Cell-Free DNA Tissue Damage Mapping in Transplant Patients Infected with COVID-19

PURPOSE: Patients with COVID-19 show variable clinical course; transplant patients often show worse outcomes. The effect of COVID-19 on the allograft and the sources of tissue injury that contribute to such poor outcomes are poorly defined. This study leverages cell-free DNA (cfDNA) to measure allograft injury as donor-derived cfDNA (ddcfDNA) and injury from different tissue types using tissue-specific DNA methylomic signatures. METHODS: 14 consecutive COVID-19 transplant patients (8 Kidney, 3 Lung, 1 Heart, 1 Liver, and one multi-organ transplant patients) and 30 healthy controls were included. Plasma nuclear cfDNA (ncfDNA) and mitochondrial cfDNA (mtcfDNA) level were measured via digital droplet PCR, and ddcfDNA using AlloSure (CareDx). cfDNA whole-genome bisulfite sequencing was performed to identify cfDNA tissues of origin leveraging tissue specific DNA methylomes and deconvolution algorithm. RESULTS: 75% of the COVID-19 transplant patients showed high ddcfDNA level compared to published quiescent values, including all lung, 50% of the kidney, liver and multi-organ transplant patients (8.5, 4.4, 30 and 16-X fold change, respectively). Total ncfDNA and mtcfDNA were 15X and 310X higher in COVID-19 transplant patients compared to controls, respectively; < 0.0001.The predominant tissues contributing to cfDNA were hematopoietic cells (80%) (Figure). More importantly, COVID-19 transplant patients showed 10 to 100 fold higher tissue specific cfDNA derived from monocyte, neutrophil, erythroblast, vascular endothelium, adipocyte, hepatocyte, kidney, heart and lung compared to controls. Analysis comparing cfDNA in transplant and non-transplant COVID-19 patients is on-going. CONCLUSION: The allograft undergoes significant injury following COVID-19. Further, cfDNA from multiple tissue types is significantly higher in COVID-19 transplant patients. Future studies in a larger cohorts of transplant and non-transplant patients are needed to elucidate why transplant patients show worse COVID-19 outcomes.