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Oligogenic inheritance of congenital heart disease involving a NKX2-5 modifier [mouse]

ABSTRACT: Complex genetic inheritance is thought to underlie many human diseases, yet experimental proof of this model has been elusive. Here, we show that a human congenital heart defect, left ventricular non-compaction (LVNC), can be caused by a combination of rare, inherited heterozygous missense single nucleotide variants. Whole exome sequencing of a nuclear family revealed novel single nucleotide variants of MYH7 and MKL2 in an asymptomatic father while the offspring with severe childhood-onset LVNC harbored an additional missense variant in the cardiac transcription factor, NKX2-5, inherited from an unaffected mother. Mice bred to compound heterozygosity for the orthologous missense variants in Myh7 and Mkl2 had mild cardiac pathology; the additional inheritance of the Nkx2-5 variant yielded a more severe LVNC-like phenotype in triple compound heterozygotes. RNA sequencing identified genes associated with endothelial and myocardial development that were dysregulated in hearts from triple heterozygote mice and human induced pluripotent stem cell–derived cardiomyocytes harboring the three variants, with evidence for NKX2-5’s contribution as a modifier on the molecular level. These studies demonstrate that the deployment of efficient gene editing tools can provide experimental evidence for complex inheritance of human disease.

ORGANISM(S): Mus musculus

PROVIDER: GSE111394 | GEO | 2019/05/31

REPOSITORIES: GEO

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Oligogenic inheritance of congenital heart disease involving a NKX2-5 modifier [human]

Project description:Complex genetic inheritance is thought to underlie many human diseases, yet experimental proof of this model has been elusive. Here, we show that a human congenital heart defect, left ventricular non-compaction (LVNC), can be caused by a combination of rare, inherited heterozygous missense single nucleotide variants. Whole exome sequencing of a nuclear family revealed novel single nucleotide variants of MYH7 and MKL2 in an asymptomatic father while the offspring with severe childhood-onset LVNC harbored an additional missense variant in the cardiac transcription factor, NKX2-5, inherited from an unaffected mother. Mice bred to compound heterozygosity for the orthologous missense variants in Myh7 and Mkl2 had mild cardiac pathology; the additional inheritance of the Nkx2-5 variant yielded a more severe LVNC-like phenotype in triple compound heterozygotes. RNA sequencing identified genes associated with endothelial and myocardial development that were dysregulated in hearts from triple heterozygote mice and human induced pluripotent stem cell–derived cardiomyocytes harboring the three variants, with evidence for NKX2-5’s contribution as a modifier on the molecular level. These studies demonstrate that the deployment of efficient gene editing tools can provide experimental evidence for complex inheritance of human disease.

2019-05-31 | GSE131322 | GEO

A human hereditary cardiomyopathy shares a genetic substrate with bicuspid aortic valve

Project description:The complex genetics underlying human cardiac disease is evidenced by its heterogenous manifestation, multigenic basis and sporadic occurrence. These features have hampered disease modelling and mechanistic understanding. Here, we show that two structural cardiac diseases, left ventricular non-compaction (LVNC) and bicuspid aortic valve (BAV), can be caused by a combined set of inherited heterozygous mutations. We used CRISPR-Cas9 gene editing to generate mice harboring two mutations in the NOTCH ligand regulator MINDBOMB1 identified in LVNC families. One Mib1 mutation causes LVNC only in heteroallelic combination with a conditional Mib1 allele, while the other leads to BAV in a NOTCH-sensitized genetic background. These data suggest that the LVNC phenotype may be influenced by genetic modifiers present in these families, while valve defects are very sensitive to NOTCH haploinsufficiency. Whole-exome sequencing revealed single-nucleotide variants in the ASXL3, APCDD1 and TMX3, CEP192 and BCL7A genes, co-segregating with the MIB1 mutations and LVNC. We generated mice harboring the orthologous variants in the corresponding Mib1 backgrounds. Triple heterozygous Mib1 Apcdd1 Asxl3 mutants show LVNC, while quadruple heterozygous Mib1 Cep192 Tmx3;Bcl7a mice show BAV and other valve-associated defects. Biochemical assays suggest interactions between CEP192, BCL7A and NOTCH. Gene profiling of murine hearts and human induced pluripotent stem cell-derived cardiomyocytes reveals defective metabolic maturation. These findings provide evidence for a common genetic substrate for LVNC and BAV involving MIB1 and genetic modifiers

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Chromatin Remodeling Complex Dosage Modulates Transcription Factor Function in Heart Development

Project description:Dominant mutations in cardiac transcription factor genes cause human inherited congenital heart defects (CHDs), but their molecular basis is not understood. Transcription factors and Brg1/Brm-associated factor (BAF) chromatin remodeling complex interactions suggest potential mechanisms, but the role of BAF complexes in cardiogenesis is not known. Here we show that dosage of Brg1 is critical for mouse and zebrafish cardiogenesis. Disrupting the balance between Brg1 and disease-causing cardiac transcription factors, including Tbx5, Tbx20, and Nkx2-5, causes severe cardiac anomalies, revealing an essential allelic balance between Brg1 and these cardiac transcription factor genes. This suggests that relative levels of transcription factors and BAF complexes are important for heart development, which is supported by reduced occupancy of Brg1 at cardiac genes in Tbx5 haploinsufficient hearts. Our results reveal complex dosage-sensitive interdependence between transcription factors and BAF complexes, providing a potential mechanism underlying transcription factor haploinsufficiency, with implications for multigenic inheritance of CHDs. We performed transcriptional profiling of E11.5 hearts from mice heterozygous for deletions of Brg1, Tbx5, or Nkx2-5, and mice that were compound heterozygotes for Brg1 and each transcription factor gene (Tbx5 and Nkx2-5).

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CRaTER enrichment for on-target gene-editing enables generation of variant libraries in hiPSCs

Project description:Generation of transgenic cell lines is limited by inefficient gene editing requiring genotypic screening of hundreds to thousands of colonies to isolate correctly gene-edited cells. Here, we describe a novel method called CRISPRa On-Target Editing Retrieval (CRaTER) that enriches for cells with on-target knock-in of a promoterless cDNA-fluorescent reporter transgene by transiently overexpressing the targeted endogenous genetic locus and sorting for fluorescent cells. We use CRaTER to enrich for rare cells with heterozygous, biallelic-editing of the endogenous, transcriptionally-inactive MYH7 locus in human induced pluripotent stem cells (hiPSC), resulting in a 9-fold enrichment compared to antibiotics selection alone. We leveraged CRaTER to enrich for heterozygous knock-in of a library of single nucleotide variants (SNV) in MYH7, a gene encoding for sarcomeric MHC-β wherein autosomal dominant missense mutations cause cardiac and skeletal myopathies. CRaTER enabled 90% enrichment of heterozygous, biallelically-edited hiPSCs – a 38.6-fold enrichment compared to antibiotics selection alone – to generate 113 SNVs comprising 78 missense variants in MYH7. hiPSCs that have undergone CRaTER enrichment can differentiate to cardiomyocytes and exhibit expected localization and expression of MHC-β fusion proteins. Together, CRaTER substantially reduces the screening required for isolation of gene-edited cells, enabling the generation of transgenic cell lines at unprecedented scale.

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NAA15 haploinsufficiency can cause congenital heart disease and perturbs protein levels in induced pluripotent stem cells

Project description:NAA15 is a component of the NatA complex that acetylates amino terminal (Nt) protein residues and influences protein synthesis. We identified multiple damaging NAA15 variants in congenital heart disease patients, including four loss-of-function (LoF) variants, one missense (R276W) de novo variant and 15 rare inherited missense variants. To understand the effects of these variants on NatA complex activity, we introduced heterozygous LoF, compound heterozygous and missense residues iPS cells using CRISPR/Cas9. Haploinsufficient NAA15 iPS cells differentiate into cardiomyocytes, unlike NAA15-null iPS cells, presumably due to alterations in the amount and composition of the NatA complex. Mass spectrometry (MS)-based N-terminomics analyses showed that nearly 80% of iPS cell proteins displayed partial or complete Nt-acetylation. Between null and haploinsufficient NAA15 cells, 32 and 9 NatA-specific targeted proteins differed in their Nt-acetylation degree, respectively. In addition, the steady-state protein levels of more than 560 proteins were altered in mutant compared to wild type cells. While most NatA-specific Nt-acetylated proteins were fully acetylated, ~19 proteins were partially acetylated. NAA15-haploinsufficiency abrogated Nt-acetylation of 4 of these proteins but did not affect the acetylation of the other 15 proteins. Similar patterns of acetylation loss in few proteins were observed in both NAA15 haploinsufficient and NAA15 R276W iPS cells. These studies define human proteins that appear to require the full NAA15 complex for normal acetylation and imply that deficiencies in one or more of these NAA15 target proteins contribute to normal cardiac development. The current dataset contains all N-terminomics data related to this study.

2021-08-30 | PXD018013 | Pride

NAA15 haploinsufficiency can cause congenital heart disease and perturbs protein levels in induced pluripotent stem cells

2021-07-07 | PXD017672 | Pride

Deletion of Nkx2-5 in trabecular myocardium reveals the developmental origins of pathological heterogeneity associated with ventricular non-compaction cardiomyopathy

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2018-04-18 | GSE113251 | GEO

Identification of RPL9 variants incorporated in mature ribosomes from patient's Lymphoblastoid cell line

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Myocardin-like Protein (MKL)-2 Regulates TGF-β Signaling in Embryonic Stem Cells and the Developing Vasculature

Project description:Signal transduction from the extracellular matrix to the arterial wall plays a critical role during development of the vasculature. We now report the discovery of a Myocardin-like Protein (MKL)2/TGF-β signaling pathway that is required for maturation and stabilization of the vasculature. Mkl2-/- null embryos exhibit profound derangements in the tunica media leading to aneurismal dilation, dissection and hemorrhage. TGFβ expression, signaling and TGF-β-regulated genes are down-regulated in Mkl2-/- ES cells and in the vasculature of Mkl2-/- embryos. Transcription of Tgfβ2 is activated via binding of a MKL 2/SRF complex to a conserved CArG element in the Tgfβ2 promoter. In this data set we include expression data from wild type and Mkl2-/- ES cells A total of 5 samples with mRNA of sufficient quality were analyzed. Samples consisted of mRNA from independent cell culture of 2 wild-type and 3 Mkl2-/- undifferentiated Embryonic Stem Cells

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