Gene expression signatures in Tif1b, Hp1a or Hp1g knockdown hematopoietic progenitors
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Satoru Miyagi
PROVIDER: E-GEOD-48897 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Gene expression analyses of Tif1b, Hp1a or Hp1g knockdown hematopoietic progenitors. Growth of hematopoietic stem cells (HSCs) are significantly impaired upon knockdown of Hp1a and Hp1g. Results provide insight into the role of these factors in hematopoiesis.
2014-08-01 | GSE48897 | GEO
Project description:The transcription factor Meis1 is preferentially expressed in hematopoietic stem cells (HSCs) and over-expressed in certain leukemias. However, the functions of Meis1 in hematopoiesis remain largely unknown. Using inducible knock-out mice, we found that Meis1 is required for the maintenance of hematopoiesis under stress and over long term while steady-state hematopoiesis was sustained in the absence of Meis1. Bone marrow cells of Meis1 deficient mice showed reduced colony formation, contained significantly fewer numbers of long- term HSCs and these Meis1-deficient HSCs exhibited loss of quiescence. Further, we found that Meis1 deletion led to the accumulation of reactive oxygen species (ROS) in HSCs and decreased expression of genes implicated in hypoxia response. Finally, ROS scavenging by N-acetyl cysteine or stabilization of hypoxia-signaling by knockdown of the VHL protein led to reversal of the effects of Meis1-deletion. Taken together, these results demonstrate that Meis1 protects and preserves HSCs by restricting oxidative metabolism. Lineage negative cells were harvested from Meis1-flox/CreER or control mice and incubated with 4-OHT for 48 hours. Total RNA was extracted and used for the profiling experiment.
2012-09-26 | E-GEOD-41133 | biostudies-arrayexpress
Project description:Umbilical cord blood (CB) is a non-invasive, convenient and broadly used source of hematopoietic stem cells (HSCs) for allogeneic stem cell transplantation. However, limiting numbers of HSCs remain a major constraint for its clinical application. One feasible option would be to expand HSCs to improve therapeutic outcome, however available protocols and the molecular mechanisms governing the self-renewal of HSC are unclear. Here we show that ectopic expression of a single miRNA, miR-125a, in purified murine and human multipotent progenitors (MPP) resulted in increased self-renewal and robust long-term multi-lineage repopulation in transplanted recipient mice. Using quantitative proteomics and Western blot analysis, we identified a restricted set of miR-125a targets which revealed the involvement of the MAP kinase signaling pathway in conferring long-term repopulating capacity to multipotent progenitors in human and mice. Our findings offer the innovative potential to use MPP with enhanced self-renewal activity to augment limited sources of HSC to improve clinical protocols.
2017-01-11 | PXD003931 | Pride
Project description:Hematopoietic differentiation is strictly regulated by complex network of transcription factors that are controlled by ligands binding to cell surface receptors. Disruptions of the intricate sequences of transcriptional activation and suppression of multiple genes cause hematological diseases, such as leukemias, myelodysplastic syndromes or myeloproliferative syndromes. From a clinical standpoint, deciphering the pattern of gene expression during hematopoiesis may help unravel disease-specific mechanisms in hematopoietic malignancies. Herein, we describe a human in vitro hematopoietic model system where lineage specific differentiation of CD34+ cells was accomplished using specific cytokines. Microarray and RNAseq based whole transcriptome and exome analysis was performed on the differentiated erythropoietic, granulopoietic and megakaryopoietic cells to delineate changes in expression of whole transcripts and exons. Analysis on the Human 1.0 ST exon arrays indicated differential expression of 172 genes (P< 0.0000001) and significant splicing of 86 genes during differentiation. Pathway analysis identified these genes to be involved in Rac/RhoA signaling, Wnt/B-catenin signaling and alanine/aspartate metabolism. Comparison of the microarray data to next generation RNAseq analysis during erythroid differentiation demonstrated a high degree of correlation in gene (R= 0.72) and exon (R=0. 62) expression. Our data provides a molecular portrait of events that regulate differentiation of hematopoietic cells. Knowledge of molecular processes by which the cells acquire their cell specific fate would be beneficial in developing cell-based therapies for human diseases. Comparison of gene expression patterns between CD34, E, M and G groups
2011-11-22 | E-GEOD-29989 | biostudies-arrayexpress
Project description:Hematopoietic stem cells (HSCs) are located in the bone marrow in a specific microenvironment referred as the hematopoietic stem cell niche, where HSCs interact with a variety of stromal cells. Though several components of the stem cell niche have been identified, the regulatory mechanisms through which such components regulate the stem cell fate are still unknown. In order to address this issue, we investigated how osteoblasts (OBs) can affect the molecular and functional phenotype of HSCs and vice versa. Our data showed that CD34+ cells cultured with OBs give rise to higher total cell numbers, produce more CFU and maintain a higher percentage of CD34+CD38- cells compared to control culture. Moreover, clonogenic assay and long-term culture results showed that OBs enhance HSC differentiation towards the mono/macrophage lineage at the expense of the granulocytic and erythroid ones. Finally, GEP analysis allowed us to identify several cytokine-receptor networks, such as WNT pathway, and transcription factors, as TWIST1 and FOXC1, that could be activated by co-culture with OBs and could be responsible for the biological effects reported above. Altogether our results indicate that OBs are able to affect both HPC maintenance and differentiation capacity by modulating mono/macrophage and erythroid commitment. We set up a co-culture system composed of human CD34+ cells in culture with human OBs. After coculture, CD34+ cells and the hematopoietic cell fraction were separated from OBs and analyzed by gene expression profiling (GEP), clonogenic assay and long-term culture.
2013-05-10 | E-GEOD-38091 | biostudies-arrayexpress
Project description:Gene expression analyses of hematopoietic stem cells (HSCs), progenitor cells (HPCs), and differentiated cell. Gene expressions of long-term HSCs (CD34-ckit+Sca1+Lineage-), short term HSCs (CD34+ckit+Sca1+Lineage-), Progenitor cells (ckit+Sca1- Lineage-), and differentiated cels (Lineage+) were examined by microarray. Results provide insight into the mechanism of hematopoietic cell differentiation. Long-term HSCs (CD34-ckit+Sca1+Lineage-), Short term-HSCs (CD34+ckit+Sca1+Lineage-), Progenitor cells (ckit+Sca1- Lineage-, and Lineage+), and differentiated cell (Lineage+) were sorted from mouse bone marraw and were examined by microarray. Results provide insight into the mechanism of hematopoietic cell differentiation.
2013-11-06 | E-GEOD-48986 | biostudies-arrayexpress
Project description:To determine the molecules involved in beta3 integrin signaling in HSCs, we carried out DNA microarray analyses using HSCs stimulated with ligand-mimic antibody for intetegrin beta3 in the presence of stem cell factor(SCF) and/or thrombopoietin (TPO). All experiments were performed in duplicate or triplicate using sorted cells that were independently prepared in separate experiments. After CD34-KSL HSCs were cultured with 2C9.G2 or control IgG for 5 days in S-Clone SF-03 medium supplemented with 50 ng/ml SCF and/or 50 ng/ml TPO, gene expression profiles were examimed using 5,000 sorted CD48-KSL cells from each sample.
2011-11-16 | E-GEOD-33696 | biostudies-arrayexpress
Project description:Epigenetic mechanisms including histone modifications have emerged as important factors influencing cell fate determination. The functional role of H3K4 methylation, however, remains largely unclear in the maintenance and differentiation of hematopoietic stem/progenitor cells (HSC/HPCs). Here we show that DPY30, a shared core subunit of the SET1/MLL family methyltransferase complexes and a facilitator of their H3K4 methylation activity, is important for ex vivo proliferation and differentiation of human CD34+ HPCs. DPY30 promotes HPC proliferation by directly regulating the expression of genes critical for cell proliferation. Interestingly, while DPY30 knockdown (KD) in HPCs impaired their differentiation into the myelomonocytic lineage, it potently promoted hemoglobin production and affected the kinetics of their differentiation into the erythroid lineage. In an in vivo model, we show that morpholino-mediated dpy30 KD resulted in severe defects in the development of the zebrafish hematopoietic system, which could be partially rescued by co-injection of dpy30 mRNA. Taken together, our results establish a critical role of DPY30 in the proliferation and appropriate differentiation of hematopoietic progenitor cells as well as in animal hematopoiesis. Finally, we also demonstrate a crucial role of DPY30 in the growth of several MLL1-fusion-mediated leukemia cell lines. Total RNAs from control (scr) or knockdown (hD2, hD5) cells before and after culturing under condition promoting myelomonocytic differentiation were subjected to Illumina microarray analyses.
2014-09-01 | E-GEOD-59643 | biostudies-arrayexpress
Project description:The derivation of functional, transplantable HSCs from an pluripotent stem cells in vitro holds great promise for clinical therapies, but is unachieved. In order to achieve full functionality of HSCs, it is vital to determine the extent to which PSCs can currently be differentiated to the HSC program in vitro and identify the remaining dysregulated genetic pathways. Microarrays were used to compare the transcritomes of ESC-derived immunophenotypic HSPCs to endogenous HSPCs from various stages of development to determine the programs important for human HSC development and function, and which programs were lacking in ESC-derived hematopoietic cells. CD34+CD38-CD43+CD90+ HSPCs were sorted from human placenta and embryoid bodies, and CD34+CD38-CD45+CD90+ HSPCs sorted from fetal liver and embryoid bodies co-cultured on OP9-M2 stroma, the RNA was extracted, library created and hybridized to the Affymetrix microarray
2016-05-16 | E-GEOD-64865 | biostudies-arrayexpress
Project description:MicroRNA plays a critical role in a wide variety of biological processes and regulate genes associated with different biological processes such as development, proliferation, apoptosis, stress response, and tumourigenesis. Profiling miRNA expression during differentiation of embryonic stem cells will help to understand the regulation pathway of differentiation, which in turn may elucidate disease mechanisms. In human hematopoiesis that requires a tight control of gene expression, lineage-specific transcription factors have long been known to act as key regulators of gene expression in multiple cell-fate decisions that govern cell differentiation. Given the important role of miRNAs in development and differentiation, it would be beneficial to elucidate the role of miRNAs in hematopoiesis for identifying novel drug targets. We undertook the current study of examining the expression of miRNA expression in CD34+ before and after differentiation into erythropoietic, granulopoietic and megakaryocytic cells using Affymetrix V 2.0 miRNA genechips. We identified 388 probesets representing 140 miRNAs, snoRNAs and stemloop RNAs to be significantly altered during lineage specific differentiation of CD34+ cells. Of these differentially expressed miRNAs with functional roles in cellular growth and proliferation, differentiation and apoptosis, 16 downregulated miRNAs were found to overlap between the E, M and G groups, hsa-miR150 was significantly downregulated and hsa-miR 210 and hsa-miR-1260b were found to be uniquely upregulated during granulopoiesis while hsa-miR486 was found to be upregulated during erythropoiesis and downregulated in megakaryopoiesis. Megakaryopoitic differentiation specifically resulted in significant down regulation of many miRNAs such as mir -150, mir -155, mir-15, mir-181, mir-221 that seem to play critical roles in the regulation of B and T cell differentiation . An integrated analysis of the differentially expressed miRNA and mRNA identified specific gene targets that are regulated by the significantly altered micro RNAs during lineage specific hematopoiesis. We believe that this study would enhance our understanding of the role of miRNA in lineage specific gene expression. CD34+ cells were compared to differentiated Erythropoitic, granulopoietic and megakaryopoiteic groups to identify differentially expressed microRNAs Human hematopoietic progenitor cells
2013-01-04 | E-GEOD-35532 | biostudies-arrayexpress