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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Highly efficient derivation of ventricular cardiomyocytes from induced pluripotent stem cells with a distinct epigenetic signature

ABSTRACT: The generation of sufficient numbers of mature ventricular myocytes for effective cell-based therapy is a central barrier for cardiac regenerative medicine. Here we demonstrate that induced pluripotent stem cells (iPSCs) can be derived from murine ventricular myocytes, and consistent with other reports of iPSCs derived from various somatic cell types, ventricular myocyte derived iPSCs (ViPSCs) exhibit a markedly higher propensity to differentiate into beating cardiomyocytes as compared to genetically-matched embryonic stem cells (ESCs) or iPSCs derived from tail-tip fibroblasts. Strikingly, ViPSC-derived cardiomyocytes form up to 99% ventricular myocytes suggesting that ventricular myocyte-derived iPSCs may be a viable strategy to generate specific cardiomyocyte subtypes for cell-based therapies. The enhanced ventricular myogenesis in ViPSCs is mediated via increased numbers of cardiovascular progenitors at early stages of differentiation. In order to investigate the mechanism of enhanced ventricular myogenesis from ViPSCs, we performed global gene expression and DNA methylation analysis, which revealed a distinct epigenetic signature that may be involved in specifying the ventricular myocyte fate in pluripotent stem cells. Total RNA was extracted from mouse ES cells, tail tip fibroblasts (TTFs), ventricular myocytes (VMs), TTF-derived induced pluripotent stem cells (TiPSCs) and VM-derived induced pluripotent stem cells (ViPSCs). Global gene expression profiling was performed using affymetrix mouse 430 2.0 gene arrays.

ORGANISM(S): Mus musculus

SUBMITTER: Kenneth Chien

PROVIDER: E-GEOD-32598 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Highly efficient derivation of ventricular cardiomyocytes from induced pluripotent stem cells with a distinct epigenetic signature

Project description:The generation of sufficient numbers of mature ventricular myocytes for effective cell-based therapy is a central barrier for cardiac regenerative medicine. Here we demonstrate that induced pluripotent stem cells (iPSCs) can be derived from murine ventricular myocytes, and consistent with other reports of iPSCs derived from various somatic cell types, ventricular myocyte derived iPSCs (ViPSCs) exhibit a markedly higher propensity to differentiate into beating cardiomyocytes as compared to genetically-matched embryonic stem cells (ESCs) or iPSCs derived from tail-tip fibroblasts. Strikingly, ViPSC-derived cardiomyocytes form up to 99% ventricular myocytes suggesting that ventricular myocyte-derived iPSCs may be a viable strategy to generate specific cardiomyocyte subtypes for cell-based therapies. The enhanced ventricular myogenesis in ViPSCs is mediated via increased numbers of cardiovascular progenitors at early stages of differentiation. In order to investigate the mechanism of enhanced ventricular myogenesis from ViPSCs, we performed global gene expression and DNA methylation analysis, which revealed a distinct epigenetic signature that may be involved in specifying the ventricular myocyte fate in pluripotent stem cells.

2011-10-05 | GSE32598 | GEO

Minicircle-derived iPS cells - Affymetrix Data

Project description:Owing to the risk of insertional mutagenesis, viral transduction has been increasingly replaced by nonviral methods to generate induced pluripotent stem (iPS) cells. We report the use of âminicircleâ DNA, a vector type that is free of bacterial DNA and capable of high expression in cells. Here we use a single minicircle vector to generate transgene-free iPSCs from adult human adipose stem cells. (Note: Our Nature Methods publication included analysis of array data from GSM378832 (Foreskin), GSM378833-GSM378838 (JT-iPSC), and GSM378817-GSM378820 (H1, H7, H9, H13, H14) in conjunction with this series). Total RNA from human adipose stem cells (hASC, n = 3 replicate samples), hASC-derived iPS cells using lentiviral factors (lenti-iPSC, n = 3 replicate samples), and minicircle-derived human iPS cells (mc-iPSC, n = 3 subclones from adipose tissue of three individual patients) was hybridized to nine Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays.

2010-02-21 | E-GEOD-20033 | biostudies-arrayexpress

The developmental potential of iPSCs is greatly influenced by the selection of the reprogramming factors (SNEL iPSC and H2A.X deposition pattern)

Project description:Induced pluripotent stem cells (iPSCs) are commonly generated by transduction of Oct4, Sox2, Klf4 and Myc (OSKM) into somatic cells. Though iPSCs are pluripotent, they frequently exhibit high variation in their quality as measured by chimera contribution and tetraploid (4n) complementation. Thus, improving the quality of iPSCs is an indispensable prerequisite for future iPSC-based therapy. Here we show that one major determinant for iPSCs quality is the selection of the reprogramming factors combination. Ectopic expression of Sall4, Nanog, Esrrb and Lin28 (SNEL) in MEFs efficiently generated high quality iPSCs as compared to other combinations of factors. SNEL-iPSCs produced approximately 5 times more efficiently “all-iPSC” mice compared to OSKM-iPSCs. While differentially methylated regions, transcript number of master regulators, establishment of ESC-specific super enhancers, and global aneuploidy were comparable between the lines, aberrant expression of 1,765 genes, trisomy of chromosome 8 and abnormal H2A.X deposition were frequently observed in poor quality OSKM-iPSCs. For high-quality iPSCs, H2A.X pattern of SNEL is most similar to that of ESC, OSK and OSKM have more devoid regions than SNEL iPSCs. Compare H2A.X deposition pattern of the OSKM 4-factor iPS cell lines (4N-), SNEL 4-factor iPS cell lines (4N+) with ChIP-Seq. The same background ES cell line as the control line.

2014-09-07 | E-GEOD-55731 | biostudies-arrayexpress

Transcription profiling of H2O2 treated rat cardiac myocytes

Project description:Title: Changes in gene expression affected by H2O2 in cardiac myocytes. Description: We aim to identify the changes in gene expression in response to oxidative stress in rat neonatal ventricular myocytes. Oxidative stress will be induced by dosing neonatal ventricular myocyte cultures with 0.2, 0.1 and 0.04mM hydrogen peroxide at 2, 4 and 8 hr time points using unstimulated myocytes as control.

2011-11-08 | E-MIMR-12 | biostudies-arrayexpress

Effect of oocyte-enriched histones Th2a, Th2b, and histone chaperone Npm on mouse iPS cell generation

Project description:Expression of key transcription factors Klf4, Oct3/4, Sox2, and c-Myc (KOSM) in embryonic stem cells can reprogram somatic cells into pluripotent cells. We found that two histone variants, TH2A and TH2B, and histone chaperone Npm enhance the KOSM-dependent generation of induced pluripotent cells (iPSCs) and produce iPSCs only with Klf4 and Oct3/4. To identify directly affected genes by these histone variants during reprogramming, we carried out gene expression profiling of MEFs overexpressing TH2A/TH2B/Npm and TH2A/TH2B deficient MEFs after infection with retroviruses expressing KOSM. A total of 21 Affymetrix Mouse Gene ST array were done for mRNA expression profiling of ES cells, iPS cells induced by Klf4, Oct4, Sox2, and c-Myc (KOSM) or Klf4, Oct4, Th2a, Th2b, and p-Npm (KOBAN), wild-type MEFs infected with retrovirus vectors expressing KOSM, KOSMBAN, or empty vector and Th2a/Th2b-deficient MEFs infected with retrovirus vector expressing KOSM.

2013-12-25 | E-GEOD-53637 | biostudies-arrayexpress

All-iPS cell mice generated from terminally differentiated B cells

Project description:The generation of induced pluripotent stem cells (iPSCs) often results in aberrant silencing of the imprinted Dlk1-Dio3 gene cluster, which compromises their ability to generate entirely iPSC-derived mice (âall-iPSC miceâ). Here, we show that reprogramming in the presence of ascorbic acid attenuates hypermethylation of Dlk1-Dio3 by enabling a chromatin configuration at its imprint control region that interferes with abnormal binding of the DNA methyltransferase Dnmt3a. This approach allowed us to generate adult all-iPSC mice from mature B cells, which have thus far failed to support the development of exclusively iPSC-derived postnatal mice. Our data demonstrate that factor-mediated reprogramming can endow a defined, terminally differentiated cell type with a developmental potential equivalent to that of embryonic stem cells. More generally, these findings indicate that the choice of culture conditions used for transcription factor-mediated reprogramming can strongly influence the epigenetic and biological properties of resultant iPSCs. This series consists of quadruplicated mRNA expression microarray data (Affymetrix mouse 430_2 3'-IVT array) for iPS cells derived from MEF cells under cell culture conditions with or without ascorbic acid supplementation. iPS cells were generated from MEFs of the Col-OKSM reprogrammable mice. In the presence of doxycycline, the reprogramming transcription factors Oct4, Sox2, Klf4, and cMyc were induced in MEFs to derivate iPS cells. Total RNA was isolated from iPS cells derivated in the presence or absence of ascorbic acid in culture medium.

2012-02-01 | E-GEOD-34761 | biostudies-arrayexpress

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. This experiment was reloaded in November 2010 after additional curation

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

Reprogramming-associated aberrant DNA methylation determines hematopoietic differentiation capacity of human induced pluripotent stem cells [iPSC_ESC_lines]

Project description:The variation among induced pluripotent stem cells (iPSCs) in their differentiation capacity to specific lineages is frequently attributed to somatic memory. In this study, we compared hematopoietic differentiation capacity of 35 human iPSC lines derived from four different tissues and four embryonic stem cell lines. The analysis revealed that hematopoietic commitment capacity (PSCs to hematopoietic precursors) is correlated with the expression level of the IGF2 gene independent of the iPSC origins. In contrast, maturation capacity (hematopoietic precursors to mature blood) is affected by iPSC origin; blood-derived iPSCs showed the highest capacity. However, some fibroblast-derived iPSCs showed higher capacity than blood-derived clones. Tracking of DNA methylation changes during reprogramming reveals that maturation capacity is highly associated with aberrant DNA methylation acquired during reprogramming, rather than the types of iPSC origins. These data demonstrated that variations in the hematopoietic differentiation capacity of iPSCs are not attributable to somatic memories of their origins. Human iPSCs after hematopoietic differentiation (n = 2), human iPSCs after neural differentiation (n = 1), human iPSCs with different culture conditions (n = 8), and human iPSC line forced to express IGF2 gene (n = 1), and its control (n = 1).

2016-06-29 | E-GEOD-75096 | biostudies-arrayexpress

Fibronectin Induced Cardiac Myocyte Hypertrophy

Project description:Gene expression changes in neonatal rat ventricular myocytes plated in fibronectin (2 samples) or uncoated plates (2 samples). Keywords = Hypertrophy Cardiac Myocyte Fibronectin Keywords: repeat sample

2004-08-19 | GSE1055 | GEO

Proteome landscape of schizophrenia in patient-derived cerebral organoids

Project description:We utilized patient-derived induced pluripotent stem cells (iPSCs) to generate 3D cerebral organoids to model neuropathology of Scz during this critical period. We discovered that Scz organoids exhibited ventricular neuropathology resulting in altered progenitor survival and disrupted neurogenesis. cz organoids principally differed not in their proteomic diversity, but specifically in their total quantity of disease and neurodevelopmental factors at the molecular level. Provides unique insights into the proteome landscape of schizophrenia in patient-derived cerebral organoids

2021-11-17 | PXD027812 | Pride

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