Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GFI1B and LSD1 repress myeloid traits during megakaryocyte differentiation

ABSTRACT: Mutations in transcription factor Growth Factor Independence 1B (GFI1B) cause inherited bleedings with varying intensity possibly caused by different effects on the transcriptional function of GFI1B. We studied transcriptomic changes of normal and GFI1BT174N,H181Y,R184P,Q287* mutants in megakaryoblast MEG01 cells using RNA-sequencing. Compared to normal GFI1B each variant affected different gene modules with limited overlap between variants. Remarkably, GFI1BQ287* specifically activated a myeloid-associated gene module. Based on this finding we studied megakaryocyte differentiation using normal and GFI1BQ287* patient-derived induced pluripotent stem cells (IPSC) followed by single cell RNA-sequencing. This revealed a 45-fold decrease in the megakaryocyte/myeloid cell ratio in the GFI1BQ287* versus control condition. Moreover, myeloid specific genes were expressed within GFI1BQ287* but not normal megakaryocytes. Finally, we studied how megakaryocyte development was affected by inhibiting binding of GFI1B to Lysine Specific Demethylase 1 (LSD1), an interaction required for megakaryocyte development. Treatment of both MEG01 cells and normal IPSC-derived developing megakaryocytes with the small-molecule inhibitor GSK-LSD1 resulted in profound activation of myeloid gene programs within megakaryocytes, while the IPSC-derived megakaryocyte/myeloid ratio dropped two-fold. We conclude that GFI1B and LSD1 suppress myeloid differentiation allowing for proper megakaryocyte development. LSD1 inhibitor and GFI1BQ287*-mediated perturbation of this function causes myeloid skewing during megakaryocyte development.

ORGANISM(S): Homo sapiens

PROVIDER: GSE244609 | GEO | 2024/03/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

GFI1B and LSD1 repress myeloid traits during megakaryocyte differentiation

Project description:The transcription factor Growth Factor Independence 1B (GFI1B) recruits Lysine Specific Demethylase 1A (LSD1/KDM1A) to stimulate gene programs relevant for megakaryocyte and platelet biology. Inherited pathogenic GFI1B variants result in thrombocytopenia and bleeding propensities with varying intensity. Whether these affect similar gene programs is unknow. Here we studied transcriptomic effects of four patient-derived GFI1B variants (GFI1BT174N,H181Y,R184P,Q287*) in MEG01 megakaryoblasts. Compared to normal GFI1B, each variant affected different gene programs with GFI1BQ287* uniquely failing to repress myeloid traits. In line with this, single cell RNA-sequencing of induced pluripotent stem cell (iPSC)-derived megakaryocytes revealed a 4.5-fold decrease in the megakaryocyte/myeloid cell ratio in GFI1BQ287* versus normal conditions. Inhibiting the GFI1B-LSD1 interaction with small molecule GSK-LSD1 resulted in activation of myeloid genes in normal iPSC-derived megakaryocytes similar as observed for GFI1BQ287* iPSC-derived megakaryocytes. Thus, GFI1B and LSD1 facilitate gene programs relevant for megakaryopoiesis while simultaneously repressing programs that induce myeloid differentiation.

2024-03-28 | PXD050401 | Pride

Transcriptomic changes induced by GFI1B variants

Project description:Mutations in transcription factor Growth Factor Independence 1B (GFI1B) cause inherited bleedings with varying intensity possibly caused by different effects on the transcriptional function of GFI1B. We studied transcriptomic changes of normal and GFI1BT174N,H181Y,R184P,Q287* mutants in megakaryoblast MEG01 cells using RNA-sequencing. Compared to normal GFI1B each variant affected different gene modules with limited overlap between variants. Remarkably, GFI1BQ287* specifically activated a myeloid-associated gene module. Based on this finding we studied megakaryocyte differentiation using normal and GFI1BQ287* patient-derived induced pluripotent stem cells (IPSC) followed by single cell RNA-sequencing. This revealed a 45-fold decrease in the megakaryocyte/myeloid cell ratio in the GFI1BQ287* versus control condition. Moreover, myeloid specific genes were expressed within GFI1BQ287* but not normal megakaryocytes. Finally, we studied how megakaryocyte development was affected by inhibiting binding of GFI1B to Lysine Specific Demethylase 1 (LSD1), an interaction required for megakaryocyte development. Treatment of both MEG01 cells and normal IPSC-derived developing megakaryocytes with the small-molecule inhibitor GSK-LSD1 resulted in profound activation of myeloid gene programs within megakaryocytes, while the IPSC-derived megakaryocyte/myeloid ratio dropped two-fold. We conclude that GFI1B and LSD1 suppress myeloid differentiation allowing for proper megakaryocyte development. LSD1 inhibitor and GFI1BQ287*-mediated perturbation of this function causes myeloid skewing during megakaryocyte development.

2024-03-28 | GSE244756 | GEO

Pathogenesis of dominant-negative mutant GFI1B and associated proteomic abnormalities in megakaryocytes and platelets

Project description:Dominant-negative mutations in transcription factor Growth Factor Independence-1B (GFI1B) cause a bleeding disorder characterized by a plethora of megakaryocyte and platelet abnormalities. The deregulated molecular mechanisms and pathways are unknown. Here we show that normal and mutant GFI1B interacted most strongly with the LSD1-RCOR-HDAC corepressor complex in megakaryoblasts. Sequestration of this complex by mutant GFI1B and chemical separation of GFI1B from LSD1 induced abnormalities in normal megakaryocytes comparable to those seen in patients. Megakaryocytes derived from GFI1B-mutant induced pluripotent stem cells (iPSC) also phenocopied abnormalities seen in patients. Proteome studies on normal and mutant iPSC-derived megakaryocytes identified a multitude of deregulated pathways downstream of mutant GFI1B. Proteome studies on primary normal and GFI1B-mutant platelets showed reduced expression of proteins implicated in platelet function, and sustained expression of proteins normally downregulated during megakaryocyte differentiation. Thus, GFI1B regulates a broad developmental program during megakaryopoiesis. Mutant GFI1B deregulates this program through LSD1-RCOR-HDAC sequestering.

2019-01-25 | PXD009020 | Pride

ChIP-Seq analysis for GFI1B, Beta-Catenin, LSD1 and histone marks in response to Wnt treatment

Project description:Gfi1b is a DNA binding transcriptional repressor highly expressed in hematopoietic stem cells (HSCs) and megakaryocytes (MKs). Gfi1b deficiency leads to the expansion of both cell types and abrogates the ability of MKs to respond to integrin substrates with spreading and movement. Here we show that Gfi1b is present in complexes with ²-catenin and its co-factors Pontin52, CHD8, TLE3 and CtBP1 and can regulate Wnt/²-catenin dependent gene expression. In reporter assays, Gfi1b can activate TCF-dependent transcription and this activation is enhanced upon treatment with Wnt3a. This requires the interaction between Gfi1b and lysine demethylase 1 (LSD1), but is independent of the ability of Gfi1b to bind DNA. This suggests that a tripartite ²-catenin/Gfi1b/LSD1 complex exists that regulates Wnt/²-catenin target genes. Consistently, expression of many canonical Wnt/²-catenin target genes is deregulated in Gfi1b-deficient cells and many of these target genes are co-occupied by Gfi1b, ²-catenin and LSD1 at promoter sites. When Gfi1b deficient cells were treated with Wnt3a, their normal cellularity was restored and Gfi1b-deficient MKs regained their ability to spread on integrin substrates. This suggests that Gfi1b controls both the cellularity and functional integrity of HSCs and MKs by regulating Wnt/²-catenin signaling pathway.

2019-02-21 | GSE117944 | GEO

Expression data from trisomy 21 and euploid induced pluripotent stem cell hematopoietic progenitors

Project description:We modeled human Trisomy 21 primitive hematopoiesis using induced pluripotent stem cells (iPSCs). Primitive multipotent progenitor populations generated from Trisomy 21 iPSCs showed normal proliferative capacity and megakaryocyte production, enhanced erythropoiesis and reduced myeloid development compared to euploid iPSCs. CD41+/235+ iPSC-derived progenitor cells were flow cytometrically sorted for RNA extraction and hybridization onto Affymetrix microarrays.

2012-09-24 | E-GEOD-35561 | biostudies-arrayexpress

RNA-Seq Analysis of Gfi1b KO Hematopoietic Stem Cells

Project description:The zinc finger protein and SNAG domain transcription factor Gfi1b is highly expressed in hematopoietic stem cells (HSC) and in megakaryocytes (MKs). Deletion of Gfi1b in mice leads to a drastic expansion of both cell types, suggesting that Gfi1b controls their proliferation. Here we present evidence that Gfi1b exerts this control by modulating the Wnt/beta-catenin signaling pathway. We can show that Gfi1b binds to beta-catenin and is part of a larger complex that contains β-catenin co-factors. Gfi1b activates beta-catenin/TCF mediated transcription and is required for the activity of beta-catenin target gene promoter driven reporter genes in vivo. This is dependent of the ability of Gfi1b to recruit the histone modifying enzyme lysine demethylase 1 (LSD1) to β-catenin containing complexes. Moreover, LSD1 enhances the Gfi1b-mediated activation of beta-catenin/TCF dependent transcription. Both Gfi1b deficient HSCs and MKs show de-regulation of expression of many sets on Wnt/β-catenin target genes and Gfi1b and β-catenin co-occupy the promoters of many common target genes. Finally, activating the Wnt/β-catenin signaling pathway in Gfi1b deficient HSCs and MKs significantly reduces their expansion, which confirms that Gfi1b is a critical factor controlling the cellularity of HSCs and MKs and exerts this function by regulating the Wnt/β-catenin pathway in these cells.

2017-09-01 | GSE85737 | GEO

PF4-Cre mediated deletion of SRF in murine megakaryocytes.

Project description:Srf is a MADS-box transcription factor that is critical for muscle differentiation. Its function in hematopoiesis has not yet been revealed. Mkl1, a cofactor of Srf, is part of the t(1;22) translocation in acute megakaryoblastic leukemia, and plays a critical role in megakaryopoiesis. In order to test the role of Srf in megakaryocyte development, we crossed Pf4-Cre mice, which express Cre recombinase in cells committed to the megakaryocytic lineage, to SrfF/F mice in which functional Srf is no longer expressed after Cre-mediated excision. Pf4-Cre/SrfF/F (KO) mice are born with normal mendelian frequency, but have significant macrothrombocytopenia with approximately 50% reduction in platelet count. In contrast, the BM has increased numbers and percentages of CD41+ megakaryocytes (WT: 0.41+/-0.06%; KO: 1.92+/-0.12%) with significantly reduced ploidy. KO mice show significantly increased megakaryocyte progenitors in the BM by both FACS analysis and CFU-Mk. Megakaryocytes lacking Srf have abnormal stress fiber and demarcation membrane formation and platelets lacking Srf have abnormal actin distribution. In vitro and in vivo assays reveal platelet function defects in KO mice. Critical actin cytoskeletal genes are downregulated in KO megakaryocytes. Thus, Srf is required for normal megakaryocyte maturation and platelet production, due at least in part, to regulation of cytoskeletal genes. C-kit+CD41+ megakaryocyte progenitors from PF4-Cre/SRF C57BL/6 SRF WT (3) and C57BL/6 SRF KO (3) mice were sorted by flow cytometry and cultured for three days in thrombopoietin.

2010-07-13 | E-GEOD-21859 | biostudies-arrayexpress

A Critical Role of RUNX1 in Governing Megakaryocyte-Primed Hematopoietic Stem Cell Differentiation [Single MK RNAseq]

Project description:RUNX1 is crucial for multiple stages of hematopoiesis and its mutation can cause familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML). We aim to study the role of RUNX1 in megakaryocyte-biased HSCs differentiation to megakaryocytes.

2023-01-20 | GSE211937 | GEO

A Critical Role of RUNX1 in Governing Megakaryocyte-Primed Hematopoietic Stem Cell Differentiation [10x scRNAseq]

2023-01-20 | GSE211861 | GEO

RNA-Seq Analysis of Gfi1b KO Megakaryocytes

Project description:Megakaryocytes isolated from Gfi1b flox/flox mice carrying PF4-Cre or not, and from Gfi1b flox/flox mice carrying ROSA-Cre-ERT with or without tamoxifen injection were analyzed for differential expression by RNA-Seq

2017-01-21 | GSE71310 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data