Cell-free Chromatin Immunoprecipitation to detect molecular pathways in Physiological and Disease States

Abstract

Patient monitoring is a cornerstone in clinical practice to define disease phenotypes and guide clinical management. Unfortunately, this is often reliant on invasive and/or less sensitive methods that do not provide deep phenotype assessments of disease state to guide treatment. This paper examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) to define molecular gene sets in physiological and heart transplant patients taking immunosuppression medications. We show cfChIP-seq reliably detect gene signals that correlate with gene expression. In healthy controls and in heart transplant patients, cfChIP-seq reliably detected housekeeping genes. cfChIP-seq identified differential gene signals of the relevant immune and non-immune molecular pathways that were predominantly downregulated in immunosuppressed heart transplant patients compared to healthy controls. cfChIP-seq also identified tissue sources of cfDNA, detecting greater cell-free DNA from cardiac, hematopoietic, and other non-hematopoietic tissues such as the pulmonary, digestive, and neurological tissues in transplant patients than healthy controls. cfChIP-seq gene signals were reproducible between patient populations and blood collection methods. cfChIP-seq may therefore be a reliable approach to provide dynamic assessments of molecular pathways and tissue injury associated to disease.

Circulating, cell-free methylated DNA indicates cellular sources of allograft injury after liver transplant

“…However, there are many situations when genetic differences cannot be used to identify allograft-derived DNA; for example, when the genotype is unknown, multiple genotypes exist in the host, and when the donor is closely related to the recipient (13). Instead, epigenetic modifications can be used to identify cfDNA that is recipient or allograft-derived by using tissue-and cell-type specific marks that are independent of genotype differences between the donor and recipient (19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29). Allograft injury can thus be detected in an organ specific fashion, which is of critical importance in recipients of multi-organ transplants and recipients of hematopoietic cell transplant (HCT) who develop Graft-versus-Host disease (GvHD) (30)(31)(32).…”