Engineering a haematopoietic stem cell niche by reprogramming mesenchymal stromal cells (ATAC-Seq)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA445309 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6881201_1.fastq.gz | Fastqsanger.gz | |||
| SRR6881201_2.fastq.gz | Fastqsanger.gz | |||
| SRR6881211_1.fastq.gz | Fastqsanger.gz | |||
| SRR6881211_2.fastq.gz | Fastqsanger.gz | |||
| SRR6881202_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Engineering a haematopoietic stem cell niche by reprogramming mesenchymal stromal cells
| PRJNA445306 | ENA
Project description:Engineering a haematopoietic stem cell niche by reprogramming mesenchymal stromal cells (RNA-Seq)
| PRJNA445310 | ENA
Project description:Haematopoietic stem cells (HSCs) reside in bone marrow (BM) niches where they are maintained to replenish all blood cell lineages throughout life. Among the constituents of the murine HSC niches, various cell types such as CXCL12-abundant reticular (CAR) cells, Nestin-GFP+ perivascular cells, leptin receptor (LepR)+ cells, endothelial cells, osteoblasts, sympathetic nerves, macrophages and megakaryocytes in the BM have been proposed to contribute to HSC niche activity. When niche cells are removed from their natural habitat, the ability to maintain HSCs ex vivo is markedly diminished. Mesenchymal-derived stromal cells (MSCs) identified by Nestin-GFP express high levels of niche factors in vivo, but their expression is downregulated rapidly upon culture, suggesting that alterations in transcriptional rewiring may contribute to the reduced HSC maintenance potential. We found that the enforced expression of 5 genes (Klf7, Ostf1, Xbp1, Irf3 and Irf7) markedly restored HSC niche function in cultured BM-derived MSCs. These revitalized MSCs (rMSCs) exhibited boosted synthesis of HSC niche factors while retaining their mesenchymal lineage differentiation capacity. By contrast to HSCs co-cultured with control MSCs, HSCs expanded with rMSCs showed significantly higher repopulation capacity. To evaluate to what extent rMSCs are reprogrammed toward freshly isolated MSCs, we compared, by RNA-seq analysis, the transcriptome of freshly sorted CD45(-) Ter119(-) CD31(-) Scf-GFP(-) cells, CD45(-) Ter119(-) CD31(-) Scf-GFP(+) cells, rMSCs and control vector-transduced stroma. HSC niche-associated genes were highly expressed in both native Scf-GFP(+) stromal cells and rMSCs compared to the Scf-GFP cell fraction and control MSCs. With the motif analysis of ATAC-seq data, we found that myocyte enhancer factor 2c (Mef2c) is one of the key factor in the revitalization of MSCs. These results suggest that rMSC may provide a promising platform for curative transplantation therapies.
2019-04-05 | GSE112232 | GEO
Project description:Haematopoietic stem cells (HSCs) reside in bone marrow (BM) niches where they are maintained to replenish all blood cell lineages throughout life. Among the constituents of the murine HSC niches, various cell types such as CXCL12-abundant reticular (CAR) cells, Nestin-GFP+ perivascular cells, leptin receptor (LepR)+ cells, endothelial cells, osteoblasts, sympathetic nerves, macrophages and megakaryocytes in the BM have been proposed to contribute to HSC niche activity. When niche cells are removed from their natural habitat, the ability to maintain HSCs ex vivo is markedly diminished. Mesenchymal-derived stromal cells (MSCs) identified by Nestin-GFP express high levels of niche factors in vivo, but their expression is downregulated rapidly upon culture, suggesting that alterations in transcriptional rewiring may contribute to the reduced HSC maintenance potential. We found that the enforced expression of 5 genes (Klf7, Ostf1, Xbp1, Irf3 and Irf7) markedly restored HSC niche function in cultured BM-derived MSCs. These revitalized MSCs (rMSCs) exhibited boosted synthesis of HSC niche factors while retaining their mesenchymal lineage differentiation capacity. By contrast to HSCs co-cultured with control MSCs, HSCs expanded with rMSCs showed significantly higher repopulation capacity. To evaluate to what extent rMSCs are reprogrammed toward freshly isolated MSCs, we compared, by RNA-seq analysis, the transcriptome of freshly sorted CD45(-) Ter119(-) CD31(-) Scf-GFP(-) cells, CD45(-) Ter119(-) CD31(-) Scf-GFP(+) cells, rMSCs and control vector-transduced stroma. HSC niche-associated genes were highly expressed in both native Scf-GFP(+) stromal cells and rMSCs compared to the Scf-GFP cell fraction and control MSCs. With the motif analysis of ATAC-seq data, we found that myocyte enhancer factor 2c (Mef2c) is one of the key factor in the revitalization of MSCs. These results suggest that rMSC may provide a promising platform for curative transplantation therapies.
2019-04-05 | GSE112231 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2019-04-05 | GSE112233 | GEO
Project description:Haematopoietic stem cells (HSCs) are maintained by bone marrow niches in vivo1,2, but the ability of niche cells to maintain HSCs ex vivo is markedly diminished. Expression of niche factors by Nestin-GFP+ mesenchymal-derived stromal cells (MSCs) is downregulated upon culture, suggesting that transcriptional rewiring may contribute to this reduced HSC maintenance potential. Using an RNA sequencing screen, we identified five genes encoding transcription factors (Klf7, Ostf1, Xbp1, Irf3 and Irf7) that restored HSC niche function in cultured bone marrow-derived MSCs. These revitalized MSCs (rMSCs) exhibited enhanced synthesis of HSC niche factors while retaining their mesenchymal differentiation capacity. In contrast to HSCs co-cultured with control MSCs, HSCs expanded with rMSCs showed higher repopulation capacity and protected lethally irradiated recipient mice. Competitive reconstitution assays revealed an approximately sevenfold expansion of functional HSCs by rMSCs. rMSCs prevented the accumulation of DNA damage in cultured HSCs, a hallmark of ageing and replication stress. Analysis of the reprogramming mechanisms uncovered a role for myocyte enhancer factor 2c (Mef2c) in the revitalization of MSCs. These results provide insight into the transcriptional regulation of the niche with implications for stem cell-based therapies.
| S-EPMC6499646 | biostudies-literature
Project description:We cultured bone marrow haematopoietic stem and progenitor cells with bone marrow mesenchymal stromal cells to understand the interaction between the two cell types.
2023-05-21 | GSE151584 | GEO
Project description:Microenvironment cues received by haematopoietic stem cells (HSC) are important in regulating the choice between self-renewal and differentiation. On the basis of the differential expression of cell-surface markers, here we identify a mesenchymal stromal progenitor hierarchy, where CD45(-)Ter119(-)CD31(-)CD166(-)CD146(-)Sca1(+)(Sca1(+)) progenitors give rise to CD45(-)Ter119(-)CD31(-)CD166(-)CD146(+)(CD146(+)) intermediate and CD45(-)Ter119(-)CD31(-)CD166(+)CD146(-)(CD166(+)) mature osteo-progenitors. All three progenitors preserve HSC long-term multi-lineage reconstitution capability in vitro; however, their in vivo fates are different. Post-transplantation, CD146(+) and CD166(+) progenitors form bone only. While Sca1(+) progenitors produce CD146(+), CD166(+) progenitors, osteocytes and CXCL12-producing stromal cells. Only Sca1(+) progenitors are capable of homing back to the marrow post-intravenous infusion. Ablation of Sca1(+) progenitors results in a decrease of all three progenitor populations as well as haematopoietic stem/progenitor cells. Moreover, suppressing production of KIT-ligand in Sca1(+) progenitors inhibits their ability to support HSCs. Our results indicate that Sca1(+) progenitors, through the generation of both osteogenic and stromal cells, provide a supportive environment for hematopoiesis.
| S-EPMC5062560 | biostudies-other
Project description:Haematopoietic differentiation of embryonic stem (ES) cells in vitro has been used as a model to study early haematopoietic development and it is well documented that haematopoietic differentiation can be enhanced by over-expression of HOXB4. HOXB4 is expressed in haematopoietic progenitor cells (HPC) where it promotes self-renewal, but it is also expressed in the primitive streak of the gastrulating embryo. This led us to hypothesise that HOXB4 might modulate gene expression in pre- haematopoietic mesoderm and that this property might contribute to its pro-haematopoietic effect in differentiating ES cells. To test our hypothesis we developed a conditionally activated HOXB4 expression system using the mutant oestrogen receptor (ERT2) and showed that a pulse of HOXB4 prior to HPC emergence in differentiating ES cells led to an increase in haematopoietic differentiation. Expression profiling revealed an increase in the expression of genes associated with paraxial mesoderm that gives rise to the haematopoietic niche. Cell mixing experiments suggest that HOXB4 activation can indeed have a paracrine, as well as a cell autonomous, effect on haematopoietic differentiation. We provide evidence that this may, in part, be mediated by modulation of the Wnt pathway via the HOXB4 target gene, Frzb. Constructs: HOXB4-ERT2 constructs were generated that utilised the CAG promoter to drive expression of the Hoxb4ERT2 fusion cDNA followed by an IRES element and the puromycin resistance gene (pCAG Hoxb4ERT2IP); CGR8.5 cells bearing Hoxb4VP16 fusion construct. Fusion of HOXB4-ERT2 with the transactivation domain of the Herpes simplex VP16 (Brickman et al. 2000) (Zamparini et al. 2006) was generated by PCR as were 2 mutants: Hoxb4 (N266P)VP16/Pcs2+ and Hoxb4 (d266)VP16/Pcs2+ which had mutations in an asparagine (residue 266) in the third helix of the homeodomain which functions in DNA recognition (Hanes and Brent 1989).
2011-02-05 | E-MTAB-547 | biostudies-arrayexpress
Project description:Comprehensive transcriptional characterization of bone marrow stromal cells by RNA sequencing was performed to determine the molecular properties/signatures of endothelium during niche formation.Here, we identify a rare subset of cells in the human fetal BM that co-express endothelial and stromal markers, including low-affinity nerve growth factor receptor (LNGFR/CD271). They display transcriptional reprogramming consistent with endothelial-to-mesenchymal transition (EndoMT), reflected in their potential to generate stromal cells with in vivo BM niche forming capacity.
| EGAS00001004946 | EGA