Engineered Heart Tissues Facilitate Noncoding Variant Studies in Cardiomyopathy

Area of Science:

• Cardiovascular Genetics
• Stem Cell Biology
• Epigenomics

Background:

• Cardiomyopathies often stem from rare genetic variants, but genome-wide association studies (GWAS) indicate significant polygenic contributions.
• Many GWAS loci are in noncoding DNA, necessitating experimental validation within a human genome context.

Purpose of the Study:

• To develop and utilize engineered heart tissues (EHTs) for functional characterization of noncoding variants associated with cardiomyopathy.
• To integrate multi-omics data for fine-mapping GWAS loci and identifying regulatory elements influencing cardiac function.

Main Methods:

• Created EHTs from human induced pluripotent stem cell-derived cardiomyocytes and cardiac fibroblasts.
• Generated single-cell gene expression and chromatin accessibility maps to create genome-wide regulatory maps.
• Integrated open chromatin regions with chromatin contact data for fine-mapping GWAS single-nucleotide polymorphisms (SNPs) and validated using reporter assays and genome editing.

Main Results:

• EHT single-cell RNA-seq demonstrated advanced cardiomyocyte maturation. Over 400,000 open chromatin regions were identified and cell-typed.
• Functional fine-mapping prioritized 5,817 variants, with reporter assays confirming allele-specific enhancer activity.
• An intergenic locus (chr3p25.1) showed long-range interactions with SLC6A6 and GRIP2; CRISPR deletion reduced gene expression and EHT contractile function.

Conclusions:

• EHTs provide a tractable platform for testing the functional impact of noncoding variants in cardiomyopathy.
• Fine-mapped variants using EHT regulatory maps have functional consequences and prioritize sites for studying polygenic heart failure.