Identification of novel hypermethylated or hypomethylated CpG sites and genes associated with anthracycline-induced cardiomyopathy

• Type of Material: Article
• Authors: Purnima Singh, University of Alabama Birmingham; Liting Zhou, University of Alabama Birmingham; Disheet A Shah, Northwestern University; Romina B Cejas, Northwestern University; David K Crossman, University of Alabama Birmingham; Mariam Jouni, Northwestern University; Tarek Magdy, Northwestern University; Xuexia Wang, Florida International University; Noha Sharafeldin, University of Alabama Birmingham; Lindsey Hageman, University of Alabama Birmingham; Donald E McKenna, Northwestern University; Steve Horvath, University of California Los Angeles; Saro H Armenian, City of Hope, Duarte; Frank M Balis, Childrens Hospital of Philadelphia; Douglas S Hawkins, Seattle Children’s Hospital; Frank G Keller, Emory University; Melissa M Hudson, St. Jude Children’s Research Hospital; Joseph P Neglia, University of Minnesota; A. Kim Ritchey, Childrens Hosp Pittsburgh UPMC; Jill P Ginsberg, Childrens Hospital of Philadelphia; Wendy Landier, University of Alabama Birmingham; Paul W Burridge, Northwestern University; Smita Bhatia, University of Alabama Birmingham
• Language: English
• Date: 2023-08-04
• Publisher: NATURE PORTFOLIO
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2023
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1038/s41598-023-39357-2
• Title of Journal or Parent Work: SCIENTIFIC REPORTS
• Volume: 13
• Issue: 1
• Start Page: 12683
• End Page: 12683
• Grant/Funding Information: NCI (R35CA220502; PI: S Bhatia), LLS (6563-19; PI: S Bhatia), The V Foundation (DT2019-010; PI: S Bhatia). This work was supported in part by the American Cancer Society Institutional Research Grant (#IRG-60-001-53-IRG) and the Kaul Pediatric Research Institute Research Grant (to P.S.). The Children’s Oncology Group study (COG-ALTE03N1; NCT00082745; PI-Bhatia) reported here is supported by the National Clinical Trials Network (NCTN) Operations Center Grant (U10CA180886; PI-Hawkins); the NCTN Statistics & Data Center Grant (U10CA180899; PI-Alonzo); the Children’s Oncology Group Chair’s Grant (U10CA098543; PI-Adamson); The COG Statistics & Data Center Grant (U10CA098413; PI-Anderson); the NCI Community Oncology Research Program (NCORP) Grant (UG1CA189955; PI-Pollock); and the Community Clinical Oncology Program (CCOP) Grant (U10CA095861; PI-Pollock), and the St Baldrick’s Foundation through an unrestricted grant.
• Keywords: EPIGENOME-WIDE ASSOCIATION; RNA; STRESS; Science & Technology - Other Topics; HYPERTROPHY; Multidisciplinary Sciences; Science & Technology; HEART-FAILURE; EPIGENETICS; EXPRESSION; CHILDHOOD-CANCER; DISEASE; DNA METHYLATION
• Research Categories: Biology, Genetics; Health Sciences, Oncology

Abstract

Anthracycline-induced cardiomyopathy is a leading cause of late morbidity in childhood cancer survivors. Aberrant DNA methylation plays a role in de novo cardiovascular disease. Epigenetic processes could play a role in anthracycline-induced cardiomyopathy but remain unstudied. We sought to examine if genome-wide differential methylation at ‘CpG’ sites in peripheral blood DNA is associated with anthracycline-induced cardiomyopathy. This report used participants from a matched case–control study; 52 non-Hispanic White, anthracycline-exposed childhood cancer survivors with cardiomyopathy were matched 1:1 with 52 survivors with no cardiomyopathy. Paired ChAMP (Chip Analysis Methylation Pipeline) with integrated reference-based deconvolution of adult peripheral blood DNA methylation was used to analyze data from Illumina HumanMethylation EPIC BeadChip arrays. An epigenome-wide association study (EWAS) was performed, and the model was adjusted for GrimAge, sex, interaction terms of age at enrollment, chest radiation, age at diagnosis squared, and cardiovascular risk factors (CVRFs: diabetes, hypertension, dyslipidemia). Prioritized genes were functionally validated by gene knockout in human induced pluripotent stem cell cardiomyocytes (hiPSC-CMs) using CRISPR/Cas9 technology. DNA-methylation EPIC array analyses identified 32 differentially methylated probes (DMP: 15 hyper-methylated and 17 hypo-methylated probes) that overlap with 23 genes and 9 intergenic regions. Three hundred and fifty-four differential methylated regions (DMRs) were also identified. Several of these genes are associated with cardiac dysfunction. Knockout of genes EXO6CB, FCHSD2, NIPAL2, and SYNPO2 in hiPSC-CMs increased sensitivity to doxorubicin. In addition, EWAS analysis identified hypo-methylation of probe ‘cg15939386’ in gene RORA to be significantly associated with anthracycline-induced cardiomyopathy. In this genome-wide DNA methylation profile study, we observed significant differences in DNA methylation at the CpG level between anthracycline-exposed childhood cancer survivors with and without cardiomyopathy, implicating differential DNA methylation of certain genes could play a role in pathogenesis of anthracycline-induced cardiomyopathy.