MiRNA expression data from multilineage differentiation of hiPSC
Ontology highlight
ABSTRACT:
ORGANISM(S): synthetic construct Homo sapiens
PROVIDER: GSE97952 | GEO | 2018/06/18
REPOSITORIES: GEO
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Project description:Pluripotent stem cell (PSC)-derived organoids are emerging as novel human-based microphysiological models but display immature phenotypes with limited subsets of endothelial or stromal cells. Here we demonstrate that in vitro manipulation of gene regulatory networks (GRNs) in PSC-derived liver organoids selected either through computational analysis or targeted tissue design can advance tissue maturation in vitro. Through an unbiased comparison with the genetic signature of mature livers, we identify downregulated GRNs in fetal liver organoids compared to adult livers. We demonstrate that overexpression of PROX1 and ATF5, together with targeted CRISPR-based transcriptional activation of endogenous CYP3A4, drives maturation in vitro. Single cell analyses reveal hepatobiliary-, endothelial-, and stellate-like cell populations. The engineered organoids demonstrate enhanced vasculogenesis, capture native liver characteristics (e.g. FXR signaling, CYP3A4 activity), and exhibit therapeutic potential in mice. Collectively, our approach provides a genetically guided framework for engineering developmentally advanced multilineage tissues from hiPSCs.
2020-12-07 | GSE159491 | GEO
Project description:RNA-seq of Multilineage differentiating stress-enduring enriched cells (MECs) derived from MenSCs
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Project description:The production of hematopoietic stem cells (HSCs) from induced pluripotent stem cells (iPSCs) would have significant implications for medicine and biotechnology. We differentiated iPSCs to blood cells resembling the first repopulating HSCs of the human embryo. In immune deficient mice transplanted with iPSC-derived CD34+ cells, long term, low level bone marrow engraftment was seen in most animals. Although many animals were engrafted by myeloid, or myeloid and B lymphoid restricted progeny, 18% of mice receiving cells exposed to retinoids at day 3 of differentiation developed multilineage erythroid, myeloid and lymphoid cell engraftment (MLE), reflecting in vitro generation of HSCs or MPPs (termed iPSC-derived (i)HSCs). In a second cohort of mice, we observed in 36% of animals transplanted with cells receiving retinoids throughout differentiation. These studies identify conditions that yield engrafting iHSCs differentiated from human iPSCs and provide a foundation for the generation of cells for clinical translation.
2024-08-03 | GSE232710 | GEO
Project description:Pluripotent stem cells provide a scalable approach to analyse molecular regulation of cell differentiation across multiple any developmental lineage trajectories. In this study, we engineered barcoded iPSCs to generate an atlas of multilineage differentiation from pluripotency, encompassing a time-course of WNT-induced differentiation perturbed using modulators of WNT, BMP, and VEGF signalling. Computational mapping of in vitro cell types to in vivo developmental lineages revealed a diversity of iPSC-derived cell types comprising mesendoderm lineage cell types including lateral plate and paraxial mesoderm, neural crest, and primitive gut. Coupling this atlas of in vitro differentiation with Summary data-based Mendelian Randomisation analysis of human complex traits, we identify the WNT-inhibitor protein TMEM88 as a putative regulator of mesendodermal cell types governing development of diverse cardiovascular and anthropometric traits. Using genetic loss of function models, we show that TMEM88 is required for differentiation of diverse endoderm and mesoderm cell lineages in vitro and that TMEM88 knockout in vivo results in a significant dysregulation of arterial blood pressure. This study provides an atlas of multilineage iPSC differentiation coupled with new molecular, computational, and statistical genetic tools to dissect genetic determinants of mammalian developmental physiology.
2024-12-05 | GSE279710 | GEO
Project description:Embryonic development commences with the formation of three germ layers from the primitive streak during gastrulation. The endoderm layer gives rise to the gut tube, leading to development of several internal organs, including the thyroid, thymus, lungs, stomach, liver, pancreas, and intestines. We differentiated human induced pluripotent stem cells (hiPSCs) to embryonic endoderm and sought to identify a tipping point at which the developing system did not recover from perturbations caused by exposure to a known teratogen, all-trans retinoic acid (ATRA). Differentiating iPSC-derived endoderm was exposed to five concentrations of ATRA between 0.001 and 10 µM at 6h, 96h, or 192h and assessed for forkhead box A2 (FOXA2) protein expression and global gene transcript expression measured by RNA-sequencing. A tipping point of 17±11 nM was identified where patterns of differentially expressed genes supported a shift in the developmental trajectory away from embryonic endoderm in favor of mesoderm and extraembryonic endoderm.
2019-10-31 | GSE131921 | GEO
Project description:To gain insight into the molecular regulation of human heart development, a detailed comparison of the mRNA and miRNA transcriptomes across differentiating human-induced pluripotent stem cell (hiPSC)–derived cardiomyocytes and biopsies from fetal, adult, and hypertensive human hearts was performed. Gene ontology analysis of the mRNA expression levels of the hiPSCs differentiating into cardiomyocytes revealed 3 distinct groups of genes: pluripotent specific, transitional cardiac specification, and mature cardiomyocyte specific. Hierarchical clustering of the mRNA data revealed that the transcriptome of hiPSC cardiomyocytes largely stabilizes 20 days after initiation of differentiation. Nevertheless, analysis of cells continuously cultured for 120 days indicated that the cardiomyocytes continued to mature toward a more adult-like gene expression pattern. Analysis of cardiomyocyte-specific miRNAs (miR-1, miR-133a/b, and miR-208a/b) revealed a miRNA pattern indicative of stem cell to cardiomyocyte specification. A biostatistitical approach integrated the miRNA and mRNA expression profiles revealing a cardiomyocyte differentiation miRNA network and identified putative mRNAs targeted by multiple miRNAs. Together, these data reveal the miRNA network in human heart development and support the notion that overlapping miRNA networks re-enforce transcriptional control during developmental specification. miRNA expression profiling of differentiating human-induced pluripotent stem cell (hiPSC)–derived cardiomyocytes (days 0-120)
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Project description:This SuperSeries is composed of the following subset Series: GSE35671: Comparison of mRNA expression profiling of differentiating human-induced pluripotent stem cell (hiPSC)–derived cardiomyocytes, biopsies from fetal, adult and hypertensive human hearts and primary cardiomyocytes GSE35672: miRNA expression profiling of differentiating human-induced pluripotent stem cell (hiPSC)-derived cardiomyocytes Refer to individual Series
2012-02-10 | E-GEOD-35673 | biostudies-arrayexpress
Project description:The increasing interest in multilineage differentiating stress-enduring (Muse) cells within the field of regenerative medicine is attributed to their exceptional homing capabilities, prolonged viability in adverse conditions, and enhanced three-germ-layer differentiate ability, surpassing their parent mesenchymal stem cells. Given their abundant sources, non-invasive collection procedure, and periodic availability, human menstrual blood-derived endometrium stem cells (MenSCs) have been extensively investigated as a potential resource for stem cell-based therapies. However, there is no established modality to isolate Muse cells from MenSCs and disparity in gene expression profiles between Muse cells and MenSCs remain unknown. In this study, Muse cells were isolated from MenSCs by long-time trypsin incubation method. Muse cells expressed pluripotency markers and could realize trilineage differentiation in vitro. Compared with MenSCs, Muse cells showed enhanced homing ability and superior therapeutic efficacy in animal models of acute liver injury (ALI) and intracerebral hemorrhage (ICH). Furthermore, the RNA-seq analysis offers insights into the mechanism underlying the disparity in trypsin resistance and migration ability between Muse and MenSCs cells. This research offers a significant foundation for further exploration of cell-based therapies using MenSCs-derived Muse cells in the context of various human diseases, highlighting their promising application in the field of regenerative medicine.
2024-01-01 | GSE247588 | GEO
Project description:Mesenchymal Stem/Stromal Cells (MSC) obtained from Pluripotent Stem Cells (PSC) constitute an interesting alternative to classical MSC in regenerative medicine. Amongst one of their many mechanism of action, MSC extracellular vesicles (EVs) raise as a suitable substitution of MSC in future cell-free based therapeutics approaches. EVs, unlike cells, do not elicit acute immune rejection and can be produced in large quantities and stored ready to use, until needed. Though therapeutic potential of MSC-EVs had already been proved, thorough characterization of them is still scarce. In this work we performed a label-free Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) proteomic approach to identify the most abundant proteins in EVs secreted from MSC derived from PSC (PD-MSC) and from their parental iPSC. Next, we compared both datasets finding that while iPSC EVs enclose proteins that modulates RNA and miRNA stability and protein sorting, PD-MSC EVs are rich in proteins that organize extracellular matrix, regulate locomotion and influence cell-substrate adhesion. Moreover, when compared to their respective cells, iPSC and iPSC EVs share a greater proportion of proteins while PD-MSC proteome seems to be more specific. Correlation and Principal Component Analysis consistently aggregate iPSC and iPSC EVs but segregate PD-MSC and their EVs. Altogether these findings suggest that during differentiation, PD-MSC EVs acquire a more specific set of proteins than their parental iPSC�s EVs have and that, arguably, this might confer them their therapeutic properties.
2018-01-13 | MSV000081933 | MassIVE
Project description:Single-cell RNA-sequencing was used to characterize the cellular diversity of dissociated cells from day 100 multilineage and gut organoids.
2021-06-15 | GSE153075 | GEO