Dynamic Gene Expression Response to TGF-β Stimulation in Multipotent Progenitors and Common Dendritic Cell Progenitors
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE46109 | GEO | 2014/04/15
SECONDARY ACCESSION(S): PRJNA197280
REPOSITORIES: GEO
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Project description:Multipotent progenitors (MPP) and common dendritic cell progenitors (CDP) were obtained from mouse bone marrow, followed by in vitro culture with a specific cytokine cocktail and FACS sorting (Felker et al., 2010; Sere et al., 2012). Cells were treated with 10 ng/ml recombinant human TGF-b1 (R&D Systems, Minneapolis, USA) for 2, 4, 8, 12 and 24 h as described (Felker et al., 2010) or left untreated. Untreated multipotent progenitor (MPP) - MPP_0h_1 - MPP_0h_2 - MPP_0h_3 TGF-beta1 treated (2 hours) MPP - MPP_2h_1 - MPP_2h_2 - MPP_2h_3 TGF-beta1 treated (4 hours) MPP - MPP_4h_1 - MPP_4h_2 - MPP_4h_3 TGF-beta1 treated (8 hours) MPP - MPP_8h_1 - MPP_8h_2 - MPP_8h_3 TGF-beta1 treated (12 hours) MPP - MPP_12h_1 - MPP_12h_2 - MPP_12h_3 TGF-beta1 treated (24 hours) MPP - MPP_24h_1 - MPP_24h_2 - MPP_24h_3 Untreated common dendritic cell progenitor (CDP) - CDP_0h_1 - CDP_0h_2 - CDP_0h_3 TGF-beta1 treated (2 hours) CDP - CDP_2h_1 - CDP_2h_2 - CDP_2h_3 TGF-beta1 treated (4 hours) CDP - CDP_4h_1 - CDP_4h_2 - CDP_4h_3 TGF-beta1 treated (8 hours) CDP - CDP_8h_1 - CDP_8h_2 - CDP_8h_3 TGF-beta1 treated (12 hours) CDP - CDP_12h_1 - CDP_12h_2 - CDP_12h_3 TGF-beta1 treated (24 hours) CDP - CDP_24h_1 - CDP_24h_2 - CDP_24h_3
2014-04-15 | E-GEOD-46109 | biostudies-arrayexpress
Project description:Dendritic cells (DC) are professional antigen presenting cells that develop from multipotent progenitors (MPP) and DC committed common DC progenitors (CDP) and further differentiate into different subsets: classical DC type 1 and 2 (cDC1 and cDC2, respectively) and plasmacytoid DC (pDC). In this study MPP, CDP, cDC1, cDC2 and pDC were obtained in a two-step in vitro culture system according to Felker et al., J. Immunol. 185, 5326-5335, 2010. Briefly, mouse bone marrow cells were first amplified with a specific cytokine cocktail and then induced to differentiate into DC with Flt3 ligand. MPP, CDP, cDC1, cDC2 and pDC were obtained by FACS sorting as follows: MPP: Gr1- CD117hi CD135low/-; CDP: Gr1- CD117int CD135+ CD115+; cDC1: CD11c+ CD11blow/- XCR1+; cDC2: CD11c+ CD11b+ XCR1- and pDC: CD11c+ CD11b- B220+. FACS sorted cells were then subjected to Omni-ATAC-seq, nuclear-titrated (NuTi) Capture-C targeting Irf8 promoter, and RNA-seq analysis. ATAC-seq data of cDC1 and pDC are published (Li et al., Genome Biol. 20, 45, 2019; GSE118221). ATAC-seq data of MPP, CDP and cDC2, NuTi Capture-C and RNA-seq data of MPP, CDP, cDC1, cDC2 and pDC are published here. CD11c+ CD11b+ B220- cDC and CD11c+ CD11b- B220+ pDC were obtained by FACS sorting and subjected to ChIP-seq analysis of IRF8 and are published here.
2023-03-01 | GSE198651 | GEO
Project description:Dendritic cells (DC) are professional antigen presenting cells that develop from hematopoietic stem cells in bone marrow by successive steps of lineage commitment and differentiation. Different DC subsets were identified based on phenotype, localisation and function: (i) classical DC (cDC) and plasmacytoid DC (pDC) are found in lymphoid organs and (ii) migratory tissue DC are spread throughout peripheral organs, including Langerhans cells, the cutaneous contingent of DC. We have developed a two-step culture system that recapitulates DC development in vitro (Felker et al., J. Immunol. 185, 5326-5335, 2010). In this system multipotent hematopoietic progenitors (MPP) progress into DC-restricted common DC progenitors (CDP) and further into the two major DC subsets cDC and pDC. We employed chromatin immunoprecipitation (ChIP) with deep sequencing (ChIP-seq) to determine the dynamics of H3K27ac occupancy in MPP, CDP, cDC and pDC. Additionally, we monitored changes in gene expression in MPP, CDP, cDC and pDC by RNA-seq.
2016-08-03 | GSE73143 | GEO
Project description:Dendritic cells (DC) are professional antigen presenting cells that develop from hematopoietic stem cells in bone marrow by successive steps of lineage commitment and differentiation. Different DC subsets were identified based on phenotype, localisation and function: (i) classical DC (cDC) and plasmacytoid DC (pDC) are found in lymphoid organs and (ii) migratory tissue DC are spread throughout peripheral organs, including Langerhans cells, the cutaneous contingent of DC. We have developed a two-step culture system that recapitulates DC development in vitro (Felker et al., J. Immunol. 185, 5326-5335, 2010). In this system multipotent hematopoietic progenitors (MPP) progress into DC-restricted common DC progenitors (CDP) and further into the two major DC subsets cDC and pDC. We employed chromatin immunoprecipitation (ChIP) with deep sequencing (ChIP-seq) to determine the dynamics of H3K27ac occupancy in MPP, CMP, cDC and pDC. Histone modification H3K27ac and RNA-Seq in MPP, CDP, cDC and pDC
2016-08-03 | E-GEOD-73143 | biostudies-arrayexpress
Project description:An investigation of the global gene expression signatures of murine hematopoietic stem cell differentiation during steady state hematopoiesis. This data compliments the miniChIP-chip data obtained from the same cell types as described in Weishaupt et al., 2009 (Blood). An Affymetrix genechip study using total RNA recovered from three separate FACS isolated HSC and MPP samples. The HSC and MPP gene expression data was analyzed alongside the PreMegEs and CD4+ T cells datasets obtained from our previous work (Pronk et al., 2007, Rolf et al. 2008). HSCs are phenotypically identified in bone marrow as lineage-, cKit+, Sca1+, CD150+, Flk2/Flt3- (LSKCD150+ cells). MPPs are phenotypically identified in bone marrow as lineage-, cKit+, Sca1+, CD150-, Flk2/Flt3+ (LSKCD150- cells). PreMegEs are phenotypically identified in bone marrow as lineage-, cKit+, Sca1-, CD150+, CD105- and CD41- as described in Pronk et al., 2007. Splenic-derived CD4+ T cells are phentypically identified as CD4+, CD8-, B220-, Nk1.1- cells as described in Rolf et al., 2008.
2009-11-09 | E-GEOD-18669 | biostudies-arrayexpress
Project description:An optimized whole genome bisulfite sequencing protocol (µWGBS, Farlik et al. 2015 Cell Reports) was used to establish DNA methylation profiles of FACS-purified stem and progenitor cells types of the human blood lineage. Most cell types were sorted from the peripheral blood of three donors each (43 donors total) with eight pools of ten cells, two pools of 50 cells, and one pool of 1000 cells. Additionally, two cell types (HSC, MPP) were sorted from bone marrow, fetal liver, and cord blood; single-cell methylome sequencing (scWGBS, Farlik et al. 2015 Cell Reports) was done for selected cell types (HSC, MPP, CMP, GMP, CLP, MLP0); and gene expression profiling using the Smart-seq2 protocol (Picelli et al. 2013 Nature Methods) was done on all stem/progenitor cell types (HSC, MPP, CMP, MEP, GMP, CLP, MLP0, MLP1, MLP2, MLP3).
2016-11-06 | GSE87196 | GEO
Project description:An optimized whole genome bisulfite sequencing protocol (µWGBS, Farlik et al. 2015 Cell Reports) was used to establish DNA methylation profiles of FACS-purified stem and progenitor cells types of the human blood lineage. Most cell types were sorted from the peripheral blood of three donors each (43 donors total) with eight pools of ten cells, two pools of 50 cells, and one pool of 1000 cells. Additionally, two cell types (HSC, MPP) were sorted from bone marrow, fetal liver, and cord blood; single-cell methylome sequencing (scWGBS, Farlik et al. 2015 Cell Reports) was done for selected cell types (HSC, MPP, CMP, GMP, CLP, MLP0); and gene expression profiling using the Smart-seq2 protocol (Picelli et al. 2013 Nature Methods) was done on all stem/progenitor cell types (HSC, MPP, CMP, MEP, GMP, CLP, MLP0, MLP1, MLP2, MLP3).
2016-11-06 | GSE87195 | GEO
Project description:Dendritic cells (DC) develop from hematopoietic stem cells, which is guided by instructive signals through cytokines. DC development progresses from multipotent progenitors (MPP) via common DC progenitors (CDP) into DC. Flt3 ligand (Flt3L) signaling via the Flt3/Stat3 pathway is of pivotal importance for DC development under steady state conditions. Additional factors produced during steady state or inflammation, such as TGF-beta1 or GM-CSF, also influence the differentiation potential of MPP and CDP. Here, we studied how gp130, GM-CSF and TGF-beta1 signaling influence DC lineage commitment from MPP to CDP and further into DC. We observed that activation of gp130 signaling promotes expansion of MPP. Additionally, gp130 signaling inhibited Flt3L-driven DC differentiation, but had little effect on GM-CSF-driven DC development. The inflammatory cytokine GM-CSF induces differentiation of MPP into inflammatory DC and blocks steady state DC development. Global transcriptome analysis revealed a GM-CSF-driven gene expression repertoire that primes MPP for differentiation into inflammatory DC. Finally, TGF-beta1 induces expression of DC-lineage affiliated genes in MPP, including Flt3, Irf-4 and Irf-8. Under inflammatory conditions, however, the effect of TGF- beta1 is altered: Flt3 is not upregulated, indicating that an inflammatory environment inhibits steady state DC development. Altogether, our data indicate that distinct cytokine signals produced during steady state or inflammation have a different outcome on DC lineage commitment and differentiation. 6 samples in total. Multipotent progenitor - GM-MPP_1 - GM-MPP_2 Dendritic cell - GM-DC_1 - GM-DC_2 Dendritic cell plus TNFa - GM-TNFa-DC_1 - GM-TNFa-DC_2
2011-11-13 | E-GEOD-29241 | biostudies-arrayexpress
Project description:Dendritic cells (DCs) in lymphoid tissue comprise conventional DCs (cDCs) and plasmacytoid DCs (pDCs) that develop from common DC progenitors (CDPs). CDPs are Flt3+c-kitintM-CSFR+ and reside in bone marrow. Here we describe a two-step culture system that recapitulates DC development from c-kithiFlt3-/lo multipotent progenitors (MPPs) into CDPs and further into cDC and pDC subsets. MPPs and CDPs are amplified in vitro with Flt3 ligand, stem cell factor, hyper-IL-6 and insulin- like growth factor-1. The four-factor cocktail readily induces self-renewal of MPPs and their progression into CDPs and has no self-renewal activity on CDPs. The amplified CDPs respond to all known DC poietins and generate all lymphoid tissue DCs in vivo and in vitro. Additionally, in vitro CDPs recapitulate the cell surface marker and gene expression profile of in vivo CDPs and possess a DC-primed transcription profile. Transforming growth factor-β1 (TGF-β1) impacts on CDPs and directs their differentiation towards cDCs. Genome-wide gene expression profiling of TGF-β1-induced genes identified transcription factors, such as interferon regulatory factor-4 (IRF-4) and RelB, that are implicated as instructive factors for cDC subset specification. TGF-β1 also induced the transcription factor inhibitor of differentiation/DNA binding 2 (Id2) that suppresses pDC development. Thus, TGF-β1 directs CDP differentiation into cDC by inducing both cDC instructive factors and pDC inhibitory factors.
2010-10-04 | GSE22432 | GEO
Project description:Dendritic cells (DC) develop from hematopoietic stem cells, which is guided by instructive signals through cytokines. DC development progresses from multipotent progenitors (MPP) via common DC progenitors (CDP) into DC. Flt3 ligand (Flt3L) signaling via the Flt3/Stat3 pathway is of pivotal importance for DC development under steady state conditions. Additional factors produced during steady state or inflammation, such as TGF-beta1 or GM-CSF, also influence the differentiation potential of MPP and CDP. Here, we studied how gp130, GM-CSF and TGF-beta1 signaling influence DC lineage commitment from MPP to CDP and further into DC. We observed that activation of gp130 signaling promotes expansion of MPP. Additionally, gp130 signaling inhibited Flt3L-driven DC differentiation, but had little effect on GM-CSF-driven DC development. The inflammatory cytokine GM-CSF induces differentiation of MPP into inflammatory DC and blocks steady state DC development. Global transcriptome analysis revealed a GM-CSF-driven gene expression repertoire that primes MPP for differentiation into inflammatory DC. Finally, TGF-beta1 induces expression of DC-lineage affiliated genes in MPP, including Flt3, Irf-4 and Irf-8. Under inflammatory conditions, however, the effect of TGF- beta1 is altered: Flt3 is not upregulated, indicating that an inflammatory environment inhibits steady state DC development. Altogether, our data indicate that distinct cytokine signals produced during steady state or inflammation have a different outcome on DC lineage commitment and differentiation.
2011-11-13 | GSE29241 | GEO