Abstract
BACKGROUND: While genome-wide association studies (GWAS) have shown that genetic variants are linked to diabetic nephropathy (DN), the precise gene responsible for influencing risk remains largely unidentified, and the issue of missing heritability persists. This study seeks to identify new pathogenic genes using transcriptome-wide association study (TWAS) analysis in a cohort with renal biopsy-proven DN. METHODS: A TWAS was conducted to investigate potential DN risk genes whose expression mediates the genotype effect on the phenotype. Gene expression levels were entered into our existing DN GWAS cohort including 2,279 renal biopsy-proven DN and 3,762 type 2 diabetes more than 10 years without any microvascular complications by using GEMMA software. The TWAS P-values were calculated using logistic regression models. Public data from ENCODE and GEO were obtained to annotate the function of genes and variants. Pathway enrichment analysis was performed with co-expressed genes. The role of GYS1 in DN was determined using Gys1-antisense oligonucleotide (ASO) in db/db mice. RESULTS: The expression levels of 4,703 cis-heritable genes were analyzed from our renal biopsy-proven DN GWAS dataset. The TWAS results identified 17 genes (9 glomerular-only, 5 tubulointerstitial-only, and 3 shared) that were statistically significantly associated with DN susceptibility in both glomerular and tubulointerstitial regions. Notably, GYS1 and FOXJ2 emerged as novel findings. Furthermore, a gene prioritization strategy was developed, involving gene differential expression validation, clinical and pathological indicator correlation, and functional variant exploration. This approach identified GYS1 as the top causal gene. Risk variants (rs116573491 and rs111518556) of GYS1 were both discovered to increase GYS1 expression in vitro. GYS1 was found to be enriched in glomerular mesangial cells and was elevated in DN compared to healthy controls. Additionally, the level of GYS1 in glomeruli was inversely correlated with estimated GFR (eGFR) and positively correlated with 24-h proteinuria in DN patients. Gys1-ASO therapy halted the progression and development of DKD in db/db mice by reducing Gys1 expression. CONCLUSIONS: This biopsy-based TWAS identifies 17 DN susceptibility genes and prioritized GYS1 as a probable driver of DN, links genetic risk to mesangial dysfunction, and demonstrates that Gys1 suppression mitigates disease progression, supporting GYS1 as a therapeutic target. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-025-01590-x.