Gene expression analysis of hematopoietic stem/progenitor cells in the zebrafish kidney
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE132927 | GEO | 2019/10/15
REPOSITORIES: GEO
Similar Datasets
Project description:Infections are associated with extensive consumption of blood platelets representing a high risk for health. How the hematopoietic system coordinates the rapid and efficient regeneration of this particular lineage during such stress scenarios remains unclear. Here we report that the phenotypic hematopoietic stem cell (HSC) compartment contains highly potent megakaryocyte-committed progenitors (hipMkPs), a cell population that shares many features with multipotent HSCs and serves as a lineage-restricted emergency pool for inflammatory insults. Our data show that during homeostasis, hipMkPs are maintained in a primed but quiescent state, thus contributing little to steady-state megakaryopoiesis. Moreover, homeostatic hipMkPs show expression of megakaryocyte lineage priming transcripts for which protein synthesis is suppressed. We demonstrate that acute inflammatory signaling instructs activation of hipMkPs, as well as Mk protein production from pre-existing transcripts and drives a rapid maturation of hipMkPs and other Mk progenitors. This results in an efficient regeneration of platelets that are lost during inflammatory insult. Thus, our study reveals an elegant emergency machinery that counteracts life-threating depletions in the platelet pool during acute inflammation.
2015-08-26 | PXD001500 | Pride
Project description:Hamey2017 - Blood stem cell regulatory
network
This model is described in the article:
Reconstructing blood stem
cell regulatory network models from single-cell molecular
profiles
Fiona K. Hamey, Sonia Nestorowa,
Sarah J. Kinston, David G. Kent, Nicola K. Wilson, and Berthold
Göttgens
Proceedings of the National Academy of
Sciences of the United States of America
Abstract:
Adult blood contains a mixture of mature cell types, each
with specialized functions. Single hematopoietic stem cells
(HSCs) have been functionally shown to generate all mature cell
types for the lifetime of the organism. Differentiation of HSCs
toward alternative lineages must be balanced at the population
level by the fate decisions made by individual cells.
Transcription factors play a key role in regulating these
decisions and operate within organized regulatory programs that
can be modeled as transcriptional regulatory networks. As
dysregulation of single HSC fate decisions is linked to fatal
malignancies such as leukemia, it is important to understand
how these decisions are controlled on a cell-by-cell basis.
Here we developed and applied a network inference method,
exploiting the ability to infer dynamic information from
single-cell snapshot expression data based on expression
profiles of 48 genes in 2,167 blood stem and progenitor cells.
This approach allowed us to infer transcriptional regulatory
network models that recapitulated differentiation of HSCs into
progenitor cell types, focusing on trajectories toward
megakaryocyte–erythrocyte progenitors and lymphoid-primed
multipotent progenitors. By comparing these two models, we
identified and subsequently experimentally validated a
difference in the regulation of nuclear factor, erythroid 2
(Nfe2) and core-binding factor, runt domain, alpha subunit 2,
translocated to, 3 homolog (Cbfa2t3h) by the transcription
factor Gata2. Our approach confirms known aspects of
hematopoiesis, provides hypotheses about regulation of HSC
differentiation, and is widely applicable to other hierarchical
biological systems to uncover regulatory relationships.
This model is hosted on
BioModels Database
and identified by:
MODEL1610060000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-06-09 | MODEL1610060000 | BioModels
Project description:Hamey2017 - Blood stem cell regulatory
network (LMPP network)
This model is described in the article:
Reconstructing blood stem
cell regulatory network models from single-cell molecular
profiles
Fiona K. Hamey, Sonia Nestorowa,
Sarah J. Kinston, David G. Kent, Nicola K. Wilson, and Berthold
Göttgens
Proceedings of the National Academy of
Sciences of the United States of America
Abstract:
Adult blood contains a mixture of mature cell types, each
with specialized functions. Single hematopoietic stem cells
(HSCs) have been functionally shown to generate all mature cell
types for the lifetime of the organism. Differentiation of HSCs
toward alternative lineages must be balanced at the population
level by the fate decisions made by individual cells.
Transcription factors play a key role in regulating these
decisions and operate within organized regulatory programs that
can be modeled as transcriptional regulatory networks. As
dysregulation of single HSC fate decisions is linked to fatal
malignancies such as leukemia, it is important to understand
how these decisions are controlled on a cell-by-cell basis.
Here we developed and applied a network inference method,
exploiting the ability to infer dynamic information from
single-cell snapshot expression data based on expression
profiles of 48 genes in 2,167 blood stem and progenitor cells.
This approach allowed us to infer transcriptional regulatory
network models that recapitulated differentiation of HSCs into
progenitor cell types, focusing on trajectories toward
megakaryocyte–erythrocyte progenitors and lymphoid-primed
multipotent progenitors. By comparing these two models, we
identified and subsequently experimentally validated a
difference in the regulation of nuclear factor, erythroid 2
(Nfe2) and core-binding factor, runt domain, alpha subunit 2,
translocated to, 3 homolog (Cbfa2t3h) by the transcription
factor Gata2. Our approach confirms known aspects of
hematopoiesis, provides hypotheses about regulation of HSC
differentiation, and is widely applicable to other hierarchical
biological systems to uncover regulatory relationships.
This model is hosted on
BioModels Database
and identified by:
MODEL1610060001.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-06-09 | MODEL1610060001 | BioModels
Project description:Transcriptome data from zebrafish single and bulk cells from blood and testes. Blood cells were collected from adult Tg(cd4:mCherry), Tg(cd41:EGFP), Tg(gata1a:GFP), Tg(lyz:DsRed2), Tg(mfap4:tdTomato), Tg(mpx:EGFP), Tg(runx1:mCherry), Tg(tal1:EGFP) and Tubingen Long Fin wild type fish.
2017-11-17 | E-MTAB-5530 | biostudies-arrayexpress
Project description:We isolated by fluorescence-activated cell sorting highly purified populations (long term hematopoietic stem cells (LT-HSCs), short term hematopoietic stem cells (ST-HSCs), multipotent progenitors (MPPs), common myeloid progenitor (CMPs), granulocyte and monocyte progenitors (GMPs), multilymphoid progenitors (MLPs), Myeloid-erythorid Progenitor (MEP), Granulocytes, Monocytes, B cells, T cells, Dendritic cells, Natural Killer cells and Erythrocyte Progenitors from 3 to 4 cord blood pools. We extracted RNA from 5K cells of each population and performed RNA-sequencing.
| EGAS00001004968 | EGA
Project description:Disrupting mutations of the RUNX1 gene are found in 10% of patients with myelodysplasia (MDS) and 30% of patients with acute myeloid leukemia (AML). Previous studies have revealed an increase in hematopoietic stem cells (HSCs) and multipotent progenitor (MPP) cells in conditional Runx1-knockout (KO) mice, but the molecular mechanism is unresolved. We investigated the myeloid progenitor (MP) compartment in KO mice, arguing that disruptions at the HSC/MPP level may be amplified in downstream cells. We demonstrate that the MP compartment is increased more than fivefold in Runx1 KO mice, with a prominent skewing toward megakaryocyte (Meg) progenitors. Runx1- deficient granulocyte-macrophage progenitors are characterized by increased cloning capacity, impaired development into mature cells, and HSC and Meg transcription signatures. An HSC/MPP subpopulation expressing Meg markers was also increased in Runx1-deficient mice. Rescue experiments coupled with transcriptome analysis and Runx1 DNA-binding assays demonstrated that commitment is marked by Runx1 suppression of genes encoding adherence and motility proteins (Tek, Jam3, Plxnc1, Pcdh7, and Selp) that support HSCâMeg interactions with the BM niche. In vitro assays confirmed that enforced Tek expression in HSCs/MPPs increases Meg output. Interestingly, besides this key repressor function of Runx1 to control lineage decisions and cell numbers in progenitors, our study also revealed a critical activating function in erythroblast differentiation, in addition to its known importance in Meg and granulocyte/monocyte (G/M) maturation. Thus both repressor and activator functions of Runx1 at multiple hematopoietic stages and lineages likely contribute to the tumor suppressor activity in MDS and AML. GMP were isolated either from Runx1+/+-Tg(vav-Cre) and Runx1fl/fl-Tg(vav-Cre) mice or from mice transplanted with Runx1fl/fl-Tg(vav-Cre) progenitors engineered to express GFP with RUNX1-ERt2 or ERt2. RUNX1-ERt2 activity was induced by i.p. injection of tamoxifen on 3 consecutive days prior to GMP isolation.
2016-07-01 | E-GEOD-81177 | biostudies-arrayexpress
Project description:The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover, transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney, termed the "kidney marrow", providing an attractive tool for studying hematopoietic niches. Here, we isolated two candidate niche cell populations from the zebrafish kidney, pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low-density lipoprotein (Ac-LDL), whereas pericytes can be labeled by pdgfrb expression. Therefore, pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488-conjugated Ac-LDL, respectively. In addition, we also utilized a cell line generated from the zebrafish kidney, zebrafish kidney stromal (ZKS), which have been shown to support proliferation of various hematopoietic precursors (Stachula et al., 2009). In this study, we performed RNA-seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ (DP) hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells (DP_uncul), gata2a+ runx1+ cells co-cultured with ZKS cells (DP_cocul), and gata2a+ runx1+ cells co-cultured with ZKS cells in the presence of both IWR-1-endo and Thpo (DP_IW+Th).
2022-10-21 | GSE186298 | GEO
Project description:Hematopoietic stem and progenitor cell (HSPC) formation and lineage differentiation involve gene expression programs orchestrated by transcription factors and epigenetic regulators. Knockdown of the chromatin remodeler chromodomain-helicase-DNA-binding protein 7 (CHD7) expanded phenotypic HSPCs, erythroid, and myeloid lineages in zebrafish and mouse embryos. CHD7 acts to suppress hematopoietic differentiation in a cell autonomous manner in the embryo and adult. We performed gene expression analysis to determine the expression of chd7 in adult sorted HSPC populations. Loss of Chd7 in long term hematopoietic stem cells (LT-HSCs) results in upregulation of genes that function in hematopoietic system development and function. Genes representative of each blood lineage including erythroid, myeloid, and lymphoid were upregulated, suggesting that Chd7 deficiency results in LT-HSCs that are more primed for multilineage differentiation. Together with the physical and genetic interaction, the data support a model in which CHD7 interacts with and modulates Runx1 activity to provide proper timing and function of HSPCs as they emerge during hematopoietic development or mature in adults. This represents a distinct and evolutionarily conserved control mechanism to ensure accurate hematopoietic lineage differentiation. We used microarrays to detail the expression of Chd7 in adult sorted HSPC populations.
2023-01-01 | GSE84127 | GEO
Project description:Epigenetic mechanisms regulate the multilineage differentiation capacity of hematopoietic stem cells (HSCs) into a variety of blood and immune cells. Our recent work revealed evidence of multilineage gene priming in HSCs, where open cis-regulatory elements (CREs) exclusively shared between HSCs and unipotent lineage cells were enriched for DNA binding motifs of known lineage-specific transcription factors. To test the hypothesis that HSC-primed lineage-specific CREs remain accessible throughout differentiation, we used ATAC-seq to map the temporal dynamics of chromatin remodeling during blood cell differentiation. We observed epigenetic-driven clustering of oligopotent and unipotent progenitors into distinct erythromyeloid and lymphoid branches, with multipotent HSCs and MPPs associating with the erythromyeloid lineage. We mapped the dynamics of lineage-primed CREs throughout hematopoiesis and identified both unique and shared CREs as potential lineage reinforcement mechanisms at fate branch points in hematopoiesis. These findings provide insight into the regulation of stem cell multipotency and lineage commitment throughout hematopoiesis and serve as a resource to test functional drivers of hematopoietic lineage fate.
2023-03-30 | GSE184851 | GEO
Project description:Human pluripotent stem cells were differentiated into hematopoietic progenitors, which were then re-specified using defined transcription factors to resemble hematopoietic stem cells (HSC) We used microarrays to establish the similarity between converted cells and purified human HSCs. The samples analyzed were: starting embryoid body progenitors, transcription factor-converted cells, and primary HSCs and progenitors from fetal liver and cord blood. All samples were flow sorted for CD34+ and CD38- to compare across a similar population of primitive cells.
2013-11-01 | E-GEOD-49938 | biostudies-arrayexpress