Novel target genes and a valid biomarker panel identified for cholangiocarcinoma

Abstract

Cholangiocarcinoma is notoriously difficult to diagnose, and the mortality rate is high due to late clinical presentation. CpG island promoter methylation is frequently seen in cancer development. In the present study, we aimed at identifying novel epigenetic biomarkers with the potential to improve the diagnostic accuracy of cholangiocarcinoma. Microarray data analyses of cholangiocarcinoma cell lines treated with epigenetic drugs and their untreated counterparts were compared with previously published gene expression profiles of primary tumors and with non-malignant controls. Genes responding to the epigenetic treatment that were simultaneously downregulated in primary cholangiocarcinoma compared with controls (n = 43) were investigated for their promoter methylation status in cancer cell lines from the gastrointestinal tract. Genes commonly methylated in cholangiocarcinoma cell lines were subjected to quantitative methylation-specific polymerase chain reaction in a total of 93 clinical samples (cholangiocarcinomas and non-malignant controls). CDO1, DCLK1, SFRP1 and ZSCAN18, displayed high methylation frequencies in primary tumors and were unmethylated in controls. At least one of these four biomarkers was positive in 87% of the tumor samples, with a specificity of 100%. In conclusion, the novel methylation-based biomarker panel showed high sensitivity and specificity for cholangiocarcinoma. The potential of these markers in early diagnosis of this cancer type should be further explored.

Methylation and liver cancer

“…[49]. Andresen et al identified CDO1, DCLK1 and ZSCAN18 as novel frequently methylated biomarkers in CCA, and confirmed frequent methylation of SFRP1 [52]. These findings suggest that many signaling pathways can be involved in the development and progression of CCA and DNA methylation may be a potential source of diagnostic, prognostic and predictive biomarkers [49].…”

“…The methylation of a specific CpG site in the TTP promoter leads to its silencing and consequent Hypermethylation Trascriptional regulator [52] increased level of c-Myc, blocking the effect of TGF-␤1. DNMT3A seems to be the prominent responsible for the methylation of TTP promoter [45].…”

Pathogenesis of cholangiocarcinoma: From genetics to signalling pathways

“…For example, the promoter of SOCS3, which is the upstream regulator of JAK/STAT cytokine signaling was frequently hypermethylated in CCA [35,39]. The Wnt signaling modulator, SFRP1 was also hypermethylated in CCA at frequencies as high as 85% [40]. On the other hand, hypermethylation of SFRP2 promoter leading to its lower M A N U S C R I P T A C C E P T E D ACCEPTED MANUSCRIPT 7 expression, was correlated with poor prognosis [41].…”

Methylated Cysteine Dioxygenase-1 Gene Promoter in the Serum Is a Potential Biomarker for Hepatitis B Virus-Related Hepatocellular Carcinoma

“…Bisulphite modified DNA samples were PCR-amplified using either an unmethylation-specific (CDO1U) or methylation-specific (CDO1M) primer pairs described before ( Fig. 2) (Andresen et al 2012). The methylation primer sense was 5′-TTGGGACGTCGGAGATAAC-3′ and antisense, 5′-GACCCT CGAAAAAAAA ACGA-3′.…”