DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE24676 | GEO | 2011/04/14
SECONDARY ACCESSION(S): PRJNA132363
REPOSITORIES: GEO
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Project description:We examined genome-wide DNA methylation with 22 human iPSC lines derived from different cell types and human ESC lines using Illumina’s Infinium HumanMethylation27 and focused on aberrant methylation sites in iPSCs for up to 42-week continuous cultivation. The iPSCs exhibited distinct epigenetic distances from ESCs at early passage. Continuous passaging of the iPSCs diminishes these differences between iPSCs and ESCs. Bisulphite converted DNA from the 47 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2
2011-04-14 | E-GEOD-24676 | biostudies-arrayexpress
Project description:Here, we determined the DNA methylation profiles of 12 human cell lines, including 2 ESC lines, 2 pESC lines,4 virally-delivered iPSC lines, 2 episomal-delivered iPSC lines, and 2 parent cell lines that iPSCs derived from using Illumina’s Infinium HumanMethylation450. The iPSCs exhibited a hypermethylation status similarly to ESCs but distinct differences from the parent cells. Genes of common methylation pattern between iPSCs and ESCs were regarded as critical factors for stemness, while differences existing between iPSCs and ESCs implied that iPSCs partly retained the parental characteristics and gained de novo methylation aberrances during cell reprogramming. No significant variant was identified between virally- and episomal- systems. De novo differentiated methylation regions as the signature of particular stem cell lines were figured out in detail in this study. 2 ESC lines, 2 pESC lines,4 virally-delivered iPSC lines, 2 episomal-delivered iPSC lines, and 2 parent cell lines that iPSCs derived from
2014-05-29 | E-GEOD-57992 | biostudies-arrayexpress
Project description:Here, we determined the DNA methylation profiles of 12 human cell lines, including 2 ESC lines, 2 pESC lines,4 virally-delivered iPSC lines, 2 episomal-delivered iPSC lines, and 2 parent cell lines that iPSCs derived from using Illumina’s Infinium HumanMethylation450. The iPSCs exhibited a hypermethylation status similarly to ESCs but distinct differences from the parent cells. Genes of common methylation pattern between iPSCs and ESCs were regarded as critical factors for stemness, while differences existing between iPSCs and ESCs implied that iPSCs partly retained the parental characteristics and gained de novo methylation aberrances during cell reprogramming. No significant variant was identified between virally- and episomal- systems. De novo differentiated methylation regions as the signature of particular stem cell lines were figured out in detail in this study.
2014-05-29 | GSE57992 | GEO
Project description:We examined genome-wide DNA methylation with 20 human iPSC lines derived from five different cell types,and 7 human ESC lines using Illumina’s Infinium HumanMethylation450K and compared among iPSCs by retrovirus, Sendai virus or episomal vectors.
2017-11-06 | GSE73938 | GEO
Project description:Induced pluripotent stem cells (iPSCs) have been derived from various somatic cell populations through ectopic expression of defined factors. It remains unclear whether iPSCs generated from different cell types are molecularly and functionally similar. Here, we show that iPSCs obtained from fibroblasts, hematopoietic and myogenic cells exhibit distinct transcriptional and epigenetic patterns. Moreover, we demonstrate that cellular origin influences the in vitro differentiation potentials of iPSCs into embryoid bodies (EBs) and different hematopoietic cells. Importantly, continuous passaging of iPSCs largely attenuates these differences. Our results suggest that low-passage iPSCs retain a transient epigenetic memory of their somatic cells of origin, which manifests as differential gene expression and ltered differentiation capacity. These observations might affect ongoing attempts to use iPSCs for disease modeling and also could be exploited for potential therapeutic applications to enhance differentiation into desired cell lineages. Keywords: DNA methylation profiling Direct comparison of DNA methylation in iPS cells derived from different tissues
2010-07-19 | E-GEOD-22827 | biostudies-arrayexpress
Project description:Induced pluripotent stem cells (iPSCs) outwardly appear to be indistinguishable from embryonic stem cells (ESCs). A study of gene expression profiles of mouse and human ESCs and iPSCs suggests that, while iPSCs are quite similar to their embryonic counterparts, a recurrent gene expression signature appears in iPSCs regardless of their origin or the method by which they were generated. Upon extended culture, hiPSCs adopt a gene expression profile more similar to hESCs; however, they still retain a gene expression signature unique from hESCs that extends to miRNA expression. Genome-wide data suggested that the iPSC signature gene expression differences are due to differential promoter binding by the reprogramming factors. High-resolution array profiling demonstrated that there is no common specific subkaryotypic alteration that is required for reprogramming and that reprogramming does not lead to genomic instability. Together, these data suggest that iPSCs should be considered a unique subtype of pluripotent cell. Detailed analysis comparing induced pluripotent stem cells revealed functional gene expression differences to hESCs that are changed with long term passaging. We used microarrays to detail the changes that are made throughout passaging to hiPSC lines.
2009-07-10 | GSE16654 | GEO
Project description:We mapped long-range chromatin interactions in embryonic stem cells (ESCs), iPSCs, and fibroblasts, and uncovered an ESC-specific genome organization that is gradually re-established during reprogramming. Confirming previous results, we show that open, accessible and closed chromatin character is the primary determinant of long-range chromatin interaction preferences. Importantly, we find that in ESCs, genomic regions extensively occupied by the pluripotency factors Oct4, Sox2, and Nanog preferentially co-localize. Similarly, regions strongly enriched for Polycomb-proteins and H3K27me3 frequently interact, and loss of the Polycomb-protein Eed diminishes these interactions without dramatically changing overall chromosome-conformation. Consistent with a spatial segregation of transcriptional networks in ESCs, Nanog and Polycomb-proteins occupy distinct nuclear spaces. Together, our data reveal that transcriptional networks that govern ESC identity play a role in genome-organization. 4C-seq was performed using a variety of baits on range of mouse cell lines, namely, ESCs, reprogrammed iPSCs, partially reprogrammed pre-iPSCs, and differentiated MEFs. Additionally, 4C-seq was performed on a partially overlapping set of baits for a Eed mutant mouse ESC line and a sibling wild-type ESC line.
2013-09-12 | E-GEOD-50029 | biostudies-arrayexpress
Project description:Human pluripotent stem cells can be derived from somatic cells by forced expression of defined factors, and more recently by nuclear-transfer into human oocytes, revitalizing a debate on whether one reprogramming approach might be advantageous over the other. Here we compared the genetic and epigenetic stability of human nuclear-transfer embryonic stem cell (NT-ESC) lines and isogenic induced pluripotent stem cell (iPSC) lines, derived from the same somatic cell cultures of fetal, neonatal and adult origin. Both cell types shared similar genome-wide gene expression and DNA methylation profiles. Importantly, NT-ESCs and iPSCs have comparable numbers of de novo coding mutations but significantly higher than parthenogenetic ESCs. Similar to iPSCs NT-ESCs displayed clone- and gene-specific aberrations in DNA methylation and allele-specific expression of imprinted genes, similarly to iPSCs. The occurrence of these genetic and epigenetic defects in both NT-ESCs and iPSCs suggests that they are inherent to reprogramming, regardless of the underlying technique. Genome-wide DNA methylation profiling by Illumina Infinium HumanMethylation 450K Beadchip was performed on a total of 21 human cell lines, including: an isogenic set of 3 nuclear-transfer embryonic stem cell (NT-ESC) lines, 2 RNA-reprogrammed induced pluripotent stem cell (iPSC) lines and their parental neonatal fibroblast cell line; an isogenic set of 1 NT-ESC line, 6 iPSC lines and their parental adult fibroblast cell line (derived from a type 1 diabetic subject); as well as 7 control embryonic stem cell (ESC) lines.
2014-11-06 | E-GEOD-61461 | biostudies-arrayexpress
Project description:Induced pluripotent stem cells (iPSCs) have been derived from various somatic cell populations through ectopic expression of defined factors. It remains unclear whether iPSCs generated from different cell types are molecularly and functionally similar. Here, we show that iPSCs obtained from fibroblasts, hematopoietic and myogenic cells exhibit distinct transcriptional and epigenetic patterns. Moreover, we demonstrate that cellular origin influences the in vitro differentiation potentials of iPSCs into embryoid bodies (EBs) and different hematopoietic cells. Importantly, continuous passaging of iPSCs largely attenuates these differences. Our results suggest that low-passage iPSCs retain a transient epigenetic memory of their somatic cells of origin, which manifests as differential gene expression and ltered differentiation capacity. These observations might affect ongoing attempts to use iPSCs for disease modeling and also could be exploited for potential therapeutic applications to enhance differentiation into desired cell lineages. Keywords: DNA methylation profiling
2010-07-19 | GSE22827 | GEO
Project description:Induced pluripotent stem cells (iPSCs) can be derived from somatic cells through ectopic expression of transcriptional factors or chemical cocktails. Chemical reprogramming might be safe than transcriptional factors since there is no integration of exogenous genes. However, there is still little direct evidence to prove this hypothesis. In this study, we have performed whole genome profiling of the DNA methylomes of mouse chemical iPSCs (CiPSCs), transcriptional factors induced iPSCs (TF-iPSCs) and embryonic stem cells (ESCs). We find that the methylation levels of high-CpG-density promoters (HCPs) and intermediate- CpG-density promoters (ICPs) have no significant difference among them, but low-CpG-density promoters (LCP) and three retrotransposons (LINEs, LTRs and SINEs) show preference to different methylation levels. Surprisingly, CiPSCs are hypomethylated than TF-iPSCs and the major difference of methylation levels lies in the intergenic regions while two iPSCs lines are generally hypermethylated compared to ESCs. Moveover, we find the methylation states of imprinting control regions (ICRs) and the expression of imprinted genes of CiPSCs are more resemble ESCs than TF-iPSCs. Our data first provide the epigenetic states of chemical induced pluripotent stem cells and compare the difference of mouse CiPSCs, TF-iPSCs and ESCs. These observations might affect ongoing choices of reprogramming methods for disease modeling and give some guides for potential therapeutic applications.
2017-06-28 | GSE92984 | GEO