The Methylome Landscape Of Cholangiocarcinoma: Crosstalk With Chromatin Regulation And Cancer Driver Mutations

Akram GHANTOUS, International Agency for Research on Cancer, France
HERCEG Z. 1 , LIMPAIBOON T. 2 , BOCK C. 3 , KUNKEAW N. 1 , CAHAIS V. 1 , SRIRAKSA R. 1, 2

1 Epigenetics Group, International Agency for Research on Cancer, Lyon, France
2 The Liver Fluke and Cholangiocarcinoma Research Center, Khon Kaen University, Khon Kaen, Thailand
3 CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria

Cholangiocarcinoma (CCA), a malignancy of the biliary epithelium, exhibits incidence rates that vary widely between geographic regions, reflecting potentially different underlying etiologies. For example, CCA is endemic to Thailand and neighboring regions with high prevalence of liver fluke infections but shows recent incidence increases elsewhere. Exome-sequencing recently identified mutation signatures specific to liver fluke- versus non-fluke-related CCA. However, the epigenomic landscape of CCA is poorly characterized. Using HM27 array and next-generation sequencing (RRBS), we recently identified differentially methylated CpGs associated with specific target genes (mainly Homeobox) of the Polycomb Repressor Complexes (PRCs), which are required for long term epigenetic silencing of chromatin through histone methylation. Homeobox genes that were hypermethylated in gene body regions were highly expressed in CCA tumor tissues and cell lines compared to normal counterparts. Homeobox gene expression also correlated with chromatin status, which was less condensed in CCA cells, as evident by the absence of PRC-mediated repressive histone methylation marks, relative to normal biliary cells. This further supports a role for PRCs in CCA development, as suggested by the methylome-wide analysis. The strongest differences in DNA methylation and expression between tumor and normal cells were evident in HoxA3 and HoxB7. Knock-down of HoxB7 selectively decreased the proliferation of CCA tumor but not normal biliary cells; whereas, HoxA3 knock-down had an inverse effect, highlighting a potential causal role for HoxB7 in CCA tumorigenesis. This study represents the largest epigenome-wide analysis of CCA using cutting-edge technology and can identify epigenetic markers of CCA risk which are being integrated with data on exposure factors and mutation profiles currently under investigation. Moreover, coupled to CCA in vitro models, this work enables a better understanding of the mechanistic insights of this disease, which involves an intricate interplay between DNA methylation, mutation and chromatin regulation. [Acknowledgement: IARC Postdoctoral Fellowship-Marie-Curie-Actions-People-COFUND].