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Induction of Ground-State Pluripotency by Minimal Factor Episomal-Expression in Single Cell Format

ABSTRACT: Human pluripotent stem cells in culture are often associated with the prime state which represents a more developed state relative to the naïve state which is often associated with the inner cell mass and thought to have the potential to give rise to all cell types. We have developed a small molecule-driven cocktail FMM that maintains human pluripotent stem cells in a state similar to the naive state as defined by several properties including gene expression profile. We used global gene expression to compare and contrast induced pluripotent stem cells -- from various starting points -- cultured in either small molecule medium FMM or conventional medium. Somatic cells were induced to reprogram by various methods and maintained in various culture conditions. Each culture condition was analyzed by various methods including global gene expression.

ORGANISM(S): Homo sapiens

SUBMITTER: Dave Robbins

PROVIDER: E-GEOD-50868 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Induction of Ground-State Pluripotency by Minimal Factor Episomal-Expression in Single Cell Format

Project description:Human pluripotent stem cells in culture are often associated with the prime state which represents a more developed state relative to the naïve state which is often associated with the inner cell mass and thought to have the potential to give rise to all cell types. We have developed a small molecule-driven cocktail FMM that maintains human pluripotent stem cells in a state similar to the naive state as defined by several properties including gene expression profile. We used global gene expression to compare and contrast induced pluripotent stem cells -- from various starting points -- cultured in either small molecule medium FMM or conventional medium.

2014-03-03 | GSE50868 | GEO

Transcription profiling by array of human hepatic cells derived from foreskin fibroblast cell line and from embryonic stem cells.

Project description:Reprogrammed somatic cells offer a valuable source of pluripotent cells that have the potential to differentiate into many cells types and provide a new tool for regenerative medicine. In the present study we differentiated induced pluripotent stem cells (iPS cells) into hepatic cells. We first showed that mouse iPS cells could from a complete liver in mouse embryo (E14.5) including hepatocytes, endothelial cells, sinusoidal cells and resident macrophages. We then designed a highly efficient hepatocyte differentiation protocol using defined factors on human embryonic stem cells (ES cells). This protocol was found to generate more than 80% albumin expressing cells that show hepatic functions and express most of liver genes as shown by microarray analyses. Similar results were obtained when human iPS cells were induced to differentiate following the same procedure. Experiment Overall Design: Total RNA was harvested from the following sources and used for Affymetrix array analysis following manufacturer defined protocols: Experiment Overall Design: 1) human foreskin fibroblasts, ATCC cell line CRL2097, 3 independent cultures Experiment Overall Design: 2) induced pluripotent stem (iPS) cells derived from CRL2097, 3 independent undifferentiated cultures Experiment Overall Design: 3) induced pluripotent stem (iPS) cells derived from CRL2097, 3 independent cultures harvested at day 20 (d20) of a hepatic differentiation protocol Experiment Overall Design: 4) WAO9 human embryonic stem cells, 3 independent undifferentiated cultures Experiment Overall Design: 5) WAO9 human embryonic stem cells, 3 independent cultures harvested at day 20 (d20) of a hepatic differentiation protocol. <br><br>This experiment was reloaded in November 2010 after additional curation

2009-08-07 | E-GEOD-14897 | biostudies-arrayexpress

Induction of pluripotency in human somatic cells via a primitive streak-like state

Project description:During mammalian embryonic development, the primitive streak is initiates the differentiation of pluripotent epiblast cells into germ layers. Pluripotency can be reacquired in committed somatic cells using a combination of handful transcription factors, such as OCT3/4, SOX2, KLF4 and c-MYC (hereafter referred to as OSKM), albeit with low efficiency . Here we show that, during the OSKM-induced reprogramming process toward pluripotency in human cells, intermediate cells transiently show gene expression profiles resembling mesendoderm, which is a major component of the primitive streak. Based on these findings, we discover that forkhead box H1 (FOXH1), a transcription factor required for anterior primitive streak specification during early development, significantly enhances the reprogramming efficiency of human fibroblasts by promoting their maturation, including the mesenchymal to epithelial transition and the activation of late pluripotent markers. These results demonstrate that during the reprogramming process, human somatic cells go through a transient state that resembles mesendoderm. Human differentiated progeny derived from pluripotent stem cells, N=13 Human undifferentiated pluripotent stem cells, N=6 Transgenic ESC line, N=6 Human tissues, N=29 Human tissue-derived cells, N=20 Human nascent reprogrammed cells, N=95 Mouse cells, N=12

2014-04-24 | E-GEOD-50206 | biostudies-arrayexpress

DNA methylome analysis of human pluripotent stem cells reprogrammed with CRISPRa

Project description:Comparison of DNA methylation in CRISPRa induced human pluripotent stem cell lines, control iPSC line induced with Sendai viral vectors, H9 embryonic stem cell line and human foreskin fibroblasts.

2018-06-07 | E-MTAB-6194 | biostudies-arrayexpress

STRT RNAseq of pluripotent stem cells reprogrammed with CRISPRa

Project description:Transcriptome comparison of CRISPRa induced human pluripotent stem cell lines, control iPSC line induced with Sendai viral vectors, H9 embryonic stem cell line and human foreskin fibroblasts.

2018-06-07 | E-MTAB-6185 | biostudies-arrayexpress

Expression data from human pluripotent stem cells and differentiated cells treated with pluripotent-specific inhibitors

Project description:The use of human pluripotent stem cells (hPSCs) in cell therapy is hindered by the tumorigenic risk from residual undifferentiated cells. Here we performed a high-throughput screen of over 52,000 small molecules, and identified 15 highly selective cytotoxic inhibitors of hPSCs (PluriSIns). Cellular and molecular analyses revealed that the most selective compound, PluriSIn #1, is a pluripotent-specific inhibitor of stearoyl-coA desaturase (SCD1), the key enzyme in the biosynthesis of monounsaturated fatty acids (MUFA). SCD1 inhibition in hPSCs induced ER stress, protein synthesis attenuation, and apoptosis of these cells, revealing that MUFA biosynthesis is crucial for their survival. PluriSIn #1 was also cytotoxic toward the ICM cells of mouse embryos, indicating that the dependence on SCD1 is inherent to the pluripotent state. Finally, application of PluriSIn #1 prevented teratoma formation from tumorigenic undifferentiated cells. Our novel method to eliminate undifferentiated cells from culture should thus increase the safety of hPSC-based treatments. Expression data from undifferentiated and differentiated human embryonic stem cells. Total RNA was isolated from undifferentiated human pluripotent stem cells grown on matrigel with mTeSR1 medium, or from early endodermal progenitor cells differentiated from human embryonic stem cells.

2013-01-22 | E-GEOD-37040 | biostudies-arrayexpress

Gene expression profiles of induced multipotent germline stem cells and other pluripotent stem cells

Project description:Spermatogonial stem cells (SSCs) have pluripotent potential. However, frequency of pluripotent cell derivation is low and the mechanism of culture-induced reprogramming remains unknown. Here we report that epigenetic instability of germline stem (GS) cells, cultured SSCs, induces pluripotent cell derivation. GS cells undergo DNA demethylation in H19 differentially methylated region under low-density culture. When H19 demethylation was induced by Dnmt1 depletion, they converted into embryonic stem (ES)-like cells. Dnmt1 depletion downregulated Dmrt1 expression, whose depletion also induced pluripotency. Functional screening of Dmrt1 target gene revealed that Dmrt1 depletion upregulates Sox2, the key molecule responsible for generating induced pluripotent stem cells. Although Sox2 transfection upregulated Oct4 and produced pluripotent cells, this conversion was inhibited by Oct1 overexpression, suggesting that the balance of Oct proteins maintains SSC identity. These results suggest that culture-induced reprogramming is caused by unstable DNA methylation, and that Dmrt1-Sox2 cascade is critical for regulating pluripotency in SSCs. Pluripotent stem-like cells were induced from GS cells by down-regulation of Dnmt/Dmrt, or up-regulation of Sox2/Oct4 in combination with p53 knock-down and their total RNA samples were subjected to microarray analysis to compare their gene expression profile with other pluripotent stem cells such as ES cells or iPS cells.

2013-10-21 | E-GEOD-43850 | biostudies-arrayexpress

Expression analysis in H9-hESCs to induce naive pluripotency

Project description:Human preimplantation embryo development involves complex dynamic cellular and molecular events that lead to the establishment of the three lineages of the blastocyst â the trophectoderm, primitive endoderm and epiblast. Owing to limited resources of biological specimens, our understanding of how the earliest lineage commitments are regulated is limited. Here, we examined role for MCRS1, TET1, and THAP11 in inducing naive pluripotency in human embryonic stem cells in vitro. Human embryonic stem cells (H9) were nucleofected with piggybac constructs that encode for three genes (MCRS1, THAP11, TET1) followed by neomycin selection for 2 weeks to ensure stable integration. Overexpression of genes can be induced by doxycycline (dox) administration to the culture medium. Prior to dox treatment cells were cultured in conventional feeder-free conditions and then transferred to a feeder layer. Culture medium was switched from mTeSR to W8. Administration of dox and media change into 2i/LIF (2 inhibitors against MEK and GSK3 pathway + leukemia inhibitory factor) induces the overexpression of piggybac constructs and over time transitions primed pluripotent hESCs into a naive pluripotent state. Both pluripotent states were examined with microarrays in three biological replicates for each condition. MCRS1 = microspherule protein 1; TET1 = tet methylcytosine dioxygenase 1; THAP11 = THAP domain containing 11

2016-08-31 | E-MTAB-4567 | biostudies-arrayexpress

Tesk1 iPSC Comparison

Project description:This experiment is to compared shTESK1 transduced induced pluripotent stem cells (iPSCs) with wild type embryonic stem cells (mES) and mouse embryonic fibroblasts (MEFs) in order to confirm that shTESK1 iPSCs are more close to ES-like state but not to their parental MEF cells. This ArrayExpress experiment includes data from two stable cell clones of shTESK1 transduced iPSCs. Microarray data for mES and MEFs have been archived in ArrayExpress under accession number E-MTAB-1188 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1188/).

2015-01-24 | E-MTAB-2258 | biostudies-arrayexpress

The impact of early WNT pathway inhibition (day 1 of differentiation) during human pluripotent stem cell differentiation towards cardiomyocytes

Project description:Human pluripotent stem cells were aggregated in mTeSR medium for 4 days and subjected to an optimzed small molecule-based cardiac differentiation protocol (modified from Kempf et. al., Stem Cell Reports, 2014) in agitated Erlenmeyer flasks. Differentiation was induced using 7.5µM CHIR99021 (day 0). Cardiac mesoderm specification was carried out using 5µM IWP2 either directly after CHIR99021 exposure after 24h (day 1; optimized protocol) or after 72h hours (day 3; standard procedure). RNA samples were harvested at undifferentiated state (day 0), after differentiation induction (day 1) and after 3 days with and without IWP2 treatment.

2019-01-13 | E-MTAB-6828 | biostudies-arrayexpress

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