Applications of donor-derived cell-free DNA in kidney transplantation healthcare: view from a prospective single-center study

Non-invasive biomarkers enable effective assessment of allograft status without compromising patient’s quality of life. Donor-derived cell-free DNA (dd-cfDNA) has recently emerged as a promising biomarker in solid organ transplants. In this study, we developed a cost-effective, scalable targeted sequencing approach to assess dd-cfDNA performance in monitoring kidney transplant (KTx) integrity. We quantified dd-cfDNA with a customized probe set of 1,000 SNPs specifically designed for the East Asian population. Longitudinal analyses were conducted on 322 blood samples collected from a single-center cohort of 39 KTx patients over an observational period of up to five years. We showed that elevated dd-cfDNA levels are associated with various forms of acute rejection and graft injury in KTx patients. In particular, dd-cfDNA levels effectively distinguished between acute rejection and non-rejection in KTx patients (p = 1.9×10⁻⁴), aligning with serum markers and histological evidences. The surges of dd-cfDNA were evident in antibody-mediated rejection and diverse types of kidney injuries. Additionally, donor bleeding volume was found to influence the stabilization of dd-cfDNA levels during the early post-transplant period. We also reported a unique correlation between dd-cfDNA and Tacrolimus trough levels (Spearman’s rho = -0.25, p = 0.008), which was not observed with other serum markers, underscoring its potential in guiding immunosuppressive therapy. Our study demonstrates the robust role of dd-cfDNA as a responsive biomarker for detecting acute rejection and monitoring kidney integrity. Furthermore, the proposed methodology offers proof-of-concept for scalable diagnostic applications in transplant healthcare.