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Marrer-Berger E, Nicastri A, Augustin A, Kramar V, Liao H, Hanisch LJ, Carpy A, Weinzierl T, Durr E, Schaub N, Nudischer R, Ortiz-Franyuti D, Breous-Nystrom E, Stucki J, Hobi N, Raggi G, Cabon L, Lezan E, Umaña P, Woodhouse I, Bujotzek A, Klein C, Ternette N. The physiological interactome of TCR-like antibody therapeutics in human tissues. Nat Commun 2024; 15:3271. [PMID: 38627373 PMCID: PMC11021511 DOI: 10.1038/s41467-024-47062-5] [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: 07/05/2022] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Selective binding of TCR-like antibodies that target a single tumour-specific peptide antigen presented by human leukocyte antigens (HLA) is the absolute prerequisite for their therapeutic suitability and patient safety. To date, selectivity assessment has been limited to peptide library screening and predictive modeling. We developed an experimental platform to de novo identify interactomes of TCR-like antibodies directly in human tissues using mass spectrometry. As proof of concept, we confirm the target epitope of a MAGE-A4-specific TCR-like antibody. We further determine cross-reactive peptide sequences for ESK1, a TCR-like antibody with known off-target activity, in human liver tissue. We confirm off-target-induced T cell activation and ESK1-mediated liver spheroid killing. Off-target sequences feature an amino acid motif that allows a structural groove-coordination mimicking that of the target peptide, therefore allowing the interaction with the engager molecule. We conclude that our strategy offers an accurate, scalable route for evaluating the non-clinical safety profile of TCR-like antibody therapeutics prior to first-in-human clinical application.
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Affiliation(s)
- Estelle Marrer-Berger
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Annalisa Nicastri
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK
| | - Angelique Augustin
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Vesna Kramar
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland
| | - Hanqing Liao
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK
| | | | - Alejandro Carpy
- Roche Pharma Research & Early Development, Roche Innovation Center Munich, 82377, Penzberg, Germany
| | - Tina Weinzierl
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland
| | - Evelyne Durr
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Nathalie Schaub
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Ramona Nudischer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Daniela Ortiz-Franyuti
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Ekaterina Breous-Nystrom
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Janick Stucki
- Alveolix AG, Swiss Organs-on-Chip Innovation, 3010, Bern, Switzerland
| | - Nina Hobi
- Alveolix AG, Swiss Organs-on-Chip Innovation, 3010, Bern, Switzerland
| | - Giulia Raggi
- Alveolix AG, Swiss Organs-on-Chip Innovation, 3010, Bern, Switzerland
| | - Lauriane Cabon
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Emmanuelle Lezan
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Pablo Umaña
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland
| | - Isaac Woodhouse
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK
| | - Alexander Bujotzek
- Roche Pharma Research & Early Development, Roche Innovation Center Munich, 82377, Penzberg, Germany
| | - Christian Klein
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland.
| | - Nicola Ternette
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK.
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK.
- Department of Pharmaceutical Sciences, University of Utrecht, 3584, CH, Utrecht, The Netherlands.
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Nolle A, van Dijken I, Waelti CM, Calini D, Bryois J, Lezan E, Golling S, Augustin A, Foo L, Hoozemans JJM. Enrichment of Glial Cells From Human Post-mortem Tissue for Transcriptome and Proteome Analysis Using Immunopanning. Front Cell Neurosci 2021; 15:772011. [PMID: 34966261 PMCID: PMC8711556 DOI: 10.3389/fncel.2021.772011] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
Glia cells have a crucial role in the central nervous system and are involved in the majority of neurological diseases. While glia isolation techniques are well established for rodent brain, only recent advances in isolating glial cells from human brain enabled analyses of human-specific glial-cell profiles. Immunopanning that is the prospective purification of cells using cell type-specific antibodies, has been successfully established for isolating glial cells from human fetal brain or from tissue obtained during brain surgeries. Here, we describe an immunopanning protocol to acutely isolate glial cells from post-mortem human brain tissue for e.g. transcriptome and proteome analyses. We enriched for microglia, oligodendrocytes and astrocytes from cortical gray matter tissue from three donors. For each enrichment, we assessed the presence of known glia-specific markers at the RNA and protein levels. In this study we show that immunopanning can be employed for acute isolation of glial cells from human post-mortem brain, which allows characterization of glial phenotypes depending on age, disease and brain regions.
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Affiliation(s)
- Anna Nolle
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Irene van Dijken
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Ciril M Waelti
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland
| | - Daniela Calini
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland
| | - Julien Bryois
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland
| | - Emmanuelle Lezan
- Pharmaceutical Sciences, Biomarkers, Bioinformatics and Omics and Pathology (MT, JL, AA), Roche Innovation Center Basel, Basel, Switzerland
| | - Sabrina Golling
- Pharmaceutical Sciences, Biomarkers, Bioinformatics and Omics and Pathology (MT, JL, AA), Roche Innovation Center Basel, Basel, Switzerland
| | - Angelique Augustin
- Pharmaceutical Sciences, Biomarkers, Bioinformatics and Omics and Pathology (MT, JL, AA), Roche Innovation Center Basel, Basel, Switzerland
| | - Lynette Foo
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland
| | - Jeroen J M Hoozemans
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
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Personnic N, Striednig B, Lezan E, Manske C, Welin A, Schmidt A, Hilbi H. Quorum sensing modulates the formation of virulent Legionella persisters within infected cells. Nat Commun 2019; 10:5216. [PMID: 31740681 PMCID: PMC6861284 DOI: 10.1038/s41467-019-13021-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 10/14/2019] [Indexed: 12/21/2022] Open
Abstract
The facultative intracellular bacterium Legionella pneumophila replicates in environmental amoebae and in lung macrophages, and causes Legionnaires' disease. Here we show that L. pneumophila reversibly forms replicating and nonreplicating subpopulations of similar size within amoebae. The nonreplicating bacteria are viable and metabolically active, display increased antibiotic tolerance and a distinct proteome, and show high virulence as well as the capacity to form a degradation-resistant compartment. Upon infection of naïve or interferon-γ-activated macrophages, the nonreplicating subpopulation comprises ca. 10% or 50%, respectively, of the total intracellular bacteria; hence, the nonreplicating subpopulation is of similar size in amoebae and activated macrophages. The numbers of nonreplicating bacteria within amoebae are reduced in the absence of the autoinducer synthase LqsA or other components of the Lqs quorum-sensing system. Our results indicate that virulent, antibiotic-tolerant subpopulations of L. pneumophila are formed during infection of evolutionarily distant phagocytes, in a process controlled by the Lqs system.
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Affiliation(s)
- Nicolas Personnic
- Institute for Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland.
| | - Bianca Striednig
- Institute for Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland
| | - Emmanuelle Lezan
- Proteomics Core Facility, Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Christian Manske
- Max von Pettenkofer Institute, Ludwig-Maximilians University Munich, Pettenkoferstrasse 9a, 80336, Munich, Germany
| | - Amanda Welin
- Institute for Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Hubert Hilbi
- Institute for Medical Microbiology, University of Zürich, Gloriastrasse 30, 8006, Zürich, Switzerland
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