Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer

Matteo D′Antonio,Christopher Deboever,Florence Coulet,Angelo Arias,Emma K Farley,Hakan Alakus,Richard B Schwab,Donate Weghorn,Andrea L Richardson,Shamil R Sunyaev,Katrina M Olson,Kelly A Frazer,Agnieszka D′Antonio-Chronowska,Frauke Drees

doi:10.1038/s41467-017-00100-x

Abstract

Efforts to identify driver mutations in cancer have largely focused on genes, whereas non-coding sequences remain relatively unexplored. Here we develop a statistical method based on characteristics known to influence local mutation rate and a series of enrichment filters in order to identify distal regulatory elements harboring putative driver mutations in breast cancer. We identify ten DNase I hypersensitive sites that are significantly mutated in breast cancers and associated with the aberrant expression of neighboring genes. A pan-cancer analysis shows that three of these elements are significantly mutated across multiple cancer types and have mutation densities similar to protein-coding driver genes. Functional characterization of the most highly mutated DNase I hypersensitive sites in breast cancer (using in silico and experimental approaches) confirms that they are regulatory elements and affect the expression of cancer genes. Our study suggests that mutations of regulatory elements in tumors likely play an important role in cancer development.

Highlights

Efforts to identify driver mutations in cancer have largely focused on genes, whereas non-coding sequences remain relatively unexplored
We focused on analyzing DNase I hypersensitive sites (DHSs) as previous pan-cancer analyses of non-coding sequences have shown that regulatory elements associated with DHSs have decreased somatic mutation rates compared with the rest of the non-coding genome, suggesting that mutations in these regions have a driver role in cancer[11,12,13]
Given the fact that local mutation density is extremely variable across the genome[14, 15], in this study we developed a statistical method that takes into account the influence of DNA sequence characteristics, replication timing, and chromatin on local mutation rates[15]

Summary

Introduction

Efforts to identify driver mutations in cancer have largely focused on genes, whereas non-coding sequences remain relatively unexplored. Functional characterization of the most highly mutated DNase I hypersensitive sites in breast cancer (using in silico and experimental approaches) confirms that they are regulatory elements and affect the expression of cancer genes. We have analyzed whole genome sequences for 657 breast cancer samples and more than one thousand tumors across 19 additional cancer types to detect non-coding driver mutations. We focused on analyzing DNase I hypersensitive sites (DHSs) as previous pan-cancer analyses of non-coding sequences have shown that regulatory elements associated with DHSs have decreased somatic mutation rates compared with the rest of the non-coding genome, suggesting that mutations in these regions have a driver role in cancer[11,12,13]. We functionally characterized the four DHSs most highly mutated in breast cancer with a combination of in silico and experimental approaches, including CRISPR and animal models, and confirmed they are regulatory elements of known cancer genes

Methods

Results

Conclusion