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Mhanna V, Barennes P, Vantomme H, Fourcade G, Coatnoan N, Six A, Klatzmann D, Mariotti-Ferrandiz E. Enhancing comparative T cell receptor repertoire analysis in small biological samples through pooling homologous cell samples from multiple mice. CELL REPORTS METHODS 2024; 4:100753. [PMID: 38614088 PMCID: PMC11045977 DOI: 10.1016/j.crmeth.2024.100753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/28/2024] [Accepted: 03/19/2024] [Indexed: 04/15/2024]
Abstract
Accurate characterization and comparison of T cell receptor (TCR) repertoires from small biological samples present significant challenges. The main challenge is the low material input, which compromises the quality of bulk sequencing and hinders the recovery of sufficient TCR sequences for robust analyses. We aimed to address this limitation by implementing a strategic approach to pool homologous biological samples. Our findings demonstrate that such pooling indeed enhances the TCR repertoire coverage, particularly for cell subsets of constrained sizes, and enables accurate comparisons of TCR repertoires at different levels of complexity across T cell subsets with different sizes. This methodology holds promise for advancing our understanding of T cell repertoires in scenarios where sample size constraints are a prevailing concern.
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Affiliation(s)
- Vanessa Mhanna
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Pierre Barennes
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Hélène Vantomme
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Gwladys Fourcade
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France
| | - Nicolas Coatnoan
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Adrien Six
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France
| | - David Klatzmann
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Encarnita Mariotti-Ferrandiz
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France; Institut Universitaire de France, France.
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Boschert T, Kromer K, Lerner T, Lindner K, Haltenhof G, Tan CL, Jähne K, Poschke I, Bunse L, Eisele P, Grassl N, Mildenberger I, Sahm K, Platten M, Lindner JM, Green EW. H3K27M neoepitope vaccination in diffuse midline glioma induces B and T cell responses across diverse HLA loci of a recovered patient. SCIENCE ADVANCES 2024; 10:eadi9091. [PMID: 38306431 PMCID: PMC10836722 DOI: 10.1126/sciadv.adi9091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
H3K27M, a driver mutation with T and B cell neoepitope characteristics, defines an aggressive subtype of diffuse glioma with poor survival. We functionally dissect the immune response of one patient treated with an H3K27M peptide vaccine who subsequently entered complete remission. The vaccine robustly expanded class II human leukocyte antigen (HLA)-restricted peripheral H3K27M-specific T cells. Using functional assays, we characterized 34 clonally unique H3K27M-reactive T cell receptors and identified critical, conserved motifs in their complementarity-determining region 3 regions. Using detailed HLA mapping, we further demonstrate that diverse HLA-DQ and HLA-DR alleles present immunogenic H3K27M epitopes. Furthermore, we identified and profiled H3K27M-reactive B cell receptors from activated B cells in the cerebrospinal fluid. Our results uncover the breadth of the adaptive immune response against a shared clonal neoantigen across multiple HLA allelotypes and support the use of class II-restricted peptide vaccines to stimulate tumor-specific T and B cells harboring receptors with therapeutic potential.
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Affiliation(s)
- Tamara Boschert
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Helmholtz Institute for Translational Oncology (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany
| | - Kristina Kromer
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- BioMed X GmbH, Heidelberg, Germany
| | | | - Katharina Lindner
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Immune Monitoring Unit, DKFZ and National Center for Tumour Diseases (NCT), Heidelberg, Germany
| | - Gordon Haltenhof
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chin Leng Tan
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Kristine Jähne
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Isabel Poschke
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Immune Monitoring Unit, DKFZ and National Center for Tumour Diseases (NCT), Heidelberg, Germany
| | - Lukas Bunse
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, MCTN Heidelberg University, Mannheim, Germany
| | - Philipp Eisele
- Department of Neurology, Medical Faculty Mannheim, MCTN Heidelberg University, Mannheim, Germany
| | - Niklas Grassl
- Department of Neurology, Medical Faculty Mannheim, MCTN Heidelberg University, Mannheim, Germany
| | - Iris Mildenberger
- Department of Neurology, Medical Faculty Mannheim, MCTN Heidelberg University, Mannheim, Germany
| | - Katharina Sahm
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, MCTN Heidelberg University, Mannheim, Germany
| | - Michael Platten
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Helmholtz Institute for Translational Oncology (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany
- Immune Monitoring Unit, DKFZ and National Center for Tumour Diseases (NCT), Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, MCTN Heidelberg University, Mannheim, Germany
- DKFZ Hector Cancer Institute at the University Medical Center Mannheim, Mannheim Germany
| | | | - Edward W Green
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, MCTN Heidelberg University, Mannheim, Germany
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de Greef PC, Lanfermeijer J, Hendriks M, Cevirgel A, Vos M, Borghans JAM, van Baarle D, de Boer RJ. On the feasibility of using TCR sequencing to follow a vaccination response - lessons learned. Front Immunol 2023; 14:1210168. [PMID: 37520553 PMCID: PMC10374308 DOI: 10.3389/fimmu.2023.1210168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
T cells recognize pathogens by their highly specific T-cell receptor (TCR), which can bind small fragments of an antigen presented on the Major Histocompatibility Complex (MHC). Antigens that are provided through vaccination cause specific T cells to respond by expanding and forming specific memory to combat a future infection. Quantification of this T-cell response could improve vaccine monitoring or identify individuals with a reduced ability to respond to a vaccination. In this proof-of-concept study we use longitudinal sequencing of the TCRβ repertoire to quantify the response in the CD4+ memory T-cell pool upon pneumococcal conjugate vaccination. This comes with several challenges owing to the enormous size and diversity of the T-cell pool, the limited frequency of vaccine-specific TCRs in the total repertoire, and the variation in sample size and quality. We defined quantitative requirements to classify T-cell expansions and identified critical parameters that aid in reliable analysis of the data. In the context of pneumococcal conjugate vaccination, we were able to detect robust T-cell expansions in a minority of the donors, which suggests that the T-cell response against the conjugate in the pneumococcal vaccine is small and/or very broad. These results indicate that there is still a long way to go before TCR sequencing can be reliably used as a personal biomarker for vaccine-induced protection. Nevertheless, this study highlights the importance of having multiple samples containing sufficient T-cell numbers, which will support future studies that characterize T-cell responses using longitudinal TCR sequencing.
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Affiliation(s)
- Peter C. de Greef
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Josien Lanfermeijer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Marion Hendriks
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Alper Cevirgel
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Martijn Vos
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - José A. M. Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Debbie van Baarle
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Rob J. de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
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