DNA–Methylome Analysis of Mouse Intestinal Adenoma Identifies a Tumour-Specific Signature That Is Partly Conserved in Human Colon Cancer

Christina Grimm,Markus Morkel,Bernhard G Herrmann,Bernd Timmermann,Lukas Chavez,Matthias Lienhard,Hans Lehrach,Jörn Walter,Phillip Grote,Ralf Herwig,Sascha Tierling,Jörn Dietrich,Michal R Schweiger,Julia W Böhm,Alexandra L Farrall,Mireia Vilardell,Dirk Schübeler

doi:10.1371/journal.pgen.1003250

Abstract

Aberrant CpG methylation is a universal epigenetic trait of cancer cell genomes. However, human cancer samples or cell lines preclude the investigation of epigenetic changes occurring early during tumour development. Here, we have used MeDIP-seq to analyse the DNA methylome of APCMin adenoma as a model for intestinal cancer initiation, and we present a list of more than 13,000 recurring differentially methylated regions (DMRs) characterizing intestinal adenoma of the mouse. We show that Polycomb Repressive Complex (PRC) targets are strongly enriched among hypermethylated DMRs, and several PRC2 components and DNA methyltransferases were up-regulated in adenoma. We further demonstrate by bisulfite pyrosequencing of purified cell populations that the DMR signature arises de novo in adenoma cells rather than by expansion of a pre-existing pattern in intestinal stem cells or undifferentiated crypt cells. We found that epigenetic silencing of tumour suppressors, which occurs frequently in colon cancer, was rare in adenoma. Quite strikingly, we identified a core set of DMRs, which is conserved between mouse adenoma and human colon cancer, thus possibly revealing a global panel of epigenetically modified genes for intestinal tumours. Our data allow a distinction between early conserved epigenetic alterations occurring in intestinal adenoma and late stochastic events promoting colon cancer progression, and may facilitate the selection of more specific clinical epigenetic biomarkers.

Highlights

Epigenetic mechanisms play critical roles in controlling the cellular transcript repertoire and cellular phenotypes
We show that mouse adenomas acquire a multitude of epigenetic alterations, which are recurring in mouse adenoma and in human colon cancer, representing early and advanced tumours, respectively
The use of a mouse model allowed us to uncover a sequence of epigenetic changes occurring in tumours, which may facilitate the identification of novel clinical colon cancer biomarkers

Summary

Introduction

Epigenetic mechanisms play critical roles in controlling the cellular transcript repertoire and cellular phenotypes. The methylation of cytosine bases of CpG dinucleotides, as well as the covalent modification of histone proteins represent major target sites of the protein complexes involved in epigenetic control. The Polycomb Repressive Complexes (PRC1 and PRC2) and Trithorax Group Complexes (TrxG) are major histone modifying protein complexes setting repressive or activating marks, respectively, while CpG methylation patterns are set and propagated by DNA methlytransferases (DNMTs). A major role of the PRC2 complex in development is to tag gene regulatory sequences with a specific tri-methyl mark on lysine 27 of histone 3 (H3K27me3), resulting in short-term transcriptional repression [3]. PRC2 complexes can interact with DNMTs, and initiate long-term silencing of genes via de-novo CpG methylation [4]. Non-transformed cells are characterized by high genome-wide CpG methylation, with the exception of CpG islands (CGIs), which are mostly unmethylated [1,2,5]

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