Resurrection of a clinical antibody: Template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-α antibody

Proteomics

Volumn 11, Issue 3, 2011, Pages 395-405

  Castellana, Natalie E ^a   McCutcheon, Krista ^b   Pham, Victoria C ^b   Harden, Kristin ^b   Nguyen, Allen ^b   Young, Judy ^b   Adams, Camellia ^b   Schroeder, Kurt ^b   Arnott, David ^b   Bafna, Vineet ^a   Grogan, Jane L ^b   Lill, Jennie R ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b GENENTECH INC   (United States)

Author keywords

Antibody; Biomedicine; De novo sequencing; Lymphotoxin ; Reverse engineering

Indexed keywords

IMMUNOGLOBULIN F(AB) FRAGMENT; IMMUNOGLOBULIN G; IMMUNOGLOBULIN HEAVY CHAIN; IMMUNOGLOBULIN LIGHT CHAIN; LYMPHOTOXIN; LYMPHOTOXIN ALPHA ANTIBODY; MONOCLONAL ANTIBODY; PROTEIN ANTIBODY; RECOMBINANT DNA; TRANSFORMING GROWTH FACTOR BETA ANTIBODY; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ANTIBODY ENGINEERING; ANTIBODY ISOLATION; ANTIBODY SPECIFICITY; ANTIGEN BINDING; ARTICLE; ASCITES; CONTROLLED STUDY; FLUORESCENCE ACTIVATED CELL SORTING; GENOMICS; HEAVY CHAIN; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; LIGHT CHAIN; MASS SPECTROMETRY; MOLECULAR CLONING; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ENGINEERING; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN SYNTHESIS; PROTEOMICS; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS; TANDEM MASS SPECTROMETRY; TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PERIODIC SYNDROME; UMBILICAL VEIN ENDOTHELIAL CELL;

AMINO ACID SEQUENCE; ANIMALS; ANTIBODIES, ANTI-IDIOTYPIC; ANTIBODIES, MONOCLONAL; CELLS, CULTURED; ENDOTHELIUM, VASCULAR; GENETIC ENGINEERING; GENOMICS; HYBRIDOMAS; LYMPHOTOXIN-ALPHA; MICE; MOLECULAR SEQUENCE DATA; PROTEOMICS; RECOMBINANT PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; UMBILICAL VEINS;

EID: 79251500018     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000487     Document Type: Article

References (23)

1. Waldmann, T. A., Immunotherapy: past, present and future. Nat. Med. 2003, 9, 269-277.
2. Martin, F., Chan, A. C., B cell immunobiology: evolving concepts from the clinic. Annu. Rev. Immunol. 2006, 24, 467-496.
3. Taylor, P. C., Feldmann, M., Anti-TNF biologic agents: still the therapy of choice for rheumatoid arthritis. Nat. Rev. Rheumatol. 2009, 5, 578-582.
4. Ouyang, W., Filvaroff, E., Hu, Y., Grogan, J., Novel therapeutic targets along the Th17 pathway. Eur. J. Immunol. 2009, 39, 670-675.
5. Ware, C. F., Network communications: lymphotoxins, LIGHT and TNF. Annu. Rev. Immunol. 2005, 23, 787-819.
6. Weyand, C. M., Immunopathologic aspects of rheumatoid arthritis: who is the conductor and who plays the immunologic instrument? J. Rheumatol. Suppl. 2007, 79, 9-14.
7. Takemura, S., Lymphoid neogenesis in rheumatoid synovitis. J. Immunol. 2001, 167, 1072-1080.
8. Chiang, E. Y., Kolumam, G. A., Yu, X., Francesco, M. et al., Targeted depletion of lymphotoxin-alpha-expressing TH1 and TH17 cells inhibits autoimmune disease. Nat. Med. 2009, 15, 766-773.
9. Wong, G. H., Kaspar, R. L., Zweiger, G., Carlson, C. et al., Strategies for manipulating apoptosis for cancer therapy with tumor necrosis factor and lymphotoxin. J. Cell Biochem. 1996, 60, 56-60.
10. Bandeira, N., Pham, V., Pevzner, P., Arnott, D., Lill, J. R., Automated de novo protein sequencing of monoclonal antibodies. Nat. Biotechnol. 2008, 26, 1336-1338.
11. Castellana, N., Pham, V., Arnott, A., Lill, J. R., Bafna, V., Template proteogenomics: a novel method for sequencing monoclonal antibodies. Mol. Cell. Proteomics 2010, 9, 1260-1270.
12. Lefranc, M. P., Giudicelli, V., Ginestoux, C., Bodmer, J. et al., IMGT, the international ImMunoGeneTics database. Nucleic Acids Res. 1999, 27, 209-212.
13. Tsur, D., Tanner, S., Zandi, E., Bafna, V., Pevzner, P. A., Identification of post-translational modifications by blind search of mass spectra. Nat. Biotechnol. 2005, 23, 1562-1567.
14. Tanner, S., Shu, H., Frank, A., Wang, L. C. et al., InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 2005, 77, 4626-4639.
15. Henikoff, S., Henikoff, J. G., Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 1992, 89, 10915-10919.
16. Gonzalez, L. C., Loyet, K. M., Calemine-Fenaux, J., Chauhan, V. et al., A coreceptor interaction between the CD28 and TNF receptor family members B and T lymphocyte attenuator and herpes virus entry mediator. Proc. Natl. Acad. Sci. USA 2005, 102, 1116-1121.
17. Kunkel, T. A., Bebenek, K., McClary, J., Efficient site-directed mutagenesis using uracil-containing DNA.Methods Enzymol. 1991, 204, 125-139.
18. Young, J., Yu, X., Wolslegel, K., Nguyen, A. et al., Lymphotoxin-ab heterotrimers are cleaved by metalloproteinases and contribute to synovitis in rheumatoid arthritis. Cytokine, 2010, 51, 71-86.
19. Pham, V., Henzel, W. J., Arnott, D., Hymowitz, S. et al., De novo proteomic sequencing of a monoclonal antibody raised against OX40 ligand. Anal. Biochem. 2006, 352, 77-86.
20. Neuberger, M. S., Antibody diversification by somatic mutation: from Burnet onwards. Immunol. Cell Biol. 2008, 86, 124-132.
21. Hochman, P. S., Majeau, G. R., Mackay, F., Browning, J. L., Pro-inflammatory responses are efficiently induced by homotrimeric but not heterotrimeric lymphotoxin ligands. J. Inflamm. 1995, 46, 220-234.
22. Nissim, A., Chernajovsky, Y., Historical development of monoclonal antibody therapeutics. Handbook Exp. Pharmacol. 2008, 181, 3-18.
23. Bostrom, J., Fuh, G., Design and construction of synthetic phage-displayed Fab libraries. Methods Mol. Biol. 2009, 562, 17-35.