Comparing the Protein Expression Profiles of Human Mesenchymal Stem Cells and Human Osteoblasts Using Gene Ontologies

Stem cells: shibboleths of development, part II: Toward a functional definition

Our previous discourse on stem cell characteristics led to the conclusion that the qualities deemed essential for a cell to be considered a "stem cell" are neither firmly established nor universally accepted, and this we accept as editorial policy. In that study, self-renewal, asymmetric division, phenotypic markers, and other attributes touted as being indicative of cells being stem cells were critically questioned as fundamental to the definition of a stem cell, leading us to seek a functional definition instead. Here, we offer further considerations, and elaborate on the characteristics that diverse investigators feel are essential for a cell to function as a stem cell, either in development or body maintenance. We hope that this discourse will promote further reflection, culminating with a definition that is widely accepted and universally applicable. We confess this goal has not been reached, neither here nor elsewhere. The outstanding goal of understanding what stem cells are, a prerequisite of characterizing what stem cells do and how they do it, is still outstanding.

Focusing of Gene Expression as the Basis of Stem Cell Differentiation

In a prior report (Stem Cells Dev 14(4):354-366, 2005), we employed two-dimensional gel electrophoresis followed by advanced proteomics and the Database for Annotation, Visualization and Integrated Discovery (DAVID) to compare the protein expression profiles of mesenchymal stem cells to that of fully differentiated osteoblasts. These data were reported to advance technical approaches to define the basis of differentiation, but also led us to suggest that osteogenic differentiation of stem cells may result from the focusing of gene expression in functional clusters (e.g., calcium-regulated signaling proteins or adherence proteins) rather than simply from the induced expression of new genes, as many have assumed. Here, we have employed these analytical techniques to compare protein expression by mesenchymal stem cells directly with that of cells derived from them after induced osteogenic differentiation. Our results support the concept of gene focusing as the basis of differentiation. Specifically, induced differentiation results in a decrease in the number of mesenchymal cell markers and calcium-mediated signaling molecules expressed by their differentiated progeny. This effect was seen in parallel to increased expression of specific extracellular matrix (ECM) molecules and their receptors. These results strongly imply that changes in the ECM have a direct impact on stem cell differentiation, and that osteogenic differentiation of stem cells directed by matrix clues results from focusing of the expression of genes involved in Ca2+-dependent signaling pathways.