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A cell atlas of the human outflow tract of the heart and its adult derivatives - 10X visium samples

ABSTRACT: Congenital heart disease (CHD) is a major birth defect affecting ~1% of new born babies. The OFT carries blood away from the heart into the great arteries. Defects specifically affecting the outflow tract (OFT) of the heart represent a third of all CHD cases. In humans the formation and remodelling of the OFT is a relatively rapid process, occurring over a 3-week period (Carnegie Stage (CS)13 – CS22). The morphological changes underlying OFT formation are orchestrated by two main cell lineages, second heart field (SHF)-derived myocardium and endothelium, and neural crest cells (NCC). Here, we present comprehensive transcriptomic data on the developing OFT at two distinct timepoint (embryonic and fetal) and its adult derivatives, providing a large reference framework of OFT cell repertoires and their gene expression profiles. This submission has the Spatial Transcriptomics of this work.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Syed Murtuza Baker

PROVIDER: E-MTAB-13461 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A cell atlas of the human outflow tract of the heart and its adult derivatives

Project description:Congenital heart disease (CHD) is a major birth defect affecting ~1% of new born babies. The OFT carries blood away from the heart into the great arteries. Defects specifically affecting the outflow tract (OFT) of the heart represent a third of all CHD cases. In humans the formation and remodelling of the OFT is a relatively rapid process, occurring over a 3-week period (Carnegie Stage (CS)13 – CS22). The morphological changes underlying OFT formation are orchestrated by two main cell lineages, second heart field (SHF)-derived myocardium and endothelium, and neural crest cells (NCC). Here, we present comprehensive transcriptomic data on the developing OFT at two distinct timepoint (embryonic and fetal) and its adult derivatives, providing a large reference framework of OFT cell repertoires and their gene expression profiles.

2025-06-09 | E-MTAB-13447 | biostudies-arrayexpress

A cell atlas of the human outflow tract of the heart and its adult derivatives - Adult samples

2025-06-09 | E-MTAB-13453 | biostudies-arrayexpress

A cell atlas of the human outflow tract of the heart and its adult derivatives - CS16-17 Replicate 1

2025-06-09 | E-MTAB-13456 | biostudies-arrayexpress

A spatial map of human liver cirrhosis reveals the patho-architecture and gene signatures associated with cell state transitions during liver disease - Spatial Transcriptomics (10X Visium) validation cohort

Project description:Liver fibrosis is a major cause of death worldwide. As a progressive step in chronic liver disease, fibrosis is almost always diagnosed too late with limited treatment options. Here, we uncover the spatial transcriptional landscape driving human liver fibrosis using single nuclei RNA and Assay for Transposase-Accessible Chromatin (ATAC) sequencing to deconvolute multi-cell spatial transcriptomic profiling in human liver cirrhosis.Through multi-modal data integration,we define molecular signatures driving cell state transitions in liver disease and define an impaired cellular response and directional trajectory from hepatocytes to cholangiocytes associated with disease remodelling.We identifypro-fibrogenic signatures in non-parenchymal cell subpopulations co-localised within the fibrotic niche and localise transitional cell states at the scar interface. This combined approach providesa spatial atlas of gene regulation and defines molecular signatures associated liver diseasefor targeted therapeutics or as early diagnostic markers of progressive liver disease. This is the 10X Visium data for the work.

2025-04-04 | E-MTAB-14960 | biostudies-arrayexpress

A spatial map of human liver cirrhosis reveals the patho-architecture and gene signatures associated with cell state transitions during liver disease - Spatial Transcriptomics (10X Visium)

2025-03-14 | E-MTAB-13132 | biostudies-arrayexpress

A multi-omics approach using a mouse model of cardiac malformations for prioritization of human congenital heart disease contributing genes [scRNA-seq]

Project description:Congenital heart disease (CHD) is the most common type of birth defect, affecting ~1% of all live births. Malformations of the cardiac outflow tract (OFT) account for ~30% of all CHD and include a range of CHDs from bicuspid aortic valve (BAV) to tetralogy of Fallot (TOF). We hypothesized that transcriptomic profiling of a mouse model of CHD would highlight disease-contributing genes implicated in congenital cardiac malformations in humans. To test this hypothesis, we utilized global transcriptional profiling differences from a mouse model of OFT malformations to prioritize damaging, de novo variants identified from exome sequencing datasets from published cohorts of CHD patients. Notch1+/-;Nos3-/- mice display a spectrum of cardiac OFT malformations ranging from BAV, semilunar valve (SLV) stenosis to TOF. Global transcriptional profiling of the E13.5 Notch1+/-;Nos3-/- mutant mouse OFTs and wildtype controls was performed by RNA sequencing (RNA-Seq). Analysis of the RNA-Seq dataset demonstrated genes belonging to the Hif1α, Tgf-β, Hippo, and Wnt signaling pathways were differentially expressed in the mutant OFT. Mouse to human comparative analysis was then performed to determine if patients with TOF and SLV stenosis display an increased burden of damaging, genetic variants in gene homologs that were dysregulated in Notch1+/-; Nos3-/- OFT. We found an enrichment of de novo variants in the TOF population among the 1,352 significantly differentially expressed genes in Notch1+/-;Nos3-/- mouse OFT but not the SLV population. This association was not significant when compared to only highly expressed genes in the murine OFT and of de novo variants in the TOF population. These results suggest that transcriptomic datasets generated from the appropriate temporal, anatomic and cellular tissues from murine models of CHD may provide a novel approach for the prioritization of disease-contributing genes in patients with CHD.

2021-06-28 | GSE171238 | GEO

A multi-omics approach using a mouse model of cardiac malformations for prioritization of human congenital heart disease contributing genes [RNA-seq]

2021-06-28 | GSE171237 | GEO

Retinoic acid signaling coordinates the behavior of multiple cell lineages during cardiac outflow morphogenesis

Project description:Retinoic acid (RA), the bioactive derivative of vitamin A, is essential for vertebrate heart development. Both excess and reduced RA signaling lead to cardiovascular malformations, particularly affecting the cardiac outflow tract (OFT). The cellular mechanisms underlying the effects of RA signaling during OFT morphogenesis are not fully understood. To address this question, we used transient maternal RA supplementation to rescue the early lethality resulting from inactivation of the murine retinaldehyde dehydrogenase 2 (Raldh2) gene. By embryonic day 13.5, Raldh2-/- hearts exhibited OFT septation defects. Although cardiac neural crest cells (cNCC) were present in OFT cushions of Raldh2-/- mutant embryos, we observed that cNCC were ectopically located in the peripheral region of the endocardial cushions, closer to the myocardium rather than immediately subjacent to the endocardium. Mislocated cNCC were aligned in parallel instead of perpendicular arrays to the endocardial surface within the proximal OFT. Supernumerary mesenchyme was generated both in and ex vivo within the cushions by Raldh2-/- mutant endocardium and found in place of the cNCC in a subendocardial, medial position. Although mislocated and misoriented, mutant cNCC resembled wildtype cells in their compaction density and individually elongated shape. Our data show that RA signaling acts on cNCC orientation relative to the septation plane and position within OFT cushions during septation process. Transcriptomic analysis and pathway-specific readout suggest that up-regulation of the Bmp pathway may be responsible for increased endothelial-to-mesenchymal transition, leading thereby to displacement of cNCC.

2015-12-21 | GSE64556 | GEO

The role of SMC3 in heart development by regulating super-enhancer associated genes

Project description:Abnormal cardiac development has been observed in individuals with Cornelia de Lange Syndrome (CdLS) due to mutations in genes encoding members of the cohesin complex. But the precise role of cohesin in heart development remains elusive. In this study, we aimed to elucidate the indispensable role of SMC3, a component of the cohesin complex, in cardiac development and its underlying mechanism. Our investigation revealed an association between SMC3 mutations and congenital heart disease (CHD) in CdLS patients. To further explore this relationship, we utilized heart-specific Smc3-knockout (SMC3-cKO) mice, which displayed varying degrees of outflow tract (OFT) abnormalities. Additionally, we identified 16 rare SMC3 variants with potential pathogenicity in individuals with isolated CHD. Employing single nucleus RNA sequencing and 3C-high-throughput genome-wide translocation sequencing, we unveiled that Smc3 deletion downregulates the expression of key genes, including Ets2, in OFT cardiac muscle cells by specifically decreasing interactions between super-enhancers (SE) and promoters. Notable, Ets2-SE-null mice also exhibit delayed OFT development in the heart. Our research uncovers a novel role for SMC3 in heart development by regulating SE-associated genes, suggesting its potential relevance as one of the CHD-related genes and providing crucial insights into the molecular basis of cardiac development.

2023-09-14 | GSE242974 | GEO

Expression data from outflow region at E9.5

Project description:A high concentration of maternal retinoic acid (RA), the active derivative of vitamin A, is well known as a teratogenic agent which can cause developmental defects. Our previous studies have shown that the maternal administration of RA to mice within a narrow developmental window induces outflow tract (OFT) septum defects, which closely resembles human transposition of the great arteries (TGA), although the responsible factors and pathogenic mechanisms of the TGA induced by RA still remain unknown. To identify the candidate genes involved in the altered development of the OFT in RA-induce TGA model, we isolated the RNA from E9.5 control and RA-treated OFT regions, and performed a microarray analysis. Approximately 200 outflow tract region were isolated from control and RA-treated embryos (embryonic day 9.5). We sought to obtain the candidate genes involved in the altered development of the OFT in RA-induce heart defects.

2011-11-08 | E-GEOD-33472 | biostudies-arrayexpress

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