DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer.

Andrew E Teschendorff,Martin Widschwendter,David L Wachter,Allison Jones,Yang Gao,Peter A Fasching,Matthias Ruebner,Matthias W Beckmann

doi:10.1038/ncomms10478

Abstract

Identifying molecular alterations in normal tissue adjacent to cancer is important for understanding cancer aetiology and designing preventive measures. Here we analyse the DNA methylome of 569 breast tissue samples, including 50 from cancer-free women and 84 from matched normal cancer pairs. We use statistical algorithms for dissecting intra- and inter-sample cellular heterogeneity and demonstrate that normal tissue adjacent to breast cancer is characterized by tens to thousands of epigenetic alterations. We show that their genomic distribution is non-random, being strongly enriched for binding sites of transcription factors specifying chromatin architecture. We validate the field defects in an independent cohort and demonstrate that over 30% of the alterations exhibit increased enrichment within matched cancer samples. Breast cancers highly enriched for epigenetic field defects, exhibit adverse clinical outcome. Our data support a model where clonal epigenetic reprogramming towards reduced differentiation in normal tissue is an important step in breast carcinogenesis.

Highlights

Identifying molecular alterations in normal tissue adjacent to cancer is important for understanding cancer aetiology and designing preventive measures
By measuring DNA methylation in almost half a million CpG sites, and using a statistical paradigm for feature selection, we demonstrate the existence of widespread epigenetic field defects in normal tissues adjacent to breast cancers, with these defects becoming enriched in the progression to breast cancer
Fat content did not vary significantly between the normal and normal-adjacent samples (Supplementary Fig. 3A), and adjustment for fat content did not have a major impact on differential methylation analysis, with differentially methylated CpGs between normal and normal-adjacent tissue not attaining genome-wide significance (minimum false discovery rate (FDR) 1⁄4 0.3) in either adjusted or unadjusted analysis (Supplementary Fig. 3B)

Summary

Introduction

Identifying molecular alterations in normal tissue adjacent to cancer is important for understanding cancer aetiology and designing preventive measures. By measuring DNA methylation in almost half a million CpG sites, and using a statistical paradigm for feature selection, we demonstrate the existence of widespread epigenetic field defects in normal tissues adjacent to breast cancers, with these defects becoming enriched in the progression to breast cancer. These data are consistent with a model in which epigenetic alterations predate the emergence of cancer

Methods

Results

Conclusion