Identification of M2 macrophage-related biomarkers for a predictive model of interstitial fibrosis and tubular atrophy after kidney transplantation by machine learning algorithms.

Background: Interstitial fibrosis and tubular atrophy (IFTA) represent significant histopathological manifestations contributing to long-term kidney allograft failure after transplantation. Identifying M2 macrophage (Mφ2)-related biomarkers could enhance early diagnosis and prognosis prediction, improving patient outcomes. This study aimed to explore Mφ2-related biomarkers for IFTA via bioinformatics and machine learning approaches.

Methods: RNA sequencing (RNA-seq) data from the GSE98320 dataset were analyzed to identify differentially expressed genes (DEGs). Immune cell profiling using the CIBERSORT algorithm and weighted gene co-expression network analysis (WGCNA) was performed to elucidate Mφ2-related biomarkers modules. Three machine learning algorithms were applied to identify hub genes. A nomogram model was developed and validated using multiple external datasets. Consensus clustering was employed to stratify patients into high-risk and low-risk groups based on hub gene expression.

Results: We obtained three hub genes (ALOX5, ARL4C, and MS4A6A) significantly associated with IFTA. The nomogram model demonstrated robust discriminatory power with an area under the curve (AUC) of 0.738 in the training cohort and 0.78-0.88 in external validation cohorts. Consensus clustering stratified patients into high-risk (cluster 1) and low-risk (cluster 2) groups, with elevated hub gene expression correlating with accelerated graft loss (P<0.001). Functional enrichment analysis revealed immune dysregulation and activation of fibrosis-related pathways in the high-risk group.

Conclusions: Our findings uncovered novel Mφ2-related biomarkers for IFTA, offering diagnostic, prognostic, and therapeutic targets to improve kidney allograft outcomes. This study highlighted the potential of integrating bioinformatics and machine learning approaches to advance personalized medicine in kidney transplantation.