Identification of de novo mutations and rare variants in hypoplastic left heart syndrome

2011 ◽  
Vol 81 (6) ◽  
pp. 542-554 ◽  
Author(s):  
M Iascone ◽  
R Ciccone ◽  
L Galletti ◽  
D Marchetti ◽  
F Seddio ◽  
...  
Keyword(s):  
Hypoplastic Left Heart Syndrome ◽  
Rare Variants ◽  
De Novo ◽  
Left Heart ◽  
De Novo Mutations ◽  
Hypoplastic Left Heart ◽  
Left Heart Syndrome

Abstract 193: RNA-sequencing of Disease-specific iPSC as a New Filter to Identify Genes Associated With Hypoplastic Left Heart Syndrome

2015 ◽  
Vol 117 (suppl_1) ◽  
Author(s):  
Almudena Martinez Fernandez ◽  
Xing Li ◽  
Jeanne L Theis ◽  
Andre Terzic ◽  
Timothy M Olson ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Hypoplastic Left Heart Syndrome ◽  
De Novo ◽  
Nuclear Family ◽  
Cardiac Differentiation ◽  
Left Heart ◽  
Hypoplastic Left Heart ◽  
Differentiated Cells ◽  
Left Heart Syndrome

Hypoplastic Left Heart Syndrome (HLHS) is a complex multifactorial disease for which no definitive genetic causes have been found. Current genetic filtering strategies render lists of genes with unknown relevance in terms of pathogenesis. A complementary filter based on biological evidence would create a new approach to prioritize relevant candidate genes and mutations. In our study, 5 members of a nuclear family including a child with HLHS were evaluated using echocardiography and their genetic information was obtained through whole genome sequencing (WGS). Data filtering including rarity, functional impact and mode of inheritance was implemented, resulting in identification of 34 genes with recessive or de novo variants potentially involved in the pathogenesis of HLHS. Additionally, iPSC were derived from proband and parents and subjected to RNA-sequencing at the undifferentiated state and following spontaneous differentiation. Comparative transcriptional analyses identified genes differentially expressed in proband samples at each stage. These gene sets were used as an additional filter for the previously generated WGS data. This strategy revealed that out of 34 mutated genes originally identified, 10 displayed transcriptional differences in undifferentiated iPSC from the HLHS-affected individual while 16 out of 34 mutated genes showed significantly different expression levels in differentiated cells from proband. Furthermore, expression dynamics were studied during guided cardiac differentiation for the 9 genes fulfilling all applied criteria. Two genes not previously linked to HLHS, ELF4 and HSPG2 were found to behave significantly different in HLHS-iPSC when compared to control counterparts. In summary, filtering WGS data according to a new layer of transcriptional information that leverages iPSC plasticity allows prioritization of genes associated with HLHS in an in vitro model of disease.

scholarly journals Single-Cell RNA-Seq Reveals Endocardial Defect in Hypoplastic Left Heart Syndrome

2019 ◽  
Author(s):  
Yifei Miao ◽  
Lei Tian ◽  
Marcy Martin ◽  
Sharon L. Paige ◽  
Francisco X. Galdos ◽  
...  
Keyword(s):  
Single Cell ◽  
Hypoplastic Left Heart Syndrome ◽  
De Novo ◽  
Heart Diseases ◽  
Heart Tissue ◽  
Abnormal Development ◽  
Left Heart ◽  
Hypoplastic Left Heart ◽  
Mesenchymal Transition ◽  
Left Heart Syndrome

SummaryHypoplastic left heart syndrome (HLHS) is one of the most challenging forms of congenital heart diseases. Previous studies were mainly focused on intrinsic defects in myocardium. However, this does not sufficiently explain the abnormal development of the cardiac valve, septum, and vasculature, known to originate from the endocardium. Here, using single-cell RNA profiling, induced pluripotent stem cells, and human fetal heart tissue with an underdeveloped left ventricle, we identified a developmentally impaired endocardial population in HLHS. The intrinsic endocardial deficits contributed to abnormal endothelial to mesenchymal transition, NOTCH signaling, and extracellular matrix organization, all of which are key factors in valve formation. Consequently, endocardial abnormalities conferred reduced proliferation and maturation of cardiomyocytes through a disrupted fibronectin-integrin interaction. Several recently described HLHS de novo mutations were associated with abnormal endocardial gene and FN1 regulation and expression. Our studies provide a rationale for considering endocardial function in future regenerative strategies for HLHS.

Prenatal diagnosis of hypoplastic left heart syndrome associated with Noonan Syndrome and de novo RAF1 mutation

2012 ◽  
Vol 32 (10) ◽  
pp. 1016-1018 ◽  
Author(s):  
Solveig Schulz ◽  
Rosemarie Fröber ◽  
Cornelia Kraus ◽  
Uwe Schneider
Keyword(s):  
Prenatal Diagnosis ◽  
Hypoplastic Left Heart Syndrome ◽  
Noonan Syndrome ◽  
De Novo ◽  
Left Heart ◽  
Hypoplastic Left Heart ◽  
Left Heart Syndrome

Abstract 46: Identification of Novel Alternate Splicing Events in Humans With RBFOX2 Mutations and Hypoplastic Left Heart Syndrome

2015 ◽  
Vol 117 (suppl_1) ◽  
Author(s):  
Craig C Benson ◽  
David McKean ◽  
Jason Homsy ◽  
Richard Kim ◽  
Josh Gorham ◽  
...  
Keyword(s):  
Target Genes ◽  
Rna Binding ◽  
De Novo ◽  
Rna Binding Protein ◽  
Left Heart ◽  
Rna Seq ◽  
De Novo Mutations ◽  
Alternate Splicing ◽  
Hypoplastic Left Heart ◽  
Left Heart Syndrome

Alternative splicing (AS) of protein isoforms is an integral mechanism for cardiac development. RNA Binding Protein, Fox-1 Homolog (C. Elegans) 2 (RBFOX2) is an RNA binding protein preferentially expressed in muscle and neuronal cells and regulates tissue-specific alternate exon splicing in ~2,100 target genes by binding the conserved RNA sequence motif (U)GCAUG. RBFOX2 was recently implicated in the pathogenesis of abnormal cardiac and cerebral development via loss-of-function studies in zebrafish and mouse. However, convincing evidence remains incomplete, as the full complement of RBFOX2 target genes and differential exon usage (DEU) in human cardiovascular cell lines are incompletely defined. We identified de novo mutations in RBFOX2 from four human cases of congenital heart disease (CHD) with hypoplastic left heart syndrome (HLHS) via whole exome sequencing. To test the hypothesis that RBFOX2 mutations alter DEU in known target genes, we performed RNA-seq on ductus arteriosus tissue from human CHD cases with and without RBFOX2 mutation. Analysis of RNA-seq for DEU was performed with DEXSeq. To limit the effect of differential gene expression, we restricted analysis to subjects with high global gene expression correlation (r2 > 0.9, case=1 vs. control=5). DEU in known RBFOX2 target genes were highly enriched compared to all known genes (115/2,100 vs. 589/26,310, p=5.78e-15). A high percentage of the DEU genes (60.0%, 69/115) have high heart expression (HHE) in the developing mouse (mean expression of four cardiac chambers at e14.5). DEU genes with HHE include VCL, TPM1, FN1, ACTN1, and CALD1. Functional annotation clustering reveals enrichment for several actin, cytoskeletal, and contractile Gene Ontology terms, suggesting a possible role in the epithelial-mesenchymal transition (EMT) developmental processes active during early cardiac formation. We also identified enrichment from genes implicated in CHD by allelic specific expression or de novo mutations (44/1,263 vs. 589/26,310, p=0.007). These results are the first in humans to identify differentially expressed exons associated with RBFOX2 mutations in CHD and suggests RBFOX2-mediated alternate splicing may influence EMT pathways implicated in the pathogenesis of HLHS.

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