An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE152906 | GEO | 2021/02/16
REPOSITORIES: GEO
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Project description:The Hox genes play a key role in specifying the axial identity of neural crest cells (NCCs) migrating into the pharyngeal arches of the developing mouse embryo. In the absence of Hoxa2, NCC derivatives of the second pharyngeal arch (PA2) duplicate those formed by NCCs of the first arch (PA1). In this study, we use bulk and single-cell RNAseq to establish the molecular mechanisms driving this phenotypic reversion to a ground state. Comparing the transcriptomes of PA1 and PA2 in wildtype and Hoxa2-/- embryos during NCC migration and differentiation, we find that Hoxa2-/- PA2 does not revert to a molecular ‘ground state’ corresponding to the NCC derivatives. This separation of phenotypic and molecular states has significant implications for our understanding of NCC biology. We also identify putative targets through which HOXA2 likely acts to impart PA2 identity. The heterogenous expression of these targets within the PAs and their responses to the absence of HOXA2 suggest that subsets of NCCs may respond to HOXA2 activity in distinct manners related to their ultimate fate. To understand the heterogeneity of neural crest cells (NCCs) and other tissues of pharyngeal arches (PAs) 1 and 2 in the mouse embryo at E10.5, during NCC differentiation, we collected PA1 and PA2 from wildtype embryos and Hoxa2-/- embryos. We used the 10x Chromium single-cell sequencing system to compare the transcriptional profiles between PA1 and PA2 as well as wildtype and Hoxa2-/- PAs.
2021-02-09 | GSE164108 | GEO
Project description:The Hox genes play a key role in specifying the axial identity of neural crest cells (NCCs) migrating into the pharyngeal arches of the developing mouse embryo. In the absence of Hoxa2, NCC derivatives of the second pharyngeal arch (PA2) duplicate those formed by NCCs of the first arch (PA1). In this study, we use bulk and single-cell RNAseq to establish the molecular mechanisms driving this phenotypic reversion to a ground state. Comparing the transcriptomes of PA1 and PA2 in wildtype and Hoxa2-/- embryos during NCC migration and differentiation, we find that Hoxa2-/- PA2 does not revert to a molecular ‘ground state’ corresponding to the NCC derivatives. This separation of phenotypic and molecular states has significant implications for our understanding of NCC biology. We also identify putative targets through which HOXA2 likely acts to impart PA2 identity. The heterogenous expression of these targets within the PAs and their responses to the absence of HOXA2 suggest that subsets of NCCs may respond to HOXA2 activity in distinct manners related to their ultimate fate. To understand the specification of axial identity in neural crest cells (NCCs), we collected pharyngeal arches (PAs) 1 and 2 from mouse embryos at four time points during NCC migration and the beginning of differentiation (E9.0, E9.5, E10.0, and E10.5). We collected these tissues from both wildtype embryos and embryos homozygous for a mutation abrogating Hoxa2 expression. By performing comparative analysis of these tissues, we set out to understand the molecular underpinnings of NCC axial identity, as well as the mechanistic role of Hoxa2 in establishing PA2 identity.
2021-02-09 | GSE164110 | GEO
Project description:S23 experiment: We sought to identify the microRNAs (miRNAs) enriched in the neural crest cell (NCC) population from E11.5 mouse embryos. To accomplish this, we utilized a transgenic mouse line harboring Cre-recombinase under the control of the Wnt1 NCC-specific promoter and also carrying the R26R-YFP allele. We sorted YFP+ (NCCs) and YFP- (non-NCCs) from E11.5 Wnt1Cre-R26R mouse embryos via FACS and compared the relative enrichment of miRNAs in the YFP+ population by miRNA microarray. 220 experiment: We sought to identify the microRNAs (miRNAs) enriched in the neural crest cell (NCC) population from E10.5 mouse embryos. To accomplish this, we utilized a transgenic mouse line harboring Cre-recombinase under the control of the Wnt1 NCC-specific promoter and also carrying the R26R-YFP allele. We sorted YFP+ (NCCs) and YFP- (non-NCCs) from E10.5 Wnt1Cre-R26R mouse embryos via FACS and compared the relative enrichment of miRNAs in the YFP+ population by miRNA microarray. 221 experiment: Our research has shown that heterozygous deletion of the miRNA processing enzyme Dicer leads to developmental delay of the thymus in mouse embryos. We sought to identify the microRNAs (miRNAs) affected by the loss of a single copy of Dicer in the neural crest cell (NCC) population from E10.5 mouse embryos. To accomplish this, we utilized a transgenic mouse line harboring a floxed allele of Dicer, Cre-recombinase under the control of the Wnt1 NCC-specific promoter, and also carrying the R26R-YFP allele. We sorted YFP+ (NCCs) cells from E10.5 Dicerfl/+,Wnt1Cre,R26R and Dicer+/+,Wnt1Cre,R26R mouse embryos via FACS and compared the relative expression of miRNAs in the Dicer-heterozygotes compared to Dicer-wildtypes by miRNA microarray. S23 experiment: RNA from YFP+ (NCCs) and YFP- (non-NCCs) cells sorted by FACS from E11.5 Wnt1Cre-R26R mouse embryos was isolated and hybridized to Exiqon miRNA microarrays v10. Cells from five E11.5 embryos were sorted into YFP+ and YFP- populations and pooled. 220 experiment: RNA from YFP+ (NCCs) and YFP- (non-NCCs) cells sorted by FACS from E10.5 Wnt1Cre-R26R mouse embryos was isolated and hybridized to Exiqon miRNA microarrays v10. Cells from ten E10.5 embryos were sorted into YFP+ and YFP- populations and pooled. 221 experiment: RNA from YFP+ (NCCs) cells sorted by FACS from E10.5 Dicerfl/+,Wnt1Cre,R26R and Dicer+/+,Wnt1Cre,R26R mouse embryos was isolated and hybridized to Exiqon miRNA microarrays v10. Cells from ten embryos were sorted into YFP+ populations and pooled for each genotype.
2010-11-10 | E-GEOD-25256 | biostudies-arrayexpress
Project description:Hirschsprung’s disease (HSCR) is a congenital disease which is characterized by the reduction or absence of neurons and glial cells in the enteric nervous system (ENS). Failure of neural crest cells (NCCs) to colonize the gut during the embryonic development has been considered as one of the possible causes of the disease. In this study, the migration and gene expression of sacral NCCs from the spontaneous mouse mutant Dominant megacolon (Dom) which is a HSCR animal model expressing a mutated transcription factor Sox10, were analyzed in order to identify candidate genes which may possibly affect the NCC migration in the mutant.
2020-11-17 | GSE161579 | GEO
Project description:Neural crest cells (NCCs) are highly multipotent stem cells. A long-standing controversy exists over the mechanism of NCC fate specification, specifically regarding the presence and potency of intermediate progenitors. The direct fate restriction (DFR) model, based on early in vivo clonal studies, hypothesised that intermediates are absent and that migrating cells maintain full multipotency1-6. However, most authors favour progressive fate restriction (PFR) models, with fully multipotent early NCCs (ENCCs) transitioning to partially- restricted intermediates before committing to individual fates7-12. Here, single cell transcriptional profiling of zebrafish pigment cell development leads to us proposing a Cyclical Fate Restriction mechanism of NCC development that reconciles the DFR and PFR models. Our clustering of single NCC Nanostring transcriptional profiles identifies only broadly multipotent intermediate states between ENCCs and differentiated melanocytes and iridophores. Leukocyte tyrosine kinase (Ltk) marks the multipotent progenitor and iridophores, consistent with biphasic ltk expression13-15. Ltk inhibitor and constitutive activation studies support expression at an early multipotent stage, whilst lineage-tracing of ltk-expressing cells reveals their multipotency extends beyond pigment cell-types to neural fates. We conclude that pigment cell development does not involve a conventional PFR mechanism, but instead occurs directly and more dynamically from a broadly multipotent intermediate state.
2021-10-09 | GSE185592 | GEO
Project description:Neural crest cells (NCCs) are a transient population which contributes to the majority of craniofacial tissue. The development of craniofacial tissue involves highly complex intermingled processes of cell fate specification and migration in densely packed mesenchyme. The establishment of appropriate in vitro models would be helpful for understanding these complicated processes. Thus, we developed a new method to induce NCCs in aggregates of human pluripotent stem cells (hPSCs). To gain insight into the process of aggregate development we performed single cell RNA sequencing (scRNA-seq) on day 2, 3, 4, and 5. scRNA-seq analysis revealed that hPSCs in the aggregates acquired neural plate border NPB-like identity before NCC induction. scRNA-seq also revealed that NCCs showed changes in the gene expression associated with epithelial mesenchymal transition as in vivo developmental process.
2024-01-03 | GSE199158 | GEO
Project description:S23 experiment: We sought to identify the microRNAs (miRNAs) enriched in the neural crest cell (NCC) population from E11.5 mouse embryos. To accomplish this, we utilized a transgenic mouse line harboring Cre-recombinase under the control of the Wnt1 NCC-specific promoter and also carrying the R26R-YFP allele. We sorted YFP+ (NCCs) and YFP- (non-NCCs) from E11.5 Wnt1Cre-R26R mouse embryos via FACS and compared the relative enrichment of miRNAs in the YFP+ population by miRNA microarray. 220 experiment: We sought to identify the microRNAs (miRNAs) enriched in the neural crest cell (NCC) population from E10.5 mouse embryos. To accomplish this, we utilized a transgenic mouse line harboring Cre-recombinase under the control of the Wnt1 NCC-specific promoter and also carrying the R26R-YFP allele. We sorted YFP+ (NCCs) and YFP- (non-NCCs) from E10.5 Wnt1Cre-R26R mouse embryos via FACS and compared the relative enrichment of miRNAs in the YFP+ population by miRNA microarray. 221 experiment: Our research has shown that heterozygous deletion of the miRNA processing enzyme Dicer leads to developmental delay of the thymus in mouse embryos. We sought to identify the microRNAs (miRNAs) affected by the loss of a single copy of Dicer in the neural crest cell (NCC) population from E10.5 mouse embryos. To accomplish this, we utilized a transgenic mouse line harboring a floxed allele of Dicer, Cre-recombinase under the control of the Wnt1 NCC-specific promoter, and also carrying the R26R-YFP allele. We sorted YFP+ (NCCs) cells from E10.5 Dicerfl/+,Wnt1Cre,R26R and Dicer+/+,Wnt1Cre,R26R mouse embryos via FACS and compared the relative expression of miRNAs in the Dicer-heterozygotes compared to Dicer-wildtypes by miRNA microarray.
2010-11-10 | GSE25256 | GEO
Project description:Individuals with mutations in CHD8 present with gastrointestinal complaints, yet the underlying mechanisms are understudied. Here, utilizing a stable constitutive chd8 mutant zebrafish model, we found that the loss of chd8 leads to reduced number of vagal neural crest cells (NCCs), enteric neural and glial progenitors, emigrating from the neural tube and that their early migration capability was altered. At later stages, although the intestinal colonization by the NCCs was complete, we found decreased numbers of both serotonin-producing enterochromaffin cells and NCC-derived serotonergic neurons, suggesting an intestinal hyposerotonemia in absence of chd8. Further, transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last, single-cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8, NCC development, intestinal homeostasis, and autism-associated gastrointestinal complaints.
2022-10-21 | GSE184363 | GEO
Project description:Individuals with mutations in CHD8 present with gastrointestinal complaints, yet the underlying mechanisms are understudied. Here, utilizing a stable constitutive chd8 mutant zebrafish model, we found that the loss of chd8 leads to reduced number of vagal neural crest cells (NCCs), enteric neural and glial progenitors, emigrating from the neural tube and that their early migration capability was altered. At later stages, although the intestinal colonization by the NCCs was complete, we found decreased numbers of both serotonin-producing enterochromaffin cells and NCC-derived serotonergic neurons, suggesting an intestinal hyposerotonemia in absence of chd8. Further, transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last, single-cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8, NCC development, intestinal homeostasis, and autism-associated gastrointestinal complaints.
2022-10-21 | GSE184359 | GEO
Project description:The enteric nervous system (ENS) of the gastrointestinal (GI) tract controls many diverse functions including motility and epithelial permeability. Perturbations in ENS development or function are common, yet a human model to study ENS-intestinal biology is lacking. We have used a tissue engineering approach with pluripotent stem cells (PSCs) to generate human intestinal tissue containing a functional ENS. We recapitulated normal intestinal ENS development by combining PSC-derived neural crest cells (NCCs) with developing human intestinal organoids (HIOs). When cultured alone, NCCs had full differentiation potential in vitro, however when recombined with HIOs they differentiated into neurons and glial cells. NCC-derived ENS neurons self-assembled within the developing intestinal mesenchyme and exhibited neuronal activity as measured by rhythmic waves of calcium transients. ENS-containing HIOs grown in vivo formed neuroglial structures similar to a myenteric and submucosal plexus, formed interstitial cells of Cajal, and had an electro-mechanical coupling that regulated waves of propagating contraction. This is the first demonstration of a human PSC-derived intestinal tissue with a functional ENS.
2016-11-23 | GSE84666 | GEO