Additional Diagnoses Other Than Rejection in the Kidney Allograft Biopsy: Pitfalls for Biopsy-based Transcript Diagnostics

Background. Biopsy-based transcripts associated with antibody-mediated rejection (AMR) hold promise as substitutes for C4d positivity. However, their utility in cases with additional diagnoses other than rejection remains inadequately studied. Methods. In our comprehensive analysis of 326 kidney allograft biopsies, assessed by histology and the Molecular Microscope Diagnostic System, we identified 68 cases characterized by additional pathologies, including pyelonephritis (n = 15), BK nephropathy (n = 20), acute interstitial nephritis (n = 5), and glomerular diseases (n = 28). Results. Among cases with pyelonephritis, 7 of 15 cases (46%) showed a rejection-like signal, 4 above (16%) and 3 (20%) below diagnostic thresholds. Notably, the T cell–mediated rejection (TCMR) archetype score R2 (median, 0.13; interquartile range [IQR], 0.04–0.34) predominantly contributed to this observation. In BK nephropathy, 13 of 20 cases (65%) showed a rejection-like signal, 10 (50%) above and 3 (15%) below diagnostic thresholds. Elevated TCMR R2 (median, 0.07; IQR, 0.00–0.41) and all AMR archetype scores R4–6 (median, 0.23; IQR, 0.07–0.53) were driving factors. Among cases with acute interstitial nephritis, 3 of 5 cases (60%) showed TCMR-like signal with elevated R2 scores (median, 0.13; IQR, 0.00–0.54). Conversely, only 5 of 28 cases (18%) showed a rejection-like signal in glomerular disease cases, whereas 57% displayed all AMR archetype scores of ≥0.30. Conclusions. Additional pathologies can affect the Molecular Microscope Diagnostic System output, giving a molecular rejection-like signal. The prevalence of rejection-like signals below diagnostic thresholds is noteworthy, warranting caution and prompting further investigation.