Single cell transcriptomics of hiPSC-derived forward programmed megakaryocytes
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ABSTRACT:
PROVIDER: PRJNA497828 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Microarray gene expression data is used to compare the transcriptomics of hiPSC, hiPSC derived forward programmed-, hiPSC derived directed differentiated- megakaryoctes AND cord- blood derived megakaryocytes
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Project description:We have published a novel method for the large-scale in vitro generation of megakaryocytes (MKs), the blood platelet precursors, by applying a transcription factor (TF) driven forward programming strategy to human pluripotent stem cells (hPSCs). We have demonstrated that the concurrent expression of GATA1, FLI1 and TAL1 in hPSCs and chemically defined culture conditions with minimal supportive cytokines produce highly pure MK cultures with long-term growth and release of functional platelets. Unravelling the molecular mechanisms underlying MK forward programming will bring biological insights that shall lead to improvements of the MK programming technology. Particularly, we have been focusing on the characterisation of the MK progenitor that allows long-term expansion of pure MK cultures, which is a key asset of the method. Using single cell RNA sequencing of long-term cultures, we have started to identify and functionally confirmed surface markers of the MK progenitor.
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Project description:This dataset consists of single-cell RNA-seq (Smart-seq2) data from 95 forward programmed cells derived from human induced pluripotent stem cells (hiPSCs). Cells conditionally expressing either ATOH1, ETV2 or NKX3-1 under the control of a tetracycline-response element (Tet-ON system) were co-cultured on Matrigel in 2 dimensions. Data was used to explore the forward-programming potential of these transcription factors (TFs) when cell lines with the capacity to differentiate in isolation are cultured together.
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Project description:Megakaryocytes are bone marrow (BM) resident cells that derive from hematopoietic stem cells. A pivotal function of megakaryocytes is the generation of platelets through the release of long protrusions called proplatelets into sinusoidal vessels. single-cell RNA-sequencing on murine BM megakaryocytes has previously revealed transcriptional heterogeneity with segmentation into four distinct categories. These studies postulated functions beyond platelet production with evidence for immunoregulatory and stem cell niche supporting subtypes, as well as a cycling population. The spatial context and transcriptional heterogeneity of megakaryocytes is of great interest as localization of for instance the vasculature is a necessity for platelet production. For single-cell RNA sequencing this spatial orientation is however lost due to the dissociation of tissues. Recent technological advances have enabled the interrogation of gene expression profiles of tissues in situ. This enables the integration of morphological, situational and transcriptional information to classify cells in the context of their microenvironment. In the following we present, for the first time, the application of this technology to BM megakaryocytes at a single cell level.
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Project description:The purpose of this experiment was to compare the transcriptome of FoP-Heps, with undifferentiated hiPSCs, HLCs generated by direct differentiation, and primary samples (adult and fetal). FoP-Heps where generated in vitro from hESCs by forward programming (FoP) using a combination of 4 transcription factors (HNF1A, FOXA3, HNF6, RORc). Human fetal liver samples where obtained from first trimester embryos.
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Project description:Adult and fetal megakaryocytes are morphologically different. These differences contribute to neonatal thrombocytopenia in premature neonates and in neonates after infection and also contribute to poor megakaryocytes engraftment after umbilical cord blood transplant. We found that Dyrk1a kinase inhibition shift the fetal megakaryocytes phenotype toward adult phenotype. This effect is mediated by MKL1 the master regulator of megakaryocytes morphogenesis. To identify differences between adult and fetal megakaryocytes we performed RNA seq of adult derived megakaryocytes and fetal derived megakaryocytes treated and untreated with Dyrk inhibitors. Through this approach we identified cohorts of genes co-regulated in adult megakaryocytes and fetal megakaryocytes treated with the dyrk inhibitors. More importantly, we found that the dyrk inhibition in fetal megakaryocytes leads to upregulation of a significant number of MKL1 target genes.
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Project description:Adult and fetal megakaryocytes are morphologically different. These differences contribute to neonatal thrombocytopenia in premature neonates and in neonates after infection and also contribute to poor megakaryocytes engrafment after umbilical cord blood transplant. We found that Dyrk1a kinase inhibition shift the fetal megakaryocytes phenotype toward adult phenotype. This effect is mediated by MKL1 the master regulator of megakaryocytes morphogenesis. To identify deferences between adult and fetal megakaryocytes we performed RNA seq of adult derived megakaryocytes and fetal derived megakaryocytes treated and untreated with Dyrk inhibitors. Through this approach we identified cohorts of genes co-regulated in adult megakaryocytes and fetal megakaryoctes treated with the dyrk inhibitors. More importantly, we found that the dyrk inhibition in fetal megakaryocytes leads to upregulation of a significant number of MKL1 target genes.
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