| Experiment ID | EXP00302 |
| Reference | Title: Integrative genomics analysis of genes with biallelic loss and its relation tothe expression of mRNA and micro-RNA in esophageal squamous cell carcinoma. Author: Hu N, Wang C, Clifford RJ, Yang HH, Su H, Wang L, Wang Y, XuY, Tang ZZ, Ding T, Zhang T, Goldstein AM, Giffen C, LeeMP, Taylor PR. Journal: BMC Genomics. 2015 Sep 26;16(1):732. doi: 10.1186/s12864-015-1919-0. Abstract: BACKGROUND: Genomic instability plays an important role in human cancers. Wepreviously characterized genomic instability in esophageal squamous cellcarcinomas (ESCC) in terms of loss of heterozygosity (LOH) and copy number (CN)changes in tumors. In the current study we focus on biallelic loss and itsrelation to expression of mRNA and miRNA in ESCC using results from 500 K SNP,mRNA, and miRNA arrays in 30 cases from a high-risk region of China.RESULTS: (i) Biallelic loss was uncommon but when it occurred it exhibited aconsistent pattern: only 77 genes (<0.5%) showed biallelic loss in at least 10%of ESCC samples, but nearly all of these genes were concentrated on just fourchromosomal arms (i.e., 42 genes on 3p, 14 genes on 9p, 10 genes on 5q, and sevengenes on 4p). (ii) Biallelic loss was associated with lower mRNA expression: 52of the 77 genes also had RNA expression data, and 41 (79%) showed lowerexpression levels in cases with biallelic loss compared to those without. (iii)The relation of biallelic loss to miRNA expression was less clear but appeared tofavor higher miRNA levels: of 60 miRNA-target gene pairs, 34 pairs (57%) hadhigher miRNA expression with biallelic loss than without, while 26 pairs (43%)had lower miRNA expression. (iv) Finally, the effect of biallelic loss on therelation between miRNA and mRNA expression was complex. Biallelic loss was mostcommonly associated with a pattern of elevated miRNA and reduced mRNA (43%), but a pattern of both reduced miRNA and mRNA was also common (35%).CONCLUSION: Our results indicate that biallelic loss in ESCC is uncommon, butwhen it occurs it is localized to a few specific chromosome regions and isassociated with reduced mRNA expression of affected genes. The effect ofbiallelic loss on miRNA expression and on the relation between miRNA and mRNAexpressions was complex. PMID: 26409826 |
| Expressiion Profile | Description: Integrative genomics analysis of genes with biallelic loss and its relation to the expression of mRNA and micro-RNA in esophageal squamous cell carcinoma Organism: Homo sapiens GEO ID: GSE66274 Platform: GPL19823 Number of samples: 60 |
| Design and Sample | Cancer Type: esophageal cancer Cancer SubType: N/D Cell Line: N/D Experimental Design: cancer vs normal Case Sample: esophageal cancer Control Sample: normal tissue Num of Case: 30 Num of Control: 30 Quantification Software: Limma Num of miRNAs: 577 |
| Identification | Num of Up: 27 Num of Down: 26 |