Comparative proteome and transcriptome analyses of embryonic stem cells during embryoid body-based differentiation.
Gene expression analyses of embryonic stem cells (ESCs) will help to uncover or further define signaling pathways and molecular mechanisms involved in the maintenance of self-renewal and pluripotency. We employed a 2-DE-based proteomics approach to analyze human ESC line, Royan H5, in undifferentiated cells and different stages of spontaneous differentiation (days 3, 6, 12, and 20) by embryoid body formation. Out of 945 proteins reproducibly detected on gels, the expression of 96 spots changed during differentiation. Using MS, 87 ESC-associated proteins were identified including several proteins involved in cell proliferation, cell apoptosis, transcription, translation, mRNA processing, and protein folding. Transcriptional changes accompanying differentiation of Royan H5 were also analyzed using microarrays. We developed a comprehensive data set that shows the use of human ESC lines in vitro to mimic gastrulation and organogenesis. Our results showed that proteomics and transcriptomics data are complementary rather than duplicative. Although regulation of many genes during differentiation were observed only at transcript level, modulation of several proteins was revealed only by proteome analysis.
Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
Ali
A
Fathi
Mohammad
M
Pakzad
Adele
A
Taei
Thore C
TC
Brink
Leila
L
Pirhaji
Guifré
G
Ruiz
Mohammad
M
Sharif Tabe Bordbar
Hamid
H
Gourabi
James
J
Adjaye
Hossein
H
Baharvand
Ghasem Hosseini
GH
Salekdeh
D002454:Cell Differentiation; D002460:Cell Line; D053595:Embryonic Stem Cells / Q000737:chemistry* / Q000166:cytology*; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D014176:Protein Biosynthesis; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D014158:Transcription, Genetic
D020543:Proteome