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Weisbrod L, Capriotti L, Hofmann M, Spieler V, Dersch H, Voedisch B, Schmidt P, Knake S. FASTMAP-a flexible and scalable immunopeptidomics pipeline for HLA- and antigen-specific T-cell epitope mapping based on artificial antigen-presenting cells. Front Immunol 2024; 15:1386160. [PMID: 38779658 PMCID: PMC11109385 DOI: 10.3389/fimmu.2024.1386160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
The study of peptide repertoires presented by major histocompatibility complex (MHC) molecules and the identification of potential T-cell epitopes contribute to a multitude of immunopeptidome-based treatment approaches. Epitope mapping is essential for the development of promising epitope-based approaches in vaccination as well as for innovative therapeutics for autoimmune diseases, infectious diseases, and cancer. It also plays a critical role in the immunogenicity assessment of protein therapeutics with regard to safety and efficacy concerns. The main challenge emerges from the highly polymorphic nature of the human leukocyte antigen (HLA) molecules leading to the requirement of a peptide mapping strategy for a single HLA allele. As many autoimmune diseases are linked to at least one specific antigen, we established FASTMAP, an innovative strategy to transiently co-transfect a single HLA allele combined with a disease-specific antigen into a human cell line. This approach allows the specific identification of HLA-bound peptides using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Using FASTMAP, we found a comparable spectrum of endogenous peptides presented by the most frequently expressed HLA alleles in the world's population compared to what has been described in literature. To ensure a reliable peptide mapping workflow, we combined the HLA alleles with well-known human model antigens like coagulation factor VIII, acetylcholine receptor subunit alpha, protein structures of the SARS-CoV-2 virus, and myelin basic protein. Using these model antigens, we have been able to identify a broad range of peptides that are in line with already published and in silico predicted T-cell epitopes of the specific HLA/model antigen combination. The transient co-expression of a single affinity-tagged MHC molecule combined with a disease-specific antigen in a human cell line in our FASTMAP pipeline provides the opportunity to identify potential T-cell epitopes/endogenously processed MHC-bound peptides in a very cost-effective, fast, and customizable system with high-throughput potential.
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Affiliation(s)
- Luisa Weisbrod
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Luigi Capriotti
- Analytical Biochemistry, Research and Development, CSL Behring AG, Bern, Switzerland
| | - Marco Hofmann
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Valerie Spieler
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Herbert Dersch
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Bernd Voedisch
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Peter Schmidt
- Protein Biochemistry, Bio21 Institute, CSL Limited, Parkville, VIC, Australia
| | - Susanne Knake
- Department of Neurology, Epilepsy Center Hessen, Philipps University Marburg, Marburg, Germany
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Porcheddu V, Lhomme G, Giraudet R, Correia E, Maillère B. The self-reactive FVIII T cell repertoire in healthy individuals relies on a short set of epitopes and public clonotypes. Front Immunol 2024; 15:1345195. [PMID: 38510258 PMCID: PMC10951066 DOI: 10.3389/fimmu.2024.1345195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/31/2024] [Indexed: 03/22/2024] Open
Abstract
Non-mutated FVIII-specific CD4 T cell epitopes have been recently found to contribute to the development of inhibitors in patients with hemophilia A (HA), while auto-reactive CD4 T cells specific to FVIII circulate in the blood of healthy individuals at a frequency close to the foreign protein ovalbumin. Thus, although FVIII is a self-protein, the central tolerance raised against FVIII appears to be low. In this study, we conducted a comprehensive analysis of the FVIII CD4 T cell repertoire in 29 healthy donors. Sequencing of the CDR3β TCR region from isolated FVIII-specific CD4 T cells revealed a limited usage and pairing of TRBV and TRBJ genes as well as a mostly hydrophobic composition of the CDR3β region according to their auto-reactivity. The FVIII repertoire is dominated by a few clonotypes, with only 13 clonotypes accounting for half of the FVIII response. Through a large-scale epitope mapping of the full-length FVIII sequence, we identified 18 immunodominant epitopes located in the A1, A3, C1, and C2 domains and covering half of the T cell response. These epitopes exhibited a broad specificity for HLA-DR or DP molecules or both. T cell priming with this reduced set of peptides revealed that highly expanded clonotypes specific to these epitopes were responsible individually for up to 32% of the total FVIII repertoire. These FVIII T cell epitopes and clonotypes were shared among HLA-unrelated donors tested and previously reported HA patients. Our study highlights the role of the auto-reactive T cell response against FVIII in HA and its similarity to the response observed in healthy individuals. Thus, it provides valuable insights for the development of new tolerance induction and deimmunization strategies.
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Affiliation(s)
- Valeria Porcheddu
- Université de Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut national de recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Département Médicaments et Technologies pour la Santé, Service d’Ingénierie Moléculaire pour la Santé (SIMoS), Gif-sur-Yvette, France
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Siegel M, Steiner G, Franssen LC, Carratu F, Herron J, Hartman K, Looney CM, Ducret A, Bray-French K, Rohr O, Hickling TP, Smith N, Marban-Doran C. Validation of a Dendritic Cell and CD4+ T Cell Restimulation Assay Contributing to the Immunogenicity Risk Evaluation of Biotherapeutics. Pharmaceutics 2022; 14:pharmaceutics14122672. [PMID: 36559166 PMCID: PMC9781343 DOI: 10.3390/pharmaceutics14122672] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
Immunogenicity, defined as the ability to provoke an immune response, can be either wanted (i.e., vaccines) or unwanted. The latter refers to an immune response to protein or peptide therapeutics, characterized by the production of anti-drug antibodies, which may affect the efficacy and/or the safety profiles of these drugs. Consequently, evaluation of the risk of immunogenicity early in the development of biotherapeutics is of critical importance for defining their efficacy and safety profiles. Here, we describe and validate a fit-for-purpose FluoroSpot-based in vitro assay for the evaluation of drug-specific T cell responses. A panel of 24 biotherapeutics with a wide range of clinical anti-drug antibody response rates were tested in this assay. We demonstrated that using suitable cutoffs and donor cohort sizes, this assay could identify most of the compounds with high clinical immunogenicity rates (71% and 78% for sensitivity and specificity, respectively) while we characterized the main sources of assay variability. Overall, these data indicate that the dendritic cell and CD4+ T cell restimulation assay published herein could be a valuable tool to assess the risk of drug-specific T cell responses and contribute to the selection of clinical candidates in early development.
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Affiliation(s)
- Michel Siegel
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Guido Steiner
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Linnea C. Franssen
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Francesca Carratu
- Lonza Biologics, Chesterford Research Park, Saffron Walden CB10 1XL, UK
| | - James Herron
- Lonza Biologics, Chesterford Research Park, Saffron Walden CB10 1XL, UK
| | - Katharina Hartman
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Cary M. Looney
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Axel Ducret
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Katharine Bray-French
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Olivier Rohr
- UR 7292, IUT Louis Pasteur, Université de Strasbourg, 67300 Schiltigheim, France
| | - Timothy P. Hickling
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Noel Smith
- Lonza Biologics, Chesterford Research Park, Saffron Walden CB10 1XL, UK
| | - Céline Marban-Doran
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, 4070 Basel, Switzerland
- Correspondence:
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Ducret A, Ackaert C, Bessa J, Bunce C, Hickling T, Jawa V, Kroenke MA, Lamberth K, Manin A, Penny HL, Smith N, Terszowski G, Tourdot S, Spindeldreher S. Assay format diversity in pre-clinical immunogenicity risk assessment: Toward a possible harmonization of antigenicity assays. MAbs 2021; 14:1993522. [PMID: 34923896 PMCID: PMC8726688 DOI: 10.1080/19420862.2021.1993522] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
A major impediment to successful use of therapeutic protein drugs is their ability to induce anti-drug antibodies (ADA) that can alter treatment efficacy and safety in a significant number of patients. To this aim, in silico, in vitro, and in vivo tools have been developed to assess sequence and other liabilities contributing to ADA development at different stages of the immune response. However, variability exists between similar assays developed by different investigators due to the complexity of assays, a degree of uncertainty about the underlying science, and their intended use. The impact of protocol variations on the outcome of the assays, i.e., on the immunogenicity risk assigned to a given drug candidate, cannot always be precisely assessed. Here, the Non-Clinical Immunogenicity Risk Assessment working group of the European Immunogenicity Platform (EIP) reviews currently used assays and protocols and discusses feasibility and next steps toward harmonization and standardization.
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Affiliation(s)
- Axel Ducret
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, Basel, Switzerland
| | - Chloé Ackaert
- ImmunXperts SA (A Nexelis Group Company), Gosselies, Belgium
| | - Juliana Bessa
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, Basel, Switzerland
| | | | - Timothy Hickling
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, Basel, Switzerland
| | - Vibha Jawa
- Biotherapeutics and Bioanalysis Non-Clinical Development, Bristol Myers Squibb, Princeton, NJ, USA
| | - Mark A Kroenke
- Clinical Immunology-Translational Medicine, Amgen Inc, Thousand Oaks, CA, USA
| | - Kasper Lamberth
- Analysis & Characterisation, Global Research Technologies, Novo Nordisk A/S, Måløv, Denmark
| | - Anaïs Manin
- Abzena, Babraham Research Campus, Cambridge, UK
| | - Hweixian L Penny
- Clinical Immunology-Translational Medicine, Amgen Inc, Thousand Oaks, CA, USA
| | - Noel Smith
- Lonza Biologics, Chesterford Research Park, Saffron Walden, UK
| | - Grzegorz Terszowski
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
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