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Spatial and single-nucleus multi-omics profiling reveals heterogeneous endothelial cell overabundance in endocardial fibroelastosis

ABSTRACT: Endocardial fibroelastosis (EFE) is a lethal fibrotic complication that affects up to 70% of patients with hypoplastic left heart syndrome (HLHS). The absence of effective therapies for EFE stems from a fundamental lack of understanding of its underlying cellular and molecular mechanisms. Progress in investigating EFE pathogenesis has been further constrained by the scarcity of patient-derived samples. Our study directly addresses this critical knowledge gap by performing an integrative multi-omics study—combining single-nucleus RNA/ATAC sequencing and high-resolution spatial transcriptomics (MERFISH) on human EFE and healthy heart tissues.

ORGANISM(S): Homo sapiens

PROVIDER: GSE311511 | GEO | 2026/08/29

REPOSITORIES: GEO

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Spatial and single-nucleus multi-omics profiling reveals heterogeneous endothelial cell overabundance in endocardial fibroelastosis [MERFISH]

Project description:Endocardial fibroelastosis (EFE) is a lethal fibrotic complication that affects up to 70% of patients with hypoplastic left heart syndrome (HLHS). The absence of effective therapies for EFE stems from a fundamental lack of understanding of its underlying cellular and molecular mechanisms. Progress in investigating EFE pathogenesis has been further constrained by the scarcity of patient-derived samples. Our study directly addresses this critical knowledge gap by performing an integrative multi-omics study—combining single-nucleus RNA/ATAC sequencing and high-resolution spatial transcriptomics (MERFISH) on human EFE and healthy heart tissues.

2026-08-29 | GSE315408 | GEO

Spatial and single-nucleus multi-omics profiling reveals heterogeneous endothelial cell overabundance in endocardial fibroelastosis [bulk RNA-seq]

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Single-Cell RNA-Seq and Patient-Specific iPSCs Reveal Endocardial Abnormalities in Hypoplastic Left Heart Syndrome

Project description:Hypoplastic left heart syndrome (HLHS) is one of the most devastating forms of congenital heart defects. Previous studies have only focused on intrinsic defects in the myocardium. However, this does not sufficiently explain the abnormal development of the cardiac valve, septum, and vasculature, which are known to originate from the endocardium. Here, using single-cell RNA profiling, induced pluripotent stem cells, and fetal heart tissue with an underdeveloped left ventricle, we identified a developmentally impaired endocardial cell 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. Consequentially, endocardial abnormalities conferred reduced proliferation and maturation of cardiomyocytes through a disrupted fibronectin-integrin interaction. Several known HLHS de novo mutations all contributed to the abnormal endocardial gene expression through the alteration of promoter/enhancer activities. These mechanistic discoveries provide an alternative angle for early intervention and heart regeneration in HLHS.

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Project description:Single cell transcriptome analysis was performed on one Hypoplastic Left Heart Synrome (HLHS) cell line and one control cell line.

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Sequential defects in cardiac lineage commitment and maturation cause hypoplastic left heart syndrome

Project description:Complex molecular programs in specific cell lineages govern human heart development. Hypoplastic left heart syndrome (HLHS) is the most severe congenital heart defect encompassing a spectrum of left-ventricular hypoplasia occurring in association with outflow-tract obstruction. The current clinical paradigm assumes HLHS is largely of hemodynamic origin. Here, by combining whole-exome sequencing of 87 HLHS parent-offspring trios and transcriptome of cardiomycytes (CMs) from healthy and patient native ventricles at different stages of development we identified perturbations in coherent gene programs controlling ventricular muscle lineage development. Single-cell and 3D molecular/functional modeling with iPSCs demonstrated intrinsic defects in the cell-cycle/ciliogenesis/autophagy hub resulting in disrupted differentiation of early cardiac progenitor (CP) lineages and ultimate defective CM-subtype differentiation/maturation in HLHS. Moreover, premature cellcycle exit of ventricular CM prevents tissue response to cues of developmental growth leading to multinucleation/polyploidy, accumulation of DNA damage, exacerbated apoptosis, and eventually ventricle hypoplasia. Our results highlight how genetic heterogeneity in HLHS converges in perturbations of sequential cellular processes driving cardiogenesis and facilitate potential novel nodes for therapy beside surgical intervention.

2022-02-15 | PXD014812 | Pride

Spatial and single-nucleus multi-omics profiling reveals heterogeneous endothelial cell overabundance in endocardial fibroelastosis [MERFISH]

Project description:Spatial and single-nucleus multi-omics profiling reveals heterogeneous endothelial cell overabundance in endocardial fibroelastosis [MERFISH]

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Label-free quantitative Proteomics Analysis Reveals Distinct Molecular characteristics in Endocardial Endothelium

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2018-06-29 | PXD009194 | Pride

Homo sapiens

Project description:Genetic Etiology of Hypoplastic Left Heart Syndrome (HLHS)

| PRJNA356956 | ENA

Genetic Etiology of Hypoplastic Left Heart Syndrome (HLHS)

Project description:Genetic Etiology of Hypoplastic Left Heart Syndrome (HLHS)

| PRJNA356955 | ENA

RNA-seq of fetal lamb heart treated with coiled implantation in left atrium against untreated controls

Project description:We created a fetal lamb model of hypoplastic left heart syndrome (HLHS), by implanting coils in the left atrium in mid-gestation. We performed bulk RNA sequencing of left ventricles (LV), right ventricles (RV), ascending aortae (AAo) and pulmonary arteries (PA). Single nucleus RNA sequencing was performed on LV free wall tissue (n = 4 coiled samples, n = 3 controls).

2023-05-31 | E-MTAB-12327 | biostudies-arrayexpress

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