Validating the concept of mutational signatures with isogenic cell models

Xueqing Zou,Serena Nik-Zainal,Stephen P Jackson,Joanna I Loizou,Rebecca Harris,Michel Owusu

doi:10.1038/s41467-018-04052-8

Abstract

The diversity of somatic mutations in human cancers can be decomposed into individual mutational signatures, patterns of mutagenesis that arise because of DNA damage and DNA repair processes that have occurred in cells as they evolved towards malignancy. Correlations between mutational signatures and environmental exposures, enzymatic activities and genetic defects have been described, but human cancers are not ideal experimental systems—the exposures to different mutational processes in a patient’s lifetime are uncontrolled and any relationships observed can only be described as an association. Here, we demonstrate the proof-of-principle that it is possible to recreate cancer mutational signatures in vitro using CRISPR-Cas9-based gene-editing experiments in an isogenic human-cell system. We provide experimental and algorithmic methods to discover mutational signatures generated under highly experimentally-controlled conditions. Our in vitro findings strikingly recapitulate in vivo observations of cancer data, fundamentally validating the concept of (particularly) endogenously-arising mutational signatures.

Highlights

The diversity of somatic mutations in human cancers can be decomposed into individual mutational signatures, patterns of mutagenesis that arise because of DNA damage and DNA repair processes that have occurred in cells as they evolved towards malignancy
We conclusively identified seven mutational signatures from nine gene knockouts in this HAP1based experimental system: two substitution signatures were induced by knockouts of EXO1 and MSH6 (Fig. 3); three indel signatures produced by knockouts of EXO1, FANCC and MSH6 (Fig. 4); and two rearrangement signatures associated with knockouts of EXO1 and FANCC (Fig. 5), as described in detail below
These principles lend themselves to a thorough, systematic screen of all genes involved in maintaining genome integrity and of all potential genotoxic agents in order to comprehensively understand the repertoire of mutational signatures in human cells

Summary

Introduction

The diversity of somatic mutations in human cancers can be decomposed into individual mutational signatures, patterns of mutagenesis that arise because of DNA damage and DNA repair processes that have occurred in cells as they evolved towards malignancy. Correlations between mutational signatures and environmental exposures, enzymatic activities and genetic defects have been described, but human cancers are not ideal experimental systems —the exposures to different mutational processes in a patient’s lifetime are uncontrolled and any relationships observed can only be described as an association. Our in vitro findings strikingly recapitulate in vivo observations of cancer data, fundamentally validating the concept of () endogenously-arising mutational signatures. There are multiple algorithms to extract mutational signatures[5,9,10,11,12], though each has its own mathematical idiosyncrasies leading to results that are broadly similar, but never identical This has caused some to question the robustness of the concept. Even if mutational signatures could be reproduced using in vitro techniques, it is not known whether these signatures would mimic what is observed in vivo

Methods

Results

Conclusion