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Williams L, Li L, Yazaki PJ, Wong P, Hong T, Poku EK, Hui S, Ghimire H, Shively JE, Kujawski M. Comparison of IL-2-antibody to IL-2-Fc with or without stereotactic radiation therapy in CEA immunocompetent mice with CEA positive tumors. Cancer Med 2024; 13:e6909. [PMID: 38317590 PMCID: PMC10905250 DOI: 10.1002/cam4.6909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/31/2023] [Accepted: 12/04/2023] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND The potent immune effects of interleukin-2 (IL-2) for cancer therapy can be increased by genetic fusion of IL-2 to the Fc domain of an antibody (IL-2-Fc) or tumor targeted by genetic fusion to a whole antibody known as an immunocytokine (ICK). METHODS An anti-CEA ICK (M5A-IL-2) was compared to an IL-2-Fc fusion protein using tumor therapy and PET imaging in CEA transgenic immunocompetent mice bearing CEA positive colon or breast tumors. Combination with stereotactic radiation therapy (SRT) was performed with either ICK or IL-2-Fc. RESULTS ICK and IL-2-Fc had comparable antitumor effects in both tumor models, although ICK had higher tumor uptake and slower blood clearance than an IL-2-Fc. Analysis of IFNγ+ /CD8+ and FoxP3+ /CD4+ T cells revealed higher levels of IFNγ-producing CD8+ T cells in ICK treated mice versus more efficient Treg elimination in IL-2-Fc treated mice. No significant or lasting toxicity was detected for either agent. Combination therapies with SRT revealed comparable efficacy and induction of immune memory for both ICK and IL-2-Fc when mice were rechallenged post-therapy. CONCLUSIONS IL-2-Fc had comparable antitumor efficacy to CEA-targeted M5A-IL-2 ICK, while both fusion proteins induced immune memory when combined with SRT. Differences in the therapeutic mechanisms of both agents were observed.
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Affiliation(s)
- Lindsay Williams
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research InstituteBeckman Research Institute of City of HopeDuarteCaliforniaUSA
| | - Lin Li
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research InstituteBeckman Research Institute of City of HopeDuarteCaliforniaUSA
| | - Paul J. Yazaki
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research InstituteBeckman Research Institute of City of HopeDuarteCaliforniaUSA
| | - Patty Wong
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research InstituteBeckman Research Institute of City of HopeDuarteCaliforniaUSA
| | - Teresa Hong
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research InstituteBeckman Research Institute of City of HopeDuarteCaliforniaUSA
| | - Erasmus K. Poku
- RadiopharmacyCity of HopeDuarteCaliforniaUSA
- Beckman Research Institute of City of HopeDuarteCaliforniaUSA
| | - Susanta Hui
- Department of Radiation OncologyCity of HopeDuarteCaliforniaUSA
- City of Hope Medical CenterDuarteCaliforniaUSA
| | - Hemendra Ghimire
- Department of Radiation OncologyCity of HopeDuarteCaliforniaUSA
- City of Hope Medical CenterDuarteCaliforniaUSA
| | - John E. Shively
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research InstituteBeckman Research Institute of City of HopeDuarteCaliforniaUSA
| | - Maciej Kujawski
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research InstituteBeckman Research Institute of City of HopeDuarteCaliforniaUSA
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Pérez-Massón B, Quintana-Pérez Y, Tundidor Y, Pérez-Martínez D, Castro-Martínez C, Pupo-Meriño M, Orosa I, Relova-Hernández E, Villegas R, Guirola O, Rojas G. Studying SARS-CoV-2 interactions using phage-displayed receptor binding domain as a model protein. Sci Rep 2024; 14:712. [PMID: 38184672 PMCID: PMC10771503 DOI: 10.1038/s41598-023-50450-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/20/2023] [Indexed: 01/08/2024] Open
Abstract
SARS-CoV-2 receptor binding domain (RBD) mediates viral entry into human cells through its interaction with angiotensin converting enzyme 2 (ACE2). Most neutralizing antibodies elicited by infection or vaccination target this domain. Such a functional relevance, together with large RBD sequence variability arising during viral spreading, point to the need of exploring the complex landscape of interactions between RBD-derived variants, ACE2 and antibodies. The current work was aimed at developing a simple platform to do so. Biologically active and antigenic Wuhan-Hu-1 RBD, as well as mutated RBD variants found in nature, were successfully displayed on filamentous phages. Mutational scanning confirmed the global plasticity of the receptor binding motif within RBD, highlighted residues playing a critical role in receptor binding, and identified mutations strengthening the interaction. The ability of vaccine-induced antibodies to inhibit ACE2 binding of many mutated RBD variants, albeit at different extents, was shown. Amino acid replacements which could compromise such inhibitory potential were underscored. The expansion of our approach could be the starting point for a large-scale phage-based exploration of diversity within RBD of SARS-CoV-2 and related coronaviruses, useful to understand structure-function relationships, to engineer RBD proteins, and to anticipate changes to watch during viral evolution.
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Affiliation(s)
- Beatriz Pérez-Massón
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Yazmina Quintana-Pérez
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Yaima Tundidor
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Dayana Pérez-Martínez
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Camila Castro-Martínez
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Mario Pupo-Meriño
- Universidad de Ciencias Informáticas, Carretera a San Antonio de los Baños, km 2 1/2, Torrens, Boyeros, CP 19370, Havana, Cuba
| | - Ivette Orosa
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Ernesto Relova-Hernández
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Rosmery Villegas
- Universidad de Ciencias Informáticas, Carretera a San Antonio de los Baños, km 2 1/2, Torrens, Boyeros, CP 19370, Havana, Cuba
| | - Osmany Guirola
- Center for Genetic Engineering and Biotechnology, Ave 31 E/158 y 190, Cubanacán, Playa, CP 11300, Havana, Cuba
| | - Gertrudis Rojas
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba.
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Williams L, Li L, Yazaki PJ, Wong P, Miller A, Hong T, Poku EK, Bhattacharya S, Shively JE, Kujawski M. Generation of IL-2-Fc-antibody conjugates by click chemistry. Biotechnol J 2023; 18:e2300115. [PMID: 37300381 DOI: 10.1002/biot.202300115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/10/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND Immunocytokines (ICKs) are antibody directed cytokines produced by genetic fusion of an antibody to a cytokine. METHODS We now show that antibodies conjugated by click chemistry to interleukin-2 (IL-2)-Fc form fully active conjugates, and in one example, equivalent activity to a genetically produced ICK. RESULTS An IL-2-Fc fusion protein was optimized for click chemistry at hinge cysteines using protein stabilizing IL-2 mutations at Lys35 and Cys125 and Fc hinge mutations at Cys142 and Cys148. The IL-2-Fc fusion protein with K35E and C125S mutations with 3 intact hinge cysteines, designated as IL-2-Fc Par, was selected based on its minimal tendency to aggregate. IL-2-Fc-antibody clicked conjugates retained high IL-2 activity and bound target antigens comparable to parent antibodies. An IL-2-Fc-anti-CEA click conjugate showed comparable anti-tumor activity to an anti-CEA-IL-2 ICK in immunocompetent CEA transgenic mice bearing CEA positive orthotopic breast tumors. Significant increases in IFNγ+ /CD8+ and decreases in FoxP3+ /CD4+ T-cells were found for the clicked conjugate and ICK therapies, suggesting a common mechanism of tumor reduction. CONCLUSION The production of antibody targeted IL-2 therapy via a click chemistry approach is feasible with comparable activity to genetically produced ICKs with the added advantage of multiplexing with other monoclonal antibodies.
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Affiliation(s)
- Lindsay Williams
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Lin Li
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Paul J Yazaki
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Patty Wong
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Aaron Miller
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Teresa Hong
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Erasmus K Poku
- Radiopharmacy, City of Hope, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Supriyo Bhattacharya
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - John E Shively
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Maciej Kujawski
- Department of Immunology and Theranostics, Riggs Diabetes, Metabolism, and Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
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Rojas G, Relova-Hernández E, Pérez-Riverón A, Castro-Martínez C, Diaz-Bravo O, Infante YC, Gómez T, Solozábal J, DíazBravo AB, Schubert M, Becker M, Pérez-Massón B, Pérez-Martínez D, Alvarez-Arzola R, Guirola O, Chinea G, Graca L, Dübel S, León K, Carmenate T. Molecular reshaping of phage-displayed Interleukin-2 at beta chain receptor interface to obtain potent super-agonists with improved developability profiles. Commun Biol 2023; 6:828. [PMID: 37558752 PMCID: PMC10412584 DOI: 10.1038/s42003-023-05188-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 07/27/2023] [Indexed: 08/11/2023] Open
Abstract
Interleukin-2 (IL-2) engineered versions, with biased immunological functions, have emerged from yeast display and rational design. Here we reshaped the human IL-2 interface with the IL-2 receptor beta chain through the screening of phage-displayed libraries. Multiple beta super-binders were obtained, having increased receptor binding ability and improved developability profiles. Selected variants exhibit an accumulation of negatively charged residues at the interface, which provides a better electrostatic complementarity to the beta chain, and faster association kinetics. These findings point to mechanistic differences with the already reported superkines, characterized by a conformational switch due to the rearrangement of the hydrophobic core. The molecular bases of the favourable developability profile were tracked to a single residue: L92. Recombinant Fc-fusion proteins including our variants are superior to those based on H9 superkine in terms of expression levels in mammalian cells, aggregation resistance, stability, in vivo enhancement of immune effector responses, and anti-tumour effect.
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Affiliation(s)
- Gertrudis Rojas
- Center of Molecular Immunology, calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, La Habana, Cuba.
| | - Ernesto Relova-Hernández
- Center of Molecular Immunology, calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, La Habana, Cuba
| | - Annia Pérez-Riverón
- Center of Molecular Immunology, calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, La Habana, Cuba
| | - Camila Castro-Martínez
- Center of Molecular Immunology, calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, La Habana, Cuba
| | - Osmany Diaz-Bravo
- Center of Molecular Immunology, calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, La Habana, Cuba
| | - Yanelys Cabrera Infante
- Center of Molecular Immunology, calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, La Habana, Cuba
| | - Tania Gómez
- Center of Molecular Immunology, calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, La Habana, Cuba
| | - Joaquín Solozábal
- Center of Molecular Immunology, calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, La Habana, Cuba
| | - Ana Beatriz DíazBravo
- Center of Molecular Immunology, calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, La Habana, Cuba
| | - Maren Schubert
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Marlies Becker
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Beatriz Pérez-Massón
- Center of Molecular Immunology, calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, La Habana, Cuba
| | - Dayana Pérez-Martínez
- Center of Molecular Immunology, calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, La Habana, Cuba
| | - Rydell Alvarez-Arzola
- Center of Molecular Immunology, calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, La Habana, Cuba
| | - Osmany Guirola
- Center of Genetic Engineering and Biotechnology, Ave 31 e/ 158 y 190, apartado 6162, Playa, CP 11300, La Habana, Cuba
| | - Glay Chinea
- Center of Genetic Engineering and Biotechnology, Ave 31 e/ 158 y 190, apartado 6162, Playa, CP 11300, La Habana, Cuba
| | - Luis Graca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
| | - Stefan Dübel
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Kalet León
- Center of Molecular Immunology, calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, La Habana, Cuba
| | - Tania Carmenate
- Center of Molecular Immunology, calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, La Habana, Cuba
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5
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Corria-Osorio J, Carmona SJ, Stefanidis E, Andreatta M, Ortiz-Miranda Y, Muller T, Rota IA, Crespo I, Seijo B, Castro W, Jimenez-Luna C, Scarpellino L, Ronet C, Spill A, Lanitis E, Romero P, Luther SA, Irving M, Coukos G. Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8 + T cells. Nat Immunol 2023; 24:869-883. [PMID: 37081150 PMCID: PMC10154250 DOI: 10.1038/s41590-023-01477-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 03/01/2023] [Indexed: 04/22/2023]
Abstract
To date, no immunotherapy approaches have managed to fully overcome T-cell exhaustion, which remains a mandatory fate for chronically activated effector cells and a major therapeutic challenge. Understanding how to reprogram CD8+ tumor-infiltrating lymphocytes away from exhausted effector states remains an elusive goal. Our work provides evidence that orthogonal gene engineering of T cells to secrete an interleukin (IL)-2 variant binding the IL-2Rβγ receptor and the alarmin IL-33 reprogrammed adoptively transferred T cells to acquire a novel, synthetic effector state, which deviated from canonical exhaustion and displayed superior effector functions. These cells successfully overcame homeostatic barriers in the host and led-in the absence of lymphodepletion or exogenous cytokine support-to high levels of engraftment and tumor regression. Our work unlocks a new opportunity of rationally engineering synthetic CD8+ T-cell states endowed with the ability to avoid exhaustion and control advanced solid tumors.
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Affiliation(s)
- Jesus Corria-Osorio
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland.
- AGORA Cancer Research Center, Lausanne, Switzerland.
| | - Santiago J Carmona
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Evangelos Stefanidis
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
| | - Massimo Andreatta
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Yaquelin Ortiz-Miranda
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Tania Muller
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Ioanna A Rota
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Isaac Crespo
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Bili Seijo
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Wilson Castro
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Cristina Jimenez-Luna
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
| | | | - Catherine Ronet
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Aodrenn Spill
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Evripidis Lanitis
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
| | - Pedro Romero
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Sanjiv A Luther
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Melita Irving
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland.
- AGORA Cancer Research Center, Lausanne, Switzerland.
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6
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Gene-based delivery of immune-activating cytokines for cancer treatment. Trends Mol Med 2023; 29:329-342. [PMID: 36828711 DOI: 10.1016/j.molmed.2023.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/24/2023]
Abstract
Tumors evolve together with the tumor microenvironment (TME) and reshape it towards immunosuppression. Immunostimulating cytokines can be used to revert this state leading to effective antitumor immune responses, but their exploitation as anticancer drugs has been hampered by severe toxicity associated with systemic administration. Local, TME-targeted delivery of immune activating cytokines can deploy their antitumoral function more effectively than systemic administration while, at the same time, avoiding exposure of healthy organs and limiting toxicity. Here, we review different gene and cell therapy platforms developed for tumor-directed cytokine delivery highlighting their potential for clinical translation.
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7
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Wang JY(J, Khmelinskaia A, Sheffler W, Miranda MC, Antanasijevic A, Borst AJ, Torres SV, Shu C, Hsia Y, Nattermann U, Ellis D, Walkey C, Ahlrichs M, Chan S, Kang A, Nguyen H, Sydeman C, Sankaran B, Wu M, Bera AK, Carter L, Fiala B, Murphy M, Baker D, Ward AB, King NP. Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proc Natl Acad Sci U S A 2023; 120:e2214556120. [PMID: 36888664 PMCID: PMC10089191 DOI: 10.1073/pnas.2214556120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/03/2023] [Indexed: 03/09/2023] Open
Abstract
Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.
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Affiliation(s)
- Jing Yang (John) Wang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA98195
| | - Alena Khmelinskaia
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Transdisciplinary Research Area “Building Blocks of Matter and Fundamental Interactions”, University of Bonn, 53113Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53121Bonn, Germany
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Marcos C. Miranda
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Aleksandar Antanasijevic
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
| | - Andrew J. Borst
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Susana V. Torres
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Chelsea Shu
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Yang Hsia
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Una Nattermann
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA98195
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA98195
| | - Carl Walkey
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Maggie Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Sidney Chan
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA94720
- Berkeley Center for Structural Biology, Lawrence Berkeley Laboratory, Berkeley, CA94720
| | - Mengyu Wu
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Andrew B. Ward
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
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Rojas G, Carmenate T, García-Pérez G, Pérez-Martínez D. Phagekines: Directed Evolution and Characterization of Functional Cytokines Displayed on Phages. Methods Mol Biol 2023; 2702:149-189. [PMID: 37679619 DOI: 10.1007/978-1-0716-3381-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The current chapter focuses on the use of filamentous phages to display and modify biologically active cytokines, with special emphasis on directed evolution of novel variants showing improved receptor binding. Cytokines are essential protein mediators involved in cell-to-cell communication. Their functional importance and the complexity of their interactions with multichain receptors make cytokine engineering a promising tool for the discovery and optimization of therapeutic molecules. Protocols used at the laboratory are illustrated through examples of manipulation of interleukin-2 and interleukin-6, two members of the family of alpha-helix-bundle cytokines playing pivotal roles in immunity and inflammation.
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Jin D, Jiang Y, Chang L, Wei J, Sun J. New therapeutic strategies based on biasing IL-2 mutants for cancers and autoimmune diseases. Int Immunopharmacol 2022; 110:108935. [PMID: 35732097 DOI: 10.1016/j.intimp.2022.108935] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/05/2022]
Abstract
Interleukin-2 (IL-2) is an immunomodulatory multifunctional cytokine. High-dose IL-2 was first approved by the U.S. Food and Drug Administration (FDA) in the 1990s for the treatment of metastatic renal cell carcinoma and metastatic melanoma. However, the short half-life of IL-2 and its toxicity caused by high-dose IL-2 limit the clinical use of IL-2. Recently, the development of cell-type-selective engineered IL-2 products become a hot research filed, mainly because IL-2 stimulates both regulatory T cells (Treg) and effector T cells (Teff) in vivo. The selective effect of IL-2 on Treg and Teff can be improved by designing biased IL-2 mutants, which showed reduced toxicity while being more effective in stimulating anti-tumor effector immunity or ameliorating autoimmune diseases. In this review we summarize the biological properties of IL-2 mutants reported so far. The design process and principle of IL-2 mutants, IL-2 mutant antibody complexes and IL-2 fusion proteins were discussed, which provided research basis for the design and application of IL-2 mutants in the future.
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Affiliation(s)
- Dongfu Jin
- Department of Molecular and Cellular Pharmacology, Tianjin University, Tianjin 300072, PRChina
| | - Yaxin Jiang
- Department of Molecular and Cellular Pharmacology, Tianjin University, Tianjin 300072, PRChina
| | - Lu Chang
- Department of Molecular and Cellular Pharmacology, Tianjin University, Tianjin 300072, PRChina
| | - Jing Wei
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PRChina.
| | - Jian Sun
- Department of Molecular and Cellular Pharmacology, Tianjin University, Tianjin 300072, PRChina; Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PRChina.
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Wang Q. Building Personalized Cancer Therapeutics through Multi-Omics Assays and Bacteriophage-Eukaryotic Cell Interactions. Int J Mol Sci 2021; 22:ijms22189712. [PMID: 34575870 PMCID: PMC8468737 DOI: 10.3390/ijms22189712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 12/11/2022] Open
Abstract
Bacteriophage-eukaryotic cell interaction provides the biological foundation of Phage Display technology, which has been widely adopted in studies involving protein-protein and protein-peptide interactions, and it provides a direct link between the proteins and the DNA encoding them. Phage display has also facilitated the development of new therapeutic agents targeting personalized cancer mutations. Proteins encoded by mutant genes in cancers can be processed and presented on the tumor cell surface by human leukocyte antigen (HLA) molecules, and such mutant peptides are called Neoantigens. Neoantigens are naturally existing tumor markers presented on the cell surface. In clinical settings, the T-cell recognition of neoantigens is the foundation of cancer immunotherapeutics. This year, we utilized phage display to successfully develop the 1st antibody-based neoantigen targeting approach for next-generation personalized cancer therapeutics. In this article, we discussed the strategies for identifying neoantigens, followed by using phage display to create personalized cancer therapeutics-a complete pipeline for personalized cancer treatment.
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Affiliation(s)
- Qing Wang
- Complete Omics Inc., 1448 S. Rolling Rd, Baltimore, MD 21227, USA
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Korn J, Schäckermann D, Kirmann T, Bertoglio F, Steinke S, Heisig J, Ruschig M, Rojas G, Langreder N, Wenzel EV, Roth KDR, Becker M, Meier D, van den Heuvel J, Hust M, Dübel S, Schubert M. Baculovirus-free insect cell expression system for high yield antibody and antigen production. Sci Rep 2020; 10:21393. [PMID: 33288836 PMCID: PMC7721901 DOI: 10.1038/s41598-020-78425-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/20/2020] [Indexed: 11/09/2022] Open
Abstract
Antibodies are essential tools for therapy and diagnostics. Yet, production remains expensive as it is mostly done in mammalian expression systems. As most therapeutic IgG require mammalian glycosylation to interact with the human immune system, other expression systems are rarely used for production. However, for neutralizing antibodies that are not required to activate the human immune system as well as antibodies used in diagnostics, a cheaper production system would be advantageous. In our study, we show cost-efficient, easy and high yield production of antibodies as well as various secreted antigens including Interleukins and SARS-CoV-2 related proteins in a baculovirus-free insect cell expression system. To improve yields, we optimized the expression vector, media and feeding strategies. In addition, we showed the feasibility of lyophilization of the insect cell produced antibodies. Furthermore, stability and activity of the antibodies was compared to antibodies produced by Expi293F cells revealing a lower aggregation of antibodies originating from High Five cell production. Finally, the newly established High Five expression system was compared to the Expi293F mammalian expression system in regard of yield and costs. Most interestingly, all tested proteins were producible in our High Five cell expression system what was not the case in the Expi293F system, hinting that the High Five cell system is especially suited to produce difficult-to-express target proteins.
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Affiliation(s)
- Janin Korn
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Dorina Schäckermann
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Toni Kirmann
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
- Medical Faculty, Carl Ludwig Institute for Physiology, Universität Leipzig, Liebigstraße 27, 04103, Leipzig, Germany
| | - Federico Bertoglio
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Stephan Steinke
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Janyn Heisig
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
- Department Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Maximilian Ruschig
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Gertrudis Rojas
- Center of Molecular Immunology, PO Box 16040, 11300, Havana, Cuba
| | - Nora Langreder
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Esther Veronika Wenzel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Kristian Daniel Ralph Roth
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Marlies Becker
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Doris Meier
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Joop van den Heuvel
- Department Structure and Function of Proteins, Helmholtz-Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Stefan Dübel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Maren Schubert
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany.
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Affinity-matured variants derived from nimotuzumab keep the original fine specificity and exhibit superior biological activity. Sci Rep 2020; 10:1194. [PMID: 31988343 PMCID: PMC6985160 DOI: 10.1038/s41598-019-57279-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/26/2019] [Indexed: 12/11/2022] Open
Abstract
Nimotuzumab is a humanized monoclonal antibody against the Epidermal Growth Factor Receptor with a long history of therapeutic use, recognizing an epitope different from the ones targeted by other antibodies against the same antigen. It is also distinguished by much less toxicity resulting in a better safety profile, which has been attributed to its lower affinity compared to these other antibodies. Nevertheless, the ideal affinity window for optimizing the balance between anti-tumor activity and toxic effects has not been determined. In the current work, the paratope of the phage-displayed nimotuzumab Fab fragment was evolved in vitro to obtain affinity-matured variants. Soft-randomization of heavy chain variable region CDRs and phage selection resulted in mutated variants with improved binding ability. Two recombinant antibodies were constructed using these variable regions, which kept the original fine epitope specificity and showed moderate affinity increases against the target (3-4-fold). Such differences were translated into a greatly enhanced inhibitory capacity upon ligand-induced receptor phosphorylation on tumor cells. The new antibodies, named K4 and K5, are valuable tools to explore the role of affinity in nimotuzumab biological properties, and could be used for applications requiring a fine-tuning of the balance between binding to tumor cells and healthy tissues.
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