Proteomics Applied to Stem Cells

Cell Stem Cell, August 6, 2009

Scientists at The Scripps Research Institute and the Burnham Institute for Medical Research have just completed a large-scale comparative phosphoproteomic analysis of human embryonic stem cells (hESCs). The accomplishment is the first of its kind and also includes a detailed analysis of differentiated derivatives of hESCs. Data from the study may ultimately allow for greater control over the molecular mechanisms that determine whether or not stem cells differentiate into more specialized cells, or merely divide without differentiating.

Protein phosphorylation, a biochemical process which is essential for cell signaling, involves the modification of protein activity via the addition of a phosphate molecule. It is one of the most widely studied aspects of protein modification and commonly employed as a fundamental tool of proteomics. A logical extension of "genomics", proteomics is defined as the large-scale study of proteins, and in particular of the mechanisms by which the 3-dimensional structure of any particular protein influences biochemical function and activity. Similar to the concept of a genome, the "proteome" consists of the entire complement of proteins which any particular biological system or organism produces.

Combining both areas of specialization, the scientists in the current study used methods of "phosphoproteomic" analysis to catalogue 2,546 phosphorylation sites on 1,602 phosphoproteins, the identification of which has now shed new light on signaling pathways. Follow-up experiments further confirmed specific phosphoproteins and cell pathways that the researchers had identified using the phosphoproteomic data as a predictive tool in target samples. Among other findings, the scientists observed the various roles that phosphorylation plays in determining cell fate, especially in the phosphorylation of various kinases as well as specific transcription regulators such as epigenetic and transcription factors. In particular, proteins that are involved in the JNK (Jun N-terminal kinase) signaling transduction pathway were observed to be phosphorylated in undifferentiated hESCs, a finding which would suggest that JNK signaling inhibition may be involved in cell differentiation, as independently confirmed by other hESC studies. Additionally, phosphoproteins involved in the RTK (receptor tyrosine kinase) signaling pathways were found to be especially numerous in undifferentiated hESCs, and follow-up studies demonstrated that multiple RTKs can maintain hESCs in an undifferentiated state.

According to Dr. Laurence Brill, a member of the team of researchers who conducted the study, "This research will be a big boost for stem cell scientists. The protein phosphorylation sites identified in this study are freely available to the broader research community, and researchers can use these data to study the cells in greater depth and determine how phosphorylation events determine a cell's fate."

Prior to this particular study, protein phosphorylation was poorly understood in hESCs, and even though the process is still not yet fully elucidated, the study nevertheless demonstrates the utility of phosphoproteomic data as a predictive and analytic tool in the determination of cell fate, at least within hESCs. Extrapolation to mechanisms of differentiation and cell fate in adult stem cells should prove to be of even greater and more immediate clinical utility, however, since adult stem cells are already being used in the treatment of a wide variety of diseases and injuries, unlike hESCs, which have yet to advance beyond the experimental laboratory stage.

Along with Dr. Laurence Brill, the team of scientists who conducted the study also include Drs. Sheng Ding and Evan Y. Snyder.