Genetic regulation of alternative splicing in the human heart: a splice QTL analysis

Background Heart failure remains a leading cause of morbidity and mortality globally, highlighting a need to identify novel therapeutic targets. The importance of alternative splicing in heart failure pathogenesis and progression is increasingly recognized, but the molecular mechanisms that regulate specific splicing events is still largely unexplored. Purpose We aimed to map genetic loci associated with alternative splicing events in the human failing heart, employing a functional genomics approach. Methods Whole genome sequencing and RNA-sequencing data derived from explanted left ventricular tissue of 94 transplant recipients with heart failure were used to map splicing quantitative trait loci (sQTL) across the human genome. Alternative splicing events based on intron excision ratios were identified in RNA-sequencing data using Leafcutter v. 0.2.9 and used as phenotypes for cis-sQTL mapping with tensorQTL, adjusting for age, sex and sampling site. Results We identified 3932 cis-sQTLs (FDR<0.05, allele frequency>0.05), including 2053 unique alternative splicing events in a total of 1602 genes (sGenes). Lead sQTL variants were primarily intronic and located in close proximity to the alternative splicing event (mean distance 2 kb). sGenes included Mendelian cardiomyopathy risk genes (FHL1, MYL3, RBM20) as well as genes where alternative splicing plays important roles for cardiac development and disease (PDLIM5, CAMK2D). For example, we identified seven sQTLs regulating alternative splicing events generating the nuclear CAMK2D-B isoform, the expression of which has been linked to heart failure progression. Conclusions We provide a comprehensive map of regulatory loci associated with alternative splicing in the failing heart, providing new molecular insights into cardiac biology and disease.