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Intergrated analysis of array-miRNAs and matched Affymetrix gene

ABSTRACT: MicroRNAs are considered to be essential regulators during post-transcription in gene expression that mainly through repression mechanism to regulate target mRNAs. We generate expression data from profiling of 664 miRNA in 113 paired tumors and non-tumors of esophageal squamous carcinoma (ESCC), along with matched genome-wide mRNA gene expression data and extensive analysis association study with clinical viable. We identified an expanded list of miRNA dysregulated with Bonferroni correction at 0.05 and genes expression over 2 fold changes in esophageal squamous cell carcinoma. We also found of sixteen miRNAs significant associated with 195 genes. Further analysis show a group of miRNAs correlated with clinical variables including tumor metastasis, tumor stage, grade, and location, family history of UGI cancer, tobacco or alcohol use and pickled vegetable consumption. Survival correlation with either miRNAs or mRNAs was done. Finally, intersect genes correlated with survival and regulated by miRNAs are pulled out. This study provides a comprehensive dataset that can be used as groundwork for further studies of the involvement of miRNA and targeted mRNAs in ESCC and a group of genes may potential serve as biomarkers for prognosis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE44021 | GEO | 2020/05/12

REPOSITORIES: GEO

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Project description:MicroRNAs (miRNAs) are an endogenous conserved class of non-coding 20–22 nt small RNAs that regulate gene expression at post-transcriptional level by mostly binding to 3′-UTR of target mRNAs, leading to mRNA degradation or translation inhibition. Recent reports demonstrate a role for miRNA expression in the disease progression and outcome. By now, many researcher focusing on miRNA expression profiles in Barrett's esophagus and esophageal adenocarcinoma have been reported. Nevertheless, there is still a little information available about specific miRNA expression pattern and their roles in ESCC. To develop novel diagnostic and therapeutic targets for esophageal squamous cancer, we first investigated the expression profile of miRNA in three pairs of ESCC clinical samples. Tissues of ESCC and the matched normal counterparts were obtained from surgical specimens immediately after resection from patients undergoing primary surgical treatment of esophageal carcinoma from the Department of Tumor Surgery of Shantou Central Hospital, China. RNA labeling and hybridization were completed by KangChen Bio-tech Inc. (Shanghai, China) according to the manufacturer's instructions. Briefly, total RNA from three pairs of esophageal carcinoma and matched normal tissues were isolated by Trizol (Invitrogen, USA) and purified by RNeasy mini kit (QIAGEN, German). The concentration and quality of total RNA were measured by NanoDrop ND-1000 at 260 and 280 nm (A260/280) and checked by gel electrophoresis. Each RNA sample from three pairs of ESCC was separately labeled either using the miRCURY Hy3/Hy5 labeling kit and hybridized on the six miRCURYTM locked nucleic acid (LNA) array version 11.0 (Exiqon, Denmark), which contains probes for 1700 mature miRNA. Scans were quantified by using GenePix software (Molecular Devices). The data were exported to Microsoft Excel worksheets, log2 transformed, normalized using global Lowess (Locally Weighted Scatter plot Smoothing) regression algorithm (MIDAS, TIGR Microarray Data Analysis System).

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Intergrated analysis of array-miRNAs and matched Affymetrix gene

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