Following the Differentiation of Human Pluripotent Stem Cells by Proteomic Identification of Biomarkers

Proteome of mesenchymal stem cells

Proteomics has evolved, in recent years, into effective tools for basic and applied stem cell research, and has been extensively used to facilitate the identification of changes in signal transduction components, especially with regard to plasticity, proliferation, and differentiation. Several recent reports have also employed proteomic strategies to characterize human mesenchymal stem cells (hMSC) and their differentiated derivatives. Although these approaches have yielded valuable data, the results highlight the fact that only the limited numbers of proteins are characterized at the protein level in these cells, thus necessitating expandable MSC proteome dataset. This review presents, for the first time, an expandable list of MSC proteins, which will function as a starting point for the generation of a comprehensive reference map of their proteome. Also, the better way to bridge current gap between genomics and proteomics study such as integrated proteomic and transcriptomic analyses is discussed.

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

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.

Umbilical cord-derived stem cells for tissue therapy: current and future uses

Organ and tissue transplants provide a means to correct disease but are limited, mostly owing to the lack of available donor tissue. Tissue matching and speed of procurement are important parameters that must be met for a successful graft, however the lack of available donors leads to expanding waiting lists and suboptimal human leukocyte antigen-matching, often leading to reduced transplant success. The discovery of embryonic stem cells and tissue-specific stem cells has provided hope for many patients. Stem cell-based therapy has provided possible new sources of human leukocyte antigen-matched tissue but, before routine clinical application of stem cells becomes a reality, many obstacles must first be overcome. Focusing on umbilical cord blood cells, we discuss some of the challenges that stem cell therapy faces, including obtaining clinically relevant numbers of stem cells and the ability of stem cells to provide for permanent engraftment of multiple tissue types. We discuss possible solutions to these problems, such as in vitro stem cell expansion and the differentiation potential of tissue-specific stem cells.

Can large-scale analysis of the proteome identify effective new markers for embryonic stem cells?

Evaluation of: van Hoof D, Passier R, Ward-Van Oostwaard D et al.: A quest for human and mouse embryonic stem cell specific proteins. Mol. Cell. Proteomics 5, 1261–1273 (2006) [1] . Embryonic stem cells (ESCs) are broadly regarded as the most promising source of future cell-based regenerative therapies, although current limitations in our ability to accurately define and monitor their behavior will have to be overcome. The search for new cell-specific markers, as well as the desire to better understand stem cells at the molecular level, is a major driving force behind the use of proteomics in stem cell systems. In 2006, a high-throughput proteomic strategy was adopted to identify ESC-exclusive proteins in human and mouse ESC lines. The study identified novel putative ESC-specific markers and incorporated substantial immunological validation. Analysis of the proteome on this scale represents a significant step in bridging the gap between gene expression data and observed cellular behavior and demonstrates the potential of proteomics for the identification of valid stem cell biomarkers.

Application of proteomic technology to neural stem cell science and neurology

There is widespread recognition of the potential that stem cells hold for the treatment and repair of a large number of disorders affecting the human CNS. Therefore, stem cell research will go hand in hand with progress in specific areas of neuroscience. Proteomics has great potential to make important contributions to the basic understanding of neurological processes, and to deliver much needed cellular biomarkers in both of these fields. This review focuses on the importance of proteomic research in neuroscience, in particular the application of biomarker discovery in stem cells and degenerative diseases of the CNS.