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Comprehensive Proteogenomic Analysis of Human Embryonic and Induced Pluripotent Stem Cells

ABSTRACT: Comprehensive Proteogenomic Analysis of Human Embryonic and Induced Pluripotent Stem Cells

PROVIDER: PRJNA479972 | ENA |

REPOSITORIES: ENA

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Comprehensive Proteogenomic Analysis of Human Embryonic and Induced Pluripotent Stem Cells

Project description:Although the concepts of reprogramming and human induced pluripotent stem cells (hiPSCs) generation have undergone to several analysis to strengthen the usefulness of these cells in research and clinic, it still remains controversial whether the hiPSCs are really equivalent to human embryonic stem cells, pointing to the need of further characterizations in order to gain a more comprehensive understanding of human stem cells pluripotency. Most of the experimental evidence comes from the transcriptome analysis, while a little information is available on protein data, and even less is known about the post-translational modifications. Here we report a combined strategy of nLC-MS/MS and gene expression profiling for proteogenomic analysis of two distinct stem cell lines, the commercially available hESCs H9 and the hiPSCs, obtained in our laboratory by reprogramming of peripheral blood T-lymphocytes with the Sendai virus-driven Yamanaka’s 4-transcription factors cocktail. The analysis was further enriched by the study of the phosphoproteomic profile of the two PSC lines. The results obtained through this integrated, multi -“omics” approach, indicate that a small number of distinct pathways is enriched in reprogrammed versus naïve pluripotent stem cells, supporting the view that pluripotency is an extremely complex, multifaceted phenomenon, with peculiarities that are characteristic of each cell type.

2019-06-02 | GSE116716 | GEO

Metabolomics Workbench ST000003 - GNPS - Metabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells

Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis

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Metabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells

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Comprehensive proteogenomic analysis of human embryonic and induced pluripotent stem cells.

Project description:Although the concepts of somatic cell reprogramming and human-induced pluripotent stem cells (hiPSCs) generation have undergone several analyses to validate the usefulness of these cells in research and clinic, it remains still controversial whether the hiPSCs are equivalent to human embryonic stem cells (hESCs), pointing to the need of further characterization for a more comprehensive understanding of pluripotency. Most of the experimental evidence comes from the transcriptome analysis, while a little is available on protein data, and even less is known about the post-translational modifications. Here, we report a combined strategy of mass spectrometry and gene expression profiling for proteogenomic analysis of reprogrammed and embryonic stem cells. The data obtained through this integrated, multi-"omics" approach indicate that a small, but still significant, number of distinct pathways is enriched in reprogrammed versus embryonic stem cells, supporting the view that pluripotency is an extremely complex, multifaceted phenomenon, with peculiarities that are characteristic of each cell type.

| S-EPMC6653499 | biostudies-literature

N-glycoproteomics of induced pluripotent stem cells, embryonic stem cells, and parental cells

Project description:We tried to understand the N-glycoproteom molecular differences between induced pluripotent stem cells and embryonic stem cells. This is important to improve the reprograming process and induced pluripotency in the context of post translational protein N-glycosylation

2016-12-23 | PXD004366 | Pride

Proteogenomic characterization and comprehensive integrative genomic analysis of human colorectal cancer liver metastasis

Project description:Colorectal cancer (CRC) is the third most common cancer worldwide and liver metastasis remains the major cause of death in CRC. Extensive genomic analysis provided valuable insight into the pathogenesis and progression of CRC. However, the major proteogenomic characterization of CRC liver metastasis is still unknown. We investigated proteogenomic characterization and performed comprehensive integrative genomic analysis of human colorectal cancer liver metastasis.

2019-12-27 | GSE93286 | GEO

The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells

Project description:Assessing relevant molecular differences between human-induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs) is important, given that such differences may impact their potential therapeutic use. Controversy surrounds recent gene expression studies comparing hiPSCs and hESCs. Here, we present an in-depth quantitative mass spectrometry-based analysis of hESCs, two different hiPSCs and their precursor fibroblast cell lines. Our comparisons confirmed the high similarity of hESCs and hiPSCS at the proteome level as 97.8% of the proteins were found unchanged. Nevertheless, a small group of 58 proteins, mainly related to metabolism, antigen processing and cell adhesion, was found significantly differentially expressed between hiPSCs and hESCs. A comparison of the regulated proteins with previously published transcriptomic studies showed a low overlap, highlighting the emerging notion that differences between both pluripotent cell lines rather reflect experimental conditions than a recurrent molecular signature. See the Data Processing section of the published paper concerning the bioinformatics pipeline used. PMCID: PMC3261715 PMID: 22108792 Mol Syst Biol. 2011 Nov 22;7:550. doi: 10.1038/msb.2011.84. The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Munoz J, Low TY, Kok YJ, Chin A, Frese CK, Ding V, Choo A, Heck AJ. Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.

2013-02-01 | PXD000134 | Pride

Human induced pluripotent stem cells display a similar mutation burden as embryonic pluripotent cells in vivo

Project description:Induced pluripotent stem cells (iPSCs) hold great promise for regenerative medicine, but genetic instability is a major concern. Embryonic pluripotent cells also accumulate mutations during early development, but how this relates to the mutation burden in iPSCs remains unknown. Here, we directly compared the mutation burden of cultured iPSCs with their isogenic embryonic cells during human embryogenesis. We generated developmental lineage trees of human fetuses by phylogenetic inference from somatic mutations in the genomes of multiple stem cells, which were derived from different germ layers. Using this approach, we characterized the mutations acquired pre-gastrulation and found a rate of 1.65 mutations per cell division. When cultured in hypoxic conditions, iPSCs generated from fetal stem cells of the assessed fetuses displayed a similar mutation rate and spectrum. Our results show that iPSCs maintain a genomic integrity during culture at a similar degree as their pluripotent counterparts do in vivo.

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1H NMR metabolite monitoring during the differentiation of human induced pluripotent stem cells provides new insights into the molecular events that regulate embryonic chondrogenesis

Project description:The integration of cell metabolism with signalling pathways, transcription factor networks and epigenetic mediators is critical in coordinating molecular and cellular events during embryogenesis. Induced pluripotent stem cells (IPSCs) are an established model for embryogenesis, germ layer specification and cell lineage differentiation, advancing the study of human embryonic development and the translation of innovations in drug discovery, disease modelling and cell-based therapies. The metabolic regulation of IPSC pluripotency is mediated by balancing glycolysis and oxidative phosphorylation, but there is a paucity of data regarding the influence of individual metabolite changes during cell lineage differentiation. We used <sup>1</sup>H NMR metabolite fingerprinting and footprinting to monitor metabolite levels as IPSCs are directed in a three-stage protocol through primitive streak/mesendoderm, mesoderm and chondrogenic populations. Metabolite changes were associated with central metabolism, with aerobic glycolysis predominant in IPSC, elevated oxidative phosphorylation during differentiation and fatty acid oxidation and ketone body use in chondrogenic cells. Metabolites were also implicated in the epigenetic regulation of pluripotency, cell signalling and biosynthetic pathways. Our results show that <sup>1</sup>H NMR metabolomics is an effective tool for monitoring metabolite changes during the differentiation of pluripotent cells with implications on optimising media and environmental parameters for the study of embryogenesis and translational applications.

2023-05-24 | MTBLS4854 | MetaboLights

Comparison of the transcription of palmitoylcarnitine induced pluripotent stem cells, normal induced pluripotent stem cells and embryonic stem cells through RNA-seq

Project description:We sequenced mRNA from 2 clones of palmitoylcarnitine induced pluripotent stem cells, 2 clones of normal induced pluripotent stem cells, 1 embryonic stem cell, and 1 mouse embryonic fibroblast strain to compare the expression profiles

2020-05-01 | GSE85272 | GEO

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