A systematic pan-cancer analysis of genetic heterogeneity reveals associations with epigenetic modifiers

© 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).Intratumor genetic heterogeneity (ITH) is the main obstacle to effective cancer treatment and a major mechanism of drug resistance. It results from the continuous evolution of different clones of a tumor over time. However, the molecular features underlying the emergence of genetically-distinct subclonal cell populations remain elusive. Here, we conducted an exhaustive characterization of ITH across 2807 tumor samples from 16 cancer types. Integration of ITH scores and somatic variants detected in each tumor sample revealed that mutations in epigenetic modifier genes are associated with higher ITH levels. In particular, genes that regulate genome-wide histone and DNA methylation emerged as being determinant of high ITH. Indeed, the knockout of histone methyltransferase SETD2 or DNA methyltransferase DNMT3A using the CRISPR/Cas9 system on cancer cells led to significant expansion of genetically-distinct clones and culminated in highly heterogeneous cell populations. The ITH scores observed in knockout cells recapitulated the heterogeneity levels observed in patient tumor samples and correlated with a better mitochondrial bioenergetic performance under stress conditions. Our work provides new insights into tumor development, and discloses new drivers of ITH, which may be useful as either predictive biomarkers or therapeutic targets to improve cancer treatment.This research was funded by: PTDC/BIM-ONC/0016-2014 and PTDC/BIA-MOL/30438/2017 to S.F.d.A., PTDC/MED-ONC/28660/2017 to A.R.G, EMBO-IG-3309, ERC-StG-679168 and FCT/IF/01693/2014/CP1236/CT0003 to V.A.M.; LISBOA-01-0145-FEDER-016394 project co-funded by FEDER, through POR Lisboa, Portugal 2020-Programa Operacional Regional de Lisboa, PORTUGAL 2020 and Fundação para a Ciência e Tecnologia (FCT); UID/BIM/50005/2019 through Fundação para a Ciência e Tecnologia (FCT)/Ministério da Ciência, Tecnologia e Ensino Superior (MCTES)-Fundos do Orçamento de Estado; the iMM-Laço Fund. A.R.G. is the recipient of an FCT Investigator grant (IF/00510/2014). M.R.d.M. is recipient of a PhD fellowship: SFRH/BD/92208/2013. F.S.C. is the recipient of the fellowship iMM/BPD/122-2016.