Embryonic stem cell proteomics

References

• Keller G. Embryonic stem cell differentiation: emergence of a new era in biology and medicine. Genes Dev.19, 1129–1155 (2005).
   PubMed Web of Science ®Google Scholar
• Bradley A, Evans M, Kaufman MH, Robertson E. Formation of germ-line chimaeras from embryo-derived teratocarcinoma cell lines. Nature309, 255–256 (1984).
   PubMed Web of Science ®Google Scholar
• Evans MJ, Kaufman MH. Establishment in culture of pluripotential cells from mouse embryos. Nature292, 154–156 (1981).
   PubMed Web of Science ®Google Scholar
• Martin GR. Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc. Natl Acad. Sci. USA 78, 7634–7638 (1981).
   PubMed Web of Science ®Google Scholar
• Thomson JA, Itskovitz-Eldor J, Shapiro SS et al. Embryonic stem cell lines derived from human blastocysts. Science282, 1145–1147 (1998).
   PubMed Web of Science ®Google Scholar
• Reubinoff BE, Pera MF, Fong CY, Trounson A, Bongso A. Embryonic stem cell lines from human blastocysts: somatic differentiation in vitro. Nat. Biotechnol.18, 399–404 (2000).
   PubMed Web of Science ®Google Scholar
• Cowan CA, Klimanskaya I, McMahon J et al. Derivation of embryonic stem-cell lines from human blastocysts. N. Eng. J. Med.350, 1353–1356 (2004).
   PubMed Web of Science ®Google Scholar
• Daheron L, Opitz SL, Zaehres H et al. LIF/STAT3 signaling fails to maintain self-renewal of human embryonic stem cells. Stem Cells22, 770–778 (2004).
   PubMed Web of Science ®Google Scholar
• Williams RL, Hilton DJ, Pease S et al. Myeloid leukaemia inhibitory factor maintains the developmental potential of embryonic stem cells. Nature336,684–687 (1988).
   PubMed Web of Science ®Google Scholar
• Smith AG, Heath JK, Donaldson DD, et al. Inhibition of pluripotential embryonic stem cell differentiation by purified polypeptides. Nature336, 688–690 (1988).
   PubMed Web of Science ®Google Scholar
• Rao M. Conserved and divergent paths that regulate self-renewal in mouse and human embryonic stem cells. Dev. Biol.275, 269–286 (2004).
   PubMed Web of Science ®Google Scholar
• Boiani M, Scholer HR. Regulatory networks in embryo-derived pluripotent stem cells. Mol. Cell Biol.6, 872–884 (2005).
   Google Scholar
• Smith A. Embryonic stem cells. In: Stem Cell Biology. Marshak DR, Gardner RL, Gottlieb D (Eds). Cold Spring Harbor Laboratory Press, NY, USA, 205–230 (2001).
   Google Scholar
• Pera MF, Trounson AO. Human embryonic stem cells: prospects for development. Development131, 5515–5525 (2004).
   PubMed Web of Science ®Google Scholar
• Wobus AM, Boheler KR. Embryonic stem cells: prospects for developmental biology and cell therapy. Physiol. Rev.85, 635–678 (2005).
   PubMed Web of Science ®Google Scholar
• Sekkai D, Gruel G, Herry M et al. Microarray analysis of LIF/Stat3 transcriptional targets in embryonic stem cells. Stem Cells23, 1634–1642 (2005).
   PubMedGoogle Scholar
• Andrews PW, Benvenisty N, McKay R et al. The International Stem Cell Initiative: toward benchmarks for human embryonic stem cell research. Nat. Biotechnol.23, 795–797 (2005).
   PubMed Web of Science ®Google Scholar
• Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 422, 198–207 (2003).
   PubMed Web of Science ®Google Scholar
• Patterson SD, Aebersold RH. Proteomics: the first decade and beyond. Nat. Genet.33, 311–323 (2003).
   PubMed Web of Science ®Google Scholar
• Unwin RD, Gaskell SJ, Evans CA, Whetton AD. The potential for proteomic definition of stem cell populations. Exp. Hematol.31, 1147–1159 (2003).
   PubMed Web of Science ®Google Scholar
• Beausoleil SA, Jedrychowski M, Schwartz D et al. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl Acad. Sci.USA101, 12130–12135 (2004).
   PubMed Web of Science ®Google Scholar
• De Hoog CL, Mann M. Proteomics. Annu. Rev. Genomics Hum. Genet.5, 267–293 (2004).
   PubMed Web of Science ®Google Scholar
• Kelly DL, Rizzino A. DNA microarray analyses of genes regulated during the differentiation of embryonic stem cells. Mol. Reprod. Dev.56, 113–123 (2000).
   PubMed Web of Science ®Google Scholar
• Ramalho-Santos M, Yoon S, Matsuzaki Y, Mulligan RC, Melton DA. ‘Stemness’: transcriptional profiling of embryonic and adult stem cells. Science298, 597–600 (2002)
   PubMed Web of Science ®Google Scholar
• Ivanova NB, Dimos JT, Schaniel C et al. A stem cell molecular signature. Science298, 601–604 (2002).
   PubMed Web of Science ®Google Scholar
• Sato N, Sanjuan IM, Heke M et al. Molecular signature of human embryonic stem cells and its comparison with the mouse. Dev. Biol.260, 404–413 (2003).
   PubMed Web of Science ®Google Scholar
• Ginis I, Luo Y, Miura T et al. Differences between human and mouse embryonic stem cells. Dev. Biol.269, 360–380 (2004).
   PubMed Web of Science ®Google Scholar
• Palmqvist L, Glover CH, Hsu L et al. Correlation of murine embryonic stem cell gene expression profiles with functional measures of pluripotency. Stem Cells23, 663–680 (2005).
   PubMedGoogle Scholar
• Anisimov SV, Tarasov KV, Tweedie D et al. SAGE identification of gene transcripts with profiles unique to pluripotent mouse R1 embryonic stem cells. Genomics79, 169–176 (2002).
   PubMedGoogle Scholar
• Wei CL, Miura T, Robson P et al. Transcriptome profiling of human and murine ESCs identifies divergent paths required to maintain the stem cell state. Stem Cells23, 166–185 (2005).
   PubMed Web of Science ®Google Scholar
• Guo X, Ying W, Wan J et al. Proteomic characterization of early-stage differentiation of mouse embryonic stem cells into neural cells induced by all-trans retinoic acid in vitro. Electrophoresis22, 3067–3075 (2001).
   PubMed Web of Science ®Google Scholar
• Elliott ST, Crider DG, Garnham CP, Boheler KR, Van Eyk JE. Two-dimensional gel electrophoresis database of murine R1 embryonic stem cells. Proteomics4, 3813–3832 (2004).
   PubMed Web of Science ®Google Scholar
• Nagano K, Taoka M, Yamauchi Y, et al. Large-scale identification of proteins expressed in mouse embryonic stem cells. Proteomics5, 1346–1361 (2005).
   PubMed Web of Science ®Google Scholar
• Niwa H, Miyazaki J, Smith AG. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat. Genet.24, 372–376 (2000).
   PubMed Web of Science ®Google Scholar
• Okuda A, Fukushima A, Nishimoto M et al. UTF1, a novel transcriptional coactivator expressed in pluripotent embryonic stem cells and extra-embryonic cells. EMBO J.17, 2019–2032 (1998).
   PubMed Web of Science ®Google Scholar
• Nunomura K, Nagano K, Itagaki C et al. Cell surface labeling and mass spectrometry reveal diversity of cell surface markers and signaling molecules expressed in undifferentiated mouse embryonic stem cells. Mol. Cell. Proteomics4, 1968–1976 (2005).
   PubMed Web of Science ®Google Scholar
• Hirokawa T, Boon-Chieng S, Mitaku S. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics14, 378–379 (1998).
   PubMed Web of Science ®Google Scholar
• 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 (2006) Published ahead of print April 6, 2006; DOI 10.1074/mcp.M500405-MCP200.
   PubMedGoogle Scholar
• Ying QL, Nichols J, Chambers I, Smith A. BMP induction of Id proteins suppresses differentiation and sustains embryonic stem cell self-renewal in collaboration with STAT3. Cell115, 281–292 (2003).
   PubMed Web of Science ®Google Scholar
• Kurisaki A, Hamazaki TS, Okabayashi K et al. Chromatin-related proteins in pluripotent mouse embryonic stem cells are downregulated after removal of leukemia inhibitory factor. Biochem. Biophys. Res. Comm.335, 667–675 (2005).
   PubMedGoogle Scholar
• Lilley KS, Friedman DB. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev. Proteomics1, 401–409 (2004).
   PubMed Web of Science ®Google Scholar
• Wang D, Gao L. Proteomic analysis of neural differentiation of mouse embryonic stem cells. Proteomics5, 4414–4426 (2005).
   PubMedGoogle Scholar
• Hu Y, Zhang Z, Torsney E et al. Abundant progenitor cells in the adventitia contribute to atherosclerosis of vein grafts in ApoE-deficient mice. J. Clin. Invest.113, 1258–1265 (2004).
   PubMed Web of Science ®Google Scholar
• Yin X, Mayr M, Xiao Q et al. Proteomic dataset of Sca-1+ progenitor cells. Proteomics5, 4533–4545 (2005).
   PubMed Web of Science ®Google Scholar
• Prudhomme W, Daley GQ, Zandstra P, Lauffenburger DA. Multivariate proteomic analysis of murine embryonic stem cell self-renewal versus differentiation signaling. Proc. Natl Acad. Sci.USA101, 2900–2905 (2004).
   PubMed Web of Science ®Google Scholar
• Puente LG, Borris DJ, Carriere JF, Kelly JF, Megeney LA. Identification of candidate regulators of embryonic stem cell differentiation by comparative phosphoprotein-affinity profiling. Mol. Cell. Proteomics5, 57–67 (2006).
   PubMedGoogle Scholar
• Perez-Iratxeta C, Palidwor G, Porter CJ et al. Study of stem cell function using microarray experiments. FEBS Lett.579, 1795–1801 (2005).
   Google Scholar
• Richards M, Tan SP, Tan JH, Chan WK, Bongso A. The transcriptome profile of human embryonic stem cells as defined by SAGE. Stem Cells22, 51–64 (2004).
   PubMed Web of Science ®Google Scholar
• Abeyta MJ, Clark AT, Rodriguez RT et al. Unique gene expression signatures of independently-derived human embryonic stem cell lines. Hum. Mol. Genet.13, 601–608 (2004).
   PubMed Web of Science ®Google Scholar
• Brandenberger R, Wei H, Zhang S et al. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. Nat. Biotechnol.22, 707–716 (2004).
   PubMed Web of Science ®Google Scholar
• Bhattacharya B, Miura T, Brandenberger R et al. Gene expression in human embryonic stem cell lines: unique molecular signature. Blood103, 2956–2964 (2004).
   PubMed Web of Science ®Google Scholar
• Zenzmaier C, Kollroser M, Gesslbauer B et al. Preliminary 2D chromatographic investigation of the human stem cell proteome. Biochem. Biophys. Res. Comm.310, 483–490 (2003).
   PubMedGoogle Scholar
• Tao W, Wang M, Voss ED et al. Comparative proteomic analysis of human CD34+ stem/progenitor cells and mature CD15+ myeloid cells. Stem Cells22, 1003–1014 (2004).
   PubMed Web of Science ®Google Scholar
• Wang D, Park JS, Chu JS et al. Proteomic profiling of bone marrow mesenchymal stem cells upon transforming growth factor beta1 stimulation. J. Biol. Chem.279, 43725–43734 (2004).
   PubMed Web of Science ®Google Scholar
• Salasznyk RM, Westcott AM, Klees RF et al. Comparing the protein expression profiles of human mesenchymal stem cells and human osteoblasts using gene ontologies. Stem Cells14, 354–366 (2005).
   Google Scholar
• Foster LJ, Zeemann PA, Li C, Mann M, Jensen ON, Kassem M. Differential expression profiling of membrane proteins by quantitative proteomics in a human mesenchymal stem cell line undergoing osteoblast differentiation. Stem Cells23, 1367–1377 (2005).
   PubMed Web of Science ®Google Scholar
• Maurer MH, Feldmann RE Jr, Bromme JO, Kalenka A. Comparison of statistical approaches for the analysis of proteome expression data of differentiating neural stem cells. J. Proteome Res.496 (2005).
   PubMedGoogle Scholar
• Zenzmaier C, Gesslbauer B, Grobuschek N, Jandrositz A, Preisegger KH, Kungl AJ. Proteomic profiling of human stem cells derived from umbilical cord blood. Biochem. Biophys. Res. Comm.328, 968–972 (2005).
   PubMedGoogle Scholar
• Feldmann RE Jr, Bieback K, Maurer MH, et al. Stem cell proteomes: a profile of human mesenchymal stem cells derived from umbilical cord blood. Electrophoresis26, 2749–2758 (2005).
   PubMed Web of Science ®Google Scholar
• DeLany JP, Floyd ZE, Zvonic S et al. Proteomic analysis of primary cultures of human adipose-derived stem cells: modulation by adipogenesis. Mol. Cell. Proteomics4, 731–740 (2005).
   PubMed Web of Science ®Google Scholar
• Hayman MW, Przyborski SA. Proteomic identification of biomarkers expressed by human pluripotent stem cells. Biochem. Biophys. Res. Comm.316, 918–923 (2004).
   PubMed Web of Science ®Google Scholar
• Unwin RD, Smith DL, Blinco D et al. Quantitative proteomics reveals post-translational control as a regulatory factor in primary hematopoietic stem cells. Blood (2006) in press.
   PubMedGoogle Scholar
• Doetschman TC, Eistetter H, Katz M, Schmidt W, Kemler R. The in vitro development of blastocyst-derived embryonic stem cell lines: formation of visceral yolk sac, blood islands and myocardium. J. Embryol. Exp. Morphol.87, 27–45 (1985).
   PubMedGoogle Scholar
• Mummery CL, Slager H, Kruijer W et al. Expression of transforming growth factor beta 2 during the differentiation of murine embryonal carcinoma and embryonic stem cells. Dev. Biol.137, 161–170 (1990).
   PubMed Web of Science ®Google Scholar
• Van de Stolpe A, Van den Brink S, Van Rooijen M et al. Human embryonic stem cells: towards therapies for cardiac disease. Derivation of a Dutch human embryonic stem cell line. Reprod Biomed Online11, 476–485 (2005).
   PubMedGoogle Scholar
• Hoffman LM, Carpenter MK. Characterization and culture of human embryonic stem cells. Nat. Biotechnol.23, 699–708 (2005).
   PubMed Web of Science ®Google Scholar
• Lim JW, Bodnar A. Proteome analysis of conditioned medium from mouse embryonic fibroblast feeder layers which support the growth of human embryonic stem cells. Proteomics2, 1187–1203 (2002).
   PubMedGoogle Scholar
• Richards M, Fong CY, Chan WK, Wong PC, Bongso A. Human feeders support prolonged undifferentiated growth of human inner cell masses and embryonic stem cells. Nat. Biotechnol.20, 933–936 (2002).
   PubMed Web of Science ®Google Scholar
• Prowse AB, McQuade LR, Bryant KJ, Van Dyk DD, Tuch BE, Gray PP. A proteome analysis of conditioned media from human neonatal fibroblasts used in the maintenance of human embryonic stem cells. Proteomics5, 978–989 (2005).
   PubMed Web of Science ®Google Scholar
• Heck AJ, Krijgsveld J. Mass spectrometry-based quantitative proteomics. Expert Rev. Proteomics1, 317–326 (2004).
   PubMed Web of Science ®Google Scholar
• Pinkse MW, Uitto PM, Hilhorst MJ, Ooms B, Heck AJR. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal. Chem.76, 3935–3943 (2004).
   PubMed Web of Science ®Google Scholar
• Ong SE, Mann M. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol.1, 252–262 (2005).
   PubMed Web of Science ®Google Scholar
• Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol.17, 994–999 (1999).
   PubMed Web of Science ®Google Scholar
• Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics3, 1154–1169 (2004).
   PubMed Web of Science ®Google Scholar
• Blagoev B, Ong SE, Kratchmarova I, Mann M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat. Biotechnol.22, 1139–1145 (2004).
   PubMed Web of Science ®Google Scholar
• Martin MJ, Muotri A, Gage F, Varki A. Human embryonic stem cells express an immunogenic nonhuman sialic acid. Nat. Medicine11, 228–232 (2005).
   PubMed Web of Science ®Google Scholar
• Wu WW, Wang G, Baek SJ, Shen RF. Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF. J. Proteome Res.5, 651–658 (2006).
   PubMed Web of Science ®Google Scholar
• Jensen ON. Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Curr. Opin. Chem. Biol.8, 33–41 (2004).
   PubMed Web of Science ®Google Scholar
• Gruhler A, Olsen JV, Mohammed S et al. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell. Proteomics4, 310–327 (2005).
   PubMed Web of Science ®Google Scholar