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Open Access Research article

Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells

Kristin P Bennett1*, Charles Bergeron1, Evrim Acar2, Robert F Klees3, Scott L Vandenberg4, Bülent Yener2 and George E Plopper3

Author Affiliations

1 Department of Mathematical Sciences, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA

2 Department of Computer Science, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA

3 Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA

4 Department of Computer Science, Siena College, 515 Loudon Road, Loudonville, NY 12211, USA

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BMC Genomics 2007, 8:380  doi:10.1186/1471-2164-8-380

Published: 19 October 2007

Abstract

Background

Recently, we demonstrated that human mesenchymal stem cells (hMSC) stimulated with dexamethazone undergo gene focusing during osteogenic differentiation (Stem Cells Dev 14(6): 1608–20, 2005). Here, we examine the protein expression profiles of three additional populations of hMSC stimulated to undergo osteogenic differentiation via either contact with pro-osteogenic extracellular matrix (ECM) proteins (collagen I, vitronectin, or laminin-5) or osteogenic media supplements (OS media). Specifically, we annotate these four protein expression profiles, as well as profiles from naïve hMSC and differentiated human osteoblasts (hOST), with known gene ontologies and analyze them as a tensor with modes for the expressed proteins, gene ontologies, and stimulants.

Results

Direct component analysis in the gene ontology space identifies three components that account for 90% of the variance between hMSC, osteoblasts, and the four stimulated hMSC populations. The directed component maps the differentiation stages of the stimulated stem cell populations along the differentiation axis created by the difference in the expression profiles of hMSC and hOST. Surprisingly, hMSC treated with ECM proteins lie closer to osteoblasts than do hMSC treated with OS media. Additionally, the second component demonstrates that proteomic profiles of collagen I- and vitronectin-stimulated hMSC are distinct from those of OS-stimulated cells. A three-mode tensor analysis reveals additional focus proteins critical for characterizing the phenotypic variations between naïve hMSC, partially differentiated hMSC, and hOST.

Conclusion

The differences between the proteomic profiles of OS-stimulated hMSC and ECM-hMSC characterize different transitional phenotypes en route to becoming osteoblasts. This conclusion is arrived at via a three-mode tensor analysis validated using hMSC plated on laminin-5.