Wasson, L. K. | bioRxiv Science

bioRxiv2022

A Missense Mutation in Human CHD4 Causes Ventricular Noncompaction by Repressing ADAMTS1-mediated Trabeculation Cessation

BackgroundLeft ventricular noncompaction (LVNC) is a prevalent cardiomyopathy associated with excessive trabeculation and thin compact myocardium. Patients with LVNC are vulnerable to cardiac dysfunction and at high risk of sudden death. Although sporadic and inherited mutations in cardiac genes are implicated in LVNC, understanding of the mechanisms responsible for human LVNC is limited. MethodsWe screened the complete exome sequence database of the Pediatrics Cardiac Genomics Consortium and identified a cohort with a de novo chromodomain helicase DNA-binding protein 4 (CHD4) proband, CHD4M202I, with congenital heart defects. We engineered a patient-specific model of CHD4M202I (mouse CHD4M195I). Histological analysis, immunohistochemistry, flow cytometry, transmission electron microscopy, and echocardiography were used to analyze cardiac anatomy and function. Ex vivo culture, immunopurification coupled with mass spectrometry, transcriptional profiling, and chromatin immunoprecipitation were performed to deduce the mechanism of CHD4M195I-mediated ventricular wall defects. ResultsCHD4M195I/M195I mice developed biventricular hypertrabeculaion and noncompaction and died at birth. Proliferation of cardiomyocytes was significantly increased in CHD4M195I hearts, and the excessive trabeculation was associated with accumulation of extracellular matrix (ECM) proteins and a reduction of ADAMTS1, an ECM protease. We rescued the hyperproliferation and hypertrabeculation defects in CHD4M195I hearts by administration of ADAMTS1. Mechanistically, the CHD4M195I protein showed augmented affinity to endocardial BRG1. This enhanced affinity resulted in failure of derepression of Adamts1 transcription such that ADAMTS1-mediated trabeculation termination was impaired. ConclusionsOur study reveals how a single mutation in the chromatin remodeler CHD4, in mice or humans, modulates ventricular chamber maturation and that cardiac defects associated with the missense mutation CHD4M195I can be attenuated by the administration of ADAMTS1. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIA patient-specific mouse model of CHD4M202I develops ventricular hypertrabeculation and dies at birth. C_LIO_LIProliferation of cardiomyocytes is significantly enhanced in CHD4M195I mice. C_LIO_LIADAMTS1 is significantly downregulated in CHD4M195I mice. C_LIO_LIClose interaction between CHD4M195I and BRG1 robustly and continuously represses Adamts1 transcription, which impairs ADAMTS1-mediated termination of trabeculation in the developing mutant heart. C_LI What Are the Clinical Implications?O_LIThis study provides a unique mouse model of ventricular noncompaction cardiomyopathy that faithfully reflects human patients genetic condition without disturbing the target genes expression and localization. C_LIO_LITranscriptional repression of ECM protease ADAMTS1 by CHD4-BRG1 interaction is detrimental to ventricular wall maturation; maintaining appropriate ADAMTS1 levels in the heart could be a promising therapeutic approach for treating ventricular noncompaction cardiomyopathy. C_LI

developmental biology↗

bioRxiv2021

CHD4 is recruited by GATA4 and NKX2-5 silencers to repress non-cardiac gene programs in the developing heart

The Nucleosome Remodeling and Deacetylase (NuRD) complex is one of the central chromatin remolding complexes that mediate gene repression. NuRD is essential for numerous developmental events, including heart development. Clinical and genetic studies have provided direct evidence for the role of chromodomain helicase DNA-binding protein 4 (CHD4), the catalytic component of NuRD, in congenital heart disease (CHD), including atrial and ventricular septal defects. Further, it has been demonstrated that CHD4 is essential for mammalian cardiomyocyte formation and function. A key unresolved question is how CHD4/NuRD is localized to specific cardiac targets genes, as neither CHD4 nor NuRD can directly bind DNA. Here, we coupled a bioinformatics-based approach with mass spectrometry analyses to demonstrate that CHD4 interacts with the core cardiac transcription factors GATA4, NKX2-5 and TBX5 during embryonic heart development. Using transcriptomics and genome-wide occupancy data, we have characterized the genomic landscape of GATA4, NKX2-5 and TBX5 repression and defined the direct cardiac gene targets of GATA4-CHD4, NKX2-5-CHD4 and TBX5-CHD4 complexes. These data were used to identify putative cis-regulatory elements regulated controlled by these complexes. We genetically interrogated two of these silencers in vivo, Acta1 and Myh11. We show that deletion of these silencers leads to inappropriate skeletal and smooth muscle gene mis-expression, respectively, in the embryonic heart. These results delineate how CHD4/NuRD is localized to specific cardiac loci and explicates how mutations in the broadly expressed CHD4 protein lead to cardiac specific disease states.

genomics↗

bioRxiv2019

A TBX5 dosage-sensitive gene regulatory network for human congenital heart disease

Haploinsufficiency of transcriptional regulators causes human congenital heart disease (CHD). However, underlying CHD gene regulatory network (GRN) imbalances are unknown. Here, we define transcriptional consequences of reduced dosage of the CHD-linked 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 cardiomyocyte function and CHD genetics--in discrete subpopulations of cardiomyocytes. GRN analysis identified vulnerable nodes enriched for CHD genes, indicating that cardiac network stability is sensitive to TBX5 dosage. A GRN-predicted genetic interaction between Tbx5 and Mef2c was validated in mouse, manifesting as ventricular septation defects. These results demonstrate exquisite sensitivity to TBX5 dosage by diverse transcriptional responses in heterogeneous subsets of iPSC-derived cardiomyocytes. This predicts candidate GRNs for human CHDs, with implications for quantitative transcriptional regulation in disease.

developmental biology↗