Epitope mapping of antibodies using a cell array-based polypeptide library

Journal of Biomolecular Screening

Volumn 15, Issue 4, 2010, Pages 418-426

  Mater, Richard H ^a,b   Maier, Christina J ^a,b   Rid, Raphaela ^b   Hintner, Helmut ^b   Bauer, Johann W ^b   Önder, Kamil ^b  

^a UNIVERSITY OF SALZBURG   (Austria)

^b PARACELSUS MEDICAL UNIVERSITY   (Austria)

Author keywords

Autoantibodies; Epitope mapping; Mono polyclonal antibodies; Peptide array; Peptide library; Protein chip

Indexed keywords

ANTIBODY; DNA; MONOCLONAL ANTIBODY; POLYCLONAL ANTIBODY; POLYPEPTIDE; VITAMIN D RECEPTOR;

ANTIGEN DETECTION; ARTICLE; CONTROLLED STUDY; ENZYME LINKED IMMUNOSORBENT ASSAY; EPITOPE MAPPING; GENE EXPRESSION SYSTEM; HUMAN; HUMAN TISSUE; IMMUNOFLUORESCENCE TEST; LABORATORY AUTOMATION; MICROARRAY ANALYSIS; MOLECULAR LIBRARY; MOLECULAR RECOGNITION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEOMICS; SEQUENCE ALIGNMENT; SKIN; WESTERN BLOTTING;

AMINO ACID SEQUENCE; ANTIBODIES, MONOCLONAL; BLOTTING, WESTERN; EPITOPE MAPPING; EPITOPES; FLUORESCENT ANTIBODY TECHNIQUE; HUMANS; IMMUNOGLOBULIN ISOTYPES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE LIBRARY; RECEPTORS, CALCITRIOL; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SKIN; TISSUE ARRAY ANALYSIS;

BACTERIA (MICROORGANISMS);

EID: 77952336120     PISSN: 10870571     EISSN: 1552454X     Source Type: Journal    
DOI: 10.1177/1087057110363821     Document Type: Article

References (49)

1. Joosten V, Lokman C, Van Den Hondel CA, Punt PJ: The production of antibody fragments and antibody fusion proteins by yeasts and filamentous fungi. Microb Cell Fact 2003;2:1. (Pubitemid 38751434)
2. Bui HH, Sidney J, Li W, Fusseder N, Sette A: Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics 2007;8:361. (Pubitemid 351659643)
3. Flego M, Mennella V, Moretti F, Poloni F, Dupuis ML, Ascione A, et al: Identification by phage display of the Linear continuous MRPrl epitope in the multidrug resistance-associated protein (MRP1). Biol Chem 2003; 384:139-142. (Pubitemid 36322639)
4. Bublil EM, Freund NT, Mayrose I, Perm O, Roitburd-Berman A, Rubinstein ND, et al: Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins 2007;68:294-304. (Pubitemid 46871603)
5. van Dolleweerd CJ, Kelly CG, Chargelegue D, Ma JK: Peptide mapping of a novel discontinuous epitope of the major surface adhesin from Streptococcus mutans. J Biol Chem 2004;279:22198-22203. (Pubitemid 38679414)
6. Spisak S, Tulassay Z, Moinar B, Guttman A: Protein microchips in biomedicine and biomarker discovery. Electrophoresis 2007;28:4261-4273. (Pubitemid 350259027)
7. Lueking A, Possling A, Huber O, Beveridge A, Horn M, Eickhoff H, et al; A nonredundant human protein chip for antibody screening and serum profiling. Mol Cell Proteomics 2003;2:1342-1349.
8. Hu YH, Warnatz HJ, Vanhecke D, Wagner F, Fiebitz A, Thamm S, et al: Cell array-based intracellular localization screening reveals novel functional features of human chromosome 21 proteins. BMC Genomics 2006;7:155. (Pubitemid 44219155)
9. Mannherz O, Mertens D, Hahn M, Lichter P: Functional screening for proapoptotic genes by reverse transfection cell array technology. Genomics 2006;87:665-672.
10. Tao SC, Zhu H: Protein chip fabrication by capture of nascent polypeptides. Nat Biotechnol 2006;24:1253-1254. (Pubitemid 44564770)
11. Ramachandran N, Hainsworth E, Bhullar B, Eisenstein S, Rosen B, Lau AY, et al: Self-assembling protein microarrays. Science 2004;305:86-90.
12. Liu R, Barrick JE, Szostak JW, Roberts RW: Optimized synthesis of RNAprotein fusions for in vitro protein selection. Methods Enzymol 2000;318:268-293. (Pubitemid 30421654)
13. Zhu H, Bilgin M, Snyder M: Proteomics. Annu Rev Biochem 2003;72: 783-812.
14. Frank R: The SPOT-synthesis technique: synthetic peptide arrays on membrane supports-principles and applications. J Immunol Methods 2002;267:13-26.
15. Beutling U, Stading K, Stradal T, Frank R: Large-scale analysis of proteinprotein interactions using cellulose-bound peptide arrays. Adv Biochem Eng Biotechnol 2008;110:115-152.
16. Lesear J, Stouracova R, Riottot MM, Chitarra V, Biynda J, Fabry M, et al: Three-dimensional structure of an Fab-peptide complex: structural basis of HIV-1 protease inhibition by a monoclonal antibody. J Mol Biol 1997;267:1207-1222. (Pubitemid 27192633)
17. Tormo J, Blaas D, Parry NR, Rowlands D, Stuart D, Fita I: Ciystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2. EMBO /1994;13:2247-2256. (Pubitemid 24157598)
18. Wishart D: NMR spectroscopy and protein structure determination: applications to drug discovery and development. Curr Pharm Biotechnol 2005;6:105-120. (Pubitemid 40637384)
19. Liu HL, Hsu JP: Recent developments in structural proteomics for protein structure determination. Proteomics 2005;5:2056-2068.
20. Dhungana S, Williams JG, Fessier MB, Tomer KB: Epitope mapping by proteolysis of antigen-antibody complexes. Methods Mol Biol 2009;524: 87-101.
21. Zhao Y, Chalt BT: Protein epitope mapping by mass spectrometry. Anal Chem 1994;66:3723-3726. (Pubitemid 24985411)
22. Lu X, DeFelippis MR, Huang L: Linear- epitope mapping by native mass spectrometry. Anal Biochem 2009;395:100-107.
23. Geysen HM, Rodda SJ, Mason TJ, Tribbick G, Schoofs PG: Strategies for epitope analysis using peptide synthesis. J Immunol Methods 1987; 102: 259-274. (Pubitemid 17139413)
24. Robinson WH, Steinman L, Utz PJ: Protein arrays for autoantibody profiling and fine-specificity mapping. Proteomics 2003;3:2077-2084. (Pubitemid 37414072)
25. Lapiere JC, Woodley DT, Parente MG, Iwasaki T, Wynn KC, Christiano AM, et al: Epitope mapping of type VII collagen: identification of discrete peptide sequences recognized by sera from patients with acquired epidermolysis bullosa. J Clin Invest 1993;92:1831-1839. (Pubitemid 23304550)
26. Zillikens D, Rose PA, Balding SD, Liu Z, Olague-Marchan M, Diaz LA, et al: Tight clustering of extracellular BP180 epitopes recognized by bullous pemphigoid autoantibodies. J Invest Dermatol 1997;109:573-579. (Pubitemid 27433604)
27. Haussler MR, Haussler CA, Bartik L, Whitfield GK, Hsieh JC, Slater S, et al: Vitamin D receptor: molecular signaling and actions of nutritional ligands in disease prevention. Nutr Rev 2008;66:S98-S112.
28. Maier R, Brandner C, Hintner H, Bauer J, Onder K: Construction of a reading frame-independent yeast two-hybrid vector system for site-specific recombinational cloning and protein interaction screening. Biotechniques 2008;45:235-244.
29. Walhout AJ, Temple GF, Brasch MA, Hartley JL, Lorson MA, van den Heuvel S, et al: GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol 2000;328:575-592.
30. Hartley JL, Temple GF, Brasch MA: DNA cloning using in vitro sitespecific recombination. Genome Res 2000;10:1788-1795.
31. Sanger F, Nicklen S, Coulson AR: DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977;74:5463-5467.
32. Smith LM, Sanders JZ, Kaiser RJ, Hughes P, Dodd C, Connell CR, et al: Fluorescence detection in automated DNA sequence analysis. Nature 1986;321:674-679. (Pubitemid 16044126)
33. Brandner CJ, Maier RH, Henderson DS, Hintner H, Bauer JW, Onder K: The ORFeome of Staphylococcus aureus v 1.1. BMC Genomics 2008;9:321.
34. Rockberg J, Lofblom J, Hjelm B, Uhlen M, Stahl S: Epitope mapping of antibodies using bacterial surface display. Nat Methods 2008;5:1039-1045.
35. Bussow K, Cahill D, Nietfeld W, Bancroft D, Scherzinger E, Lehrach H, et al: A. method for global protein expression and antibody screening on high-density filters of an arrayed cDNA library. Nucleic Acids Res 1998;26:5007-5008. (Pubitemid 28491184)
36. Holz C, Lueking A, Bovekamp L, Gutjahr C, Bolotina N, Lehrach H, et al: A human cDNA expression library in yeast enriched for open reading frames. Genome Res 2001;11:1730-1735. (Pubitemid 33040500)
37. Lueking A, Holz C, Gotthold C, Lehrach H, Cahill D: A system for dual protein expression in Pichia pastoris and Escherichia coli. Protein Expr Purif 2000;20:372-378.
38. Albala JS, Franke K, McConnell IR, Pak KL, Folta PA, Rubinfeld B, et al: From genes to proteins: high-throughput expression and purification of the human proteome. J Cell Biochem 2000;80:187-191. (Pubitemid 32011952)
39. Woodley DT, Briggaman RA, O'Keefe EJ, Inman AO, Queen LL, Gammon WR: Identification of the skin basement-membrane autoantigen in epidermolysis bullosa acquisita. N Engl J Med 1984;310:1007-1013.
40. Sahin U, Tureci O, Schmitt H, Cochlovius B, Johannes T, Schmits R, et al: Human neoplasms elicit multiple specific immune responses in the autologous host. Proc Natl Acad Sci USA 1995;92:11810-11813. (Pubitemid 26014201)
41. Chen YT, Gure AO, Tsang S, Stockert E, Jager E, Knuth A, et al: Identification of multiple cancer/testis antigens by allogeneic antibody Screening of a melanoma cell line library. Proc Natl Acad Sci USA 1998;95:6919-6923. (Pubitemid 28278082)
42. Stockert E, Jager E, Chen YT, Scanlan MJ, Gout I, Karbach J, et al: A survey of the humoral immune response of cancel' patients to a panel of human tumor antigens. J Exp Med 1998;187:1349-1354. (Pubitemid 28189124)
43. Michaud GA, Salcius M, Zhou F, Bangham R, Bonin J, Guo H, et al: Analyzing antibody specificity with whole proteome microarrays. Nat Biotechnol 2003;21:1509-1512. (Pubitemid 37522714)
44. Carter PJ: Potent antibody therapeutics by design. Nat Rev Immunol 2006;6:343-357.
45. Hoogenboom HR: Selecting and screening recombinant antibody libraries. Nat Biotechnol 2005;23:1105-1116.
46. Lonberg N: Human antibodies from transgenic animals. Nat Biotechnol 2005;23:1117-1125.
47. Carter P: Improving the efficacy of antibody-based cancer therapies. Nat Rev Cancer 2001;1:118-129.
48. Presta LG: Engineering antibodies for therapy. Curr Pharm Biotechnol 2002;3:237-256.
49. Chowdhury PS, Wu H: Tailor-made antibody therapeutics. Methods 2005;36:11-24.