Genetic Control of Alternative Splicing in the Kidneys Illuminates Cardiovascular-Kidney-Metabolic Disease Risk

Background: Multiple transcripts derived from a single protein-coding gene through alternative splicing contribute to functional diversity, yet short-read RNA sequencing typically aggregates isoforms, limiting the resolution of variant-specific regulation. Methods: Splicing events from short read RNA sequencing in 404 human kidney cortex samples were quantified with Leafcutter, and associations between splicing isoforms and disease markers—such as glomerular filtration rate (GFR) and fibrosis—were analyzed via linear regression adjusted for age and sex. PacBio long-read sequencing was conducted on 8 samples, with differential isoform usage analysis performed using tappAS. Splicing quantitative trait locus (sQTL) analysis was integrated the results with genome-wide association study (GWAS) data for estimated glomerular filtration rate (eGFR) and other cardiovascular-kidney-metabolic (CKM) traits. Results: Linear regression revealed 496 significant genes associated with GFR, enriched for membrane transport and ion-handling pathways, and 1875 genes associated with fibrosis, enriched across broader pathways. Long-read sequencing identified 51.4% novel transcripts, and differential isoform analysis highlighted 475 genes significantly altered in CKD versus control samples. We identified 1,948 genes with significant sQTLs, of which 30 showed evidence of shared genetic regulation with eGFR through both Bayesian colocalization and summary-based Mendelian randomization. Six genes—including PRKAG2, INHBC, HNF1A, and SLC34A1—demonstrated concordant regulation across sQTL, expression QTL (eQTL), and protein QTL (pQTL) datasets, implicating transcript-level regulation as a key mediator of disease-associated variation for kidney function. Similarly, a confluence of evidence nominated the importance of CLCNK splice variant for blood pressure. To further resolve transcript structure, we performed long-read RNA sequencing, identifying novel isoforms and validating short-read junction-based quantifications. These data nominate specific isoforms, including those of MANBA and GSTA2, as mediators of kidney disease risk. Conclusion: Our findings highlight transcript-specific genetic regulation in the human kidney and emphasize the importance of isoform-resolved analyses for understanding complex trait biology.