Parallel Identification Of Gene-Environment Interactions In Cardiac Development Using Human Induced Pluripotent Stem Cells

Most human diseases are influenced by both genetic factors and environmental factors. However, it is not easy to identify causative combinations of genes and environmental factors that interplay in disease development. Congenital heart defects (CHDs), which is the most common birth defect occurring 1% of newborns in the US, are primarily caused by genetic mutations. On the other hand, phenotypes of CHDs are typically inconsistent among individuals with the same variants and the penetrance is often incomplete, which suggests the important role of environmental factors. Environmental factors known to be involved in the development of CHDs include maternal smoking, diabetes, inflammation, and use of certain medications. Here, we investigated gene-environmental interactions in cardiac development. First, we developed a CRISPR-screen system that screens essential genes in cardiac differentiation from human induced pluripotent stem cells (iPSCs). Our custom CRISPRi library targets ~ 700 genes, which are enriched in human adult or fetal hearts. Our screen system successfully identified positive control genes such as TNNT2, TNNC1, and TBX20 as well as genes that have not been intensively investigated in human cardiac development such as BAMBI and SMAD6. Second, to identify gene-environment interactions, we used the system under the exposure to various environmental stresses such as nicotine, ethanol, inflammatory cytokines, and multiple teratogenic drugs and identified stress-specific gene-environment interactions. This approach is applicable to any other screens of gene-environment interactions.