Abstract 46: Identification of Novel Alternate Splicing Events in Humans With RBFOX2 Mutations and Hypoplastic Left Heart Syndrome

Abstract

Alternative splicing (AS) of protein isoforms is an integral mechanism for cardiac development. RNA Binding Protein, Fox-1 Homolog (C. Elegans) 2 (RBFOX2) is an RNA binding protein preferentially expressed in muscle and neuronal cells and regulates tissue-specific alternate exon splicing in ~2,100 target genes by binding the conserved RNA sequence motif (U)GCAUG. RBFOX2 was recently implicated in the pathogenesis of abnormal cardiac and cerebral development via loss-of-function studies in zebrafish and mouse. However, convincing evidence remains incomplete, as the full complement of RBFOX2 target genes and differential exon usage (DEU) in human cardiovascular cell lines are incompletely defined. We identified de novo mutations in RBFOX2 from four human cases of congenital heart disease (CHD) with hypoplastic left heart syndrome (HLHS) via whole exome sequencing. To test the hypothesis that RBFOX2 mutations alter DEU in known target genes, we performed RNA-seq on ductus arteriosus tissue from human CHD cases with and without RBFOX2 mutation. Analysis of RNA-seq for DEU was performed with DEXSeq. To limit the effect of differential gene expression, we restricted analysis to subjects with high global gene expression correlation (r2 > 0.9, case=1 vs. control=5). DEU in known RBFOX2 target genes were highly enriched compared to all known genes (115/2,100 vs. 589/26,310, p=5.78e-15). A high percentage of the DEU genes (60.0%, 69/115) have high heart expression (HHE) in the developing mouse (mean expression of four cardiac chambers at e14.5). DEU genes with HHE include VCL, TPM1, FN1, ACTN1, and CALD1. Functional annotation clustering reveals enrichment for several actin, cytoskeletal, and contractile Gene Ontology terms, suggesting a possible role in the epithelial-mesenchymal transition (EMT) developmental processes active during early cardiac formation. We also identified enrichment from genes implicated in CHD by allelic specific expression or de novo mutations (44/1,263 vs. 589/26,310, p=0.007). These results are the first in humans to identify differentially expressed exons associated with RBFOX2 mutations in CHD and suggests RBFOX2-mediated alternate splicing may influence EMT pathways implicated in the pathogenesis of HLHS.