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Review

Proteomics for biomarker discovery in malignant melanoma

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Pages 209-220 | Published online: 10 Jan 2014

References

  • Markovic S, Erickson L, Rao R et al. Malignant melanoma in the 21st Century, part 1: epidemiology, risk factors, screening, prevention, and diagnosis. Mayo Clin. Proc.82(3), 364–380 (2007).
  • Brochez L, Naeyaert J. Serological markers for melanoma. Br. J. Dermatol.143(2), 256–268 (2000).
  • Linette G, Carlson J, Slominski A, Mihm M, Ross J. Biomarkers in melanoma: stage III and IV disease. Expert Rev. Mol. Diagn.5(1), 65–74 (2005).
  • Torabian S, Kashani-Sabet M. Biomarkers for melanoma. Curr. Opin. Oncol.17(2), 167–171 (2005).
  • Utikal J, Schadendorf D, Ugurel S. Serologic and immunohistochemical prognostic biomarkers of cutaneous malignancies. Arch. Dermatol. Res.298(10), 469–477 (2007).
  • Bosserhoff A. Novel biomarkers in malignant melanoma. Clin. Chim. Acta367(1–2), 28–35 (2006).
  • Rifai N, Gillette M, Carr S. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol.24(8), 971–983 (2006).
  • Wulfkuhle JD, Paweletz CP, Steeg PS, Petricoin REF, Liotta L. Proteomic approaches to the diagnosis, treatment, and monitoring of cancer. Adv. Exp. Med. Biol.532, 59–68 (2003).
  • Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature422(6928), 198–207 (2003).
  • Hortin G. The MALDI-TOF mass spectrometric view of the plasma proteome and peptidome. Clin. Chem.52(7), 1223–1237 (2006).
  • Ahn N, Shabb J, Old W, Resing K. Achieving in-depth proteomics profiling by mass spectrometry. ACS Chem. Biol.2(1), 39–52 (2007).
  • Tannu N, Hemby S. Two-dimensional fluorescence difference gel electrophoresis for comparative proteomics profiling. Nat. Protoc.1(4), 1732–1742 (2006).
  • Maurya P, Meleady P, Dowling P, Clynes M. Proteomic approaches for serum biomarker discovery in cancer. Anticancer Res.27(3A), 1247–1255 (2007).
  • Clauser K, Hall S, Smith D et al. Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE. Proc. Natl Acad. Sci. USA92(11), 5072–5076 (1995).
  • de Souza G, Godoy L, Teixeira V et al. Proteomic and SAGE profiling of murine melanoma progression indicates the reduction of proteins responsible for ROS degradation. Proteomics6(5), 1460–1470 (2006).
  • Buscà R, Berra E, Gaggioli C et al. Hypoxia-inducible factor 1a is a new target of microphthalmia-associated transcription factor (MITF) in melanoma cells. J. Cell Biol.170(1), 49–59 (2005)
  • Sinha P, Kohl S, Fischer J et al. Identification of novel proteins associated with the development of chemoresistance in malignant melanoma using two-dimensional electrophoresis. Electrophoresis21(14), 3048–3057 (2000).
  • Poland J, Schadendorf D, Lage H et al. Study of therapy resistance in cancer cells with functional proteome analysis. Clin. Chem. Lab. Med.40(3), 221–234 (2002).
  • Sinha P, Poland J, Kohl S et al. Study of the development of chemoresistance in melanoma cell lines using proteome analysis. Electrophoresis24(14), 2386–2404 (2003).
  • Carta F, Demuro P, Zanini C et al. Analysis of candidate genes through a proteomics-based approach in primary cell lines from malignant melanomas and their metastases. Melanoma Res.15(4), 235–244 (2005).
  • Anderson N, Polanski M, Pieper R et al. The human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol. Cell. Proteomics3(4), 311–326 (2004).
  • Bernard K, Litman E, Fitzpatrick J et al. Functional proteomic analysis of melanoma progression. Cancer Res.63(20), 6716–6725 (2003).
  • Pardo M, Garcia A, Thomas B et al. Proteome analysis of a human uveal melanoma primary cell culture by 2-DE and MS. Proteomics5(18), 4980–4993 (2005).
  • Zuidervaart W, Hensbergen P, Wong M-C et al. Proteomic analysis of uveal melanoma reveals novel potential markers involved in tumor progression. Invest. Ophthalmol. Vis. Sci.47(3), 786–793 (2006).
  • Pardo M, Dwek R, Zitzmann N. Proteomics in uveal melanoma research: opportunities and challenges in biomarker discovery. Expert Rev. Proteomics4(2), 273–286 (2007).
  • Pardo M, Garcia A, Thomas B et al. The characterization of the invasion phenotype of uveal melanoma tumour cells shows the presence of MUC18 and HMG-1 metastasis markers and leads to the identification of DJ-1 as a potential serum biomarker. Int. J. Cancer119(5), 1014–1022 (2006).
  • Culp W, Neal R, Massey R et al. Proteomic analysis of tumor establishment and growth in the B16-F10 mouse melanoma model. J. Proteome Res.5(6), 1332–1343 (2006).
  • Issaq H, Veenstra T. The role of electrophoresis in disease biomarker discovery. Electrophoresis28(12), 1980–1988 (2007).
  • Hoffman S, Won AJ, Echan L, Speicher D. Higher dimensional (Hi-D) separation strategies dramatically improve the potential for cancer biomarker detection in serum and plasma. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.849(1–2), 43–52 (2007).
  • Deutsch E, Eng J, Zhang H et al. Human Plasma PeptideAtlas. Proteomics5(13), 3497–3500 (2005).
  • States D, Omenn G, Blackwell T et al. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol.24(3), 333–338 (2006).
  • Lee H-J, Lee E-Y, Kwon M-S, Paik Y-K. Biomarker discovery from the plasma proteome using multidimensional fractionation proteomics. Curr. Opin. Chem. Biol.10(1), 42–49 (2006).
  • Zhang Z, Bast JRC, Yu Y et al. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res.64(16), 5882–5890 (2004).
  • Pusch W, Flocco M, Leung S-M, Thiele H, Kostrzewa M. Mass spectrometry-based clinical proteomics. Pharmacogenomics4(4), 463–476 (2003).
  • Villanueva J, Philip J, Entenberg D et al. Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry. Anal. Chem.76(6), 1560–1570 (2004).
  • Lopez M, Mikulskis A, Kuzdzal S et al. A novel, high-throughput workflow for discovery and identification of serum carrier protein-bound peptide biomarker candidates in ovarian cancer samples. Clin. Chem.53(6), 1067–1074 (2007).
  • Tomecki K, Montague P, Hearing JV. Serum and urine protein differences in patients with malignant melanoma. J. Natl Cancer Inst.64(1), 29–32 (1980).
  • Ferrari L, Seraglia R, Rossi C et al. Protein profiles in sera of patients with malignant cutaneous melanoma. Rapid Commun. Mass Spectrom.14(13), 1149–1154 (2000).
  • Wilson L, Tran L, Morton D, Hoon D. Detection of differentially expressed proteins in early-stage melanoma patients using SELDI-TOF mass spectrometry. Ann. NY Acad. Sci.1022, 317–322 (2004).
  • Mian S, Ugurel S, Parkinson E et al. Serum proteomic fingerprinting discriminates between clinical stages and predicts disease progression in melanoma patients. J. Clin. Oncol.23(22), 5088–5093 (2005).
  • Matharoo-Ball B, Ratcliffe L, Lancashire L et al. Diagnostic biomarkers differentiating metastatic melanoma patients from healthy controls identified by an integrated MALDI-TOF mass spectrometry/bioinformatic approach. Proteomics Clin. Applic.1(6), 605–620 (2007).
  • Ragazzi E, Vogliardi S, Allegri G et al. Cluster analysis of serum proteins in malignant cutaneous melanoma: search for disease markers. Rapid Commun. Mass Spectrom.17(13), 1511–1515 (2003).
  • Seraglia R, Vogliardi S, Allegri G et al. Search for melanoma markers in plasma and serum samples. Eur. J. Mass Spectrom.11(3), 353–360 (2005).
  • Mischak H, Apweiler R, Banks R et al. Clinical proteomics: a need to define the field and to begin to set adequate standards. Proteomics Clin. Applic.1(2), 148–156 (2007).
  • Deichmann M, Kahle B, Moser K, Wacker J, Wüst K. Diagnosing melanoma patients entering American Joint Committee on Cancer stage IV, C-reactive protein in serum is superior to lactate dehydrogenase. Br. J. Cancer91(4), 699–702 (2004).
  • Koomen J, Zhao H, Li D et al. Diagnostic protein discovery using liquid chromatography/mass spectrometry for proteolytic peptide targeting. Rapid Commun. Mass Spectrom.19(12), 1624–1636 (2005).
  • Missotten G, Beijnen J, Keunen J, Bonfrer J. Proteomics in uveal melanoma. Melanoma Res.13(6), 627–629 (2003).
  • Kaiser T, Wittke S, Just I et al. Capillary electrophoresis coupled to mass spectrometer for automated and robust polypeptide determination in body fluids for clinical use. Electrophoresis25(13), 2044–2055 (2004).
  • Brouard M, Saurat JH, Ghanem G, Siegenthaler G. Urinary excretion of epidermal-type fatty acid-binding protein and S100A7 protein in patients with cutaneous melanoma. Melanoma Res.12(6), 627–631 (2002).
  • Kolch W, Neusüss C, Pelzing M, Mischak H. Capillary electrophoresis-mass spectrometry as a powerful tool in clinical diagnosis and biomarker discovery. Mass Spectrom. Rev.24(6), 959–977 (2005).
  • Weissinger E, Wittke S, Kaiser T et al. Proteomic patterns established with capillary electrophoresis and mass spectrometry for diagnostic purposes. Kidney Int.65(6), 2426–2434 (2004).
  • Theodorescu D, Fliser D, Wittke S et al. Pilot study of capillary electrophoresis coupled to mass spectrometry as a tool to define potential prostate cancer biomarkers in urine. Electrophoresis26(14), 2797–2808 (2005).
  • Decramer S, Wittke S, Mischak H et al. Predicting the clinical outcome of congenital unilateral ureteropelvic junction obstruction in newborn by urinary proteome analysis. Nat. Med.12(4), 398–400 (2006).
  • Theodorescu D, Wittke S, Ross M et al. Discovery and validation of new protein biomarkers for urothelial cancer: a prospective analysis. Lancet Oncol.7(3), 230–240 (2006).
  • Schiffer E, Mischak H, Novak J. High resolution proteome/peptidome analysis of body fluids by capillary electrophoresis coupled with MS. Proteomics6(20), 5615–5627 (2006).
  • Diamandis E. Point: proteomic patterns in biological fluids: do they represent the future of cancer diagnostics? Clin. Chem.49(8), 1272–1275 (2003).
  • Garber K. Debate rages over proteomic patterns. J. Natl Cancer Inst.96(11), 816–818 (2004).
  • Diamandis E. Serum proteomic profiling by matrix-assisted laser desorption–ionization time-of-flight mass spectrometry for cancer diagnosis: next steps. Cancer Res.66(11), 5540–5541 (2006).
  • Petricoin E, Ardekani A, Hitt B et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet359(9306), 572–577 (2002).
  • Baggerly K, Morris J, Coombes K. Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics20(5), 777–785 (2004).
  • Check E, Proteomics and cancer: running before we can walk? Nature429(6991), 496–497 (2004).
  • Semmes O, Cazares L, Ward M et al. Discrete serum protein signatures discriminate between human retrovirus-associated hematologic and neurologic disease. Leukemia19(7), 1229–1238 (2005).
  • McLerran D, Grizzle WE, Feng Z et al. analytical validation of serum proteomic profiling for diagnosis of prostate cancer: sources of sample bias. Clin. Chem.54(1), 44–52 (2008).
  • McLerran D, Grizzle WE, Feng Z et al. SELDI-TOF MS whole serum proteomic profiling with IMAC surface does not reliably detect prostate cancer. Clin. Chem.54(1), 53–60 (2008).
  • Banks R, Stanley A, Cairns D et al. Influences of blood sample processing on low-molecular-weight proteome identified by surface-enhanced laser desorption/ionization mass spectrometry. Clin. Chem.51(9), 1637–1649 (2005).
  • Findeisen P, Sismanidis D, Riedl M, Costina V, Neumaier A. Preanalytical impact of sample handling on proteome profiling experiments with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clin. Chem.51(12), 2409–2411 (2005).
  • Baumann S, Ceglarek U, Fiedler G et al. Standardized approach to proteome profiling of human serum based on magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clin. Chem.51(6), 973–980 (2005).
  • West-Nielsen M, Hogdall E, Marchiori E et al. Sample handling for mass spectrometric proteomic investigations of human sera. Anal. Chem.77(16), 5114–5123 (2005).
  • West-Norager M, Kelstrup C, Schou C et al. Unravelling in vitro variables of major importance for the outcome of mass spectrometry-based serum proteomics. J. Chromatogr. B847(1), 30–37 (2007).
  • Karsan A, Eigl B, Flibotte S et al. Analytical and preanalytical biases in serum proteomic pattern analysis for breast cancer diagnosis. Clin. Chem.51(8), 1525–1528 (2005).
  • Ransohoff D. Lessons from controversy: ovarian cancer screening and serum proteomics. J. Natl Cancer Inst.97(4), 315–319 (2005).
  • Hong H, Dragan Y, Epstein J et al. Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS). BMC Bioinformatics6(Suppl. 2), 5 (2005).
  • Villanueva J, Philip J, Chaparro C et al. Correcting common errors in identifying cancer-specific serum peptide signatures. J. Proteome Res.4(4), 1060–1072 (2005).
  • Hu J, Coombes K, Morris J, Baggerly K. The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales. Brief. Funct. Genomic. Proteomic.3(4), 322–331 (2005).
  • Taylor C, Paton N, Lilley K et al. The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol.25(8), 887–893 (2007).
  • Brazma A, Krestyaninova M, Sarkans U. Standards for systems biology. Nat. Rev. Genet.7(8), 593–605 (2006).
  • Anderson N, Anderson N. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics1(11), 845–867 (2002).
  • Koomen J, Li D, Xiao L-C et al. Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. J. Proteome Res.4(3), 972–981 (2005).
  • Villanueva J, Shaffer DR, Philip J et al. Differential exoprotease activities confer tumor-specific serum peptidome patterns. J. Clin. Invest.116(1), 271–284 (2006).
  • Omenn G. Strategies for plasma proteomic profiling of cancers. Proteomics6(20), 5662–5673 (2006).
  • Whiteaker J, Zhang H, Eng J et al. Head-to-head comparison of serum fractionation techniques. J. Proteome Res.6(2), 828–836 (2007).
  • Diamandis E. Oncopeptidomics: a useful approach for cancer diagnosis? Clin. Chem.53(6), 1004–1006 (2007).
  • Bossuyt P, Reitsma J, Bruns D et al. The STARD statement for reporting studies of diagnostic accuracy: explanation and elaboration. Clin. Chem.49(1), 7–18 (2003).
  • Diamandis E. Peptidomics for cancer diagnosis: present and future. J. Proteome Res.5(9), 2079–2082 (2006).
  • Lopez-Otin C, Overall C. Protease degradomics: a new challenge for proteomics. Nat. Rev. Mol. Cell Biol.3(7), 509–519 (2002).
  • Villanueva J, Martorella A, Lawlor K et al. Serum peptidome patterns that distinguish metastatic thyroid carcinoma from cancer-free controls are unbiased by gender and age. Mol. Cell. Proteomics5(10), 1840–1852 (2006).
  • Capon F, Emonard H, Hornebeck W, Maquart F, Bernard P. Expression and activation of pro-gelatinase A by human melanoma cell lines with different tumorigenic potential. Clin. Exp. Metastasis17(6), 463–469 (1999).
  • Ntayi C, Labrousse A-L, Debret R et al. Elastin-derived peptides upregulate matrix metalloproteinase-2-mediated melanoma cell invasion through elastin-binding protein. J. Invest. Dermatol.122(2), 256–265 (2004).
  • Jessani N, Niessen S, Wei B et al. A streamlined platform for high-content functional proteomics of primary human specimens. Nat. Methods2(9), 691–697 (2005).
  • Conrads T, Hood B, Veenstra T. Sampling and analytical strategies for biomarker discovery using mass spectrometry. Biotechniques40(6), 799–805 (2006).
  • Findeisen P, Post S, Wenz F, Neumaier M. Addition of exogenous reporter peptides to serum samples before mass spectrometry-based protease profiling provides advantages over profiling of endogenous peptides. Clin. Chem.53(10), 1864–1866 (2007).
  • Villanueva J, Nazarian A, Lawlor K et al. A sequence-specific exopeptidase activity test (SSEAT) for ‘functional’ biomarker discovery. Mol. Cell. Proteomics7(3), 509–518 (2008).
  • Nedelkov D, Kiernan U, Niederkofler E, Tubbs K, Nelson R. Investigating diversity in human plasma proteins. Proc. Natl Acad. Sci. USA102(31), 10852–10857 (2005).
  • Jin M, Cataland S, Bissell M, Wu HM. A rapid test for the diagnosis of thrombotic thrombocytopenic purpura using surface enhanced laser desorption/ionization time-of-flight (SELDI-TOF)-mass spectrometry. J. Thromb. Haemost.4(2), 333–338 (2006).
  • Mueller L, Rinner O, Schmidt A et al. SuperHirn – a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics7(19), 3470–3480 (2007).
  • Keshishian H, Addona T, Burgess M, Kuhn E, Carr SA. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics6(12), 2212–2229 (2007).
  • Anderson L, Hunter C. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics5(4), 573–588 (2006).
  • Bondar OP, Barnidge DR, Klee EW, Davis BJ, Klee GG. LC-MS/MS quantification of Zn-α2 glycoprotein: a potential serum biomarker for prostate cancer. Clin. Chem.53(4), 673–678 (2007).
  • Hortin GL. A new era in protein quantification in clinical laboratories: application of liquid chromatography-tandem mass spectrometry. Clin. Chem.53(4), 543–544 (2007).
  • Veenstra T. Global and targeted quantitative proteomics for biomarker discovery. J. Chromatogr. B847(1), 3–11 (2007).
  • Stahl-Zeng J, Lange V, Ossola R et al. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics6(10), 1809–1817 (2007).
  • Ackermann B, Berna M. Coupling immunoaffinity techniques with MS for quantitative analysis of low-abundance protein biomarkers. Expert Rev. Proteomics4(2), 175–186 (2007).
  • Ueda K, Katagiri T, Shimada T et al. Comparative profiling of serum glycoproteome by sequential purification of glycoproteins and 2-nitrobenzensulfenyl (NBS) stable isotope labeling: a new approach for the novel biomarker discovery for cancer. J. Proteome Res.6(9), 3475–3483 (2007).
  • Caron M, Choquet-Kastylevsky GV, Joubert-Caron R. Cancer immunomics using autoantibody signatures for biomarker discovery. Mol. Cell. Proteomics6(7), 1115–1122 (2007).
  • Usener D, Gerhardt A, Schadendorf D, Eichmüller S. Seroreactivity against MAGE-A and LAGE-1 proteins in melanoma patients. Br. J. Dermatol.149(2), 282–288 (2003).
  • Hartmann T, Bazhin A, Schadendorf D, Eichmüller S. SEREX identification of new tumor antigens linked to melanoma-associated retinopathy. Int. J. Cancer114(1), 88–93 (2005).
  • Ladewig G, Reinhold U, Thirkill C et al. Incidence of antiretinal antibodies in melanoma: screening of 77 serum samples from 51 patients with American Joint Committee on Cancer stage I-IV. Br. J. Dermatol.152(5), 931–938 (2005).
  • Hardouin J, Lasserre J-P, Sylvius LK, Joubert-Caron R, Caron M. Cancer immunomics: from serological proteome analysis to multiple affinity protein profiling. Ann. NY Acad. Sci.1107, 223–230 (2007).

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