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 nonpathogenic mitral valves by an assay for transposase-accessible chromatin with high-throughput sequencing. Open chromatin peaks were globally similar between pathogenic and nonpathogenic valves. Compared with the heart tissue and cardiac fibroblasts, we found that MV-specific assay for transposase-accessible chromatin with high-throughput sequencing peaks are enriched near genes involved in extracellular matrix organization, chondrocyte differentiation, and connective tissue development. One of the most enriched motifs in MV-specific open chromatin peaks was for the nuclear factor of activated T cells family of TFs (transcription factors) involved in valve endocardial and interstitial cell formation. We also found that MVP-associated variants were significantly enriched (P<0.05) in mitral valve open chromatin peaks. Integration of the assay for transposase-accessible chromatin with high-throughput sequencing 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. Circular chromatin conformation capture followed by high-throughput sequencing 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 chromosome 2. Conclusions: Here, we describe unprecedented genome-wide open chromatin profiles from human pathogenic and nonpathogenic MVs and report specific gene regulation profiles, compared with 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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | E84-E101 |
| Journal | Circulation research |
| Volume | 128 |
| Issue number | 5 |
| DOIs | |
| State | Published - Mar 5 2021 |
Funding
This study was supported by French Agency of Research (ANR-16-CE17-0015-02) to N. Bouatia-Naji and a PhD scholarship from the China Scholarship Council to M. Yu. A. Georges, S. Kyryachenko, and N. Bouatia-Naji are supported by a European Research Council grant (ERC-Stg-ROSALIND-716628), French Society of Cardiology affiliated Fondation Coeur et Recherche and Federation Francaise de Cardi- ologie. This work was supported by grants from the Deutsche Forschungsgemein-schaft (DFG) to N. Voigt (VO 1568/4-1, VO 1568/3-1, IRTG1816, SFB1002 project A13, under Germany\u2019s Excellence Strategy \u2013 EXC 2067/1-390729940); the Else-Kr\u00F6ner-Fresenius Foundation to N. Voigt (EKFS 2016_A20) and from the German Center for Cardiovascular Research to N. Voigt (DZHK GOE MD3 and SE181); National Institutes of Health to I. Efimov and K. Aras (R44 HL139248, 3OT2OD023848, and 1K99HL148523-01A1), and to R. Norris (HL131546, GM103444, HL149696, HL122906); American Heart Association to I. Efimov (2019 Center Arrhythmias sudden cardiac death Strategically Focused Research Network), to R. Norris (19TPA34850095, 20SRG35540029, 19TPA34900016, 17CSA33590067), and to L. Guo (18PRE34080172); Leducq Foundation grant RHYTHM to I. Efimov. The work at Medical University of South Carolina (MUSC) was performed in a facility constructed with support from the National Institutes of Health grant number C06 RR018823 from the Extramural Research Facilities Program of the National Center for Research Resources. This study was supported by French Agency of Research (ANR-16-CE17-0015-02) to N. Bouatia-Naji and a PhD scholarship from the China Scholarship Council to M. Yu. A. Georges, S. Kyryachenko, and N. Bouatia-Naji are supported by a European Research Council grant (ERC-Stg-ROSALIND-716628), French Society of Cardiology affiliated Fondation Coeur et Recherche and Federation Francaise de Cardiologie. This work was supported by grants from the Deutsche Forschungsgemeinschaft (DFG) to N. Voigt (VO 1568/4-1, VO 1568/3-1, IRTG1816, SFB1002 project A13, under Germany\u2019s Excellence Strategy \u2013 EXC 2067/1- 390729940); the Else-Kr\u00F6ner-Fresenius Foundation to N. Voigt (EKFS 2016_A20) and from the German Center for Cardiovascular Research to N. Voigt (DZHK GOE MD3 and SE181); National Institutes of Health to I. Efimov and K. Aras (R44 HL139248, 3OT2OD023848, and 1K99HL148523-01A1), and to R. Norris (HL131546, GM103444, HL149696, HL122906); American Heart Association to I. Efimov (2019 Center Arrhythmias sudden cardiac death Strategically Focused Research Network), to R. Norris (19TPA34850095, 20SRG35540029, 19TPA34900016, 17CSA33590067), and to L. Guo (18PRE34080172); Leducq Foundation grant RHYTHM to I. Efimov. The work at Medical University of South Carolina (MUSC) was performed in a facility constructed with support from the National Institutes of Health grant number C06 RR018823 from the Extramural Research Facilities Program of the National Center for Research Resources.
Keywords
- chromatin
- extracellular matrix
- fibroblast
- genome wide association studies
- mitral valve prolapse
- single nucleotide polymorphism
ASJC Scopus subject areas
- Physiology
- Cardiology and Cardiovascular Medicine