In-depth exploration of cerebrospinal fluid by combining peptide ligand library treatment and label-free protein quantification

Molecular and Cellular Proteomics

Volumn 9, Issue 5, 2010, Pages 1006-1021

  Mouton Barbosa, Emmanuelle ^a,b   Roux Dalvai, Florence ^a,b   Bouyssié, David ^a,b   Berger, François ^c   Schmidt, Eric ^d   Righetti, Pier Giorgio ^e   Guerrier, Luc ^f   Boschetti, Egisto ^f   Burlet Schiltz, Odile ^a,b   Monsarrat, Bernard ^a,b   De Peredo, Anne Gonzalez ^a,b  

^a INSTITUT DE PHARMACOLOGIE ET DE BIOLOGIE STRUCTURALE   (France)

^b UNIVERSITÉ DE TOULOUSE   (France)

^c INSERM   (France)

^d CHU PURPAN   (France)

^e POLITECNICO DI MILANO   (Italy)

^f CEA SACLAY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE LIBRARY;

ARTICLE; BIOINFORMATICS; CEREBROSPINAL FLUID; CLINICAL STUDY; COMBINATORIAL PEPTIDE LIGAND LIBRARY TECHNOLOGY; GENE TECHNOLOGY; HUMAN; HUMAN TISSUE; LIQUID CHROMATOGRAPHY; LUMBAR PUNCTURE; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONTENT;

EID: 77951838202     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M900513-MCP200     Document Type: Article

References (56)

1. Hühmer, A. F., Biringer, R. G., Amato, H., Fonteh, A. N., and Harrington, M. G. (2006) Protein analysis in human cerebrospinal fluid: physiological aspects, current progress and future challenges. Dis. Markers 22, 3-26 (Pubitemid 41831602)
2. Johanson, C. E., Duncan, J. A., 3rd, Klinge, P. M., Brinker, T., Stopa, E. G., and Silverberg, G. D. (2008) Multiplicity of cerebrospinal fluid functions: new challenges in health and disease. Cerebrospinal Fluid Res. 5, 10 (Pubitemid 351803829)
3. Speake, T., Whitwell, C., Kajita, H., Majid, A., and Brown, P. D. (2001) Mechanisms of CSF secretion by the choroid plexus. Microsc. Res. Tech. 52, 49-59
4. Reiber, H. (1994) Flow rate of cerebrospinal fluid (CSF) - a concept common to normal blood-CSF barrier function and to dysfunction in neurological diseases. J. Neurol. Sci. 122, 189-203
5. Tu, G. F., Cole, T., Southwell, B. R., and Schreiber, G. (1990) Expression of the genes for transthyretin, cystatin C and beta A4 amyloid precursor protein in sheep choroid plexus during development. Brain Res. Dev. Brain Res. 55, 203-208
6. Reiber, H. (2001) Dynamics of brain-derived proteins in cerebrospinal fluid. Clin. Chim. Acta 310, 173-186
7. Goldman, D., Merril, C. R., and Ebert, M. H. (1980) Two-dimensional gel electrophoresis of cerebrospinal fluid proteins. Clin. Chem. 26, 1317-1322
8. Guillaume, E., Zimmermann, C., Burkhard, P. R., Hochstrasser, D. F., and Sanchez, J. C. (2003) A potential cerebrospinal fluid and plasmatic marker for the diagnosis of Creutzfeldt-Jakob disease. Proteomics 3, 1495-1499 (Pubitemid 37048075)
9. Sickmann, A., Dormeyer, W., Wortelkamp, S., Woitalla, D., Kuhn, W., and Meyer, H. E. (2000) Identification of proteins from human cerebrospinal fluid, separated by two-dimensional polyacrylamide gel electrophoresis. Electrophoresis 21, 2721-2728 (Pubitemid 30646308)
10. Terry, D. E., and Desiderio, D. M. (2003) Between-gel reproducibility of the human cerebrospinal fluid proteome. Proteomics 3, 1962-1979 (Pubitemid 37305891)
11. Pan, S., Zhu, D., Quinn, J. F., Peskind, E. R., Montine, T. J., Lin, B., Goodlett, D. R., Taylor, G., Eng, J., and Zhang, J. (2007) A combined dataset of human cerebrospinal fluid proteins identified by multi-dimensional chromatography and tandem mass spectrometry. Proteomics 7, 469-473 (Pubitemid 46293989)
12. Abdi, F., Quinn, J. F., Jankovic, J., McIntosh, M., Leverenz, J. B., Peskind, E., Nixon, R., Nutt, J., Chung, K., Zabetian, C., Samii, A., Lin, M., Hattan, S., Pan, C., Wang, Y., Jin, J., Zhu, D., Li, G. J., Liu, Y., Waichunas, D., Montine, T. J., and Zhang, J. (2006) Detection of biomarkers with a multiplex quantitative proteomic platform in cerebrospinal fluid of patients with neurodegenerative disorders. J. Alzheimers Dis. 9, 293-348 (Pubitemid 44253348)
13. Zougman, A., Pilch, B., Podtelejnikov, A., Kiehntopf, M., Schnabel, C., Kumar, C., and Mann, M. (2008) Integrated analysis of the cerebrospinal fluid peptidome and proteome. J. Proteome Res. 7, 386-399 (Pubitemid 351171153)
14. Zhang, J., Goodlett, D. R., Quinn, J. F., Peskind, E., Kaye, J. A., Zhou, Y., Pan, C., Yi, E., Eng, J., Wang, Q., Aebersold, R. H., and Montine, T. J. (2005) Quantitative proteomics of cerebrospinal fluid from patients with Alzheimer disease. J. Alzheimers Dis. 7, 125-133; discussion 173-180 (Pubitemid 40592186)
15. Roy, S., Josephson, S. A., Fridlyand, J., Karch, J., Kadoch, C., Karrim, J., Damon, L., Treseler, P., Kunwar, S., Shuman, M. A., Jones, T., Becker, C. H., Schulman, H., and Rubenstein, J. L. (2008) Protein biomarker identification in the CSF of patients with CNS lymphoma. J. Clin. Oncol. 26, 96-105
16. Guerrier, L., Thulasiraman, V., Castagna, A., Fortis, F., Lin, S., Lomas, L., Righetti, P. G., and Boschetti, E. (2006) Reducing protein concentration range of biological samples using solid-phase ligand libraries. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 833, 33-40
17. Righetti, P. G., Boschetti, E., Lomas, L., and Citterio, A. (2006) Protein Equalizer Technology: the quest for a "democratic proteome". Proteomics 6, 3980-3992
18. Righetti, P. G., and Boschetti, E. (2008) The ProteoMiner and the FortyNiners: searching for gold nuggets in the proteomic arena. Mass Spectrom. Rev. 27, 596-608
19. Boschetti, E., and Righetti, P. G. (2009) The art of observing rare protein species in proteomes with peptide ligand libraries. Proteomics 9, 1492-1510
20. Castagna, A., Cecconi, D., Sennels, L., Rappsilber, J., Guerrier, L., Fortis, F., Boschetti, E., Lomas, L., and Righetti, P. G. (2005) Exploring the hidden human urinary proteome via ligand library beads. J. Proteome Res. 4, 1917-1930 (Pubitemid 41814257)
21. Sennels, L., Salek, M., Lomas, L., Boschetti, E., Righetti, P. G., and Rappsilber, J. (2007) Proteomic analysis of human blood serum using peptide library beads. J. Proteome Res. 6, 4055-4062 (Pubitemid 350032568)
22. Guerrier, L., Claverol, S., Fortis, F., Rinalducci, S., Timperio, A. M., Antonioli, P., Jandrot-Perrus, M., Boschetti, E., and Righetti, P. G. (2007) Exploring the platelet proteome via combinatorial, hexapeptide ligand libraries. J. Proteome Res. 6, 4290-4303 (Pubitemid 350158505)
23. Roux-Dalvai, F., Gonzalez de Peredo, A., Simó, C., Guerrier, L., Bouyssié, D., Zanella, A., Citterio, A., Burlet-Schiltz, O., Boschetti, E., Righetti, P. G., and Monsarrat, B. (2008) Extensive analysis of the cytoplasmic proteome of human erythrocytes using the peptide ligand library technology and advanced mass spectrometry. Mol. Cell. Proteomics 7, 2254-2269
24. Bouyssié, D., Gonzalezde Peredo, A., Mouton, E., Albigot, R., Roussel, L., Ortega, N., Cayrol, C., Burlet-Schiltz, O., Girard, J. P., and Monsarrat, B. (2007) Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human endothelial cells. Mol. Cell. Proteomics 6, 1621-1637
25. Aruga, J., Yokota, N., and Mikoshiba, K. (2003) Human SLITRK family genes: genomic organization and expression profiling in normal brain and brain tumor tissue. Gene 315, 87-94 (Pubitemid 37214900)
26. Stanislas, T., Bouyssie, D., Rossignol, M., Vesa, S., Fromentin, J., Morel, J., Pichereaux, C., Monsarrat, B., and Simon-Plas, F. (2009) Quantitative proteomics reveals a dynamic association of proteins to detergent-resistant membranes upon elicitor signaling in tobacco. Mol. Cell. Proteomics 8, 2186-2198
27. Fang, Q., Strand, A., Law, W., Faca, V. M., Fitzgibbon, M. P., Hamel, N., Houle, B., Liu, X., May, D. H., Poschmann, G., Roy, L., Stühler, K., Ying, W., Zhang, J., Zheng, Z., Bergeron, J. J., Hanash, S., He, F., Leavitt, B. R., Meyer, H. E., Qian, X., and McIntosh, M. W. (2009) Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease. Mol. Cell. Proteomics 8, 451-466
28. Candiano, G., Dimuccio, V., Bruschi, M., Santucci, L., Gusmano, R., Boschetti, E., Righetti, P. G., and Ghiggeri, G. M. (2009) Combinatorial peptide ligand libraries for urine proteome analysis: investigation of different elution systems. Electrophoresis 30, 2405-2411
29. Pan, S., Wang, Y., Quinn, J. F., Peskind, E. R., Waichunas, D., Wimberger, J. T., Jin, J., Li, J. G., Zhu, D., Pan, C., and Zhang, J. (2006) Identification of glycoproteins in human cerebrospinal fluid with a complementary proteomic approach. J. Proteome Res. 5, 2769-2779 (Pubitemid 44595178)
30. Zhang, J., Goodlett, D. R., Peskind, E. R., Quinn, J. F., Zhou, Y., Wang, Q., Pan, C., Yi, E., Eng, J., Aebersold, R. H., and Montine, T. J. (2005) Quantitative proteomic analysis of age-related changes in human cerebrospinal fluid. Neurobiol. Aging 26, 207-227 (Pubitemid 39610462)
31. Xu, J., Chen, J., Peskind, E. R., Jin, J., Eng, J., Pan, C., Montine, T. J., Goodlett, D. R., and Zhang, J. (2006) Characterization of proteome of human cerebrospinal fluid. Int. Rev. Neurobiol. 73, 29-98
32. Reiber, H. (2003) Proteins in cerebrospinal fluid and blood: barriers, CSF flow rate and source-related dynamics. Restor. Neurol. Neurosci. 21, 79-96
33. Reiber, H., and Peter, J. B. (2001) Cerebrospinal fluid analysis: disease-related data patterns and evaluation programs. J. Neurol. Sci. 184, 101-122
34. Thompson, E. J. (1988) The CSF Proteins: a Biochemical Approach, Elsevier, Amsterdam
35. Silva, J. C., Gorenstein, M. V., Li, G. Z., Vissers, J. P., and Geromanos, S. J. (2006) Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol. Cell. Proteomics 5, 144-156
36. Yazdani, U., and Terman, J. R. (2006) The semaphorins. Genome Biol. 7, 211
37. Kruger, R. P., Aurandt, J., and Guan, K. L. (2005) Semaphorins command cells to move. Nat. Rev. Mol. Cell Biol. 6, 789-800
38. Geretti, E., and Klagsbrun, M. (2007) Neuropilins: novel targets for antiangiogenesis therapies. Cell Adh. Migr. 1, 56-61
39. Karayan-Tapon, L., Wager, M., Guilhot, J., Levillain, P., Marquant, C., Clarhaut, J., Potiron, V., and Roche, J. (2008) Semaphorin, neuropilin and VEGF expression in glial tumours: SEMA3G, a prognostic marker? Br. J. Cancer 99, 1153-1160
40. Rich, J. N., Hans, C., Jones, B., Iversen, E. S., McLendon, R. E., Rasheed, B. K., Dobra, A., Dressman, H. K., Bigner, D. D., Nevins, J. R., and West, M. (2005) Gene expression profiling and genetic markers in glioblastoma survival. Cancer Res. 65, 4051-4058 (Pubitemid 40775641)
41. Yang, X., Cao, W., Lin, H., Zhang, W., Lin, W., Cao, L., Zhen, H., Huo, J., and Zhang, X. (2009) Isoform-specific expression of 14-3-3 proteins in human astrocytoma. J. Neurol. Sci. 276, 54-59
42. Pennington, C., Chohan, G., Mackenzie, J., Andrews, M., Will, R., Knight, R., and Green, A. (2009) The role of cerebrospinal fluid proteins as early diagnostic markers for sporadic Creutzfeldt-Jakob disease. Neurosci. Lett. 455, 56-59
43. Undén, J., Strandberg, K., Malm, J., Campbell, E., Rosengren, L., Stenflo, J., Norrving, B., Romner, B., Lindgren, A., and Andsberg, G. (2009) Explorative investigation of biomarkers of brain damage and coagulation system activation in clinical stroke differentiation. J. Neurol. 256, 72-77
44. Bloomfield, S. M., McKinney, J., Smith, L., and Brisman, J. (2007) Reliability of S100B in predicting severity of central nervous system injury. Neurocrit. Care 6, 121-138 (Pubitemid 46934023)
45. Gonçalves, C. A., Leite, M. C., and Nardin, P. (2008) Biological and methodological features of the measurement of S100B, a putative marker of brain injury. Clin. Biochem. 41, 755-763
46. Sharif, A., Canton, B., Junier, M. P., and Chneiweiss, H. (2003) PEA-15 modulates TNFalpha intracellular signaling in astrocytes. Ann. N.Y. Acad. Sci. 1010, 43-50
47. Balenci, L., Saoudi, Y., Grunwald, D., Deloulme, J. C., Bouron, A., Bernards, A., and Baudier, J. (2007) IQGAP1 regulates adult neural progenitors in vivo and vascular endothelial growth factor-triggered neural progenitor migration in vitro. J. Neurosci. 27, 4716-4724 (Pubitemid 46663565)
48. Tsui, C. C., Copeland, N. G., Gilbert, D. J., Jenkins, N. A., Barnes, C., and Worley, P. F. (1996) Narp, a novel member of the pentraxin family, promotes neurite outgrowth and is dynamically regulated by neuronal activity. J. Neurosci. 16, 2463-2478 (Pubitemid 26122671)
49. Pang, Z., Zuo, J., and Morgan, J. I. (2000) Cbln3, a novel member of the precerebellin family that binds specifically to Cbln1. J. Neurosci. 20, 6333-6339
50. Patapoutian, A., and Reichardt, L. F. (2001) Trk receptors: mediators of neurotrophin action. Curr. Opin. Neurobiol. 11, 272-280
51. Schindowski, K., Belarbi, K., and Buée, L. (2008) Neurotrophic factors in Alzheimer's disease: role of axonal transport. Genes Brain Behav. 7, Suppl. 1, 43-56
52. da Costa, C. A. (2007) DJ-1: a newcomer in Parkinson's disease pathology. Curr. Mol. Med. 7, 650-657
53. Ross, C. A., and Pickart, C. M. (2004) The ubiquitin-proteasome pathway in Parkinson's disease and other neurodegenerative diseases. Trends Cell Biol. 14, 703-711
54. Mattson, M. P., Gleichmann, M., and Cheng, A. (2008) Mitochondria in neuroplasticity and neurological disorders. Neuron 60, 748-766
55. Hartwig, S., Czibere, A., Kotzka, J., Passlack, W., Haas, R., Eckel, J., and Lehr, S. (2009) Combinatorial hexapeptide ligand libraries (ProteoMiner): an innovative fractionation tool for differential quantitative clinical proteomics. Arch. Physiol. Biochem. 115, 155-160
56. Simó, C., Bachi, A., Cattaneo, A., Guerrier, L., Fortis, F., Boschetti, E., Podtelejnikov, A., and Righetti, P. G. (2008) Performance of combinatorial peptide libraries in capturing the low-abundance proteome of red blood cells. 1. Behavior of mono- to hexapeptides. Anal. Chem. 80, 3547-3556