1
|
Chung DH, Kong S, Young NJ, Chuo SW, Shiah JV, Connelly EJ, Rohweder PJ, Born A, Manglik A, Grandis JR, Johnson DE, Craik CS. Rare antibody phage isolation and discrimination (RAPID) biopanning enables identification of high-affinity antibodies against challenging targets. Commun Biol 2023; 6:1036. [PMID: 37828150 PMCID: PMC10570357 DOI: 10.1038/s42003-023-05390-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
In vitro biopanning platforms using synthetic phage display antibody libraries have enabled the identification of antibodies against antigens that were once thought to be beyond the scope of immunization. Applying these methods against challenging targets remains a critical challenge. Here, we present a new biopanning pipeline, RAPID (Rare Antibody Phage Isolation and Discrimination), for the identification of rare high-affinity antibodies against challenging targets. RAPID biopanning uses fluorescent labeled phage displayed fragment antigen-binding (Fab) antibody libraries for the isolation of high-affinity binders with fluorescent activated sorting. Subsequently, discriminatory hit screening is performed with a biolayer interferometry (BLI) method, BIAS (Biolayer Interferometry Antibody Screen), where candidate binders are ranked and prioritized according to their estimated kinetic off rates. Previously reported antibodies were used to develop the methodology, and the RAPID biopanning pipeline was applied to three challenging targets (CHIP, Gαq, and CS3D), enabling the identification of high-affinity antibodies.
Collapse
Affiliation(s)
- Dong Hee Chung
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Sophie Kong
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Nicholas J Young
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Shih-Wei Chuo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jamie V Shiah
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Emily J Connelly
- The Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Peter J Rohweder
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Alexandra Born
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jennifer R Grandis
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Daniel E Johnson
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA.
- The Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA.
| |
Collapse
|
3
|
Zhang Z, Rohweder PJ, Ongpipattanakul C, Basu K, Bohn MF, Dugan EJ, Steri V, Hann B, Shokat KM, Craik CS. A covalent inhibitor of K-Ras(G12C) induces MHC class I presentation of haptenated peptide neoepitopes targetable by immunotherapy. Cancer Cell 2022; 40:1060-1069.e7. [PMID: 36099883 PMCID: PMC10393267 DOI: 10.1016/j.ccell.2022.07.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 05/26/2022] [Accepted: 07/11/2022] [Indexed: 12/27/2022]
Abstract
Immunotargeting of tumor-specific antigens is a powerful therapeutic strategy. Immunotherapies directed at MHC-I complexes have expanded the scope of antigens and enabled the direct targeting of intracellular oncoproteins at the cell surface. We asked whether covalent drugs that alkylate mutated residues on oncoproteins could act as haptens to generate unique MHC-I-restricted neoantigens. Here, we report that KRAS G12C mutant cells treated with the covalent inhibitor ARS1620 present ARS1620-modified peptides in MHC-I complexes. Using ARS1620-specific antibodies identified by phage display, we show that these haptenated MHC-I complexes can serve as tumor-specific neoantigens and that a bispecific T cell engager construct based on a hapten-specific antibody elicits a cytotoxic T cell response against KRAS G12C cells, including those resistant to direct KRAS G12C inhibition. With multiple K-RAS G12C inhibitors in clinical use or undergoing clinical trials, our results present a strategy to enhance their efficacy and overcome the rapidly arising tumor resistance.
Collapse
Affiliation(s)
- Ziyang Zhang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Peter J Rohweder
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Chayanid Ongpipattanakul
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Koli Basu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Markus-Frederik Bohn
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Eli J Dugan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Veronica Steri
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Preclinical Therapeutics Core, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Byron Hann
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Preclinical Therapeutics Core, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
4
|
Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio CM, Dai SA, Dickinson MS, Elledge SK, Helsell CVM, Hendel NL, Kang E, Kern N, Khoroshkin MS, Kirkemo LL, Lewis GR, Lou K, Marin WM, Maxwell AM, McTigue PF, Myers-Turnbull D, Nagy TL, Natale AM, Oltion K, Pourmal S, Reder GK, Rettko NJ, Rohweder PJ, Schwarz DMC, Tan SK, Thomas PV, Tibble RW, Town JP, Tsai MK, Ugur FS, Wassarman DR, Wolff AM, Wu TS, Bogdanoff D, Li J, Thorn KS, O'Conchúir S, Swaney DL, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS. Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biol Open 2018; 7:7/7/bio036103. [PMID: 30037883 PMCID: PMC6078352 DOI: 10.1242/bio.036103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the difference between fitness under laboratory culture conditions and the selective pressures in changing environments over evolutionary timescales. Building on our previous work (Mavor et al., 2016), we used deep mutational scanning to determine how twelve new chemicals (3-Amino-1,2,4-triazole, 5-fluorocytosine, Amphotericin B, CaCl2, Cerulenin, Cobalt Acetate, Menadione, Nickel Chloride, p-Fluorophenylalanine, Rapamycin, Tamoxifen, and Tunicamycin) reveal novel mutational sensitivities of ubiquitin residues. Collectively, our experiments have identified eight new sensitizing conditions for Lys63 and uncovered a sensitizing condition for every position in Ub except Ser57 and Gln62. By determining the ubiquitin fitness landscape under different chemical constraints, our work helps to resolve the inconsistencies between deep mutational scanning experiments and sequence conservation over evolutionary timescales.
Collapse
Affiliation(s)
- David Mavor
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Kyle A Barlow
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Daniel Asarnow
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Yuliya Birman
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Derek Britain
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Weilin Chen
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Evan M Green
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Lillian R Kenner
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Bruk Mensa
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Leanna S Morinishi
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Charlotte A Nelson
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Erin M Poss
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Pooja Suresh
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Ruilin Tian
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Taylor Arhar
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Beatrice E Ary
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - David P Bauer
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Ian D Bergman
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Rachel M Brunetti
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Cynthia M Chio
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Shizhong A Dai
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Miles S Dickinson
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Susanna K Elledge
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Cole V M Helsell
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Nathan L Hendel
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Emily Kang
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Nadja Kern
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Matvei S Khoroshkin
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Lisa L Kirkemo
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Greyson R Lewis
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Kevin Lou
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Wesley M Marin
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Alison M Maxwell
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Peter F McTigue
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | | | - Tamas L Nagy
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Andrew M Natale
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Keely Oltion
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Sergei Pourmal
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Gabriel K Reder
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Nicholas J Rettko
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Peter J Rohweder
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Daniel M C Schwarz
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Sophia K Tan
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Paul V Thomas
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Ryan W Tibble
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Jason P Town
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Mary K Tsai
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Fatima S Ugur
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Douglas R Wassarman
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Alexander M Wolff
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Taia S Wu
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Derek Bogdanoff
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Jennifer Li
- Department of Chemistry Undergraduate Program, University of California, Davis 95616, USA
| | - Kurt S Thorn
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Shane O'Conchúir
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Daniel N Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester 01655, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Martin Kampmann
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA .,Institute for Neurodegenerative Diseases, University of California, San Francisco 94158, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
| |
Collapse
|