A large-scale proteomic analysis of human embryonic stem cells

BMC Genomics. 2007 Dec 27;8:478. doi: 10.1186/1471-2164-8-478.


Background: Much of our current knowledge of the molecular expression profile of human embryonic stem cells (hESCs) is based on transcriptional approaches. These analyses are only partly predictive of protein expression however, and do not shed light on post-translational regulation, leaving a large gap in our knowledge of the biology of pluripotent stem cells.

Results: Here we describe the use of two large-scale western blot assays to identify over 600 proteins expressed in undifferentiated hESCs, and highlight over 40 examples of multiple gel mobility variants, which are suspected protein isoforms and/or post-translational modifications. Twenty-two phosphorylation events in cell signaling molecules, as well as potential new markers of undifferentiated hESCs were also identified. We confirmed the expression of a subset of the identified proteins by immunofluorescence and correlated the expression of transcript and protein for key molecules in active signaling pathways in hESCs. These analyses also indicated that hESCs exhibit several features of polarized epithelia, including expression of tight junction proteins.

Conclusion: Our approach complements proteomic and transcriptional analysis to provide unique information on human pluripotent stem cells, and is a framework for the continued analyses of self-renewal.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Blotting, Western
  • Embryonic Stem Cells / metabolism*
  • Fluorescent Antibody Technique
  • Humans
  • Immunohistochemistry
  • Membrane Proteins / genetics
  • Membrane Proteins / metabolism
  • Occludin
  • Phosphoproteins / genetics
  • Phosphoproteins / metabolism
  • Phosphoric Monoester Hydrolases / genetics
  • Phosphoric Monoester Hydrolases / metabolism
  • Phosphorylation
  • Protein Isoforms / genetics
  • Protein Isoforms / metabolism
  • Protein Kinases / genetics
  • Protein Kinases / metabolism
  • Protein Processing, Post-Translational
  • Proteome / classification
  • Proteome / genetics
  • Proteome / metabolism*
  • Proteomics / methods*
  • Transcription, Genetic
  • Zonula Occludens-1 Protein


  • Membrane Proteins
  • OCLN protein, human
  • Occludin
  • Phosphoproteins
  • Protein Isoforms
  • Proteome
  • TJP1 protein, human
  • Zonula Occludens-1 Protein
  • Protein Kinases
  • Phosphoric Monoester Hydrolases