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Tongwu Zhang, Jiyeon Choi, Michael A Kovacs, Jianxin Shi, Mai Xu, Alisa M Goldstein, Adam J Trower, D Timothy Bishop, Mark M Iles, David L Duffy, Stuart MacGregor, Laufey T Amundadottir, Matthew H Law, Stacie K Loftus, William J Pavan, Kevin M Brown
Most expression quantitative trait locus (eQTL) studies to date have been performed in heterogeneous tissues as opposed to specific cell types. To better understand the cell-type-specific regulatory landscape of human melanocytes, which give rise to melanoma but account for <5% of typical human skin biopsies, we performed an eQTL analysis in primary melanocyte cultures from 106 newborn males. We identified 597,335 cis -eQTL SNPs prior to linkage disequilibrium (LD) pruning and 4997 eGenes (FDR < 0.05)...
October 17, 2018: Genome Research
Jianan Chen, Yan Yu, Chen Xue, Xiaolong Chen, Guangying Cui, Juan Li, Kongfei Li, Zhigang Ren, Ranran Sun
BACKGROUND: microRNA-139 (miR-139) is dysregulated in various types of tumors and plays a key role in carcinogenesis. miR-139 may be used as a diagnostic and prognostic biomarker of cancers. However, the data from the literature are not consistent. The present study aimed to verify the prognostic and diagnostic values of miR-139 in solid tumors. DATA SOURCES: PubMed, Web of Science and Embase databases were searched and publications from January 2011 to August 2017 were included...
September 26, 2018: Hepatobiliary & Pancreatic Diseases International: HBPD INT
Peixin Dong, Ying Xiong, Junming Yue, Sharon J B Hanley, Hidemichi Watari
Although the role of PD-L1 in suppressing the anti-tumor immune response is extensively documented, recent discoveries indicate a distinct tumor-intrinsic role for PD-L1 in modulating epithelial-to-mesenchymal transition (EMT), cancer stem cell (CSC)-like phenotype, metastasis and resistance to therapy. In this review, we will focus on the newly discovered functions of PD-L1 in the regulation of cancer development, describe underlying molecular mechanisms responsible for PD-L1 upregulation and discuss current insights into novel components of PD-L1 signaling...
2018: Frontiers in Oncology
Yuexiong Yi, Yanyan Liu, Wanrong Wu, Kejia Wu, Wei Zhang
This study aims to investigate the role of miR-106b-5p in cervical cancer by performing a comprehensive analysis on its expression and identifying its putative molecular targets and pathways based on The Cancer Genome Atlas (TCGA) dataset, Gene Expression Omnibus (GEO) dataset, and literature review. Significant upregulation of miR-106b-5p in cervical cancer is confirmed by meta-analysis with the data from TCGA, GEO, and literature. Moreover, the expression of miR-106b-5p is significantly correlated with the number of metastatic lymph nodes...
2018: Cell Death Discovery
Sara S Oltra, Maria Peña-Chilet, Victoria Vidal-Tomas, Kirsty Flower, María Teresa Martinez, Elisa Alonso, Octavio Burgues, Ana Lluch, James M Flanagan, Gloria Ribas
MiRNAs are part of the epigenetic machinery, and are also epigenetically modified by DNA methylation. MiRNAs regulate expression of different genes, so any alteration in their methylation status may affect their expression. We aimed to identify methylation differences in miRNA encoding genes in breast cancer affecting women under 35 years old (BCVY), in order to identify potential biomarkers in these patients. In Illumina Infinium MethylationEPIC BeadChip samples (metEPICVal), we analysed the methylation of 9,961 CpG site regulators of miRNA-encoding genes present in the array...
September 26, 2018: Scientific Reports
Wei-Ning Cen, Jin-Shu Pang, Jia-Cheng Huang, Jia-Yin Hou, Wen-Guang Bao, Rong-Quan He, Jie Ma, Zhi-Gang Peng, Xiao-Hua Hu, Fu-Chao Ma
BACKGROUND: The specific expression level and clinical significance of miR-375-3p in HNSCC had not been fully stated, as well as the overall biological function and molecular mechanisms. Therefore, we purpose to carry out a comprehensive meta-analysis to further explore the clinical significance and potential function mechanism of miR-375-3p in HNSCC. METHODS: HNSCC-related data was gained from Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), and peer-reviewed journals...
September 13, 2018: Pathology, Research and Practice
Kumardeep Chaudhary, Olivier B Poirion, Liangqun Lu, Sijia Huang, Travers Ching, Lana X Garmire
Although driver genes in hepatocellular carcinoma (HCC) have been investigated in various previous genetic studies, prevalence of key driver genes among heterogeneous populations is unknown. Moreover, the phenotypic associations of these driver genes are poorly understood. This report aims to reveal the phenotypic impacts of a group of consensus driver genes in HCC. We used MutSigCV and OncodriveFM modules implemented in the IntOGen pipeline to identify consensus driver genes across six HCC cohorts comprising 1,494 samples in total...
September 21, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Kashif Rafiq Zahid, Shiming Han, Fuling Zhou, Umar Raza
BACKGROUND: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-associated deaths worldwide. Although recent studies have proposed different biomarkers for HCC progression and therapy resistance, a better understanding of the molecular mechanisms underlying HCC progression and recurrence, as well as the identification of molecular markers with a higher diagnostic accuracy, are necessary for the development of more effective clinical management strategies. Here, we aimed to identify novel players in HCC progression...
September 20, 2018: Cellular Oncology (Dordrecht)
Jie Ruan, Peipei Xu, Wei Fan, Qiaoling Deng, Mingxia Yu
Epigenetic alteration of P16INK4a is conventionally thought to induce the initiation of carcinoma. However, the role of P16INK4a methylation in ovarian cancer still remains controversial. Therefore, we performed a meta-analysis to further elucidate the relationship between P16INK4a promoter methylation and ovarian cancer. A total of 24 studies, including 20 on risk, 10 on clinicopathological features, and 3 on prognosis, were included in our meta-analysis. Our results indicated that the frequency of P16INK4a methylation in cancer tissues was significantly higher than normal tissues and low malignant potential tumor tissues (odds ratio [OR] =5...
2018: Cancer Management and Research
Chunbo Zhuang, Lei Zheng, Pei Wang
Background: Long non-coding RNAs (LncRNAs) play important roles in tumorigenesis and progression. Recent studies have demonstrated that LncRNA HNF1A antisense RNA 1 ( HNF1A-AS1 ) is aberrantly expressed in several types of cancers and is associated with poor outcomes. This meta-analysis was conducted to investigate the relationship between HNF1A-AS1 expression and clinical outcomes in cancer patients. Methods: We searched PubMed, Embase, Web of Science, China National Knowledge Infrastructure (CNKI), and Wan Fang databases (updated until December 31, 2017) for literature...
2018: OncoTargets and Therapy
Jixi Li, Kang Liu, Tingting Zhang, Zhendong Yang, Rensheng Wang, Gang Chen, Min Kang
HNSCC is the sixth most common cancer worldwide and is characterized as an aggressive, malignant tumor. MiR-34a-5p (miR-34a) expression has been strongly linked to HNSCC development. However, the exact target gene of miRNA-34a-as well as its biological and mechanistic pathways-are unclear. It is critical that the clinical value of HNSCC receive further study. We conducted a continuous variable, meta-analysis from data found in the cancer literature as well as that provided by the Cancer Genome Atlas (TCGA) to estimate miR-34a expression in HNSCC...
2018: American Journal of Translational Research
GaoFeng Hu, QianWen Lv, JiaXiu Yan, LiJun Chen, Juan Du, Ke Zhao, Wei Xu
Integrated studies of accumulated data can be performed to obtain more reliable information and more feasible measures for investigating potential diagnostic biomarkers of gastric cancer (GC) and to explore related molecular mechanisms. This study aimed to identify microRNAs involved in GC by integrating data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus. Through our analysis, we identified hsa-miR-17 (miR-17) as a suitable candidate. We performed a meta-analysis of published studies and analyzed clinical data from TCGA to evaluate the clinical significance and diagnostic value of miR-17 in GC...
September 2018: FEBS Open Bio
Zhigang Zhang, Bing Pan, Shaocheng Lv, Zhiwei Ji, Qian Wu, Ren Lang, Qiang He, Xin Zhao
BACKGROUND/AIMS: MicroRNAs (miRNAs) are promising biomarkers for pancreatic cancer (PaCa). However, systemic and unified evaluations of the diagnostic value of miRNAs are lacking. Therefore, we performed a systematic evaluation based on miRNA expression profiling studies. METHODS: We obtained miRNA expression profiling studies from Gene Expression Omnibus (GEO) and ArrayExpress (AE) databases and calculated the pooled sensitivity, specificity, and summary area under a receiver operating characteristic (ROC) curve for every miRNA...
2018: Cellular Physiology and Biochemistry
Quinn T Ostrom, Ben Kinnersley, Georgina Armstrong, Terri Rice, Yanwen Chen, John K Wiencke, Lucie S McCoy, Helen M Hansen, Christopher I Amos, Jonine L Bernstein, Elizabeth B Claus, Jeanette E Eckel-Passow, Dora Il'yasova, Christoffer Johansen, Daniel H Lachance, Rose K Lai, Ryan T Merrell, Sara H Olson, Siegal Sadetzki, Joellen M Schildkraut, Sanjay Shete, Joshua B Rubin, Ulrika Andersson, Preetha Rajaraman, Stephen J Chanock, Martha S Linet, Zhaoming Wang, Meredith Yeager, Richard S Houlston, Robert B Jenkins, Margaret R Wrensch, Beatrice Melin, Melissa L Bondy, Jill S Barnholtz-Sloan
Glioblastoma (GBM) is the most common malignant brain tumor in the United States. Incidence of GBM increases with age, and younger age-at-diagnosis is significantly associated with improved prognosis. While the relationship between candidate GBM risk SNPs and age-at-diagnosis has been explored, genome-wide association studies (GWAS) have not previously been stratified by age. Potential age-specific genetic effects were assessed in autosomal SNPs for GBM patients using data from four previous GWAS. Using age distribution tertiles (18-53, 54-64, 65+) datasets were analyzed using age-stratified logistic regression to generate p values, odds ratios (OR), and 95% confidence intervals (95%CI), and then combined using meta-analysis...
August 27, 2018: International Journal of Cancer. Journal International du Cancer
Xiaoliang Chen, Yueying Yang, Yong Cao, Changjun Wu, Shuxian Wu, Zhan Su, Hongwei Jin, Dongli Wang, Gengxin Zhang, Wei Fan, Jinbo Lin, Yunhong Zeng, Dongsheng Hu
Purpose: Long noncoding RNA PVT1 is dysregulated in some human tumors and has been found to increase the risk of tumor progression and poor prognosis. This study aimed to reanalyze the effect of PVT1 on tumorous prognosis. Materials and methods: The effect of PVT1 on metastasis and survival were analyzed by univariate logistic regression and Cox proportional hazards model for 32 types of cancer in the Cancer Genome Atlas database (TCGA), and the relationship between PVT1 level and expression of relative genes was assessed by Pearson correlation analysis...
2018: Cancer Management and Research
Chaojie Liang, Jinghong Zhang, Hua Ge, Yingchen Xu, Shulin Ren, Chaosen Yue, Guangming Li, Jixiang Wu
BACKGROUND AND AIM: Recently, several studies have reported that the long non-coding RNA cancer susceptibility 2 (CASC2) is downregulated in human solid tumors. However, as the sample size in those studies was limited, the role of CASC2 in cancer remains unknown. Accordingly, we conducted this meta-analysis to explore the role of CASC2 in solid tumors. METHODS: We systematically searched the PubMed, Medline, Cochrane Library, Web of Science, EMBASE, Ovid, Chinese CNKI, and Chinese WanFang databases...
August 23, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
Lingling Yu, Shengsong Chen, Hui Bao, Weifang Zhang, Minqi Liao, Qian Liang, Xiaoshu Cheng
Background: Cancer susceptibility candidate 2 (CASC2) is characterized as a tumor suppressor, which was first identified to be downregulated in endometrial carcinoma. Accumulating evidence was provided to testify the function of CASC2 in malignant tumors. However, a systematic and quantitative assessment is not available. The present study was designed to evaluate the role of CASC2 in multiple carcinomas through meta-analysis and bioinformatics. Materials and methods: A systematic assessment of the relationship of CASC2 with tumors was performed by using several computerized databases from inception to December 1, 2017...
2018: OncoTargets and Therapy
Bin-Liang Gan, Rong-Quan He, Yu Zhang, Dan-Ming Wei, Xiao-Hua Hu, Gang Chen
Recent studies have indicated that homeobox A3 (HOXA3) functions as a carcinogen in colon cancer and the methylation level of HOXA3 is significantly increased in lung adenocarcinoma (LUAD) tissues. However, at least to the best of our knowledge, few studies to date have been performed on HOXA3 in non-small cell lung cancer (NSCLC). Therefore, further studies on HOXA3 expression in NSCLC and the potential regulatory mechanisms are urgently required. In this study, HOXA3 expression in 55 tissues of cases of NSCLC and corresponding non-lung cancer tissues was detected by reverse transcription-quantitative PCR (RT-qPCR)...
October 2018: International Journal of Oncology
Xue-Bin Wang, Ning-Hua Cui, Xia-Nan Liu, Jun-Fen Ma, Qing-Hua Zhu, Shu-Ren Guo, Jun-Wei Zhao, Liang Ming
Background: Promoter hypermethylation in death-associated protein kinase 1 ( DAPK1 ) gene has been long linked to cervical neoplasia, but the established results remained controversial. Here, we performed a meta-analysis to assess the associations of DAPK1 promoter hypermethylation with low-grade intra-epithelial lesion (HSIL), high-grade intra-epithelial lesion (HSIL), cervical cancer (CC), and clinicopathological features of CC. Methods: Published studies with qualitative methylation data were initially searched from PubMed, Web of Science, EMBASE, and China National Knowledge Infrastructure databases (up to March 2018)...
2018: Frontiers in Genetics
Zhicong Chen, Yonghao Zhan, Jieshan Chi, Shuyuan Guo, Xinliang Zhong, Anbang He, Jianrong Zheng, Yanqing Gong, Xuesong Li, Liqun Zhou
BACKGROUND: MicroRNAs(miRNAs) are involved in the formation, maintenance, and metastasis of urologic cancer. Here, we aim to gather and evaluate all of the evidence regarding the potential role of miRNAs as novel predictors of urologic cancer survival. METHODS: A systematic review was performed to identify and score all of the published studies that evaluated the prognostic effects of miRNAs in kidney (KCa), bladder (BCa) or prostate cancer (PCa). Where appropriate, the summary effects of miRNAs on urologic cancer were meta-analysed...
August 2018: EBioMedicine
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