Microarray Analysis of Cohesin Mutant HSPC
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE73224 | GEO | 2015/11/03
SECONDARY ACCESSION(S): PRJNA296396
REPOSITORIES: GEO
Similar Datasets
Project description:Transciptome analysis of CD34+ enriched human HSPC lentivirally transduced with cohesin WT or mutant CD34+ enriched HSPCs from cord blood were transduced with a constitutive lentiviral vector expressing cohesin WT or mutant tagged to GFP. After 72hrs cells were GFP+ sorted and subjected to downstream microarray protocol.
2015-11-03 | E-GEOD-73224 | biostudies-arrayexpress
Project description:Understanding the impact of cohesin mutations on HSPC chromatin structure We examined chromatin structure using ATAC-seq in CD34+ enriched-human HSPC that were transduced with either cohesin WT, mutant or empty vector controls
2015-11-03 | E-GEOD-73206 | biostudies-arrayexpress
Project description:Decreased levels of Cohesin proteins increases the amount of primitive hematopoietic stem and progenitor cells in an in vitro setting. We used microarrays to detail the changes in global transcription programme to understand the underlying mechanisms behind this phenotype. Of note, we discover that hematopoietic stem cell-specific genes are upregulated in cells with decreased Cohesin levels. CD34 positive cells were isolated from human cord blood (not older than 24h), lentivirally transduced with shRNA targeting different members of the Cohesin complex. In order to focus on immediate changes, transduced cells were sorted 36 hours post transduction and analyzed.
2016-03-17 | E-GEOD-74824 | biostudies-arrayexpress
Project description:Understanding the impact of cohesin mutations on HSPC chromatin structure
2015-11-03 | GSE73206 | GEO
Project description:The occurrence of clonal perturbations and leukemia in patients transplanted with retrovirally-transduced autologous hematopoietic stem and progenitor cells (HSPCs) has stimulated extensive investigation, demonstrating that proviral insertions perturb adjacent proto-oncogene expression. Although enhancer-deleted lentiviruses are less likely to result in insertional oncogenesis, there is evidence that they may perturb transcript splicing, and one patient with a benign clonal expansion of lentivirally-transduced HPSC has been reported. The rhesus macaque model provides an opportunity for informative long-term analysis to ask whether transduction impacts on long-term HSPC properties. We utilized two techniques to examine whether lentivirally-transduced HSPCs from eight rhesus macaques transplanted 1-13.5 years previously are perturbed at a population level, comparing telomere length as a measure of replicative history and gene expression profile of vector positive versus vector negative cells. There were no differences in telomere lengths between sorted GFP+ and GFP- blood cells, suggesting that lentiviral transduction did not globally disrupt replicative patterns. Bone marrow GFP+ and GFP- CD34+ cells showed no differences in gene expression using unsupervised and principal component analysis. These studies did not uncover any global long-term perturbation of proliferation, differentiation, or other important functional parameters of transduced HSPCs in the rhesus macaque model. CD34+ hematopoietic stem and progenitor cells were purified from bone marrow aspirates obtained from 4 rhesus macaques 3-9 years following transplantation with lentivirally-transduced autologous hematopoietic stem and progenitor cells. All lentiviral vectors contained the GFP marker gene. The CD34+ cells from each animal were sorted via flow cytometry into GFP+ and GFP- fractions, and RNA from these cells was used for Affymetrix gene expression analysis as detailed below. There were two samples, GFP+ and GFP-, from each of 4 animals.
2013-11-05 | E-GEOD-46032 | biostudies-arrayexpress
Project description:The occurrence of clonal perturbations and leukemia in patients transplanted with retrovirally-transduced autologous hematopoietic stem and progenitor cells (HSPCs) has stimulated extensive investigation, demonstrating that proviral insertions perturb adjacent proto-oncogene expression. Although enhancer-deleted lentiviruses are less likely to result in insertional oncogenesis, there is evidence that they may perturb transcript splicing, and one patient with a benign clonal expansion of lentivirally-transduced HPSC has been reported. The rhesus macaque model provides an opportunity for informative long-term analysis to ask whether transduction impacts on long-term HSPC properties. We utilized two techniques to examine whether lentivirally-transduced HSPCs from eight rhesus macaques transplanted 1-13.5 years previously are perturbed at a population level, comparing telomere length as a measure of replicative history and gene expression profile of vector positive versus vector negative cells. There were no differences in telomere lengths between sorted GFP+ and GFP- blood cells, suggesting that lentiviral transduction did not globally disrupt replicative patterns. Bone marrow GFP+ and GFP- CD34+ cells showed no differences in gene expression using unsupervised and principal component analysis. These studies did not uncover any global long-term perturbation of proliferation, differentiation, or other important functional parameters of transduced HSPCs in the rhesus macaque model.
2013-11-05 | GSE46032 | GEO
Project description:Cohesin shapes the nuclear chromatin architecture, including enhancer-promoter interactions,
and its components, of which especially STAG2 and RAD21, are frequently mutated in myeloid
malignancies. To elucidate mechanisms of leukemogenesis associated with cohesin mutations
in humans, we comprehensively characterized genetic, epigenetic, transcriptional, and
chromatin conformational changes in acute myeloid leukemia (AML). To corroborate our
findings, we performed complementary siRNA-mediated depletion of STAG2, its paralogue
STAG1 or RAD21 in cord blood-derived CD34+ primary human hematopoietic stem and
progenitor cells (HSPCs). We show that STAG2 mutations consistently lead to the loss of
STAG2 protein and are associated with a specific set of co-occurring mutations, while STAG1
was never mutated in AML. Loss of STAG2 was frequently compensated by STAG1. Still,
specific loci displayed altered cohesin occupancy, gene expression and corresponding changes
in local chromatin activation as measured by H3K27ac enrichment and chromatin accessibility.
High-throughput chromosome conformation capture (in-situ Hi-C) revealed significantly
altered chromatin looping in cohesin-mutated AMLs, including weakened enhancer-promoter
contacts with reduced, cohesin-dependent promoter activity. In HSPCs, we detected
transcriptomic and epigenetic effects overlapping STAG2-mutant AML-specific changes
following STAG2 knockdown (KD), that were not invoked by the depletion of STAG1. We
also found that STAG2 loss in cultured HSPCs impaired the differentiation capacity, especially
erythroid colony formation which maintained HSPC-like gene expression. This work
establishes STAG2 as a key regulator of cohesin-associated chromatin architecture, gene
expression and differentiation in the human hematopoietic system and identifies candidate
target genes that may be implicated in leukemogenesis.
| EGAS00001007405 | EGA
Project description:RNA-seq of vehicle and doxycycline treated Rad21-TEV primary neuron transduced with NLS-TEV, inducing extended cohesin depletion
2021-02-28 | GSE161797 | GEO
Project description:We demonstrated to examine the effect of AhR antagonists on the specific lineage-biased differentiation of HSPC. To confirm this, CD34+ cells isolated from cord blood were cultured with two antagonists (CH223191 and StemRegenin 1) for 14 days to monitor their phenotype, and chromatin immunoprecipitation DNA was extracted from cultured cells on the 14th day of culture. We sought to explain the relationship between the action of AhR-antagonist complex and the megakaryocyte lineage-biased differentiation of HSPC with these ChIP-seq results.
2022-06-01 | GSE184778 | GEO