Modeling Human TBX5 Haploinsufficiency Predicts Regulatory Networks for Congenital Heart Disease

Haploinsufficiency of transcriptional regulators causes human congenital heart disease (CHD); however, the underlying CHD gene regulatory network (GRN) imbalances are unknown. Here, we define transcriptional consequences of reduced dosage of the CHD transcription factor, TBX5, in individual cells du...

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Published in:	Developmental cell Vol. 56; no. 3; pp. 292 - 309.e9
Main Authors:	Kathiriya, Irfan S., Rao, Kavitha S., Iacono, Giovanni, Devine, W. Patrick, Blair, Andrew P., Hota, Swetansu K., Lai, Michael H., Garay, Bayardo I., Thomas, Reuben, Gong, Henry Z., Wasson, Lauren K., Goyal, Piyush, Sukonnik, Tatyana, Hu, Kevin M., Akgun, Gunes A., Bernard, Laure D., Akerberg, Brynn N., Gu, Fei, Li, Kai, Speir, Matthew L., Haeussler, Maximilian, Pu, William T., Stuart, Joshua M., Seidman, Christine E., Seidman, J.G., Heyn, Holger, Bruneau, Benoit G.
Format:	Journal Article
Language:	English
Published:	United States Elsevier Inc 08-02-2021
Subjects:	Animals Body Patterning - genetics cardiomyocyte differentiation Cell Differentiation congenital heart disease disease modeling Gene Dosage gene regulation Gene Regulatory Networks haploinsufficiency Haploinsufficiency - genetics Heart Defects, Congenital - genetics Heart Ventricles - pathology human induced pluripotent stem cells Humans MEF2 Transcription Factors - metabolism Mice Models, Biological Mutation - genetics Myocytes, Cardiac - metabolism single cell transcriptomics T-Box Domain Proteins - genetics transcription factor Transcription, Genetic cardiomyocyte differentiation transcription factor human induced pluripotent stem cells haploinsufficiency gene regulatory networks gene regulation single cell transcriptomics disease modeling congenital heart disease gene dosage
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Summary:	Haploinsufficiency of transcriptional regulators causes human congenital heart disease (CHD); however, the underlying CHD gene regulatory network (GRN) imbalances are unknown. Here, we define transcriptional consequences of reduced dosage of the CHD transcription factor, TBX5, in individual cells during cardiomyocyte differentiation from human induced pluripotent stem cells (iPSCs). We discovered highly sensitive dysregulation of TBX5-dependent pathways—including lineage decisions and genes associated with heart development, cardiomyocyte function, and CHD genetics—in discrete subpopulations of cardiomyocytes. Spatial transcriptomic mapping revealed chamber-restricted expression for many TBX5-sensitive transcripts. GRN analysis indicated that cardiac network stability, including vulnerable CHD-linked nodes, is sensitive to TBX5 dosage. A GRN-predicted genetic interaction between Tbx5 and Mef2c, manifesting as ventricular septation defects, was validated in mice. These results demonstrate exquisite and diverse sensitivity to TBX5 dosage in heterogeneous subsets of iPSC-derived cardiomyocytes and predicts candidate GRNs for human CHDs, with implications for quantitative transcriptional regulation in disease. [Display omitted] •Modeling human TBX5 haploinsufficiency manifests disease-related cellular defects•Subpopulations of cardiomyocytes show distinct responses to reduced TBX5 dosage•TBX5-sensitive genes are linked to congenital heart disease and cardiac function•TBX5 dose-dependent gene networks in humans predict genetic interactions in mice Reduced cardiac transcription factor dosage causes congenital heart disease. Kathiriya et al. investigate genome-edited human iPSC-derived cardiomyocytes to model TBX5 haploinsufficiency. Single-cell RNA-seq reveals discrete cell types with altered expression of disease-related genes. Gene regulatory networks disrupted by reduced TBX5 dosage identify nodes for congenital heart disease.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Author Contributions. I.S.K. and B.G.B conceived and designed the project. B.I.G., L.K.W., L.B., T.S. and I.S.K. performed gene targeting and isolation of mutant iPSCs. B.I.G., K.S.R, P.G., T.S., and I.S.K. performed in vitro differentiation and harvested samples. P.G. performed the Western analysis. M.H.L. performed electrophysiology analyses. R.T. performed statistical analyses for electrophysiology. K.S.R. performed immunostaining and scoring of cardiomyocytes. G.A.A., K.S.R., and K.M.H. performed RNAscope and flow cytometry. K.S.R., A.P.B. and I.S.K. performed Seurat analysis. K.S.R., A.P.B., H.Z.G., and I.S.K. performed pseudotime analyses. A.P.B. employed machine learning for the cell type classifier and mapping of spatial transcriptomics. H.Z.G., A.P.B., M.L.S., and M.H. implemented the cell browser. G.I. performed gene regulatory network analyses. W.P.D. and I.S.K. performed phenotype analyses of mutant mice. B.N.A., F.G., K.L., and W.T.P. performed ChIP-seq experiments and peak calling. S.K.H. and R.T. performed association analyses of co-occupancy, gene expression and disease candidates. J.M.S., W.T.P., C.E.S., J.G.S., and H.H. supervised and advised. I.S.K. and B.G.B. wrote the manuscript, with comments and contributions from all authors. Lead contact
ISSN:	1534-5807 1878-1551
DOI:	10.1016/j.devcel.2020.11.020