Proteomik

Genomik çalışmalardan elde edilen bilgiler sınırlı olduğundan, genomiğin devamı olan proteomik biyolojik olayların açıklanmasında önem kazanmıştır. Proteomik belli şartlar altında ve belli bir dokuda genom tarafından kodlanan tüm proteinlerin, yani proteomun analiz edilmesi işlemidir. Proteomik çalışmalarının esas amacı bütün hücre, doku ve vücut sıvılarındaki proteinleri, özellikleri ve seviyelerini de içerecek şekilde belirleyerek tanımlamaktır. Proteomik çalışmaları proteinlerin ayrılması, miktarlarının belirlenmesi ve bu proteinlerin tanımlanması teknolojilerine ihtiyaç duyar. Bu makalede biz iki yönlü jel elektroforezi (2-DE), iki yönlü differential jel elektroforezi (2D-DIGE), tek ve iki yönlü sıvı kromatografisi (1D-LC ve 2D-LC), kütle spektrofotometresi (MS) ve protein mikroarray teknolojileri olan son proteomik teknolojileri üzerinde durduk. Aynı zamanda biyomarker keşfi, özellikle erken kanser tanısı olmak üzere bazı diğer hastalıkların tanı ve tedavisi ile toplumsal proteomik çalışmalarında proteomik teknolojisinin yerini belirlemeye çalıştık.

Proteomics

Since information obtained from genomic studies is limited, proteomics, which is an advance of genomics, become more important in the evaluation of the biological events. Proteomics is to analyse proteins expressed by genom under certain conditions and in a spesific tissue, that is proteomics is to identify proteom. The main goal of proteomics studies is the understanding of proteins including their identification, characterization, and quantification of proteins in whole cells, tissues, or body fluids. Proteomics methodologies require techniques to separate and quantify individual proteins and identify those proteins. In this article, we review the current proteomics technologies which include two-dimensional gel electrophoresis (2-DE), two-dimensional differential ingel electrophoresis (2D-DIGE), one-and two-dimensional liquid chromatography (1D-LC and 2D-LC), mass spectrometry (MS) and protein microarray technology. We will also review proteomics technology in biomarker discovery, especially early detection of cancer and diagnosis and treatment of some other diseases and population proteomics.

PDF

___

1. Del Boccio P, Urbani A. Homo sapiens proteomics: clinical perspectives. Ann Ist Super Sanita 2005;41: 479-82.
2. Denizli A. Protein Analizi. BİLİM ve TEKNİK 2007;476: 66-9.
3. Arthur JM. Proteomics. Curr Opin Nephrol Hypertens 2003;12: 423-30.
4. Anderson L, Seilhamer J. A comparision of selected mRNA and protein abundances in human liver. Electrophoresis 1997;18: 533-7.
5. Graham DR, Elliott ST, Van Eyk JE. Broad-based proteomic strategies: a practical guide to proteomics and functional screening. J Physiol 2005;563: 1–9.
6. Guo Y, Fu Z, Van Eyk JE. A proteomic primer for the clinician. Proc Am Thorac Soc 2007;4: 9-17.
7. Chen Y, Guo Z, Wang X, Qiu C. Sample preparation. J Chromatogr A 2008;1184: 191-219.
8. Von Eggeling F, Gawriljuk A, Fiedler W, Ernst G, Blaussen U, Klose J, et al. Fluorescent dual colour 2D-protein gel electrophoresis for rapid detection of differences in protein patter with standard image analysis software. Int J Mol Med 2001;8: 373–7
9. Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, et al. Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics techonology. Proteomics 2001;1: 377-96.
10. Neverova I, Van Eyk JE. Role of chromatographic techniques in proteomic analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 815: 51–63.
11. Sheng S, Chen D, Van Eyk JE. Multidimensional liquid chromatography separation of intact proteins by chromatographic focusing and reversed phase of the human serum proteome: optimization and protein database. Mol Cell Proteomics 2006;5: 26-34.
12. Hilario M, Kalousis A, Pellegrini C, Müller M. Processing and classification of protein mass spectra. Mass Spectrom Rev 2006;25: 409-49.
13. Nedelkov D, Kiernan UA, Niederkofler EE, Tubbs KA, Nelson RW. Population proteomics: the concept, attributes, and potential for cancer biomarker research. Mol Cell Proteomics 2006;5: 1811-18.
14. Tang N, Tornatore P, Weinberger SR. Current developments in SELDI affinity technology. Mass Spectrom Rev 2004;23: 34–44.
15. Kallweit U, Börnsen OK, Kresbach GM, Widmer HM. Matrix compatible buffers for analysis of proteins with matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 1996;10: 845-9.
16. Hall DA, Ptacek J, Snyder M. Protein microarray technology. Mech Ageing Dev 2007;128: 161-7.
17. Han MH, Hwang SI, Roy DB, Lundgren DH, Price JV, Ousman SS, et al. Proteomic analysis of active multiple sclerosis lesions reveals therapeutic targets. Nature 2008;451: 1076-81.
18. Pasinetti GM, Ungar LH, Lange DJ, Yemul S, Deng H, Yuan X, et al. Identification of potential CSF biomarkers in ALS. Neurology 2006;66: 1218-22.
19. Junker H, Späte K, Suofu Y, Walther R, Schwarz G, Kammer W, et al. Proteomic identification of the involvement of the mitochondrial rieske protein in epilepsy. Epilepsia 2005;46: 339-43.
20. McGregor E, Dunn MJ. Proteomics of the Heart Unraveling Disease. Circ Res 2006;98: 309-21.
21. Vidal BC, Bonventre JV, I-Hong Hsu S. Towards the application of proteomics in renal disease diagnosis. Clin Sci (Lond) 2005;109: 421-30.
22. Johann DJ Jr, McGuigan MD, Patel AR, Tomov S, Ross S, Conrads TP, et al. Clinical proteomics and biomarker discovery Ann N Y Acad Sci 2004;1022: 295–305.
23. Wulfkuhle JD, Liotta L A, Petricoin EF. Proteomic applications for the early detection of cancer. Nat Rev Cancer 2003;3: 267–75.
24. Chuthapisith S, Layfield R, Kerr ID, Eremin O. Principles of proteomics and its applications in cancer. Surgeon 2007;5: 14–22.
25. Kuramitsu Y, Nakamura K, Kuramitsu Y, Nakamura K. Proteomic analysis of cancer tissues: shedding light on carcinogenesis and possible biomarkers. Proteomics 2006;6: 5650–61.
26. Petricoin EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, Steinberg SM, et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002;359: 572–7.
27. Zinkin NT, Grall F, Bhaskar K, Otu HH, Spentzos D, Kalmowitz B, et al. Serum proteomics and biomarkers in hepatocellular carcinoma and chronic liver disease. Clin Cancer Res 2008;14: 470-7.
28. Okusaka T, Yamada T, Maekawa M, Okusaka T, Yamada T, Maekawa M. Serum tumor markers for pancreatic cancer: the dawn of new era? JOP 2006;7: 332–6.
29. Xiao X, Liu D, Tang Y, Guo F, Xia L, Liu J, et al. Development of proteomic patterns for detecting lung cancer. Dis Markers 2003-2004;19: 33-9.
30. Ye B, Cramer DW, Skates SJ, Gygi SP, Pratomo V, Fu L, et al. Haptoglobin-alpha subunit as potential serum biomarker in ovarian cancer: identification and characterization using proteomic profiling and mass spectrometry. Clin Cancer Res 2003;9: 2904–11.
31. Zhang Z, Bast RC Jr, Yu Y, Li J, Sokoll LJ, Rai AJ, et al. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res 2004;64: 5882-90.
32. Le L, Chi K, Tyldesley S, Flibotte S, Diamond DL, Kuzyk MA, et al. Identification of serum amyloid A as a biomarker to distinguish prostate cancer patients with bone lesions. Clin Chem 2005; 51: 695-707.
33. Hlavaty JJ, Partin AW, Shue MJ, Mangold LA, Derby J, Javier T, et al. Identification and preliminary clinical evaluation of a 50.8-kDa serum marker for prostate cancer. Urology 2003;61: 1261-5.
34. Malik G, Ward MD, Gupta SK, Trosset MW, Grizzle WE, Adam BL, et al. Serum levels of an isoform of apolipoprotein A-II as a potential marker for prostate cancer. Clin Cancer Res 2005;11: 1073-85.
35. Parekh DJ, Ankerst DP, Troyer D, Srivastava S, Thompson IM. Biomarkers for prostate cancer detection. J Urol 2007;178: 2252-9.
36. Li J, Orlandi R, White CN, Rosenzweig J, Zhao J, Seregni E, et al. Independent validation of candidate breast cancer serum biomarkers identified by mass spectrometry. Clin Chem 2006;52: 771-2.
37. Rho JH, Qin S, Wang JY, Roehrl MH. Proteomic expression analysis of surgical human colorectal cancer tissues: up-regulation of PSB7, PRDX1, and SRP9 and hypoxic adaptation in cancer. J Proteome Res 2008;7: 2959-72.
38. Nedelkov D. Population proteomics: investigation of protein diversity in human populations. Proteomics 2008;8: 779-86.
39. Nedelkov D, Kiernan UA, Niederkofler EE, Tubbs KA, Nelson RW. Investigating human plasma proteins diversity. Proc Natl Acad Sci USA 2005;102: 10852–7.
40. Connors LH, Lim A, Prokaeva T, Roskens VA, Costello CE. Tabulation of human transthyretin (TTR) variants. Amyloid 2003;10: 160–84.
41. Mahley RW, Huang Y. Apolipoprotein E: from atherosclerosis to Alzheimer’s disease and beyond. Curr Opin Lipidol 1999;10: 207–17.
42. Nedelkov D, Phillips DA, Tubbs KA, Nelson RW. Investigation of human protein variants and their frequency in the general population. Mol Cell Proteomics 2007;6: 1183-7.