Human iPSCs-based modeling unveils a dominant role of SETBP1 mutation in shaping stable chromatin accessibility landscape in GATA2 deficiency
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE265824 | GEO | 2025/10/02
REPOSITORIES: GEO
Similar Datasets
Project description:Patients with GATA2 deficiency are predisposed to developing myelodysplastic syndrome (MDS), which can progress to acute myeloid leukemia (AML). This progression is often associated with the acquisition of additional cytogenetic and somatic alterations. Mutations in SETBP1 and ASXL1 genes are frequently observed in pediatric GATA2 patients, but their roles in disease progression remain poorly understood. Genome editing of induced pluripotent stem cells (iPSCs) enabled precise reconstruction of mutation combinations found in patients. Here we developed a human hiPSC-based model to study the impact of SETBP1 and ASXL1 mutations in context of GATA2 deficiency. We show that germline heterozygous GATA2 mutation alone showed no significant effect on myeloid development, while the addition of SETBP1 and ASXL1 mutations impaired myelopoiesis, resulting in monocytopenia. We identified a key role of the SETBP1 mutation in promoting chromatin remodeling near genes involved in myeloid neoplasms, which likely initiated the blockage of myeloid differentiation observed in vitro. Motif analysis of more accessible chromatin regions in the SETBP1 and SETBP1/ASXL1 mutant background highlighted an enrichment for MEIS1, PU.1, RUNX1, and HOXA9, implicating these factors in the disease progression. Our study establishes a novel humanized model system for studying GATA2 deficiency. We demonstrate that SETBP1 mutations act as a primary driver in hematopoietic impairment, providing insights that may inform future therapeutic strategies for patients progressing to MDS/AML.
2025-10-01 | GSE300314 | GEO
Project description:GATA2 deficient patients are prone to develop myelodysplastic syndrome (MDS) that can evolve to acute myeloid leukemia (AML). The MDS progression is usually associated with the acquisition of cytogenetic and/or additional somatic alterations. Mutations in SETBP1 and ASXL1 genes are frequently observed in pediatric GATA2 patients, although how they contribute to the disease progression remains poorly understood. Here we develop a human induced pluripotent stem cells (hiPSCs)-based model to study the impact of germline GATA2 mutation along with selected somatic mutations on GATA2 deficiency progression. We found that, while germline heterozygous GATA2 mutation alone is insufficient to induce an impairment of myeloid development, SETBP1 and ASXL1 mutations lead to a significant decrease of myeloid differentiation potential with a complete monocytopenia. The prominent loss of myeloid progenitor was associated with a down regulation of myeloid-specific genes and an up-regulation of leukemic stem cell markers. Through epigenomic profiling, we found that mutation in SETBP1 promotes chromatin remodeling in genes involved in myeloid neoplasms that preceded the blockage of myeloid differentiation, a state that persisted after the acquisition of the ASXL1 mutation. Finally, transcription factors motif analysis revealed an enrichment for MEIS1, PU.1, RUNX1 and HOXA9 motifs in more accessible chromatin regions, suggesting their cooperation in disease progression. Beyond establishing a valuable tool for studying the molecular mechanisms underlying GATA2 deficiency, our findings suggest that mutated SETBP1 primes the onset of hematopoietic impairment at transcriptomic and epigenomic level in GATA2 deficiency, a process exacerbated by the acquisition of the ASXL1 mutation.
2025-10-02 | GSE264140 | GEO
Project description:Clinical GATA2 deficiency syndromes arise from germline haploinsufficiency inducing mutations in GATA2, resulting in immunodeficiency that evolves to myelodysplastic syndrome (MDS)/acute myeloid leukemia (AML). How GATA2 haploinsufficiency disrupts the function and transcriptional network of hematopoietic stem/progenitors (HSCs/HSPCs) to facilitate the shift from immunodeficiency sequalae to pre-leukemia is poorly characterised. Using a conditional mouse model harboring a single allele deletion of Gata2 when HSCs emerge in utero, we identify pervasive defects in HSPC differentiation from young adult Gata2 haploinsufficient mice during B-cell maturation, early erythroid specification, megakaryocyte maturation to platelets and inflammatory cell generation. Gata2 haploinsufficiency abolishes HSC self-renewal and multi-lineage differentiation capacity following transplantation. These alterations closely associate with deregulated DNA damage responses and inflammatory signalling conveyed from Gata2 haploinsufficient HSCs. We also identify functional interplay between Gata2 and Asxl1, a driver of DNA damage and inflammation and, notably, a recurrent secondary mutation found in GATA2 haploinsufficiency disease progression to MDS/AML. shRNA mediated knockdown of Asxl1 in Gata2 haploinsufficient HSPCs led to a differentiation block in committed progenitor formation beyond that in Gata2 haploinsufficient HSPCs. By analysis of HSCs from young adult compound Gata2/Asxl1 haploinsufficient mice, we discover hyperproliferation of double haploinsufficent HSCs, which are also functionally compromised in transplantation compared to their single haploinsufficient counterparts. Through both Gata2/Asxl1 dependent and unique transcriptional programs, HSCs from young adult compound Gata2/Asxl1 haploinsufficient mice fortify deregulated DNA damage responses and inflammatory signalling in HSCs initiated in Gata2 haploinsufficient mice and establish a broad pre-leukemic program. Our data reveal how Gata2 haploinsufficiency initially drives deregulation of HSC genome integrity and suggest the mechanisms of how secondary mutations like ASXL1 take advantage of HSC genomic instability to nurture a pre-leukemic state in GATA2 haploinsufficiency syndromes.
2025-08-27 | GSE283399 | GEO
Project description:Clinical GATA2 deficiency syndromes arise from germline haploinsufficiency inducing mutations in GATA2, resulting in immunodeficiency that evolves to myelodysplastic syndrome (MDS)/acute myeloid leukemia (AML). How GATA2 haploinsufficiency disrupts the function and transcriptional network of hematopoietic stem/progenitors (HSCs/HSPCs) to facilitate the shift from immunodeficiency sequalae to pre-leukemia is poorly characterised. Using a conditional mouse model harboring a single allele deletion of Gata2 when HSCs emerge in utero, we identify pervasive defects in HSPC differentiation from young adult Gata2 haploinsufficient mice during B-cell maturation, early erythroid specification, megakaryocyte maturation to platelets and inflammatory cell generation. Gata2 haploinsufficiency abolishes HSC self-renewal and multi-lineage differentiation capacity following transplantation. These alterations closely associate with deregulated DNA damage responses and inflammatory signalling conveyed from Gata2 haploinsufficient HSCs. We also identify functional interplay between Gata2 and Asxl1, a driver of DNA damage and inflammation and, notably, a recurrent secondary mutation found in GATA2 haploinsufficiency disease progression to MDS/AML. shRNA mediated knockdown of Asxl1 in Gata2 haploinsufficient HSPCs led to a differentiation block in committed progenitor formation beyond that in Gata2 haploinsufficient HSPCs. By analysis of HSCs from young adult compound Gata2/Asxl1 haploinsufficient mice, we discover hyperproliferation of double haploinsufficent HSCs, which are also functionally compromised in transplantation compared to their single haploinsufficient counterparts. Through both Gata2/Asxl1 dependent and unique transcriptional programs, HSCs from young adult compound Gata2/Asxl1 haploinsufficient mice fortify deregulated DNA damage responses and inflammatory signalling in HSCs initiated in Gata2 haploinsufficient mice and establish a broad pre-leukemic program. Our data reveal how Gata2 haploinsufficiency initially drives deregulation of HSC genome integrity and suggest the mechanisms of how secondary mutations like ASXL1 take advantage of HSC genomic instability to nurture a pre-leukemic state in GATA2 haploinsufficiency syndromes.
2025-08-27 | GSE283398 | GEO
Project description:Recurrent mutations in ASXL1 are found in various hematological malignancies and are associated with poor prognosis. In particular, ASXL1 mutations are frequently found in patients with hematological malignancies associated with myelodysplasia including myelodysplastic syndromes (MDS), and chronic myelomonocytic leukemia. Although loss-of-function ASXL1 mutations promote myeloid transformation, a large subset of ASXL1 mutations is thought to result in stable truncation of ASXL1. Here we demonstrate that C-terminal truncating ASXL1 mutations (ASXL1-MT) inhibit myeloid differentiation and induce MDS-like disease in mice, displaying all the features of human MDS including multi-lineage myelodysplasia, pancytopenia and occasional progression to overt leukemia. Concerning the molecular mechanisms, ASXL1-MT derepressed expression of Hoxa9 and miR-125a through inhibiting PRC2-mediated methylation of H3K27. miR-125a targeted expression of a surface receptor Clec5a, which was found to supports for myeloid differentiation. In addition, HOXA9 expression was high in MDS patients with ASXL1 mutations while Clec5a expression was generally low in MDS patients. Thus, ASXL1-MT induced MDS-like disease in mice via derepression of Hoxa9 and miR-125a, and Clec5a downregulation. Our data provide evidence for a novel axis of MDS pathogenesis (ASXL1 mutations-upregulation of HoxA9 and miR-125a-downregulation of Clec5a) and implicate both ASXL1 mutants and miR-125a as therapeutic targets in MDS.
2013-07-31 | GSE49118 | GEO
Project description:Recurrent mutations in ASXL1 are found in various hematological malignancies and are associated with poor prognosis. In particular, ASXL1 mutations are frequently found in patients with hematological malignancies associated with myelodysplasia including myelodysplastic syndromes (MDS), and chronic myelomonocytic leukemia. Although loss-of-function ASXL1 mutations promote myeloid transformation, a large subset of ASXL1 mutations is thought to result in stable truncation of ASXL1. Here we demonstrate that C-terminal truncating ASXL1 mutations (ASXL1-MT) inhibit myeloid differentiation and induce MDS-like disease in mice, displaying all the features of human MDS including multi-lineage myelodysplasia, pancytopenia and occasional progression to overt leukemia. Concerning the molecular mechanisms, ASXL1-MT derepressed expression of Hoxa9 and miR-125a through inhibiting PRC2-mediated methylation of H3K27. miR-125a targeted expression of a surface receptor Clec5a, which was found to supports for myeloid differentiation. In addition, HOXA9 expression was high in MDS patients with ASXL1 mutations while Clec5a expression was generally low in MDS patients. Thus, ASXL1-MT induced MDS-like disease in mice via derepression of Hoxa9 and miR-125a, and Clec5a downregulation. Our data provide evidence for a novel axis of MDS pathogenesis (ASXL1 mutations-upregulation of HoxA9 and miR-125a-downregulation of Clec5a) and implicate both ASXL1 mutants and miR-125a as therapeutic targets in MDS.
2013-07-31 | GSE49117 | GEO
Project description:Recurrent mutations in ASXL1 are found in various hematological malignancies and are associated with poor prognosis. In particular, ASXL1 mutations are frequently found in patients with hematological malignancies associated with myelodysplasia including myelodysplastic syndromes (MDS), and chronic myelomonocytic leukemia. Although loss-of-function ASXL1 mutations promote myeloid transformation, a large subset of ASXL1 mutations is thought to result in stable truncation of ASXL1. Here we demonstrate that C-terminal truncating ASXL1 mutations (ASXL1-MT) inhibit myeloid differentiation and induce MDS-like disease in mice, displaying all the features of human MDS including multi-lineage myelodysplasia, pancytopenia and occasional progression to overt leukemia. Concerning the molecular mechanisms, ASXL1-MT derepressed expression of Hoxa9 and miR-125a through inhibiting PRC2-mediated methylation of H3K27. miR-125a targeted expression of a surface receptor Clec5a, which was found to supports for myeloid differentiation. In addition, HOXA9 expression was high in MDS patients with ASXL1 mutations while Clec5a expression was generally low in MDS patients. Thus, ASXL1-MT induced MDS-like disease in mice via derepression of Hoxa9 and miR-125a, and Clec5a downregulation. Our data provide evidence for a novel axis of MDS pathogenesis (ASXL1 mutations-upregulation of HoxA9 and miR-125a-downregulation of Clec5a) and implicate both ASXL1 mutants and miR-125a as therapeutic targets in MDS. BM cells derived from mock-transplanted mice and ASXL1-MT transplanted mice were incubated with biotinylated antibodies for CD3e, B220, and TER-119, followed by incubation with streptavidin Micro Beads (Miltenyi Biotec). The marker-negative fraction was separated with LS Columns (Miltenyi Biotec). Using the sorted-BM cells, we compared the expression proliles between 3 sorted-BM cells with mock and 3 sorted-BM cells with ASXL1-MT. Total RNA was extracted by Trizol reagent (Invitrogen) according to the manufacturer’s protocol. Double-stranded cDNA was synthesized from 5 μg of total RNA with oligo (dT)24 T7 primer, amplified with T7 RNA polymerase up to approximately 50 μg of cRNA, and hybridized to Affymetrix Mouse Expression array 430A, which contains 45000 probe sets for 39000 transcripts and variants from over 34000 well-characterized mouse genes (Affymetrix). After washing and staining, the arrays were scanned on the GeneChip system confocal scanner (Affymetrix). The intensity for each feature of the array was captured with Affymetrix Microarray Suite (MAS) Version 5.0 software. Gene set enrichment analysis was performed by using Gene Ontology gene sets from the Molecular Signatures Database (http://www.broad.mit.edu/gsea/msigdb/).
2013-07-31 | E-GEOD-49118 | biostudies-arrayexpress
Project description:Recurrent mutations in ASXL1 are found in various hematological malignancies and are associated with poor prognosis. In particular, ASXL1 mutations are frequently found in patients with hematological malignancies associated with myelodysplasia including myelodysplastic syndromes (MDS), and chronic myelomonocytic leukemia. Although loss-of-function ASXL1 mutations promote myeloid transformation, a large subset of ASXL1 mutations is thought to result in stable truncation of ASXL1. Here we demonstrate that C-terminal truncating ASXL1 mutations (ASXL1-MT) inhibit myeloid differentiation and induce MDS-like disease in mice, displaying all the features of human MDS including multi-lineage myelodysplasia, pancytopenia and occasional progression to overt leukemia. Concerning the molecular mechanisms, ASXL1-MT derepressed expression of Hoxa9 and miR-125a through inhibiting PRC2-mediated methylation of H3K27. miR-125a targeted expression of a surface receptor Clec5a, which was found to supports for myeloid differentiation. In addition, HOXA9 expression was high in MDS patients with ASXL1 mutations while Clec5a expression was generally low in MDS patients. Thus, ASXL1-MT induced MDS-like disease in mice via derepression of Hoxa9 and miR-125a, and Clec5a downregulation. Our data provide evidence for a novel axis of MDS pathogenesis (ASXL1 mutations-upregulation of HoxA9 and miR-125a-downregulation of Clec5a) and implicate both ASXL1 mutants and miR-125a as therapeutic targets in MDS. Using 32Dcl3 cells transduced with pMYs-IG (mock) and pMYs-FLAG-ASXL1-MT-IG, we compared the expression profiles of 32Dcl3 cells with mock or ASXL1-MT under G-CSF stimulation at 4 time points, including 0hr (IL-3), 2hr, 6hr and 24hrs. Total RNA was extracted by Trizol reagent (Invitrogen) according to the manufacturer’s protocol. Double-stranded cDNA was synthesized from 5 μg of total RNA with oligo (dT)24 T7 primer, amplified with T7 RNA polymerase up to approximately 50 μg of cRNA, and hybridized to Affymetrix Mouse Expression array 430A, which contains 45000 probe sets for 39000 transcripts and variants from over 34000 well-characterized mouse genes (Affymetrix). After washing and staining, the arrays were scanned on the GeneChip system confocal scanner (Affymetrix). The intensity for each feature of the array was captured with Affymetrix Microarray Suite (MAS) Version 5.0 software. Gene set enrichment analysis was performed by using Gene Ontology gene sets from the Molecular Signatures Database (http://www.broad.mit.edu/gsea/msigdb/)
2013-07-31 | E-GEOD-49117 | biostudies-arrayexpress
Project description:GATA2 deficiency is an autosomal dominant germline disorder of immune dysfunction and bone marrow failure with a high propensity for leukemic transformation in adolescents, present in up to 7% of pediatric myelodysplastic syndrome (MDS) and 15% of advanced MDS cases. While sequencing studies have identified several secondary mutations thought to contribute to malignancy, the mechanisms of disease progression have been difficult to identify due to a lack of disease-specific experimental models. Here, we generated a murine model of one of the most common GATA2 mutations associated with leukemic progression in GATA2 deficiency, Gata2R396Q/+. While mutant mice exhibit mild defects in peripheral blood output throughout life, they display significant hematopoietic abnormalities in the bone marrow (BM), including a reduction in hematopoietic stem cell (HSC) function and intrinsic biases toward specific stem cell subsets that differ from previous models of GATA2 loss. Supporting this observation, single-cell RNA sequencing of BM hematopoietic progenitors revealed a loss of HSC stemness, myeloid-bias, and accelerated ageing phenotype. Importantly, we show that Gata2R396Q/+ exerts effects early in hematopoietic development, as mutant mice generate fewer HSCs in the aorta gonad mesonephros, and fetal liver HSCs have reduced function. This reduced pool of HSCs and aged phenotype could be potential contributors to leukemic transformation in patients, and our model provides a useful tool to study the mechanisms of malignant transformation in GATA2 deficiency.
2024-12-23 | GSE275213 | GEO
Project description:Germline heterozygous GATA2 mutations cause GATA2 deficiency, a complex disorder characterized by bone marrow failure, immunodeficiency, and a high risk of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). The disease evolves variably among patients, leading to anxiety for families. Due to phenotypic diversity and clinical overlap, timely diagnosis is often challenging. GATA2 carriers exhibit variable expressivity, with some developing early-onset MDS while others remain asymptomatic, suggesting that genetic and epigenetic factors influence disease progression. While advances in diagnostics through whole-exome sequencing (WES) and whole genome sequencing (WGS) have been made, few epigenetic studies have focused on GATA-related MDS. We present a familial case of four GATA2 carriers, two of whom are asymptomatic and two have developed MDS. Notably, we conducted a longitudinal epigenome analysis of one patient, tracking progression from asymptomatic to MDS, providing key insights with potential clinical applications
2025-04-16 | GSE280776 | GEO