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Dobersberger M, Sumesgutner D, Zajc CU, Salzer B, Laurent E, Emminger D, Sylvander E, Lehner E, Teufl M, Seigner J, Bobbili MR, Kunert R, Lehner M, Traxlmayr MW. An engineering strategy to target activated EGFR with CAR T cells. Cell Rep Methods 2024; 4:100728. [PMID: 38492569 PMCID: PMC11045874 DOI: 10.1016/j.crmeth.2024.100728] [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] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/18/2024] [Accepted: 02/16/2024] [Indexed: 03/18/2024]
Abstract
Chimeric antigen receptor (CAR) T cells have shown remarkable response rates in hematological malignancies. In contrast, CAR T cell treatment of solid tumors is associated with several challenges, in particular the expression of most tumor-associated antigens at lower levels in vital organs, resulting in on-target/off-tumor toxicities. Thus, innovative approaches to improve the tumor specificity of CAR T cells are urgently needed. Based on the observation that many human solid tumors activate epidermal growth factor receptor (EGFR) on their surface through secretion of EGFR ligands, we developed an engineering strategy for CAR-binding domains specifically directed against the ligand-activated conformation of EGFR. We show, in several experimental systems, that the generated binding domains indeed enable CAR T cells to distinguish between active and inactive EGFR. We anticipate that this engineering concept will be an important step forward to improve the tumor specificity of CAR T cells directed against EGFR-positive solid cancers.
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Affiliation(s)
- Markus Dobersberger
- Department of Chemistry, Institute of Biochemistry, BOKU University, 1190 Vienna, Austria
| | - Delia Sumesgutner
- Department of Chemistry, Institute of Biochemistry, BOKU University, 1190 Vienna, Austria; CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria
| | - Charlotte U Zajc
- Department of Chemistry, Institute of Biochemistry, BOKU University, 1190 Vienna, Austria; CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria
| | - Benjamin Salzer
- CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria; St. Anna Children's Cancer Research Institute, CCRI, 1090 Vienna, Austria
| | - Elisabeth Laurent
- BOKU Core Facility Biomolecular & Cellular Analysis, BOKU University, 1190 Vienna, Austria
| | - Dominik Emminger
- CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria; St. Anna Children's Cancer Research Institute, CCRI, 1090 Vienna, Austria
| | - Elise Sylvander
- CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria; St. Anna Children's Cancer Research Institute, CCRI, 1090 Vienna, Austria
| | - Elisabeth Lehner
- Department of Chemistry, Institute of Biochemistry, BOKU University, 1190 Vienna, Austria; CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria
| | - Magdalena Teufl
- Department of Chemistry, Institute of Biochemistry, BOKU University, 1190 Vienna, Austria; CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria
| | - Jacqueline Seigner
- Department of Chemistry, Institute of Biochemistry, BOKU University, 1190 Vienna, Austria; Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology, BOKU University, 1190 Vienna, Austria
| | - Madhusudhan Reddy Bobbili
- Department of Biotechnology, Institute of Molecular Biotechnology, BOKU University, 1190 Vienna, Austria; Ludwig Boltzmann Institute for Traumatology, Research Center in Cooperation with AUVA, 1200 Vienna, Austria
| | - Renate Kunert
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology, BOKU University, 1190 Vienna, Austria
| | - Manfred Lehner
- CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria; St. Anna Children's Cancer Research Institute, CCRI, 1090 Vienna, Austria; St. Anna Children's Hospital, Department of Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Michael W Traxlmayr
- Department of Chemistry, Institute of Biochemistry, BOKU University, 1190 Vienna, Austria; CD Laboratory for Next Generation CAR T Cells, 1090 Vienna, Austria.
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Seigner J, Zajc CU, Dötsch S, Eigner C, Laurent E, Busch DH, Lehner M, Traxlmayr MW. Solving the mystery of the FMC63-CD19 affinity. Sci Rep 2023; 13:23024. [PMID: 38155191 PMCID: PMC10754921 DOI: 10.1038/s41598-023-48528-0] [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: 09/04/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023] Open
Abstract
The majority of approved CAR T cell products are based on the FMC63-scFv directed against CD19. Surprisingly, although antigen binding affinity is a major determinant for CAR function, the affinity of the benchmark FMC63-scFv has not been unambiguously determined. That is, a wide range of affinities have been reported in literature, differing by more than 100-fold. Using a range of techniques, we demonstrate that suboptimal experimental designs can cause artefacts that lead to over- or underestimation of the affinity. To minimize these artefacts, we performed SPR with strictly monomeric and correctly folded soluble CD19, yielding an FMC63-scFv affinity of 2-6 nM. Together, apart from analyzing the FMC63-scFv affinity under optimized conditions, we also provide potential explanations for the wide range of published affinities. We expect that this study will be highly valuable for interpretations of CAR affinity-function relationships, as well as for the design of future CAR T cell generations.
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Affiliation(s)
- Jacqueline Seigner
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Charlotte U Zajc
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, Vienna, Austria
| | - Sarah Dötsch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Caroline Eigner
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Elisabeth Laurent
- BOKU Core Facility Biomolecular and Cellular Analysis, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Manfred Lehner
- CD Laboratory for Next Generation CAR T Cells, Vienna, Austria
- St. Anna Children's Cancer Research Institute, CCRI, Vienna, Austria
- Department of Pediatrics, St. Anna Kinderspital, Medical University of Vienna, Vienna, Austria
| | - Michael W Traxlmayr
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria.
- CD Laboratory for Next Generation CAR T Cells, Vienna, Austria.
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Abstract
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In addition to its
biological function, the stability of a protein
is a major determinant for its applicability. Unfortunately, engineering
proteins for improved functionality usually results in destabilization
of the protein. This so-called stability–function trade-off
can be explained by the simple fact that the generation of a novel
protein function—or the improvement of an existing one—necessitates
the insertion of mutations, i.e., deviations from
the evolutionarily optimized wild-type sequence. In fact, it was demonstrated
that gain-of-function mutations are not more destabilizing than other
random mutations. The stability–function trade-off is a universal
phenomenon during protein evolution that has been observed with completely
different types of proteins, including enzymes, antibodies, and engineered
binding scaffolds. In this review, we discuss three types of strategies
that have been successfully deployed to overcome this omnipresent
obstacle in protein engineering approaches: (i) using highly stable
parental proteins, (ii) minimizing the extent of destabilization during
functional engineering (by library optimization and/or coselection
for stability and function), and (iii) repairing damaged mutants through
stability engineering. The implementation of these strategies in protein
engineering campaigns will facilitate the efficient generation of
protein variants that are not only functional but also stable and
therefore better-suited for subsequent applications.
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Affiliation(s)
- Magdalena Teufl
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, 1190 Vienna, Austria
| | - Charlotte U. Zajc
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, 1190 Vienna, Austria
| | - Michael W. Traxlmayr
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, 1190 Vienna, Austria
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Abstract
Yeast surface display is a powerful protein engineering technology that is extensively used to improve various properties of proteins, including affinity, specificity, and stability or even to add novel functions (usually ligand binding). Apart from its robustness and versatility as an engineering tool, yeast display offers a further critical advantage: Once the selection campaign is finished, usually resulting in an oligoclonal pool, these enriched protein variants can be analyzed individually on the surface of yeast without the need for any sub-cloning, soluble expression, and purification. Here, we provide detailed protocols for determining both the affinity and the thermal stability of yeast displayed proteins. In addition, we discuss the advantages, challenges, and potential pitfalls associated with affinity and stability analysis using yeast surface display.
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Affiliation(s)
- Charlotte U Zajc
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, Vienna, Austria
| | - Magdalena Teufl
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, Vienna, Austria
| | - Michael W Traxlmayr
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria.
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Zajc CU, Salzer B, Taft JM, Reddy ST, Lehner M, Traxlmayr MW. Driving CARs with alternative navigation tools - the potential of engineered binding scaffolds. FEBS J 2020; 288:2103-2118. [PMID: 32794303 PMCID: PMC8048499 DOI: 10.1111/febs.15523] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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] [Received: 05/16/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 12/11/2022]
Abstract
T cells that are genetically engineered to express chimeric antigen receptors (CAR T cells) have shown impressive clinical efficacy against B‐cell malignancies. In contrast to these highly potent CD19‐targeting CAR T cells, many of those directed against other tumor entities and antigens currently suffer from several limitations. For example, it has been demonstrated that many scFvs used as antigen‐binding domains in CARs show some degree of oligomerization, which leads to tonic signaling, T cell exhaustion, and poor performance in vivo. Therefore, in many cases alternatives to scFvs would be beneficial. Fortunately, due to the development of powerful protein engineering technologies, also non‐immunoglobulin‐based scaffolds can be engineered to specifically recognize antigens, thus eliminating the historical dependence on antibody‐based binding domains. Here, we discuss the advantages and disadvantages of such engineered binding scaffolds, in particular with respect to their application in CARs. We review recent studies, collectively showing that there is no functional or biochemical aspect that necessitates the use of scFvs in CARs. Instead, antigen recognition can also be mediated efficiently by engineered binding scaffolds, as well as natural ligands or receptors fused to the CAR backbone. Finally, we critically discuss the risk of immunogenicity and show that the extent of nonhuman amino acid stretches in engineered scaffolds—even in those based on nonhuman proteins—is more similar to humanized scFvs than might be anticipated. Together, we expect that engineered binding scaffolds and natural ligands and receptors will be increasingly used for the design of CAR T cells.
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Affiliation(s)
- Charlotte U Zajc
- Christian Doppler Laboratory for Next Generation CAR T Cells, Vienna, Austria.,Department of Chemistry, Institute of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Benjamin Salzer
- Christian Doppler Laboratory for Next Generation CAR T Cells, Vienna, Austria.,St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Joseph M Taft
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Manfred Lehner
- Christian Doppler Laboratory for Next Generation CAR T Cells, Vienna, Austria.,St. Anna Children's Cancer Research Institute, Vienna, Austria.,Department of Pediatrics, St. Anna Kinderspital, Medical University of Vienna, Austria
| | - Michael W Traxlmayr
- Christian Doppler Laboratory for Next Generation CAR T Cells, Vienna, Austria.,Department of Chemistry, Institute of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
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Salzer B, Schueller CM, Zajc CU, Peters T, Schoeber MA, Kovacic B, Buri MC, Lobner E, Dushek O, Huppa JB, Obinger C, Putz EM, Holter W, Traxlmayr MW, Lehner M. Engineering AvidCARs for combinatorial antigen recognition and reversible control of CAR function. Nat Commun 2020; 11:4166. [PMID: 32820173 PMCID: PMC7441178 DOI: 10.1038/s41467-020-17970-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [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: 08/19/2019] [Accepted: 07/23/2020] [Indexed: 12/13/2022] Open
Abstract
T cells engineered to express chimeric antigen receptors (CAR-T cells) have shown impressive clinical efficacy in the treatment of B cell malignancies. However, the development of CAR-T cell therapies for solid tumors is hampered by the lack of truly tumor-specific antigens and poor control over T cell activity. Here we present an avidity-controlled CAR (AvidCAR) platform with inducible and logic control functions. The key is the combination of (i) an improved CAR design which enables controlled CAR dimerization and (ii) a significant reduction of antigen-binding affinities to introduce dependence on bivalent interaction, i.e. avidity. The potential and versatility of the AvidCAR platform is exemplified by designing ON-switch CARs, which can be regulated with a clinically applied drug, and AND-gate CARs specifically recognizing combinations of two antigens. Thus, we expect that AvidCARs will be a highly valuable platform for the development of controllable CAR therapies with improved tumor specificity.
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MESH Headings
- Animals
- Antigens, Neoplasm/immunology
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- Cells, Cultured
- Cytokines/immunology
- Cytokines/metabolism
- Cytotoxicity, Immunologic/immunology
- Humans
- Immunotherapy, Adoptive/methods
- Lymphocyte Activation/immunology
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Neoplasms/immunology
- Neoplasms/pathology
- Neoplasms/therapy
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
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Affiliation(s)
- Benjamin Salzer
- St. Anna Children's Cancer Research Institute (CCRI), 1090, Vienna, Austria
- Christian Doppler Laboratory for Next Generation CAR T Cells, 1090, Vienna, Austria
| | | | - Charlotte U Zajc
- St. Anna Children's Cancer Research Institute (CCRI), 1090, Vienna, Austria
- Christian Doppler Laboratory for Next Generation CAR T Cells, 1090, Vienna, Austria
| | - Timo Peters
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, 1090, Vienna, Austria
| | - Michael A Schoeber
- St. Anna Children's Cancer Research Institute (CCRI), 1090, Vienna, Austria
| | - Boris Kovacic
- St. Anna Children's Cancer Research Institute (CCRI), 1090, Vienna, Austria
| | - Michelle C Buri
- St. Anna Children's Cancer Research Institute (CCRI), 1090, Vienna, Austria
| | - Elisabeth Lobner
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190, Vienna, Austria
| | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Johannes B Huppa
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, 1090, Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, 1190, Vienna, Austria
| | - Eva M Putz
- St. Anna Children's Cancer Research Institute (CCRI), 1090, Vienna, Austria
| | - Wolfgang Holter
- St. Anna Children's Cancer Research Institute (CCRI), 1090, Vienna, Austria
- Department of Pediatrics, St. Anna Kinderspital, Medical University of Vienna, 1090, Vienna, Austria
| | - Michael W Traxlmayr
- Christian Doppler Laboratory for Next Generation CAR T Cells, 1090, Vienna, Austria.
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, 1190, Vienna, Austria.
| | - Manfred Lehner
- St. Anna Children's Cancer Research Institute (CCRI), 1090, Vienna, Austria.
- Christian Doppler Laboratory for Next Generation CAR T Cells, 1090, Vienna, Austria.
- Department of Pediatrics, St. Anna Kinderspital, Medical University of Vienna, 1090, Vienna, Austria.
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