Rapid Molecular Assessment of Kidney Allograft Rejection Using the Biopsy Transport Medium
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Introduction
Timely diagnosis of kidney allograft rejection is critical for post-transplant management, yet treatment decisions may need to be made empirically while awaiting the final pathology report. We previously demonstrated that biopsy transport medium (BTM) contains molecular signals reflective of allograft rejection. Building on these findings, we developed a rapid BTM–qPCR workflow using a targeted gene panel for early molecular assessment of rejection.
Methods
Kidney transplant biopsies assessed at Leiden University Medical Center from April 2023 to November 2024 were eligible. A predefined gene panel was quantified in BTM by qPCR, while matched formalin-fixed paraffin-embedded tissues were profiled using Tempo-Seq. Elastic Net, Random Forest, and support vector machine models were developed to classify rejection and predict continuous histological indices directly from the BTM.
Results
A total of 134 paired BTM samples and biopsy tissues were analyzed. The best-performing BTM gene-panel models demonstrated good discrimination for rejection, with a median AUC of 0.80, and good calibration (median slope, 0.92; median intercept, 0.08). For continuous histological indices, the best-performing BTM gene-panel models achieved R² values of 0.33 for Activity, 0.31 for TCMR/TI, and 0.27 for AMR/MVI. Corresponding biopsy gene-panel models showed similar patterns across diagnostic outcomes.
Conclusions
The BTM–qPCR workflow captures molecular features of kidney allograft rejection and enables prediction of rejection status along the spectrum of continuous activity indices. By providing same-day molecular information while definitive biopsy interpretation is pending, this rapid approach has the potential to complement conventional histopathological diagnostics and support early clinical decision-making.
Lay Summary
Kidney transplantation is the optimal treatment for end-stage kidney disease, and effective post-transplant management is critical for long-term survival of the transplanted kidney. Therefore, prompt treatment decisions and timely interventions are essential. However, a complete and final pathological assessment of a kidney biopsy can sometimes take several days. A molecular diagnostic approach using qPCR on biopsy transport medium (BTM), the liquid used to transport biopsy samples, has the potential to complement conventional pathological assessment by providing rapid information to support clinical decision-making. Our study included 134 kidney transplant biopsy samples and measured the expression of a panel of 19 genes in BTM. These gene expression measurements were able to distinguish rejection from non-rejection and predict continuous histological indices. Our findings suggest that, while pathological assessment is pending, the BTM–qPCR approach could provide same-day molecular information to support earlier clinical decision-making.
