Proteomic applications in the study of human mesenchymal stem cells

Proteomes

Volumn 2, Issue 1, 2014, Pages 53-71

  Mateos, Jesús ^a   Pernas, Pablo Fernández ^a   Labora, Juan Fafián ^a   Blanco, Francisco ^a,b   Arufe, María del Carmen ^a  

^a UNIVERSITY OF A CORUÑA   (Spain)

^b UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

Author keywords

Characterization; Differentiation; Mesenchymal stem cell; Proteomic analysis

Indexed keywords

EID: 84947598058     PISSN: None     EISSN: 22277382     Source Type: Journal    
DOI: 10.3390/proteomes2010053     Document Type: Review

References (57)

1. Park, D.; Spencer, J.A.; Koh, B.I.; Kobayashi, T.; Fujisaki, J.; Clemens, T.L.; Lin, C.P.; Kronenberg, H.M.; Scadden, D.T. Endogenous bone marrow MSCs are dynamic, fate-restricted participants in bone maintenance and regeneration. Cell Stem Cell 2012, 10, 259-272
2. Huang, A.H.; Snyder, B.R.; Cheng, P.H.; Chan, A.W. Putative dental pulp-derived stem/stromal cells promote proliferation and differentiation of endogenous neural cells in the hippocampus of mice. Stem Cells 2008, 26, 2654-2663
3. Hayashi, E.; Hosoda, T. Therapeutic application of cardiac stem cells and other cell types. BioMed Res. Int. 2013, 2013, e736815
4. Skalnikova, H.K. Proteomic techniques for characterisation of mesenchymal stem cell secretome. Biochimie 2013, 95, 2196-2211
5. Mann, M.; Højrup, P.; Roepstorff, P. Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol. Mass Spectrom. 1993, 22, 338-345
6. Nier, A.O. Determination of isotopic masses and abundances by mass spectrometry. Science 1955, 121, 737-744
7. Ardekani, A.M.; Akhondi, M.M.; Sadeghi, M.R. Application of genomic and proteomic technologies to early detection of cancer. Arch. Iran Med. 2008, 11, 427-434
8. Mittal, V.; Nolan, D.J. Genomics and proteomics approaches in understanding tumor angiogenesis. Expert Rev. Mol. Diagn. 2007, 7, 133-147
9. Choi, Y.S. Reaching for the deep proteome: Recent nano liquid chromatography coupled with tandem mass spectrometry-based studies on the deep proteome. Arch. Pharm. Res. 2012, 35, 1861-1870
10. Salasznyk, R.M.; Westcott, A.M.; Klees, R.F.; Ward, D.F.; Xiang, Z.; Vandenberg, S.; Bennett, K.; Plopper, G.E. Comparing the protein expression profiles of human mesenchymal stem cells and human osteoblasts using gene ontologies. Stem Cells Dev. 2005, 14, 354-366
11. Feldmann, R.E.; Bieback, K.; Maurer, M.H.; Kalenka, A.; Bürgers, H.F.; Gross, B.; Hunzinger, C.; Klüter, H.; Kuschinsky, W.; Eichler, H. Stem cell proteomes: A profile of human mesenchymal stem cells derived from umbilical cord blood. Electrophoresis 2005, 26, 2749-2758
12. Roubelakis, M.G.; Pappa, K.I.; Bitsika, V.; Zagoura, D.; Vlahou, A.; Papadaki, H.A.; Antsaklis, A.; Anagnou, N.P. Molecular and proteomic characterization of human mesenchymal stem cells derived from amniotic fluid: Comparison to bone marrow mesenchymal stem cells. Stem Cells Dev. 2007, 16, 931-952
13. Mareddy, S.; Broadbent, J.; Crawford, R.; Xiao, Y. Proteomic profiling of distinct clonal populations of bone marrow mesenchymal stem cells. J. Cell Biochem. 2009, 106, 776-786
14. Li, G.; Zhang, X.A.; Wang, H.; Wang, X.; Meng, C.L.; Chan, C.Y.; Yew, D.T.; Tsang, K.S.; Li, K.; Tsai, S.N.; et al. Comparative proteomic analysis of mesenchymal stem cells derived from human bone marrow, umbilical cord, and placenta: Implication in the migration. Proteomics 2009, 9, 20-30
15. Jaishankar, A.; Barthelery, M.; Freeman, W.; Salli, U.; Ritty, T.; Vrana, K. Human embryonic and mesenchymal stem cells express different nuclear proteomes. Stem Cells Dev. 2009, 18, 793-802
16. Roche, S.; Delorme, B.; Oostendorp, R.A.; Barbet, R.; Caton, D.; Noel, D.; Boumediene, K.; Papadaki, H.A.; Cousin, B.; Crozet, C.; et al. Comparative proteomic analysis of human mesenchymal and embryonic stem cells: towards the definition of a mesenchymal stem cell proteomic signature. Proteomics 2009, 9, 223-232
17. Roche, S.; D'Ippolito, G.; Gomez, L.A.; Bouckenooghe, T.; Lehmann, S.; Montero-Menei, C.N.; Schiller, P.C. Comparative analysis of protein expression of three stem cell populations: Models of cytokine delivery system in vivo. Int. J. Pharm. 2013, 440, 72-82
18. Mindaye, S.T.; Ra, M.; Lo Surdo, J.; Bauer, S.R.; Alterman, M.A. Improved proteomic profiling of the cell surface of culture-expanded human bone marrow multipotent stromal cells. J. Proteomics 2013, 78, 1-14
19. Sun, H.J.; Bahk, Y.Y.; Choi, Y.R.; Shim, J.H.; Han, S.H.; Lee, J.W. A proteomic analysis during serial subculture and osteogenic differentiation of human mesenchymal stem cell. J. Orthop. Res. 2006, 24, 2059-2071
20. Wagner, W.; Feldmann, R.E.; Seckinger, A.; Maurer, M.H.; Wein, F.; Blake, J.; Krause, U.; Kalenka, A.; Bürgers, H.F.; Saffrich, R.; et al. The heterogeneity of human mesenchymal stem cell preparations-Evidence from simultaneous analysis of proteomes and transcriptomes. Exp. Hematol. 2006, 34, 536-548
21. Lazzarotto-Silva, C.; Binato, R.; Rocher, B.D.; Costa, J.A.; Pizzatti, L.; Bouzas, L.F.; Abdelhay, E. Similar proteomic profiles of human mesenchymal stromal cells from different donors. Cytotherapy 2009, 11, 268-277
22. Binato, R.; de Souza Fernandez, T.; Lazzarotto-Silva, C.; Du Rocher, B.; Mencalha, A.; Pizzatti, L.; Bouzas, L.F.; Abdelhay, E. Stability of human mesenchymal stem cells during in vitro culture: Considerations for cell therapy. Cell Prolif. 2013, 46, 10-22
23. Capra, E.; Beretta, R.; Parazzi, V.; Viganò, M.; Lazzari, L.; Baldi, A.; Giordano, R. Changes in the proteomic profile of adipose tissue-derived mesenchymal stem cells during passages. Proteome Sci. 2012, 10, e46
24. Lee, S.K.; Kim, Y.; Kim, S.S.; Lee, J.H.; Cho, K.; Lee, S.S.; Lee, Z.W.; Kwon, K.H.; Kim, Y.H.; Suh-Kim, H.; et al. Differential expression of cell surface proteins in human bone marrow mesenchymal stem cells cultured with or without basic fibroblast growth factor containing medium. Proteomics 2009, 9, 4389-4405
25. Madeira, A.; da Silva, C.L.; dos Santos, F.; Camafeita, E.; Cabral, J.M.; Sá-Correia, I. Human mesenchymal stem cell expression program upon extended ex-vivo cultivation, as revealed by 2-DE-based quantitative proteomics. PLoS One 2012, 7, e43523
26. Kim, H.J.; Ji, B.R.; Kim, J.S.; Lee, H.N.; Ha, D.H.; Kim, C.W. Proteomic analysis of proteins associated with cellular senescence by calorie restriction in mesenchymal stem cells. In Vitro Cell Dev. Biol. Anim. 2012, 48, 186-195
27. Kuboki, T.; Kantawong, F.; Burchmore, R.; Dalby, M.J.; Kidoaki, S. 2D-DIGE proteomic analysis of mesenchymal stem cell cultured on the elasticity-tunable hydrogels. Cell Struct. Funct. 2012, 37, 127-139
28. Wang, D.; Park, J.S.; Chu, J.S.; Krakowski, A.; Luo, K.; Chen, D.J.; Li, S. Proteomic profiling of bone marrow mesenchymal stem cells upon transforming growth factor beta1 stimulation. J. Biol. Chem. 2004, 279, 43725-43734
29. Foster, L.J.; Zeemann, P.A.; Li, C.; Mann, M.; Jensen, O.N.; Kassem, M. Differential expression profiling of membrane proteins by quantitative proteomics in a human mesenchymal stem cell line undergoing osteoblast differentiation. Stem Cells 2005, 23, 1367-1377
30. Jeong, J.A.; Ko, K.M.; Park, H.S.; Lee, J.; Jang, C.; Jeon, C.J.; Koh, G.Y.; Kim, H. Membrane proteomic analysis of human mesenchymal stromal cells during adipogenesis. Proteomics 2007, 7, 4181-4191
31. Zhang, A.X.; Yu, W.H.; Ma, B.F.; Yu, X.B.; Mao, F.F.; Liu, W.; Zhang, J.Q.; Zhang, X.M.; Li, S.N.; Li, M.T.; et al. Proteomic identification of differently expressed proteins responsible for osteoblast differentiation from human mesenchymal stem cells. Mol. Cell Biochem. 2007, 304, 167-179
32. Kim, J.S.; Lee, H.K.; Kim, M.R.; Kim, P.K.; Kim, C.W. Differentially expressed proteins of mesenchymal stem cells derived from human cord blood (hUCB) during osteogenic differentiation. Biosci. Biotechnol. Biochem. 2008, 72, 2309-2317
33. Giusta, M.S.; Andrade, H.; Santos, A.V.; Castanheira, P.; Lamana, L.; Pimenta, A.M.; Goes, A.M. Proteomic analysis of human mesenchymal stromal cells derived from adipose tissue undergoing osteoblast differentiation. Cytotherapy 2010, 12, 478-490
34. Kim, S.; Min, W.K.; Chun, S.; Lee, W.; Chung, H.J.; Choi, S.J.; Yang, S.E.; Yang, Y.S.; Yoo, J.I. Protein expression profiles during osteogenic differentiation of mesenchymal stem cells derived from human umbilical cord blood. Tohoku J. Exp. Med. 2010, 221, 141-150
35. Purmessur, D.; Schek, R.M.; Abbott, R.D.; Ballif, B.A.; Godburn, K.E.; Iatridis, J.C. Notochordal conditioned media from tissue increases proteoglycan accumulation and promotes a healthy nucleus pulposus phenotype in human mesenchymal stem cells. Arthritis Res. Ther. 2011, 13, R81
36. Lo, T.; Tsai, C.F.; Shih, Y.R.; Wang, Y.T.; Lu, S.C.; Sung, T.Y.; Hsu, W.L.; Chen, Y.J.; Lee, O.K. Phosphoproteomic analysis of human mesenchymal stromal cells during osteogenic differentiation. J. Proteome Res. 2012, 11, 586-598
37. De la Fuente, A.; Mateos, J.; Lesende-Rodríguez, I.; Calamia, V.; Fuentes-Boquete, I.; de Toro, F.J.; Arufe, M.C.; Blanco, F.J. Proteome analysis during chondrocyte differentiation in a new chondrogenesis model using human umbilical cord stroma mesenchymal stem cells. Mol. Cell Proteomics 2012, 11, M111.010496
38. Rocha, B.; Calamia, V.; Mateos, J.; Fernández-Puente, P.; Blanco, F.J.; Ruiz-Romero, C. Metabolic labeling of human bone marrow mesenchymal stem cells for the quantitative analysis of their chondrogenic differentiation. J. Proteome Res. 2012, 11, 5350-5361
39. Herencia, C.; Martínez-Moreno, J.M.; Herrera, C.; Corrales, F.; Santiago-Mora, R.; Espejo, I.; Barco, M.; Almadén, Y.; de la Mata, M.; Rodríguez-Ariza, A.; et al. Nuclear translocation of ß-catenin during mesenchymal stem cells differentiation into hepatocytes is associated with a tumoral phenotype. PLoS One 2012, 7, e34656
40. Alves, R.D.; Eijken, M.; Bezstarosti, K.; Demmers, J.A.; van Leeuwen, J.P. Activin A suppresses osteoblast mineralization capacity by altering extracellular matrix composition and impairing matrix vesicle production. Mol. Cell Proteomics 2013, doi:10.1074/mcp.M112.024927
41. Seshi, B. Proteomics strategy based on liquid-phase IEF and 2-D DIGE: Application to bone marrow mesenchymal progenitor cells. Proteomics 2007, 7, 1984-1999
42. Yi, W.; Sun, Y.; Wei, X.; Gu, C.; Dong, X.; Kang, X.; Guo, S.; Dou, K. Proteomic profiling of human bone marrow mesenchymal stem cells under shear stress. Mol. Cell Biochem. 2010, 341, 9-16
43. Zhuang, Q.; Li, J.; Wu, Z.; Zhang, J.; Sun, W.; Li, T.; Yan, Y.; Jiang, Y.; Zhao, R.C.; Qiu, G. Differential proteome analysis of bone marrow mesenchymal stem cells from adolescent idiopathic scoliosis patients. PLoS One 2011, 6, e18834
44. Kim, H.S.; Choi, D.Y.; Yun, S.J.; Choi, S.M.; Kang, J.W.; Jung, J.W.; Hwang, D.; Kim, K.P.; Kim, D.W. Proteomic analysis of microvesicles derived from human mesenchymal stem cells. J. Proteome Res. 2012, 11, 839-849
45. Han, S.; Zhu, Y.; Wu, Z.; Zhang, J.; Qiu, G. The differently expressed proteins in MSCs of degenerative scoliosis. J. Orthop. Sci. 2013, 18, 885-892
46. Ståhlberg, A.; Thomsen, C.; Ruff, D.; Åman, P. Quantitative PCR analysis of DNA, RNAs, and proteins in the same single cell. Clin. Chem. 2012, 58, 1682-1691
47. Henzel, W.J.; Billeci, T.M.; Stults, J.T.; Wong, S.C.; Grimley, C.; Watanabe, C. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. USA 1993, 90, 5011-5015
48. Knowles, M.R.; Cervino, S.; Skynner, H.A.; Hunt, S.P.; de Felipe, C.; Salim, K.; Meneses-Lorente, G.; McAllister, G.; Guest, P.C. Multiplex proteomic analysis by two-dimensional differential in-gel electrophoresis. Proteomics 2003, 3, 1162-1171
49. Percy, A.J.; Parker, C.E.; Borchers, C.H. Pre-analytical and analytical variability in absolute quantitative MRM-based plasma proteomic studies. Bioanalysis 2013, 5, 2837-2856
50. Provansal, M.; Jorgensen, C.; Lehmann, S.; Roche, S. Two dimensional gel electrophoresis analysis of mesenchymal stem cells. Methods Mol. Biol. 2011, 698, 431-442
51. Maurer, M.H. Proteomic definitions of mesenchymal stem cells. Stem Cells Int. 2011, 2011, e704256
52. Huang, P.; Lin, L.M.; Wu, X.Y.; Tang, Q.L.; Feng, X.Y.; Lin, G.Y.; Lin, X.; Wang, H.W.; Huang, T.H.; Ma, L. Differentiation of human umbilical cord Wharton's jelly-derived mesenchymal stem cells into germ-like cells in vitro. J. Cell Biochem. 2010, 109, 747-754
53. Zhang, H.; Liu, Q.; Zimmerman, L.J.; Ham, A.J.; Slebos, R.J.; Rahman, J.; Kikuchi, T.; Massion, P.P.; Carbone, D.P.; Billheimer, D.; et al. Methods for Peptide and protein quantitation by liquid chromatography-multiple reaction monitoring mass spectrometry. Mol. Cell Proteomics 2011, 10, M110.006593
54. Louie, K.B.; Bowen, B.P.; McAlhany, S.; Huang, Y.; Price, J.C.; Mao, J.H.; Hellerstein, M.; Northen, T.R. Mass spectrometry imaging for in situ kinetic histochemistry. Sci. Rep. 2013, 3, e1656
55. Pirman, D.A.; Reich, R.F.; Kiss, A.; Heeren, R.M.; Yost, R.A. Quantitative MALDI tandem mass spectrometric imaging of cocaine from brain tissue with a deuterated internal standard. Anal. Chem. 2013, 85, 1081-1089
56. Cillero-Pastor, B.; Eijkel, G.B.; Kiss, A.; Blanco, F.J.; Heeren, R.M. Matrix-assisted laser desorption ionization-imaging mass spectrometry: A new methodology to study human osteoarthritic cartilage. Arthritis Rheum. 2013, 65, 710-720
57. Mukherjee, S.; Rodriguez-Canales, J.; Hanson, J.; Emmert-Buck, M.R.; Tangrea, M.A.; Prieto, D.A.; Blonder, J.; Johann, D.J. Proteomic analysis of frozen tissue samples using laser capture microdissection. Methods Mol. Biol. 2013, 1002, 71-83