title: Nuclear proteome dynamics in differentiating embryonic carcinoma (NTERA-2) cells.
abstract: The use of stem cells for generating cell types suitable for therapy is dependent on understanding the mechanisms, and identifying biomarkers, that control cell fate into different lineages. In this study, we aimed to characterize the nuclear protein dynamics of NTERA-2 cells undergoing retinoic acid-induced differentiation. We focused specifically on the first six days of differentiation, to provide insight into the earliest differentiation events, and employed techniques to specifically monitor the nuclear proteome. Well-characterized gene expression markers were used to precisely stage cell differentiation across the experimental time course. A combination of the novel iTRAQ and ExacTag labeling technologies, together with LC-ESI tandem mass spectrometry, were then used to accurately measure nuclear protein expression changes occurring within these differentiation-staged cells. We report proteins that showed significantly altered expression over the first 6 days of differentiation. Extensive bioinformatic analysis was undertaken, resulting in the construction of a novel interactome network, which revealed the temporal dynamics of the nuclear protein network in the context of neuronal differentiation.
authors.affiliation: Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Level 4, The Jessop Wing, S10 2SF Sheffield, United Kingdom.
authors.forename: Emma
authors.initials: E
authors.lastname: Pewsey
authors.forename: Christine
authors.initials: C
authors.lastname: Bruce
authors.forename: Peter
authors.initials: P
authors.lastname: Tonge
authors.forename: Caroline
authors.initials: C
authors.lastname: Evans
authors.forename: Saw Yen
authors.initials: SY
authors.lastname: Ow
authors.forename: A Stephen
authors.initials: AS
authors.lastname: Georgiou
authors.forename: Phillip C
authors.initials: PC
authors.lastname: Wright
authors.forename: Peter W
authors.initials: PW
authors.lastname: Andrews
authors.forename: Alireza
authors.initials: A
authors.lastname: Fazeli
mesh_terms: D000704:Analysis of Variance; D015415:Biomarkers / Q000378:metabolism; D015153:Blotting, Western; D002454:Cell Differentiation / Q000187:drug effects; D002460:Cell Line; D002467:Cell Nucleus / Q000378:metabolism*; D016000:Cluster Analysis; D054278:Embryonal Carcinoma Stem Cells / Q000378:metabolism*; D006801:Humans; D007553:Isotope Labeling; D009474:Neurons / Q000378:metabolism; D009687:Nuclear Proteins / Q000737:chemistry / Q000145:classification / Q000378:metabolism*; D025941:Protein Interaction Mapping; D020543:Proteome / Q000187:drug effects / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D015398:Signal Transduction / Q000187:drug effects; D014212:Tretinoin / Q000494:pharmacology
chemical_list: D015415:Biomarkers; D009687:Nuclear Proteins; D020543:Proteome; D014212:Tretinoin