1
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Sun R, Qian MG, Zhang X. T and B cell epitope analysis for the immunogenicity evaluation and mitigation of antibody-based therapeutics. MAbs 2024; 16:2324836. [PMID: 38512798 PMCID: PMC10962608 DOI: 10.1080/19420862.2024.2324836] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
The surge in the clinical use of therapeutic antibodies has reshaped the landscape of pharmaceutical therapy for many diseases, including rare and challenging conditions. However, the administration of exogenous biologics could potentially trigger unwanted immune responses such as generation of anti-drug antibodies (ADAs). Real-world experiences have illuminated the clear correlation between the ADA occurrence and unsatisfactory therapeutic outcomes as well as immune-related adverse events. By retrospectively examining research involving immunogenicity analysis, we noticed the growing emphasis on elucidating the immunogenic epitope profiles of antibody-based therapeutics aiming for mechanistic understanding the immunogenicity generation and, ideally, mitigating the risks. As such, we have comprehensively summarized here the progress in both experimental and computational methodologies for the characterization of T and B cell epitopes of therapeutics. Furthermore, the successful practice of epitope-driven deimmunization of biotherapeutics is exceptionally highlighted in this article.
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Affiliation(s)
- Ruoxuan Sun
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
| | - Mark G. Qian
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
| | - Xiaobin Zhang
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
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2
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Harhala MA, Gembara K, Rybicka I, Kaźmierczak ZM, Miernikiewicz P, Majewska JM, Budziar W, Nasulewicz-Goldeman A, Nelson DC, Owczarek B, Dąbrowska K. Immunogenic epitope scanning in bacteriolytic enzymes Pal and Cpl-1 and engineering Pal to escape antibody responses. Front Immunol 2023; 14:1075774. [PMID: 37781366 PMCID: PMC10540205 DOI: 10.3389/fimmu.2023.1075774] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 08/16/2023] [Indexed: 10/03/2023] Open
Abstract
Bacteriolytic enzymes are promising antibacterial agents, but they can cause a typical immune response in vivo. In this study, we used a targeted modification method for two antibacterial endolysins, Pal and Cpl-1. We identified the key immunogenic amino acids, and designed and tested new, bacteriolytic variants with altered immunogenicity. One new variant of Pal (257-259 MKS → TFG) demonstrated decreased immunogenicity while a similar mutant (257-259 MKS → TFK) demonstrated increased immunogenicity. A third variant (280-282 DKP → GGA) demonstrated significantly increased antibacterial activity and it was not cross-neutralized by antibodies induced by the wild-type enzyme. We propose this variant as a new engineered endolysin with increased antibacterial activity that is capable of escaping cross-neutralization by antibodies induced by wild-type Pal. We show that efficient antibacterial enzymes that avoid cross-neutralization by IgG can be developed by epitope scanning, in silico design, and substitutions of identified key amino acids with a high rate of success. Importantly, this universal approach can be applied to many proteins beyond endolysins and has the potential for design of numerous biological drugs.
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Affiliation(s)
- Marek Adam Harhala
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
- Research and Development Centre, Regional Specialist Hospital, Wroclaw, Poland
| | - Katarzyna Gembara
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
- Research and Development Centre, Regional Specialist Hospital, Wroclaw, Poland
| | - Izabela Rybicka
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Zuzanna Maria Kaźmierczak
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
- Research and Development Centre, Regional Specialist Hospital, Wroclaw, Poland
| | - Paulina Miernikiewicz
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Joanna Marta Majewska
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Wiktoria Budziar
- Research and Development Centre, Regional Specialist Hospital, Wroclaw, Poland
| | - Anna Nasulewicz-Goldeman
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Daniel C. Nelson
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, United States
| | - Barbara Owczarek
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Krystyna Dąbrowska
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
- Research and Development Centre, Regional Specialist Hospital, Wroclaw, Poland
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3
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Fang Y, Chang AY, Verma D, Miyashita SI, Eszterhas S, Lee PG, Shen Y, Davis LR, Dong M, Bailey-Kellogg C, Griswold KE. Functional Deimmunization of Botulinum Neurotoxin Protease Domain via Computationally Driven Library Design and Ultrahigh-Throughput Screening. ACS Synth Biol 2023; 12:153-163. [PMID: 36623275 PMCID: PMC9872818 DOI: 10.1021/acssynbio.2c00426] [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: 08/05/2022] [Indexed: 01/11/2023]
Abstract
Botulinum neurotoxin serotype A (BoNT/A) is a widely used cosmetic agent that also has diverse therapeutic applications; however, adverse antidrug immune responses and associated loss of efficacy have been reported in clinical uses. Here, we describe computational design and ultrahigh-throughput screening of a massive BoNT/A light-chain (BoNT/A-LC) library optimized for reduced T cell epitope content and thereby dampened immunogenicity. We developed a functional assay based on bacterial co-expression of BoNT/A-LC library members with a Förster resonance energy transfer (FRET) sensor for BoNT/A-LC enzymatic activity, and we employed high-speed fluorescence-activated cell sorting (FACS) to identify numerous computationally designed variants having wild-type-like enzyme kinetics. Many of these variants exhibited decreased immunogenicity in humanized HLA transgenic mice and manifested in vivo paralytic activity when incorporated into full-length toxin. One variant achieved near-wild-type paralytic potency and a 300% reduction in antidrug antibody response in vivo. Thus, we have achieved a striking level of BoNT/A-LC functional deimmunization by combining computational library design and ultrahigh-throughput screening. This strategy holds promise for deimmunizing other biologics with complex superstructures and mechanisms of action.
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Affiliation(s)
- Yongliang Fang
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Andrew Y. Chang
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Deeptak Verma
- Department
of Computer Science, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Shin-Ichiro Miyashita
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department
of Food, Aroma and Cosmetic Chemistry, Tokyo
University of Agriculture, 196 Yasaka, Abashiri 099-2493, Japan
| | - Susan Eszterhas
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Pyung-Gang Lee
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yi Shen
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Lydia R. Davis
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Min Dong
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Chris Bailey-Kellogg
- Department
of Computer Science, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Karl E. Griswold
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
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4
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Prihoda D, Maamary J, Waight A, Juan V, Fayadat-Dilman L, Svozil D, Bitton DA. BioPhi: A platform for antibody design, humanization, and humanness evaluation based on natural antibody repertoires and deep learning. MAbs 2022; 14:2020203. [PMID: 35133949 PMCID: PMC8837241 DOI: 10.1080/19420862.2021.2020203] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [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: 12/20/2022] Open
Abstract
Despite recent advances in transgenic animal models and display technologies, humanization of mouse sequences remains one of the main routes for therapeutic antibody development. Traditionally, humanization is manual, laborious, and requires expert knowledge. Although automation efforts are advancing, existing methods are either demonstrated on a small scale or are entirely proprietary. To predict the immunogenicity risk, the human-likeness of sequences can be evaluated using existing humanness scores, but these lack diversity, granularity or interpretability. Meanwhile, immune repertoire sequencing has generated rich antibody libraries such as the Observed Antibody Space (OAS) that offer augmented diversity not yet exploited for antibody engineering. Here we present BioPhi, an open-source platform featuring novel methods for humanization (Sapiens) and humanness evaluation (OASis). Sapiens is a deep learning humanization method trained on the OAS using language modeling. Based on an in silico humanization benchmark of 177 antibodies, Sapiens produced sequences at scale while achieving results comparable to that of human experts. OASis is a granular, interpretable and diverse humanness score based on 9-mer peptide search in the OAS. OASis separated human and non-human sequences with high accuracy, and correlated with clinical immunogenicity. BioPhi thus offers an antibody design interface with automated methods that capture the richness of natural antibody repertoires to produce therapeutics with desired properties and accelerate antibody discovery campaigns. The BioPhi platform is accessible at https://biophi.dichlab.org and https://github.com/Merck/BioPhi.
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Affiliation(s)
- David Prihoda
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czech Republic.,R&D Informatics Solutions, MSD Czech Republic S.r.o, Prague, Czech Republic
| | - Jad Maamary
- Predictive and Clinical Immunogenicity, Merck & Co., Inc, Kenilworth, New Jersey, USA
| | - Andrew Waight
- Discovery Biologics, Protein Sciences, MRL, Merck & Co., Inc, South San Francisco, CA, USA
| | - Veronica Juan
- Discovery Biologics, Protein Sciences, MRL, Merck & Co., Inc, South San Francisco, CA, USA
| | | | - Daniel Svozil
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czech Republic.,CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
| | - Danny A Bitton
- R&D Informatics Solutions, MSD Czech Republic S.r.o, Prague, Czech Republic
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5
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Abstract
Vaccinia viral (VV) vectors are increasingly used in oncolytic virus therapy and vaccine development for cancer and infectious diseases. However, their effectiveness is hindered by the strong anti-viral immune response induced by the viral vector. In this review, we discuss the strategies to deimmunize vaccinia viral vector. One approach is to mask the virus from the neutralization antibody responses by mapping and eliminating of B-cell epitopes on the viral membrane proteins. The recombinant VVs contain one or more viral glycoproteins with mutations in the neutralizing antibody epitopes, resulting in viral escape from neutralization. In addition, a regulator of complement activation (e.g., CD55) can be expressed on the surface of the virus particle, leading to increased resistance to complement-mediated neutralization.
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Affiliation(s)
| | - Mariya Viskovska
- Icell Kealex Therapeutics, 2450 Holcombe Blvd Suite J, JALBS@TMC, Houston, TX 77021, USA;
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6
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Stickler M, Reddy A, Xiong JM, Wong MH, Akamatsu Y, Hinton PR, Harding FA. Design, creation and in vitro testing of a reduced immunogenicity humanized anti-CD25 monoclonal antibody that retains functional activity. Protein Eng Des Sel 2019; 32:543-554. [PMID: 32725169 DOI: 10.1093/protein/gzaa017] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/29/2020] [Accepted: 07/06/2020] [Indexed: 11/14/2022] Open
Abstract
Humanized and fully human sequence-derived therapeutic antibodies retain the capacity to induce anti-drug antibodies. Daclizumab (humanized version of the murine anti-Tac antibody; E.HAT) was selected for a proof of concept application of engineering approaches to reduce potential immunogenicity due to its demonstrated immunogenicity in the clinic. Reduced immunogenicity variants of E.HAT were created by identifying and modifying a CD4+ T cell epitope region in the VH region. Variant epitope region peptides were selected for their reduced capacity to induce CD4+ T cell proliferative responses in vitro. Variant antibody molecules were created, and CD25 affinity and potency were similar to the unmodified parent antibody. Fab fragments from the variant antibodies induced a lower frequency and magnitude of responses in human peripheral blood mononuclear cells proliferation tests. By the empirical selection of two amino acid mutations, fully functional humanized E.HAT antibodies with reduced potential to induce immune responses in vitro were created.
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Affiliation(s)
| | | | | | | | | | - Paul R Hinton
- Formerly of AbbVie, Redwood City, CA, USA.,IGM Biosciences, Mountain View, CA, USA
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7
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Moss DL, Park HW, Mettu RR, Landry SJ. Deimmunizing substitutions in Pseudomonas exotoxin domain III perturb antigen processing without eliminating T-cell epitopes. J Biol Chem 2019; 294:4667-4681. [PMID: 30683694 DOI: 10.1074/jbc.ra118.006704] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/23/2019] [Indexed: 11/06/2022] Open
Abstract
Effective adaptive immune responses depend on activation of CD4+ T cells via the presentation of antigen peptides in the context of major histocompatibility complex (MHC) class II. The structure of an antigen strongly influences its processing within the endolysosome and potentially controls the identity of peptides that are presented to T cells. A recombinant immunotoxin, comprising exotoxin A domain III (PE-III) from Pseudomonas aeruginosa and a cancer-specific antibody fragment, has been developed to manage cancer, but its effectiveness is limited by the induction of neutralizing antibodies. Here, we observed that this immunogenicity is substantially reduced by substituting six residues within PE-III. Although these substitutions targeted T-cell epitopes, we demonstrate that reduced conformational stability and protease resistance were responsible for the reduced antibody titer. Analysis of mouse T-cell responses coupled with biophysical studies on single-substitution versions of PE-III suggested that modest but comprehensible changes in T-cell priming can dramatically perturb antibody production. The most strongly responsive PE-III epitope was well-predicted by a structure-based algorithm. In summary, single-residue substitutions can drastically alter the processing and immunogenicity of PE-III but have only modest effects on CD4+ T-cell priming in mice. Our findings highlight the importance of structure-based processing constraints for accurate epitope prediction.
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Affiliation(s)
- Daniel L Moss
- From the Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana 70112 and
| | - Hee-Won Park
- From the Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana 70112 and
| | - Ramgopal R Mettu
- the Department of Computer Science, Tulane University, New Orleans, Louisiana 70118
| | - Samuel J Landry
- From the Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana 70112 and
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8
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Michalska M, Schultze-Seemann S, Kuckuck I, Wolf P. In Vitro Evaluation of Humanized/De-immunized Anti-PSMA Immunotoxins for the Treatment of Prostate Cancer. Anticancer Res 2018; 38:61-69. [PMID: 29277757 DOI: 10.21873/anticanres.12192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 10/27/2017] [Accepted: 11/01/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND We generated humanized/de-immunized immunotoxins targeting the prostate-specific membrane antigen (PSMA) and tested their cytotoxic activity against prostate cancer cells in vitro. MATERIALS AND METHODS The humanized/de-immunized version of our murine anti-PSMA single-chain antibody fragment (scFv) D7, termed hD7-1(VL-VH), was ligated to the 40-kDa toxin domain of Pseudomonas aeruginosa exotoxin A (PE40), and to the deimmunized 24-kDa toxin domains PE24 or PE24mut. The immunotoxins designated as hD7-1(VL-VH)-PE40, hD7-1(VL-VH)-PE24 and hD7-1(VL-VH)-PE24mut were bacterially expressed and purified by affinity chromatography. Binding and cytotoxicity were examined by flow cytometry and viability assay, respectively. RESULTS All immunotoxins revealed strong binding to prostate cancer cells expressing PSMA and specific cytotoxicity, with half-maximal inhibitory concentration values in the picomolar range. CONCLUSION We successfully created powerful anti-PSMA immunotoxins with reduced immunogenicity for further clinical development and application against advanced prostate cancer.
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Affiliation(s)
- Marta Michalska
- Department of Urology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Susanne Schultze-Seemann
- Department of Urology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Irina Kuckuck
- Department of Urology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Philipp Wolf
- Department of Urology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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9
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Salvat RS, Verma D, Parker AS, Kirsch JR, Brooks SA, Bailey-Kellogg C, Griswold KE. Computationally optimized deimmunization libraries yield highly mutated enzymes with low immunogenicity and enhanced activity. Proc Natl Acad Sci U S A 2017; 114:E5085-93. [PMID: 28607051 DOI: 10.1073/pnas.1621233114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Therapeutic proteins of wide-ranging function hold great promise for treating disease, but immune surveillance of these macromolecules can drive an antidrug immune response that compromises efficacy and even undermines safety. To eliminate widespread T-cell epitopes in any biotherapeutic and thereby mitigate this key source of detrimental immune recognition, we developed a Pareto optimal deimmunization library design algorithm that optimizes protein libraries to account for the simultaneous effects of combinations of mutations on both molecular function and epitope content. Active variants identified by high-throughput screening are thus inherently likely to be deimmunized. Functional screening of an optimized 10-site library (1,536 variants) of P99 β-lactamase (P99βL), a component of ADEPT cancer therapies, revealed that the population possessed high overall fitness, and comprehensive analysis of peptide-MHC II immunoreactivity showed the population possessed lower average immunogenic potential than the wild-type enzyme. Although similar functional screening of an optimized 30-site library (2.15 × 109 variants) revealed reduced population-wide fitness, numerous individual variants were found to have activity and stability better than the wild type despite bearing 13 or more deimmunizing mutations per enzyme. The immunogenic potential of one highly active and stable 14-mutation variant was assessed further using ex vivo cellular immunoassays, and the variant was found to silence T-cell activation in seven of the eight blood donors who responded strongly to wild-type P99βL. In summary, our multiobjective library-design process readily identified large and mutually compatible sets of epitope-deleting mutations and produced highly active but aggressively deimmunized constructs in only one round of library screening.
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10
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Grinberg Y, Benhar I. Addressing the Immunogenicity of the Cargo and of the Targeting Antibodies with a Focus on Demmunized Bacterial Toxins and on Antibody-Targeted Human Effector Proteins. Biomedicines 2017; 5:E28. [PMID: 28574434 DOI: 10.3390/biomedicines5020028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/23/2017] [Accepted: 05/31/2017] [Indexed: 12/22/2022] Open
Abstract
Third-generation immunotoxins are composed of a human, or humanized, targeting moiety, usually a monoclonal antibody or an antibody fragment, and a non-human effector molecule. Due to the non-human origin of the cytotoxic domain, these molecules stimulate potent anti-drug immune responses, which limit treatment options. Efforts are made to deimmunize such immunotoxins or to combine treatment with immunosuppression. An alternative approach is using the so-called “human cytotoxic fusion proteins”, in which antibodies are used to target human effector proteins. Here, we present three relevant approaches for reducing the immunogenicity of antibody-targeted protein therapeutics: (1) reducing the immunogenicity of the bacterial toxin, (2) fusing human cytokines to antibodies to generate immunocytokines and (3) addressing the immunogenicity of the targeting antibodies.
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11
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Mazor R, Zhang J, Xiang L, Addissie S, Awuah P, Beers R, Hassan R, Pastan I. Recombinant Immunotoxin with T-cell Epitope Mutations That Greatly Reduce Immunogenicity for Treatment of Mesothelin-Expressing Tumors. Mol Cancer Ther 2015; 14:2789-96. [PMID: 26443804 PMCID: PMC4674367 DOI: 10.1158/1535-7163.mct-15-0532] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [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: 06/25/2015] [Accepted: 08/27/2015] [Indexed: 11/16/2022]
Abstract
SS1P is a recombinant immunotoxin (RIT) that targets mesothelin. It consists of an antimesothelin Fv fused to a portion of Pseudomonas exotoxin A. In clinical studies, it has produced dramatic responses in patients with advanced mesothelioma, when combined with immunosuppressive therapy so that several treatment cycles could be given. Otherwise its activity is limited by its immunogenicity. In this work, we describe the development and characterization of LMB-T20, a highly potent RIT targeted at mesothelin-expressing cancers with low immunogenicity due to removal of its eight T-cell epitopes. LMB-T20 was more active than SS1P when tested on four different mesothelin-expressing cell lines as well as on cells obtained from patients with mesothelioma. It also has potent antitumor activity in mice, and has reduced immunogenicity as measured by cytokine secretion assays. In conclusion, LMB-T20 is a favorable candidate for evaluation in clinical trials due to its reduced immunogenicity and excellent activity.
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Affiliation(s)
- Ronit Mazor
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Jingli Zhang
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Laiman Xiang
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Selamawit Addissie
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Prince Awuah
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Richard Beers
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Raffit Hassan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland.
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12
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Schmohl JU, Todhunter D, Oh S, Vallera DA. Mutagenic Deimmunization of Diphtheria Toxin for Use in Biologic Drug Development. Toxins (Basel) 2015; 7:4067-82. [PMID: 26473923 PMCID: PMC4626721 DOI: 10.3390/toxins7104067] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/09/2015] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Targeted toxins require multiple treatments and therefore must be deimmunized. We report a method of protein deimmunization based on the point mutation of highly hydrophilic R, K, D, E, and Q amino acids on the molecular surface of truncated diphtheria-toxin (DT390). METHODS Based on their surface position derived from an X-ray-crystallographic model, residues were chosen for point mutation that were located in prominent positions on the molecular surface and away from the catalytic site. Mice were immunized with a targeted toxin containing either a mutated DT390 containing seven critical point mutations or the non-mutated parental toxin form. RESULTS Serum analysis revealed a significant 90% reduction in anti-toxin antibodies in mice immunized with the mutant, but not the parental drug form despite multiple immunizations. The experiment was repeated in a second strain of mice with a different MHC-haplotype to address whether point mutation removed T or B cell epitopes. Findings were identical indicating that B cell epitopes were eliminated from DT. The mutant drug form lost only minimal activity in vitro as well as in vivo. CONCLUSION These findings indicate that this method may be effective for deimmunizing of other proteins and that discovery of a deimmunized form of DT may lead to the development of more effective targeted toxin.
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Affiliation(s)
- Joerg U Schmohl
- University of Minnesota Masonic Cancer Center, Section of Molecular Cancer Therapeutics, Therapeutic Radiology-Radiation Oncology, University of Minnesota, Minneapolis, MN 55423, USA.
- Department for Hematology and Oncology, Department of Medicine 2, University Hospital of Tuebingen, Tuebingen 72076, Germany.
| | - Deborah Todhunter
- University of Minnesota Masonic Cancer Center, Section of Molecular Cancer Therapeutics, Therapeutic Radiology-Radiation Oncology, University of Minnesota, Minneapolis, MN 55423, USA.
| | - Seung Oh
- University of Minnesota Masonic Cancer Center, Section of Molecular Cancer Therapeutics, Therapeutic Radiology-Radiation Oncology, University of Minnesota, Minneapolis, MN 55423, USA.
| | - Daniel A Vallera
- University of Minnesota Masonic Cancer Center, Section of Molecular Cancer Therapeutics, Therapeutic Radiology-Radiation Oncology, University of Minnesota, Minneapolis, MN 55423, USA.
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13
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Salvat RS, Choi Y, Bishop A, Bailey-Kellogg C, Griswold KE. Protein deimmunization via structure-based design enables efficient epitope deletion at high mutational loads. Biotechnol Bioeng 2015; 112:1306-18. [PMID: 25655032 PMCID: PMC4452428 DOI: 10.1002/bit.25554] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 10/26/2014] [Revised: 01/09/2015] [Accepted: 01/18/2015] [Indexed: 12/31/2022]
Abstract
Anti-drug immune responses are a unique risk factor for biotherapeutics, and undesired immunogenicity can alter pharmacokinetics, compromise drug efficacy, and in some cases even threaten patient safety. To fully capitalize on the promise of biotherapeutics, more efficient and generally applicable protein deimmunization tools are needed. Mutagenic deletion of a protein's T cell epitopes is one powerful strategy to engineer immunotolerance, but deimmunizing mutations must maintain protein structure and function. Here, EpiSweep, a structure-based protein design and deimmunization algorithm, has been used to produce a panel of seven beta-lactamase drug candidates having 27-47% reductions in predicted epitope content. Despite bearing eight mutations each, all seven engineered enzymes maintained good stability and activity. At the same time, the variants exhibited dramatically reduced interaction with human class II major histocompatibility complex proteins, key regulators of anti-drug immune responses. When compared to 8-mutation designs generated with a sequence-based deimmunization algorithm, the structure-based designs retained greater thermostability and possessed fewer high affinity epitopes, the dominant drivers of anti-biotherapeutic immune responses. These experimental results validate the first structure-based deimmunization algorithm capable of mapping optimal biotherapeutic design space. By designing optimal mutations that reduce immunogenic potential while imparting favorable intramolecular interactions, broadly distributed epitopes may be simultaneously targeted using high mutational loads.
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Affiliation(s)
- Regina S Salvat
- Thayer School of Engineering, Dartmouth, 14 Engineering Dr., Hanover, New Hampshire, 03755
| | - Yoonjoo Choi
- Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, New Hampshire, 03755
| | | | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, New Hampshire, 03755.
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, 14 Engineering Dr., Hanover, New Hampshire, 03755.
- Program in Molecular and Cellular Biology, Dartmouth, Hanover, New Hampshire.
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14
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Mazor R, Eberle JA, Hu X, Vassall AN, Onda M, Beers R, Lee EC, Kreitman RJ, Lee B, Baker D, King C, Hassan R, Benhar I, Pastan I. Recombinant immunotoxin for cancer treatment with low immunogenicity by identification and silencing of human T-cell epitopes. Proc Natl Acad Sci U S A 2014; 111:8571-6. [PMID: 24799704 PMCID: PMC4060717 DOI: 10.1073/pnas.1405153111] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [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] [Indexed: 12/15/2022] Open
Abstract
Nonhuman proteins have valuable therapeutic properties, but their efficacy is limited by neutralizing antibodies. Recombinant immunotoxins (RITs) are potent anticancer agents that have produced many complete remissions in leukemia, but immunogenicity limits the number of doses that can be given to patients with normal immune systems. Using human cells, we identified eight helper T-cell epitopes in PE38, a portion of the bacterial protein Pseudomonas exotoxin A which consists of the toxin moiety of the RIT, and used this information to make LMB-T18 in which three epitopes were deleted and five others diminished by point mutations in key residues. LMB-T18 has high cytotoxic and antitumor activity and is very resistant to thermal denaturation. The new immunotoxin has a 93% decrease in T-cell epitopes and should have improved efficacy in patients because more treatment cycles can be given. Furthermore, the deimmunized toxin can be used to make RITs targeting other antigens, and the approach we describe can be used to deimmunize other therapeutically useful nonhuman proteins.
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Affiliation(s)
- Ronit Mazor
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892;Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 6998, Israel
| | - Jaime A Eberle
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Xiaobo Hu
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Aaron N Vassall
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Masanori Onda
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Richard Beers
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elizabeth C Lee
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Robert J Kreitman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Byungkook Lee
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - David Baker
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, WA 98122; and
| | - Chris King
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, WA 98122; and
| | - Raffit Hassan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892;Thoracic and Gastrointestinal Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Itai Benhar
- Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 6998, Israel
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892;
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15
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Abstract
Immune responses can make protein therapeutics ineffective or even dangerous. We describe a general computational protein design method for reducing immunogenicity by eliminating known and predicted T-cell epitopes and maximizing the content of human peptide sequences without disrupting protein structure and function. We show that the method recapitulates previous experimental results on immunogenicity reduction, and we use it to disrupt T-cell epitopes in GFP and Pseudomonas exotoxin A without disrupting function.
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Affiliation(s)
- Chris King
- Institute for Protein Design, Department of Biochemistry and
| | - Esteban N Garza
- Department of Immunology, University of Washington, Seattle, WA 98195; and
| | | | - Jonathan L Linehan
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20892
| | | | - Marion Pepper
- Department of Immunology, University of Washington, Seattle, WA 98195; and
| | - David Baker
- Institute for Protein Design, Department of Biochemistry and
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16
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Weidle UH, Tiefenthaler G, Schiller C, Weiss EH, Georges G, Brinkmann U. Prospects of bacterial and plant protein-based immunotoxins for treatment of cancer. Cancer Genomics Proteomics 2014; 11:25-38. [PMID: 24633317] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
Bacterial- and plant-derived immunotoxins have documented potential for treatment of cancer. We discuss Anthrax toxin, ribosome inactivating-toxins, such as saporin and ricin, and ADP-ribosylating toxins such as Diphtheria toxin and Pseudomonas exotoxin, with focus on the latter, which has been most thoroughly investigated. Regarding their potential as anticancer agents, critical issues such as immunogenicity and toxicity are outlined. We describe different generations of immunotoxins, the pathways for the delivery of the cytotoxic 'warheads', molecular parameters modulating efficacy, and combination therapy with other anticancer agents. Finally, we discuss deimmunization strategies based on the removal of B- and T-cell epitopes from the cytotoxic component, and highlight promising clinical proof-of-concept studies.
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Affiliation(s)
- Ulrich H Weidle
- Roche Pharma Research and Early Development (pRED), Roche Diagnostics GmbH, D-82372 Penzberg, Germany.
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17
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Mazor R, Vassall AN, Eberle JA, Beers R, Weldon JE, Venzon DJ, Tsang KY, Benhar I, Pastan I. Identification and elimination of an immunodominant T-cell epitope in recombinant immunotoxins based on Pseudomonas exotoxin A. Proc Natl Acad Sci U S A 2012; 109:E3597-603. [PMID: 23213206 PMCID: PMC3529021 DOI: 10.1073/pnas.1218138109] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [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] [Indexed: 02/04/2023] Open
Abstract
Recombinant immunotoxins (RITs) are chimeric proteins that are being developed for cancer treatment. We have produced RITs that contain PE38, a portion of the bacterial protein Pseudomonas exotoxin A. Because the toxin is bacterial, it often induces neutralizing antibodies, which limit the number of treatment cycles and the effectiveness of the therapy. Because T cells are essential for antibody responses to proteins, we adopted an assay to map the CD4(+) T-cell epitopes in PE38. We incubated peripheral blood mononuclear cells with an immunotoxin to stimulate T-cell expansion, followed by exposure to overlapping peptide fragments of PE38 and an IL-2 ELISpot assay to measure responses. Our observation of T-cell responses in 50 of 50 individuals correlates with the frequency of antibody formation in patients with normal immune systems. We found a single, highly immunodominant epitope in 46% (23/50) of the donors. The immunodominant epitope is DRB1-restricted and was observed in subjects with different HLA alleles, indicating promiscuity. We identified two amino acids that, when deleted or mutated to alanine, eliminated the immunodominant epitope, and we used this information to construct mutant RITs that are highly cytotoxic and do not stimulate T-cell responses in many donors.
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Affiliation(s)
- Ronit Mazor
- Laboratory of Molecular Biology
- Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv 69978, Israel
| | | | | | | | | | - David J. Venzon
- Biostatistics and Data Management Section, Center for Cancer Research, and
| | - Kwong Y. Tsang
- Laboratory of Tumor Immunology and Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Itai Benhar
- Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv 69978, Israel
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18
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Hansen JK, Weldon JE, Xiang L, Beers R, Onda M, Pastan I. A recombinant immunotoxin targeting CD22 with low immunogenicity, low nonspecific toxicity, and high antitumor activity in mice. J Immunother 2010; 33:297-304. [PMID: 20445350 PMCID: PMC7291874 DOI: 10.1097/cji.0b013e3181cd1164] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [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] [Indexed: 11/25/2022]
Abstract
Recombinant immunotoxins (RITs) are genetically engineered proteins designed to kill cancer cells. The RIT HA22 contains the Fv portion of an anti-CD22 antibody fused to a 38 kDa fragment of Pseudomonas exotoxin A (PE38). As PE38 is a bacterial protein, patients frequently produce antibodies that neutralize its activity, preventing retreatment. We have earlier shown in mice that PE38 contains 7 major B-cell epitopes located in domains II and III of the protein. Here we present a new mutant RIT, HA22-LR-6X, in which we removed most B-cell epitopes by deleting domain II and mutating 6 residues in domain III. HA22-LR-6X is cytotoxic to several lymphoma cell lines, has very low nonspecific toxicity, and retains potent antitumor activity in mice with CA46 lymphomas. To assess its immunogenicity, we immunized 3 MHC-divergent strains of mice with 5 microg doses of HA22-LR-6X, and found that HA22-LR-6X elicited significantly lower antibody responses than HA22 or other mutant RITs with fewer epitopes removed. Furthermore, large (50 microg) doses of HA22-LR-6X induced markedly lower antibody responses than 5 microg of HA22, indicating that high doses can be administered with low immunogenicity. Our experiments show that we have correctly identified and removed B-cell epitopes from PE38, producing a highly active immunotoxin with low immunogenicity and low animal toxicity. Future studies will determine if these properties carry over to humans with cancer.
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Affiliation(s)
- Johanna K. Hansen
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute; Bethesda, MD
- National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD
| | - John E. Weldon
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute; Bethesda, MD
- National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD
| | - Laiman Xiang
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute; Bethesda, MD
| | - Richard Beers
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute; Bethesda, MD
| | - Masanori Onda
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute; Bethesda, MD
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute; Bethesda, MD
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