Proteomic analysis of cerebrospinal fluid extracellular vesicles: A comprehensive dataset

Journal of Proteomics

Volumn 106, Issue , 2014, Pages 191-204

  Chiasserini, Davide ^a   Van Weering, Jan R T ^a   Piersma, Sander R ^a   Pham, Thang V ^a   Malekzadeh, Arjan ^a   Teunissen, Charlotte E ^a   De Wit, Heidi ^a   Jiménez, Connie R ^a  

^a VU UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Cerebrospinal fluid; Exosomes; Extracellular vesicles; Mass spectrometry; Neurological diseases; Proteomics

Indexed keywords

ALPHA SYNUCLEIN; AMYLOID BETA PROTEIN; AMYLOID PRECURSOR PROTEIN; DJ 1 PROTEIN; HEAT SHOCK PROTEIN; PRION PROTEIN; PROTEIN; PROTEOME; SYNTENIN; TETRASPANIN; BIOLOGICAL MARKER; PRION; PROTEIN CEREBROSPINAL FLUID LEVEL;

ARTICLE; BIOINFORMATICS; BRAIN BLOOD FLOW; CELL ORGANELLE; CEREBROSPINAL FLUID ANALYSIS; CONTROLLED STUDY; DEGENERATIVE DISEASE; ELECTRON MICROSCOPY; EXOSOME; EXTRACELLULAR VESICLE; HUMAN; HUMAN CELL; NERVE DEGENERATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; SPINAL CORD; TANDEM MASS SPECTROMETRY; ULTRACENTRIFUGATION; ANALYSIS; BIOLOGY; BLOOD; BRAIN; CHEMISTRY; LIQUID CHROMATOGRAPHY; METABOLISM; PRION; PROTEIN CEREBROSPINAL FLUID LEVEL; PROTEIN DATABASE;

AMYLOID BETA-PROTEIN PRECURSOR; BIOLOGICAL MARKERS; BRAIN; CEREBROSPINAL FLUID PROTEINS; CHROMATOGRAPHY, LIQUID; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; MICROSCOPY, ELECTRON; NEURODEGENERATIVE DISEASES; PRIONS; PROTEOME; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 84900036747     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2014.04.028     Document Type: Article

References (63)

1. Südhof T.C. Basic neurochemistry: molecular, cellular and medical aspects. 6th edition ed 1999, Lippincott-Raven, Philadelphia.
2. Lachenal G., Pernet-Gallay K., Chivet M., Hemming F.J., Belly A., Bodon G., et al. Release of exosomes from differentiated neurons and its regulation by synaptic glutamatergic activity. Mol Cell Neurosci 2011, 46:409-418.
3. Schneider A., Simons M. Exosomes: vesicular carriers for intercellular communication in neurodegenerative disorders. Cell Tissue Res 2013, 352:33-47.
4. Aguzzi A., Rajendran L. The transcellular spread of cytosolic amyloids, prions, and prionoids. Neuron 2009, 64:783-790.
5. Thery C., Zitvogel L., Amigorena S. Exosomes: composition, biogenesis and function. Nat Rev Immunol 2002, 2:569-579.
6. Thery C., Amigorena S., Raposo G., Clayton A. Isolation and characterization of exosomes from cell culture supernatants and biological fluids. Curr Protoc Cell Biol 2006, supplement 30:1-29.
7. Simons M., Raposo G. Exosomes-vesicular carriers for intercellular communication. Curr Opin Cell Biol 2009, 21:575-581.
8. Faure J., Lachenal G., Court M., Hirrlinger J., Chatellard-Causse C., Blot B., et al. Exosomes are released by cultured cortical neurones. Mol Cell Neurosci 2006, 31:642-648.
9. Emmanouilidou E., Melachroinou K., Roumeliotis T., Garbis S.D., Ntzouni M., Margaritis L.H., et al. Cell-produced alpha-synuclein is secreted in a calcium-dependent manner by exosomes and impacts neuronal survival. J Neurosci 2010, 30:6838-6851.
10. Antonucci F., Turola E., Riganti L., Caleo M., Gabrielli M., Perrotta C., et al. Microvesicles released from microglia stimulate synaptic activity via enhanced sphingolipid metabolism. EMBO J 2012, 31:1231-1240.
11. Haqqani A.S., Delaney C.E., Tremblay T.L., Sodja C., Sandhu J.K., Stanimirovic D.B. Method for isolation and molecular characterization of extracellular microvesicles released from brain endothelial cells. Fluids Barriers CNS 2013, 10:4.
12. Vella L.J., Greenwood D.L., Cappai R., Scheerlinck J.P., Hill A.F. Enrichment of prion protein in exosomes derived from ovine cerebral spinal fluid. Vet Immunol Immunopathol 2008, 124:385-393.
13. Street J.M., Barran P.E., Mackay C.L., Weidt S., Balmforth C., Walsh T.S., et al. Identification and proteomic profiling of exosomes in human cerebrospinal fluid. J Transl Med 2012, 10:5.
14. Harrington M.G., Fonteh A.N., Oborina E., Liao P., Cowan R.P., McComb G., et al. The morphology and biochemistry of nanostructures provide evidence for synthesis and signaling functions in human cerebrospinal fluid. Cerebrospinal Fluid Res 2009, 6:10.
15. Piersma S.R., Warmoes M.O., de Wit M., de Reus I., Knol J.C., Jimenez C.R. Whole gel processing procedure for GeLC-MS/MS based proteomics. Proteome Sci 2013, 11:17.
16. Cox J., Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008, 26:1367-1372.
17. Pham T.V., Jimenez C.R. An accurate paired sample test for count data. Bioinformatics 2012, 28:i596-i602. (Oxford, England).
18. Huang da W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
19. Eden E., Navon R., Steinfeld I., Lipson D., Yakhini Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinforma 2009, 10:48.
20. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns 1998, 95:14863-14868.
21. von Mering C., Huynen M., Jaeggi D., Schmidt S., Bork P., Snel B. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res 2003, 31:258-261.
22. Enright A.J., Van Dongen S., Ouzounis C.A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002, 30:1575-1584.
23. Morris J.H., Apeltsin L., Newman A.M., Baumbach J., Wittkop T., Su G., et al. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinforma 2011, 12:436.
24. Maere S., Heymans K., Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 21:3448-3449. (Oxford, England).
25. Kalra H., Simpson R.J., Ji H., Aikawa E., Altevogt P., Askenase P., et al. Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation. PLoS Biol 2012, 10:e1001450.
26. Looze C., Yui D., Leung L., Ingham M., Kaler M., Yao X., et al. Proteomic profiling of human plasma exosomes identifies PPARgamma as an exosome-associated protein. Biochem Biophys Res Commun 2009, 378:433-438.
27. Pisitkun T., Shen R.F., Knepper M.A. Identification and proteomic profiling of exosomes in human urine. Proc Natl Acad Sci U S A 2004, 101:13368-13373.
28. Bellingham S.A., Guo B.B., Coleman B.M., Hill A.F. Exosomes: vehicles for the transfer of toxic proteins associated with neurodegenerative diseases?. Front Physiol 2012, 3:124.
29. Mathivanan S., Ji H., Simpson R.J. Exosomes: extracellular organelles important in intercellular communication. J Proteome 2010, 73:1907-1920.
30. Vlassov A.V., Magdaleno S., Setterquist R., Conrad R. Exosomes: current knowledge of their composition, biological functions, and diagnostic and therapeutic potentials. Biochim Biophys Acta 1820, 2012:940-948.
31. Baietti M.F., Zhang Z., Mortier E., Melchior A., Degeest G., Geeraerts A., et al. Syndecan-syntenin-ALIX regulates the biogenesis of exosomes. Nat Cell Biol 2012, 14:677-685.
32. Rink J., Ghigo E., Kalaidzidis Y., Zerial M. Rab conversion as a mechanism of progression from early to late endosomes. Cell 2005, 122:735-749.
33. Savina A., Vidal M., Colombo M.I. The exosome pathway in K562 cells is regulated by Rab11. J Cell Sci 2002, 115:2505-2515.
34. Stenmark H., Parton R.G., Steele-Mortimer O., Lutcke A., Gruenberg J., Zerial M. Inhibition of rab5 GTPase activity stimulates membrane fusion in endocytosis. EMBO J 1994, 13:1287-1296.
35. Iliff J.J., Wang M., Liao Y., Plogg B.A., Peng W., Gundersen G.A., et al. A paravascular pathway facilitates CSF flow through the brain parenchyma and the clearance of interstitial solutes including amyloid beta. Sci Transl Med 2012, 4:147ra11.
36. Fitzner D., Schnaars M., van Rossum D., Krishnamoorthy G., Dibaj P., Bakhti M., et al. Selective transfer of exosomes from oligodendrocytes to microglia by macropinocytosis. J Cell Sci 2011, 124:447-458.
37. Hooper C., Sainz-Fuertes R., Lynham S., Hye A., Killick R., Warley A., et al. Wnt3a induces exosome secretion from primary cultured rat microglia. BMC Neurosci 2012, 13:144.
38. Ahn S.M., Byun K., Cho K., Kim J.Y., Yoo J.S., Kim D., et al. Human microglial cells synthesize albumin in brain. PLoS One 2008, 3:e2829.
39. Thery C., Ostrowski M., Segura E. Membrane vesicles as conveyors of immune responses. Nat Rev Immunol 2009, 9:581-593.
40. Colombo E., Borgiani B., Verderio C., Furlan R. Microvesicles: novel biomarkers for neurological disorders. Front Physiol 2012, 3:63.
41. Fevrier B., Vilette D., Archer F., Loew D., Faigle W., Vidal M., et al. Cells release prions in association with exosomes. Proc Natl Acad Sci U S A 2004, 101:9683-9688.
42. Blennow K., Hampel H., Weiner M., Zetterberg H. Cerebrospinal fluid and plasma biomarkers in Alzheimer disease. Nat Rev Neurol 2010, 6:131-144.
43. Rajendran L., Honsho M., Zahn T.R., Keller P., Geiger K.D., Verkade P., et al. Alzheimer's disease beta-amyloid peptides are released in association with exosomes. Proc Natl Acad Sci U S A 2006, 103:11172-11177.
44. Bastos-Amador P., Royo F., Gonzalez E., Conde-Vancells J., Palomo-Diez L., Borras F.E., et al. Proteomic analysis of microvesicles from plasma of healthy donors reveals high individual variability. J Proteome 2012, 75:3574-3584.
45. Choi D.S., Yang J.S., Choi E.J., Jang S.C., Park S., Kim O.Y., et al. The protein interaction network of extracellular vesicles derived from human colorectal cancer cells. J Proteome Res 2012, 11:1144-1151.
46. Gonzalez-Begne M., Lu B., Han X., Hagen F.K., Hand A.R., Melvin J.E., et al. Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). J Proteome Res 2009, 8:1304-1314.
47. Wang Z., Hill S., Luther J.M., Hachey D.L., Schey K.L. Proteomic analysis of urine exosomes by multidimensional protein identification technology (MudPIT). Proteomics 2012, 12:329-338.
48. Kokubo H., Lemere C.A., Yamaguchi H. Localization of flotillins in human brain and their accumulation with the progression of Alzheimer's disease pathology. Neurosci Lett 2000, 290:93-96.
49. Kim H.J., Kim N.C., Wang Y.D., Scarborough E.A., Moore J., Diaz Z., et al. Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS. Nature 2013, 495:467-473.
50. Saman S., Kim W., Raya M., Visnick Y., Miro S., Saman S., et al. Exosome-associated tau is secreted in tauopathy models and is selectively phosphorylated in cerebrospinal fluid in early Alzheimer disease. J Biol Chem 2012, 287:3842-3849.
51. McKhann G.M., Knopman D.S., Chertkow H., Hyman B.T., Jack C.R., Kawas C.H., et al. The diagnosis of dementia due to Alzheimer's disease: recommendations from the National Institute on Aging-Alzheimer's Association workgroups on diagnostic guidelines for Alzheimer's disease. Alzheimers Dement 2011, 7:263-269.
52. Albert M.S., Dekosky S.T., Dickson D., Dubois B., Feldman H.H., Fox N.C., et al. The diagnosis of mild cognitive impairment due to Alzheimer's disease: recommendations from the National Institute on Aging and Alzheimer's Association workgroup. Alzheimers Dement 2011, 7:270-279.
53. Mattsson N., Zetterberg H., Hansson O., Andreasen N., Parnetti L., Jonsson M., et al. CSF biomarkers and incipient Alzheimer disease in patients with mild cognitive impairment. JAMA 2009, 302:385-393.
54. Bonifati V., Rizzu P., van Baren M.J., Schaap O., Breedveld G.J., Krieger E., et al. Mutations in the DJ-1 gene associated with autosomal recessive early-onset parkinsonism. Science 2003, 299:256-259.
55. Hong Z., Shi M., Chung K.A., Quinn J.F., Peskind E.R., Galasko D., et al. DJ-1 and alpha-synuclein in human cerebrospinal fluid as biomarkers of Parkinson's disease. Brain 2010, 133:713-726.
56. Maita C., Tsuji S., Yabe I., Hamada S., Ogata A., Maita H., et al. Secretion of DJ-1 into the serum of patients with Parkinson's disease. Neurosci Lett 2008, 431:86-89.
57. Waragai M., Nakai M., Wei J., Fujita M., Mizuno H., Ho G., et al. Plasma levels of DJ-1 as a possible marker for progression of sporadic Parkinson's disease. Neurosci Lett 2007, 425:18-22.
58. Waragai M., Wei J., Fujita M., Nakai M., Ho G.J., Masliah E., et al. Increased level of DJ-1 in the cerebrospinal fluids of sporadic Parkinson's disease. Biochem Biophys Res Commun 2006, 345:967-972.
59. Tsuboi Y., Munemoto H., Ishikawa S., Matsumoto K., Iguchi-Ariga S.M., Ariga H. DJ-1, a causative gene product of a familial form of Parkinson's disease, is secreted through microdomains. FEBS Lett 2008, 582:2643-2649.
60. Bibl M., Esselmann H., Otto M., Lewczuk P., Cepek L., Ruther E., et al. Cerebrospinal fluid amyloid beta peptide patterns in Alzheimer's disease patients and nondemented controls depend on sample pretreatment: indication of carrier-mediated epitope masking of amyloid beta peptides. Electrophoresis 2004, 25:2912-2918.
61. Tokuda T., Qureshi M.M., Ardah M.T., Varghese S., Shehab S.A., Kasai T., et al. Detection of elevated levels of alpha-synuclein oligomers in CSF from patients with Parkinson disease. Neurology 2010, 75:1766-1772.
62. Tauro B.J., Greening D.W., Mathias R.A., Ji H., Mathivanan S., Scott A.M., et al. Comparison of ultracentrifugation, density gradient separation, and immunoaffinity capture methods for isolating human colon cancer cell line LIM1863-derived exosomes. Methods 2012, 56:293-304.
63. Vizcaino J.A., Cote R.G., Csordas A., Dianes J.A., Fabregat A., Foster J.M., et al. The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 2013, 41:D1063-D1069.