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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from human keratinocyte and PBMC-derived iPS cells

ABSTRACT: Induced pluripotent stem cell (iPSC) technology allows for the generation of patient-specific pluripotent stem cells, from somatic cell sources, thereby providing a novel cell therapy platform for severe degenerative diseases. One of the key issues for clinical-grade iPSC derivation is the accessibility of donor cells used for reprogramming and subsequent feasiblity of reprogramming into a pluripotent state. We used microarrays to detail the global gene expression profiles from blood cells. The use of blood cells allows for minimally invasive tissue procurement under GMP conditions and rapid cellular reprogramming, mobilized HPCs and unmobilized PBMCs would be ideal somatic cell sources for clinical-grade iPSC derivation. We examined the feasibility of reprogramming mobilized GMP-grade hematopoietic progenitor cells (HPCs) and mononuclear myeloid cells and tested the pluripotency of derived iPS clones.

ORGANISM(S): Homo sapiens

SUBMITTER: Yasuhiro Ikeda

PROVIDER: E-GEOD-33536 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from human keratinocyte and PBMC-derived iPS cells

Project description:Induced pluripotent stem cell (iPSC) technology allows for the generation of patient-specific pluripotent stem cells, from somatic cell sources, thereby providing a novel cell therapy platform for severe degenerative diseases. One of the key issues for clinical-grade iPSC derivation is the accessibility of donor cells used for reprogramming and subsequent feasiblity of reprogramming into a pluripotent state. We used microarrays to detail the global gene expression profiles from blood cells. The use of blood cells allows for minimally invasive tissue procurement under GMP conditions and rapid cellular reprogramming, mobilized HPCs and unmobilized PBMCs would be ideal somatic cell sources for clinical-grade iPSC derivation.

2011-11-09 | GSE33536 | GEO

Transgene-free iPSCs generated from small volume peripheral blood nonmobilized CD34+ cells

Project description:A variety of somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs), but the small number of CD34+ hematopoietic stem cells (HSCs) present in non-mobilized peripheral blood (PB) would be a convenient and desirable starting target. We report here a simple method for targeting derivation of iPSC from non-mobilized PB CD34+ HSCs using immunobead purification and 2-4 day culture to achieve enrichment of CD34+ HSCs to 80±9%, followed by reprogramming transduction with loxP-flanked polycistronic (Oct4, Klf4, Sox2, and c-Myc) STEMCCA-loxP lentivector at an MOI of 2. Our yield was 4.7±2.2 iPSC colonies (n=12) per 20 mL non-mobilized peripheral blood, where most colonies had single copy STEMCCA-loxP that was easily excised by transient transfection expression of Cre. Resultant iPSC clones expressed pluripotent cell markers, had genomic methylation pattern closely matching embryonic stem cells, and generated teratomas containing tissues of all three germ lineages in immunodeficient mice. Furthermore, we conclude that these iPSC are derived from the non-mobilized CD34+ HSCs enriched from PB rather than from any lymphocyte or monocyte contaminants because they lacked somatic rearrangements typical of T or B lymphocytes, and because we demonstrated that purified CD14+ monocytes do not yield iPSC colonies under these reprogramming conditions.

2013-04-26 | GSE40790 | GEO

Nanog Independent Reprogramming to iPSCs with Canonical Factors

Project description:It has been suggested that the transcription factor Nanog is essential for the establishment of pluripotency during the derivation of embryonic stem (ES) cells and induced pluripotent stem (iPS) cells. However, successful reprogramming to pluripotency with a growing list of divergent transcription factors, at ever increasing efficiencies, suggests that there may be many distinct routes to a pluripotent state. Here, we have investigated whether Nanog is necessary for reprogramming murine fibroblasts under highly efficient conditions using the canonical reprogramming factors Oct4, Sox2, Klf4 and cMyc. In agreement with prior results, the efficiency of reprogramming Nanog-/- fibroblasts was significantly lower than that of control fibroblasts. However, in contrast to previous findings, we were able to reproducibly generate iPS cells from Nanog-/- fibroblasts that effectively contributed to chimeric mice. Thus while Nanog may be an important mediator of reprogramming it is not required for establishing pluripotency in the mouse, even under standard conditions. In order to further evaluate the equivalency of Nanog null iPSC to nanog null ESCs, we have performed RNAseq on two independent nanog null iPSC lines, as well as Nanog Null ESC, WT ESC and iPSCs as well as MEFs. As a negativve control for reprogramming we have analyzed a partially reprogrammed iPSC line. 2-4 biological replicates each of 7 conditions (WT MEFs, WT ESC, WT iPSC, WT partially reprogrammed iPSC (piPS), Nanog null ESC, Nanog null iPSC clone G2 and Nanog null iPSC clone G5)

2014-01-01 | E-GEOD-53212 | biostudies-arrayexpress

Finger-prick iPSCs Facilitate the Development of Stem cell banking

Project description:Induced pluripotent stem cells (iPSCs) derived from somatic cells of patients can be a good model for studying human diseases and for future therapeutic regenerative medicine. Current initiatives to establish iPSC banking face challenges in recruiting large numbers of donors with diverse diseased, genetic and phenotypic representations. Here, we describe the derivation of transgene-free iPSCs from human finger-prick blood. Fingerprick samples collection can be performed “DIY (Do-it-yourself)” by donors and sent to the iPSC facility for reprogramming. We show that single drop volumes of finger-prick samples are sufficient for performing cellular reprogramming, DNA sequencing and blood serotyping in parallel. Our novel strategy will facilitate the development of large scale iPSC banking world-wide. Total RNA from PBMC, hES cells, or iPS cells from PBMC was labeled with biotin. Samples were hybridized to HumanHT-12v4 Beadchip (Illumina) according to manufacturer’s protocol.

2014-03-28 | E-GEOD-53485 | biostudies-arrayexpress

Transcription profiling of IPS cells derived from peripheral blood cells: Reprogramming of T Cells from Human Peripheral Blood

Project description:Human induced pluripotent stem (iPS) cells derived from somatic cells of patients hold great promise for modelling human diseases. Dermal fibroblasts are frequently used for reprogramming, but require an invasive skin biopsy and a prolonged period of expansion in cell culture prior to use. Here, we report the derivation of iPS cells from multiple human blood sources including peripheral blood mononuclear cells (PBMCs) harvested by routine venipuncture. Peripheral blood-derived human iPS lines are comparable to human embryonic stem (ES) cells with respect to morphology, expression of surface antigens, activation of endogenous pluripotency genes, DNA methylation and differentiation potential. Analysis of Immunoglobulin and T-cell receptor gene rearrangement revealed that some of the PBMC iPS cells were derived from T-cells, documenting derivation of iPS cells from terminally differentiated cell types. Importantly, peripheral blood cells can be isolated with minimal risk to the donor and can be obtained in sufficient numbers to enable reprogramming without the need for prolonged expansion in culture. Reprogramming from blood cells thus represents a fast, safe and efficient way of generating patient-specific iPS cells. We isolated RNA from multiple human blood sources including peripheral blood mononuclear iPS cells, multiple somatic cells and iPS cells and human embryonic cells and hybridized them to Affymetrix gene expression microarrays.

2010-06-23 | E-GEOD-22167 | biostudies-arrayexpress

Finger-prick iPSCs Facilitate the Development of Stem cell banking

2014-03-28 | GSE53485 | GEO

Small molecules facilitate rapid and synchronous iPSC generation

Project description:The reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) upon overexpression of OCT4, KLF4, SOX2 and c-MYC (OKSM) provides a powerful system to interrogate basic mechanisms of cell fate change. However, iPSC formation with standard methods is typically protracted and inefficient, resulting in heterogeneous cell populations. We show that exposure of OKSM-expressing cells to both ascorbic acid and a GSK3-β inhibitor (AGi) facilitates more synchronous and rapid iPSC formation from several mouse cell types. AGi treatment restored the ability of refractory cell populations to yield iPSC colonies, and it attenuated the activation of developmental regulators commonly observed during the reprogramming process. Moreover, AGi supplementation gave rise to chimera-competent iPSCs after as little as 48 h of OKSM expression. Our results offer a simple modification to the reprogramming protocol, facilitating iPSC induction at unparalleled efficiencies and enabling dissection of the underlying mechanisms in more homogeneous cell populations. 18 samples were analyzed in total, samples represent bulk cultures of reprogrammable-MEFs (Rep-MEFs) that express OKSM and were supplemented with ascorbic acid and GSK3i during iPS cell induction. Control samples represent similar bulk cultures of reprogrammable-MEFs that express OKSM but were not supplemented with ascorbic acid and GSK3i during iPS cell induction. GMP-iPSCs were generated using 48 hours of OKSM+AGi induction. Fibroblast-iPSCs were generated using 96 hours of OKSM+AGi induction.

2014-09-23 | E-GEOD-57774 | 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

Comparison of the transcriptome and chromatin state between human cord blood HSC and human iPSC derived hematopoietic progenitor using next-generation sequencing

Project description:We analyzed the transcriptome and transposase accessible chromatin–using RNAseq and ATAC-seq, respectively–of human cord blood hematopoietic stem cells and human iPSC derived hematopoietic progenitors. iPSC-derived HPCs were FACS sorted CD34+/CD43+ cells. We also examined the effect of inhibiting Wnt signaling during the second week of hematopoietic differentiation of hiPSC. The integrated transcriptomic, epigenomic and functional analyses not only uncovered novel molecular differences between hPSC- HPCs and native HSCs, but also enabled us to target these differences with small molecules to improve derivation and function of hPSC derived HPCs. The strategies here delineated could also be useful for increasing the production of blood cell types such as erythrocytes for therapeutic purposes. Given the existence of a multitude of small molecules specifically targeting a wide range of molecular pathways, our approach could provide a comprehensive strategy for reconstituting the authentic HSC regulatory program and thus open up new avenues for de novo generation of HSCs from hPSCs.

2019-01-01 | GSE69932 | GEO

CD44 is a negative cell surface marker for pluripotent stem cell identification during human fibroblast reprogramming

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