Pluripotent stem cell heterogeneity and the evolving role of proteomic technologies in stem cell biology

Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
Proteomics (Impact Factor: 3.81). 10/2011; 11(20):3947-61. DOI: 10.1002/pmic.201100100
Source: PubMed


Stem cells represent obvious choices for regenerative medicine and are invaluable for studies of human development and drug testing. The proteomic landscape of pluripotent stem cells (PSCs), in particular, is not yet clearly defined; consequently, this field of research would greatly benefit from concerted efforts designed to better characterize these cells. In this concise review, we provide an overview of stem cell potency, highlight the types and practical implications of heterogeneity in PSCs and provide a detailed analysis of the current view of the pluripotent proteome in a unique resource for this rapidly evolving field. Our goal in this review is to provide specific insights into the current status of the known proteome of both mouse and human PSCs. This has been accomplished by integrating published data into a unified PSC proteome to facilitate the identification of proteins, which may be informative for the stem cell state as well as to reveal areas where our current view is limited. These analyses provide insight into the challenges faced in the proteomic analysis of PSCs and reveal one area--the cell surface subproteome--that would especially benefit from enhanced research efforts.

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    • "Molecular and functional heterogeneities in cell populations is not unique to hBMSCs; it is a widespread phenomenon among stem cells including embryonic (Canham et al., 2010), hematopoietic (Schroeder, 2010), neural (Suslov et al., 2002), and cancer stem cells (Wong et al., 2012). The analysis of major proteomic studies (n = 34) of human and mouse pluripotent stem cells (hPSCs and mPSCs) by Gundry et al. highlighted the degree of heterogeneity among pluripotent stem cell populations (Gundry et al., 2011). "
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    ABSTRACT: The clinical application of human bone marrow stromal cells (hBMSCs) largely depends on their capacity to expand in vitro. We have conducted a comprehensive comparative proteomic analysis of culture-expanded hBMSCs obtained from different human donors. The data reveal extensive donor-to-donor proteomic heterogeneity. Processing and database-searching of the tandem MS data resulted in a most comprehensive to date proteomic dataset for hBMSC. A total of 7753 proteins including 712 transcription and translation regulators, 384 kinases, 248 receptor proteins, and 29 cytokines were confidently identified. The proteins identified are mainly nuclear (43.2%) and the share of proteins assigned to more than one subcellular location constitutes 10% of the identified proteome. Bioinformatics tools (IPA, DAVID, and PANTHER) were used to annotate proteins with respect to cellular locations, functions, and other physicochemical characteristics. We also compared the proteomic profile of hBMSCs to recently compiled datasets for human and mouse pluripotent stem cells. The result shows the extent of similarity between the three cell populations and also identified 253 proteins expressed uniformly by all lines of hBMSCs but not reported in the proteomic datasets of the two pluripotent stem cells. Overall, the proteomic database reported in this paper can serve as a reference map for extensive evaluation of hBMSC to explain their biology as well as identify possible marker candidates for further evaluation.
    Stem Cell Research 06/2013; 11(2):793-805. DOI:10.1016/j.scr.2013.05.006 · 3.69 Impact Factor
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    • "Another reason for us to believe the detected diversity at least partially specific to stem cells is the population heterogeneity inherent to stem cells [75], which increases the likelihood to observe different membrane proteins. For example, the examination of the proteomes of 7 mES cell studies, each with >1000 protein identifications, yielded only a small overlap of 27% among themselves; and about 61% of the proteins were identified only in one or two studies [75]. "
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    ABSTRACT: E14.Tg2a mouse embryonic stem (mES) cells are a widely used host in gene trap and gene targeting techniques. Molecular characterization of host cells will provide background information for a better understanding of functions of the knockout genes. Using a highly selective glycopeptide-capture approach but ordinary liquid chromatography coupled mass spectrometry (LC-MS), we characterized the N-glycoproteins of E14.Tg2a cells and analyzed the close relationship between the obtained N-glycoproteome and cell-surface proteomes. Our results provide a global view of cell surface protein molecular properties, in which receptors seem to be much more diverse but lower in abundance than transporters on average. In addition, our results provide a systematic view of the E14.Tg2a N-glycosylation, from which we discovered some striking patterns, including an evolutionarily preserved and maybe functionally selected complementarity between N-glycosylation and the transmembrane structure in protein sequences. We also observed an environmentally influenced N-glycosylation pattern among glycoenzymes and extracellular matrix proteins. We hope that the acquired information enhances our molecular understanding of mES E14.Tg2a as well as the biological roles played by N-glycosylation in cell biology in general.
    PLoS ONE 02/2013; 8(2):e55722. DOI:10.1371/journal.pone.0055722 · 3.23 Impact Factor
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    • "Compared with published proteomic studies of PSCs (i.e. 34 studies of mouse and human PSC lines; herein referred to as the " PSC proteome " (Gundry et al., 2011), 187 proteins (37% of the current data) have not been reported among the 7487 proteins previously described in mouse PSCs (Fig. 1D), and 128 proteins (25% of the current data) were identified in only a single other study. For 175 proteins, UniProt annotations for experimental data do not exist at the protein level in mouse (i.e. "
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    ABSTRACT: Induction of a pluripotent state in somatic cells through nuclear reprogramming has ushered in a new era of regenerative medicine. Heterogeneity and varied differentiation potentials among induced pluripotent stem cell (iPSC) lines are, however, complicating factors that limit their usefulness for disease modeling, drug discovery, and patient therapies. Thus, there is an urgent need to develop nonmutagenic rapid throughput methods capable of distinguishing among putative iPSC lines of variable quality. To address this issue, we have applied a highly specific chemoproteomic targeting strategy for de novo discovery of cell surface N-glycoproteins to increase the knowledge-base of surface exposed proteins and accessible epitopes of pluripotent stem cells. We report the identification of 500 cell surface proteins on four embryonic stem cell and iPSCs lines and demonstrate the biological significance of this resource on mouse fibroblasts containing an oct4-GFP expression cassette that is active in reprogrammed cells. These results together with immunophenotyping, cell sorting, and functional analyses demonstrate that these newly identified surface marker panels are useful for isolating iPSCs from heterogeneous reprogrammed cultures and for isolating functionally distinct stem cell subpopulations.
    Molecular &amp Cellular Proteomics 04/2012; 11(8):303-16. DOI:10.1074/mcp.M112.018135 · 6.56 Impact Factor
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