Integration of transcriptomics, machine learning, and molecular simulations identifies key microvascular-protective...

Diabetic kidney disease (DKD) is a microvascular complication of diabetes that can progress to renal failure. Tert-butylhydroquinone (TBHQ) exhibits renal protective effects in type II diabetes, but its regulatory role on microvascular protection-related genes in DKD requires further elucidation. This study aimed to identify key TBHQ-targeted genes involved in microvascular protection in DKD. In this study, we employed a tert-butyl hydroperoxide (t-BHP)-induced human renal glomerular endothelial cell (HRGEC) model to identify differentially expressed genes (DEGs) (|log2FC|>1, P < 0.05) in TBHQ-treated groups through transcriptomic analysis. Concurrently, two DKD datasets from the GEO database were analyzed using weighted gene co-expression network analysis (WGCNA) to identify DKD-highly correlated genes. After obtaining potential targets by intersecting these two gene sets, we further refined key genes using LASSO regression and SVM-RFE algorithms. The study identified VEGFA and BIRC3 as two key TBHQ-targeted genes for microvascular protection in DKD. Single-gene GSEA analysis revealed significant enrichment of these genes in inflammation, apoptosis and vascular development-related pathways. Molecular docking and molecular dynamics (MD) simulations confirmed good binding affinity between TBHQ and key genes, with their expression changes further validated by RT-qPCR and Western blot in HRGECs. These findings suggest TBHQ mitigates microvascular endothelial injury via modulation of VEGFA and BIRC3, offering novel insights into therapeutic strategies for DKD.