Remote allograft rejection diagnosis by epigenetic changes in circulating cell-free DNA in kidney transplanted patients.

Kidney transplantation (KT) is the preferred treatment for patients with end-stage kidney disease, but long-term graft survival is still compromised by a rate of alloimmune rejection of about 15%. At present, there are no available non-invasive biomarkers that can accurately predict or detect graft rejection. In this PhD project we will explore cell-free DNA (cfDNA) as a novel, non-invasive, and accurate biomarker for monitoring KT recipients. CfDNA is a mixture of circulating DNA fragments released from cells into the bloodstream, and other bodily fluids, upon cell death. In the plasma of KT recipients, cfDNA fragments originating from graft dying cells (donor-derived cfDNA) are mixed with those originating from the recipient. Recent studies indicated that the donor-derived cfDNA fraction is a sensitive marker for graft injury, but not specific for rejection. As DNA epigenetic changes have proved to play a leading role in defining susceptibility to graft rejection and to be also highly tissue specific, we will implement and optimize a new pipeline for cfDNA fragmentation and methylation pattern analysis, able to detect and characterize graft rejection, even at an early stage, and to pinpoint tissue-of-origin of cfDNA fragments. This new non-invasive approach will allow to accurately stratify KT patients, providing then prompt intervention for those at high risk of rejection, while reducing immunosuppressive treatment in clinically stable patients at low risk of rejection.