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Intrahepatic cholangiocarcinoma (ICC) is a rare but fatal tumor. The isocitrate dehydrogenase 1 and 2 ( IDH1 / 2 ) genes are known to be mutated in ICC.  IDH1 / 2  mutations tend to be accompanied by enhanced hypermethylation at a subset of genomic loci. We sought to clarify the clinicopathological features, including prognostic value, of ICCs with  IDH1 / 2  mutation-associated hypermethylation at a subset of genes. The mutation status of  IDH1 / 2  and methylation status of 30 gene CpG island loci were analyzed in 172 cases of ICC using pyrosequencing and the MethyLight assay, respectively. The mutation status of  IDH1 / 2  was correlated with clinicopathological features and the DNA methylation status at 30 gene loci. Then, the clinicopathological characteristics were analyzed regarding three-tiered methylation statuses in genes showing  IDH1 / 2  mutation-associated methylation.  IDH1 / 2  mutations were found in 9.3% of ICCs, and  IDH1 / 2 -mutated tumors were associated with the histological subtype, including the bile ductular type and small duct type, and poor differentiation. Eight DNA methylation markers showed associations with  IDH1 / 2  mutations, and ICCs with > 5/8 methylated markers were associated with the bile ductular type or small duct type, absence of mucin production, absence of biliary intraepithelial neoplasia, and presence of chronic liver disease. > 5/8 methylated markers were an independent prognostic marker associated with better survival in both cancer-specific survival and recurrence-free survival. In summary, by analyzing the association between  IDH1 / 2  mutations and DNA methylation in individual genes, we developed a panel of DNA methylation markers that were significantly associated with  IDH1 / 2  mutations and were able to identify a subset of ICC with better clinical outcomes.

Intrahepatic cholangiocarcinomas with IDH1/2 mutation-associated hypermethylation at selective genes and their clinicopathological features