# Biopsy proteome-based classification of T cell-mediated kidney allograft rejection

## TL;DR

This study explores using kidney biopsy proteomes to better classify T cell-mediated rejection in kidney transplants, potentially improving patient diagnosis and treatment.

## Contribution

A proteomic panel of four proteins is proposed for classifying kidney transplant rejection, with GNB4 and PDK1 showing promise for immune cell and macrophage-based classification.

## Key findings

- Proteomic analysis identified 2547 proteins with strong concordance between borderline and acute rejection groups.
- GNB4 and AGXT significantly differentiated borderline and acute rejection groups.
- PDK1 and CD73 best classified samples in binary analysis, with IHC confirming GNB4 upregulation in immune cells and PDK1 in macrophages.

## Abstract

T cell-mediated rejection (TCMR) remains a challenge in kidney transplantation. Based on a histopathological biopsy examination, patients can be classified into groups such as no rejection (NR), borderline rejection (BR; Banff category 3), and acute rejection (AR; Banff category 4). Yet, this classification is not sufficient, since for the borderline cases a number of patients may require a clinical intervention. Thus, a robust classification by biopsy proteome profiling may provide a solution.

In this work, kidney tissue from patients classified into NR, BR, and AR were subjected to MS-based proteomic profiling. Subsequently, a panel of four proteins (GNB4, PDK1, AGXT, CD73) was selected for validation by immunohistochemistry (IHC). This retrospective study was approved by the Bioethics Committee of the Medical University of Gdańsk, no. NKBBN/201/2021.

Proteomic analysis identified 2547 proteins whose abundance profiles demonstrated strong concordance between the BR and AR groups. In a quantitative comparison between the BR and AR groups, GNB4 and AGXT emerged as significantly differentiating. Moreover, AGXT was indicated as a potential biomarker following ROC analysis. PDK1 and CD73 were found to best classify the samples in a binary analysis. IHC confirmed only upregulation of GNB4 in immune cells and PDK1 in macrophages, with no significant changes in the tubular epithelium.

Thus, GNB4 and PDK1 in immune cells and macrophages have been identified as a potential target for further extensive studies. If their relevance were to be confirmed in a larger patient cohort, their IHC analysis could serve as an extension of established histopathological classification in the context of kidney transplant rejection.

The online version contains supplementary material available at 10.1186/s12967-025-07116-8.