Mass spectrometric and computational analysis of cytokine-induced alterations in the astrocyte secretome

Proteomics

Volumn 9, Issue 3, 2009, Pages 768-782

  Keene, Sarah Dunn ^a   Greco, Todd M ^a   Parastatidis, Loannis ^a   Lee, Seon Hwa ^b   Hughes, Ethan G ^b   Balice Gordon, Rita J ^b   Speicher, David W ^c   Ischiropoulos, Harry ^a,b  

^a CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c WISTAR INSTITUTE   (United States)

Author keywords

Astrocytes; Comparative proteomics; Cytokines; Development; Protein secretion

Indexed keywords

CYCLOOXYGENASE 2; CYTOKINE; INTERLEUKIN 6; NERVE GROWTH FACTOR; NITRIC OXIDE; STROMELYSIN;

ALGORITHM; ANIMAL TISSUE; ARTICLE; ASTROCYTE; CENTRAL NERVOUS SYSTEM; ENZYME ACTIVATION; MASS SPECTROMETRY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN SECRETION;

ANIMALS; ASTROCYTES; CELLS, CULTURED; CYTOKINES; MICE; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 60549100723     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200800385     Document Type: Article

References (57)

1. Garcia, A. D., Doan, N. B., Imura, T., Bush, T. G., Sofroniew, M. V., GFAP-expressing progenitors are the principal source of constitutive neurogenesis in adult mouse forebrain. Nat. Neurosci. 2004, 7, 1233-1241.
2. Mauch, D. H., Nagler, K., Schumacher, S., Goritz, C. et al., CNS synaptogenesis promoted by glia-derived cholesterol. Science 2001, 294, 1354-1357.
3. Pascual, O., Casper, K. B., Kubera, C., Zhang, J. et al., Astrocytic purinergic signaling coordinates synaptic networks. Science 2005, 370, 113-116.
4. Volterra, A., Meldolesi, J., Astrocytes, from brain glue to communication elements: the revolution continues. Nat. Rev. Neurosci. 2005, 6, 626-640.
5. Mulligan, S. J., MacVicar, B. A., Calcium transients in astrocyte endfeet cause cerebrovascular constrictions. Nature 2004, 437, 195-199.
6. Zonta, M., Angulo, M. C., Gobbo, S., Rosengarten, B. et al., Neuron-to-astrocyte signaling is central to the dynamic control of brain microcirculation. Nat. Neurosci. 2003, 6, 43-50.
7. Bernardinelli, Y., Magistretti, P. J., Chatton, J. Y., Astrocytes generate Na+-mediated metabolic waves. Proc. Natl. Acad. Sci. USA 2004, 707, 14937-14942.
8. Escartin, C., Valette, J., Lebon, V., Bonvento, G., Neuronastrocyte interactions in the regulation of brain energy metabolism: a focus on NMR spectroscopy. J. Neurochem. 2006, 99, 393-401.
9. Christopherson, K. S., Ullian, E. M., Stokes, C. C., Mullowney, C. E. et al., Thrombospondins are astrocyte-secreted proteins that promote CNS synaptogenesis. Cell 2005, 720, 421-433.
10. Koistinaho, M., Lin, S., Wu, X., Esterman, M. et al., Apolipoprotein E promotes astrocyte colocalization and degradation of deposited amyloid-beta peptides. Nat. Med. 2004, 70, 719-726.
11. Delcourt, N., Jouin, P., Poncet, J., Demey, E. et al., Difference in mass analysis using labeled lysines (DIMAL-K): a new, efficient proteomic quantification method applied to the analysis of astrocytic secretomes. Mol. Cell. Proteomics 2005, 4, 1085-1094.
12. Lafon-Cazal, M., Adjali, O., Galeotti, N., Poncet, J. et al., Proteomic analysis of astrocytic secretion in the mouse. Comparison with the cerebrospinal fluid proteome. J. Biol. Chem. 2003, 278, 24438-24448.
13. Egnaczyk, G. F., Pomonis, J. D., Schmidt, J. A., Rogers, S. D. et al., Proteomic analysis of the reactive phenotype of astrocytes following endothelin-1 exposure. Proteomics 2003, 3, 689-698.
14. Yang, J. W., Rodrigo, R., Felipo, V., Lubec, G., Proteome analysis of primary neurons and astrocytes from rat cerebellum. J. Proteome Res. 2005, 4, 768-788.
15. Dong, Y., Benveniste, E. N., Immune function of astrocytes. Glia 2001, 36, 180-190.
16. Antony, J. M., van Marle, G.,Opii, W., Butterfield, D. A. et al., Human endogenous retrovirus glycoprotein-mediated induction of redox reactants causes oligodendrocyte death and demyelination. Nat. Neurosci. 2004, 7, 1088-1095.
17. Cassina, P., Pehar, M., Vargas, M. R., Castellanos, R. et al., Astrocyte activation by fibroblast growth factor-1 and motor neuron apoptosis: implications for amyotrophic lateral sclerosis. J. Neurochem. 2005, 93, 38-46.
18. Di Giorgio, F. P., Carrasco, M. A., Siao, M. C., Maniatis, T., Eggan, K., Noncell autonomous effect of glia on motor neurons in an embryonic stem cell-based ALS model. Nat. Neurosci. 2007, 10, 608-614.
19. Nagai, M., Re, D. B., Nagata, T., Chalazonitis, A. et al., Astrocytes expressing ALS-linked mutated SOD1 release factors selectively toxic to motor neurons. Nat. Neurosci. 2007, 10, 615-622.
20. Vargas, M. R., Pehar, M., Cassina, P., Martinez-Palma, L. et al., Fibroblast growth factor-1 induces heme oxygenase-1 via nuclear factor erythroid 2-related factor 2 (Nrf2) in spinal cord astrocytes: consequences for motor neuron survival. J. Biol. Chem. 2005, 280, 25571-25579.
21. Tang, H. Y., Ali-Khan, N., Echan, L. A., Levenkova, N. et al.,A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes. Proteomics 2005, 5, 3329-3342.
22. Speicher, K., Kolbas, O., Harper, S., Speicher, D., Systematic analysis of peptide recoveries from in-gel digestions for protein identifications in proteome studies. J. Biomol. Tech. 2000, 11, 74-86.
23. Keller, A., Nesvizhskii, A. I., Kolker, E., Aebersold, R., Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74, 5383-5392.
24. Nesvizhskii, A. I., Keller, A., Kolker, E., Aebersold, R., A statistical model for identifying proteins by MS/MS. Anal. Chem. 2003, 75, 4646-4658.
25. Maere, S., Heymans, K., Kuiper, M., BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 27, 3448-3449.
26. Chukkapalli, G., Guda, C., Subramaniam, S., SledgeHM-MER: a web server for batch searching the Pfam database. Nucleic Acids Res. 2004, 32, W542-W544.
27. Villoslada, P., Genain, C. P., Role of nerve growth factor and other trophic factors in brain inflammation. Prog. Brain Res. 2004, 146, 403-414.
28. Lukes, A., Mun-Bryce, S., Lukes, M., Rosenberg, G. A., Extracellular matrix degradation by metalloproteinases and central nervous system diseases. Mol. Neurobiol. 1999, 19, 267-284.
29. Nair, R., Rost, B., Mimicking cellular sorting improves prediction of subcellular localization. J. Mol. Biol. 2005, 348,85-100.
30. Klee, E. W., Sosa, C. P., Computational classification of classically secreted proteins. Drug Discov. Today 2007, 72, 234-240.
31. Hawkins, J., Boden, M., Detecting and sorting targeting peptides with neural networks and support vector machines. J. Bioinform. Comput. Biol. 2006, 4, 1-18.
32. Nickel, W., Unconventional secretory routes: direct protein export across the plasma membrane of mammalian cells. Traffic 2005, 6, 607-614.
33. Bendtsen, J. D., Jensen, L. J., Blom, N., Von Heijne, G., Bru- nak, S., Feature-based prediction of nonclassical and lea- derless protein secretion. Protein Eng. Des. Sel. 2004, 17, 349-356.
34. Mor-Vaknin, N., Punturieri, A., Sitwala, K., Markovitz, D. M., Vimentin is secreted by activated macrophages. Nat. Cell Biol. 2003, 5, 59-63.
35. Zhao, W. Q., Chen, G. H., Chen, H., Pascale, A. et al., Secretion of Annexin II via activation of insulin receptor and insulin-like growth factor receptor. J. Biol. Chem. 2003, 278, 4205-4215.
36. Suzuki, J., Jin, Z. G., Meoli, D. F., Matoba, T., Berk, B. C., Cyclophilin A is secreted by a vesicular pathway in vascular smooth muscle cells. Circ. Res. 2006, 98, 811-817.
37. Liu, H., Sadygov, R. G., Yates, J. R., III, A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
38. Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G. et al., Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics 2005, 4, 1487-1502.
39. Rappsilber, J., Ryder, U., Lamond, A. I., Mann, M., Largescale proteomic analysis of the human spliceosome. Ge-nome Res. 2002, 12, 1231-1245.
40. Schmidt, M. W., Houseman, A., Ivanov, A. R., Wolf, D. A., Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe. Mol. Syst. Biol. 2007, 3, 79.
41. Liu, Q., Tan, G., Levenkova, N., Li, T. et al., The proteome of the mouse photoreceptor sensory cilium Complex. Mol. Cell. Proteomics 2007, 6, 1299-1317.
42. Ishihama, Y., Oda, Y., Tabata, T., Sato, T. et al., Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 2005, 4, 1265-1272.
43. Grimmond, S. M., Miranda, K. C., Yuan, Z., Davis, M.J. et al., The mouse secretome: functional classification of the proteins secreted into the extracellular environment. Genome Res. 2003, 13, 1350-1359.
44. Pekny, M., Nilsson, M., Astrocyte activation and reactive gliosis. Glia 2005, 50, 427-434.
45. Donsante, A., Levy, B., Vogler, C., Sands, M. S., Clinical response to persistent, low-level beta-glucuronidase expression in the murine model of mucopolysaccharidosis type VII. J. Inherit. Metab. Dis. 2007, 30, 227-238.
46. Denny, C. A., Alroy, J., Pawlyk, B. S., Sandberg, M. A. et al., Neurochemical, morphological, and neurophysiological abnormalities in retinas of Sandhoff and GM1 gang- liosidosis mice. J. Neurochem. 2007, 101, 1294-1302.
47. Bezzi, P., Domercq, M., Brambilla, L., Galli, R. et al., CXCR4-activated astrocyte glutamate release via TNFalpha: amplification by microglia triggers neurotoxicity. Nat. Neurosci. 2001, 4, 702-710.
48. Babcock, A. A., Kuziel, W. A., Rivest, S., Owens, T., Chemokine expression by glial cells directs leukocytes to sites of axonal injury in the CNS. J. Neurosci. 2003, 23, 7922-7930.
49. Tsai, H. H., Frost, E., To, V., Robinson, S. et al., The chemokine receptor CXCR2 controls positioning of oligodendrocyte precursors in developing spinal cord by arresting their migration. Cell 2002, 110, 373-383.
50. Imitola, J., Raddassi, K., Park, K. I., Mueller, F. J. et al.,Directed migration of neural stem cells to sites of CNS injury by the stromal cell-derived factor 1alpha/CXC chemokine receptor 4 pathway. Proc. Natl. Acad. Sci. USA 2004, 101, 18117-18122.
51. Glabinski, A. R., Tani, M., Strieter, R. M., Tuohy, V. K., Ransohoff, R. M., Synchronous synthesis of alpha-and beta-chemokines by cells of diverse lineage in the central nervous system of mice with relapses of chronic experimental autoimmune encephalomyelitis. Am. J. Pathol. 1997, 150, 617-630.
52. Combrinck, M., Williams, J., De Berardinis, M. A., Warden, D. et al., Levels of CSF prostaglandin E2, cognitive decline, and survival in Alzheimer's disease. J. Neurol. Neurosurg. Psychiatry 2006, 77, 85-88.
53. Flieger, O., Engling, A., Bucala, R., Lue, H. et al., Regulated secretion of macrophage migration inhibitory factor is mediated by a nonclassical pathway involving an ABC transporter. FEBS Lett. 2003, 551, 78-86.
54. Guidotti, A., Forchetti, C. M., Corda, M. G., Konkel, D. et al., Isolation, characterization, and purification to homogeneity of an endogenous polypeptide with agonistic action on benzodiazepine receptors. Proc. Natl. Acad. Sci. USA 1983, 80, 3531-3535.
55. Hengst, U., Albrecht, H., Hess, D., Monard, D., The phos- phatidylethanolamine-binding protein is the prototype of a novel family of serine protease inhibitors. J. Biol. Chem. 2001, 276, 535-540.
56. Kinseth, M. A., Anjard, C., Fuller, D., Guizzunti, G. et al., The Golgi-associated protein GRASP is required for unconventional protein secretion during development. Cell 2007, 130, 524-534.
57. Nishino, J., Yamashita, K., Hashiguchi, H., Fujii, H. et al., Meteorin: a secreted protein that regulates glial cell differentiation and promotes axonal extension. EMBO J. 2004, 23, 1998-2008.