Membrane proteomics: The development of diagnostics based on protein shedding

Current Opinion in Molecular Therapeutics

Volumn 11, Issue 6, 2009, Pages 623-631

  Lai, Zon W ^a   Steer, David L ^a   Smith, A Ian ^a  

^a MONASH UNIVERSITY   (Australia)

Author keywords

Biomarker; Membrane protein; Membrane shaving; Protein shedding; Proteolysis; Proteomics

Indexed keywords

AMPHIREGULIN; AMYLOID PRECURSOR PROTEIN; EPIREGULIN; HEPARIN BINDING EPIDERMAL GROWTH FACTOR; MEMBRANE PROTEIN; TRANSFORMING GROWTH FACTOR ALPHA; TUMOR NECROSIS FACTOR ALPHA;

CELL SURFACE; DIAGNOSTIC ACCURACY; ELECTROSPRAY MASS SPECTROMETRY; HUMAN; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; REVIEW; TANDEM MASS SPECTROMETRY;

BIOLOGICAL MARKERS; CELL MEMBRANE; DIAGNOSIS, DIFFERENTIAL; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; HUMANS; MASS SPECTROMETRY; MEMBRANE PROTEINS; PROTEOME; PROTEOMICS;

EID: 72449183681     PISSN: 14648431     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (86)

1. Caprioli RM, Farmer TB, Gile J: Molecular imaging of biological samples: Localization of peptides and proteins using MALDI-TOF MS. Anal Chem (1997) 69(23):4751-4760.
2. Chaurand P, Stoeckli M, Caprioli RM: Direct profiling of proteins in biological tissue sections by MALDI mass spectrometry. Anal Chem (1999) 71(23):5263-5270. (Pubitemid 129563241)
3. Stoeckli M, Farmer TB, Caprioli RM: Automated mass spectrometry imaging with a matrix-assisted laser desorption ionization time-of-flight instrument. J Am Soc Mass Spectrom (1999) 10(1):67-71.
4. Goshe MB, Blonder J, Smith RD: Affinity labeling of highly hydrophobic integral membrane proteins for proteome-wide analysis. J Proteome Res (2003) 2(2):153-161.
5. Tao WA, Aebersold R: Advances in quantitative proteomics via stable isotope tagging and mass spectrometry. Curr Opin Biotechnol (2003) 14(1):110-118.
6. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S et al: Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics (2004) 3(12):1154-1169.
7. Bykova NV, Egsgaard H, Moller IM: Identification of 14 new phosphoproteins involved in important plant mitochondrial processes. FEBS Lett (2003) 540(1-3):141-146.
8. Jensen ON: Modification-specific proteomics: Characterization of post-translational modifications by mass spectrometry. Curr Opin Chem Biol (2004) 8(1):33-41.
9. Fenselau C: A review of quantitative methods for proteomic studies. J Chromatogr B Analyt Technol Biomed Life Sci (2007) 855(1):14-20.
10. Mann M, Kelleher NL: Precision proteomics: The case for high resolution and high mass accuracy. Proc Natl Acad Sci USA (2008) 105(47):18132-18138.
11. Demirev PA, Fenselau C: Mass spectrometry in biodefense. J Mass Spectrom (2008) 43(11):1441-1457.
12. Baginsky S: Plant proteomics: Concepts, applications, and novel strategies for data interpretation. Mass Spectrom Rev (2009) 28(1):93-120.
13. Clemens S, Naumann B, Hippler M: Proteomics of metal mediated protein dynamics in plants - iron and cadmium in the focus. Front Biosci (2009) 14:1955-1969.
14. Wiseman JM, Ifa DR, Zhu Y, Kissinger CB, Manicke NE, Kissinger PT, Cooks RG: Desorption electrospray ionization mass spectrometry: Imaging drugs and metabolites in tissues. Proc Natl Acad Sci USA (2008) 105(47):18120-18125.
15. Zinkernagel RM, Doherty PC: Restriction of in vitro T cell-mediated cytotoxicity in lymphocytic choriomeningitis within a syngeneic or semiallogeneic system. Nature (1974) 248(450):701-702.
16. Cossart P, Sansonetti PJ: Bacterial invasion: The paradigms of enteroinvasive pathogens. Science (2004) 304(5668):242-248.
17. Burrell LM, Risvanis J, Kubota E, Dean RG, MacDonald PS, Lu S, Tikellis C, Grant SL, Lew RA, Smith AI, Cooper ME et al: Myocardial infarction increases ACE2 expression in rat and humans. Eur Heart J (2005) 26(4):369-375.
18. Seliger B: Molecular mechanisms of MHC class I abnormalities and APM components in human tumors. Cancer Immunol Immunother (2008) 57(11):1719-1726.
19. Whelan SA, Lu M, He J, Yan W, Saxton R, Faull KF, Whitelegge JP, Chang H: Mass spectrometry (LC-MS/MS) site-mapping of N-glycosylated membrane proteins for breast cancer biomarkers. J Proteome Res (2009) 8(8):4151-4160.
20. Arcinas AJ, Yen TY, Kebebew E, Macher BA: Cell surface and secreted protein profiles of human thyroid cancer cell lines reveal distinct glycoprotein patterns. J Proteome Res (2009) 8(8):3958-3968.
21. Harkness L, Christiansen H, Nehlin J, Barington T, Andersen JS, Kassem M: Identification of a membrane proteomic signature for human embryonic stem cells independent of culture conditions. Stem Cell Res (2008) 1(3):219-227.
22. Zhang L, Lun Y, Yan D, Yu L, Ma W, Du B, Zhu X: Proteomic analysis of macrophages: A new way to identify novel cell-surface antigens. J Immunol Methods (2007) 321(1-2):80-85.
23. Anderson NL, Anderson NG: The human plasma proteome: History, character, and diagnostic prospects. Mol Cell Proteomics (2002) 1(11):845-867.
24. Santoni V, Molloy M, Rabilloud T: Membrane proteins and proteomics: Un amour impossible? Electrophoresis (2000) 21(6):1054-1070.
25. Zheng YZ, Foster LJ: Biochemical and proteomic approaches for the study of membrane microdomains. J Proteomics (2009) 72(1):12-22.
26. Helenius A, Simons K: Solubilization of membranes by detergents. Biochim Biophys Acta (1975) 415(1):29-79.
27. Griffiths WJ, Wang Y: Mass spectrometry: From proteomics to metabolomics and lipidomics. Chem Soc Rev (2009) 38(7):1882-1896.
28. Poetz O, Hoeppe S, Templin MF, Stoll D, Joos TO: Proteome wide screening using peptide affinity capture. Proteomics (2009) 9(6):1518-1523.
29. Yocum AK, Chinnaiyan AM: Current affairs in quantitative targeted proteomics: Multiple reaction monitoring-mass spectrometry. Brief Funct Genomic Proteomic (2009) 8(2):145-157.
30. Schluesener D, Fischer F, Kruip J, Rogner M, Poetsch A: Mapping the membrane proteome of Corynebacterium glutamicum. Proteomics (2005) 5(5):1317-1330.
31. Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM, Yates JR 3rd: Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol (1999) 17(7):676-682.
32. Washburn MP, Wolters D, Yates JR 3rd: Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol (2001) 19(3):242-247. (Pubitemid 32220565)
33. Aggarwal K, Choe LH, Lee KH: Shotgun proteomics using the iTRAQ isobaric tags. Brief Funct Genomic Proteomic (2006) 5(2):112-120.
34. Collins MO, Choudhary JS: Mapping multiprotein complexes by affinity purification and mass spectrometry. Curr Opin Biotechnol (2008) 19(4):324-330.
35. Kimple ME, Sondek J: Overview of affinity tags for protein purification. Curr Protoc Protein Sci (2004) Chapter 9(Unit 9.9).
36. Yang Z, Hancock WS: Approach to the comprehensive analysis of glycoproteins isolated from human serum using a multi-lectin affinity column. J Chromatogr A (2004) 1053(1-2):79-88.
37. Aebersold R, Goodlett DR: Mass spectrometry in proteomics. Chem Rev (2001) 101(2):269-295.
38. Aebersold R, Mann M: Mass spectrometry-based proteomics. Nature (2003) 422(6928):198-207.
39. Krutchinsky AN, Kalkum M, Chait BT: Automatic identification of proteins with a MALDI-quadrupole ion trap mass spectrometer. Anal Chem (2001) 73(21):5066-5077.
40. Loboda AV, Krutchinsky AN, Bromirski M, Ens W, Standing KG: A tandem quadrupole/time-of-flight mass spectrometer with a matrix-assisted laser desorption/ionization source: Design and performance. Rapid Commun Mass Spectrom (2000) 14(12):1047-1057.
41. Medzihradszky KF, Campbell JM, Baldwin MA, Falick AM, Juhasz P, Vestal ML, Burlingame AL: The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. Anal Chem (2000) 72(3):552-558.
42. Powlesland AS, Hitchen PG, Parry S, Graham SA, Barrio MM, Elola MT, Mordoh J, Dell A, Drickamer K, Taylor ME: Targeted glycoproteomic identification of cancer cell glycosylation. Glycobiology (2009) 19(8):899-909.
43. Edman P: Sequence determination. Mol Biol Biochem Biophys (1970) 8:211-255.
44. Driessen HP, de Jong WW, Tesser GI, Bloemendal H: The mechanism of N-terminal acetylation of proteins. CRC Crit Rev Biochem (1985) 18(4):281-325.
45. Tsunasawa S, Sakiyama F: Amino-terminal acetylation of proteins: An overview. Methods Enzymol (1984) 106:165-170.
46. Leite JF, Amoscato AA, Cascio M: Coupled proteolytic and mass spectrometry studies indicate a novel topology for the glycine receptor. J Biol Chem (2000) 275(18):13683-13689.
47. Rodríguez-Ortega MJ, Norais N, Bensi G, Liberatori S, Capo S, Mora M, Scarselli M, Doro F, Ferrari G, Garaguso I, Maggi T et al: Characterization and identification of vaccine candidate proteins through analysis of the group A Streptococcus surface proteome. Nat Biotechnol (2006) 24(2):191-197.
48. Severin A, Nickbarg E, Wooters J, Quazi SA, Matsuka YV, Murphy E, Moutsatsos IK, Zagursky RJ, Olmsted SB: Proteomic analysis and identification of Streptococcus pyogenes surfaceassociated proteins. J Bacteriol (2007) 189(5):1514-1522.
49. Tjalsma H, Lambooy L, Hermans PW, Swinkels DW: Shedding & shaving: Disclosure of proteomic expressions on a bacterial face. Proteomics (2008) 8(7):1415-1428.
50. Sabarth N, Hurvitz R, Schmidt M, Zimny-Arndt U, Jungblut PR, Meyer TF, Bumann D: Identification of Helicobacter pylori surface proteins by selective proteinase K digestion and antibody phage display. J Microbiol Methods (2005) 62(3): 345-349.
51. Elortza F, Mohammed S, Bunkenborg J, Foster LJ, Nuhse TS, Brodbeck U, Peck SC, Jensen ON: Modification-specific proteomics of plasma membrane proteins: Identification and characterization of glycosylphosphatidylinositol- anchored proteins released upon phospholipase D treatment. J Proteome Res (2006) 5(4):935-943.
52. Le Bihan T, Goh T, Stewart II, Salter AM, Bukhman YV, Dharsee M, Ewing R, Wi?niewski JR: Differential analysis of membrane proteins in mouse fore- and hindbrain using a label-free approach. J Proteome Res (2006) 5(10):2701-2710.
53. Massague J, Pandiella A: Membrane-anchored growth factors. Annu Rev Biochem (1993) 62:515-541.
54. Rosen SD, Bertozzi CR: The selectins and their ligands. Curr Opin Cell Biol (1994) 6(5):663-673.
55. Tracey KJ, Cerami A: Metabolic responses to cachectin/TNF. A brief review. Ann NY Acad Sci (1990) 587:325-331.
56. Jia HP, Look DC, Tan P, Shi L, Hickey M, Gakhar L, Chappell MC, Wohlford-Lenane C, McCray PB Jr: Ectodomain shedding of angiotensin converting enzyme 2 in human airway epithelia. Am J Physiol Lung Cell Mol Physiol (2009) 297(1):L84-96.
57. Pruessmeyer J, Ludwig A: The good, the bad and the ugly substrates for ADAM10 and ADAM17 in brain pathology, inflammation and cancer. Semin Cell Dev Biol (2009) 20(2): 164-174.
58. Black RA, Rauch CT, Kozlosky CJ, Peschon JJ, Slack JL, Wolfson MF, Castner BJ, Stocking KL, Reddy P, Srinivasan S, Nelson N et al: A metalloproteinase disintegrin that releases tumour-necrosis factor-? from cells. Nature (1997) 385(6618):729-733.
59. Moss ML, Jin SL, Milla ME, Bickett DM, Burkhart W, Carter HL, Chen WJ, Clay WC, Didsbury JR, Hassler D, Hoffman CR et al: Cloning of a disintegrin metalloproteinase that processes precursor tumour-necrosis factor-?. Nature (1997) 385(6618):733-736.
60. Althoff K, Mullberg J, Aasland D, Voltz N, Kallen K, Grotzinger J, Rose-John S: Recognition sequences and structural elements contribute to shedding susceptibility of membrane proteins. Biochem J (2001) 353(Pt 3):663-672.
61. Borrell-Pages M, Rojo F, Albanell J, Baselga J, Arribas J: TACE is required for the activation of the EGFR by TGF-? in tumors. Embo J (2003) 22(5):1114-1124.
62. Kenny PA, Bissell MJ: Targeting TACE-dependent EGFR ligand shedding in breast cancer. J Clin Invest (2007) 117(2):337-345.
63. Peschon JJ, Slack JL, Reddy P, Stocking KL, Sunnarborg SW, Lee DC, Russell WE, Castner BJ, Johnson RS, Fitzner JN, Boyce RW et al: An essential role for ectodomain shedding in mammalian development. Science (1998) 282(5392):1281-1284.
64. Sahin U, Weskamp G, Kelly K, Zhou HM, Higashiyama S, Peschon J, Hartmann D, Saftig P, Blobel CP: Distinct roles for ADAM10 and ADAM17 in ectodomain shedding of six EGFR ligands. J Cell Biol (2004) 164(5):769-779.
65. Schafer B, Gschwind A, Ullrich A: Multiple G-protein-coupled receptor signals converge on the epidermal growth factor receptor to promote migration and invasion. Oncogene (2004) 23(4):991-999.
66. Gschwind A, Hart S, Fischer OM, Ullrich A: TACE cleavage of proamphiregulin regulates GPCR-induced proliferation and motility of cancer cells. Embo J (2003) 22(10):2411-2421.
67. Buxbaum JD, Thinakaran G, Koliatsos V, O'Callahan J, Slunt HH, Price DL, Sisodia SS: Alzheimer amyloid protein precursor in the rat hippocampus: Transport and processing through the perforant path. J Neurosci (1998) 18(23):9629-9637.
68. Slack BE, Ma LK, Seah CC: Constitutive shedding of the amyloid precursor protein ectodomain is up-regulated by tumour necrosis factor-? converting enzyme. Biochem J (2001) 357 (Pt 3):787-794.
69. VM, Ventura AP, Fitzgibbon MP, Pereira-Faça SR, Pitteri SJ, Green AE, Ireton RC, Zhang Q, Wang H, O'Briant KC, Drescher CW et al: Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extracellular domains. PLoS One (2008) 3(6):e2425.
70. Gardiner EE, Karunakaran D, Shen Y, Arthur JF, Andrews RK, Berndt MC: Controlled shedding of platelet glycoprotein (GP) VI and GPIb-IX-V by ADAM family metalloproteinases. J Thromb Haemost (2007) 5(7):1530-1537.
71. Seubert P, Oltersdorf T, Lee MG, Barbour R, Blomquist C, Davis DL, Bryant K, Fritz LC, Galasko D, Thal LJ et al: Secretion of ?-amyloid precursor protein cleaved at the amino terminus of the ?-amyloid peptide. Nature (1993) 361(6409):260-263.
72. Xu X Secretase catalyzes sequential cleavages of the A?PP transmembrane domain. J Alzheimers Dis (2009) 16(2):211-224.
73. Armstrong RA: Amyloid plaques: Stages in life history or independent origin? Dement Geriatr Cogn Disord (1998) 9(4):227-238.
74. Farfara D, Lifshitz V, Frenkel D: Neuroprotective and neurotoxic properties of glial cells in the pathogenesis of Alzheimer's disease. J Cell Mol Med 2008, 12(3):762-780.
75. Guillozet AL, Weintraub S, Mash DC, Mesulam MM: Neurofibrillary tangles, amyloid, and memory in aging and mild cognitive impairment. Arch Neurol (2003) 60(5):729-736.
76. Selkoe DJ: Alzheimer's disease: Genes, proteins, and therapy. Physiol Rev (2001) 81(2):741-766.
77. Lambert JC, Schraen-Maschke S, Richard F, Fievet N, Rouaud O, Berr C, Dartigues JF, Tzourio C, Alpérovitch A, Buée L, Amouyel P: Association of plasma amyloid ? with risk of dementia: The prospective Three-City Study. Neurology (2009) 73(11):847-853.
78. Verwey NA, Veerhuis R, Twaalfhoven HA, Wouters D, Hoozemans JJ, Bollen YJ, Killestein J, Bibl M, Wiltfang J, Hack CE, Scheltens P et al: Quantification of amyloid-? 40 in cerebrospinal fluid. J Immunol Methods (2009) 348(1-2):57-66.
79. Li W, Moore MJ, Vasilieva N, Sui J, Wong SK, Berne MA, Somasundaran M, Sullivan JL, Luzuriaga K, Greenough TC, Choe H et al: Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature (2003) 426(6965):450-454.
80. Hofmann H, Geier M, Marzi A, Krumbiegel M, Peipp M, Fey GH, Gramberg T, Pohlmann S: Susceptibility to SARS coronavirus S protein-driven infection correlates with expression of angiotensin converting enzyme 2 and infection can be blocked by soluble receptor. Biochem Biophys Res Commun (2004) 319(4):1216-1221.
81. Clemetson JM, Polgar J, Magnenat E, Wells TN, Clemetson KJ: The platelet collagen receptor glycoprotein VI is a member of the immunoglobulin superfamily closely related to Fc?R and the natural killer receptors. J Biol Chem (1999) 274(41):29019-29024.
82. Massberg S, Gawaz M, Grüner S, Schulte V, Konrad I, Zohlnhöfer D, Heinzmann U, Nieswandt B: A crucial role of glycoprotein VI for platelet recruitment to the injured arterial wall in vivo. J Exp Med (2003) 197(1):41-49.
83. Bigalke B, Lindemann S, Ehlers R, Seizer P, Daub K, Langer H, Schonberger T, Kremmer E, Siegel-Axel D, May AE, Gawaz M: Expression of platelet collagen receptor glycoprotein VI is associated with acute coronary syndrome. Eur Heart J (2006) 27(18):2165-2169.
84. Yamazaki S, Iwamoto R, Saeki K, Asakura M, Takashima S, Yamazaki A, Kimura R, Mizushima H, Moribe H, Higashiyama S, Endoh M et al: Mice with defects in HB-EGF ectodomain shedding show severe developmental abnormalities. J Cell Biol (2003) 163(3):469-475.
85. Ebos JM, Lee CR, Bogdanovic E, Alami J, Van Slyke P, Francia G, Xu P, Mutsaers AJ, Dumont DJ, Kerbel RS: Vascular endothelial growth factor-mediated decrease in plasma soluble vascular endothelial growth factor receptor-2 levels as a surrogate biomarker for tumor growth. Cancer Res (2008) 68(2):521-529.
86. Isserlin R, Emili A: Interpretation of large-scale quantitative shotgun proteomic profiles for biomarker discovery. Curr Opin Mol Ther (2008) 10(3):231-242.