Quantitative proteomic analysis of mouse embryonic fibroblasts and induced pluripotent stem cells using 16O/ 18O labeling

Xin Huang, Changhai Tian, Miao Liu, Yongxiang Wang, Aleksey V. Tolmachev, Seema Sharma, Fang Yu, Kai Fu, Jialin C Zheng, Shi Jian Ding

Research output: Contribution to journalArticle

8 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)2091-2102
Number of pages12
JournalJournal of proteome research
Volume11
Issue number4
DOIs
StatePublished - Apr 6 2012

Fingerprint

Induced Pluripotent Stem Cells
Fibroblasts
Stem cells
Proteomics
Labeling
Proteins
DNA Replication
Intracellular Signaling Peptides and Proteins
DNA Polymerase II
Regenerative Medicine
Chromatin Assembly and Disassembly
RNA Polymerase II
DNA
Proteome
Electric network analysis
Nuclear Proteins
Tandem Mass Spectrometry
Epigenomics
Chromatin
Mass spectrometry

Keywords

  • Hdac1
  • O/ O labeling
  • Pcna
  • UNiquant
  • quantitative proteomics
  • reprogramming
  • stem cell proteomics

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Quantitative proteomic analysis of mouse embryonic fibroblasts and induced pluripotent stem cells using 16O/ 18O labeling. / Huang, Xin; Tian, Changhai; Liu, Miao; Wang, Yongxiang; Tolmachev, Aleksey V.; Sharma, Seema; Yu, Fang; Fu, Kai; Zheng, Jialin C; Ding, Shi Jian.

In: Journal of proteome research, Vol. 11, No. 4, 06.04.2012, p. 2091-2102.

Research output: Contribution to journalArticle

Huang, Xin ; Tian, Changhai ; Liu, Miao ; Wang, Yongxiang ; Tolmachev, Aleksey V. ; Sharma, Seema ; Yu, Fang ; Fu, Kai ; Zheng, Jialin C ; Ding, Shi Jian. / Quantitative proteomic analysis of mouse embryonic fibroblasts and induced pluripotent stem cells using 16O/ 18O labeling. In: Journal of proteome research. 2012 ; Vol. 11, No. 4. pp. 2091-2102.
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