Screening aberrant methylation profile in esophageal squamous cell carcinoma for Kazakhs in Xinjiang area of China

Abstract

To screen the aberrant methylation genes in esophageal squamous cell carcinoma (ESCC) for Kazakh nationality in Xinjiang, and the aberrant DNA methylation genes pattern provides a clue for deeply study on ESCC mechanism. Illumina Human Methylation 450 K chip was used to screen the genome-wide methylation on six cancer tissues and six adjacent normal tissues of ESCC in Kazakh people. Meanwhile, mRNA library was constructed by scanning the RNA expression on two cancer tissues and two adjacent normal tissues by Hiseq2000. After association study between the methylation profile and expression profile, aberrant DNA methylated genes were screened out and were uploaded to the GoMiner and the KEGG, completing the bioinformatic analysis. There were 227 hypermethylation genes and 6 hypomethylated genes in cancer tissue, mRNA expression varied from 0.0312 to 8,192 in cancer tissues compared with 0.0312-1,024 in adjacent normal tissues. The correlation study indicated that there were 10 loci in 10 down-regulated genes of hypermethylated in negative correlation group. Additionally, there were 11 loci in 10 up-regulated genes in negative group. Using GoMiner to do GO analysis on aberrant DNA methylation genes, RAPGEFL1, TP53AIP1, KIAA1522, DUOXA2 were identified not involved in any biological processes. ALDH1L1 participated in folinic acid catabolism and CAPN1 positively regulated the cell proliferation. And ALDH1L1 involved in one carbon metabolism and CAPN1 participate in the apoptosis process by applying pathway analysis. The aberrant DNA methylation profiles were established and provided a clue for deeply study on ESCC of Kazakh nationality.