Real-time quantitative RT-PCR measurements of an additional 32 pairs of samples further confirmed the three subgroups. The altered expression of ligand activators between myometrium and leiomyoma suggest that tyrosine kinases regulated by CYR61 and EFNA4 may be exploited as therapeutic targets to develop non-surgical treatments of symptomatic leiomyomas.
   

 Ind Health. 2011, 49(1):8-14.
 Changes in Oxidative Stress Biomarker and Gene Expression Levels in Workers Exposed to Volatile Organic Compounds.
 
 
 Kim JH, Moon JY, Park EY, Lee KH, Hong YC.
  Abstract
Exposure to volatile organic compounds (VOCs) was known to result in immunologic, respiratory, carcinogenic, reproductive, neurologic, and cardiovascular effects. However, the mechanisms by which VOCs induce these adverse health effects are not well understood. To evaluate the change of oxidative stress biomarker and gene expression levels in workers exposed to VOCs, we obtained urine and blood samples from 21 subjects before and after occupational exposure to VOCs. We measured levels of muconic acid (MuA), hippuric acid (HA), mandelic acid (MaA), and methyl hippuric acid (MHA) as urinary exposure biomarkers for benzene, toluene, ethylbenzene, and xylene (collectively BTEX), and malondialdehyde (MDA) and 8-hydroxydeoxyguanine (8-OHdG) as oxidative stress biomarkers in all subjects. We also evaluated BTEX-mediated RNA expression using cDNA microarray in 14 subjects. HA and MHA levels were higher following occupational exposure to VOCs (p < 0.01). In the linear regression analysis, HA ratios of after- and before-exposure were found to be significantly associated with increase of MDA ratios of after- and before-exposure after controlling for age, body mass index, and smoking (£] = 0.06, p = 0.031). Evaluation of the gene expressions by HA showed that 23 gene expressions were found to be significantly associated with HA levels after adjusting for age, body mass index, and smoking (p < 0.001). In particular, expressions of ENO3 and CDNA FLJ39461 fis among the 23 genes were significantly associated with the change in MDA level (p < 0.05). Our study results suggest that exposure to VOCs, specifically toluene, induces oxidative stress and various gene expression change of which some may be responsible for oxidative stress.
   

 BMC Microbiology. 2010, 10:244. doi: 10.1186/1471-2180-10-244.
 Coxiella burnetii Nine Mile II proteins modulate gene expression of monocytic host cells during infection.
 
 
 Saugata Mahapatra, Patricia Ayoubi, Edward I Shaw.
  Abstract
Coxiella burnetii is an intracellular bacterial pathogen that causes acute and chronic disease in humans. Bacterial replication occurs within enlarged parasitophorous vacuoles (PV) of eukaryotic cells, the biogenesis and maintenance of which is dependent on C. burnetii protein synthesis. These observations suggest that C. burnetii actively subverts host cell processes, however little is known about the cellular biology mechanisms manipulated by the pathogen during infection. Here, we examined host cell gene expression changes specifically induced by C. burnetii proteins during infection. We have identified 36 host cell genes that are specifically regulated when de novo C. burnetii protein synthesis occurs during infection using comparative microarray analysis. Two parallel sets of infected and uninfected THP-1 cells were grown for 48 h followed by the addition of chloramphenicol (CAM) to 10 £gg/ml in one set. Total RNA was harvested at 72 hpi from all conditions, and microarrays performed using Phalanx Human OneArray? slides. A total of 784 (mock treated) and 901 (CAM treated) THP-1 genes were up or down regulated ?2 fold in the C. burnetii infected vs. uninfected cell sets, respectively. Comparisons between the complementary data sets (using >0 fold), eliminated the common gene expression changes. A stringent comparison (?2 fold) between the separate microarrays revealed 36 host cell genes modulated by C. burnetii protein synthesis. Ontological analysis of these genes identified the innate immune response, cell death and proliferation, vesicle trafficking and development, lipid homeostasis, and cytoskeletal organization as predominant cellular functions modulated by C. burnetii protein synthesis. Collectively, these data indicate that C. burnetii proteins actively regulate the expression of specific host cell genes and pathways. This is in addition to host cell genes that respond to the presence of the pathogen whether or not it is actively synthesizing proteins. These findings indicate that C. burnetii modulates the host cell gene expression to avoid the immune response, preserve the host cell from death, and direct the development and maintenance of a replicative PV by controlling vesicle formation and trafficking within the host cell during infection.
   

 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.
   

 NATURE. 2010, 466(7305):503-7. doi: 10.1038/nature09261.
 Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development.
 
 
 Hank H. Qi, Madathia Sarkissian, Gang-Qing Hu, Zhibin Wang, Arindam Bhattacharjee, D. Benjamin Gordon, Michelle Gonzales, Fei Lan, Pat P. Ongusaha, Maite Huarte, Nasser K. Yaghi, Huijun Lim, Benjamin A. Garcia, Leonardo Brizuela, Keji Zhao, Thomas M. Roberts, Yang Shi.
  Abstract
X-linked mental retardation (XLMR) is a complex human disease that causes intellectual disability. Causal mutations have been found in approximately 90 X-linked genes; however, molecular and biological functions of many of these genetically defined XLMR genes remain unknown. PHF8 (PHD (plant homeo domain) finger protein 8) is a JmjC domain-containing protein and its mutations have been found in patients with XLMR and craniofacial deformities. Here we provide multiple lines of evidence establishing PHF8 as the first mono-methyl histone H4 lysine 20 (H4K20me1) demethylase, with additional activities towards histone H3K9me1 and me2. PHF8 is located around the transcription start sites (TSS) of approximately 7,000 RefSeq genes and in gene bodies and intergenic regions (non-TSS). PHF8 depletion resulted in upregulation of H4K20me1 and H3K9me1 at the TSS and H3K9me2 in the non-TSS sites, respectively, demonstrating differential substrate specificities at different target locations. PHF8 positively regulates gene expression, which is dependent on its H3K4me3-binding PHD and catalytic domains. Importantly, patient mutations significantly compromised PHF8 catalytic function. PHF8 regulates cell survival in the zebrafish brain and jaw development, thus providing a potentially relevant biological context for understanding the clinical symptoms associated with PHF8 patients. Lastly, genetic and molecular evidence supports a model whereby PHF8 regulates zebrafish neuronal cell survival and jaw development in part by directly regulating the expression of the homeodomain transcription factor MSX1/MSXB, which functions downstream of multiple signalling and developmental pathways. Our findings indicate that an imbalance of histone methylation dynamics has a critical role in XLMR.
   

 European Journal of Cell Biology. 2010, 89(7):537-46. doi: 10.1016/j.ejcb.2010.01.005.
 Expression of the homeobox gene, HOPX, is modulated by cell differentiation in human keratinocytes and is involved in the expression of differentiation markers.
 
 
 Jun-Mo Yang, Seon Mi Sim, Hyo-Yeon Kim, Geon Tae Park.
  Abstract
Homeodomain only protein X (HOPX), an unusual homeodomain protein, was originally identified as a key regulator of cardiac development. We first demonstrated that the expression of HOPX was dependent on the differentiation of human keratinocytes and has an effect on the expression of differentiation markers. HOPX was suppressed in proliferating human keratinocytes and was gradually induced by calcium-triggered differentiation of human keratinocytes. In the epidermis, HOPX is highly expressed in the terminally differentiated suprabasal layers. Among the transcript variants of HOPX, the variant 3 driven by promoter A was the main transcript and it was regulated by cell differentiation in human keratinocytes. The expression of HOPX was induced through the phorbol-12-myristate-13-acetate (PMA)-dependent protein kinase C (PKC) signaling pathway, and not by the demethylating agent, 5-aza-dC (5-aza-2'-deoxycitidine) suggesting the suppression of HOPX is not associated with DNA methylation in human keratinocytes. The RNA interference (RNAi) silencing experiment showed that the knockdown of HOPX expression resulted in the increase of such differentiation markers as involucrin and loricrin. Exogenous expression of HOPX down-regulated the expression of differentiation marker genes in immortalized human keratinocytes (HaCaT). Collectively, HOPX is modulated by cell differentiation in human keratinocytes and this might contribute to homeostasis of keratinocytes by controlling differentiation-dependent genes.
   

 Vaccine. 2010, 28(31):4945-54.
 Immunomodulatory and adjuvant activities of a polysaccharide extract of Ganoderma lucidum in vivo and in vitro.
 
 
 Lai CY, Hung JT, Lin HH, Yu AL, Chen SH, Tsai YC, Shao LE, Yang WB, Yu J.
  Abstract
We had isolated a high molecular weight polysaccharide fraction, designated as F3, and performed a comprehensive analysis of its immunomodulatory and adjuvant activities in vivo and in vitro. In vivo, F3-treated mice showed an increase in the number of dendritic cells as well as CD4, CD8, regulatory T, B, plasma, NK, and NKT cells in the spleen. F3 also elevated the levels of multiple cytokines and chemokines in the blood of mice. F3 displayed potent adjuvant activity for tetanus toxoid in the absence of alum and potentiated antibody responses to alum-containing tetanus toxoid in mice. In addition, F3 also boosted Th1 and Th2 response in vivo. In vitro, F3 induced the maturation of dendritic cells derived from human monocytes by upregulating CD40, CD54, CD80, CD83, CD86, and HLA-DR, enhanced mixed lymphocyte reaction, and stimulated the production of ten cytokines and six chemokines. In microarray analysis, expressions of 7688 genes were modulated in dendritic cells after treatment with F3, including cytokine and chemokine genes. These results provide F3 polysaccharide extract further insight into the mechanisms of action for these immunomodulatory and adjuvant activities of from Ganoderma lucidum and also offer preclinical evidence for its development as a vaccine adjuvant.
   

 Basic & Clinical Medicine. 2010, 30:5.
 Expression and regulation of HES1 in sperms with low motility from asthenospermia patients.
 
 
 LI Yan,WEN Liu,CHEN De-yu.
  Abstract
To analyze the expression and regulation of HES1 in sperms with low motility.MethodsThirty semen samples from asthenospermia patients and 20 semen samples from healthy and fertile adults were collected,total RNAs were extracted to produce cDNAs probes.Hybridization with Phalanx OneArrayTM containing 30 968 probes was carried out after the labeled cDNAs were purified by PCR product purification kit.Realtime RT-PCR was used to analyze the expression of hsa-miR-487a and hsa-miR-193b;the expression of the target genes of hsa-miR-487a and hsa-miR-193b were searched from gene-expression profiles in asthenospermia patients' sperms.Results The expression level of HES1 in low motility sperms was up-regulated.The expression level of hsa-miR-193b in low motility sperms was 2.19 times higher than that in high motility sperms,hsa-miR-487a was 0.43% of that in high motility sperms.Conclusion The expression level of HES1 in low motility sperms was up-regulated.Hsa-miR-487a and hsa-miR-193b may affect the expression of HES1 and so regulate sperm motility.
   

 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.
   

 Biochemical and Biophysical Research Communications. 2010, 393(3):420-5. doi: 10.1016/j.bbrc.2010.02.010.
 SOX2 modulates alternative splicing in transitional cell carcinoma.
 
 
 Chun-Liang Tung, Pei-Hsuan Hou, Yung-Ling Kao, Yu-Wn Huang, Chiung-Chun Shen, Yi-Hsin Cheng, Shu-Fen Wu, Moon-Sing Lee, Chin Li
  Abstract
Aberrant alternative splicing of key cellular regulators may play a pivotal role in cancer development. To investigate the potential influence of altered alternative splicing on the development of transitional cell carcinoma (TCC), splicing activity in the TCC cell lines TSGH8301 and BFTC905 was examined using the SV40-immortalized uroepithelial cell line SV-HUC-1 as a reference. Our results indicate a significant alteration in splice site selection in the TCC cell lines. By gene expression profiling and subsequent validation, we discovered that sex-determining region Y-box protein 2 (SOX2) is specifically upregulated in BFTC905. Furthermore, ectopic expression of SOX2 modulates alternative splicing of the splicing reporter in vivo. More significantly, using an in vitro pull-down assay, it was found that SOX2 exhibits RNA-binding capability. Our observations suggest that SOX2 modulates alternative splicing by functioning as a splicing factor.
   

 BLOOD. 2009, 114(15):3181-90. doi: 10.1182/blood-2009-02-205708.
 Characterization of Gaucher disease bone marrow mesenchymal stromal cells reveals an altered in?ammatory secretome.
 
 
 Philippe M. Campeau, Moutih Rafei, Marie-No ?le Boivin, Ying Sun, Gregory A. Grabowski, Jacques Galipeau
  Abstract
Gaucher disease causes pathologic skeletal changes that are not fully explained. Considering the important role of mesenchymal stromal cells (MSCs) in bone structural development and maintenance, we analyzed the cellular biochemistry of MSCs from an adult patient with Gaucher disease type 1 (N370S/L444P mutations). Gaucher MSCs possessed a low glucocerebrosidase activity and consequently had a 3-fold increase in cellular glucosylceramide. Gaucher MSCs have a typical MSC marker phenotype, normal osteocytic and adipocytic differentiation, growth, exogenous lactosylceramide trafficking, cholesterol content, lysosomal morphology, and total lysosomal content, and a marked increase in COX-2, prostaglandin E2, interleukin-8, and CCL2 production compared with normal controls. Transcriptome analysis on normal MSCs treated with the glucocerebrosidase inhibitor conduritol B epoxide showed an up-regulation of an array of inflammatory mediators, including CCL2, and other differentially regulated pathways. These cells also showed a decrease in sphingosine-1-phosphate. In conclusion, Gaucher disease MSCs display an altered secretome that could contribute to skeletal disease and immune disease manifestations in a manner distinct and additive to Gaucher macrophages themselves.
   

 JOURNAL OF VIROLOGY. 2009, 83(20):10548-56. doi: 10.1128/JVI.01250-09.
 Baculovirus Transduction of Mesenchymal Stem Cells Triggers the Toll-Like Receptor 3 Pathway.
 
 
 Guan-Yu Chen, Hsiao-Chiao Shiah, Hung-Ju Su, Chi-Yuan Chen, Yung-Jen Chuang, Wen-Hsin Lo, Jie-Len Huang, Ching-Kuang Chuang, Shiaw-Min Hwang, Yu-Chen Hu
  Abstract
Human mesenchymal stem cells (hMSCs) can be genetically modified with viral vectors and hold promise as a cell source for regenerative medicine, yet how hMSCs respond to viral vector transduction remains poorly understood, leaving the safety concerns unaddressed. Here, we explored the responses of hMSCs against an emerging DNA viral vector, baculovirus (BV), and discovered that BV transduction perturbed the transcription of 816 genes associated with five signaling pathways. Surprisingly, Toll-like receptor-3 (TLR3), a receptor that generally recognizes double-stranded RNA, was apparently upregulated by BV transduction, as confirmed by microarray, PCR array, flow cytometry, and confocal microscopy. Cytokine array data showed that BV transduction triggered robust secretion of interleukin-6 (IL-6) and IL-8 but not of other inflammatory cytokines and beta interferon (IFN-beta). BV transduction activated the signaling molecules (e.g., Toll/interleukin-1 receptor domain-containing adaptor-inducing IFN-beta, NF-kappaB, and IFN regulatory factor 3) downstream of TLR3, while silencing the TLR3 gene with small interfering RNA considerably abolished cytokine expression and promoted cell migration. These data demonstrate, for the first time, that a DNA viral vector can activate the TLR3 pathway in hMSCs and lead to a cytokine expression profile distinct from that in immune cells. These findings underscore the importance of evaluating whether the TLR3 signaling cascade plays roles in the immune response provoked by other DNA vectors (e.g., adenovirus). Nonetheless, BV transduction barely disturbed surface marker expression and induced only transient and mild cytokine responses, thereby easing the safety concerns of using BV for hMSCs engineering.
   

 Biochemical and Biophysical Research Communications. 2009, 387(2):239-44. doi: 10.1016/j.bbrc.2009.06.128.
 Dual knockdown of N-ras and epiregulin synergistically suppressed the growth of human hepatoma cells.
 
 
 Meng Zhao, Hong-wei He, Huan-xing Sun, Kai-huan Ren, Rong-guang Shao
  Abstract
Hepatocellular carcinoma (HCC) is a major challenge because of its resistance to conventional cytotoxic chemotherapy and radiotherapy. Multi-targeted therapy might be a new option for HCC treatment. Our previous study showed that N-ras gene was activated in HCC and was inhibited by RNA interference. In the present study, we investigated the alternation of gene expression by microarray in N-Ras-siRNA-treated HepG2 cells. The results revealed that the EREG gene, encoding epiregulin, was dramatically up-regulated in response to silence of N-ras. We speculated that the up-regulation of epiregulin was involved in the compensatory mechanism of N-ras knockdown for cell growth. Therefore, we evaluated whether dual silence of N-ras and epiregulin display a greater suppression of cell growth. The results confirmed that dual knockdown of N-ras and epiregulin synergistically inhibited cell growth. Our results also showed that dual knockdown of N-ras and epiregulin significantly induced cell arrest at G0/G1 phase. Furthermore, Western blot assay showed that dual knockdown of N-ras and epiregulin markedly reduced the phosphorylations of ERK1/2, Akt and Rb, and inhibited the expression of cyclin D1. Our findings imply that multi-targeted silence of oncogenes might be an effective treatment for HCC.
   

 Platelets. 2009, 20(5):289-96. doi: 10.1080/09537100902993022.
 Clinical manifestation and molecular genetic characterization of MYH9 disorders.
 
 
 Vera Geierova, Tereza Kumstyrova, Roman Kotlin, Dana Mikulenkova, Kamila Zurkova, Vaclav Matoska, Ingrid Hrachovinova, Simon Rittich, Dana Provaznikova
  Abstract
Currently, the May-Hegglin anomaly (MHA), Sebastian (SBS), Fechtner (FTNS) and Epstein (EPS) syndrome are considered to be distinct clinical manifestations of a single disease caused by mutations of the MYH9 gene encoding the heavy chain of non-muscle myosin IIA (NMMHC-IIA). Manifestations of these disorders include giant platelets, thrombocytopenia and combinations of the presence of granulocyte inclusions, deafness, cataracts and renal failure. We examined 15 patients from 10 unrelated families on whom we performed immunostaining of NMMHC-IIA in blood samples. Polymerase chain reaction (PCR) analysis of selected exons of the MYH9 gene revealed mutations in nine samples with one novel mutation. Results of fluorescence and mutational analysis were compared with clinical manifestations of the MYH9 disorder. We also determined the number of glycoprotein sites on the surface of platelets. Most patients had an increased number of glycoproteins, which could be due to platelet size.
   

 EXPERIMENTAL and MOLECULAR MEDICINE. 2009, 41(7):462-70. doi: 10.3858/emm.2009.41.7.051.
 Integrated analysis of copy number alteration and RNA expression profiles of cancer using a high-resolution whole-genome oligonucleotide array.
 
 
 Seung-Hyun Jung, Seung-Hun Shin,Seon-Hee Yim, Hye-Sun Choi, Sug-Hyung Lee and Yeun-Jun Chung.
  Abstract
Recently, microarray-based comparative genomic hybridization (array-CGH) has emerged as a very efficient technology with higher resolution for the genome-wide identification of copy number alterations (CNA). Although CNAs are thought to affect gene expression, there is no platform currently available for the integrated CNA-expression analysis. To achieve high-resolution copy number analysis integrated with expression profiles, we established human 30k oligoarray-based genome-wide copy number analysis system and explored the applicability of this system for integrated genome and transcriptome analysis using MDA-MB-231 cell line. We compared the CNAs detected by the oligoarray with those detected by the 3k BAC array for validation. The oligoarray identified the single copy difference more accurately and sensitively than the BAC array. Seventeen CNAs detected by both platforms in MDA-MB-231 such as gains of 5p15.33-13.1, 8q11.22-8q21.13, 17p11.2, and losses of 1p32.3, 8p23.3-8p11.21, and 9p21 were consistently identified in previous studies on breast cancer. There were 122 other small CNAs (mean size 1.79 mb) that were detected by oligoarray only, not by BAC-array. We performed genomic qPCR targeting 7 CNA regions, detected by oligoarray only, and one non-CNA region to validate the oligoarray CNA detection. All qPCR results were consistent with the oligoarray-CGH results. When we explored the possibility of combined interpretation of both DNA copy number and RNA expression profiles, mean DNA copy number and RNA expression levels showed a significant correlation. In conclusion, this 30k oligoarray-CGH system can be a reasonable choice for analyzing whole genome CNAs and RNA expression profiles at a lower cost.
   

 British Journal of Pharmacology. 2009, 157(5):746-56. doi: 10.1111/j.1476-5381.2009.00223.x.
 Comprehensive evaluation of a novel nuclear factor-kB inhibitor, quinoclamine, by transcriptomic analysis.
 
 
 Cheng WY, Lien JC, Hsiang CY, Wu SL, Li CC, Lo HY, Chen JC, Chiang SY, Liang JA, Ho TY.
  Abstract
The transcription factor nuclear factor-kappaB (NF-kappaB) has been linked to the cell growth, apoptosis and cell cycle progression. NF-kappaB blockade induces apoptosis of cancer cells. Therefore, NF-kappaB is suggested as a potential therapeutic target for cancer. Here, we have evaluated the anti-cancer potential of a novel NF-kappaB inhibitor, quinoclamine (2-amino-3-chloro-1,4-naphthoquinone). In a large-scale screening test, we found that quinoclamine was a novel NF-kappaB inhibitor. The global transcriptional profiling of quinoclamine in HepG2 cells was therefore analysed by transcriptomic tools in this study. Quinoclamine suppressed endogenous NF-kappaB activity in HepG2 cells through the inhibition of IkappaB-alpha phosphorylation and p65 translocation. Quinoclamine also inhibited induced NF-kappaB activities in lung and breast cancer cell lines. Quinoclamine-regulated genes interacted with NF-kappaB or its downstream genes by network analysis. Quinoclamine affected the expression levels of genes involved in cell cycle or apoptosis, suggesting that quinoclamine exhibited anti-cancer potential. Furthermore, quinoclamine down-regulated the expressions of UDP glucuronosyltransferase genes involved in phase II drug metabolism, suggesting that quinoclamine might interfere with drug metabolism by slowing down the excretion of drugs. This study provides a comprehensive evaluation of quinoclamine by transcriptomic analysis. Our findings suggest that quinoclamine is a novel NF-kappaB inhibitor with anti-cancer potential.
   

 BMC Biology. 2009, 7:35. doi: 10.1186/1741-7007-7-35.
 Effect of hydroxyurea on the promoter occupancy profiles of tumor suppressor p53 and p73.
 
 
 Vera Huang, Xin Lu, Yong Jiang and Jean YJ Wang.
  Abstract
The p53 tumor suppressor and its related protein, p73, share a homologous DNA binding domain, and mouse genetics studies have suggested that they have overlapping as well as distinct biological functions. Both p53 and p73 are activated by genotoxic stress to regulate an array of cellular responses. Previous studies have suggested that p53 and p73 independently activate the cellular apoptotic program in response to cytotoxic drugs. The goal of this study was to compare the promoter-binding activity of p53 and p73 at steady state and after genotoxic stress induced by hydroxyurea.We employed chromatin immunoprecipitation, the NimbleGen promoter arrays and a model-based algorithm for promoter arrays to identify promoter sequences enriched in anti-p53 or anti-p73 immunoprecipitates, either before or after treatment with hydroxyurea, which increased the expression of both p53 and p73 in the human colon cancer cell line HCT116-3(6). We calculated a model-based algorithm for promoter array score for each promoter and found a significant correlation between the promoter occupancy profiles of p53 and p73. We also found that after hydroxyurea treatment, the p53-bound promoters were still bound by p73, but p73 became associated with additional promoters that that did not bind p53. In particular, we showed that hydroxyurea induces the binding of p73 but not p53 to the promoter of MLH3, which encodes a mismatch repair protein, and causes an up-regulation of the MLH3 mRNA.These results suggest that hydroxyurea exerts differential effects on the promoter-binding functions of p53 and p73 and illustrate the power of model-based algorithm for promoter array in the analyses of promoter occupancy profiles of highly homologous transcription factors.
   

 International Journal of Food Microbiology. 2009, 131(2-3):224-32. doi: 10.1016/j.ijfoodmicro.2009.03.002.
 Interactive transcriptome analysis of enterohemorrhagic Escherichia coli+H23 (EHEC) O157:H7 and intestinal epithelial HT-29 cells after bacterial attachment.
 
 
 Younghoon Kim , Sejong Oh , Sungsu Park , Sae Hun Kim.
  Abstract
Here, the gene expression profiles of EHEC O157:H7 and HT-29 during the attachment stage were investigated by using duplex whole transcriptome analysis. After the initial attachment (3 h), the gene regulation systems of both the EHEC O157:H7 and HT-29 host cells were immediately remodeled. A total of 326 genes of the HT-29 cells, which involved proteins associated with the detoxification process, stress response proteins, anti-apoptosis/inflammation proteins, immune response protein, and oxidative stress proteins, were differentially regulated by more than 2.0-fold during EHEC attachment. In contrast, when HT-29 was attached to EHEC the expression of 611 genes was induced and the expression of 384 genes was reduced by more than twofold when compared to RPMI 1640-grown EHEC (16.14% of the total hybridized genes). Among the genes that were classified according to biological function, the mRNA levels of the genes involved in stress response, oxidative stress, cell signaling and cell surface proteins were significantly altered after the attachment of EHEC O157:H7. Therefore, the results of this study provide crucial insight into the genetic networks that provide host cell protection and the strategy of EHEC O157:H7 pathogenesis in gastro-intestinal (GI) tracts.
   

 BIOINFORMATICS. 2009, 25(8):981-8. doi: 10.1093/bioinformatics/btp106.
 A neural network model for constructing endophenotypes of common complex diseases: an application to male young-onset hypertension microarray data.
 
 
 Lynn KS, Li LL, Lin YJ, Wang CH, Sheng SH, Lin JH, Liao W, Hsu WL, Pan WH
  Abstract
Identification of disease-related genes using high-throughput microarray data is more difficult for complex diseases as compared with monogenic ones. We hypothesized that an endophenotype derived from transcriptional data is associated with a set of genes corresponding to a pathway cluster. We assumed that a complex disease is associated with multiple endophenotypes and can be induced by their up/downregulated gene expression patterns. Thus, a neural network model was adopted to simulate the gene-endophenotype-disease relationship in which endophenotypes were represented by hidden nodes. RESULTS: We successfully constructed a three-endophenotype model for Taiwanese hypertensive males with high identification accuracy. Of the three endophenotypes, one is strongly protective, another is weakly protective and the third is highly correlated with developing young-onset male hypertension. Sixteen of the involved 101 genes were highly and consistently influential to the endophenotypes. Identification of SLC4A5, SLC5A10 and LDOC1 indicated that sodium/bicarbonate transport, sodium/glucose transport and cell-proliferation regulation may play important upstream roles and identification of BNIP1, APOBEC3F and LDOC1 suggested that apoptosis, innate immune response and cell-proliferation regulation may play important downstream roles in hypertension. The involved genes not only provide insights into the mechanism of hypertension but should also be considered in future gene mapping endeavors.
   

 Zhonghua Xin Xue Guan Bing Za Zhi. 2009, 37(2):120-125.
 Identification of differentially expressed genes in myocardium of patients with heart failure by human whole genomic oligonucleotide microarray-assisted pathways analysis.
 
 
 Wu XX, Wan T, Wu HJ, Zhi G, Xiao CS, Gao CQ, WU Jia-jin
  Abstract
To identify the differentially expressed gene profiles in myocardium of patients with heart failure using human whole genomic oligonucleotide microarray-assisted pathway analysis. Phalanx whole genomic oligonucleotide microarrays were used to detect the gene expression profiles of myocardium in four patients died of heart failure and 4 brain died patients without heart diseases. The microarray findings were confirmed by real-time quantitative reverse transcriptase-polymerase chain reaction. The genes with a threshold of 1.2 times fold-change were selected and BioCarta Pathway and KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway databases were used to identify functionallyrelated gene pathways. A total of 2806 genes with differentially expression were detected between the failing and non-failing heart samples,expression changes of 399 genes were more than 2-folds. Eleven pathways were identified by BioCarta pathway database and sixteen pathways were identified by KEGG PATHWAY Database. Genomic microarray-assisted pathway analysis could help to identify gene expression profiles in failing heart.
   

 MOLECULAR PHARMACOLOGY. 2009, 75(1):151-7. doi: 10.1124/mol.108.049502.
 Vanillin Inhibits Matrix Metalloproteinase-9 Expression through Down-Regulation of Nuclear Factor- B Signaling Pathway in Human Hepatocellular Carcinoma Cells.
 
 
 Liang JA, Wu SL, Lo HY, Hsiang CY, Ho TY
  Abstract
Vanillin has been reported to exhibit anti-invasive and antimetastatic activities by suppressing the enzymatic activity of matrix metalloproteinase-9 (MMP-9). However, the underlying mechanism of anti-invasive activity remains unclear so far. Herein we demonstrate that vanillin reduced 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced MMP-9 gelatinolytic activity and suppressed cell invasion through the down-regulation of MMP-9 gene transcription in HepG2 cells. Vanillin significantly reduced the 6.6-fold invasive capacity of HepG2 cells in noncytotoxic concentrations, and this anti-invasive effect was concentration-dependent in the Matrigel invasion assay. Moreover, vanillin significantly suppressed the TPA-induced enzymatic activity of MMP-9 and decreased the induced mRNA level of MMP-9. Analysis of the transcriptional regulation indicated that vanillin suppressed MMP-9 transcription by inhibiting nuclear factor-kappaB (NF-kappaB) activity. Western blot further confirmed that vanillin inhibited NF-kappaB activity through the inhibition of IkappaB-alpha phosphorylation and degradation. In conclusion, vanillin might be a potent antiinvasive agent that suppresses the MMP-9 enzymatic activity via NF-kappaB signaling pathway.
   

 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.
   

 Beijing Journal of Stomatology. 2008, 16(6):309-311.
 Differential gene expression related to oxidative stress in oral cancer and oral precancerous lesion cells.
 
 
 Zhang Xin Yan, Zhang Min, Sun Zheng, TANG Xiao-fei
  Abstract
To identify differentially expressed genes related to oxidative stress in oral squamous cell carcinoma and oral precancerous lesion cells and investigate the mechanism and relationship between oxidative damage and oral cancer development. cDNA microarray analysis was used to examine the differences in gene expression between oral carcinoma cell lines Tca8113, KB and oral precancerous lesion cell line DOK. Twenty-eight differentially expressed genes related to oxidative stress were detected in oral squamous cell carcinoma and oral precancerous lesion cells1 Among them, 9 genes were separately up-regulated from two folds to six folds, including PRDX, SOD, GSS, GST, TXNRD, SEPX1, etc. High expression of cytokeratin 10, 17 and 7 were also observed in the cells of oral squamous cell carcinomas. Oxidative damage may be related to the carcinogenesis of oral cancer, and oxidative stress damage may activate some signal pathway related to cytokeratinization which leads to carcinogenesis.
   

 INTERNATIONAL JOURNAL OF ONCOLOGY. 2008, 33(4):767-76. doi: 10.3892/ijo_00000063.
 Histone deacetylase inhibitor scriptaid induces cell cycle arrest and epigenetic change in colon cancer cells.
 
 
 EUN JU LEE1, BO BIN LEE, SOON-JA KIM, YONG-DOO PARK, JOOBAE PARK, Duk-Hwan Kim
  Abstract
Histone deacetylase inhibitors (HDACIs) are involved in cell growth, apoptosis and differentiation. This study aimed to investigate the effects of HDACI scriptaid on histone modification, demethylation, cell growth, cell cycle and apoptosis in the RKO colorectal cancer cell line and screening for scriptaid-induced genes. RKO cells were treated with 5-aza-2'-deoxycytidine (5-aza-dC), trichostatin A (TSA) or scriptaid at different concentrations. Histone modification and methylation status of a silenced p16 gene were analyzed using chromatin immunoprecipitation and methylation-specific PCR, respectively. Flow cytometry was performed for the analysis of cell cycle and apoptosis. Scriptaid-induced expression was analyzed using Human OneArray chip. Scriptaid resulted in the demethylation and re-expression of a hypermethylated p16 gene along with 5-aza-dC synergistically in the RKO cells, but not alone. Scriptaid induced modifications of core histone tails important in euchromatin structure: increases in acetyl-H3-K9 and dimethyl-H3-K4 and a decrease in dimethyl-H3-K9. Cell growth was inhibited by scriptaid in a dose-dependent manner. Cell cycle analysis showed that scriptaid induced G1 arrest at 0.5 and 1.0 microM concentrations and G1 and G2/M arrest at 2.0 microM. Scriptaid did not have a significant effect on apoptosis in RKO cells. An altered expression of 278 genes was observed in RKO cells in response to scriptaid treatment. In conclusion, the present study suggests that scriptaid may be effective in growth suppression and cell cycle arrest and in the reversal of repressive chromatin marks at the promoter region of a hypermethylated p16 gene in colorectal cancer.
   

 Genomics & Informatics. 2008, 6(3):126-129.
 CGHscape: A Software Framework for the Detection and Visualization of Copy Number Alterations.
 
 
 Yong-Bok Jeong, Tae-Min Kim, Yeun- Jun Chung
  Abstract
The robust identification and comprehensive profiling of copy number alterations (CNAs) is highly challenging. The amount of data obtained from high-throughput technologies such as array-based comparative genomic hybridization is often too large and it is required to develop a comprehensive and versatile tool for the detection and visualization of CNAs in a genome-wide scale. With this respective, we introduce a software framework, CGHscape that was originally developed to explore the CNAs for the study of copy number variation (CNV) or tumor biology. As a standalone program, CGHscape can be easily installed and run in Microsoft Windows platform. With a user-friendly interface, CGHscape provides a method for data smoothing to cope with the intrinsic noise of array data and CNA detection based on SW-ARRAY algorithm. The analysis results can be demonstrated as log2 plots for individual chromosomes or genomic distribution of identified CNAs. With extended applicability, CGHscape can be used for the initial screening and visualization of CNAs facilitating the cataloguing and characterizing chromosomal alterations of a cohort of samples.
   

 The American Journal of Chinese Medicine. 2008, 36(4):783-97. doi: 10.1142/S0192415X08006235.
 Relationship Between San-Huang-Xie-Xin-Tang and Its Herbal Components on the Gene Expression Profiles in HepG2 Cells.
 
 
 Cheng WY, Wu SL, Hsiang CY, Li CC, Lai TY, Lo HY, Shen WS, Lee CH, Chen JC, Wu HC, Tin-Yun Ho
  Abstract
Traditional Chinese medicine (TCM) has been used for thousands of years. Most Chinese herbal formulae consist of several herbal components and have been used to treat various diseases. However, the mechanisms of most formulae and the relationship between formulae and their components remain to be elucidated. Here we analyzed the putative mechanism of San-Huang-Xie-Xin-Tang (SHXXT) and defined the relationship between SHXXT and its herbal components by microarray technique. HepG2 cells were treated with SHXXT or its components and the gene expression profiles were analyzed by DNA microarray. Gene set enrichment analysis indicated that SHXXT and its components displayed a unique anti-proliferation pattern via p53 signaling, p53 activated, and DNA damage signaling pathways in HepG2 cells. Network analysis showed that most genes were regulated by one molecule, p53. In addition, hierarchical clustering analysis showed that Rhizoma Coptis shared a similar gene expression profile with SHXXT. These findings may explain why Rhizoma Coptis is the principle herb that exerts the major effect in the herbal formula, SHXXT. Moreover, this is the first report to reveal the relationship between formulae and their herbal components in TCM by microarray and bioinformatics tools.
   

 Journal of Applied Physiology. 2008, 105(1):30-6. doi: 10.1152/japplphysiol.00119.2008.
 Effects of cardiotonic steroids on dermal collagen synthesis and wound healing.
 
 
 Nasser El-Okdi, Sleiman Smaili, Vanamala Raju, Amjad Shidyak, Shalini Gupta, Larisa Fedorova, Jihad Elkareh, Sankaridrug Periyasamy, Anna P. Shapiro, M. Bashar Kahaleh, Deepak Malhotra, Zijian Xie, Khew Voon Chin, Joseph I. Shapiro
  Abstract
We previously reported that cardiotonic steroids stimulate collagen synthesis by cardiac fibroblasts in a process that involves signaling through the Na-K-ATPase pathway (Elkareh et al. Hypertension 49: 215-224, 2007). In this study, we examined the effect of cardiotonic steroids on dermal fibroblasts collagen synthesis and on wound healing. Increased collagen expression by human dermal fibroblasts was noted in response to the cardiotonic steroid marinobufagenin in a dose- and time-dependent fashion. An eightfold increase in collagen synthesis was noted when cells were exposed to 10 nM marinobufagenin for 24 h (P < 0.01). Similar increases in proline incorporation were seen following treatment with digoxin, ouabain, and marinobufagenin (10 nM x 24 h, all results P < 0.01 vs. control). The coadministration of the Src inhibitor PP2 or N-acetylcysteine completely prevented collagen stimulation by marinobufagenin. Next, we examined the effect of digoxin, ouabain, and marinobufagenin on the rate of wound closure in an in vitro model where human dermal fibroblasts cultures were wounded with a pipette tip and monitored by digital microscopy. Finally, we administered digoxin in an in vivo wound healing model. Olive oil was chosen as the digoxin carrier because of a favorable partition coefficient observed for labeled digoxin with saline. This application significantly accelerated in vivo wound healing in rats wounded with an 8-mm biopsy cut. Increased collagen accumulation was noted 9 days after wounding (both P < 0.01). The data suggest that cardiotonic steroids induce increases in collagen synthesis by dermal fibroblasts, as could potentially be exploited to accelerate wound healing.
   

 Cancer Biology & Therapy. 2008, 7(4):577-86. doi: 10.1371/journal.pone.0030107.
 Molecular mechanisms underlying selective cytotoxic activity of BZL101, an extract of Scutellaria barbata, towards breast cancer cells.
 
 
 Fong S, Shoemaker M, Cadaoas J, Lo A, Liao W, Tagliaferri M, Cohen I, Emma Shtivelman
  Abstract
We studied the mechanism of the cytotoxic activity of BZL101, an aqueous extract from the herb Scutellaria barbata D. Don, which is currently in phase II clinical trial in patients with advanced breast cancer. The phase I trial showed favorable toxicity profile and promising efficacy. We report here that BZL101 induces cell death in breast cancer cells but not in non-transformed mammary epithelial cells. This selective cytotoxicity is based on strong induction by BZL101 of reactive oxygen species (ROS) in tumor cells. As a consequence, BZL101 treated cancer cells develop extensive oxidative DNA damage and succumb to necrotic death. Data from the expression profiling of cells treated with BZL101 are strongly supportive of a death pathway that involves oxidative stress, DNA damage and activation of death-promoting genes. In breast cancer cells oxidative damage induced by BZL101 leads to the hyperactivation of poly (ADP-ribose) polymerase (PARP), followed by a sustained decrease in levels of NAD and depletion of ATP, neither of which are observed in non-transformed cells. The hyperactivation of PARP is instrumental in the necrotic death program induced by BZL101, because inhibition of PARP results in suppression of necrosis and activation of the apoptotic death program. BZL101 treatment leads to the inhibition of glycolysis selectively in tumor cells, evident from the decrease in the enzymatic activities within the glycolytic pathway and the inhibition of lactate production. Because tumor cells frequently rely on glycolysis for energy production, the observed inhibition of glycolysis is likely a key factor in the energetic collapse and necrotic death that occurs selectively in breast cancer cells. The promising selectivity of BZL101 towards cancer cells is based on metabolic differences between highly glycolytic tumor cells and normal cells.
   

 Pharmacological research. 2007, 56(6):474-82. doi:10.1016/j.phrs.2007.09.009.
 Microarray analysis of vanillin-regulated gene expression profile in human hepatocarcinoma cells.
 
 
 Cheng WY, Hsiang CY, Bau DT, Chen JC, Shen WS, Li CC, Lo HY, Wu SL, Chiang SY, Tin-Yun Ho
  Abstract
Vanillin is one of the most widely used flavor compounds in food and personal products. It has been reported that vanillin is able to inhibit mutagenesis induced by chemical and physical mutagens, and to suppress the invasion and migration of cancer cells. Herein we used the oligonucleotide microarray approach to study gene expression profile of vanillin-treated human hepatocarcinoma cells. Microarray data followed by gene ontology (GO) investigation displayed that vanillin-affected clusters of genes involved in cell cycle and apoptosis. Genes down-regulated by vanillin were grouped into three GO categories, regulation of cellular process, cell cycle, and death. Furthermore, most of the down-regulated genes were associated with cancer progression. Knowledge-based analysis further indicated that Fos may play a central role in the regulation of gene expression network. Analysis of Fos-related transcription factor, activator protein 1 (AP-1), showed that vanillin inhibited AP-1 activity in a dose-dependent manner. Furthermore, the phosphorylation of extracellular signal-regulated protein kinase (ERK) was diminished with increasing concentrations of vanillin, indicating that vanillin-regulated AP-1 activity via ERK pathway. In conclusion, our data suggested that vanillin exhibited the anticancer potential by the regulations of cell cycle and apoptosis. Moreover, its regulation may involve the suppression of a central molecule, AP-1.
   

 Genetic Epidemiology. 2006, 30(2):143-54. doi: 10.1002/gepi.20136.
 Using Endophenotypes for Pathway Clusters to Map Complex Disease Genes.
 
 
 Pan WH, Lynn KS, Chen CH, Wu YL, Lin CY, Chang HY, Wen-Ham Pan
  Abstract
Nature determines the complexity of disease etiology and the likelihood of revealing disease genes. While culprit genes for many monogenic diseases have been successfully unraveled, efforts to map major complex disease genes have not been as productive as hoped. The conceptual framework currently adopted to deal with the heterogeneous nature of complex diseases focuses on using homogeneous internal features of the disease phenotype for mapping. However, phenotypic homogeneity does not equal genotypic homogeneity. In this report, we advocate working with well-measured phenotypes portrayed by amounts of transcripts and activities of gene products or their metabolites, which are pertinent to relatively small pathway clusters. Reliable and controlled measures for oligogenic traits resulting from proper dissection efforts may enhance statistical power. The large amounts of information obtained on gene and protein expression from technological advances can add to the power of gene finding, particularly for diseases with unclear etiology. Data-mining tools for dimension reduction can assist biologists to reveal novel molecular endophenotypes. However, there are still hurdles to overcome, including high cost, relatively poor reproducibility and comparability among platforms, the cross-sectional nature of the information, and the accessibility of human tissues. Concerted efforts are required to carry out large-scale prospective studies that are integrated at the levels of phenotype characterization, high throughput experimental techniques, data analyses, and beyond.