Differential Denaturation of Serum Proteome Reveals a Significant Amount of Hidden Information in Complex Mixtures of Proteins

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Verdoliva, Vincenzo ^a   Senatore, Cinzia ^a   Polci, Maria Letizia ^a   Rossi, Stefania ^a   Cordella, Martina ^a   Carlucci, Giuseppe ^a   Marchetti, Paolo ^b   Antonini Cappellini, Giancarlo ^c   Facchiano, Antonio ^c   D'Arcangelo, Daniela ^c   Facchiano, Francesco ^a  

^a ISTITUTO SUPERIORE DI SANITÀ   (Italy)

^b SAPIENZA UNIVERSITY OF ROME   (Italy)

^c LABORATORIO DI PATOLOGIA VASCOLARE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA 2 MACROGLOBULIN; APOLIPOPROTEIN A1; APOLIPOPROTEIN E; GELSOLIN; PLASMA PROTEIN; PROTEOME;

ADULT; AGED; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CONTROLLED STUDY; CUTANEOUS MELANOMA; DISEASE MARKER; DNA SEQUENCE; DOT HYBRIDIZATION; DOWN REGULATION; ELECTROPHORETIC MOBILITY; FEMALE; HUMAN; LIQUID CHROMATOGRAPHY; MALE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PROTEIN ANALYSIS; PROTEIN BLOOD LEVEL; PROTEIN CONTENT; PROTEIN DENATURATION; PROTEIN DETERMINATION; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN LOCALIZATION; TANDEM MASS SPECTROMETRY; TRIDENT ANALYSIS; UPREGULATION; WESTERN BLOTTING;

ANIMALS; BLOOD PROTEINS; CELL LINE, TUMOR; CELLS, CULTURED; COMPUTATIONAL BIOLOGY; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HUMANS; MALE; MASS SPECTROMETRY; MICE; MICE, INBRED C57BL; PROTEIN FOLDING; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 84875299090     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0057104     Document Type: Article

References (47)

1. Doolittle RF (1975) Fibrinogen and Fibrin, in The Plasma Proteins: Structure, Function and Genetic Control. In: Putnam FW editor. New York: Academic Press. pp. 109-156.
2. Mitchell P, (2010) Proteomics retrenches. Nat Biotechnol 28: 665-670.
3. Liotta LA, Ferrari M, Petricoin E, (2003) Clinical proteomics: written in blood. Nature 425: 905.
4. Pieper R, Su Q, Gatlin CL, Huang ST, Anderson NL, et al. (2003) Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome. Proteomics 3: 422-432.
5. Righetti PG, Boschetti E, Lomas L, Citterio A, (2006) Protein Equalizer Technology: the quest for a "democratic proteome". Proteomics 6: 3980-3992.
6. Ray S, Reddy PJ, Jain R, Gollapalli K, Moiyadi A, et al. (2011) Proteomic technologies for the identification of disease biomarkers in serum: advances and challenges ahead. Proteomics 11: 2139-2161.
7. Di Girolamo F, Boschetti E, Chung MC, Guadagni F, Righetti PG, (2011) "Proteomineering" or not? The debate on biomarker discovery in sera continues. J Proteomics 74: 589-594.
8. Witzmann FA, Richardson MR, (2006) Two-dimensional gels for toxicological drug discovery applications. Expert Opin Drug Metab Toxicol 2: 103-111.
9. Lopez JL, (2007) Two-dimensional electrophoresis in proteome expression analysis. J Chromatogr B Analyt Technol Biomed Life Sci 849: 190-202.
10. Shevchenko A, Wilm M, Vorm O, Mann M, (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 68: 850-858.
11. Lentini A, Vidal-Vanaclocha F, Facchiano F, Caraglia M, Abbruzzese A, et al. (2000) Theophylline administration markedly reduces hepatic and pulmonary implantation of B16-F10 melanoma cells in mice. Melanoma Res 10: 435-443.
12. Faraone D, Aguzzi MS, Toietta G, Facchiano AM, Facchiano F, et al. (2009) Platelet-derived growth factor-receptor alpha strongly inhibits melanoma growth in vitro and in vivo. Neoplasia 11: 732-742.
13. Aguzzi MS, D'Arcangelo D, Giampietri C, Capogrossi MC, Facchiano A, (2011) RAM, an RGDS Analog, Exerts Potent Anti-Melanoma Effects In Vitro and In Vivo. PLoS One 6 (10):: e25352 doi:10.1371/journal.pone.0025352 Epub 2011 Oct 3.
14. Facchiano F, D'Arcangelo D, Russo K, Fogliano V, Mennella C, et al. (2006) Glycated fibroblast growth factor-2 is quickly produced in vitro upon low-millimolar glucose treatment and detected in vivo in diabetic mice. Mol Endocrinol 20: 2806-2818.
15. Yates JR 3rd, Eng JK, McCormack AL, Schieltz D, (1995) Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem 67: 1426-1436.
16. Ping P, Vondriska TM, Creighton CJ, Gandhi TK, Yang Z, et al. (2005) A functional annotation of subproteomes in human plasma. Proteomics 5: 3506-3519.
17. Chromy BA, Gonzales AD, Perkins J, Choi MW, Corzett MH, et al. (2004) Proteomic analysis of human serum by two-dimensional differential gel electrophoresis after depletion of high-abundant proteins. J Proteome Res 3: 1120-1127.
18. Anderson NL, Polanski M, Pieper R, Gatlin T, Tirumalai RS, et al. (2004) The human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol Cell Proteomics 3: 311-326.
19. Liu T, Qian WJ, Gritsenko MA, Xiao W, Moldawer LL, et al. (2006) High dynamic range characterization of the trauma patient plasma proteome. Mol Cell Proteomics 5: 1899-1913.
20. Anderson NL, Anderson NG, (2002) The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 1: 845-867.
21. Bernhard OK, Kapp EA, Simpson RJ, (2007) Enhanced analysis of the mouse plasma proteome using cysteine-containing tryptic glycopeptides. J Proteome Res 6: 987-995.
22. Chan KC, Lucas DA, Hise D, Schaefer CF, Xiao Z, et al. (2004) Analysis of the human serum proteome. Clinical Proteomics 1: 101-225.
23. Poste G, (2011) Bring on the biomarkers. Nature 469: 156-157.
24. Mouawad R, Spano JP, Khayat D, (2010) Old and new serological biomarkers in melanoma: where we are in 2009. Melanoma Res 20: 67-76.
25. Zhang H, Fu T, McGettigan S, Kumar S, Liu S, et al. (2011) IL8 and Cathepsin B as Melanoma Serum Biomarkers. Int J Mol Sci 12: 1505-18.
26. Findeisen P, Zapatka M, Peccerella T, Matzk H, Neumaier M, et al. (2009) Serum amyloid A as a prognostic marker in melanoma identified by proteomic profiling. J Clin Oncol 27: 2199-2208.
27. Longo C, Gambara G, Espina V, Luchini A, Bishop B, et al. (2011) A novel biomarker harvesting nanotechnology identifies Bak as a candidate melanoma biomarker in serum. Exp Dermatol 20: 29-34.
28. Boschetti E, Bindschedler LV, Tang C, Fasoli E, Righetti PG, (2009) Combinatorial peptide ligand libraries and plant proteomics: a winning strategy at a price. J Chromatogr A 1216: 1215-1222.
29. Rak J, (2010) Microparticles in cancer. Semin Thromb Hemost 36: 888-906.
30. Bourboulia D, Stetler-Stevenson WG, (2010) Matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs): Positive and negative regulators in tumor cell adhesion. Semin Cancer Biol 20: 161-168.
31. Baker AH, Edwards DR, Murphy G, (2002) Metalloproteinase inhibitors: biological actions and therapeutic opportunities. J Cell Sci 115: 3719-3727.
32. Lizonova A, Bizik J, Grofova M, Vaheri A, (1990) Coexpression of tumor-associated alpha 2-macroglobulin and growth factors in human melanoma cell lines. J Cell Biochem 43: 315-325.
33. Kancha RK, Stearns ME, Hussain MM, (1994) Decreased expression of the low density lipoprotein receptor-related protein/alpha 2-macroglobulin receptor in invasive cell clones derived from human prostate and breast tumor cells. Oncol Res 6: 365-372.
34. Harthun NL, Weaver AM, Brinckerhoff LH, Deacon DH, Gonias SL, et al. (1998) Activated alpha 2-macroglobulin reverses the immunosuppressive activity in human breast cancer cell-conditioned medium by selectively neutralizing transforming growth factor-beta in the presence of interleukin-2. J Immunother 21: 85-94.
35. Katerinaki E, Evans GS, Lorigan PC, MacNeil S, (2003) TNF-alpha increases human melanoma cell invasion and migration in vitro: the role of proteolytic enzymes. Br J Cancer 89: 1123-1129.
36. Lisowska-Myjak B, Pachecka J, Kaczynska B, Miszkurka G, Kadziela K, (2006) Serum protease inhibitor concentrations and total antitrypsin activity in diabetic and non-diabetic children during adolescence. Acta Diabetol 43: 88-92.
37. Arinola G, Arowojolu A, Bamgboye A, Akinwale A, Adeniyi A, (2006) Serum concentrations of immunoglobulins and acute phase proteins in Nigerian women with preeclampsia. Reprod Biol 6: 265-274.
38. Okano T, Kondo T, Kakisaka T, Fujii K, Yamada M, et al. (2006) Plasma proteomics of lung cancer by a linkage of multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis. Proteomics 6: 3938-3948.
39. Chen Z, Gu J, (2007) Immunoglobulin G expression in carcinomas and cancer cell lines. Faseb J 21: 2931-2938.
40. Yang Y, Chung EK, Zhou B, Blanchong CA, Yu CY, et al. (2003) Diversity in intrinsic strengths of the human complement system: serum C4 protein concentrations correlate with C4 gene size and polygenic variations, hemolytic activities, and body mass index. J Immunol 171: 2734-2745.
41. Leiviskä J, Sundvall J, Alfthan G, Jauhiainen M, Salomaa V, (2011) Apolipoprotein A-I, apolipoprotein B, and apolipoprotein B/apolipoprotein A-I ratio: Reference intervals compared with values in different pathophysiological conditions from the FINRISK 2007 study. Clin Chim Acta 412: 1146-1150.
42. Bernhard OK, Kapp EA, Simpson RJ, (2007) Enhanced analysis of the mouse plasma proteome using cysteine-containing tryptic glycopeptides. J Proteome Res 6: 987-995.
43. Li SQ, Yun J, Xue FB, Bai CQ, Yang SG, et al. (2007) Comparative proteome analysis of serum from acute pulmonary embolism rat model for biomarker discovery. J Proteome Res 6: 150-159.
44. Haddy N, De Bacquer D, Chemaly MM, Maurice M, Ehnholm C, et al. (2002) The importance of plasma apolipoprotein E concentration in addition to its common polymorphism on inter-individual variation in lipid levels: results from Apo Europe. Eur J Hum Genet 10: 841-850.
45. Heo SH, Lee SJ, Ryoo HM, Park JY, Cho JY, (2007) Identification of putative serum glycoprotein biomarkers for human lung adenocarcinoma by multilectin affinity chromatography and LC-MS/MS. Proteomics 7: 4292-4302.
46. Hoagland LF, Campa MJ, Gottlin EB, Herndon JE 2nd, Patz EF Jr, (2007) Haptoglobin and posttranslational glycan-modified derivatives as serum biomarkers for the diagnosis of nonsmall cell lung cancer. Cancer 110: 2260-2268.
47. Yang Y, Chung EK, Zhou B, Blanchong CA, Yu CY, et al. (2003) Diversity in intrinsic strengths of the human complement system: serum C4 protein concentrations correlate with C4 gene size and polygenic variations, hemolytic activities, and body mass index. J Immunol 171: 2734-2745.