Supplementary Material for: Transcriptomic Insights into Polyomavirus Nephropathy in Kidney Transplants: Evaluating the Utility of the B-HOT Panel

Background: Polyomavirus nephropathy (PyVN) is a significant complication following kidney transplantation, characterized by tubulointerstitial inflammation that mimics T cell-mediated rejection (TCMR). The Banff Human Organ Transplant (B-HOT) panel, a transcriptomic analysis tool comprising 770 genes, has been developed to facilitate the diagnosis of allograft rejection. However, its utility in distinguishing PyVN from TCMR remains unclear.Objective: This study aimed to evaluate the biochemical characteristics of PyVN and TCMR using the B-HOT panel, investigate changes after PyVN treatment, and assess the panel's diagnostic utility.Methods: Formalin-fixed paraffin-embedded (FFPE) tissue samples from 11 PyVN patients were analyzed at diagnosis and follow-up using the B-HOT panel. Public datasets were compared to identify differentially expressed genes (DEG) and activated pathways. Prognostic factors were explored based on viral clearance and renal function outcomes.Results: BK VP1 gene expression was significantly elevated in PyVN cases, aiding diagnosis. While tissue homeostasis pathways were upregulated in PyVN compared to TCMR in original data, no specific pathways were identified in public datasets. Successful viral clearance correlated with enhanced T cell checkpoint signaling at diagnosis, suggesting its role in immune-mediated viral elimination.Conclusion: The B-HOT panel provides limited utility for diagnosing PyVN beyond viral gene quantification. However, T cell checkpoint signaling may serve as a prognostic marker for viral clearance and renal function preservation in PyVN cases. Further studies are needed to refine molecular diagnostics for PyVN and improve transplant outcomes.