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Structure-Guided and Phage-Assisted Evolution of Therapeutic Antibodies to Reverse On-Target Point Mutation-Mediated Resistance

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Phage Engineering and Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2793))

Abstract

Resistance to therapeutic antibodies caused by on-target point mutations is a major obstacle in anticancer therapy, creating an “unmet clinical need.” To tackle this problem, researchers are developing new generations of antibody drugs that can overcome the resistance mechanisms of existing agents. We have previously reported a structure-guided and phage-assisted evolution (SGAPAE) approach to evolve cetuximab, a therapeutic antibody, to effectively reverse the resistance driven by EGFRS492R or EGFRG465R mutations, without changing the binding epitope or compromising the antibody efficacy. In this protocol, we provide detailed instructions on how to use the SGAPAE approach to evolve cetuximab, which can also be applied to other therapeutic antibodies for reversing on-target point mutation-mediated resistance. The protocol consists of four steps: structure preparation, computational prediction, phage display library construction, and antibody candidate selection.

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References

  1. Lyu X, Zhao Q, Hui J, Wang T et al (2022) The global landscape of approved antibody therapies. Antib Ther 5(4):233–257

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Misale S, Di Nicolantonio F, Sartore-Bianchi A et al (2014) Resistance to anti-EGFR therapy in colorectal cancer: from heterogeneity to convergent evolution. Cancer Discov 4(11):1269–1280

    Article  CAS  PubMed  Google Scholar 

  3. Schlam I, Tarantino P, Tolaney SM (2022) Overcoming resistance to HER2-directed therapies in breast cancer. Cancers (Basel) 14(16):3996

    Article  CAS  PubMed  Google Scholar 

  4. Torka P, Barth M, Ferdman R et al (2019) Mechanisms of resistance to monoclonal antibodies (mAbs) in lymphoid malignancies. Curr Hematol Malig Rep 14(5):426–438

    Article  PubMed  Google Scholar 

  5. Arena S, Bellosillo B, Siravegna G et al (2015) Emergence of multiple EGFR extracellular mutations during cetuximab treatment in colorectal cancer. Clin Cancer Res 21(9):2157–2166

    Article  CAS  PubMed  Google Scholar 

  6. Montagut C, Dalmases A, Bellosillo B et al (2012) Identification of a mutation in the extracellular domain of the epidermal growth factor receptor conferring cetuximab resistance in colorectal cancer. Nat Med 18(2):221–223

    Article  CAS  PubMed  Google Scholar 

  7. Newhall K, Price T, Peeters M et al (2014) Frequency of S492R mutations in the epidermal growth factor receptor: analysis of plasma dna from metastatic colorectal cancer patients treated with panitumumab or cetuximab monotherapy. Ann Oncol 25:i109

    Article  Google Scholar 

  8. Diwanji D, Trenker R, Thaker TM et al (2021) Structures of the HER2-HER3-NRG1beta complex reveal a dynamic dimer interface. Nature 600(7888):339–343

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Shin JW, Kim S, Ha S et al (2019) The HER2 S310F mutant can form an active heterodimer with the EGFR, which can be inhibited by cetuximab but not by trastuzumab as well as pertuzumab. Biomolecules 9(10):629

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Arena S, Siravegna G, Mussolin B et al (2016) MM-151 overcomes acquired resistance to cetuximab and panitumumab in colorectal cancers harboring EGFR extracellular domain mutations. Sci Transl Med 8(324):314r–324r

    Article  Google Scholar 

  11. Sanchez-Martin FJ, Bellosillo B, Gelabert-Baldrich M et al (2016) The first-in-class anti-EGFR antibody mixture Sym004 overcomes cetuximab resistance mediated by EGFR extracellular domain mutations in colorectal cancer. Clin Cancer Res 22(13):3260–3267

    Article  PubMed  Google Scholar 

  12. Harb W, Lieu C, Beeram M et al (2014) A first-in-human study evaluating the safety and pharmacology of MM-151, a novel oligoclonal anti-EGFR antibody combination in patients with refractory solid tumors. Ann Oncol 25:v152

    Article  Google Scholar 

  13. Montagut C, Argiles G, Ciardiello F et al (2018) Efficacy of Sym004 in patients with metastatic colorectal cancer with acquired resistance to anti-EGFR therapy and molecularly selected by circulating tumor DNA analyses: a phase 2 randomized clinical trial. JAMA Oncol 4(4):e175245

    Article  PubMed  PubMed Central  Google Scholar 

  14. Zhuang X, Wang Z, Fan J et al (2022) Structure-guided and phage-assisted evolution of a therapeutic anti-EGFR antibody to reverse acquired resistance. Nat Commun 13(1):4431

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Fleishman SJ, Leaver-Fay A, Corn JE et al (2011) Rosettascripts: a scripting language interface to the rosetta macromolecular modeling suite. PLoS One 6(6):e20161

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Leaver-Fay A, Tyka M, Lewis SM et al (2011) Rosetta3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol 487:545–574

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Alfaleh MA, Alsaab HO, Mahmoud AB et al (2020) Phage display derived monoclonal antibodies: from bench to bedside. Front Immunol 11:1986

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Ferrari D, Garrapa V, Locatelli M (2020) A novel nanobody scaffold optimized for bacterial expression and suitable for the construction of ribosome display libraries. Mol Biotechnol 62(1):43–55

    Article  CAS  PubMed  Google Scholar 

  19. Frenzel A, Schirrmann T, Hust M (2016) Phage display-derived human antibodies in clinical development and therapy. MAbs 8(7):1177–1194

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Correspondence to Liqiang Pan .

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© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Zhuang, X., Chen, S., Pan, L. (2024). Structure-Guided and Phage-Assisted Evolution of Therapeutic Antibodies to Reverse On-Target Point Mutation-Mediated Resistance. In: Peng, H., Liu, J., Chen, I.A. (eds) Phage Engineering and Analysis. Methods in Molecular Biology, vol 2793. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3798-2_3

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  • DOI: https://doi.org/10.1007/978-1-0716-3798-2_3

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3797-5

  • Online ISBN: 978-1-0716-3798-2

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