A SELDI mass spectrometry study of experimental autoimmune encephalomyelitis: Sample preparation, reproducibility, and differential protein expression patterns

Proteome Science

Volumn 11, Issue 1, 2013, Pages

  Azzam, Sausan ^a   Broadwater, Laurie ^a   Li, Shuo ^a   Freeman, Ernest J ^a   McDonough, Jennifer ^a   Gregory, Roger B ^a  

^a KENT STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA SUBCOMPLEX SUBUNIT 2; ATP SYNTHASE SUBUNIT E; CALPAIN; CYTOCHROME C OXIDASE; CYTOCHROME C OXIDASE SUBUNIT 4; CYTOCHROME C OXIDASE SUBUNIT 6B1; CYTOCHROME C OXIDASE SUBUNIT 6C; FLAVOPROTEIN; IRON SULFUR PROTEIN; IRON SULFUR PROTEIN 4; IRON SULFUR PROTEIN 6; MYELIN BASIC PROTEIN; MYELIN BASIC PROTEIN ISOFORM 8; NADH DEHYDROGENASE FLAVOPROTEIN 3; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE; UNCLASSIFIED DRUG;

ALLERGIC ENCEPHALOMYELITIS; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ANION EXCHANGE; ARTICLE; BRAIN; BRAIN HOMOGENATE; BRAIN MITOCHONDRION; BRAIN TISSUE; CELL FRACTIONATION; CLUSTER ANALYSIS; CONTROLLED STUDY; ELECTRON TRANSPORT; FROZEN SECTION; HISTOPATHOLOGY; MASS SPECTROMETRY; MICROCHIP ANALYSIS; MOUSE; NONHUMAN; PREDICTIVE VALUE; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN METABOLISM; PROTEIN SUBUNIT; PROTEOMICS; REPRODUCIBILITY; SURFACE ENHANCED LASER DESORPTION IONIZATION MASS SPECTROMETRY;

ANIMALIA; MUS;

EID: 84876802035     PISSN: None     EISSN: 14775956     Source Type: Journal    
DOI: 10.1186/1477-5956-11-19     Document Type: Article

References (67)

1. Compston A, Coles A. Multiple Sclerosis. Lancet 2008, 372:1502-1517. 10.1016/S0140-6736(08)61620-7, 18970977.
2. Mix E, Pahnke J, Ibrahim S. Gene-expression profiling of experimental autoimmune encephalomyelitis. Neurochem Res 2002, 27:1157-63. 10.1023/A:1020925425780, 12462414.
3. Steinman L, Zamvil S. How to successfully apply animal studies in experimental allergic encephalomyelitis to research on multiple sclerosis. Ann Neurol 2006, 60:12-21. 10.1002/ana.20913, 16802293.
4. Constantinescu C, Farooqi N, O'Brien K, Gran B. Experimental autoimmune encephalomyelitis (EAE) as a model for multiple sclerosis. Brit J Pharm 2011, 164:1079-1106.
5. Cook S. Handbook of Multiple Sclerosis 2006, New York: Taylor & Francis, 4.
6. Martin R, McFarland H. Immunological aspects of experimental allergic encephalomyelitis and multiple sclerosis. Crit Rev Clin Lab Sci 1995, 32:121-82. 10.3109/10408369509084683, 7598789.
7. Friese M, Montalban X, Willcox N, Bell J, Martin R, Fugger L. The value of animal models for drug development in multiple sclerosis. Brain 2006, 129:1940-52. 10.1093/brain/awl083, 16636022.
8. Majewska M, Zajac K, Srebro Z, Sura P, Ksiazek L, Zemelka M, Szczepanik M. Epicutaneous immunization with myelin basic protein protects from the experimental autoimmune encephalomyelitis. Pharmacol Rep 2007, 59:74-9.
9. Ballinger S. Mitochondrial dysfunction in cardiovascular disease. Free Radical Biol Med 2005, 38:1278-1295.
10. Trushina E, McMurray C. Oxidative stress and mitochondrial dysfunction in neurodegenerative diseases. Neuroscience 2007, 145:1233-1248. 10.1016/j.neuroscience.2006.10.056, 17303344.
11. Navarro A, Boveris A. Brain mitochondrial dysfunction in aging, neurodegeneration, and Parkinson's disease. Front Aging Neurosci 2010, 2:34. 2947925, 20890446.
12. Jiang Y, Wang X. Comparative mitochondrial proteomics: perspective in human diseases. J Hemtology Oncolology 2012, 5:11.
13. Inglese M, Ge Y, Filippi M, Falini A, Grossman R, Gonen O. Indirect evidence for early widespread gray matter involvement in relapsing-remitting multiple sclerosis. Neuroimage 2004, 21:1825-182. 10.1016/j.neuroimage.2003.12.008, 15050603.
14. Cader S, Johansen-Berg H, Wylezinska M, Palace J, Behrens T, Smith S, Matthews P. Discordant white matter N-acetylaspartate and diffusion MRI measures suggest that chronic dysfunction contributes to axonal pathology inmultiple sclerosis. Neuroimage 2007, 36:19-27. 10.1016/j.neuroimage.2007.02.036, 17398118.
15. Forte M, Gold B, Marracci G, Chaudhary P, Basso E, Johnsen D, Yu X, Fowlkes J, Rahder M, Stem K, Bernardi P, Bourdette D. Cyclophilin D inactivation protects axons in experimental autoimmune encephalomyelitis, an animal model of multiple sclerosis. Proc Natl Acad Sci USA 2007, 104:7558-7563. 10.1073/pnas.0702228104, 1857227, 17463082.
16. Mronga T, Stahnke T, Goldbaum O, Richter-Landsberg C. Mitochondrial pathway is involved in hydrogen-peroxide-induced apoptotic cell death of oligodendrocytes. Glia 2004, 46:446-455. 10.1002/glia.20022, 15095374.
17. Ghafourifar P, Mousavizadeh K, Parihar M, Nazarewicz R, Parihar A, Zenebe W. Mitochondria in multiple sclerosis. Front Biosci 2008, 13:3116-3126. 10.2741/2913, 17981781.
18. Mahad D, Ziabreva I, Lassman H, Turnbull D. Mitochondrial defects in acute multiple sclerosis lesions. Brain 2008, 131:1722-1735. 10.1093/brain/awn105, 2442422, 18515320.
19. Kalman B, Laitinen K, Komoly S. The involvement of mitochondria in the pathogenesis of multiple sclerosis. J Neuroimmunol 2007, 188:1-12. 10.1016/j.jneuroim.2007.03.020, 17493689.
20. Witte ME, Bø L, Rodenburg R, Belien A, Musters R, Hazes T, Wintjes L, Smeitink J, Geurts J, De Vries H, van der Valk P, Van Horssen J. Enhanced number and activity of mitochondria in multiple sclerosis lesions. J Pathol 2009, 219:193-204. 10.1002/path.2582, 19591199.
21. Pandit A, Vadnal J, Houston S, Freeman E, McDonough J. Impaired regulation of electron transport chain subunit genes by nuclear respiratory factor 2 in multiple sclerosis. J Neurol Sci 2009, 279:14-20. 10.1016/j.jns.2009.01.009, 19187944.
22. Dutta R, McDonough J, Yin X, Peterson J, Chang A, Torres T, Gudz T, Macklin B, Lewis A, Fox J, Rudick R, Mirnics K, Trapp D. Mitochondrial dysfunction as a cause of axonal degeneration in multiple sclerosis patients. Ann Neurol 2006, 59:478-489. 10.1002/ana.20736, 16392116.
23. Sowell A, Owen J, Butterfield A. Proteomics in animal models of Alzheimer's and Parkinson's diseases. Ageing Res Rev 2009, 8:1-17. 10.1016/j.arr.2008.07.003, 2630427, 18703168.
24. Zhang J, Keene D, Pan C, Montine S, Montine J. Proteomics of human neurodegenerative diseases. J Neuropathol Exp Neurol 2008, 67:923-32. 10.1097/NEN.0b013e318187a832, 2710115, 18800015.
25. Han H, Hwang I, Roy B, Lundgren H, Price V, Ousman S, Fernald G, Gerlitz B, Robinson H, Baranzini E, Grinnell W, Raine S, Sobel A, Han K, Steinman L. Proteomic analysis of active multiple sclerosis lesions reveals therapeutic targets. Nature 2008, 451:1076-81. 10.1038/nature06559, 18278032.
26. Elkabes S, Li H. Proteomic strategies in multiple sclerosis and its animal models. Proteomics Clin Appl 2007, 1(11):1393-1405. 10.1002/prca.200700315, 2744133, 19759847.
27. Dumont D, Noben P, Raus J, Stinissen P, Robben J. Proteomic analysis of cerebrospinal fluid from multiple sclerosis patients. Proteomics 2004, 4:2117-24. 10.1002/pmic.200300715, 15221773.
28. Rithidech N, Honikel L, Milazzo M, Madigan D, Troxell R, Krupp B. Protein expression profiles in pediatric multiple sclerosis: potential biomarkers. Mult Scler 2009, 15:455-64.
29. Linker A, Brechlin P, Jesse S, Steinacker P, Lee H, Asif R, Jahn O, Tumani H, Gold R, Otto M. Proteome profiling in murine models of multiple sclerosis: Identification of stage specific markers and culprits for tissue damage. PLoS One 2009, 4(10):e7624. 10.1371/journal.pone.0007624, 2765069, 19865482.
30. Fazeli S, Nasrabadi D, Sanati H, Pouya A, Ibrahim M, Baharvand H, Salekdeh H. Proteome analysis of brain in murine experimental autoimmune encephalomyelitis. Proteomics 2010, 10:2822-2832. 10.1002/pmic.200900507, 20540118.
31. Broadwater L, Pandit A, Azzam S, Clements R, Vadnal J, Sulak M, Yong W, Freeman J, Gregory R, McDonough J. Analysis of the mitochondrial proteome in multiple sclerosis cortex. Biochim Biophys Acta 1812, 2011:630-641.
32. Rosenling T, Attali A, Luider M, Bischoff R. The experimental autoimmune encephalomyelitis model for proteomic biomarker studies: From rat to human. Cinica Chimica Acta 2011, 412:812-822.
33. Farias A, Martins-de-Souza D, Guimaraes L, Pradella F, Moraes A, Facchini G, Novello J, Santos L. Proteome analysis of spinal cord during the clinical course of monophasic experimental autoimmune encephalomyelitis. Proteomics 2012, 12:2656-2662. 10.1002/pmic.201200044, 22740327.
34. Timms J, Cramer R. Difference Gel Electrophoresis. Proteomics 2008, 8:4886-4897. 10.1002/pmic.200800298, 19003860.
35. Minden J, Dowd S, Meyer H, Stuhler K. Difference Gel Electrophoresis. Electrophoresis 2009, 30:S156-S161. 10.1002/elps.200900098, 19517495.
36. Chevalier F. Highlights on the Capacities of " Gel-based" Proteomics. Proteome Science 2010, 8:23-32. 10.1186/1477-5956-8-23, 2873371, 20426826.
37. Wang G, Wu W, Zeng W, Chou L, Shen F. Label-Free Protein Quantification Using LC-Coupled Ion Trap or FT Mass Spectrometry: Reproducibility, Linearity, and Application with Complex Proteomes. J Proteome Res 2006, 5:1214-1223. 10.1021/pr050406g, 16674111.
38. Gygi P, Rist B, Gerber A, Turecek F, Gelb H, Abersold R. Quantitative Analysis of Complex Protein Mixtures using Isotope-coded Affinity Tags. Nature Biotech 1999, 17:994-999.
39. Wiese S, Reidegeld A, Meyer E, Warscheid B. Protein Labeling by iTRAQ: A New Tool for Quantitative Mass Spectrometry in Proteome Research. Proteomics 2007, 7:340-350. 10.1002/pmic.200600422, 17177251.
40. Elliott H, Smith S, Parker E, Borchers C. Current trends in Quantitative Proteomics. J Mass Spec 2009, 44:1637-1660.
41. Hutchens W, Yip T. New Desorption Strategies for the Mass Spectrometric Analysis of Macromolecules. Rapid Commun Mass Spectrom 1993, 7:576-580.
42. Issaq J, Conrads P, Prieto A, Tirumalai R, Veenstra D. SELDI -TOF-MS for Diagnostic Proteomics. Analyt Chem 2003, 75:149 A-155A.
43. Wei W, Martin A, Johnson J, Ward G. 10 Years of SELDI: What have we Learnt?. Current Proteomics 2010, 7:15-25.
44. Poon W. Opportunities and Limitations of SELDI-TOF-MS in Biomedical Research: Practical Advice. Expert Rev Proteomics 2007, 4:51-65. 10.1586/14789450.4.1.51, 17288515.
45. Woolley F, Al-Rubeai M. The Application of SELDI-TOF Mass Spectrometry to Mammalian Cell Culture. Biotech Advances 2009, 27:177-184.
46. Jackson E. A User's Guide to Principal Components 2003, Statistics: Wiley Series in Probability and.
47. Shlens J. A tutorial on Principal Components Analysis 2009, Version 3.01, http://www.snl.salk.edu/~shlens/pca.pdf.
48. Yeung K, Ruzzo W. Principal component analysis for clustering gene expression data. Bioinformatics 2001, 17:763-774. 10.1093/bioinformatics/17.9.763, 11590094.
49. Eisen B, Spellman T, Brown O, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95:14863-8. 10.1073/pnas.95.25.14863, 24541, 9843981.
50. Seno S, Teramoto R, Takenaka Y, Matsuda H. A method for clustering gene expression data based on graph structure. Genome Inform 2004, 15:151-60.
51. Katz-Jaffe G, Gardner K, Schoolcraft B. Proteomic analysis of individual human embryos to identify novel biomarkers of development and viability. Fertil Steril 2006, 85:101-7. 10.1016/j.fertnstert.2005.09.011, 16412738.
52. Hong H, Dragan Y, Epstein J, Teitel C, Chen B, Xie Q, Fang H, Shi L, Perkins R, Tong W. Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS). BMC Bioinforma 2005, 6:S5.
53. Semmes J, Cazares H, Ward D, Ward D, Qi L, Moody M, Maloney E, Morris J, Trosset W, Hisada M, Gygi S, Jacobson S. Discrete serum protein signatures discriminate between human retrovirus associated hematologic and neurologic disease. Leukemia 2005, 19:1229-38. 10.1038/sj.leu.2403781, 15889159.
54. Diao L, Clarke H, Coombes R, Hamilton R, Roth J, Mao L, Czerniak B, Baggerly A, Morris S, Fung T, Bast G. Reproducibility of SELDI Spectra Across Time and Laboratories. Cancer Informatics 2011, 10:45-64. 3085423, 21552492.
55. Selvaraju S, El Rassi Z. Liquid-phase-based separation systems for depletion, prefractionation and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis-An update covering the period 2008-2011. Electrophoresis 2012, 33:74-88. 10.1002/elps.201100431, 3516880, 22125262.
56. De Bock M, de Seny D, Meuwis A, Servais C, Minh Q, Closset J, Chapelle J, Louis E, Malaise M, Merville P, Fillet M. Comparison of three methods for fractionation and enrichment of low molecular weight proteins for SELDI-TOF-MS differential analysis. Talanta 2010, 82:245-254. 10.1016/j.talanta.2010.04.029, 20685463.
57. Lavine B, Workman J. Chemometrics. Anal Chem 2010, 82:4699-4711. 10.1021/ac101202z, 20481510.
58. Mao P, Reddy H. Is multiple sclerosis a mitochondrial disease?. BBA Mol Basis Dis 1802, 2010:66-79.
59. Qi X, Lewin S, Sun L, Hauswirth W, Guy J. Mitochondrial protein nitration primes neurodegeneration in experimental autoimmune encephalomyelitis. J Biol Chem 2006, 281:31950-31962. 10.1074/jbc.M603717200, 16920708.
60. Ravera S, Panfoli I, Calzia D, Aluigi G, Bianchini P, Diaspro A, Mancardi G, Morelli A. Evidence for aerobic ATP synthesis in isolated myelin vesicles. Int J Biochem Cell Bio 2009, 41:1581-1591.
61. Stahl L, Swanson D. Effects of freezing and storage on subcellular fractionation of guinea pig and human brain. Neurobiology 1975, 5:393-400.
62. Ottens K, Golden C, Bustamante L, Hayes L, Denslow D, Wang K. Proteolysis of multiple myelin basic protein isoforms after neurotrauma: characterization by mass spectrometry. J Neurochem 2008, 104:1404-14. 10.1111/j.1471-4159.2007.05086.x, 3584683, 18036155.
63. Shiryaev A, Savinov Y, Cieplak P, Ratnikov I, Motamedchaboki K, Smith W, Strongin Y. Matrix Metalloproteinase Proteolysis of the Myelin Basic Protein Isoforms Is a Source of Immunogenic Peptides in Autoimmune Multiple Sclerosis. PLoS One 2009, 4:e4952. 10.1371/journal.pone.0004952, 2654159, 19300513.
64. Schaecher E, Shields C, Banik L. Mechanism of myelin breakdown in experimental demyelination: a putative role for calpain. Neurochem Res 2001, 26:731-7. 10.1023/A:1010903823668, 11519732.
65. Liu C, Akle V, Zheng W, Kitlen J, O'Steen B, Larner F, Dave R, Tortella C, Hayes L, Wang K. Extensive degradation of myelin basic protein isoforms by calpain following traumatic brain injury. J Neurochem 2006, 98:700-12. 10.1111/j.1471-4159.2006.03882.x, 16893416.
66. Medveczky P, Antal J, Patthy A, Kékesi K, Juhász G, Szilágyi L, Gráf L. Myelin basic protein, an autoantigen in multiple sclerosis, is selectively processed by human trypsin 4. FEBS Lett 2006, 580:545-552. 10.1016/j.febslet.2005.12.067, 16412431.
67. Dasilva G, Yong W. Expression and regulation of matrix metalloproteinase-12 in experimental autoimmune encephalomyelitis and by bone marrow derived macrophages in vitro. J Neuroimmunol 2008, 199:24-34. 10.1016/j.jneuroim.2008.04.034, 18547653.