Kanser Araştırmalarında Proteomiks Teknikler ve Uygulamaları

Genomik ve transkriptomik tekniklerdeki ilerlemeler, kanser araştırmalarındakigelişmelere olanak sağlamasına rağmen; günümüzdeproteomiks teknikler,karsinogenezis ve kanserle ilişkili protein paternlerinin tanımlanması hakkında daha kapsamlı bilgi sağlaması bakımından,kanser araştırmalarındason derecekullanışlıve popüler hale gelmiştir. Proteomiks; zaman, yaş, durum ve dış etkenlere bağlı olarak;hücre, organ veya organizmada ifade edilen tüm protein formlarına odaklanmış, genomik ile biyoloji arasında bir köprü olarak önemli rol oynayan ve gerçekte ne olduğu hakkında bilgi sağlayan teknolojiler topluluğudur.Bu nedenle günümüzde, kanser araştırmalarında proteomiks tekniklerin kullanımı yönünde artan bir ilgi söz konusudur.Tek boyutlu (1D) ve iki boyutlu (2D) poliakrilamid jel elektroforezi, ayırıcı jel elektroforezi (DIGE), floresan ayırıcı 2D jel elektroforezi (2D-DIGE), kütle spektrometresine dayalı yöntemler (MALDI-TOF-matriks destekli lazer desorpsiyon/iyonizasyon uçuş zamanı, SELDİ-TOF-yüzey geliştirilmiş lazer desorpsiyon/iyonizasyon uçuş zamanı, ESI-TOF-elektrosprey iyonizasyon uçuş zamanı, tandem kütle spektroskopisi vs.), protein mikroarray, doku mikroarray, hücre kültüründe amino asitler ile izotopik işaretleme (SILAC), izotopla kodlanmış afinite işaretleme (ICAT),göreceli ve mutlak kantitatif izobarik işaretleme (iTRAQ) vs. teknikleri içeren günümüz proteomiks teknolojisi;detaylı proteom analizlerininyapılmasına imkan sunmakta ve aday tümör biyobelirteçlerinin saptanmasında güçlü biyolojik bilgi sağlayarak, kanserin erken teşhisi için olası çözümler sunmaktadır. Bu derlemede, günümüz kanser araştırmalarında kullanılan proteomiks teknolojileri ve uygulamaları özetlenmektedir.

___

  • Gelband H, Sankaranarayanan R, Gauvreau CL, Horton S, Anderson BO, Bray F, Gupta S. Costs, affordability, and feasibility of an essential package of cancer control interventions in low-income and middle-income countries: key messages from Disease Control Priorities. The Lancet, 2016; 387(10033), 2133-2144.
  • Cairns RA, Mak TW. The current state of cancer metabolism. Nature Reviews Cancer, 2016; 16(10), 613-614.
  • Smith RA, Andrews K, Brooks D, DeSantis CE, Fedewa SA, Lortet‐Tieulent J, Wender RC. Cancer screening in the United States, 2016: A review of current American Cancer Society guidelines and current issues in cancer screening. CA: a cancer journal for clinicians.
  • Torre LA, Siegel RL, Ward EM, Jemal A. Global cancer incidence and mortality rates and trends—an update. Cancer Epidemiology and Prevention Biomarkers, 2016; 25(1), 16-27.
  • WHO. World Health Organization. 2016. Cancer country profiles.
  • Levitsky DO, Dembitsky VM. Anti-breast Cancer Agents Derived from Plants. Natural Products & Bioprospecting, 2015; 5, 1–16.
  • Tagne RS, Telefo BP, Nyemb JN, Yemele DM, Njina SN, Goka SMC, Farooq AD. Anticancer and antioxidant activities of methanol extracts and fractions of some Cameroonian medicinal plants. Asian Pacific Journal of Tropical Medicine, 2014; 7(1), 442-447.
  • Nicolini A, Ferrari P, Masoni, MC, Fini M, Pagani S, Giampietro O, Carpi A. Malnutrition, anorexia and cachexia in cancer patients: a mini-review on pathogenesis and treatment. Biomedicine & Pharmacotherapy, 2013; 67(8), 807-817.
  • Deracinois B, Flahau, C, Duban-Deweer S, & Karamanos Y. Comparative and quantitative global proteomics approaches: an overview. Proteomes, 2013; 1(3), 180-218.
  • Löhr M, & Faissner R. Proteomics in pancreatic disease. Pancreatology, 2004; 4(2), 67-75.
  • Maron JL, Alterovitz G, Ramoni M, Johnson KL, & Bianchi DW. High‐throughput discovery and characterization of fetal protein trafficking in the blood of pregnant women. PROTEOMICS-Clinical Applications, 2009; 3(12), 1389-1396.
  • Reynolds T. Updates to staging system reflect advances in imaging, understanding. Journal of the National Cancer Institute, 2002; 94(22), 1664-1666.
  • Seo J, & Lee KJ. Post-translational modifications and their biological functions: proteomic analysis and systematic approaches. Journal of biochemistry and molecular biology, 2004; 37(1), 35-44.
  • Espina V, Geho D, Mehta AI, Petricoin III EF, Liotta LA, & Rosenblatt KP. Pathology of the future: molecular profiling for targeted therapy. Cancer investigation, 2005; 23(1), 36-46.
  • Lau ATY, He QY, & Chiu JF. Proteomic technology and its biomedical applications. Acta Biochimica Et Biophysica Sinica-Chinese Edition-, 2003; 35(11), 965-975.
  • Wilson R. Sensitivity and specificity: twin goals of proteomics assays. Can they be combined?.Expert review of proteomics, 2013; 10(2), 135-149.
  • Pearson H. Genetics: what is a gene? Nature, 2006; 441(7092), 398-401.
  • Pandey A, & Mann M. Proteomics to study genes and genomes. Nature, 2000; 405(6788), 837-846.
  • Tyers M, & Mann M. From genomics to proteomics. Nature, 2003; 422(6928), 193-197.
  • Massion PP, & Caprioli RM. Proteomic strategies for the characterization and the early detection of lung cancer. Journal of Thoracic Oncology, 2006; 1(9), 1027-1039.
  • Aebersold R, & Mann M. Mass spectrometry-based proteomics. Nature, 2003; 422(6928), 198-207.
  • Colantonio DA, & Chan DW. The clinical application of proteomics. Clinica chimica acta, 2005; 357(2), 151-158.
  • Raynie DE. Modern extraction techniques. Analytical chemistry, 2010; 82(12), 4911-4916.
  • Bodzon-Kulakowska A, Bierczynska-Krzysik A, Dylag T, Drabik A, Suder P, Noga M, et al. Methods for samples preparation in proteomic research. Journal of Chromatography B, 2007; 849(1), 1-31.
  • Xie F, Liu T, Qian WJ, Petyuk VA, & Smith RD. Liquid chromatography-mass spectrometry-based quantitative proteomics. Journal of Biological Chemistry, 2011; 286(29), 25443-25449.
  • Hao P, Guo T, Li X, Adav SS, Yang J, Wei M, & Sze SK. Novel application of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) in shotgun proteomics: comprehensive profiling of rat kidney proteome. Journal of proteome research, 2010; 9(7), 3520-3526.
  • Rabilloud T, & Lelong C. Two-dimensional gel electrophoresis in proteomics: a tutorial. Journal of proteomics, 2011; 74(10), 1829-1841.
  • Craven R. A, Totty, N, Harnden P, Selby PJ, & Banks RE. Laser capture microdissection and two-dimensional polyacrylamide gel electrophoresis: evaluation of tissue preparation and sample limitations. The American journal of pathology, 2002; 160(3), 815-822.
  • Peng J, Elias JE, Thoreen CC, Licklider LJ, & Gygi SP. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. Journal of proteome research, 2003; 2(1), 43-50.
  • Riederer BM. Non-covalent and covalent protein labeling in two-dimensional gel electrophoresis. Journal of proteomics, 2008; 71(2), 231-244.
  • Zhou S, Bailey MJ, Dunn MJ, Preedy VR, & Emery PW. A quantitative investigation into the losses of proteins at different stages of a two‐dimensional gel electrophoresis procedure. Proteomics, 2005; 5(11), 2739-2747.
  • Anderson NL, & Anderson NG. Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis, 1998; 19(11), 1853-1861.
  • Groth SFDS, Webster RG, & Datyner A. Two new staining procedures for quantitative estimation of proteins on electrophoretic strips. Biochimica et biophysica acta, 1963; 71, 377-391.
  • Merril CR, Switzer RC, & Van Keuren ML. Trace polypeptides in cellular extracts and human body fluids detected by two-dimensional electrophoresis and a highly sensitive silver stain. Proceedings of the National Academy of Sciences, 1979; 76(9), 4335-4339.
  • Minden JS, Dowd SR, Meyer HE, & Stühler K. Difference gel electrophoresis. Electrophoresis, 2009; 30(S1), S156-S161.
  • Angel TE, Aryal UK, Hengel SM, Baker ES, Kelly RT, Robinson EW, & Smith RD. Mass spectrometry-based proteomics: existing capabilities and future directions. Chemical Society Reviews, 2012; 41(10), 3912-3928.
  • Fenn JB, Mann M, Meng CK, Wong SF, & Whitehouse CM. Electrospray ionization for mass spectrometry of large biomolecules. Science, 1989; 246(4926), 64-71.
  • Yamashita M, & Fenn JB. Electrospray ion source. Another variation on the free-jet theme. The Journal of Physical Chemistry, 1984; 88(20), 4451-4459.
  • Walther TC, & Mann M. Mass spectrometry–based proteomics in cell biology. The Journal of cell biology, 2010; 190(4), 491-500.
  • Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 2002; 415(6868), 180-183.
  • Bonk T, & Humeny A. MALDI-TOF-MS analysis of protein and DNA. The Neuroscientist, 2001; 7(1), 6-12.
  • Tanaka K, Waki H, Ido Y, Akita S, Yoshida Y, Yoshida T, & Matsuo T. Protein and polymer analyses up to m/z 100 000 by laser ionization time? of flight mass spectrometry. Rapid communications in mass spectrometry, 1988; 2(8), 151-153.
  • Karas M, & Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Analytical chemistry, 1988; 60(20), 2299-2301.
  • Harvey DJ. Matrix-assisted laser desorption/ionisation mass spectrometry of oligosaccharides and glycoconjugates. Journal of chromatography A, 1996; 720(1), 429-446.
  • Zaluzec EJ, Gage DA, & Watson JT. Matrix-assisted laser desorption ionization mass spectrometry: applications in peptide and protein characterization. Protein expression and purification, 1995; 6(2), 109-123.
  • Hillenkamp F, Karas M, Beavis RC, & Chait BT. Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Analytical chemistry, 1991; 63(24), 1193A-1203A.
  • Lewis JK, Wei J, & Siuzdak G. Matrix‐Assisted Laser Desorption/Ionization Mass Spectrometry in Peptide and Protein Analysis. Encyclopedia of Analytical Chemistry; 2000.
  • Marvin LF, Roberts MA, & Fay LB. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in clinical chemistry. Clinica chimica acta, 2003; 337(1), 11-21.
  • Blueggel M, Chamrad D, & Meyer HE. Bioinformatics in proteomics. Current pharmaceutical biotechnology, 2004; 5(1), 79-88.
  • Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D.et al. Approaching clinical proteomics: current state and future fields of application in cellular proteomics. Cytometry Part A, 2009; 75(10), 816-832.
  • Hutchens TW, & Yip TT. New desorption strategies for the mass spectrometric analysis of macromolecules. Rapid Communications in Mass Spectrometry, 1993; 7(7), 576-580.
  • Cazares LH, Leung SM, Nasim S, Adam BL, Yip TT, Schellhammer PF.et al. Proteinchip (R) surface enhanced laser desorption/ionization (SELDI) mass spectrometry: a novel protein biochip technology for detection of prostate cancer biomarkers in complex protein mixtures. Prostate cancer and prostatic diseases, 1999; 2(5/6), 264-276.
  • Issaq HJ, Veenstra TD, Conrads TP, & Felschow D. The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. Biochemical and biophysical research communications, 2002; 292(3), 587-592.
  • Ahram M, & Petricoin EF. Proteomics discovery of disease biomarkers. Biomarker insights, 2008; 3, 325.
  • Tang N, Tornatore P, & Weinberger SR. Current developments in SELDI affinity technology. Mass spectrometry reviews, 2004; 23(1), 34-44.
  • Banerjee S, & Mazumdar S. Electrospray ionization mass spectrometry: a technique to access the information beyond the molecular weight of the analyte. International journal of analytical chemistry, 2012.
  • Ho CS, Lam CWK, Chan MHM, Cheung RCK, Law LK, Lit LCW. et al. Electrospray ionisation mass spectrometry: principles and clinical applications. Clinical Biochemist Reviews, 2003; 24(1), 3-12.
  • Arenkov P, Kukhtin A, Gemmell A, Voloshchuk S, Chupeeva V, & Mirzabekov A. Protein microchips: use for immunoassay and enzymatic reactions. Analytical Biochemistry, 2000; 278(2), 123-131.
  • Haab BB, Dunham MJ, & Brown PO. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol, 2001; 2(2), 1-13.
  • Paweletz CP, Charboneau L, Bichsel VE, Simone NL, Chen T, Gillespie JW.et al. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene, 2001; 20(16), 1981-1989.
  • Wu W, Hu W, & Kavanagh JJ. Proteomics in cancer research. International Journal of Gynecological Cancer, 2002; 12(5), 409-423.
  • Kim WH. Tissue array technology for translational research. From gene discovery to application]. Experimental & molecular medicine, 2001; 33(1 Suppl), 135-148.
  • Bantscheff M, Schirle M, Sweetman G, Rick J, & Kuster B. Quantitative mass spectrometry in proteomics: a critical review. Analytical and bioanalytical chemistry, 2007; 389(4), 1017-1031.
  • Akpınar G, Kasap M, Cantürk Z, & Cantürk NZ. Proteomiks nedir? Tiroid hastalıklarıyla ilgili araştırmalarda proteomiks. Journal of Dialog in Endocrinology/Endokrinolide Diyalog Dergisi, 2011; 8(4).
  • Munday DC, Surtees R, Emmott E, Dove BK, Digard P, Barr JN. et al. Using SILAC and quantitative proteomics to investigate the interactions between viral and host proteomes. Proteomics, 2012; 12(4‐5), 666-672.
  • Yohannes E, Ghosh SK, Jiang B, McCormick TS, Sevgi Gezici / DERLEME, 10 (2): 54-61, 2017, www.nobel.gen.tr 9 Weinberg A, Hill E.et al. Proteomic signatures of human oral epithelial cells in HIV-infected subjects. PloS one,2011; 6(11), e27816.
  • Kubach J, Lutter P, Bopp T, Stoll S, Becker C, Huter E. Et al. Human CD4+ CD25+ regulatory T cells: proteome analysis identifies galectin-10 as a novel marker essential for their anergy and suppressive function. Blood, 2007; 110(5), 1550-1558.
  • Nedelkov D, Kiernan UA, Niederkofler EE, Tubbs KA, & Nelson RW. Population Proteomics The Concept, Attributes, and Potential for Cancer Biomarker Research. Molecular & Cellular Proteomics, 2006; 5(10), 1811-1818.
  • Plebani M. Proteomics: the next revolution in laboratory medicine? Clinica chimica acta, 2005; 357(2), 113-122.
  • Gygi SP, Corthals GL, Zhang Y, Rochon Y, & Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proceedings of the National Academy of Sciences, 2000; 97(17), 9390-9395.
  • Gasteiger E, Hoogland C, Gattiker A, Duvaud SE, Wilkins MR, Appel RD, & Bairoch A. Protein identification and analysis tools on the ExPASy server; 2005. (pp. 571-607). Humana Press.
  • Roy P, & Shukla Y. Applications of proteomic techniques in cancer research. Cancer Therapy, 2008; 6(2).
  • Yates JR. Mass spectrometry: from genomics to proteomics. Trends in Genetics, 2000; 16(1), 5-8.
  • Hanash S, & Taguchi A. The grand challenge to decipher the cancer proteome. Nature reviews cancer, 2010; 10(9), 652-660.
  • Petricoin EF, & Liotta LA. Proteomic approaches in cancer risk and response assessment. Trends in molecular medicine, 2004; 10(2), 59-64.
  • Etzioni R, Urban N, Ramsey S, McIntosh M, Schwartz S, Reid B, et al. The case for early detection. Nature Reviews Cancer, 2003; 3(4), 243-252.
  • Mayr M, Zhang J, Greene AS, Gutterman D, Perloff J, & Ping P. Proteomics-based Development of Biomarkers in Cardiovascular Disease Mechanistic, Clinical, and Therapeutic Insights. Molecular & Cellular Proteomics, 2006; 5(10), 1853-1864.
  • Robaye B, Døskeland AP, Suarez‐Huerta N, Døskeland SO, & Dumont JE. Apoptotic cell death analyzed at the molecular level by two‐dimensional gel electrophoresis. Electrophoresis, 1994; 15(1), 503-510.