Complementary Roles of Tissue-based Gene Expression and Donor-derived Cell-free DNA for Therapy of Mild and Moderate T-cell–mediated Rejection in Kidney Transplants

BACKGROUND: We recently reported on the Molecular Microscope Diagnostic System (MMDx) to guide T-cell-mediated rejection (TCMR) therapy. Donor-derived cell-free DNA (dd-cfDNA) could also assist in risk stratification of TCMR. METHODS: In this cohort of 141 adult kidney transplant recipients, we assessed 3 groups based on histology, MMDx findings, and treatment decisions: untreated histologic TCMR with molecular quiescence (H+M-Rx-); treated histologic and molecular TCMR (H+M+Rx+; high-dose steroids and/or anti-thymocyte globulin); and controls without rejection (H-M-Rx-). We evaluated a 12-mo composite outcome comprising graft loss, patient death, recurrent rejection, or a ≥30% decline in estimated glomerular filtration rate from baseline. Serial dd-cfDNA levels were trended at biopsy and post-biopsy. RESULTS: At biopsy, median dd-cfDNA was higher in H+M+Rx+ (0.94%; interquartile range [IQR], 0.38%-2.30%) versus H+M-Rx- (0.30%; IQR, 0.17%-0.40%) and H-M-Rx- (0.26%; IQR, 0.18%-0.51%; P < 0.001). Median MMDx TCMR scores and molecular acute kidney injury (AKI) scores were higher in H+M+Rx+ (TCMR: 0.40; AKI: 0.93) than H+M-Rx- (TCMR: 0.01; AKI: 0.23) and H-M-Rx- (TCMR: 0.01; AKI: 0.12; both P < 0.001). Over 12 mo, dd-cfDNA decreased in H+M+Rx+ with therapy and remained stably low in H+M-Rx- and H-M-Rx-. In a Cox proportional hazards model, molecular AKI (hazard ratio [HR], 3.20; 95% confidence interval [CI], 1.54-6.66; P = 0.002), histologic chronic interstitial fibrosis/tubular atrophy (HR, 1.39 per unit; 95% CI, 1.09-1.77; P = 0.008), and dd-cfDNA at index biopsy (HR, 1.28; 95% CI, 1.04-1.57; P = 0.02) predicted the composite outcome. CONCLUSIONS: dd-cfDNA correlated more closely with molecular TCMR than with histologic tubulitis and interstitial inflammation. Untreated histologic TCMR with molecular quiescence (by MMDx and dd-cfDNA) had clinical outcomes comparable to cases without rejection, and serial dd-cfDNA remained low despite lack of TCMR therapy.