Abstract
High-throughput ligand discovery and evolution—via genotype-phenotype linkage strategies—empower molecularly targeted therapy, diagnostics, and fundamental science. Maintaining high-quality target antigen in these selections, particularly for membrane targets, is often a technical challenge. Panning yeast-displayed ligand libraries on intact mammalian cells expressing the molecular target has emerged as an effective strategy. Herein we describe the techniques used to select target-binding ligands via this approach including the use of target-negative cells to deplete non-specific binders and avidity reduction to preferentially select high-affinity ligands.
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References
James ML, Gambhir SS (2012) A molecular imaging primer: modalities, imaging agents, and applications. Physiol Rev 92:897–965
Dijkstra S, Mulders PFA, Schalken JA (2014) Clinical use of novel urine and blood based prostate cancer biomarkers: a review. Clin Biochem 47:889–896
Husseinzadeh N (2011) Status of tumor markers in epithelial ovarian cancer has there been any progress? A review. Gynecol Oncol 120:152–157
Yotsukura S, Mamitsuka H (2015) Evaluation of serum-based cancer biomarkers: a brief review from a clinical and computational viewpoint. Crit Rev Oncol Hematol 93:103–115
Leader B, Baca QJ, Golan DE (2008) Protein therapeutics: a summary and pharmacological classification. Nat Rev Drug Discov 7:21–39
Mäbert K, Cojoc M, Peitzsch C et al (2014) Cancer biomarker discovery: current status and future perspectives. Int J Radiat Biol 90:659–677
Zahnd C, Amstutz P, Plückthun A (2007) Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target. Nat Methods 4:269–279
Mattheakis LC, Bhatt RR, Dower W (2012) An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc Natl Acad Sci 91:9022:9026
Dreier B, Pluckthun A (2012) Rapid selection of high affinity binders using ribosome display. Methods Mol Biol 805:261-286
Josephson K, Ricardo A, Szostak JW (2014) MRNA display: from basic principles to macrocycle drug discovery. Drug Discov Today 19:388–399
Lipovsek D, Plückthun A (2004) In-vitro protein evolution by ribosome display and mRNA display. J Immunol Methods 290:51–67
Roberts RW, Szostak JW (1997) RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc Natl Acad Sci 94:12297–12302
Smith GP (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the viron surface. Science (80) 228:1315–1317
Bratkovic T (2010) Progress in phage display: evolution of the technique and its application. Cell Mol Life Sci 67:749–767
Sidhu SS, Lowman HB, Cunningham BC et al (2000) Phage display for selection of novel binding peptides. Methods Enzymol 328:333–363
Boder ET, Wittrup KD (1997) Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol 15:553–557
Gai SA, Wittrup KD (2007) Yeast surface display for protein engineering and characterization. Curr Opin Struct Biol 17:467–473
Ho M, Pastan I (2009) Mammalian cell display for antibody engineering. Methods Mol Biol 525:337–351
Beerli RR, Bauer M, Buser RB et al (2008) Isolation of human monoclonal antibodies by mammalian cell display. Proc Natl Acad Sci U S A 105:14336–14341
Bowley DR, Labrijn AF, Zwick MB et al (2007) Antigen selection from an HIV-1 immune antibody library displayed on yeast yields many novel antibodies compared to selection from the same library displayed on phage. Protein Eng Des Sel 20:81–90
Shusta EV, Kieke MC, Parke E et al (1999) Yeast polypeptide fusion surface display levels predict thermal stability and soluble secretion efficiency. J Mol Biol 292:949–956
Swers JS, Kellogg BA, Wittrup KD (2004) Shuffled antibody libraries created by in vivo homologous recombination and yeast surface display. Nucleic Acids Res 32:e36
Ackerman M, Levary D, Tobon G et al (2009) Highly avid magnetic bead capture: an efficient selection method for de novo protein engineering utilizing yeast surface display. Biotechnol Prog 25:774–783
Chen TF, de Picciotto PS, Hackel BJ et al (2013) Engineering fibronectin-based binding proteins by yeast surface display. Methods Enzymol 523:303–326
Gera N, Hussain M, Rao BM (2013) Protein selection using yeast surface display. Methods 60:15–26
Friedman M, Nordberg E, Höidén-Guthenberg I et al (2007) Phage display selection of affibody molecules with specific binding to the extracellular domain of the epidermal growth factor receptor. Protein Eng Des Sel 20:189–199
Stefan N, Martin-Killias P, Wyss-Stoeckle S et al (2011) DARPins recognizing the tumor-associated antigen EpCAM selected by phage and ribosome display and engineered for multivalency. J Mol Biol 413:826–843
Kruziki MA, Bhatnagar S, Woldring DR et al (2015) A 45-amino-acid scaffold mined from the PDB for high-affinity ligand engineering. Chem Biol 22:946–956
Hackel BJ, Ackerman ME, Howland SW et al (2010) Stability and CDR composition biases enrich binder functionality landscapes. J Mol Biol 401:84–96
Horak E, Heitner T, Robinson MK et al (2005) Isolation of scFvs to in vitro produced extracellular domains of EGFR family members. Cancer Biother Radiopharm 20:603–613
Zielonka S, Weber N, Becker S et al (2014) Shark attack: high affinity binding proteins derived from shark vNAR domains by stepwise in vitro affinity maturation. J Biotechnol 191:236–245
Iwasaki K, Goto Y, Katoh T et al (2015) A fluorescent imaging probe based on a macrocyclic scaffold that binds to cellular EpCAM. J Mol Evol 81:210–217
Mazzei GJ, Edgerton MD, Losberger C et al (1995) Recombinant soluble trimeric CD40 ligand is biologically active. J Biol Chem 270:7025–7028
Singer E, Landgraf R, Horan T et al (2001) Identification of a heregulin binding site in HER3 extracellular domain. J Biol Chem 276:44266–44274
Stern LA, Lown PS, Kobe AC et al (2019) Cellular-based selections aid yeast-display discovery of genuine cell-binding ligands: targeting oncology vascular biomarker CD276. ACS Comb Sci 21:207–222
Zorniak M, Clark PA, Umlauf BJ, et al (2017) Yeast display biopanning identifies human antibodies targeting glioblastoma stemlike cells. Sci Rep 7:1–12
Tillotson BJ, Cho YK, Shusta EV. (2013) Cells and cell lysates: A direct approach for engineering antibodies against membrane proteins using yeast surface display. Methods 60:27–37
Williams RM, Hajiran CJ, Nayeem S, Sooter LJ (2014) Identification of an antibody fragment specific for androgen-dependentprostate cancer cells. BMC Biotechnol 14:81
Dangaj D, Lanitis E, Zhao A, et al (2013) Novel recombinant human B7-H4 antibodies overcome tumoral immune escape to potentiate T-cell antitumor responses. Cancer Res 73:4820–4829
Wang XX, Cho YK, Shusta E V (2007) Mining a yeast library for brain endothelial cell-binding antibodies. Nat Methods 4:143–145
Wang XX, Shusta E V (2005) The use of scFv-displaying yeast in mammalian cell surface selections. J Immunol Methods 304:30–42
Even-desrumeaux K, Chames P (2012) Phage Display and Selections in Cells. In: Antibody Engineering. pp 225–235
Watters JM, Telleman P, Junghans RP (1997) An optimized method for cell-based phage display panning. Immunotechnology 3:21–29
Jones AR, Stutz CC, Zhou Y, et al (2014) Identifying blood-brain-barrier selective single-chain antibody fragments. Biotechnol J 9:664–674
Newton J and Deutscher SL (2008) Phage peptide display. in Handbook of Experimental Pharmacology 145–163
Sanchez-Martin D, Sorensen MD, Lykkemark S, et al (2015) Selection strategies for anticancer antibody discovery: searching off the beaten path. Trends Biotechnol 33:292–301
Stern LA, Schrack IA, Johnson SM et al (2016) Geometry and expression enhance enrichment of functional yeast-displayed ligands via cell panning. Biotechnol Bioeng 113:2328–2341
Watters JM, Telleman P, Junghans RP (1997) An optimized method for cell-based phage display panning. Immunotechnology 3:21–29
Stern LA, Csizmar CM, Woldring DR et al (2017) Titratable avidity reduction enhances affinity discrimination in mammalian cellular selections of yeast-displayed ligands ACS Comb Sci. 19(5):315–323
Even-Desrumeaux K, Chames P (2012) Phage display and selections in cells. Methods Mol Biol 907:225–235
Patrick WM, Firth AE, Blackburn JM (2003) User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries. Protein Eng Des Sel 16:451–457
Stevens R, Stevens L, Price N (1983) The stabilities of various thiol compounds used in protein purifications. Biochem Educ 11:70
Acknowledgments
This chapter describes work funded by the American Cancer Society (130418-RSG-17-110-01-TBG to B.J.H.), the National Institutes of Health (R01 EB023339 to B.J.H.), and the California Tobacco-Related Disease Research Grants Program Office of the University of California (28FT-0072 to L.A.S.).
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Stern, L.A., Lown, P.S., Hackel, B.J. (2020). Ligand Engineering via Yeast Surface Display and Adherent Cell Panning. In: Zielonka, S., Krah, S. (eds) Genotype Phenotype Coupling. Methods in Molecular Biology, vol 2070. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9853-1_17
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DOI: https://doi.org/10.1007/978-1-4939-9853-1_17
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