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Stem Cells. 2015 Sep;33(9):2712-25. doi: 10.1002/stem.2067. Epub 2015 Jun 23.

Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells.

Author information

1
Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
2
Cambridge Systems Biology Centre, Wellcome Trust Stem Cell building, University of Cambridge, Cambridge, United Kingdom.
3
Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
4
Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
5
Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
6
Department of Computer Engineering, Bogazici University, Istanbul, Turkey.
7
Neusentis, Pfizer Worldwide Research and Development, Granta Park Science Park, Great Abington, Cambridge, United Kingdom.
8
The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom.

Abstract

During mammalian preimplantation development, the cells of the blastocyst's inner cell mass differentiate into the epiblast and primitive endoderm lineages, which give rise to the fetus and extra-embryonic tissues, respectively. Extra-embryonic endoderm (XEN) differentiation can be modeled in vitro by induced expression of GATA transcription factors in mouse embryonic stem cells. Here, we use this GATA-inducible system to quantitatively monitor the dynamics of global proteomic changes during the early stages of this differentiation event and also investigate the fully differentiated phenotype, as represented by embryo-derived XEN cells. Using mass spectrometry-based quantitative proteomic profiling with multivariate data analysis tools, we reproducibly quantified 2,336 proteins across three biological replicates and have identified clusters of proteins characterized by distinct, dynamic temporal abundance profiles. We first used this approach to highlight novel marker candidates of the pluripotent state and XEN differentiation. Through functional annotation enrichment analysis, we have shown that the downregulation of chromatin-modifying enzymes, the reorganization of membrane trafficking machinery, and the breakdown of cell-cell adhesion are successive steps of the extra-embryonic differentiation process. Thus, applying a range of sophisticated clustering approaches to a time-resolved proteomic dataset has allowed the elucidation of complex biological processes which characterize stem cell differentiation and could establish a general paradigm for the investigation of these processes.

KEYWORDS:

Differentiation; Extra-embryonic endoderm stem cells; Pluripotency; Quantitative proteomics; Tandem mass tags

PMID:
26059426
DOI:
10.1002/stem.2067
[Indexed for MEDLINE]
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