Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional Signature and Memory Retention of Human-induced Pluripotent Stem Cells

ABSTRACT: Transient expression of two factors, or from Oct4 alone, resulted in efficient generation of human iPSCs. The reprogramming strategy described revealed a potential transcriptional signature for human iPSCs yet retaining the gene expression of donor cells in human reprogrammed cells free of viral and transgene interference. Genetic reprogramming of somatic cells to a pluripotent state (induced pluripotent stem cells or iPSCs) by over-expression of specific genes has been accomplished using mouse and human cells. However, it is still unclear how similar human iPSCs are to human Embryonic Stem Cells (hESCs). Here, we describe the transcriptional profile of human iPSCs generated without viral vectors or genomic insertions, revealing that these cells are in general similar to hESCs but with significant differences. For the generation of human iPSCs without viral vectors or genomic insertions, pluripotent factors Oct4 and Nanog were cloned in episomal vectors and transfected into human fetal neural progenitor cells. The transient expression of these two factors, or from Oct4 alone, resulted in efficient generation of human iPSCs. The reprogramming strategy described here revealed a potential transcriptional signature for human iPSCs yet retaining the gene expression of donor cells in human reprogrammed cells free of viral and transgene interference. Moreover, the episomal reprogramming strategy represents a safe way to generate human iPSCs for clinical purposes and basic research.

ORGANISM(S): Homo sapiens

PROVIDER: GSE18618 | GEO | 2009/10/20

SECONDARY ACCESSION(S): PRJNA121451

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcription profiling of human induced pluripotent stem cells signature and memory retention

Project description:Transient expression of two factors, or from Oct4 alone, resulted in efficient generation of human iPSCs. The reprogramming strategy described revealed a potential transcriptional signature for human iPSCs yet retaining the gene expression of donor cells in human reprogrammed cells free of viral and transgene interference. Genetic reprogramming of somatic cells to a pluripotent state (induced pluripotent stem cells or iPSCs) by over-expression of specific genes has been accomplished using mouse and human cells. However, it is still unclear how similar human iPSCs are to human Embryonic Stem Cells (hESCs). Here, we describe the transcriptional profile of human iPSCs generated without viral vectors or genomic insertions, revealing that these cells are in general similar to hESCs but with significant differences. For the generation of human iPSCs without viral vectors or genomic insertions, pluripotent factors Oct4 and Nanog were cloned in episomal vectors and transfected into human fetal neural progenitor cells. The transient expression of these two factors, or from Oct4 alone, resulted in efficient generation of human iPSCs. The reprogramming strategy described here revealed a potential transcriptional signature for human iPSCs yet retaining the gene expression of donor cells in human reprogrammed cells free of viral and transgene interference. Moreover, the episomal reprogramming strategy represents a safe way to generate human iPSCs for clinical purposes and basic research. Experiment Overall Design: Gene expression profiles measured using human genome Affymetrix Gene Chip arrays were grouped by hierarchical clustering, and correlation coefficients were computed for all pair-wise comparisons

2009-12-19 | E-GEOD-18618 | biostudies-arrayexpress

Establishing and improving retroviral episome transfer of transcription factors to achieve cell fate conversion and reprogramming

Project description:Gene transfer of distinct cocktails of transcription factors enables the targeted modification of cell fate. Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) via ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc allows creation of pluripotent cells with the potential to differentiate into any cell type of the body. To achieve a high degree of biosafety for future application of converted cells, technologies are required to express the required transcription factors without affecting the target cell genome. Retroviral vectors are widely employed gene transfer vehicles and can be converted into transient gene delivery vehicles by mutation of the viral integrase, thus avoiding risks associated with retroviral integration. We improved the retroviral episome transfer system by identifying the most suitable vector architecture, by enhancing episomal expression and by tuning the activity of the transcription factor Oct4. Repeated episomal transductions allowed establishment of stable, fully reversible expression levels over time. Providing proof-of-principle in the reprogramming context, we were able to generate human iPSCs following retroviral episomal transfer of Oct4 in fibroblasts stably expressing Klf4, Sox2 and c-Myc, with a high percentage of clones not carrying residually integrated vector copies. RNA obtained from human embryonic stem cells, fibroblasts and induced pluripotent stem cell lines reprogrammed with the mentioned reprogramming protocol

2015-05-06 | E-GEOD-57378 | biostudies-arrayexpress

Establishing and improving retroviral episome transfer of transcription factors to achieve cell fate conversion and reprogramming

2015-05-06 | GSE57378 | GEO

Influence of ATM-mediated DNA damage response on genomic variation in human induced pluripotent stem cells (Affymetrix CNV)

Project description:Genome instability is a potential limitation to the research and therapeutic application of induced pluripotent stem cells (iPSCs). Observed genomic variations reflect the combined activities of DNA damage, cellular DNA damage response (DDR), and selection pressure in culture. To understand the contribution of DDR on the distribution of copy number variations (CNVs) in iPSCs, we mapped CNVs of iPSCs with mutations in the central DDR gene ATM onto genome organization landscapes defined by genome-wide replication timing profiles. We show that following reprogramming the early and late replicating genome is differentially affected by CNVs in ATM deficient iPSCs relative to wild type iPSCs. Specifically, the early replicating regions had increased CNV losses during retroviral reprogramming. This differential CNV distribution was not present after later passage or after episomal reprogramming. Comparison of different reprogramming methods in the setting of defective DNA damage response reveals unique vulnerability of early replicating open chromatin to retroviral vectors. We isolated genomic DNA from Ataxia-telangiectasia (A-T) iPSC cells derived from patient fibroblasts virus and episomal vectors, coresponding fibroblasts, normal human fibroblast derived iPSCcells, for hybridization to the Affymetrix Genome-Wide Human SNP 6.0 Array.

2016-03-29 | E-GEOD-78715 | biostudies-arrayexpress

Transcription profiling of human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (super series)

Project description:Human induced pluripotent stem (iPS) cells have previously been derived from somatic cells using viral vectors that integrate transgenes into the genome. Genomic integration, however, can allow persistent leaky expression of the transgenes and can create insertional mutations, thus limiting the utility of these cells for both research and clinical applications. Here, we describe the derivation of human iPS cells free of vector and transgene sequences using non-integrating oriP/EBNA1-based episomal vectors. The resulting iPS cells are similar to human embryonic stem (ES) cells in both proliferative and developmental potential. These results demonstrate that reprogramming of human somatic cells does not require genomic integration or the continued presence of exogenous reprogramming factors, and removes one important obstacle to the clinical applications of these cells. This SuperSeries is composed of the following subset Series:; GSE15175: Human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (fig 1.c); GSE15176: Human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (fig 4.a) Experiment Overall Design: Total 21 samples were analyzed to confirm the similarity of human iPS cells derived with episomal vectors with human ES cells, and a dissimilarity with fibroblasts. Experiment Overall Design: Refer to individual Series

2009-04-04 | E-GEOD-15148 | biostudies-arrayexpress

Transcription profiling of Transgene-Free Induced Pluripotent Stem Cells from Normal and Neoplastic Bone Marrow and Cord Blood Mononuclear Cells .

Project description:global gene expression were compared among human blood iPSC, human fibroblas iPSC, human embryonic stem cells, human bone marrow MNC and human forskin fibroblast Reprogramming blood cells to induced pluripotent stem cells (iPSCs) provides a novel tool for modeling blood diseases in vitro. we demonstrated that iPSCs free of transgene and vector sequences could be efficiently generated from human bone marrow and cord blood mononuclear cells using non-integrating episomal vectors. The reprogramming described here is up to 100 times more efficient, occurs 1 to 3 weeks faster as compared to the reprogramming of fibroblasts, and does not require isolation of progenitors or multiple rounds of transfection. This approach provides an opportunity to explore banked normal and diseased cord blood and bone marrow samples without the limitations associated with virus-based methods. Compare the global gene expression of iPSs from different sources, ESCs and Somatic cells

2011-02-04 | E-GEOD-26672 | biostudies-arrayexpress

Excluding Oct4 from Yamanaka cocktail unleashes the developmental potential of iPSCs

Project description:Oct4 is widely considered the most important among the four Yamanaka reprogramming factors. Here we show that the combination of Sox2, Klf4, and cMyc (SKM) suffices for reprogramming mouse somatic cells to induced pluripotent stem cells (iPSCs). Simultaneous induction of Sox2 and cMyc in fibroblasts triggers immediate retroviral silencing, which explains the discrepancy with previous studies that attempted but failed to generate iPSCs without Oct4 using retroviral vectors. SKM induction could partially activate the pluripotency network even in Oct4-knockout fibroblasts. Importantly, reprogramming in the absence of exogenous Oct4 results in greatly improved developmental potential of iPSCs, determined by their ability to give rise to all-iPSC mice in the tetraploid complementation assay. Our data suggest that overexpression of Oct4 during reprogramming leads to off-target gene activation during reprogramming and epigenetic aberrations in resulting iPSCs, and thereby bear major implications for further development and application of iPSC technology.

2019-11-06 | GSE137001 | GEO

Efficient Generation of Transgene-Free Induced Pluripotent Stem Cells from Normal and Neoplastic Bone Marrow and Cord Blood Mononuclear Cells

2011-02-04 | GSE26672 | GEO

Transcription profiling of human induced pluripotent stem cells free of exogenous DNA derived with episomal vectors

2009-04-04 | E-GEOD-15176 | biostudies-arrayexpress

Transcription profiling of human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (fig 1.c)

2009-04-04 | E-GEOD-15175 | biostudies-arrayexpress