A pilot study of integrative genomics analysis of genes with biallelic loss and its relation to the expression of mRNA and micro-RNA in esophageal squamous cell cancer

In the current study we focused on biallelic loss and its relation to expression of mRNA and miRNA in ESCC using arrays of 500K SNP, mRNA, and miRNA in 30 cases from a high-risk region of China. Our main results are the followings: 1) 77 genes had biallelic loss in at least 10% of ESCC samples, and most of them are located on chromosome 3p (gene number, n=42), 9p (n=14), 5q (n=10) and 4p (n=7); 2) 52 of 77 genes had signals in both tumor and matched normal on Affymetrix Hu 133 array whereas 79% of them (n=41) showed lower expression levels in patients with biallelic loss (group 1) than that without biallelic loss (group 2) and 19% (n=10) of genes showed higher expression levels in group1 than in group2; 3) 70 miRNAs targeting 35 genes were analyzed, and expression levels of 50 miRNAs (71%) were high while expression levels of their targets were low, and 20 miRNA (29%) showed low expression while their target genes showed high expression; 4) 60 miRNAs target 32 affected genes showed that 43% of (n=26) miRNA expression level were low in group 1 than in group 2 and 57% (n=34) miRNA showed higher expression levels in group 1 than in group 2; and the expression patterns of miRNA and genes affected are complex when comparison the two groups of patients.

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Hu N, Wang C, Clifford RJ, Yang HH, Su H, Wang L, Wang Y, Xu Y, Tang ZZ, Ding T, Zhang T, Goldstein AM, Giffen C, Lee MP, Taylor PR