title: Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells.
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.
authors.affiliation: Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.|Cambridge Systems Biology Centre, Wellcome Trust Stem Cell building, University of Cambridge, Cambridge, United Kingdom.|Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Claire M
authors.initials: CM
authors.lastname: Mulvey
authors.affiliation: Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Christian
authors.initials: C
authors.lastname: Schröter
authors.affiliation: Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.|Cambridge Systems Biology Centre, Wellcome Trust Stem Cell building, University of Cambridge, Cambridge, United Kingdom.|Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Laurent
authors.initials: L
authors.lastname: Gatto
authors.affiliation: Cambridge Systems Biology Centre, Wellcome Trust Stem Cell building, University of Cambridge, Cambridge, United Kingdom.|Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Duygu
authors.initials: D
authors.lastname: Dikicioglu
authors.affiliation: Department of Computer Engineering, Bogazici University, Istanbul, Turkey.
authors.forename: Isik Baris
authors.initials: IB
authors.lastname: Fidaner
authors.affiliation: Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.|Cambridge Systems Biology Centre, Wellcome Trust Stem Cell building, University of Cambridge, Cambridge, United Kingdom.|Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Andy
authors.initials: A
authors.lastname: Christoforou
authors.affiliation: Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.|Cambridge Systems Biology Centre, Wellcome Trust Stem Cell building, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Deery
authors.affiliation: Neusentis, Pfizer Worldwide Research and Development, Granta Park Science Park, Great Abington, Cambridge, United Kingdom.
authors.forename: Lily T Y
authors.initials: LT
authors.lastname: Cho
authors.affiliation: The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom.
authors.forename: Kathy K
authors.initials: KK
authors.lastname: Niakan
authors.affiliation: Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Martinez-Arias
authors.affiliation: Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.|Cambridge Systems Biology Centre, Wellcome Trust Stem Cell building, University of Cambridge, Cambridge, United Kingdom.|Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Kathryn S
authors.initials: KS
authors.lastname: Lilley
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000502:physiology*; D002478:Cells, Cultured; D004707:Endoderm / Q000166:cytology / Q000502:physiology*; D005321:Extraembryonic Membranes / Q000166:cytology / Q000502:physiology*; D051379:Mice; D000066450:Mouse Embryonic Stem Cells / Q000502:physiology*; D040901:Proteomics / Q000379:methods*
keywords: Differentiation; Extra-embryonic endoderm stem cells; Pluripotency; Quantitative proteomics; Tandem mass tags