Mammalian display to secretion switchable libraries for antibody preselection and high throughput functional screening

References

• Gérard A, Woolfe A, Mottet G, Reichen M, Castrillon C, Menrath V, Ellouze S, Poitou A, Doineau R, Briseno-Roa L, et al. High-throughput single-cell activity-based screening and sequencing of antibodies using droplet microfluidics. Nat Biotechnol. 2020;38(6):715–10. doi:10.1038/s41587-020-0466-7.
   PubMed Web of Science ®Google Scholar
• Liu G, Zeng H, Mueller J, Carter B, Wang Z, Schilz J, Horny G, Birnbaum ME, Ewert S, Gifford DK, et al. Antibody complementarity determining region design using high-capacity machine learning. Bioinformatics. 2020;36(7):2126–33. doi:10.1093/bioinformatics/btz895.
   PubMed Web of Science ®Google Scholar
• Wang Y, Jin R, Shen B, Li N, Zhou H, Wang W, Zhao Y, Huang M, Fang P, Wang S, et al. High-throughput functional screening for next-generation cancer immunotherapy using droplet-based microfluidics. Sci Adv. 2021;7(24):3839–50. doi:10.1126/sciadv.abe3839.
   Web of Science ®Google Scholar
• Zhang H, Yea K, Xie J, Ruiz D, Wilson IA, Lerner RA. Selecting agonists from single cells infected with combinatorial antibody libraries. Chem Biol. 2013;20(5):734–41. doi:10.1016/j.chembiol.2013.04.012.
   PubMedGoogle Scholar
• Nehlsen K, Schucht R, da Gama-Norton L, Krömer W, Baer A, Cayli A, Hauser H, Wirth D. Recombinant protein expression by targeting pre-selected chromosomal loci. BMC Biotechnol. 2009;9(1):1–12. doi:10.1186/1472-6750-9-100.
   PubMedGoogle Scholar
• Eguchi A, Nakakido M, Nagatoishi S, Kuroda D, Tsumoto K, Nagamune T, Kawahara M. An epitope-directed antibody affinity maturation system utilizing mammalian cell survival as readout. Biotechnol Bioeng. 2019;116(7):1742–51. doi:10.1002/bit.26965.
   PubMed Web of Science ®Google Scholar
• Matreyek KA, Stephany JJ, Chiasson MA, Hasle N, Fowler DM. An improved platform for functional assessment of large protein libraries in mammalian cells. Nucleic Acids Res. 2020;48:1–12. doi:10.1093/nar/gkz910.
   PubMed Web of Science ®Google Scholar
• Robertson N, Lopez-Anton N, Gurjar SA, Khalique H, Khalaf Z, Clerkin S, Leydon VR, Parker-Manuel R, Raeside A, Payne T, et al. Development of a novel mammalian display system for selection of antibodies against membrane proteins. J Biol Chem. 2020;295(52):18436–48. doi:10.1074/jbc.RA120.015053.
   PubMed Web of Science ®Google Scholar
• Smith ES, Zauderer M. Antibody library display on a mammalian virus vector: combining the advantages of both phage and yeast display into one technology. Curr Drug Discov Technol. 2014;11(1):48–55. doi:10.2174/157016381101140124163634.
   PubMedGoogle Scholar
• Kim H, Kim JS. A guide to genome engineering with programmable nucleases. Nat Rev Genet. 2014;15(5):321–34. doi:10.1038/nrg3686.
   PubMed Web of Science ®Google Scholar
• Parthiban K, Perera RL, Sattar M, Huang Y, Mayle S, Masters E, Griffiths D, Surade S, Leah R, Dyson MR, et al. A comprehensive search of functional sequence space using large mammalian display libraries created by gene editing. MAbs. 2019;11(5):884–98. doi:10.1080/19420862.2019.1618673.
   PubMed Web of Science ®Google Scholar
• Parola C, Neumeier D, Friedensohn S, Csepregi L, Di Tacchio M, Mason DM, Reddy ST. Antibody discovery and engineering by enhanced CRISPR-Cas9 integration of variable gene cassette libraries in mammalian cells. MAbs. 2019;11(8):1367–80. doi:10.1080/19420862.2019.1662691.
   PubMed Web of Science ®Google Scholar
• Zhou C, Jacobsen FW, Cai L, Chen Q, Shen WD. Development of a novel mammalian cell surface antibody display platform. MAbs. 2010;2(5):508–18. doi:10.4161/mabs.2.5.12970.
   PubMed Web of Science ®Google Scholar
• Luo R, Zhao Y, Fan Y, An L, Jiang T, Ma S, Hang H. High efficiency CHO cell display-based antibody maturation. Sci Rep. 2020;10(1):1–10. doi:10.1038/s41598-020-65044-7.
   PubMed Web of Science ®Google Scholar
• Jia JY, Yu D, Tian X-L, Li H-X, Zhou X-C, Kong Y, Zhang W, Zhang L, Lei C, Yang Z-L, et al. A novel and effective approach to generate germline-like monoclonal antibodies by integration of phage and mammalian cell display platforms. Acta Pharmacol Sin. 2022;43(4):954–62. doi:10.1038/s41401-021-00707-3.
   PubMed Web of Science ®Google Scholar
• Durrant MG, Fanton A, Tycko J, Hinks M, Chandrasekaran SS, Perry NT, Schaepe J, Du PP, Lotfy P, Bassik MC, et al. Large-scale discovery of recombinases for integrating DNA into the human genome. bioRxiv. 2021;2021–11. https://www.biorxiv.org/content/10.1101/2021.11.05.467528v2%0Ahttps://www.biorxiv.org/content/10.1101/2021.11.05.467528v2.abstract.
   Google Scholar
• Huhtinen O, Salbo R, Lamminmäki U, Prince S. Selection of biophysically favorable antibody variants using a modified Flp-in CHO mammalian display platform. Front Bioeng Biotechnol. 2023;11:11. doi:10.3389/fbioe.2023.1170081.
   Web of Science ®Google Scholar
• Segaliny AI, Jayaraman J, Chen X, Chong J, Luxon R, Fung A, Fu Q, Jiang X, Rivera R, Ma X, et al. A high throughput bispecific antibody discovery pipeline. Commun Biol. 2023;6(1):380. doi:10.1038/s42003-023-04746-w.
   PubMed Web of Science ®Google Scholar
• Waldmeier L, Hellmann I, Gutknecht CK, Wolter FI, Cook SC, Reddy ST, Grawunder U, Beerli RR. Transpo-mAb display: Transposition-mediated B cell display and functional screening of full-length IgG antibody libraries. MAbs. 2016;8(4):726–40. doi:10.1080/19420862.2016.1160990.
   PubMed Web of Science ®Google Scholar
• Nguyen AW, Le KC, Maynard JA. Identification of high affinity HER2 binding antibodies using CHO Fab surface display. Protein Eng Des Sel. 2018;31(3):91–101. doi:10.1093/protein/gzy004.
   PubMed Web of Science ®Google Scholar
• Bowers PM, Horlick RA, Kehry MR, Neben TY, Tomlinson GL, Altobell L, Zhang X, Macomber JL, Krapf IP, Wu BF, et al. Mammalian cell display for the discovery and optimization of antibody therapeutics. Methods. 2014;65(1):44–56. doi:10.1016/j.ymeth.2013.06.010.
   PubMed Web of Science ®Google Scholar
• Seo H, Masuda H, Asagoshi K, Uchiki T, Kawata S, Sasaki G, Yabuki T, Miyai S, Takahashi N, Hashimoto SI, et al. Streamlined human antibody generation and optimization by exploiting designed immunoglobulin loci in a B cell line. Cell Mol Immunol. 2021;18(6):1545–61. doi:10.1038/s41423-020-0440-9.
   PubMed Web of Science ®Google Scholar
• Zhou Y, Wang J, Zhou I, Lou H, Li CZ, Chen ZR, Zhang ZH, Liu S, Wu S, Tan W, et al. Simultaneous expression of displayed and secreted antibodies for antibody screen. PLoS One. 2013;8(11):2–7. doi:10.1371/journal.pone.0080005.
   Web of Science ®Google Scholar
• Dyson MR, Masters E, Pazeraitis D, Perera RL, Syrjanen JL, Surade S, Thorsteinson N, Parthiban K, Jones PC, Sattar M, et al. Beyond affinity: selection of antibody variants with optimal biophysical properties and reduced immunogenicity from mammalian display libraries. MAbs. 2020;12(1). doi:10.1080/19420862.2020.1829335.
   PubMed Web of Science ®Google Scholar
• Shembekar N, Hu H, Eustace D, M CA. Single-cell droplet microfluidic screening for antibodies Specifically binding to target cells. Cell Rep. 2018;22(8):2206–15. doi:10.1016/j.celrep.2018.01.071.
   PubMed Web of Science ®Google Scholar
• Fitzgerald V, Leonard P. Single cell screening approaches for antibody discovery. Methods. 2017;116:34–42. doi:10.1016/j.ymeth.2016.11.006.
   PubMed Web of Science ®Google Scholar
• Seah YFS, Hu H, Merten CA. Microfluidic single-cell technology in immunology and antibody screening. Mol Aspects Med. 2018;59:47–61. doi:10.1016/j.mam.2017.09.004.
   PubMed Web of Science ®Google Scholar
• Mazutis L, Gilbert J, Ung WL, Weitz DA, Griffiths AD, Heyman JA. Single-cell analysis and sorting using droplet-based microfluidics. Nat Protoc. 2013;8(5):870–91. doi:10.1038/nprot.2013.046.
   PubMed Web of Science ®Google Scholar
• Winters A, McFadden K, Bergen J, Landas J, Berry KA, Gonzalez A, Salimi-Moosavi H, Murawsky CM, Tagari P, King CT. Rapid single B cell antibody discovery using nanopens and structured light. MAbs. 2019;11(6):1025–35. doi:10.1080/19420862.2019.1624126.
   PubMed Web of Science ®Google Scholar
• Fitzgerald V, Manning B, O’Donnell B, O’Reilly B, O’Sullivan D, O’Kennedy R, Leonard P. Exploiting highly ordered subnanoliter volume microcapillaries as microtools for the analysis of antibody producing cells. Anal Chem. 2015;87(2):997–1003. doi:10.1021/ac503547j.
   PubMed Web of Science ®Google Scholar
• Jones BE, Brown-Augsburger PL, Corbett KS, Westendorf K, Davies J, Cujec TP, Wiethoff CM, Blackbourne JL, Heinz BA, Foster D, et al. LY-CoV555, a rapidly isolated potent neutralizing antibody, provides protection in a non-human primate model of SARS-CoV-2 infection. bioRxiv Prepr Serv Bio. 2020. doi:10.1101/2020.09.30.318972.
   Google Scholar
• Lim S, Chen B, Kariolis MS, Dimov IK, Baer TM, Cochran JR. Engineering high affinity Protein–Protein Interactions using a high-throughput microcapillary array platform. ACS Chem Biol. 2017;12(2):336–41. doi:10.1021/acschembio.6b00794.
   PubMed Web of Science ®Google Scholar
• Zhai J, Yi S, Jia Y, Mak PI, Martins RP. Cell-based drug screening on microfluidics. TrAC - Trends Anal Chem. 2019;117:231–41. doi:10.1016/j.trac.2019.05.018.
   Web of Science ®Google Scholar
• Yanakieva D, Elter A, Bratsch J, Friedrich K, Becker S, Kolmar H. FACS-Based functional Protein screening via microfluidic co-encapsulation of yeast secretor and mammalian reporter cells. Sci Rep. 2020;10(1):1–13. doi:10.1038/s41598-020-66927-5.
   PubMed Web of Science ®Google Scholar
• Segaliny AI, Li G, Kong L, Ren C, Chen X, Wang JK, Baltimore D, Wu G, Zhao W. Functional TCR T cell screening using single-cell droplet microfluidics. Lab Chip. 2018;18(24):3733–49. doi:10.1039/C8LC00818C.
   PubMed Web of Science ®Google Scholar
• Jones BE, Brown-Augsburger PL, Corbett KS, Westendorf K, Davies J, Cujec TP, Wiethoff CM, Blackbourne JL, Heinz BA, Foster D, et al. The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates. Sci Transl Med. 2021;13(593):eabf1906. doi:10.1126/scitranslmed.abf1906.
   PubMed Web of Science ®Google Scholar
• Journal AI, Gaa R, Kumari K, Mayer HM, Yanakieva D, Tsai S, Joshi S, Guenther R, Doerner A, Gaa R, et al. An integrated mammalian library approach for optimization and enhanced microfluidics-assisted antibody hit discovery. Artif Cells, Nanomedicine, Biotechnol. 2023;51(1):74–82. doi:10.1080/21691401.2023.2173219.
   PubMed Web of Science ®Google Scholar
• Gaa R, Menang-Ndi E, Pratapa S, Nguyen C, Kumar S, Doerner A. Versatile and rapid microfluidics-assisted antibody discovery. MAbs. 2021;13(1):1978130. doi:10.1080/19420862.2021.1978130.
   PubMed Web of Science ®Google Scholar
• Makowski EK, Kinnunen PC, Huang J, Wu L, Smith MD, Wang T, Desai AA, Streu CN, Zhang Y, Zupancic JM, et al. Co-optimization of therapeutic antibody affinity and specificity using machine learning models that generalize to novel mutational space. Nat Commun. 2022;13(1):3788. doi:10.1038/s41467-022-31457-3.
   PubMed Web of Science ®Google Scholar
• Kim S, Park I, Park SG, Cho S, Kim JH, Sipper N, Choi SS, Lee ES, Hong HJ. Generation, diversity determination, and application to antibody selection of a human naïve fab library. Mol Cells. 2017;40(9):655–66. doi:10.14348/molcells.2017.0106.
   PubMed Web of Science ®Google Scholar
• Erasmus MF, D’Angelo S, Ferrara F, Naranjo L, Teixeira AA, Buonpane R, Stewart SM, Nastri HG, Bradbury ARM. A single donor is sufficient to produce a highly functional in vitro antibody library. Commun Biol. 2021;4(1):350. doi:10.1038/s42003-021-01881-0.
   PubMed Web of Science ®Google Scholar
• Wang Y, Jin R, Shen B, Li N, Zhou H, Wang W, Zhao Y, Huang M, Fang P, Wang S, et al. High-throughput functional screening for next-generation cancer immunotherapy using droplet-based microfluidics. Sci Adv. 2021;7(24):1–14. doi:10.1126/sciadv.abe3839.
   Web of Science ®Google Scholar
• Shepherd A, Bennychen B, Marcil A, Bloemberg D, Pon R, Weeratna R, McComb S. A simplified function-first method for the discovery and optimization of bispecific immune engaging antibodies. bioRxiv. 2022;18(6):e0273884. https://www.biorxiv.org/content/early/2022/08/18/2022.08.17.504342.
   Google Scholar
• Puligedda RD, Sharma R, Al-Saleem FH, Velu AB, Kattala CD, Prendergast GC, Lynch DR, Chumakov K, Dessain SK, Velu AB, et al. Capture and display of antibodies secreted by hybridoma cells enables fluorescent on-cell screening. MAbs. 2019;11(3):546–58. doi:10.1080/19420862.2019.1574520.
   PubMed Web of Science ®Google Scholar
• Mason DM, Friedensohn S, Weber CR, Jordi C, Wagner B, Meng SM, Ehling RA, Bonati L, Dahinden J, Gainza P, et al. Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning. Nat Biomed Eng. 2021;5(6):600–12. doi:10.1038/s41551-021-00699-9.
   PubMed Web of Science ®Google Scholar
• Liu Z, Chen O, Wall JBJ, Zheng M, Zhou Y, Wang L, Vaseghi HR, Qian L, Liu J. Systematic comparison of 2A peptides for cloning multi-genes in a polycistronic vector. Sci Rep. 2017;7(1):2193. doi:10.1038/s41598-017-02460-2.
   PubMedGoogle Scholar