title: Quantitative proteomic analysis of mouse embryonic fibroblasts and induced pluripotent stem cells using 16O/18O labeling.
abstract: Induced pluripotent stem cells (iPSC) hold great promise for regenerative medicine as well as for investigations into the pathogenesis and treatment of various diseases. Understanding of key intracellular signaling pathways and protein targets that control development of iPSC from somatic cells is essential for designing new approaches to improve reprogramming efficiency. Here, we report the development and application of an integrated quantitative proteomics platform for investigating differences in protein expressions between mouse embryonic fibroblasts (MEF) and MEF-derived iPSC. This platform consists of 16O/18O labeling, multidimensional peptide separation coupled with tandem mass spectrometry, and data analysis with UNiquant software. With this platform, a total of 2481 proteins were identified and quantified from the 16O/18O-labeled MEF-iPSC proteome mixtures with a false discovery rate of 0.01. Among them, 218 proteins were significantly upregulated, while 247 proteins were significantly downregulated in iPSC compared to MEF. Many nuclear proteins, including Hdac1, Dnmt1, Pcna, Ccnd1, Smarcc1, and subunits in DNA replication and RNA polymerase II complex, were found to be enhanced in iPSC. Protein network analysis revealed that Pcna functions as a hub orchestrating complicated mechanisms including DNA replication, epigenetic inheritance (Dnmt1), and chromatin remodeling (Smarcc1) to reprogram MEF and maintain stemness of iPSC.
authors.affiliation: Department of Pathology and Microbiology, Mass Spectrometry and Proteomics Core Facility, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States.
authors.forename: Xin
authors.initials: X
authors.lastname: Huang
authors.forename: Changhai
authors.initials: C
authors.lastname: Tian
authors.forename: Miao
authors.initials: M
authors.lastname: Liu
authors.forename: Yongxiang
authors.initials: Y
authors.lastname: Wang
authors.forename: Aleksey V
authors.initials: AV
authors.lastname: Tolmachev
authors.forename: Seema
authors.initials: S
authors.lastname: Sharma
authors.forename: Fang
authors.initials: F
authors.lastname: Yu
authors.forename: Kai
authors.initials: K
authors.lastname: Fu
authors.forename: Jialin
authors.initials: J
authors.lastname: Zheng
authors.forename: Shi-Jian
authors.initials: SJ
authors.lastname: Ding
mesh_terms: D000818:Animals; D002460:Cell Line; D004622:Embryo, Mammalian / Q000166:cytology / Q000378:metabolism; D005347:Fibroblasts / Q000378:metabolism*; D057026:Induced Pluripotent Stem Cells / Q000378:metabolism*; D007553:Isotope Labeling / Q000379:methods*; D051379:Mice; D010103:Oxygen Isotopes / Q000032:analysis / Q000378:metabolism; D060066:Protein Interaction Maps; D020543:Proteome / Q000032:analysis* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*
chemical_list: D010103:Oxygen Isotopes; D020543:Proteome