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RNA-seq in human hematopoietic stem cells (HSCs) cultures on 3 different materials

ABSTRACT: RNA-seq in human hematopoietic stem cells (HSCs) cultures on 3 different materials

PROVIDER: PRJNA739969 | ENA |

REPOSITORIES: ENA

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RNA-seq in human hematopoietic stem cells (HSCs) cultures on 3 different materials

Project description:Hematopoietic stem cell transplantation (HSCT) is successfully applied since the late 1950s, however, its efficacy still needs to be improved. A promising strategy is to transplant high numbers of pluripotent hematopoietic stem cells (HSCs). Therefore, an advanced ex vivo culture system is needed that supports the proliferation and maintains the pluripotency of HSC to override possible limitations in cell numbers gained from donors. To model the natural HSC niche in vitro and thus, to amplify high numbers of undifferentiated HSCs, we used an optimized HSC cell culture medium in combination with artificial 3D bone marrow-like scaffolds made of polydimethylsiloxane (PDMS). After 14 days in vitro (DIV) cell culture, we performed transcriptome and proteome analysis of the whole cell populations. Ingenuity pathway analysis (IPA) indicated that our 3D PDMS cell culture scaffolds altered PI3K/AKT/mTOR pathways and activated SREBP, HIF1α and FOXO signaling leading to metabolic adaptations, which we confirmed by ELISA, Western blot and metabolic flux analysis. These molecular signaling pathways can promote the expansion HSCs and are involved in their pluripotency maintenance. Thus, we could show that our 3D bone marrow-like PDMS scaffolds activate key molecular signaling pathways to amplify the numbers of undifferentiated HSCs efficiently ex vivo.

2021-10-27 | GSE178657 | GEO

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Transcriptome analysis of different tissues in different materials

Project description:We used two hybrid combinations and their 4 parents as materials. One week after topping the tobacco plant, samples were taken, including three tissues: root, stalk, and leaf. The RNA of these samples was extracted, and transcriptome sequencing analysis was carried out to explore the transcriptional profile differences between hybrids and their parents, and to analyze the gene differential expression between different tissues.

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Analysis of differentially expressed genes in murine Satb1-deficient hematopoietic stem cells (HSCs) compared to wild-type HSCs

Project description:Gene expression analysis on purified murine hematopoietic stem cells (HSCs) deficient for Special AT-rich sequence-binding protein 1 (Satb1) compared to wild-type HSCs. Analysis of gene expression of bone marrow-derived CD45.2+ CD150+cKit+Sca-1+CD4-CD8a-CD19-B220-Gr-1- HSCs from congenic recipient animals transplanted >20 weeks with either wild-type or Satb1-deficient hematopoeitic cells.

2013-04-07 | E-GEOD-44107 | biostudies-arrayexpress

Transcriptome data of bone marrow hematopoietic stem cells (HSCs) with IGF-1 treatment

Project description:Insulin-like growth factor-1 (IGF-1) is known as a hematopoietic factor which impacts hematopoietic reconstitution and facilitates thrombopoiesis, although its direct effect on hematopoietic stem cells (HSCs) remains unclear. Here, we show that IGF-1 rapidly prompts megakaryocyte (Mk)-lineage differentiation of HSCs by enhancing mitochondrial activity in HSCs. To identify the phenotype switching and function variation in HSCs with IGF-1 treatment, we performed RNA-seq of HSCs from the bone marrow of mice with single-dose IGF-1 treatment (IGF-1) and their age-matched control mice (Ctrl).

2024-06-05 | GSE229985 | GEO

Analysis of differentially expressed genes in murine Satb1-deficient hematopoietic stem cells (HSCs) compared to wild-type HSCs

Project description:Gene expression analysis on purified murine hematopoietic stem cells (HSCs) deficient for Special AT-rich sequence-binding protein 1 (Satb1) compared to wild-type HSCs.

2013-04-07 | GSE44107 | GEO

Hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs)

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Igf2bp2 deletion reduces energy metabolism, gIgf2bp2 deletion reduces energy metabolism, growth signaling, and aging of hematopoietic stem cells in micerowth signaling, and aging of hematopoietic stem cells in mice

Project description:Increasing evidence links metabolic activity and cell growth to decline in hematopoietic stem cell (HSC) function during aging. The Lin28b/Hmga2 pathway controls tissue development and in the hematopoietic system the postnatal downregulation of this pathway causes a decrease in self renewal of adult HSCs compared to fetal HSCs. Igf2bp2 is an RNA binding protein and a mediator of the Lin28b/Hmga2 pathway, which regulates metabolism and growth signaling by influencing RNA stability and translation of its target genes. It is currently unknown whether Lin28/Hmga2/Igf2bp2 signaling impacts on aging-associated impairments in HSC function and hematopoiesis. Here, we analyzed homozygous Igf2bp2 germline knockout mice and wildtype control animals to address this question. The study shows that Igf2bp2 deletion rescues aging phenotypes of the hematopoietic system, such as the expansion of HSC numbers in bone marrow and the biased increase of myeloid cells in peripheral blood. This rescue of hematopoietic aging coincides with reduced mitochondrial metabolism and glycolysis in Igf2bp2-/- HSCs compared to Igf2bp2+/+ HSCs. Conversely, Igf2bp2 overexpression activates protein synthesis pathways in HSCs and leads to a rapid loss of self renewal by enhancing myeloid skewed differentiation in an mTOR/PI3K-dependent manner. Together, these results show that Igf2bp2 regulates energy metabolism and growth signaling in HSCs and that the activity of this pathways influences self renewal, differentiation, and aging of HSCs.

2024-05-21 | PXD018535 | Pride

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