Epitope characterization of an anti-PD-L1 antibody using orthogonal approaches

Journal of Molecular Recognition

Volumn 28, Issue 4, 2015, Pages 269-276

  Hao, Gang ^a   Wesolowski, John S ^a   Jiang, Xuliang ^a   Lauder, Scott ^a,b   Sood, Vanita D ^a  

^a EMD Serono Research and Development Institute Inc   (United States)

^b MERRIMACK PHARMACEUTICALS   (United States)

Author keywords

epitope mapping; hydrogen deuterium exchange; mass spectrometry; monoclonal antibody; mutagenesis; PD L1

Indexed keywords

EPITOPE; MONOCLONAL ANTIBODY; PROGRAMMED DEATH 1 LIGAND 1;

CHEMISTRY; DEUTERIUM HYDROGEN EXCHANGE; EPITOPE MAPPING; HUMAN; IMMUNOLOGY; MASS SPECTROMETRY; PROCEDURES; PROTEIN DEGRADATION;

ANTIBODIES, MONOCLONAL; ANTIGENS, CD274; DEUTERIUM EXCHANGE MEASUREMENT; EPITOPE MAPPING; EPITOPES; HUMANS; MASS SPECTROMETRY; PROTEOLYSIS;

EID: 84925452622     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.2418     Document Type: Article

References (45)

1. Amit AG, Mariuzza RA, Phillips SE, Poljak RJ,. 1986. Three-dimensional structure of an antigen antibody complex at 2.8 A resolution. Science 233: 747-753.
2. Baerga-Ortiz A, Hughes CA, Mandell JG, Komives EA,. 2002. Epitope mapping of a monoclonal antibody against human thrombin by H/D-exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein. Protein Sci. 11: 1300-1308.
3. Bai Y, Milne JS, Mayne L, Englander SW,. 1993. Primary structure effects on peptide group hydrogen exchange. Struct. Funct. Genet. 17: 75.
4. Barber DL, Wherry EJ, Masopust D, Zhu B, Allison JP, Sharpe AH, Freeman GJ, Ahmed R,. 2006. Restoring function in exhausted CD8 T cells during chronic viral infection. Nature 439: 682-687.
5. Barlow DJ, Edwards MS, Thornton JM,. 1986. Continuous and discontinuous protein antigenic determinants. Nature 322: 747-748.
6. Benjamin DC, Berzofsky JA, East IJ, Gurd FR, Hannum C, Leach SJ, Margoliash E, Michael JG, Miller A, Prager EM,. 1984. The antigenic structure of proteins: a reappraisal. Annu. Rev. Immunol. 2: 67-101.
7. Berger R, Rotem-Yehudar R, Slama G, Landes S, Kneller A, Leiba M, Koren-Michowitz M, Shimoni A, Nagler A,. 2008. Phase I safety and pharmacokinetic study of CT-011, a humanized antibody interacting with PD-1, in patients with advanced hematologic malignancies. Clin. Cancer Res. 14: 3044-3051.
8. Bhadra R, Gigley JP, Weiss LM, Khan IA,. 2011. Control of Toxoplasma reactivation by rescue of dysfunctional CD8+ T-cell response via PD-1-PDL-1 blockade. Proc. Natl. Acad. Sci. USA 108: 9196-9201.
9. Bobst CE, Kaltashov IA,. 2012. Localizing flexible regions in proteins using hydrogen deuterium exchange mass spectrometry. Methods Mol. Biol. 896: 375-85.
10. Brahmer JR, Tykodi SS, Chow LQ, Hwu WJ, Topalian SL, Hwu P, Drake CG, Camacho LH, Kauh J, Odunsi K, Pitot HC, Hamid O, Bhatia S, Martins R, Eaton K, Chen S, Salay TM, Alaparthy S, Grosso JF, Korman AJ, Parker SM, Agrawal S, Goldberg SM, Pardoll DM, Gupta A, Wigginton JM,. 2012. Safety and activity of anti-PD-L1 antibody in patients with advanced cancer. N. Engl. J. Med. 366: 2455-2465.
11. Brock A,. 2012. Fragmentation hydrogen exchange mass spectrometry: a review of methodology and applications. Protein Expr. Purif. 84: 19-37.
12. Brown JA, Dorfman DM, Ma FR, Sullivan EL, Munoz O, Wood CR, Greenfield EA, Freeman GJ,. 2003. Blockade of programmed death-1 ligands on dendritic cells enhances T cell activation and cytokine production. J. Immunol. 170: 1257-1266.
13. Carter L, Fouser LA, Jussif J, Fitz L, Deng B, Wood CR, Collins M, Honjo T, Freeman GJ, Carreno BM,. 2002. PD-1:PD-L inhibitory pathway affects both CD4(+) and CD8(+) T cells and is overcome by IL-2. Eur. J. Immunol. 32: 634-643.
14. Chalmers MJ, Busby SA, Pascal BD, West GM, Griffin PR,. 2011. Differential hydrogen/deuterium exchange mass spectrometry analysis of protein-ligand interactions. Expert Rev. Proteomics 8: 43-59.
15. Coales SJ, Tuske SJ, Tomasso JC, Hamuro Y,. 2009. Epitope mapping by amide hydrogen/deuterium exchange coupled with immobilization of antibody, on-line proteolysis, liquid chromatography and mass spectrometry. Rapid Commun. Mass Spectrom. 23: 639-647.
16. Dong H, Zhu G, Tamada K, Chen L,. 1999. B7-H1, a third member of the B7 family, co-stimulates T-cell proliferation and interleukin-10 secretion. Nat. Med. 5: 1365-1369.
17. Englander SW,. 2006. Hydrogen exchange and mass spectrometry: A historical perspective. J. Am. Soc. Mass Spectrom. 17: 1481-1489.
18. FDA. 1997. Points to Consider in the Manufacture and Testing of Monoclonal Antibody Products for Human Use. http://www.fda.gov/downloads/biologicsbloodvaccines/guidancecomplianceregulatoryinformation/otherrecommendationsformanufacturers/ucm153182.pdf: U. S. Department of Health and Human Services Food and Drug Administration Center for Biologics Evaluation and Research.
19. Freeman GJ, Long AJ, Iwai Y, Bourque K, Chernova T, Nishimura H, Fitz LJ, Malenkovich N, Okazaki T, Byrne MC, Horton HF, Fouser L, Carter L, Ling V, Bowman MR, Carreno BM, Collins M, Wood CR, Honjo T,. 2000. Engagement of the PD-1 immunoinhibitory receptor by a novel B7 family member leads to negative regulation of lymphocyte activation. J. Exp. Med. 192: 1027-1034.
20. Gerhardt S, Abbott WM, Hargreaves D, Pauptit RA, Davies RA, Needham MR, Langham C, Barker W, Aziz A, Snow MJ, Dawson S, Welsh F, Wilkinson T, Vaugan T, Beste G, Bishop S, Popovic B, Rees G, Sleeman M, Tuske SJ, Coales SJ, Hamuro Y, Russell C,. 2009. Structure of IL-17A in complex with a potent, fully human neutralizing antibody. J. Mol. Biol. 394: 905-21.
21. Geysen HM, Meloen RH, Barteling SJ,. 1984. Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid. Proc. Natl. Acad. Sci. USA 81: 3998-4002.
22. Hirano F, Kaneko K, Tamura H, Dong H, Wang S, Ichikawa M, Rietz C, Flies DB, Lau JS, Zhu G, Tamada K, Chen L,. 2005. Blockade of B7-H1 and PD-1 by monoclonal antibodies potentiates cancer therapeutic immunity. Cancer Res. 65: 1089-1096.
23. Hoofnagle AN, Resing KA, Ahn NG,. 2003. Protein analysis by hydrogen exchange mass spectrometry. Annu. Rev. Biophys. Biomol. Struct. 32: 1-25.
24. Huang RY, Garai K, Frieden C, Gross ML,. 2011. Hydrogen/deuterium exchange and electron-transfer dissociation mass spectrometry determine the interface and dynamics of apolipoprotein E oligomerization. Biochemistry 50: 9273-82.
25. Ishida Y, Agata Y, Shibahara K, Honjo T,. 1992. Induced expression of PD-1, a novel member of the immunoglobulin gene superfamily, upon programmed cell death. EMBO J. 11: 3887-3895.
26. Iwai Y, Ishida M, Tanaka Y, Okazaki T, Honjo T, Minato N,. 2002. Involvement of PD-L1 on tumor cells in the escape from host immune system and tumor immunotherapy by PD-L1 blockade. Proc. Natl. Acad. Sci. USA 99: 12293-12297.
27. Jaswal SS,. 2013. Biological insights from hydrogen exchange mass spectrometry. Biochim. Biophys. Acta 1834: 1188-1201.
28. Jemmerson R, Paterson Y,. 1986. Mapping epitopes on a protein antigen by the proteolysis of antigen-antibody complexes. Science 232: 1001-1004.
29. Kao C, Oestreich KJ, Paley MA, Crawford A, Angelosanto JM, Ali MA, Intlekofer AM, Boss JM, Reiner SL, Weinmann AS, Wherry EJ,. 2011. Transcription factor T-bet represses expression of the inhibitory receptor PD-1 and sustains virus-specific CD8+ T cell responses during chronic infection. Nat. Immunol. 12: 663-671.
30. Lin DY, Tanaka Y, Iwasaki M, Gittis AG, Su HP, Mikami B, Okazaki T, Honjo T, Minato N, Garboczi DN,. 2008. The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors. Proc. Natl. Acad. Sci. USA 105: 3011-3016.
31. Lipson EJ, Sharfman WH, Drake CG, Wollner I, Taube JM, Anders RA, Xu H, Yao S, Pons A, Chen L, Pardoll DM, Brahmer JR, Topalian SL,. 2013. Durable cancer regression off-treatment and effective reinduction therapy with an anti-PD-1 antibody. Clin. Cancer Res. 19: 462-468.
32. Lu J, Witcher DR, White MA, Wang X, Huang L, Rathnachalam R, Beals JM, Kuhstoss S,. 2005. IL-1beta epitope mapping using site-directed mutagenesis and hydrogen-deuterium exchange mass spectrometry analysis. Biochemistry 44: 11106-11114.
33. Malito E, Faleri A, Lo Surdo P, Veggi D, Maruggi G, Grassi E, Cartocci E, Bertoldi I, Genovese A, Santini L, Romagnoli G, Borgogni E, Brier S, Lo Passo C, Domina M, Castellino F, Felici F, van der Veen S, Johnson S, Lea SM, Tang CM, Pizza M, Savino S, Norais N, Rappuoli R, Bottomley MJ, Masignani V,. 2013. Defining a protective epitope on factor H binding protein, a key meningococcal virulence factor and vaccine antigen. Proc. Natl. Acad. Sci. USA 110: 3304-3309.
34. Manimala JC, Roach TA, Li Z, Gildersleeve JC,. 2007. High-throughput carbohydrate microarray profiling of 27 antibodies demonstrates widespread specificity problems. Glycobiology 17: 17C-23C.
35. Mylvaganam SE, Paterson Y, Getzoff ED,. 1998. Structural basis for the binding of an anti-cytochrome c antibody to its antigen: crystal structures of FabE8-cytochrome c complex to 1.8 A resolution and FabE8 to 2.26 A resolution. J. Mol. Biol. 281: 301-322.
36. Obungu VH, Gelfanova V, Rathnachalam R, Bailey A, Sloan-Lancaster J, Huang L,. 2009. Determination of the mechanism of action of anti-FasL antibody by epitope mapping and homology modeling. Biochemistry 48: 7251-7260.
37. Okazaki T, Maeda A, Nishimura H, Kurosaki T, Honjo T,. 2001. PD-1 immunoreceptor inhibits B cell receptor-mediated signaling by recruiting src homology 2-domain-containing tyrosine phosphatase 2 to phosphotyrosine. Proc. Natl. Acad. Sci. USA 98: 13866-13871.
38. Percy AJ, Rey M, Burns KM, Schriemer DC,. 2012. Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry-a review. Anal. Chim. Acta 721: 7-21.
39. Rand KD, Pringle SD, Morris M, Brown JM,. 2012. Site-specific analysis of gas-phase hydrogen/deuterium exchange of peptides and proteins by electron transfer dissociation. Anal. Chem. 84: 1931-40.
40. Rehm H,. 2006. Glycoproteins. In Protein biochemistry and proteomics, Rehm H, (Ed.) 4th ed. Access Online via Elsevier: Elsevier Science: New York, NY.
41. Velu V, Titanji K, Zhu B, Husain S, Pladevega A, Lai L, Vanderford TH, Chennareddi L, Silvestri G, Freeman GJ, Ahmed R, Amara RR,. 2009. Enhancing SIV-specific immunity in vivo by PD-1 blockade. Nature 458: 206-210.
42. Wales TE, Engen JR,. 2006. Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrom. Rev. 25: 158-170.
43. Wilson DS, Wu J, Peluso P, Nock S,. 2002. Improved method for pepsinolysis of mouse IgG(1) molecules to F(ab')(2) fragments. J. Immunol. Methods 260: 29-36.
44. Zhang Q, Willison LN, Tripathi P, Sathe SK, Roux KH, Emmett MR, Blakney GT, Zhang HM, Marshall AG,. 2011. Epitope mapping of a 95kDa antigen in complex with antibody by solution-phase amide backbone hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 83: 7129-7136.
45. Zhang H, Cui W, Gross ML,. 2013. Mass spectrometry for the biophysical characterization of therapeutic monoclonal antibodies. FEBS Lett. 5793: 00871-00875.