Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA115459 | ENA |
REPOSITORIES: ENA
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Project description:Emergence of induced pluripotent stem cells (iPSC) technology has paved novel routes for regenerative medicine. iPSCs offer the possibilities of disease modeling, drug toxicity studies as well as cell replacement therapies by autologous transplantation. Classical protocols of iPSC generation harness infection by retro- or lenti-viruses. Although such integrating viruses represent very robust tools for reprogramming, the presence of viral transgenes in iPSCs is deleterious as it holds the risk of insertional mutagenesis leading to malignant transformation. Moreover, remaining reprogramming transgenes have been shown to affect the differentiation potential of iPSCs. More recently, alternative protocols have been explored to derive transgene-free iPSC, including use of transposons, mRNA transfection, episomal plasmid transfection, and infection with non-integrating viruses such as Sendai virus. However, the utility of such protocols remains limited due to low efficiency and narrow range of cell specificity. In this study we aim at combining the robustness of lentiviral reprogramming with the high efficacy of Cre recombinase protein transduction to readily delete reprogramming transgenes from iPSCs. We demonstrate rapid generation of transgene-free human iPSCs by excising the loxP-flanked reprogramming cassette employing direct delivery of biologically active Cre protein. By genome-wide analysis and targeted differentiation towards the cardiomyocyte lineage, we show that transgene-free iPSCs do resemble more to human ESCs and has better differentiation potential than iPSCs before Cre transduction. Our study provides a simple, rapid and robust protocol for the generation of superior transgene-free iPSCs suitable for disease modeling, tissue engineering and cell replacement therapies. mRNA extracted from human Fibroblasts (AR1034ZIMA), human Embryonic Stem Cell line I3 (hES I3), three human induced Pluripotent Stem Cell clones 1, 1.2 and 1.4 (fl-ARiPS cl1, del-ARiPS cl 1.2, del-ARiPS cl1.4) has been hybridized on Illumina Human HT-12 (version 4 revision 2) arrays for genome wide expression analysis. Samples were run at least as duplicate technical replicates. Differential gene expression analysis has been performed on the grouped expression data with the human embryonic stem cells (hES I3) group as the reference.
2014-03-11 | E-GEOD-55725 | biostudies-arrayexpress
Project description:Induced pluripotent stem (iPS) cells can be generated from somatic cells by transduction with several transcription factors in both mouse and human. However, direct reprogramming in other species has not been reported. Here, we established an efficient method to generate monkey iPS cells from fibroblasts by retrovirus-mediated introduction of the four monkey transcription factors OCT4 (POU5F1), SOX2, KLF4, and c-MYC. The monkey iPS cells displayed ES-like morphology, expressed ES cell-marker genes, shared similar global gene profiles and methylation status in the OCT4 promoter to those of monkey ES cells, and possessed the ability to differentiate into three germ layers in vitro and in vivo. Our results suggest that the mechanism of direct reprogramming is conserved among species. The efficient generation of monkey iPS cells will allow investigation of the feasibility of therapeutic cloning in primate model with various diseases. Keywords: Induced pluripotent stem, iPS, Rhesus monkey We analysed each sample (Rhesus monkey fibroblast, embryonic stem cell (ES) and induced pluripotent stem cell (iPS)) for three replications and sought to see high similarty between iPS and ES.
2010-05-15 | E-GEOD-13146 | biostudies-arrayexpress
Project description:Direct generation of induced pluripotent stem cells from human non-mobilized blood
| PRJNA124339 | ENA
Project description:Generation of Induced Pluripotent Stem Cells using Recombinant Proteins
| PRJNA115481 | ENA
Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis
2018-08-02 | MSV000082680 | GNPS
Project description:Pluripotent cells are important and unique because of unprecedently high proliferation and differentiation potentials. The state of pluripotency is robust enough to sustain years of uninterrupted proliferation in vitro, but, once lost, there is a significant barrier for differentiated cells to regain pluripotency. By now, reprogramming of somatic cells into a pluripotent state is unambiguously proven only for methods that necessarily involve ectopic expression or direct delivery of exogenous factors inside the cells. Molecular mechanisms that provide robustness to the state of pluripotency and sustain the barrier between pluripotent and differentiated cells are not fully understood. We reprogrammed human foreskin fibroblasts into human induced pluripotent stem cells using CoMiP 4in1 plasmid without shRNA p53.
2019-08-06 | GSE135409 | GEO
Project description:Reprogramming of somatic cells to pluripotency, thereby creating induced pluripotent stem (iPS) cells, promises to boost cellular therapy. Most instances of direct reprogramming have been achieved by forced expression of defined exogenous factors using multiple viral vectors. The most used four transcription factors, OCT4, SOX2, KLF4 and C-MYC, can induce pluripotency in mouse and human fibroblasts. Here we report that a forced expression of a new combination of transcription factors (TCL-1A, C-MYC and SOX2) is sufficient to promote the reprogramming of human fibroblast into pluripotent cells. These three-factor pluripotent cells are similar to human embryonic stem cells (hESC) in morphology, in the ability to differentiate into cells of the three embryonic layers, and at the level of global gene expression. Induced pluripotent human cells generated by combination of other factors will be of great help for the understanding of reprogramming pathways. This in turn will allow us to better control cell-fate and apply this knowledge to cell therapy.
2010-10-26 | E-MEXP-2422 | biostudies-arrayexpress
Project description:We recently showed that some human induced pluripotent stem cell (iPSC) clones were defective in neural differentiation and were marked with the activation of long term repeats (LTRs) of human endogenous retroviruses (HERVs). We herein demonstrated that these LTRs were transiently overexpressed during the generation of iPSCs and contributed to reprogramming. When the generation of iPSCs was completed, LTRs were re-suppressed to levels similar to those in human ES cells. However, differentiation-defective iPSC clones maintained high LTR expression levels, which indicated that these clones failed to complete reprogramming. lincRNA-RoR, a long intergenic non-coding RNA (lincRNA) that was previously shown to support the induction and maintenance of pluripotency, was detected among the LTR-driven transcripts. Short hairpin RNAs against the conserved sequence in LTRs or lincRNA-RoR markedly reduced the efficiency of iPSC generation. Reprogramming factors including OCT3/4, SOX2, and KLF4 bound to most LTRs. The expression of KLF4 was low in normal iPSC clones, but remained high in differentiation-defective clones. The forced expression of KLF4 in human embryonic stem cells led to the activation of LTRs and defects in neural differentiation. These results demonstrated that the transient overexpression of KLF4/LTR/lincRNA-RoR played crucial roles in reprogramming toward pluripotency in humans, whereas a failure in its re-silence resulted in differentiation defects. Four human induced pluripotent stem cell lines were subcloned into 55 separate lines. Bisulfite converted genomic DNA lysates from fibroblast, induced pluripotent stem cell, intermediate reprogrammed cell and embryonic stem cell lines were hybridized to Illumina HumanMethylation450 BeadChip.
2014-08-04 | E-GEOD-54848 | biostudies-arrayexpress
Project description:Cell fate transitions involve rapid changes of gene expression patterns and global chromatin remodeling, yet the underlying regulatory pathways remain incompletely understood. Here, we used transcription-factor induced reprogramming of somatic cells into pluripotent cells to screen for novel regulators of cell fate change. We identified the RNA processing factor Nudt21, a component of the pre-mRNA cleavage and polyadenylation complex, as a potent barrier to reprogramming. Importantly, suppression of Nudt21 not only enhanced the generation of induced pluripotent stem cells but also facilitated the conversion of fibroblasts into trophoblast stem cells and delayed the differentiation of myeloid precursor cells into macrophages, suggesting a broader role for Nudt21 in restricting cell fate change. Polyadenylation site sequencing (PAS-seq) revealed that Nudt21 directs differential polyadenylation of over 1,500 transcripts in cells acquiring pluripotency. While only a fraction of these transcripts changed expression at the protein level, this fraction was strongly enriched for chromatin regulators, including components of the PAF, polycomb, and trithorax complexes. Co-suppression analysis further suggests that these chromatin factors are largely responsible for Nudt21’s effect on reprogramming, providing a mechanistic basis for our observations. Collectively, our data uncover Nudt21 as a novel post-transcriptional regulator of mammalian cell fate and establish a direct, previously unappreciated link between alternative polyadenylation and chromatin signaling.
2018-01-08 | PXD008078 | Pride
Project description:We report that the efficiency of reprogramming human somatic cells to induced pluripotent stem cells (hiPSCs) can be dramatically improved in a microfluidic environment. Microliter-volume confinement resulted in a 50-fold increase in efficiency over traditional reprogramming by delivery of synthetic mRNAs encoding transcription factors. In these small volumes, extracellular components of the TGF-β and other signaling pathways exhibited temporal regulation that appears critical to acquisition of pluripotency. The high quality and purity of the resulting hiPSCs (μ-hiPSCs) allowed direct differentiation into functional hepatocyte- and cardiomyocyte-like cells in the same platform without additional expansion.
2016-04-10 | GSE59534 | GEO