Proteomic Analysis of Mouse ES Cells

Embryonic stem (ES) cells have generated enormous interest because of their capacity to self-renew and differentiate into various cell types in vitro. Although numerous problems are encountered in the use of ES cells for regenerative medicine, such as ethical issues associated with the use of stem cells established from terminated human embryos and immunorejection due to transplantation of allogenic ES cell-derived cells into patients, recent technologies to generate induced pluripotent stem (iPS) cells from adult somatic cells have provided alternative ways to access pluripotent stem cells (Takahashi et al., 2007). However, the practical application of these pluripotent stem cells has yet to emerge, and regulatory mechanisms are not well known. Moreover, precise differentiation methodologies of ES and iPS cells have not been developed. These problems cause difficulties in the manipulation of pluripotent stem cells and derivation of functionally differentiated cells. Detailed analysis of the transcriptome has allowed elucidation of transcription networks that regulate the pluripotency of these stem cells. However, the specific nuclear infrastructures that maintain the pluripotent stem cell-specific transcription network have not yet been elucidated. We used proteomics to analyze the nuclear protein machinery in stem cells and identified some crucial components for the maintenance of pluripotent stem cells. In addition, various growth factors and extracellular matrix components regulate the pluripotency and differentiation of stem cells. Therefore, the cell surface receptors that bind these regulatory factors are important for the precise regulation of stem cells. We have also explored stem cell-specific cellsurface markers by proteomic analysis of mouse ES cells. These cell-surface membrane proteins can be useful to manipulate pluripotent stem cells. In this chapter, we describe some examples of new findings elucidated by proteomic analysis of ES cells.