Proteomics Approaches Applied to Regenerative Medicine: Perspectives in Stem Cell Proteomics

  • Saeed Heidari-Keshel
  • Mostafa Rezaei-Tavirani
  • Azam Rahimi
  • Farshid Sefat
  • Arash Khojasteh
Part of the Stem Cell Biology and Regenerative Medicine book series (STEMCELL)


Stem cells are able to maintain self-renewal for a long time. Under certain conditions, these cells may differentiate into adult and functional cell types. According to their origin and developmental capacity two essential types of stem cells are classified: embryonic and adult or mesenchymal stem cells. Human embryonic stem cells (hESCs) are able to generate adult somatic tissue cells because they are pluripotent cells but other types of stem cells are called tissue-specific because each of them is particular to specific tissue. Proteomics studies have the potency to define molecules and pathways pivotal for cell biology and the strategies by which cells can participate in transplantation and repair. The proteome is the whole protein content that expressed in an organism. The proteomics final goal is to characterize information flow, with protein analysis, pathways, and networks. In this chapter, we tried to explain proteomics studies of embryonic stem cells and discuss their extraordinary characteristics or properties which make them interesting in medical investigations. The hESCs differentiation pattern prepares a model for examining the cellular and molecular events of early development that is cellular and molecular with a significant potency for the progression of proteome analysis. Proteins expressed by a large number of genes are characterized and the pattern of expression has been compared between iPSCs and ESCs. We will investigate adult or mesenchymal stem cell proteomics and after that about the proteomic study of iPSC and finally the methodology used for both of them.


Stem cell Proteomics Regenerative medicine 


  1. 1.
    Kingham E, Oreffo R. Embryonic and induced pluripotent stem cells: understanding, creating and exploiting the nano-niche for regenerative medicine. ACS Nano. 2013;3:1867–81.CrossRefGoogle Scholar
  2. 2.
    Bernstein H, Hyun W. Strategies for enrichment and selection of stem cell-derived tissue precursors. Stem Cell Res Ther. 2012;3:1–14.CrossRefGoogle Scholar
  3. 3.
    Lorelei D, Harley I. Neural stem cells (NSC) and proteomics. Cell Proteom. 2016;15:344–54.CrossRefGoogle Scholar
  4. 4.
    Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 2003;422:198–207.CrossRefGoogle Scholar
  5. 5.
    Vlahou A, Fountoulakis M. Proteomic approaches in the search for disease biomarkers. Biomed Life Sci. 2005;814:11–9.CrossRefGoogle Scholar
  6. 6.
    Atkinson S, Armstrong L. Epigenetics in embryonic stem cells: regulation of pluripotency and differentiation. Cell Tissue Res. 2008;331:23–9.PubMedCrossRefGoogle Scholar
  7. 7.
    Aslam B, Basit M, Nisar M, Khurshid M, Rasool M. Proteomics: technologies and their applications. J Chromatogr Sci. 2017;2:182–96.CrossRefGoogle Scholar
  8. 8.
    Jungbauer A, Hahn R. Ion-exchange chromatography. Methods Enzymol. 2009;463:349–71.PubMedCrossRefPubMedCentralGoogle Scholar
  9. 9.
    Voedisch B, Thie H. Size exclusion chromatography. In: Kontermann R, Dübel S, editors. Antibody engineering. Berlin: Springer; 2010. p. 607–12.CrossRefGoogle Scholar
  10. 10.
    Hage DS, Anguizola JA, Bi C, Li R, Matsuda R, Papastavros E. Pharmaceutical and biomedical applications of affinity chromatography: recent trends and developments. J Pharm Biomed Anal. 2012;69:93–105.PubMedPubMedCentralCrossRefGoogle Scholar
  11. 11.
    Lequin RM. Enzyme immunoassay (EIA)/enzyme-linked immunosorbent assay (ELISA). Clin Chem. 2005;51:2415–8.PubMedCrossRefGoogle Scholar
  12. 12.
    Kurien B, Scofield R. Western blotting. Methods. 2006;38:283–93.PubMedCrossRefGoogle Scholar
  13. 13.
    Issaq H, Veenstra T. Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE): advances and perspectives. BioTechniques. 2008;44:697–700.PubMedCrossRefGoogle Scholar
  14. 14.
    Marouga R, David S, Hawkins E. The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem. 2005;382:669–78.PubMedCrossRefGoogle Scholar
  15. 15.
    Ong S, Mann M. Stable isotope labeling by amino acids in cell culture for quantitative proteomics. Methods Mol Biol. 2007;359:37–52.PubMedCrossRefPubMedCentralGoogle Scholar
  16. 16.
    Wiese S, Reidegeld KA, Meyer HE, Warscheid B. Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics. 2007;7:340–50.PubMedCrossRefPubMedCentralGoogle Scholar
  17. 17.
    Kroksveen AC, Jaffe JD, Aasebo E, Barsnes H, Bjorlykke Y. Quantitative proteomics suggests a decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis. Proteomics. 2015;15:3361–9.PubMedCrossRefGoogle Scholar
  18. 18.
    Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaino JA. Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics. 2015;15:930–49.PubMedPubMedCentralCrossRefGoogle Scholar
  19. 19.
    Cox J, Mann M. Is proteomics the new genomics. Cell. 2007;130:395–8.PubMedCrossRefPubMedCentralGoogle Scholar
  20. 20.
    Cravatt BF, Simon GM, Yates JR. The biological impact of mass-spectrometry-based proteomics. Nature. 2007;450:991–1000.PubMedCrossRefGoogle Scholar
  21. 21.
    Dai B, Rasmussen TP. Global epiproteomic signatures distinguish embryonic stem cells from differentiated cells. Stem Cells. 2007;25:2567–74.PubMedCrossRefGoogle Scholar
  22. 22.
    Elling U, Klasen C, Eisenberger T, Anlag K, Treier M. Murine inner cell mass-derived lineages depend on Sall4 function. Proc Natl Acad Sci U S A. 2006;103:16319–24.PubMedPubMedCentralCrossRefGoogle Scholar
  23. 23.
    Freitas MA, Sklenar AR, Parthun MR. Application of mass spectrometry to the identification and quantification of histone post-translational modifications. J Cell Biochem. 2004;92:691–700.PubMedPubMedCentralCrossRefGoogle Scholar
  24. 24.
    Ginis I, Luo Y, Miura T, Thies S, Brandenberger R, Gerecht-Nir S, Amit M, Hoke A, Carpenter MK, Itskovitz-Eldor J, Rao MS. Differences between human and mouse embryonic stem cells. Dev Biol. 2004;269:360–80.PubMedCrossRefGoogle Scholar
  25. 25.
    Harvey DJ. Proteomic analysis of glycosylation: structural determination of N- and O-linked glycans by mass spectrometry. Proteomics. 2005;2:87–101.PubMedGoogle Scholar
  26. 26.
    Ivanova N, Dobrin R, Lu R, Kotenko I, Levorse J, DeCoste C, Schafer X, Lun Y, Lemischka IR. Dissecting self-renewal in stem cells with RNA interference. Nature. 2006;442:533–8.PubMedCrossRefGoogle Scholar
  27. 27.
    Jensen ON. Interpreting the protein language using proteomics. Nat Rev Mol Cell Biol. 2006;7:391–403.PubMedCrossRefGoogle Scholar
  28. 28.
    Joephson R, Ording CJ, Liu Y, Shin S, Lakshmipathy U, Toumadje A, Love B, Chesnut JD, Andrews PW, Rao MS, Auerbach JM. Qualification of embryonal carcinoma 2102Ep as a reference for human embryonic stem cell research. Stem Cells. 2007;25:437–46.CrossRefGoogle Scholar
  29. 29.
    Kirkpatrick DS, Denison C, Gygi SP. Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nat Cell Biol. 2005;7:750–7.PubMedPubMedCentralCrossRefGoogle Scholar
  30. 30.
    Klemm M, Schrattenholz A. Neurotoxicity of active compounds establishment of hESC-lines and proteomics technologies for human embryo and neurotoxicity screening and biomarker identification. ALTEX. 2004;21(Suppl 3):41–8.PubMedGoogle Scholar
  31. 31.
    Trounson A, McDonald C. Stem cell therapies in clinical trials: progress and challenges. Cell Stem Cell. 2015;17:11–22.PubMedCrossRefGoogle Scholar
  32. 32.
    Darabi R, Perlingeiro RC. Lineage-specific reprogramming as a strategy for cell therapy. Cell Cycle. 2008;7:1732–7.PubMedCrossRefGoogle Scholar
  33. 33.
    Hassani SN, Totonchi M, Gourabi H. Signaling roadmap modulating naive and primed pluripotency. Stem Cells Dev. 2014;23:193–208.PubMedCrossRefGoogle Scholar
  34. 34.
    Hughes C, Radan L, Wing Y, William L, Dean H, Gilles A. Mass spectrometry-based proteomic analysis of the matrix microenvironment in pluripotent stem cell culture. Mol Cell Proteomics. 2012;11:1924–36.PubMedPubMedCentralCrossRefGoogle Scholar
  35. 35.
    Shekari F, Han CL, Lee J, Mirzaei M, Gupta V, Haynes PA, Lee B, Baharvand H, Chen YJ, Hosseini SG. Surface markers of human embryonic stem cells: a meta-analysis of membrane proteomics reports. Expert Rev Proteomics. 2018;55:1–21.Google Scholar
  36. 36.
    Taleahmad S, Hassani SN, Hosseini Salekdeh G, Baharvand H. Metabolic signature of pluripotent stem cells. Cell J. 2018;20:388–95.PubMedPubMedCentralGoogle Scholar
  37. 37.
    Soteriou D, Iskender B, Byron A, Humphries J, Borg-Bartolo B, Haddock M. Comparative proteomic analysis of supportive and unsupportive extracellular matrix substrates for human embryonic stem cell maintenance. J Biol Chem. 2013;26:18716–31.CrossRefGoogle Scholar
  38. 38.
    Rebekah L, Gundry W, Kenneth R. Pluripotent stem cell heterogeneity and the evolving role of proteomic technologies in stem cell biology. Proteomics. 2011;11:3947–61.CrossRefGoogle Scholar
  39. 39.
    Ong SE, Mann M. Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol. 2005;1:252–62.PubMedCrossRefGoogle Scholar
  40. 40.
    Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics. 2002;1:376–86.PubMedCrossRefPubMedCentralGoogle Scholar
  41. 41.
    Park HW, Shin JS, Kim CW. Proteome of mesenchymal stem cells. Proteomics. 2007;7:2881–94.PubMedCrossRefPubMedCentralGoogle Scholar
  42. 42.
    Pinkse MWH, Uitto PM, Hilhorst MJ, Ooms B, Heck AJR. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-Nano LC-ESI-MS/MS and titanium oxide precolumns. Anal Chem. 2004;76:3935–43.PubMedCrossRefPubMedCentralGoogle Scholar
  43. 43.
    Pinkse MWH, Mohammed S, Gouw JW, Van Breukelen B, Vos HR, Heck AJR. Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster. J Proteome Res. 2008;7:687–97.PubMedCrossRefPubMedCentralGoogle Scholar
  44. 44.
    Prowse AB, McQuade LR, Bryant KJ, Van Dyk DD, Tuch BE, Gray PP. Proteome analysis of conditioned media from human neonatal fibroblasts used in the maintenance of human embryonic stem cells. Proteomics. 2005;5:978–89.PubMedCrossRefPubMedCentralGoogle Scholar
  45. 45.
    Scott IC, Clark TG, Takahara K, Hoffman GG, Greenspan DS. Structural organization and expression patterns of the human and mouse genes for the type I procollagen COOH-terminal proteinase enhancer protein. Genomics. 1999;55:229–34.PubMedCrossRefPubMedCentralGoogle Scholar
  46. 46.
    Shevinsky LH, Knowles BB, Damjanov I, Solter D. Monoclonal antibody to murine embryos defines a stage-specific embryonic antigen expressed on mouse embryos and human teratocarcinoma cells. Cell. 1982;30:697–705.PubMedCrossRefPubMedCentralGoogle Scholar
  47. 47.
    Speers AE, Wu CC. Proteomics of integral membrane proteins theory and application. Chem Rev. 2007;107:3687–714.PubMedCrossRefPubMedCentralGoogle Scholar
  48. 48.
    Spisak S, Tulassay Z, Molnar B, Guttman A. Protein microchips in biomedicine and biomarker discovery. Electrophoresis. 2007;28:4261–73.PubMedCrossRefPubMedCentralGoogle Scholar
  49. 49.
    Stanton LW, Bakre MM. Genomic and proteomic characterization of embryonic stem cells. Curr Opin Chem Biol. 2007;11:399–404.PubMedCrossRefPubMedCentralGoogle Scholar
  50. 50.
    Sze SK, de Kleijn DP, Lai RC, Khia Way TE, Zhao H, Yeo KS, Low TY, Lian Q, Lee CN, Mitchell W, El Oakley RM, Lim SK. Elucidating the secretion proteome of human ESC derived mesenchymal stem cells. Mol Cell Proteomics. 2007;6:1680–9.PubMedCrossRefPubMedCentralGoogle Scholar
  51. 51.
    Van Hoof D, Passier R, Ward-Van Oostwaard D, Pinkse MWH, Heck AJR, Mummery CL, Krijgsveld J. A quest for human and mouse embryonic stem cell-specific proteins. Mol Cell Proteomics. 2006;5:1261–73.PubMedCrossRefGoogle Scholar
  52. 52.
    Van Hoof D, Mummery CL, Heck AJR, Krijgsveld J. Embryonic stem cell proteomics. Proteomics. 2006;3:427–37.PubMedGoogle Scholar
  53. 53.
    Van Hoof D, Pinkse MWH, Ward-Van Oostwaard D, Mummery CL, Heck AJR, Krijgsveld J. An experimental correction for arginine-to-proline conversion artifacts in SILACbased quantitative proteomics. Nat Methods. 2007;4:677–8.PubMedCrossRefGoogle Scholar
  54. 54.
    Washburn MP, Wolters D, Yates JR. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol. 2001;19:242–7.PubMedCrossRefGoogle Scholar
  55. 55.
    Wegner M, Stolt CC. From stem cells to neurons and glia: a Soxist’s view of neural development. Trends Neurosci. 2005;28:583–8.PubMedCrossRefGoogle Scholar
  56. 56.
    Wu Q, Chen X, Zhang J, Loh YH, Low TY, Zhang W, Zhang W, Sze SK, Lim B, Ng HH. Sall4 interacts with Nanog and co-occupies Nanog genomic sites in embryonic stem cells. J Biol Chem. 2006;281:24090–4.PubMedCrossRefGoogle Scholar
  57. 57.
    Xie CQ, Lin G, Luo KL, Luo SW, Lu GX. Newly expressed proteins of mouse embryonic fibroblasts irradiated to be inactive. Biochem Biophys Res Commun. 2004;315:581–8.PubMedCrossRefGoogle Scholar
  58. 58.
    Zhang J, Tam WL, Tong GQ, Wu Q, Chan HY, Soh BS, Lou Y, Yang J, Ma Y, Chai L, Ng HH, Lufkin T, Robson P, Lim B. Sall4 modulates embryonic stem cell pluripotency and early embryonic development by the transcriptional regulation of Pou5f1. Nat Cell Biol. 2006;8:1114–23.PubMedCrossRefPubMedCentralGoogle Scholar
  59. 59.
    Zhao S, Nichols J, Smith AG, Li M. SoxB transcription factors specify neuroectodermal lineage choice in ES cells. Mol Cell Neurosci. 2004;27:332–42.PubMedCrossRefGoogle Scholar
  60. 60.
    Mitsui K, Tokuzawa Y, Itoh H, Segawa K. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell. 2003;113:631–42.PubMedCrossRefGoogle Scholar
  61. 61.
    Domon B, Aebersold R. Mass spectrometry and protein analysis. Science. 2006;312:212–7.CrossRefGoogle Scholar
  62. 62.
    Kelleher NL. Top-down proteomics. Anal Chem. 2004;76:196–203.CrossRefGoogle Scholar
  63. 63.
    Siuti N, Kelleher NL. Decoding protein modifications using top-down mass spectrometry. Nat Methods. 2007;4:817–21.PubMedPubMedCentralCrossRefGoogle Scholar
  64. 64.
    Forner F, Foster LJ, Toppo S. Mass spectrometry data analysis in the proteomics era. Curr Bioinforma. 2007;2:63–93.CrossRefGoogle Scholar
  65. 65.
    Lam H, Deutsch EW, Eddes JS, Eng JK, et al. Building consensus spectral libraries for peptide identification in proteomics. Nat Methods. 2008;5:873–5.PubMedPubMedCentralCrossRefGoogle Scholar
  66. 66.
    Bendall SC, Hughes C, Campbell JL, Stewart MH, et al. An enhanced mass spectrometry approach reveals human embryonic stem cell growth factors in culture. Mol Cell Proteomics. 2008;8:421–32.PubMedCrossRefGoogle Scholar
  67. 67.
    Fang Y, Robinson DP, Foster LJ. Quantitative analysis of proteome coverage and recovery rates for upstream fractionation methods in proteomics. J Proteome Res. 2010;9:1902–12.PubMedCrossRefGoogle Scholar
  68. 68.
    Mueller LN, Brusniak MY, Mani DR, Aebersold R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res. 2008;7:51–61.PubMedCrossRefGoogle Scholar
  69. 69.
    Domon B, Aebersold R. Options and considerations when selecting a quantitative proteomics strategy. Nat Biotechnol. 2010;28:710–21.PubMedCrossRefGoogle Scholar
  70. 70.
    Mann M. Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol. 2006;7:952–8.PubMedCrossRefGoogle Scholar
  71. 71.
    Ross PL, Huang YLN, Marchese JN, Williamson B, et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics. 2004;3:1154–69.PubMedCrossRefGoogle Scholar
  72. 72.
    Bryder D, Rossi DJ, Weissman IL. Hematopoietic stem cells: the paradigmatic tissue-specific stem cell. Am J Pathol. 2006;169:338–46.PubMedPubMedCentralCrossRefGoogle Scholar
  73. 73.
    Kern S, Eichler H, Stove J, Kluter H, Bieback K. Comparative analysis of mesenchymal stem cells from bone marrow, umbilical cord blood, or adipose tissue. Stem Cells. 2006;24:1294–301.PubMedCrossRefGoogle Scholar
  74. 74.
    Pevsner-Fischer M, Levin S, Zipori D. The origins of mesenchymal stromal cell heterogeneity. Stem Cell Rev. 2011;7:560–8.CrossRefGoogle Scholar
  75. 75.
    Davies OG, Cooper PR, Shelton RM, Smith AJ, Scheven BA. A comparison of the in vitro mineralization and dentinogenic potential of mesenchymal stem cells derived from adipose tissue, bone marrow, and dental pulp. J Bone Miner Metab. 2014;33:371–82.PubMedCrossRefGoogle Scholar
  76. 76.
    Boyd NL, Robbins KR, Dhara SK, West FD, Stice SL. Human embryonic stem cell-derived mesoderm-like epithelium transitions to mesenchymal progenitor cells. Tissue Eng. 2009;15:1897–907.CrossRefGoogle Scholar
  77. 77.
    Hematti P. Human embryonic stem cell-derived mesenchymal stromal cells. Transfusion. 2011;51:138S–44S.PubMedPubMedCentralCrossRefGoogle Scholar
  78. 78.
    de Peppo GM, et al. Human embryonic mesodermal progenitors highly resemble human mesenchymal stem cells and display high potential for tissue engineering applications. Tissue Eng. 2010;16:2161–82.CrossRefGoogle Scholar
  79. 79.
    Vodyanik MA, et al. A mesoderm-derived precursor for mesenchymal stem and endothelial cells. Cell Stem Cell. 2010;7:718–29.PubMedPubMedCentralCrossRefGoogle Scholar
  80. 80.
    Kimbrel EA, et al. Mesenchymal stem cell population derived from human pluripotent stem cells displays potent immunomodulatory and therapeutic properties. Stem Cells Dev. 2014;23:1611–24.PubMedPubMedCentralCrossRefGoogle Scholar
  81. 81.
    Sanchez L, et al. Enrichment of human ESC-derived multipotent mesenchymal stem cells with immunosuppressive and anti-inflammatory properties capable to protect against experimental inflammatory bowel disease. Stem Cells. 2011;29:251–62.PubMedCrossRefGoogle Scholar
  82. 82.
    Wang X, et al. Human ESC-derived MSCs outperform bone marrow MSCs in the treatment of an EAE model of multiple sclerosis. Stem Cell Rep. 2014;3:115–30.CrossRefGoogle Scholar
  83. 83.
    Liberski AR, et al. Adaptation of a commonly used, chemically defined medium for human embryonic stem cells to stable isotope labeling with amino acids in cell culture. J Proteome Res. 2013;12:3233–45.PubMedCrossRefGoogle Scholar
  84. 84.
    Yamana R, Iwasaki M, Wakabayashi M, Nakagawa M, Yamanaka S, Ishihama Y. Rapid and deep profiling of human induced pluripotent stem cell proteome by one-shot NanoLC−MS/MS analysis with meter-scale monolithic silica columns. J Proteome Res. 2012;44:1–12.Google Scholar
  85. 85.
    Chae J, Kim D, Lee N, Jeon Y, Jeon I, Kwon J, Kim J, Soh Y, Lee D, Seo K, Choi N, Park B, Kang S, Ryu J, Oh S, Shin D, Lee D, Do J, Park I, Daley G, Song J. Quantitative proteomic analysis of induced pluripotent stem cells derived from a human Huntington’s disease patient. Biochemist. 2012;446:359–71.CrossRefGoogle Scholar
  86. 86.
    Pripuzova N, Getie-Kebtie M, Grunseich C, Sweeneyc C, Malechc H, Alterman M. Development of a protein marker panel for characterization of human induced pluripotent stem cells (hiPSCs) using global quantitative proteome analysis. Stem Cell Res. 2015;14:323–38.PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Saeed Heidari-Keshel
    • 1
  • Mostafa Rezaei-Tavirani
    • 2
  • Azam Rahimi
    • 1
  • Farshid Sefat
    • 3
    • 4
  • Arash Khojasteh
    • 1
  1. 1.Department of Tissue Engineering and Applied Cell SciencesSchool of Advanced Technologies in Medicine, Shahid Beheshti University of Medical SciencesTehranIran
  2. 2.Proteomics Research CenterShahid Beheshti University of Medical SciencesTehranIran
  3. 3.Biomedical and Electrical Engineering DepartmentSchool of Engineering, University of BradfordBradfordUK
  4. 4.Interdisciplinary Research Centre in Polymer Science and Technology (IRC Polymer), University of BradfordBradfordUK

Personalised recommendations