Proteomic profiling of serologic response to Candida albicans during host-commensal and host-pathogen interactions

Methods in Molecular Biology

Volumn 470, Issue , 2008, Pages 369-411

  Pitarch, Aida ^a   Nombela, César ^a   Gil, Concha ^a  

^a UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

Author keywords

Antibody response; Candida albicans; Immunome; Immunoproteomics; Mass spectrometry; Proteomics; SERPA; Systemic candidiasis; Two dimensional gel electrophoresis

Indexed keywords

CANDIDA; CANDIDA ALBICANS; FUNGI;

EID: 62549146596     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-204-5_26     Document Type: Article

References (55)

1. Pfaller, M. A. and Diekema, D. J. (2007) Epidemiology of invasive candidiasis: a persistent public health problem. Clin. Microbiol. Rev. 20, 133-163.
2. Calderone, R. A. and Fonzi, W. A. (2001) Virulence factors of Candida albicans. Trends Microbiol. 9, 327-335.
3. Hube, B. (2004) From commensal to pathogen: stage- and tissue-specific gene expression of Candida albicans. Curr. Opin. Microbiol. 7, 336-341.
4. Pitarch, A., Nombela, C., and Gil, C. (2006) Candida albicans biology and pathogenicity: insights from proteomics. Methods Biochem. Anal. 49, 285-330.
5. Garber, G. (2001) An overview of fungal infections. Drugs 61, 1-12.
6. Rex, J. H., Walsh, T. J., Sobel, J. D., Filler, S. G., Pappas, P. G., Dismukes, W. E., and Edwards, J. E. (2000) Practice guidelines for the treatment of candidiasis. Infectious Diseases Society of America. Clin. Infect. Dis. 30, 662-678.
7. Pitarch, A., Abian, J., Carrascal, M., Sanchez, M., Nombela, C., and Gil, C. (2004) Proteomics-based identification of novel Candida albicans antigens for diagnosis of systemic candidiasis in patients with underlying hematological malignancies. Proteomics. 4, 3084-3106.
8. Pitarch, A., Jimenez, A., Nombela, C., and Gil, C. (2006) Decoding serological response to Candida cell wall immunome into novel diagnostic, prognostic, and therapeutic candidates for systemic candidiasis by proteomic and bioinformatic analyses. Mol. Cell Proteomics. 5, 79-96.
9. Martinez, J. P., Gil, M. L., Lopez-Ribot, J. L., and Chaffin, W. L. (1998) Serologic response to cell wall mannoproteins and proteins of Candida albicans. Clin. Microbiol. Rev. 11, 121-141.
10. Ellepola, A. N. and Morrison, C.J. (2005) Laboratory diagnosis of invasive candidiasis. J. Microbiol. 43, 65-84.
11. Krah, A. and Jungblut, P. R. (2004) Immunoproteomics. Methods Mol. Med. 94, 19-32.
12. Caron, M., Choquet-Kastylevsky, G., and Joubert-Caron, R. (2007) Cancer immunomics using autoantibody signatures for biomarker discovery. Mol. Cell Proteomics. 6, 1115-1122.
13. Seliger, B. and Kellner, R. (2002) Design of proteome-based studies in combination with serology for the identification of biomarkers and novel targets. Proteomics. 2, 1641-1651.
14. Chich, J. F., David, O., Villers, F., Schaeffer, B., Lutomski, D., and Huet, S. (2007) Statistics for proteomics: experimental design and 2-DE differential analysis. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 849, 261-272.
15. Haoudi, A. and Bensmail, H. (2006) Bioinformatics and data mining in proteomics. Expert. Rev. Proteomics. 3, 333-343.
16. Phan, J. H., Quo, C. F., and Wang, M. D. (2006) Functional genomics and proteomics in the clinical neurosciences: data mining and bioinformatics. Prog. Brain Res. 158, 83-108.
17. Wilson, R. A., Curwen, R. S., Braschi, S., Hall, S. L., Coulson, P. S., and Ashton, P. D. (2004) From genomes to vaccines via the proteome. Mem. Inst. Oswaldo Cruz 99, 45-50.
18. Sette, A., Fieri, W., Peters, B., Sathiamurthy, M., Bui, H. H., and Wilson, S. (2005) A roadmap for the immunomics of category A-C pathogens. Immunity. 22, 155-161.
19. Pitarch, A., Diez-Orejas, R., Molero, G., Pardo, M., Sanchez, M., Gil, C., and Nombela, C. (2001) Analysis of the serologic response to systemic Candida albicans infection in a murine model. Proteomics. 1, 550-559.
20. Pardo, M., Ward, M., Pitarch, A., Sanchez, M., Nombela, C., Blackstock, W., and Gil, C. (2000) Cross-species identification of novel Candida albicans immunogenic proteins by combination of two-dimensional Polyacrylamide gel electrophoresis and mass spectrometry. Electrophoresis 21, 2651-2659.
21. Pitarch, A., Nombela, C., and Gil, C. (2007). Reliability of antibodies to Candida methionine synthase for diagnosis, prognosis and risk stratification in systemic candidiasis: a generic strategy for the prototype development phase of proteomic markers. Proteomics, Clin. Appl., 1, 1221-1242.
22. Fernandez-Arenas, E., Molero, G., Nombela, C., Diez-Orejas, R., and Gil, C (2004) Contribution of the antibodies response induced by a low virulent Candida albicans strain in protection against systemic candidiasis. Proteomics. 4, 1204-1215.
23. Fernandez-Arenas, E., Molero, G., Nombela, C., Diez-Orejas, R., and Gil, C. (2004) Low virulent strains of Candida albicans: unravelling the antigens for a future vaccine. Proteomics. 4, 3007-3020.
24. Pitarch, A., Pardo, M., Jimenez, A., Pla, J., Gil, C., Sanchez, M., and Nombela, C. (1999) Two-dimensional gel electrophoresis as analytical tool for identifying Candida albicans immunogenic proteins. Electrophoresis 20, 1001-1010.
25. Pitarch, A., Nombela, C., and Gil, C. (2006) Contributions of proteomics to diagnosis, treatment, and prevention of candidiasis. Methods Biochem. Anal. 49, 331-361.
26. Pitarch, A., Molero, G., Monteoliva, L., Thomas, D. P., López-Ribot, J. L., Nombela, C., and Gil, C. (2007) Proteomics in Candida species, in Candida: Comparative and Functional Genomics (d'Enfert, C and Hube, B., eds), Caister Academic Press, UK, pp. 169-194.
27. Sahin, U., Tureci, O., Schmitt, H., Cochlovius, B., Johannes, T., Schmits, R., Stenner, F., Luo, G., Schobert, I., and Pfreundschuh, M. (1995) Human neoplasms elicit multiple specific immune responses in the autologous host. Proc. Natl. Acad. Sci. U.S.A. 92, 11810-11813.
28. Lee, S. Y., Obata, Y., Yoshida, M., Stockert, E., Williamson, B., Jungbluth, A. A., Chen, Y. T., Old, L. J., and Scanlan, M. J. (2003) Immunomic analysis of human sarcoma. Proc. Natl. Acad. Sci. U.S.A. 100, 2651-2656.
29. Rollins, S. M., Peppercorn, A., Hang, L., Hillman, J. D., Calderwood, S. B., Handfield, M., and Ryan, E. T. (2005) In vivo induced antigen technology (TvTAT). Cell Microbiol. 7, 1-9.
30. Hardouin, J., Lasserre, J. P., Canelle, L., Duchateau, M., Vlieghe, C., Choquet-Kastylevsky, G., Joubert-Caron, R., and Caron, M. (2007) Usefulness of autoantigens depletion to detect autoantibody signatures by multiple affinity protein profiling. J. Sep. Sci. 30, 352-358.
31. Bradford, T. J., Wang, X., and Chinnaiyan, A. M. (2006) Cancer immunomics: using autoantibody signatures in the early detection of prostate cancer. Urol. Oncol. 24, 237-242.
32. Hess, J. L., Blazer, L., Romer, T., Faber, L., Buller, R. M., and Boyle, M. D. (2005) Immunoproteomics. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 815, 65-75.
33. Chaffin, W. L., Lopez-Ribot, J. L., Casanova, M., Gozalbo, D., and Martinez, J. P. (1998) Cell wall and secreted proteins of Candida albicans: identification, function, and expression. Microbiol. Mol. Biol. Rev. 62, 130-180.
34. Lopez-Ribot, J. L., Casanova, M., Murgui, A., and Martinez, J. P. (2004) Antibody response to Candida albicans cell wall antigens. FEMS Immunol. Med. Microbiol. 41, 187-196.
35. Pitarch, A., Nombela, C., and Gil, C. (2008) Cell wall fractionation for yeast and fungal proteomics. Methods Mol. Biol. 425, 217-239.
36. Pitarch, A., Nombela, C., and Gil, C. (2008) Collection of proteins secreted from yeast protoplasts in active cell wall regeneration. Methods Mol. Biol. 425, 241-263.
37. Pitarch, A., Sanchez, M., Nombela, C., and Gil, C. (2003) Analysis of the Candida albicans proteome. I. Strategies and applications. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 787, 101-128.
38. Rupp, S. (2004) Proteomics on its way to study host-pathogen interaction in Candida albicans. Curr. Opin. Microbiol. 7, 330-335.
39. Thomas, D. P., Pitarch, A., Monteoliva, L., Gil, C., and Lopez-Ribot, J. L. (2006) Proteomics to study Candida albicans biology and pathogenicity. Infect. Disord. Drug Targets. 6, 335-341.
40. Gorg, A., Obermaier, C., Boguth, G., Harder, A., Scheibe, B., Wildgruber, R., and Weiss, W. (2000) The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21, 1037-1053.
41. Valdes, I., Pitarch, A., Gil, C., Bermudez, A., Llorente, M., Nombela, C., and Mendez, E. (2000) Novel procedure for the identification of proteins by mass fingerprinting combining two-dimensional electrophoresis with fluorescent SYPRO red staining. J Mass Spectrom. 35, 672-682.
42. Shevchenko, A., Wilm, M., Vorm, O., and Mann, M. (1996) Mass spectrometric sequencing of proteins silver-stained Polyacrylamide gels. Anal. Chem. 68, 850-858.
43. Okamura, H., Sigal, C. T., Alland, L., and Resh, M. D. (1995) Rapid high-resolution western blotting. Methods Enzymol. 254, 535-550.
44. Pitarch, A., Sánchez, M., Nombela, C., and Gil, C. (2003). Analysis of the Candida albicans proteome. II. Protein information technology on the Net (update 2002). J Chromatogr. B Analyt. Technol. Biomed. Life Sci. 787, 129-148.
45. d'Enfert, C., Goyard, S., Rodriguez-Arnaveilhe, S., Frangeul, L., Jones, L., Tekaia, F., Bader, O., Albrecht, A., Castillo, L., Dominguez, A., Ernst, J. F., Fradin, C., Gaillardin, C., Garcia-Sanchez, S., de Groot, P., Hube, B., Klis, F. M., Krishnamurthy, S., Kunze, D., Lopez, M. C., Mavor, A., Martin, N., Moszer, I., Onesime, D., Perez, M. J., Sentandreu, R., Valentin, E., and Brown, A. J. (2005) CandidaDB: a genome database for Candida albicans pathogenomics. Nucleic Acids Res. 33, D353-D357.
46. Westermeier, R. and Naven, T. (eds.) (2002) Proteomics in Practice: A Laboratory Manual of Proteome Analysis. Wiley-VCH, Weinheim, Germany.
47. Choe, L. H. and Lee, K H. (2000) A comparison of three commercially available isoelectric focusing units for proteome analysis: the multiphor, the IPGphor and the protean IEF cell. Electrophoresis 21, 993-1000.
48. Palagi, P. M., Hernandez, P., Walther, D., and Appel, R. D. (2006) Proteome informatics I: Bioinformatics tools for processing experimental data. Proteomics 6, 5435-5444.
49. Hochstrasser, D. F., Harrington, M. G., Hochstrasser, A. C., Miller, M. J., and Merril, C. R. (1988) Methods for increasing the resolution of two-dimensional protein electrophoresis. Anal. Biochem. 173, 424-435.
50. Necas, O. (1971) Cell wall synthesis in yeast protoplasts. Bacteriol. Rev. 35, 149-170.
51. Pitarch, A., Sanchez, M., Nombela, C., and Gil, C. (2002) Sequential fractionation and two-dimensional gel analysis unravels the complexity of the dimorphic fungus Candida albicans cell wall proteome. Mol. Cell Proteomics 1, 967-982.
52. Heukeshoven, J. and Dernick, R. (1985) Simplified method for silver staining of proteins in Polyacrylamide and the mechanism of silver staining. Electrophoresis 6, 103-112.
53. Zolg, J. W. and Langen, H. (2004) How industry is approaching the search for new diagnostic markers and biomarkers. Mol. Cell Proteomics 3, 345-354.
54. Pitarch, A., Jimenez, A., Nombela, C., and Gil, C. (2008) Serological proteome analysis to identify systemic candidiasis patients in the intensive care unit: Analytical, diagnostic and prognostic validation of anti-Candida enolase antibodies on quantitative clinical platforms. Proteomics Clin. Appl. 2, 596-618.
55. Pitarch, A., Nombela, C., and Gil. (2008) The Candida immunome as a mine for clinical biomarker development for invasive candidiasis: From biomarker discovery to assay validation. In Pathogenic Fungi: Insights in Molecular Biology. (Eds., San-Bias, G. and Calderone, R.). Caister Academic Press, Norfolk, UK, pp. 103-142.