Anthracyclines induce global changes in cardiomyocyte chromatin accessibility that overlap with cardiovascular disease loci

Abstract

Breast cancer drugs including anthracyclines (ACs) and Trastuzumab increase the risk for cardiovascular diseases (CVDs) such as atrial fibrillation (AF) and heart failure (HF) that ultimately affect the heart muscle. These CVDs are associated with hundreds of genetic variants in non- coding regions of the genome. However, how these drugs affect the regulatory potential of the non-coding genome of the heart and CVD risk loci is unknown. We therefore measured global chromatin accessibility across iPSC-derived cardiomyocytes from four individuals treated with the ACs, Doxorubicin, Epirubicin, and Daunorubicin, a related non-AC, Mitoxantrone, and the monoclonal antibody Trastuzumab, or a vehicle control for three and 24 hours. We identified 155,557 high-confidence regions of open chromatin across 48 samples where the major sources of variation are associated with drug type and time. Jointly modeling the data revealed three accessibility response signatures denoted as early-acute, early-sustained, and late that correspond to 67,329 regions that open or close in response to drug treatment. Sequences associated with drug-induced chromatin opening contain motifs for DNA damage-associated transcription factors including p53 and ZBTB14, and associate with increases in active histone acetylation and gene expression. 21 AF- and HF-associated SNPs directly overlap with regions associated with drug-induced opening. A shared intronic HF and AF SNP, rs3176326, that is also an eQTL for CDKN1A in heart tissue, associates with increased chromatin accessibility, histone acetylation, and CDKN1A expression in response to all ACs. Our results demonstrate large-scale changes in chromatin accessibility in cardiomyocytes treated with ACs, which correspond to several regions harboring CVD risk loci. Author summaryAnthracyclines are a widely used class of breast cancer drugs that are linked to cardiac toxicity and the development of heart disease in some women. There are hundreds of genetic variants that associate with risk for heart disease; however their role and mechanism of action in drug- induced toxicity is unclear given that most reside in the non-coding genome. We therefore tested the effects of five breast cancer drugs on genome-wide chromatin accessibility using induced pluripotent stem cell-derived cardiomyocytes. We found tens of thousands of chromatin regions that change in accessibility after drug treatment. Regions with increased accessibility contain sequences that have been shown to bind DNA damage-associated transcription factors, and associate with increases in nearby gene expression. We find 21 heart disease-associated genetic variants in regions that increase in chromatin accessibility following treatment. This suggests that cancer drugs have large effects on the non-coding genome of heart cells including at regions associated with heart disease. This research contributes to our understanding of how genetic variants associated with disease exert their effects.