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.

背景：多瘤病毒肾病（Polyomavirus nephropathy, PyVN）是肾移植术后的严重并发症，以肾小管间质性炎症为特征，临床表现与T细胞介导的排斥反应（T cell-mediated rejection, TCMR）高度相似。班夫人类器官移植（Banff Human Organ Transplant, B-HOT）转录组分析工具包含770个基因，已被开发用于辅助诊断移植排斥反应，但该工具在区分PyVN与TCMR方面的应用价值仍不明确。
研究目的：本研究旨在借助B-HOT转录组分析工具，解析PyVN与TCMR的生化特征，探究PyVN患者接受治疗后的转录组变化，并评估该工具的诊断效能。
研究方法：本研究纳入11例PyVN患者的福尔马林固定石蜡包埋（FFPE）组织样本，在确诊时及随访阶段采用B-HOT工具进行转录组分析；通过比对公共数据集筛选差异表达基因（DEG）与激活通路，并基于病毒清除情况及肾功能结局探索预后相关影响因素。
研究结果：BK病毒VP1基因在PyVN患者样本中显著高表达，可辅助PyVN的临床诊断。在原始数据集分析中，相较于TCMR，PyVN患者的组织稳态通路存在上调，但公共数据集未筛选到特异性激活通路。确诊时较强的T细胞检查点信号通路激活与病毒成功清除呈正相关，提示该通路在免疫介导的病毒清除过程中发挥关键作用。
研究结论：除病毒基因定量检测外，B-HOT转录组分析工具在PyVN诊断中的应用价值有限。不过，T细胞检查点信号通路或可作为PyVN患者实现病毒清除及保留肾功能的预后标志物。未来仍需开展进一步研究以优化PyVN的分子诊断方案，改善肾移植术后临床结局。