Integrated Bioinformatics Analysis and Clinical Validation Identify TNFSF14 and CD40 as Novel Biomarkers for Chronic Kidney Disease Progression and Tubulointerstitial Injury

Background Chronic Kidney Disease (CKD) imposes a significant global health burden, defined by the irreversible loss of function and progressive fibrosis. There is a critical unmet need for non-invasive biomarkers that can accurately mirror renal inflammation and early-stage injury to guide diagnosis. This study combines bioinformatics with clinical validation to pinpoint pathogenic genes driving CKD progression. Methods We mined two CKD expression datasets (GSE66494 and GSE97709) from the GEO database. Using the limma R package, we screened for Differentially Expressed Genes (DEGs) and mapped their biological functions via GO and KEGG enrichment. To validate the top candidates—TNFSF14 and CD40—we analyzed a clinical cohort comprising 140 CKD patients (Stages I–V) and 60 healthy controls. Protein levels were quantified in serum and urine. Furthermore, we assessed tissue expression patterns using immunofluorescence on renal biopsies from patients with Diabetic Nephropathy, IgA Nephropathy, Membranous Nephropathy, and FSGS (n = 20 per group). Results Bioinformatics analysis highlighted TNFSF14 and CD40 as key immune-related targets, clustering heavily within the TNF signaling and cytokine-receptor interaction pathways. Clinically, both markers were markedly elevated in the serum and urine of CKD patients compared to controls (P < 0.05). Tissue staining localized this upregulation specifically to the renal tubules. Correlation analysis showed that urinary levels of these markers tracked closely with disease severity, associating positively with serum creatinine/BUN and inversely with eGFR. ROC analysis further confirmed that both TNFSF14 and CD40 exhibit high diagnostic sensitivity and specificity. Conclusions This study positions TNFSF14 and CD40 not only as robust molecular signatures of tubulointerstitial injury but also as non-invasive urinary biomarkers with high diagnostic precision. Their integration into clinical practice could refine risk stratification and uncover novel therapeutic targets for halting CKD progression.