Identification of ventricle-specific methylation patterns in cell-free DNA and correlation with myocardial apoptosis and acute cellular rejection after heart transplantation

Increased levels of donor-derived cell-free DNA (dd-cfDNA) in recipient plasma have been associated with acute cellular rejection (ACR) after heart transplantation. DNA sequence differences have been used to distinguish between donor and recipient cfDNA but epigenetic differences could also potentially identify dd-cfDNA. This study aimed to assess the feasibility of using ventricle-specific methylation patterns in human cfDNA as an alternative biomarker for ACR in cardiac transplantation. Serial samples of plasma (n=24) were collected from adult heart transplant recipients undergoing routine endomyocardial biopsy (EMB) for post- transplant rejection surveillance. Publicly available methylomes and genomic DNA from various human tissues were leveraged to identify ventricle-specific differentially methylated regions of DNA (DMRs) detectable in isolated plasma cfDNA. Correlation of these novel DMRs with pathology-graded ACR was then validated in serial plasma samples.