Congenital heart disease (CHD) is the most common birth defect, affecting approximately 1% of all live births. The cause of the majority of CHD cases is still unknown. Recently, exome sequencing of parent-offspring trios identified a subset of protein-damaging de novo mutations in CHD probands, especially in genes highly expressed in the developing heart and brain. Many CHD-associated de novo mutations were in epigenetic transcriptional regulators, in particular those involved in H3K4 and H3K27 methylation. However, protein-damaging de novo mutations only contribute to approximately 10% of CHD. The contribution of non-coding mutations to CHD is just beginning to be studied. In large part, this is because of the increased difficulty of prioritizing non-coding variants and evaluating non-coding variants for biological impact. We developed a high throughput, massively parallel reporter assay which can evaluate the enhancer activity of thousands of candidate regions. Here I will use this assay to enable the analysis of whole genome sequencing data (available for this project through collaborations with the Pediatric Cardiac Genomics Consortium) to detect pathogenic non-coding CHD mutations, through the following specific aims. First, I will use this assay to assess human cardiac enhancer activity during iPSC-derived cardiomyocyte (iPSC-CM) differentiation, and combine the active cardiac enhancers with epigenetic profiling data to develop an informatic method to predict new cardiac enhancers. These cardiac enhancer predictions will be applied to prioritize de novo non-coding variants in CHD cases. Second, I will apply my high-throughput assay to measure the impact of CHD-associated de novo variants on enhancer activity. In follow-up studies on selected variants, I will further test the impact on gene expression by introducing the variants into iPSCs and differentiating the iPSCs into CMs, and by measuring their impact on promoter-enhancer contacts. Taken together, these studies will provide new insights into human cardiogenesis and CHD pathogenesis.
|Program type||Postdoctoral Fellowship|
|Effective start/end date||01/01/2020 → 12/31/2021|