Gene regulatory networks for heart development

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PROJECT SUMMARY Congenital heart defects (CHDs) are the most prevalent and serious birth defects, occurring in over 1% of live births. Major subsets of congenital heart defects are defective septation of the atria or ventricles, and conduction system defects, which often co-exist within an individual. The molecular and cellular basis of congenital heart defects remains poorly understood, and an understanding is necessary to develop new diagnostic and therapeutic modalities. The genetic basis of human CHD is largely from dominant mutations in transcription factors (TFs) and chromatin-modifying factors, resulting in their reduced dosage. How reduced dosage of a transcriptional regulator translates to altered genomic function is not known, nor is it known how these altered gene regulatory networks then disrupt heart development to cause CHDs. TBX5 is a T-box TF, haploinsufficiency of which causes heart defects associated with Holt-Oram syndrome (HOS). We have developed an induced pluripotent stem (iPS) cell model of HOS, and in parallel, we have studied a new mouse model of TBX5-dependent CHD. Based on strong preliminary data including single cell RNAseq, we propose a project aimed at elucidating the molecular basis of TBX5-dependent gene regulatory networks in the formation of CHDs. We hypothesize that TBX5 dosage in specific, vulnerable cell populations in the developing heart, drives gene regulatory networks that control finely regulated cellular behaviors, with consequences for cardiac development. We will test this hypothesis by elucidating the genomic dysregulation that results from TBX5 haploinsufficiency in a human iPSC model of CHD, and the genetic and cellular defects in the cells that define the interventricular septum boundaries in a mouse model of TBX5 haploinsufficiency in vivo. The proposed experiments, based on single cell transcriptomics and epigenomics, will provide exciting new insights into the molecular events that lead to common CHD. We propose three specific aims. Aim 1 is todefine disrupted gene regulatory networks in discrete cell populations in a human cell model of CHD, using an allelic series of TBX5, which includes heterozygous and homozygous null iPS cell lines, and single cell RNAseq and ATACseq. Aim 2 is to identify epigenomic mechanisms for TBX5 haploinsufficiency by examining in our TBX5 allelic series chromatin occupancy of TBX5 and its TF partners, chromatin remodeler, and histone modifications. Aim 3 is to delineate the genetic and cellular basis for Tbx5 haploinsufficiency in interventricular septum progenitors in vivo by single cell RNAseq and ATACseq using lineage labeled interventricular septum cardiomyocytes, combined with spatial transcriptomics. These results will reveal in vivo gene regulatory networks dysregulated in CHD. The major impact of the proposed work will be important mechanistic insights into CHDs, and broadly generalizable mechanisms of transcription factor dosage-sensitive gene regulation.