Biopsy-Based Transcriptomics Support Rejection Monitoring Through Repeated Kidney Allograft Biopsies.

Introduction: Biopsy-based transcriptomics may detect subthreshold signals suspicious for rejection in histologically "rejection-free" biopsies, reflect antirejection treatment responses, and indicate gradual phenotyping of rejection in kidney allograft biopsies.

Methods: We investigated 80 "biopsy series" (baseline and corresponding follow-up biopsies) from 2018 to 2025, assessed by histopathology (Banff classification) and the Molecular Microscope Diagnostic System (MMDx).

Results: Baseline biopsies showed histological rejection, including partial antibody-mediated rejection (AMR) and borderline T-cell-mediated rejection (TCMR) in 55 of 80 cases (69%), with 55% molecular rejection confirmation. After a median of 9 months (interquartile range: 4-18), follow-up biopsies detected histological rejection in 9 of 25 (36%) previously "rejection-free" cases. Corresponding baseline biopsies had higher rejection (Rejection; median 0.23 vs. 0.02, = 0.008) and AMR (AMR; 0.08 vs. 0.03, = 0.002) classifier scores than those without follow-up rejection ( = 16). Histological interstitial inflammation (i) + tubulitis (t) and glomerulitis (g) + peritubular capillaritis (ptc) scores were similar ( = 0.411, = 0.602). In molecular TCMR treated conventionally, 4 of 6 (67%) had TCMR < 0.1 at follow-up, with significant reductions in i+t scores (4.5-1.5, = 0.031). Two of 6 (33%) progressed to mixed phenotypes. Among treated molecular AMR cases, AMR decreased (0.76-0.51, = 0.047), but only 1 of 7 (14%) reached AMR < 0.2, whereas g + ptc scores remained unchanged ( > 0.99). In treated mixed molecular AMR/TCMR, molecular and histological scores improved. Four of 9 (44%) showed rejection resolution, 3 of 9 (33%) shifted to molecular AMR, 1 of 9 (11%) to TCMR, and 1 of 9 (11%) remained mixed molecular phenotypes.

Conclusions: Biopsy-based transcriptomics differentiated suspicious molecular signals among histologically "rejection-free" biopsies progressing to rejection and provided a monitoring tool after antirejection treatment interventions.