Solid organ transplantation is currently the best option to treat end-stage organ disease. However, it requires lifelong immunosuppressive therapy in most cases, and the diagnosis of rejection and other types of graft injury requires invasive biopsy testing, which poses significant challenges. We developed a targeted deep sequencing assay that extends conventional donor-derived cell-free DNA (dd-cfDNA) analysis by incorporating tissue-of-origin information with the aim of improved non-invasive monitoring of transplant recipients. In this study, plasma cfDNA from liver transplant (LT) and kidney transplant (KT) recipients was analyzed alongside healthy controls to characterize cfDNA release and clearance patterns from graft and recipient cell types, and to identify potential tissue injury signatures. Our assay accurately detected low-abundance, tissue-specific cfDNA, revealing unique cfDNA release patterns associated with the transplanted organ type in recipients with stable allografts. In the early post-transplant period, LT and KT patients exhibited different cfDNA kinetics in numerous tissues, reflecting variation in the response and recovery following reperfusion injury and surgical trauma. Furthermore, the comparison of tissue- and donor-specific cfDNA proportions within 24 hours after transplantation supports a multisource donor-tissue cfDNA release. These findings suggest that incorporating tissue-of-origin information with dd-cfDNA quantification provides important additional insights for evaluating transplant recipient health.

The authors have declared no competing interest.

This study has been funded by the Swiss National Science Foundation grant number 310030_188762, the Hemmi Foundation and the Fondation Johanna Duermueller-Bol. The biobanking was financially supported by the Department for Teaching and Research of the Inselspital, University Hospital Bern, Bern, Switzerland.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Ethics committee of the Canton of Bern, Switzerland gave ethical approval for this work.

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Raw adapter trimmed FASTQ files generated in this study have been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI and the CRG, under accession number EGAS50000000987. Due to Swiss law, access to the data is restricted. Researchers wishing to obtain the data must submit an application to the responsible Data Access Committee.