Chromatin Accessibility of Human Mitral Valves and Functional Assessment of MVP Risk Loci

Authors

Kyryachenko S, Georges A, Yu M, Berrandou T, Guo L, Bruneval P, Rubio T, Gronwald J, Baraki H, Kutschka I, Aras K, Efimov IR, Norris RA, Voigt N, Bouatia-Naji N

Journal

Circulation Research

Citation

Circ Res. 2021 Jan 28.

Abstract

Rationale: Mitral valve prolapse (MVP) is a common valvopathy that leads to mitral insufficiency, heart failure and sudden death. Functional genomic studies in mitral valves are needed to better characterize MVP associated variants and target genes.

Objective: To establish the chromatin accessibility profiles and assess functionality of variants and narrow down target genes at MVP loci.

Methods and Results: We mapped the open chromatin regions in nuclei from 11 human pathogenic and 7 non-pathogenic mitral valves by an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq). Open chromatin peaks were globally similar between pathogenic and non-pathogenic valves. Compared to the heart tissue and cardiac fibroblasts, we found that MV-specific ATAC-Seq peaks are enriched near genes involved in extracellular matrix organization, chondrocyte differentiation, and connective tissue development. One of the most enriched motif in MV-specific open chromatin peaks was for the nuclear factor of activated T cells (NFATC) family of transcription factors, involved in valve endocardial and interstitial cells formation. We also found that MVP-associated variants were significantly enriched (p<0.05) in mitral valve open chromatin peaks. Integration of the ATAC-Seq data with risk loci, extensive functional annotation, and gene reporter assay suggest plausible causal variants for rs2641440 at the SMG6/SRR locus and rs6723013 at the IGFBP2/IGFBP5/TNS1 locus. CRISPR-Cas9 deletion of the sequence including rs6723013 in human fibroblasts correlated with increased expression only for TNS1. 4C-Seq experiments provided evidence for several target genes, including SRR, HIC1, and DPH1 at the SMG6/SRR locus and further supported TNS1 as the most likely target gene on Chr2.

Conclusions: Here we describe unprecedented genome-wide open chromatin profiles from human pathogenic and non-pathogenic MVs and report specific gene regulation profiles, compared to the heart. We also report in vitro functional evidence for potential causal variants and target genes at MVP risk loci involving established and new biological mechanisms.

DOI

10.1161/CIRCRESAHA.120.317581
 
Pubmed Link