TY - JOUR
T1 - Quantitative proteomic analysis of mouse embryonic fibroblasts and induced pluripotent stem cells using 16O/ 18O labeling
AU - Huang, Xin
AU - Tian, Changhai
AU - Liu, Miao
AU - Wang, Yongxiang
AU - Tolmachev, Aleksey V.
AU - Sharma, Seema
AU - Yu, Fang
AU - Fu, Kai
AU - Zheng, Jialin
AU - Ding, Shi Jian
PY - 2012/4/6
Y1 - 2012/4/6
N2 - 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.
AB - 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.
KW - Hdac1
KW - O/ O labeling
KW - Pcna
KW - UNiquant
KW - quantitative proteomics
KW - reprogramming
KW - stem cell proteomics
UR - http://www.scopus.com/inward/record.url?scp=84859586010&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84859586010&partnerID=8YFLogxK
U2 - 10.1021/pr300155r
DO - 10.1021/pr300155r
M3 - Article
C2 - 22375802
AN - SCOPUS:84859586010
SN - 1535-3893
VL - 11
SP - 2091
EP - 2102
JO - Journal of proteome research
JF - Journal of proteome research
IS - 4
ER -