Identification of methylation profile of HOX genes in extrahepatic cholangiocarcinoma

Abstract

AIM: To identify methylation profile and novel tumor marker ofextrahepatic cholangiocarcinoma (CCA) with high throughout microarray. METHODS: Differential methylation profile was compared between normal bile duct epithelial cell lines and CCA cell lines by methyl-DNA immunoprecipitation (MeDIP) microarray. Bisulfite-polymerase chain reaction (BSP) was performed to identify the methylated allels oftarget genes. Expression oftarget genes was investigated before and after the treatment with DNA demethylating agent. Expression ofcandidate genes was also evaluated by immunofluorescence in 30 specimens ofCCA tissues and 9 normal bile duct tissues. RESULTS: Methylation profile ofCCA was identified with MeDIPmicroarray in the respects ofdifferent gene functions and signaling pathways. Interestingly, 97 genes with hypermethylated CpG islands in the promoter region were homeobox genes. The top 5 hypermethylated homeobox genes validated by BSPwere HOXA2 (94.29%), HOXA5 (95.38%), HOXA11 (91.67%), HOXB4 (90.56%) and HOXD13 (94.38%). Expression ofthese genes was reactivated with 5'-aza-2'-deoxycytidine. Significant expression differences were found between normal bile duct and extrahepatic CCA tissues (66.67%-100% vs 3.33%-10%). CONCLUSION: HOXA2, HOXA5, HOXA11, HOXB4 and HOXD13 may work as differential epigenetic biomarkers between malignant and benign biliary tissues. © 2011 Baishideng. All rights reserved.