1
|
Kotikova AI, Blinova EA, Akleyev AV. Analysis of Vβ-Segment Diversity of T-cell Receptor in Techa Riverside Residents Chronically Exposed to Radiation in the Long-Term Period. DOKL BIOCHEM BIOPHYS 2025:10.1134/S1607672925700164. [PMID: 40353972 DOI: 10.1134/s1607672925700164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2025] [Revised: 02/28/2025] [Accepted: 02/28/2025] [Indexed: 05/14/2025]
Abstract
To study the repertoire of the T-cell receptor in chronically exposed persons in the long-term period. The study involved 48 people who were divided into two groups: a group of exposed persons (31 individuals with the mean accumulated dose to red bone marrow (RBM) of 981 ± 130 mGy) and a comparison group (17 individuals, the mean accumulated dose to RBM of 25.3 ± 5.91 mGy). The study groups did not differ significantly in age, gender, and ethnicity. The repertoire of Vβ-segments of the T-cell receptor of the peripheral blood T-lymphocytes of exposed persons was analyzed by flow cytometry method. 24 Vβ-segments of the T-cell receptor were studied. Statistical processing of the obtained data was carried out using the Wilcoxon signed-rank test, and a direct description of Vβ-segment repertoire of the T-cell receptor was performed using the Lorenz curve and the Gini-TCR index. The study revealed a statistically significant increase in the number of Vβ3 and Vβ5.2 T-cell receptor segments in exposed individuals relative to the comparison group (p = 0.03 and p = 0.003, respectively). It was also shown that the distribution of the Vβ-segments of the T-cell receptor was uneven in both study groups. However, there was no significant difference between the repertoires of the T-cell receptor of the studied groups by the Gini-TCR index (p = 0.14).
Collapse
Affiliation(s)
- A I Kotikova
- Urals Research Center for Radiation Medicine, Federal Medical-Biological Agency of the Russian Federation, Chelyabinsk, Russia.
| | - E A Blinova
- Urals Research Center for Radiation Medicine, Federal Medical-Biological Agency of the Russian Federation, Chelyabinsk, Russia
- Chelyabinsk State University, Chelyabinsk, Russia
| | - A V Akleyev
- Urals Research Center for Radiation Medicine, Federal Medical-Biological Agency of the Russian Federation, Chelyabinsk, Russia
- Chelyabinsk State University, Chelyabinsk, Russia
| |
Collapse
|
2
|
van de Sandt CE, McQuilten HA, Aban M, Nguyen THO, Valkenburg SA, Grant EJ, Sant S, Rossjohn J, Gras S, Crowe J, Kedzierska K. Gradual changes within long-lived influenza virus-specific CD8 + T cells are associated with the loss of public TCR clonotypes in older adults. EBioMedicine 2025; 115:105697. [PMID: 40250246 PMCID: PMC12036069 DOI: 10.1016/j.ebiom.2025.105697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Revised: 03/27/2025] [Accepted: 03/29/2025] [Indexed: 04/20/2025] Open
Abstract
BACKGROUND Susceptibility to life-threatening influenza increases with age, partly due to declining immunity. Frequency, phenotype and T-cell receptor (TCR) composition of influenza-specific CD8+ T-cells directed at the prominent A2/M158 influenza epitope change across the human lifespan. METHODS We investigated longevity and mechanisms underlying age-related changes in influenza-specific TCR repertoires by performing longitudinal analyses in young and older adults across 7-12 years within A2/M158+CD8+ T-cells using peptide-HLA tetramers directly ex vivo. Paired TCRαβ-chains were used to track clonotypes over time within individuals. FINDINGS Expanded public and private TCR clonotypes were long-lived but gradually declined over time. Loss of public clonotypes was initially compensated by expansions of clonotypes expressing public-associated features. Once these public-associated TCR clonotypes were abated in older adults, the void was filled by expansions of less similar private TCR clonotypes. Expanded older private TCR clonotypes also declined over time and were gradually replaced by other private TCR clonotypes with low similarity to public TCR clonotypes detected in adults. INTERPRETATION Despite our relatively small cohort, we provided conclusive evidence that CD8+ T-cells to a single HLA-A2-restricted influenza-epitope are long-lived. However, dynamic changes occur at the clonotypic level, which eventually result in loss of public clonotypes, indicating that T-cell-based influenza vaccines are likely more effective in adults than older adults. FUNDING This research was supported by the National Health and Medical Research Council (#1173871, #1159272), the Australian Research Council (#190102704), European Union's Horizon 2020 (#792532), the University of Melbourne. Funders had no role in design, analysis or reporting of the study.
Collapse
MESH Headings
- Humans
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Influenza, Human/immunology
- Influenza, Human/virology
- Aged
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/genetics
- Male
- Female
- Adult
- Middle Aged
- Epitopes, T-Lymphocyte/immunology
- Aged, 80 and over
- Young Adult
Collapse
Affiliation(s)
- Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Hayley A McQuilten
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Malet Aban
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Sophie A Valkenburg
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Emma J Grant
- Infection and Immunity Program, Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia; Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sneha Sant
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jamie Rossjohn
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Stephanie Gras
- Infection and Immunity Program, Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia; Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jane Crowe
- Deepdene Surgery, Deepdene, VIC 3103, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| |
Collapse
|
3
|
Kotikova AI, Blinova EA, Akleyev AV. Analysis of Vβ-Segment Diversity of T-Cell Receptor in Residents of the Techa Riverside Villages Chronically Exposed to Radiation in the Long-Term Period. DOKL BIOCHEM BIOPHYS 2025; 521:261-266. [PMID: 40216718 DOI: 10.1134/s1607672925700048] [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: 01/20/2025] [Revised: 01/29/2025] [Accepted: 01/29/2025] [Indexed: 05/16/2025]
Abstract
OBJECTIVE To study the repertoire of the T-cell receptor in persons chronically exposed to radiation in the long-term period. MATERIALS AND METHODS The study involved 48 people, who were divided into two groups: a group of exposed persons (31 individuals with the average accumulated dose to red bone marrow (RBM) of 981 ± 130 mGy) and a comparison group (17 individuals with the average accumulated dose to RBM of 25.3 ± 5.91 mGy). The study groups did not differ significantly in age, gender and ethnicity. The repertoire of Vβ-segments of the T-cell receptor of the peripheral blood T-lymphocytes of exposed persons was analyzed by flow cytometry method. 24 Vβ-segments of the T-cell receptor were studied. Statistical processing of the obtained data was carried out using the Wilcoxon signed-rank test, and a direct description of Vβ-segment repertoire of the T-cell receptor was performed using the Lorenz curve and the Gini-TCR index. RESULTS The study revealed a statistically significant increase in the number of Vβ3 and Vβ5.2 T-cell receptor segments in exposed individuals relative to the comparison group (p = 0.03 and p = 0.003, respectively). It was also shown that the distribution of the Vβ-segments of the T-cell receptor is uneven in both study groups. However, there was no significant difference between the repertoires of the T-cell receptor of the studied groups in the Gini-TCR index (p = 0.14).
Collapse
Affiliation(s)
- A I Kotikova
- Urals Research Center for Radiation Medicine, Federal Medical-Biological Agency of the Russian Federation, Chelyabinsk, Russia.
| | - E A Blinova
- Urals Research Center for Radiation Medicine, Federal Medical-Biological Agency of the Russian Federation, Chelyabinsk, Russia
- Chelyabinsk State University, Chelyabinsk, Russia
| | - A V Akleyev
- Urals Research Center for Radiation Medicine, Federal Medical-Biological Agency of the Russian Federation, Chelyabinsk, Russia
- Chelyabinsk State University, Chelyabinsk, Russia
| |
Collapse
|
4
|
Olofsson A, Humbert M, Rekha RS, Frankling MH, Lund-Johansen F, Bergman P, Björkhem-Bergman L, Karlsson AC. Adaptive immune responses against common viruses are sustained and functional in end-of-life patients. iScience 2025; 28:112082. [PMID: 40124502 PMCID: PMC11930376 DOI: 10.1016/j.isci.2025.112082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 11/22/2024] [Accepted: 02/18/2025] [Indexed: 03/25/2025] Open
Abstract
Viral infections occur with increased frequency in patients in palliative care, impacting their quality of life and increasing mortality rates. Still, the function of the immune system has never been thoroughly studied at the end of life. We investigated virus-specific humoral and cellular immune responses in elderly end-of-life patients (n = 38) and controls (n = 28). Virus-specific T cell responses were characterized using high-parameter flow cytometry, after stimulation with cytomegalovirus (CMV) and human coronavirus OC43 peptides. Although some virus-specific T cells from patients exhibited elevated expression of costimulatory and coinhibitory molecules, their functional profile remained largely intact compared to controls. The expression of the cytotoxic markers Granzyme B, CD107a, and 2B4 on CMV-specific T cells correlated closely with survival time. Significantly, our data demonstrate that both humoral and cellular immunity remain responsive and functional against common viruses in end-of-life patients.
Collapse
Affiliation(s)
- Anna Olofsson
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marion Humbert
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Rokeya S. Rekha
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Helde Frankling
- Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Fridtjof Lund-Johansen
- Institute of Clinical Medicine, University of Oslo, Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Immunology, Oslo University Hospital, ImmunoLingo Convergence Center, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Peter Bergman
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Linda Björkhem-Bergman
- Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Research and Development Unit/Palliative Care, Stockholms Sjukhem, Mariebergsgatan 22, Stockholm, Sweden
| | - Annika C. Karlsson
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
5
|
Luo S, Notaro A, Lin L. ATLAS-seq: a microfluidic single-cell TCR screen for antigen-reactive TCRs. Nat Commun 2025; 16:216. [PMID: 39746936 PMCID: PMC11696065 DOI: 10.1038/s41467-024-54675-3] [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: 09/26/2023] [Accepted: 11/18/2024] [Indexed: 01/04/2025] Open
Abstract
Discovering antigen-reactive T cell receptors (TCRs) is central to developing effective engineered T cell immunotherapies. However, the conventional technologies for isolating antigen-reactive TCRs (i.e., major histocompatibility complex (MHC) multimer staining) focus on high-affinity interactions between the TCR and MHC-antigen complex, and may fail to identify TCRs with high efficacy for activating T cells. Here, we develop a microfluidic single-cell screening method for antigen-reactive T cells named ATLAS-seq (Aptamer-based T Lymphocyte Activity Screening and SEQuencing). This technology isolates and characterizes activated T cells via an aptamer-based fluorescent molecular sensor, which monitors the cytotoxic cytokine IFNγ secretion from single T cells upon antigen stimulation, followed by single-cell RNA and single-cell TCR sequencing. We use ATLAS-seq to screen TCRs reactive to cytomegalovirus (CMV) or prostate specific antigen (PSA) from peripheral blood mononuclear cells (PBMCs). ATLAS-seq identifies distinct TCR clonotype populations with higher T cell activation levels compared to TCRs recovered by MHC multimer staining. Select TCR clonotypes from ATLAS-seq are more efficient in target cell killing than those from MHC multimer staining. Collectively, ATLAS-seq provides an efficient and broadly applicable technology to screen antigen-reactive TCRs for engineered T cell immunotherapy.
Collapse
Affiliation(s)
- Siwei Luo
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Amber Notaro
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lan Lin
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
6
|
Mahdy AKH, Lokes E, Schöpfel V, Kriukova V, Britanova OV, Steiert TA, Franke A, ElAbd H. Bulk T cell repertoire sequencing (TCR-Seq) is a powerful technology for understanding inflammation-mediated diseases. J Autoimmun 2024; 149:103337. [PMID: 39571301 DOI: 10.1016/j.jaut.2024.103337] [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: 04/19/2024] [Revised: 10/12/2024] [Accepted: 11/09/2024] [Indexed: 12/15/2024]
Abstract
Multiple alterations in the T cell repertoire were identified in many chronic inflammatory diseases such as inflammatory bowel disease, multiple sclerosis, and rheumatoid arthritis, suggesting that T cells might, directly or indirectly, be implicated in these pathologies. This has sparked a deep interest in characterizing disease-associated T cell clonotypes as well as in identifying and quantifying their contribution to the pathophysiology of different autoimmune and inflammation-mediated diseases. Bulk T cell repertoire sequencing (TCR-Seq) has emerged as a powerful method to profile the T cell repertoire of a sample in a high throughput fashion. Given the increasing utilization of TCR-Seq, we aimed here to provide a comprehensive, up-to-date review of the method, its extensions, and its ability to investigate chronic and autoimmune diseases. Specifically, we started by introducing the immunological basis of TCR repertoire generation and features, followed by discussing different experimental approach to perform TCR-Seq, then we describe different methods and frameworks for analyzing the generated datasets. Subsequently, different experimental techniques for investigating the antigenicity of T cell clonotypes are described. Lastly, we discuss recent studies that utilized TCR-Seq to understand different inflammation-mediated diseases, discuss fallbacks of the technology and potential future directions to overcome current limitations.
Collapse
Affiliation(s)
- Aya K H Mahdy
- Institute of Clinical Molecular Biology, Kiel University & University Medical Centre Schleswig-Holstein, Kiel, 24105, Germany
| | - Evgeniya Lokes
- Institute of Clinical Molecular Biology, Kiel University & University Medical Centre Schleswig-Holstein, Kiel, 24105, Germany
| | - Valentina Schöpfel
- Institute of Clinical Molecular Biology, Kiel University & University Medical Centre Schleswig-Holstein, Kiel, 24105, Germany
| | - Valeriia Kriukova
- Institute of Clinical Molecular Biology, Kiel University & University Medical Centre Schleswig-Holstein, Kiel, 24105, Germany
| | - Olga V Britanova
- Institute of Clinical Molecular Biology, Kiel University & University Medical Centre Schleswig-Holstein, Kiel, 24105, Germany
| | - Tim A Steiert
- Institute of Clinical Molecular Biology, Kiel University & University Medical Centre Schleswig-Holstein, Kiel, 24105, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University & University Medical Centre Schleswig-Holstein, Kiel, 24105, Germany.
| | - Hesham ElAbd
- Institute of Clinical Molecular Biology, Kiel University & University Medical Centre Schleswig-Holstein, Kiel, 24105, Germany.
| |
Collapse
|
7
|
Komlodi-Pasztor E, Escarra-Senmarti M, Bazer DA, Bhatnagar A, Perez Heydrich CA, Messmer M, Ambinder RF, Gladstone DE, Clayton L, Goodrich A, Schoch L, Wagner-Johnston N, VandenBussche CJ, Huang P, Holdhoff M, Rosario M. The immune response to Covid-19 mRNA vaccination among Lymphoma patients receiving anti-CD20 treatment. Front Immunol 2024; 15:1433442. [PMID: 39295862 PMCID: PMC11408186 DOI: 10.3389/fimmu.2024.1433442] [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: 05/15/2024] [Accepted: 07/15/2024] [Indexed: 09/21/2024] Open
Abstract
The monoclonal antibody rituximab improves clinical outcome in the treatment of CD20-positive lymphomatous neoplasms, and it is an established drug for treatment of these cancers. Successful mRNA COVID-19 (SARS-CoV-2) vaccination is extremely important for lymphoma patients because they tend to be elderly with comorbidities which leaves them at increased risk of poor outcomes once infected by Coronavirus. Anti-CD20 therapies such as rituximab, deplete B-cell populations and can affect vaccine efficacy. Therefore, a knowledge of the effect of COVID-19 vaccination in this group is critical. We followed a cohort of 28 patients with CD20-positive lymphomatous malignancies treated with rituximab that started prior to their course of COVID-19 vaccination, including boosters. We assayed for vaccine "take" in the humoral (IgG and IgA) and cellular compartment. Here, we show that short-term and long-term development of IgG and IgA antibodies directed toward COVID-19 spike protein are reduced in these patients compared to healthy controls. Conversely, the robustness and breath of underlying T-cell response is equal to healthy controls. This response is not limited to specific parts of the spike protein but spans the spike region, including response to the conserved Receptor Binding Domain (RBD). Our data informs on rational vaccine design and bodes well for future vaccination strategies that require strong induction of T-cell responses in these patients.
Collapse
Affiliation(s)
- Edina Komlodi-Pasztor
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Neurology, MedStar Georgetown University Hospital, Washington, DC, United States
| | - Marta Escarra-Senmarti
- Department of Pathology, Division of Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Danielle A Bazer
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Aastha Bhatnagar
- Department of Neurology, MedStar Georgetown University Hospital, Washington, DC, United States
| | - Carlos A Perez Heydrich
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Marcus Messmer
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Richard F Ambinder
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Douglas E Gladstone
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Northwell Health Cancer Institute, New Hyde Park, NY, United States
| | - Laura Clayton
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Amy Goodrich
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Laura Schoch
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Nina Wagner-Johnston
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Christopher J VandenBussche
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Pathology, Division of Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Peng Huang
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Matthias Holdhoff
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Maximillian Rosario
- Department of Pathology, Division of Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| |
Collapse
|
8
|
Chatzileontiadou DSM, Lobos CA, Robson H, Almedia CA, Szeto C, Castley A, D'Orsogna LJ, Gras S. Public T cell clonotypes are selected in HLA-B ∗57:01 +/HIV + patients independently of the viral load. Cell Rep 2024; 43:114555. [PMID: 39083376 DOI: 10.1016/j.celrep.2024.114555] [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: 05/02/2024] [Revised: 06/10/2024] [Accepted: 07/12/2024] [Indexed: 08/02/2024] Open
Abstract
HIV controllers can control viral replication and remain healthy, but the mechanism behind this control is unknown. Despite human leukocyte antigen (HLA) diversity in the population, almost 50% of HIV controllers express the HLA-B∗57:01 molecule, which presents, among others, the Gag-derived epitope TW10. Given TW10's presentation in early infection, TW10-specific T cells could participate in the control of HIV. Here, we study the strength and functionality of TW10-specific T cells from HLA-B∗57:01+/HIV+ controller and non-controller individuals. We determine the TW10-specific T cell receptor (TCR) repertoire, revealing a bias in TCR gene usage with the presence of a public TCR. We determine that the T cell response is polyfunctional regardless of the viral load, despite the low affinity of TW10-specific TCRs. We solve the crystal structure of HLA-B∗57:01-TW10 in complex with a TCR, providing the basis of recognition that underpins the strong TRBV5 bias observed in TW10-specific clonotypes.
Collapse
Affiliation(s)
- Demetra S M Chatzileontiadou
- Immunity and Infection Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, VIC 3086, Australia; Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Christian A Lobos
- Immunity and Infection Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, VIC 3086, Australia; Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Hayden Robson
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Coral-Ann Almedia
- School of Medicine, University of Western Australia, Nedlands, WA 6009, Australia
| | - Christopher Szeto
- Immunity and Infection Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, VIC 3086, Australia; Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
| | - Alison Castley
- Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Murdoch, WA 6150, Australia
| | - Lloyd J D'Orsogna
- School of Medicine, University of Western Australia, Nedlands, WA 6009, Australia; Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Murdoch, WA 6150, Australia
| | - Stephanie Gras
- Immunity and Infection Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, VIC 3086, Australia; Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| |
Collapse
|
9
|
Cai C, Keoshkerian E, Wing K, Samir J, Effenberger M, Schober K, Bull RA, Lloyd AR, Busch DH, Luciani F. Discovery of a monoclonal, high-affinity CD8 + T-cell clone following natural hepatitis C virus infection. Immunol Cell Biol 2024; 102:630-641. [PMID: 38855806 DOI: 10.1111/imcb.12791] [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: 02/26/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/11/2024]
Abstract
CD8+ T cells recognizing their cognate antigen are typically recruited as a polyclonal population consisting of multiple clonotypes with varying T-cell receptor (TCR) affinity to the target peptide-major histocompatibility complex (pMHC) complex. Advances in single-cell sequencing have increased accessibility toward identifying TCRs with matched antigens. Here we present the discovery of a monoclonal CD8+ T-cell population with specificity for a hepatitis C virus (HCV)-derived human leukocyte antigen (HLA) class I epitope (HLA-B*07:02 GPRLGVRAT) which was isolated directly ex vivo from an individual with an episode of acutely resolved HCV infection. This population was absent before infection and underwent expansion and stable maintenance for at least 2 years after infection as measured by HLA-multimer staining. Furthermore, the monoclonal clonotype was characterized by an unusually long dissociation time (half-life = 794 s and koff = 5.73 × 10-4) for its target antigen when compared with previously published results. A comparison with related populations of HCV-specific populations derived from the same individual and a second individual suggested that high-affinity TCR-pMHC interactions may be inherent to epitope identity and shape the phenotype of responses which has implications for rational TCR selection and design in the age of personalized immunotherapies.
Collapse
Affiliation(s)
- Curtis Cai
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Elizabeth Keoshkerian
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Kristof Wing
- School of Medicine and Health, Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Jerome Samir
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Manuel Effenberger
- School of Medicine and Health, Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Kilian Schober
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rowena A Bull
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Andrew R Lloyd
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Dirk H Busch
- School of Medicine and Health, Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
- German Center for Infection Research (Deutsches Zentrum für Infektionsforschung), Partner Site Munich, Munich, Germany
| | - Fabio Luciani
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- Cellular Genomics Future Institute, UNSW Sydney, Sydney, NSW, Australia
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY, USA
| |
Collapse
|
10
|
Bodansky A, Mettelman RC, Sabatino JJ, Vazquez SE, Chou J, Novak T, Moffitt KL, Miller HS, Kung AF, Rackaityte E, Zamecnik CR, Rajan JV, Kortbawi H, Mandel-Brehm C, Mitchell A, Wang CY, Saxena A, Zorn K, Yu DJL, Pogorelyy MV, Awad W, Kirk AM, Asaki J, Pluvinage JV, Wilson MR, Zambrano LD, Campbell AP, Thomas PG, Randolph AG, Anderson MS, DeRisi JL. Molecular mimicry in multisystem inflammatory syndrome in children. Nature 2024; 632:622-629. [PMID: 39112696 PMCID: PMC11324515 DOI: 10.1038/s41586-024-07722-4] [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: 06/20/2023] [Accepted: 06/14/2024] [Indexed: 08/16/2024]
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a severe, post-infectious sequela of SARS-CoV-2 infection1,2, yet the pathophysiological mechanism connecting the infection to the broad inflammatory syndrome remains unknown. Here we leveraged a large set of samples from patients with MIS-C to identify a distinct set of host proteins targeted by patient autoantibodies including a particular autoreactive epitope within SNX8, a protein involved in regulating an antiviral pathway associated with MIS-C pathogenesis. In parallel, we also probed antibody responses from patients with MIS-C to the complete SARS-CoV-2 proteome and found enriched reactivity against a distinct domain of the SARS-CoV-2 nucleocapsid protein. The immunogenic regions of the viral nucleocapsid and host SNX8 proteins bear remarkable sequence similarity. Consequently, we found that many children with anti-SNX8 autoantibodies also have cross-reactive T cells engaging both the SNX8 and the SARS-CoV-2 nucleocapsid protein epitopes. Together, these findings suggest that patients with MIS-C develop a characteristic immune response to the SARS-CoV-2 nucleocapsid protein that is associated with cross-reactivity to the self-protein SNX8, demonstrating a mechanistic link between the infection and the inflammatory syndrome, with implications for better understanding a range of post-infectious autoinflammatory diseases.
Collapse
Affiliation(s)
- Aaron Bodansky
- Department of Pediatrics, Division of Critical Care, University of California San Francisco, San Francisco, CA, USA
| | - Robert C Mettelman
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Joseph J Sabatino
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Sara E Vazquez
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Janet Chou
- Division of Immunology, Department of Pediatrics, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Tanya Novak
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Anesthesia, Harvard Medical School, Boston, MA, USA
| | - Kristin L Moffitt
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatric, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Haleigh S Miller
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, CA, USA
| | - Andrew F Kung
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, CA, USA
| | - Elze Rackaityte
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Colin R Zamecnik
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Jayant V Rajan
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Hannah Kortbawi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Aditi Saxena
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - David J L Yu
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mikhail V Pogorelyy
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Walid Awad
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Allison M Kirk
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - James Asaki
- Biomedical Sciences Program, University of California San Francisco, San Francisco, CA, USA
| | - John V Pluvinage
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Laura D Zambrano
- COVID-19 Response Team and Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Angela P Campbell
- COVID-19 Response Team and Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Paul G Thomas
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adrienne G Randolph
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Anesthesia, Harvard Medical School, Boston, MA, USA
| | - Mark S Anderson
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Francisco, San Francisco, CA, USA.
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA.
| |
Collapse
|
11
|
Bryan E, Teague JE, Eligul S, Arkins WC, Moody DB, Clark RA, Van Rhijn I. Human Skin T Cells Express Conserved T-Cell Receptors that Cross-React with Staphylococcal Superantigens and CD1a. J Invest Dermatol 2024; 144:833-843.e3. [PMID: 37951348 DOI: 10.1016/j.jid.2023.09.284] [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: 03/29/2023] [Revised: 09/06/2023] [Accepted: 09/30/2023] [Indexed: 11/14/2023]
Abstract
Human Langerhans cells highly express CD1a antigen-presenting molecules. To understand the functions of CD1a in human skin, we used CD1a tetramers to capture T cells and determine their effector functions and TCR patterns. Skin T cells from all donors showed CD1a tetramer staining, which in three cases exceeded 10% of skin T cells. CD1a tetramer-positive T cells produced diverse cytokines, including IL-2, IL-4, IL-5, IL-9, IL-17, IL-22, and IFN-γ. Conserved TCRs often recognize nonpolymorphic antigen-presenting molecules, but no TCR motifs are known for CD1a. We detected highly conserved TCRs that used TRAV34 and TRBV28 variable genes, which is a known motif for recognition of staphylococcal enterotoxin B, a superantigen associated with atopic dermatitis. We found that these conserved TCRs did not respond to superantigen presented by CD1a, but instead showed a cross-reactive response with two targets: CD1a and staphylococcal enterotoxin B presented by classical major histocompatibility complex II. These studies identify a conserved human TCR motif for CD1a-reactive T cells. Furthermore, the demonstrated cross-reaction of T cells with two common skin-specific stimuli suggests a candidate mechanism by which CD1a and skin flora could synergize during natural immune response and in Staphylococcus-associated skin diseases.
Collapse
Affiliation(s)
- Elizabeth Bryan
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jessica E Teague
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sezin Eligul
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Wellington C Arkins
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - D Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rachael A Clark
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
| |
Collapse
|
12
|
Kirk AM, Crawford JC, Chou CH, Guy C, Pandey K, Kozlik T, Shah RK, Chung S, Nguyen P, Zhang X, Wang J, Bell M, Mettelman RC, Allen EK, Pogorelyy MV, Kim H, Minervina AA, Awad W, Bajracharya R, White T, Long D, Gordon B, Morrison M, Glazer ES, Murphy AJ, Jiang Y, Fitzpatrick EA, Yarchoan M, Sethupathy P, Croft NP, Purcell AW, Federico SM, Stewart E, Gottschalk S, Zamora AE, DeRenzo C, Strome SE, Thomas PG. DNAJB1-PRKACA fusion neoantigens elicit rare endogenous T cell responses that potentiate cell therapy for fibrolamellar carcinoma. Cell Rep Med 2024; 5:101469. [PMID: 38508137 PMCID: PMC10983114 DOI: 10.1016/j.xcrm.2024.101469] [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: 08/23/2023] [Revised: 11/29/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Fibrolamellar carcinoma (FLC) is a liver tumor with a high mortality burden and few treatment options. A promising therapeutic vulnerability in FLC is its driver mutation, a conserved DNAJB1-PRKACA gene fusion that could be an ideal target neoantigen for immunotherapy. In this study, we aim to define endogenous CD8 T cell responses to this fusion in FLC patients and evaluate fusion-specific T cell receptors (TCRs) for use in cellular immunotherapies. We observe that fusion-specific CD8 T cells are rare and that FLC patient TCR repertoires lack large clusters of related TCR sequences characteristic of potent antigen-specific responses, potentially explaining why endogenous immune responses are insufficient to clear FLC tumors. Nevertheless, we define two functional fusion-specific TCRs, one of which has strong anti-tumor activity in vivo. Together, our results provide insights into the fragmented nature of neoantigen-specific repertoires in humans and indicate routes for clinical development of successful immunotherapies for FLC.
Collapse
Affiliation(s)
- Allison M Kirk
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ching-Heng Chou
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cliff Guy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kirti Pandey
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Tanya Kozlik
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ravi K Shah
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shanzou Chung
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Phuong Nguyen
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaoyu Zhang
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jin Wang
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Matthew Bell
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hyunjin Kim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anastasia A Minervina
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Walid Awad
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Resha Bajracharya
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Toni White
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Donald Long
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Brittney Gordon
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michelle Morrison
- Center for Cancer Research, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Evan S Glazer
- Center for Cancer Research, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA; Department of Surgery, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Andrew J Murphy
- Department of Surgery, The University of Tennessee Health Science Center, Memphis, TN 38163, USA; Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yixing Jiang
- Department of Medical Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Elizabeth A Fitzpatrick
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Mark Yarchoan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Sara M Federico
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elizabeth Stewart
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anthony E Zamora
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Christopher DeRenzo
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Scott E Strome
- College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| |
Collapse
|
13
|
Voogd L, Drittij AM, Dingenouts CK, Franken KL, Unen VV, van Meijgaarden KE, Ruibal P, Hagedoorn RS, Leitner JA, Steinberger P, Heemskerk MH, Davis MM, Scriba TJ, Ottenhoff TH, Joosten SA. Mtb HLA-E-tetramer-sorted CD8 + T cells have a diverse TCR repertoire. iScience 2024; 27:109233. [PMID: 38439958 PMCID: PMC10909886 DOI: 10.1016/j.isci.2024.109233] [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: 10/18/2023] [Revised: 01/05/2024] [Accepted: 02/09/2024] [Indexed: 03/06/2024] Open
Abstract
HLA-E molecules can present self- and pathogen-derived peptides to both natural killer (NK) cells and T cells. T cells that recognize HLA-E peptides via their T cell receptor (TCR) are termed donor-unrestricted T cells due to restricted allelic variation of HLA-E. The composition and repertoire of HLA-E TCRs is not known so far. We performed TCR sequencing on CD8+ T cells from 21 individuals recognizing HLA-E tetramers (TMs) folded with two Mtb-HLA-E-restricted peptides. We sorted HLA-E Mtb TM+ and TM- CD8+ T cells directly ex vivo and performed bulk RNA-sequencing and single-cell TCR sequencing. The identified TCR repertoire was diverse and showed no conservation between and within individuals. TCRs selected from our single-cell TCR sequencing data could be activated upon HLA-E/peptide stimulation, although not robust, reflecting potentially weak interactions between HLA-E peptide complexes and TCRs. Thus, HLA-E-Mtb-specific T cells have a highly diverse TCR repertoire.
Collapse
Affiliation(s)
- Linda Voogd
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Anne M.H.F. Drittij
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Calinda K.E. Dingenouts
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Kees L.M.C. Franken
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Vincent van Unen
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Paula Ruibal
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Renate S. Hagedoorn
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Judith A. Leitner
- Centre for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Medical University of Vienna, Vienna, Austria
| | - Peter Steinberger
- Centre for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Mark M. Davis
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Palo Alto, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Tom H.M. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Simone A. Joosten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| |
Collapse
|
14
|
Dibble JJ, Ferneyhough B, Roddis M, Millington S, Fischer MD, Parkinson NJ, Ponting CP. Comparison of T-cell receptor diversity of people with myalgic encephalomyelitis versus controls. BMC Res Notes 2024; 17:17. [PMID: 38178251 PMCID: PMC10768444 DOI: 10.1186/s13104-023-06616-4] [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: 07/12/2023] [Accepted: 11/06/2023] [Indexed: 01/06/2024] Open
Abstract
OBJECTIVE Myalgic Encephalomyelitis (ME; sometimes referred to as Chronic Fatigue Syndrome) is a chronic disease without laboratory test, detailed aetiological understanding or effective therapy. Its symptoms are diverse, but it is distinguished from other fatiguing illnesses by the experience of post-exertional malaise, the worsening of symptoms even after minor physical or mental exertion. Its frequent onset after infection suggests autoimmune involvement or that it arises from abnormal T-cell activation. RESULTS To test this hypothesis, we sequenced the genomic loci of α/δ, β and γ T-cell receptors (TCR) from 40 human blood samples from each of four groups: severely affected people with ME; mildly or moderately affected people with ME; people diagnosed with Multiple Sclerosis, as disease controls; and, healthy controls. Seeking to automatically classify these individuals' samples by their TCR repertoires, we applied P-SVM, a machine learning method. However, despite working well on a simulated data set, this approach did not allow statistically significant partitioning of samples into the four subgroups. Our findings do not support the hypothesis that blood samples from people with ME frequently contain altered T-cell receptor diversity.
Collapse
Affiliation(s)
- Joshua J Dibble
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Ben Ferneyhough
- Systems Biology Laboratory UK, Abingdon, Oxfordshire, OX14 4SA, UK
| | - Matthew Roddis
- Systems Biology Laboratory UK, Abingdon, Oxfordshire, OX14 4SA, UK
| | - Sam Millington
- Systems Biology Laboratory UK, Abingdon, Oxfordshire, OX14 4SA, UK
| | | | - Nick J Parkinson
- Systems Biology Laboratory UK, Abingdon, Oxfordshire, OX14 4SA, UK.
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK.
| |
Collapse
|
15
|
Hsu J, Donahue RN, Katragadda M, Lowry J, Huang W, Srinivasan K, Guntas G, Tang J, Servattalab R, Moisan J, Tsai YT, Stoop A, Palakurthi S, Chopra R, Liu K, Wherry EJ, Su Z, Gulley JL, Bayliffe A, Schlom J. A T cell receptor β chain-directed antibody fusion molecule activates and expands subsets of T cells to promote antitumor activity. Sci Transl Med 2023; 15:eadi0258. [PMID: 38019931 PMCID: PMC11421222 DOI: 10.1126/scitranslmed.adi0258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023]
Abstract
Despite the success of programmed cell death-1 (PD-1) and PD-1 ligand (PD-L1) inhibitors in treating solid tumors, only a proportion of patients respond. Here, we describe a first-in-class bifunctional therapeutic molecule, STAR0602, that comprises an antibody targeting germline Vβ6 and Vβ10 T cell receptors (TCRs) fused to human interleukin-2 (IL-2) and simultaneously engages a nonclonal mode of TCR activation with costimulation to promote activation and expansion of αβ T cell subsets expressing distinct variable β (Vβ) TCR chains. In solution, STAR0602 binds IL-2 receptors in cis with Vβ6/Vβ10 TCRs on the same T cell, promoting expansion of human Vβ6 and Vβ10 CD4+ and CD8+ T cells that acquire an atypical central memory phenotype. Monotherapy with a mouse surrogate molecule induced durable tumor regression across six murine solid tumor models, including several refractory to anti-PD-1. Analysis of murine tumor-infiltrating lymphocyte (TIL) transcriptomes revealed that expanded Vβ T cells acquired a distinct effector memory phenotype with suppression of genes associated with T cell exhaustion and TCR signaling repression. Sequencing of TIL TCRs also revealed an increased T cell repertoire diversity within targeted Vβ T cell subsets, suggesting clonal revival of tumor T cell responses. These immunological and antitumor effects in mice were recapitulated in studies of STAR0602 in nonhuman primates and human ex vivo models, wherein STAR0602 boosted human antigen-specific T cell responses and killing of tumor organoids. Thus, STAR0602 represents a distinct class of T cell-activating molecules with the potential to deliver enhanced antitumor activity in checkpoint inhibitor-refractory settings.
Collapse
Affiliation(s)
| | - Renee N Donahue
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | | | - Wei Huang
- Marengo Therapeutics, Cambridge, MA 02139, USA
| | | | | | - Jian Tang
- Marengo Therapeutics, Cambridge, MA 02139, USA
| | | | | | - Yo-Ting Tsai
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | | | - Raj Chopra
- Marengo Therapeutics, Cambridge, MA 02139, USA
| | - Ke Liu
- Marengo Therapeutics, Cambridge, MA 02139, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhen Su
- Marengo Therapeutics, Cambridge, MA 02139, USA
| | - James L Gulley
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - Jeffrey Schlom
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| |
Collapse
|
16
|
van de Sandt CE, Nguyen THO, Gherardin NA, Crawford JC, Samir J, Minervina AA, Pogorelyy MV, Rizzetto S, Szeto C, Kaur J, Ranson N, Sonda S, Harper A, Redmond SJ, McQuilten HA, Menon T, Sant S, Jia X, Pedrina K, Karapanagiotidis T, Cain N, Nicholson S, Chen Z, Lim R, Clemens EB, Eltahla A, La Gruta NL, Crowe J, Lappas M, Rossjohn J, Godfrey DI, Thomas PG, Gras S, Flanagan KL, Luciani F, Kedzierska K. Newborn and child-like molecular signatures in older adults stem from TCR shifts across human lifespan. Nat Immunol 2023; 24:1890-1907. [PMID: 37749325 PMCID: PMC10602853 DOI: 10.1038/s41590-023-01633-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/24/2023] [Indexed: 09/27/2023]
Abstract
CD8+ T cells provide robust antiviral immunity, but how epitope-specific T cells evolve across the human lifespan is unclear. Here we defined CD8+ T cell immunity directed at the prominent influenza epitope HLA-A*02:01-M158-66 (A2/M158) across four age groups at phenotypic, transcriptomic, clonal and functional levels. We identify a linear differentiation trajectory from newborns to children then adults, followed by divergence and a clonal reset in older adults. Gene profiles in older adults closely resemble those of newborns and children, despite being clonally distinct. Only child-derived and adult-derived A2/M158+CD8+ T cells had the potential to differentiate into highly cytotoxic epitope-specific CD8+ T cells, which was linked to highly functional public T cell receptor (TCR)αβ signatures. Suboptimal TCRαβ signatures in older adults led to less proliferation, polyfunctionality, avidity and recognition of peptide mutants, although displayed no signs of exhaustion. These data suggest that priming T cells at different stages of life might greatly affect CD8+ T cell responses toward viral infections.
Collapse
Affiliation(s)
- Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nicholas A Gherardin
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Jerome Samir
- School of Medical Sciences and The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | | | - Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Simone Rizzetto
- School of Medical Sciences and The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Christopher Szeto
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jasveen Kaur
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
| | - Nicole Ranson
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
| | - Sabrina Sonda
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
| | - Alice Harper
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
| | - Samuel J Redmond
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Hayley A McQuilten
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Tejas Menon
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sneha Sant
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Xiaoxiao Jia
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kate Pedrina
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Theo Karapanagiotidis
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Natalie Cain
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Suellen Nicholson
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ratana Lim
- Obstetrics, Nutrition and Endocrinology Group, Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Auda Eltahla
- School of Medical Sciences and The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Nicole L La Gruta
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jane Crowe
- Deepdene Surgery, Deepdene, Victoria, Australia
| | - Martha Lappas
- Obstetrics, Nutrition and Endocrinology Group, Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jamie Rossjohn
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Dale I Godfrey
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephanie Gras
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Katie L Flanagan
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, Victoria, Australia
- Tasmanian Vaccine Trial Centre, Clifford Craig Foundation, Launceston General Hospital, Launceston, Tasmania, Australia
| | - Fabio Luciani
- School of Medical Sciences and The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
| |
Collapse
|
17
|
Mifsud NA, Illing PT, Ho R, Tuomisto JE, Fettke H, Mullan KA, McCluskey J, Rossjohn J, Vivian J, Reantragoon R, Purcell AW. The allopurinol metabolite, oxypurinol, drives oligoclonal expansions of drug-reactive T cells in resolved hypersensitivity cases and drug-naïve healthy donors. Allergy 2023; 78:2980-2993. [PMID: 37452515 PMCID: PMC10952278 DOI: 10.1111/all.15814] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 07/18/2023]
Abstract
Allopurinol (ALP) is a successful drug used in the treatment of gout. However, this drug has been implicated in hypersensitivity reactions that can cause severe to life-threatening reactions such as Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). Individuals who carry the human leukocyte antigen (HLA)-B*58:01 allotype are at higher risk of experiencing a hypersensitivity reaction (odds ratios ranging from 5.62 to 580.3 for mild to severe reactions, respectively). In addition to the parent drug, the metabolite oxypurinol (OXP) is implicated in triggering T cell-mediated immunopathology via a labile interaction with HLA-B*58:01. To date, there has been limited information regarding the T-cell receptor (TCR) repertoire usage of reactive T cells in patients with ALP-induced SJS or TEN and, in particular, there are no reports examining paired αβTCRs. Here, using in vitro drug-treated PBMCs isolated from both resolved ALP-induced SJS/TEN cases and drug-naïve healthy donors, we show that OXP is the driver of CD8+ T cell-mediated responses and that drug-exposed memory T cells can exhibit a proinflammatory immunophenotype similar to T cells described during active disease. Furthermore, this response supported the pharmacological interaction with immune receptors (p-i) concept by showcasing (i) the labile metabolite interaction with peptide/HLA complexes, (ii) immunogenic complex formation at the cell surface, and (iii) lack of requirement for antigen processing to elicit drug-induced T cell responsiveness. Examination of paired OXP-induced αβTCR repertoires highlighted an oligoclonal and private clonotypic profile in both resolved ALP-induced SJS/TEN cases and drug-naïve healthy donors.
Collapse
Affiliation(s)
- Nicole A. Mifsud
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Patricia T. Illing
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Rebecca Ho
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Johanna E. Tuomisto
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Heidi Fettke
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Present address:
Cancer Research, Peter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Present address:
Sir Peter MacCallum Department of OncologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Kerry A. Mullan
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Present address:
ADREM Data Lab, Department of Computer ScienceUniversity of AntwerpAntwerpBelgium
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and ImmunityUniversity of MelbourneParkvilleVictoriaAustralia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Institute of Infection and ImmunityCardiff University School of MedicineCardiffUK
| | - Julian Vivian
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Present address:
St. Vincent's Institute of Medical ResearchFitzroyVictoriaAustralia
- Present address:
Department of MedicineThe University of MelbourneMelbourneVictoriaAustralia
| | - Rangsima Reantragoon
- Immunology Division, Department of Microbiology, Department of MicrobiologyChulalongkorn UniversityBangkokThailand
- Center of Excellence in Immunology and Immune‐mediated Disease, Faculty of MedicineChulalongkorn UniversityBangkokThailand
| | - Anthony W. Purcell
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| |
Collapse
|
18
|
Fast E, Dhar M, Chen B. TAPIR: a T-cell receptor language model for predicting rare and novel targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557285. [PMID: 37745475 PMCID: PMC10515850 DOI: 10.1101/2023.09.12.557285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
T-cell receptors (TCRs) are involved in most human diseases, but linking their sequences with their targets remains an unsolved grand challenge in the field. In this study, we present TAPIR (T-cell receptor and Peptide Interaction Recognizer), a T-cell receptor (TCR) language model that predicts TCR-target interactions, with a focus on novel and rare targets. TAPIR employs deep convolutional neural network (CNN) encoders to process TCR and target sequences across flexible representations (e.g., beta-chain only, unknown MHC allele, etc.) and learns patterns of interactivity via several training tasks. This flexibility allows TAPIR to train on more than 50k either paired (alpha and beta chain) or unpaired TCRs (just alpha or beta chain) from public and proprietary databases against 1933 unique targets. TAPIR demonstrates state-of-the-art performance when predicting TCR interactivity against common benchmark targets and is the first method to demonstrate strong performance when predicting TCR interactivity against novel targets, where no examples are provided in training. TAPIR is also capable of predicting TCR interaction against MHC alleles in the absence of target information. Leveraging these capabilities, we apply TAPIR to cancer patient TCR repertoires and identify and validate a novel and potent anti-cancer T-cell receptor against a shared cancer neoantigen target (PIK3CA H1047L). We further show how TAPIR, when extended with a generative neural network, is capable of directly designing T-cell receptor sequences that interact with a target of interest.
Collapse
Affiliation(s)
- Ethan Fast
- Vcreate, Inc., Menlo Park, CA, 94025, USA
| | | | | |
Collapse
|
19
|
Zheng MZ, Tan TK, Villalon-Letelier F, Lau H, Deng YM, Fritzlar S, Valkenburg SA, Gu H, Poon LL, Reading PC, Townsend AR, Wakim LM. Single-cycle influenza virus vaccine generates lung CD8 + Trm that cross-react against viral variants and subvert virus escape mutants. SCIENCE ADVANCES 2023; 9:eadg3469. [PMID: 37683004 PMCID: PMC10491285 DOI: 10.1126/sciadv.adg3469] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
Influenza virus-specific tissue-resident memory (Trm) CD8+ T cells located along the respiratory tract provide cross-strain protection against a breadth of influenza viruses. We show that immunization with a single-cycle influenza virus vaccine candidate (S-FLU) results in the deposition of influenza virus nucleoprotein (NP)-specific CD8+ Trm along the respiratory tract that were more cross-reactive against viral variants and less likely to drive the development of cytotoxic T lymphocyte (CTL) escape mutants, as compared to the lung memory NP-specific CD8+ T cell pool established following influenza infection. This immune profile was linked to the limited inflammatory response evoked by S-FLU vaccination, which increased TCR repertoire diversity within the memory CD8+ T cell compartment. Cumulatively, this work shows that S-FLU vaccination evokes a clonally diverse, cross-reactive memory CD8+ T cell pool, which protects against severe disease without driving the virus to rapidly evolve and escape, and thus represents an attractive vaccine for use against rapidly mutating influenza viruses.
Collapse
Affiliation(s)
- Ming Z. M. Zheng
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Fernando Villalon-Letelier
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Hilda Lau
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Svenja Fritzlar
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Sophie A. Valkenburg
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Haogao Gu
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Leo L. M. Poon
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Patrick C. Reading
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Alain R. Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, UK
- Centre for Translational Immunology, Chinese Academy of Medical Sciences, Oxford Institute, University of Oxford, OX3 7FZ Oxford, UK
| | - Linda M. Wakim
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| |
Collapse
|
20
|
Paschold L, Gottschick C, Langer S, Klee B, Diexer S, Aksentijevich I, Schultheiß C, Purschke O, Riese P, Trittel S, Haase R, Dressler F, Eberl W, Hübner J, Strowig T, Guzman CA, Mikolajczyk R, Binder M. T cell repertoire breadth is associated with the number of acute respiratory infections in the LoewenKIDS birth cohort. Sci Rep 2023; 13:9516. [PMID: 37308563 DOI: 10.1038/s41598-023-36144-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/30/2023] [Indexed: 06/14/2023] Open
Abstract
We set out to gain insight into peripheral blood B and T cell repertoires from 120 infants of the LoewenKIDS birth cohort to investigate potential determinants of early life respiratory infections. Low antigen-dependent somatic hypermutation of B cell repertoires, as well as low T and B cell repertoire clonality, high diversity, and high richness especially in public T cell clonotypes reflected the immunological naivety at 12 months of age when high thymic and bone marrow output are associated with relatively few prior antigen encounters. Infants with inadequately low T cell repertoire diversity or high clonality showed higher numbers of acute respiratory infections over the first 4 years of life. No correlation of T or B cell repertoire metrics with other parameters such as sex, birth mode, older siblings, pets, the onset of daycare, or duration of breast feeding was noted. Together, this study supports that-regardless of T cell functionality-the breadth of the T cell repertoire is associated with the number of acute respiratory infections in the first 4 years of life. Moreover, this study provides a valuable resource of millions of T and B cell receptor sequences from infants with available metadata for researchers in the field.
Collapse
Affiliation(s)
- Lisa Paschold
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany
| | - Cornelia Gottschick
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Susan Langer
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Bianca Klee
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Sophie Diexer
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christoph Schultheiß
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany
| | - Oliver Purschke
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Peggy Riese
- Department Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Stephanie Trittel
- Department Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Roland Haase
- Department of Neonatology and Pediatric Intensive Care, Hospital St. Elisabeth und St. Barbara, 06110, Halle (Saale), Germany
| | - Frank Dressler
- Department of Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, 30625, Hannover, Germany
| | - Wolfgang Eberl
- Department of Paediatrics, Hospital Braunschweig, 38118, Braunschweig, Germany
| | - Johannes Hübner
- Department of Paediatrics, Dr. von Hauner Children's Hospital, Ludwig- Maximilians-University Munich, 80337, Munich, Germany
| | - Till Strowig
- Department Microbial Immune Regulation, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Carlos A Guzman
- Department Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Rafael Mikolajczyk
- Interdisciplinary Center for Health Sciences, Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06112, Halle (Saale), Germany
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120, Halle (Saale), Germany.
- Division of Medical Oncology, University Hospital Basel, Petersgraben 4, 40314031, Basel, Switzerland.
| |
Collapse
|
21
|
Li X, Liang H, Fan J. Prospects of Cytomegalovirus-Specific T-Cell Receptors in Clinical Diagnosis and Therapy. Viruses 2023; 15:1334. [PMID: 37376633 DOI: 10.3390/v15061334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/03/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Human cytomegalovirus (HCMV) is responsible for widespread infections worldwide. In immunocompetent individuals it is typically latent, while infection or reactivation in immunocompromised individuals can result in severe clinical symptoms or even death. Although there has been significant progress in the treatment and diagnosis of HCMV infection in recent years, numerous shortcomings and developmental limitations persist. There is an urgent need to develop innovative, safe, and effective treatments, as well as to explore early and timely diagnostic strategies for HCMV infection. Cell-mediated immune responses are the primary factor controlling HCMV infection and replication, but the protective role of humoral immune responses remains controversial. T-cells, key effector cells of the cellular immune system, are critical for clearing and preventing HCMV infection. The T-cell receptor (TCR) lies at the heart of T-cell immune responses, and its diversity enables the immune system to differentiate between self and non-self. Given the significant influence of cellular immunity on human health and the indispensable role of the TCR in T-cell immune responses, we posit that the impact of TCR on the development of novel diagnostic and prognostic methods, as well as on patient monitoring and management of clinical HCMV infection, will be far-reaching and profound. High-throughput and single-cell sequencing technologies have facilitated unprecedented quantitative detection of TCR diversity. With these current sequencing technologies, researchers have already obtained a vast number of TCR sequences. It is plausible that in the near future studies on TCR repertoires will be instrumental in assessing vaccine efficacy, immunotherapeutic strategies, and the early diagnosis of HCMV infection.
Collapse
Affiliation(s)
- Xuejie Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Hanying Liang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Jun Fan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| |
Collapse
|
22
|
Kalinina A, Persiyantseva N, Britanova O, Lupyr K, Shagina I, Khromykh L, Kazansky D. Unique features of the TCR repertoire of reactivated memory T cells in the experimental mouse tumor model. Comput Struct Biotechnol J 2023; 21:3196-3209. [PMID: 37333858 PMCID: PMC10275742 DOI: 10.1016/j.csbj.2023.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/20/2023] Open
Abstract
T cell engineering with T cell receptors (TCR) specific to tumor antigens has become a breakthrough towards personalized cancer adoptive cell immunotherapy. However, the search for therapeutic TCRs is often challenging, and effective strategies are strongly required for the identification and enrichment of tumor-specific T cells that express TCRs with superior functional characteristics. Using an experimental mouse tumor model, we studied sequential changes in TCR repertoire features of T cells involved in the primary and secondary immune responses to allogeneic tumor antigens. In-depth bioinformatics analysis of TCR repertoires showed differences in reactivated memory T cells compared to primarily activated effectors. After cognate antigen re-encounter, memory cells were enriched with clonotypes that express α-chain TCR with high potential cross-reactivity and enhanced strength of interaction with both MHC and docked peptides. Our findings suggest that functionally true memory T cells could be a better source of therapeutic TCRs for adoptive cell therapy. No marked changes were observed in the physicochemical characteristics of TCRβ in reactivated memory clonotypes, indicative of the dominant role of TCRα in the secondary allogeneic immune response. The results of this study could further contribute to the development of TCR-modified T cell products based on the phenomenon of TCR chain centricity.
Collapse
Affiliation(s)
- Anastasiia Kalinina
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, Kashirskoe sh. 24, 115478 Moscow, Russian Federation
| | - Nadezda Persiyantseva
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, Kashirskoe sh. 24, 115478 Moscow, Russian Federation
| | - Olga Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, 117997 Moscow, Russian Federation
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova st.1, 17997 Moscow, Russian Federation
| | - Ksenia Lupyr
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoi boulevard 30c1, 121205 Moscow, Russian Federation
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova st.1,build. 1, 17997 Moscow, Russian Federation
| | - Irina Shagina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, 117997 Moscow, Russian Federation
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova st.1, 17997 Moscow, Russian Federation
| | - Ludmila Khromykh
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, Kashirskoe sh. 24, 115478 Moscow, Russian Federation
| | - Dmitry Kazansky
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, Kashirskoe sh. 24, 115478 Moscow, Russian Federation
| |
Collapse
|
23
|
Christodoulou MI, Zaravinos A. Single-Cell Analysis in Immuno-Oncology. Int J Mol Sci 2023; 24:8422. [PMID: 37176128 PMCID: PMC10178969 DOI: 10.3390/ijms24098422] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
The complexity of the cellular and non-cellular milieu surrounding human tumors plays a decisive role in the course and outcome of disease. The high variability in the distribution of the immune and non-immune compartments within the tumor microenvironments (TME) among different patients governs the mode of their response or resistance to current immunotherapeutic approaches. Through deciphering this diversity, one can tailor patients' management to meet an individual's needs. Single-cell (sc) omics technologies have given a great boost towards this direction. This review gathers recent data about how multi-omics profiling, including the utilization of single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin with sequencing (scATAC-seq), T-cell receptor sequencing (scTCR-seq), mass, tissue-based, or microfluidics cytometry, and related bioinformatics tools, contributes to the high-throughput assessment of a large number of analytes at single-cell resolution. Unravelling the exact TCR clonotype of the infiltrating T cells or pinpointing the classical or novel immune checkpoints across various cell subsets of the TME provide a boost to our comprehension of adaptive immune responses, their antigen specificity and dynamics, and grant suggestions for possible therapeutic targets. Future steps are expected to merge high-dimensional data with tissue localization data, which can serve the investigation of novel multi-modal biomarkers for the selection and/or monitoring of the optimal treatment from the current anti-cancer immunotherapeutic armamentarium.
Collapse
Affiliation(s)
- Maria-Ioanna Christodoulou
- Tumor Immunology and Biomarkers Group, Basic and Translational Cancer Research Center (BTCRC), 1516 Nicosia, Cyprus
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404 Nicosia, Cyprus
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404 Nicosia, Cyprus
- Cancer Genetics, Genomics and Systems Biology Group, Basic and Translational Cancer Research Center (BTCRC), 1516 Nicosia, Cyprus
| |
Collapse
|
24
|
Ciacchi L, van de Garde MDB, Ladell K, Farenc C, Poelen MCM, Miners KL, Llerena C, Reid HH, Petersen J, Price DA, Rossjohn J, van Els CACM. CD4 + T cell-mediated recognition of a conserved cholesterol-dependent cytolysin epitope generates broad antibacterial immunity. Immunity 2023; 56:1082-1097.e6. [PMID: 37100059 DOI: 10.1016/j.immuni.2023.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/31/2022] [Accepted: 03/30/2023] [Indexed: 04/28/2023]
Abstract
CD4+ T cell-mediated immunity against Streptococcus pneumoniae (pneumococcus) can protect against recurrent bacterial colonization and invasive pneumococcal diseases (IPDs). Although such immune responses are common, the pertinent antigens have remained elusive. We identified an immunodominant CD4+ T cell epitope derived from pneumolysin (Ply), a member of the bacterial cholesterol-dependent cytolysins (CDCs). This epitope was broadly immunogenic as a consequence of presentation by the pervasive human leukocyte antigen (HLA) allotypes DPB1∗02 and DPB1∗04 and recognition via architecturally diverse T cell receptors (TCRs). Moreover, the immunogenicity of Ply427-444 was underpinned by core residues in the conserved undecapeptide region (ECTGLAWEWWR), enabling cross-recognition of heterologous bacterial pathogens expressing CDCs. Molecular studies further showed that HLA-DP4-Ply427-441 was engaged similarly by private and public TCRs. Collectively, these findings reveal the mechanistic determinants of near-global immune focusing on a trans-phyla bacterial epitope, which could inform ancillary strategies to combat various life-threatening infectious diseases, including IPDs.
Collapse
Affiliation(s)
- Lisa Ciacchi
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Martijn D B van de Garde
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Utrecht 3721MA, the Netherlands
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK
| | - Carine Farenc
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Martien C M Poelen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Utrecht 3721MA, the Netherlands
| | - Kelly L Miners
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK
| | - Carmen Llerena
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Hugh H Reid
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jan Petersen
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK; Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK.
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK; Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK.
| | - Cécile A C M van Els
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Utrecht 3721MA, the Netherlands; Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CL, the Netherlands.
| |
Collapse
|
25
|
Barber-Axthelm IM, Wragg KM, Esterbauer R, Amarasena TH, Barber-Axthelm VR, Wheatley AK, Gibbon AM, Kent SJ, Juno JA. Phenotypic and functional characterization of pharmacologically expanded Vγ9Vδ2 T cells in pigtail macaques. iScience 2023; 26:106269. [PMID: 36936791 PMCID: PMC10014287 DOI: 10.1016/j.isci.2023.106269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/22/2022] [Accepted: 02/19/2023] [Indexed: 03/12/2023] Open
Abstract
While gaining interest as treatment for cancer and infectious disease, the clinical efficacy of Vγ9Vδ2 T cell-based immunotherapeutics has to date been limited. An improved understanding of γδ T cell heterogeneity across lymphoid and non-lymphoid tissues, before and after pharmacological expansion, is required. Here, we describe the phenotype and tissue distribution of Vγ9Vδ2 T cells at steady state and following in vivo pharmacological expansion in pigtail macaques. Intravenous phosphoantigen administration with subcutaneous rhIL-2 drove robust expansion of Vγ9Vδ2 T cells in blood and pulmonary mucosa, while expansion was confined to the pulmonary mucosa following intratracheal antigen administration. Peripheral blood Vγ9Vδ2 T cell expansion was polyclonal, and associated with a significant loss of CCR6 expression due to IL-2-mediated receptor downregulation. Overall, we show the tissue distribution and phenotype of in vivo pharmacologically expanded Vγ9Vδ2 T cells can be altered based on the antigen administration route, with implications for tissue trafficking and the clinical efficacy of Vγ9Vδ2 T cell immunotherapeutics.
Collapse
Affiliation(s)
- Isaac M. Barber-Axthelm
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Kathleen M. Wragg
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Robyn Esterbauer
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thakshila H. Amarasena
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Valerie R.B. Barber-Axthelm
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Adam K. Wheatley
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Anne M. Gibbon
- Monash Animal Research Platform, Monash University, Clayton, VIC 3800, Australia
| | - Stephen J. Kent
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Jennifer A. Juno
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| |
Collapse
|
26
|
Tracking the progeny of adoptively transferred virus-specific T cells in patients posttransplant using TCR sequencing. Blood Adv 2023; 7:812-827. [PMID: 36121440 PMCID: PMC9996373 DOI: 10.1182/bloodadvances.2022007270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 08/26/2022] [Accepted: 08/28/2022] [Indexed: 11/20/2022] Open
Abstract
Adoptive cellular therapies with T cells are increasingly used to treat a variety of conditions. For instance, in a recent phase 1/2 trial, we prophylactically administered multivirus-specific T-cell products to protect recipients of T-cell-depleted allogeneic stem cell grafts against viral reactivation. To establish treatment efficacy, it is important to determine the fate of the individual transferred T-cell populations. However, it is difficult to unequivocally distinguish progeny of the transferred T-cell products from recipient- or stem cell graft-derived T cells that survived T-cell depletion during conditioning or stem cell graft manipulation. Using messenger RNA sequencing of the T-cell receptor β-chains of the individual virus-specific T-cell populations within these T-cell products, we were able to track the multiple clonal virus-specific subpopulations in peripheral blood and distinguish recipient- and stem cell graft-derived virus-specific T cells from the progeny of the infused T-cell products. We observed in vivo expansion of virus-specific T cells that were exclusively derived from the T-cell products with similar kinetics as the expansion of virus-specific T cells that could also be detected before the T-cell product infusion. In addition, we demonstrated persistence of virus-specific T cells derived from the T-cell products in most patients who did not show viral reactivation. This study demonstrates that virus-specific T cells from prophylactically infused multiantigen-specific T-cell products can expand in response to antigen encounter in vivo and even persist in the absence of early viral reactivation.
Collapse
|
27
|
Mullan KA, Zhang JB, Jones CM, Goh SJ, Revote J, Illing PT, Purcell AW, La Gruta NL, Li C, Mifsud NA. TCR_Explore: A novel webtool for T cell receptor repertoire analysis. Comput Struct Biotechnol J 2023; 21:1272-1282. [PMID: 36814721 PMCID: PMC9939424 DOI: 10.1016/j.csbj.2023.01.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
T cells expressing either alpha-beta or gamma-delta T cell receptors (TCR) are critical sentinels of the adaptive immune system, with receptor diversity being essential for protective immunity against a broad array of pathogens and agents. Programs available to profile TCR clonotypic signatures can be limiting for users with no coding expertise. Current analytical pipelines can be inefficient due to manual processing steps, open to data entry errors and have multiple analytical tools with unique inputs that require coding expertise. Here we present a bespoke webtool designed for users irrespective of coding expertise, coined 'TCR_Explore', enabling analysis either derived via Sanger sequencing or next generation sequencing (NGS) platforms. Further, TCR_Explore incorporates automated quality control steps for Sanger sequencing. The creation of flexible and publication ready figures are enabled for different sequencing platforms following universal conversion to the TCR_Explore file format. TCR_Explore will enhance a user's capacity to undertake in-depth TCR repertoire analysis of both new and pre-existing datasets for identification of T cell clonotypes associated with health and disease. The web application is located at https://tcr-explore.erc.monash.edu for users to interactively explore TCR repertoire datasets.
Collapse
Affiliation(s)
- Kerry A. Mullan
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia,Corresponding authors.
| | - Justin B. Zhang
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Claerwen M. Jones
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Shawn J.R. Goh
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Jerico Revote
- Monash eResearch Centre, Monash University, Melbourne, VIC 3800, Australia
| | - Patricia T. Illing
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Anthony W. Purcell
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Nicole L. La Gruta
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Chen Li
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Nicole A. Mifsud
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia,Corresponding authors.
| |
Collapse
|
28
|
Blanco DB, Chapman NM, Raynor JL, Xu C, Su W, Kc A, Li W, Lim SA, Schattgen S, Shi H, Risch I, Sun Y, Dhungana Y, Kim Y, Wei J, Rankin S, Neale G, Thomas PG, Yang K, Chi H. PTEN directs developmental and metabolic signaling for innate-like T cell fate and tissue homeostasis. Nat Cell Biol 2022; 24:1642-1654. [PMID: 36302969 PMCID: PMC10080469 DOI: 10.1038/s41556-022-01011-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/12/2022] [Indexed: 01/18/2023]
Abstract
Phosphatase and tensin homologue (PTEN) is frequently mutated in human cancer, but its roles in lymphopoiesis and tissue homeostasis remain poorly defined. Here we show that PTEN orchestrates a two-step developmental process linking antigen receptor and IL-23-Stat3 signalling to type-17 innate-like T cell generation. Loss of PTEN leads to pronounced accumulation of mature IL-17-producing innate-like T cells in the thymus. IL-23 is essential for their accumulation, and ablation of IL-23 or IL-17 signalling rectifies the reduced survival of female PTEN-haploinsufficient mice that model human patients with PTEN mutations. Single-cell transcriptome and network analyses revealed the dynamic regulation of PTEN, mTOR and metabolic activities that accompanied type-17 cell programming. Furthermore, deletion of mTORC1 or mTORC2 blocks PTEN loss-driven type-17 cell accumulation, and this is further shaped by the Foxo1 and Stat3 pathways. Collectively, our study establishes developmental and metabolic signalling networks underpinning type-17 cell fate decisions and their functional effects at coordinating PTEN-dependent tissue homeostasis.
Collapse
Affiliation(s)
- Daniel Bastardo Blanco
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Nicole M Chapman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jana L Raynor
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chengxian Xu
- Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wei Su
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anil Kc
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wei Li
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Seon Ah Lim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stefan Schattgen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hao Shi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Isabel Risch
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yu Sun
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yogesh Dhungana
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yunjung Kim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun Wei
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sherri Rankin
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kai Yang
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| |
Collapse
|
29
|
Saggau C, Martini GR, Rosati E, Meise S, Messner B, Kamps AK, Bekel N, Gigla J, Rose R, Voß M, Geisen UM, Reid HM, Sümbül M, Tran F, Berner DK, Khodamoradi Y, Vehreschild MJGT, Cornely O, Koehler P, Krumbholz A, Fickenscher H, Kreuzer O, Schreiber C, Franke A, Schreiber S, Hoyer B, Scheffold A, Bacher P. The pre-exposure SARS-CoV-2-specific T cell repertoire determines the quality of the immune response to vaccination. Immunity 2022; 55:1924-1939.e5. [PMID: 35985324 PMCID: PMC9372089 DOI: 10.1016/j.immuni.2022.08.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/23/2022] [Accepted: 08/08/2022] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2 infection and vaccination generates enormous host-response heterogeneity and an age-dependent loss of immune-response quality. How the pre-exposure T cell repertoire contributes to this heterogeneity is poorly understood. We combined analysis of SARS-CoV-2-specific CD4+ T cells pre- and post-vaccination with longitudinal T cell receptor tracking. We identified strong pre-exposure T cell variability that correlated with subsequent immune-response quality and age. High-quality responses, defined by strong expansion of high-avidity spike-specific T cells, high interleukin-21 production, and specific immunoglobulin G, depended on an intact naive repertoire and exclusion of pre-existing memory T cells. In the elderly, T cell expansion from both compartments was severely compromised. Our results reveal that an intrinsic defect of the CD4+ T cell repertoire causes the age-dependent decline of immune-response quality against SARS-CoV-2 and highlight the need for alternative strategies to induce high-quality T cell responses against newly arising pathogens in the elderly.
Collapse
Affiliation(s)
- Carina Saggau
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany
| | - Gabriela Rios Martini
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany; Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany
| | - Elisa Rosati
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany; Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany
| | - Silja Meise
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany
| | - Berith Messner
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany; Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany
| | - Ann-Kristin Kamps
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany; Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany
| | - Nicole Bekel
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany; Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany
| | - Johannes Gigla
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany
| | - Ruben Rose
- Institute for Infection Medicine, Christian-Albrecht University of Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Mathias Voß
- Institute for Infection Medicine, Christian-Albrecht University of Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Ulf M Geisen
- Medical Department I, Department for Rheumatology and Clinical Immunology, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Hayley M Reid
- Medical Department I, Department for Rheumatology and Clinical Immunology, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Melike Sümbül
- Department of Dermatology, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany; Department of Internal Medicine I, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Dennis K Berner
- Medical Department I, Department for Rheumatology and Clinical Immunology, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Oliver Cornely
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Philipp Koehler
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Andi Krumbholz
- Institute for Infection Medicine, Christian-Albrecht University of Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany; Labor Dr. Krause und Kollegen MVZ GmbH, Kiel, Germany
| | - Helmut Fickenscher
- Institute for Infection Medicine, Christian-Albrecht University of Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | - Claudia Schreiber
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany; Department of Internal Medicine I, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Bimba Hoyer
- Medical Department I, Department for Rheumatology and Clinical Immunology, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany
| | - Petra Bacher
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany; Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany.
| |
Collapse
|
30
|
Xia J, Li X, Gui G, Wu J, Gong S, Shang Y, Fan J. Early immune surveillance to predict cytomegalovirus outcomes after allogeneic hematopoietic stem cell transplantation. Front Cell Infect Microbiol 2022; 12:954420. [PMID: 35992173 PMCID: PMC9382130 DOI: 10.3389/fcimb.2022.954420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThere is no method of predicting human cytomegalovirus (HCMV) outcomes in allogeneic hematopoietic stem cell transplant recipients clinically, leading in some cases to excessive or insufficient antiviral therapy. We evaluated the early immune response of recipients with disparate HCMV outcomes.MethodsThe HCMV outcomes of recipients were determined by long-term monitoring of HCMV DNA levels posttransplant. HCMV IgG and IgM concentrations at 1 week before and 1 week after transplantation, absolute lymphocyte counts, and HCMV-specific IFN-γ secreting cells at 1 month posttransplant were evaluated based on HCMV outcome.ResultsAll recipients were negative for HCMV IgM. Significant differences between recipients with and without HCMV reactivation were observed in pre- and post-transplant HCMV IgG antibody levels, absolute lymphocyte counts, and HCMV-specific IFN-γ secreting cells (P < 0.05). HCMV IgG antibody levels significantly increased after transplantation in recipients with HCMV reactivation (P = 0.032), but not in those without reactivation. Multivariate analysis revealed that except for the absolute lymphocyte count these biomarkers were related to HCMV reactivation, independent of other clinical factors. In time-to-event analyses, lower levels of these biomarkers were associated with an increased 150-day cumulative incidence of HCMV reactivation (log-rank P < 0.05). In recipients with HCMV reactivation, the duration of HCMV DNAemia had negative correlation with HCMV-specific IFN-γ-secreting cells (P = 0.015, r = -0.372). The relationships between the peak HCMV DNA load and absolute lymphocyte count and HCMV-specific IFN-γ-secreting cells followed the same trends (P = 0.026, r = -0.181 and P = 0.010, r = -0.317).ConclusionsHCMV IgG, absolute lymphocyte count, and HCMV-specific IFN-γ secreting cells represent the humoral and cellular immune response. Early monitoring of these immune markers could enable prediction of HCMV outcomes posttransplant and assessment of the severity of HCMV DNAemia.
Collapse
Affiliation(s)
- Jintao Xia
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xuejie Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Genyong Gui
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jian Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shengnan Gong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yuxin Shang
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London South Kensington Campus, London, United Kingdom
| | - Jun Fan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Jun Fan,
| |
Collapse
|
31
|
Boonpattanaporn N, Kongkaew T, Sengprasert P, Souter MNT, Lakananurak N, Rerknimitr R, Corbett AJ, Reantragoon R. Human mucosal Vα7.2 + CD161 hi T cell distribution at physiologic state and in Helicobacter pylori infection. J Leukoc Biol 2022; 112:717-732. [PMID: 35704477 DOI: 10.1002/jlb.4a0421-223rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/23/2022] [Indexed: 01/02/2023] Open
Abstract
Mucosal-associated invariant T (MAIT) cells are innate-like, unconventional T cells that are present in peripheral blood and mucosal surfaces. A clear understanding of how MAIT cells in the mucosae function and their role in host immunity is still lacking. Therefore, our aim was to investigate MAIT cell distribution and their characteristics in the gastrointestinal (GI) mucosal tissue based on Vα7.2+ CD161hi identification. We showed that Vα7.2+ CD161hi T cells are present in both intraepithelial layer and lamina propriae of the GI mucosa, but have different abundance at each GI site. Vα7.2+ CD161hi T cells were most abundant in the duodenum, but had the lowest reactivity to MR1-5-OP-RU tetramers when compared with Vα7.2+ CD161hi T cells at other GI tissue sites. Striking discrepancies between MR1-5-OP-RU tetramer reactive cells and Vα7.2+ CD161hi T cells were observed along each GI tissue sites. Vα7.2+ CD161hi TCR repertoire was most diverse in the ileum. Similar dominant profiles of TRBV usage were observed among peripheral blood, duodenum, ileum, and colon. Some TRBV chains were detected at certain intestinal sites and not elsewhere. The frequency of peripheral blood Vα7.2+ CD161hi T cells correlated with mucosal Vα7.2+ CD161hi T cells in lamina propriae ileum and lamina propriae colon. The frequency of peripheral blood Vα7.2+ CD161hi T cells in Helicobacter pylori-infected individuals was significantly lower than uninfected individuals, but this was not observed with gastric Vα7.2+ CD161hi T cells. This study illustrates the biology of Vα7.2+ CD161hi T cells in the GI mucosa and provides a basis for understanding MAIT cells in the mucosa and MAIT-related GI diseases.
Collapse
Affiliation(s)
- Norasate Boonpattanaporn
- Medical Microbiology Interdisciplinary Program, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Thidarat Kongkaew
- Medical Microbiology Interdisciplinary Program, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Panjana Sengprasert
- Immunology Division, Faculty of Medicine, Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Michael N T Souter
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Narisorn Lakananurak
- Faculty of Medicine, Department of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Rungsun Rerknimitr
- Faculty of Medicine, Department of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Rangsima Reantragoon
- Immunology Division, Faculty of Medicine, Department of Microbiology, Chulalongkorn University, Bangkok, Thailand.,Faculty of Medicine, Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok, Thailand.,Faculty of Medicine, Center of Excellence in Skeletal Disorders and Enzyme Reaction Mechanism, Chulalongkorn University, Bangkok, Thailand
| |
Collapse
|
32
|
Mettelman RC, Allen EK, Thomas PG. Mucosal immune responses to infection and vaccination in the respiratory tract. Immunity 2022; 55:749-780. [PMID: 35545027 PMCID: PMC9087965 DOI: 10.1016/j.immuni.2022.04.013] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 01/25/2023]
Abstract
The lungs are constantly exposed to inhaled debris, allergens, pollutants, commensal or pathogenic microorganisms, and respiratory viruses. As a result, innate and adaptive immune responses in the respiratory tract are tightly regulated and are in continual flux between states of enhanced pathogen clearance, immune-modulation, and tissue repair. New single-cell-sequencing techniques are expanding our knowledge of airway cellular complexity and the nuanced connections between structural and immune cell compartments. Understanding these varied interactions is critical in treatment of human pulmonary disease and infections and in next-generation vaccine design. Here, we review the innate and adaptive immune responses in the lung and airways following infection and vaccination, with particular focus on influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The ongoing SARS-CoV-2 pandemic has put pulmonary research firmly into the global spotlight, challenging previously held notions of respiratory immunity and helping identify new populations at high risk for respiratory distress.
Collapse
Affiliation(s)
- Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| |
Collapse
|
33
|
Suliman S, Kjer-Nielsen L, Iwany SK, Lopez Tamara K, Loh L, Grzelak L, Kedzierska K, Ocampo TA, Corbett AJ, McCluskey J, Rossjohn J, León SR, Calderon R, Lecca-Garcia L, Murray MB, Moody DB, Van Rhijn I. Dual TCR-α Expression on Mucosal-Associated Invariant T Cells as a Potential Confounder of TCR Interpretation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1389-1395. [PMID: 35246495 PMCID: PMC9359468 DOI: 10.4049/jimmunol.2100275] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 01/12/2022] [Indexed: 05/20/2023]
Abstract
Mucosal-associated invariant T (MAIT) cells are innate-like T cells that are highly abundant in human blood and tissues. Most MAIT cells have an invariant TCRα-chain that uses T cell receptor α-variable 1-2 (TRAV1-2) joined to TRAJ33/20/12 and recognizes metabolites from bacterial riboflavin synthesis bound to the Ag-presenting molecule MHC class I related (MR1). Our attempts to identify alternative MR1-presented Ags led to the discovery of rare MR1-restricted T cells with non-TRAV1-2 TCRs. Because altered Ag specificity likely alters affinity for the most potent known Ag, 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil (5-OP-RU), we performed bulk TCRα- and TCRβ-chain sequencing and single-cell-based paired TCR sequencing on T cells that bound the MR1-5-OP-RU tetramer with differing intensities. Bulk sequencing showed that use of V genes other than TRAV1-2 was enriched among MR1-5-OP-RU tetramerlow cells. Although we initially interpreted these as diverse MR1-restricted TCRs, single-cell TCR sequencing revealed that cells expressing atypical TCRα-chains also coexpressed an invariant MAIT TCRα-chain. Transfection of each non-TRAV1-2 TCRα-chain with the TCRβ-chain from the same cell demonstrated that the non-TRAV1-2 TCR did not bind the MR1-5-OP-RU tetramer. Thus, dual TCRα-chain expression in human T cells and competition for the endogenous β-chain explains the existence of some MR1-5-OP-RU tetramerlow T cells. The discovery of simultaneous expression of canonical and noncanonical TCRs on the same T cell means that claims of roles for non-TRAV1-2 TCR in MR1 response must be validated by TCR transfer-based confirmation of Ag specificity.
Collapse
Affiliation(s)
- Sara Suliman
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA;
- Division of Experimental Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, San Francisco, CA
| | - Lars Kjer-Nielsen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sarah K Iwany
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Kattya Lopez Tamara
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Socios en Salud Sucursal Perú, Lima, Peru
| | - Liyen Loh
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ludivine Grzelak
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Tonatiuh A Ocampo
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | | | | | | | - Megan B Murray
- Department of Global Health and Social Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Division of Global Health Equity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; and
| | - D Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA;
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| |
Collapse
|
34
|
Mudd PA, Minervina AA, Pogorelyy MV, Turner JS, Kim W, Kalaidina E, Petersen J, Schmitz AJ, Lei T, Haile A, Kirk AM, Mettelman RC, Crawford JC, Nguyen THO, Rowntree LC, Rosati E, Richards KA, Sant AJ, Klebert MK, Suessen T, Middleton WD, Wolf J, Teefey SA, O'Halloran JA, Presti RM, Kedzierska K, Rossjohn J, Thomas PG, Ellebedy AH. SARS-CoV-2 mRNA vaccination elicits a robust and persistent T follicular helper cell response in humans. Cell 2022; 185:603-613.e15. [PMID: 35026152 PMCID: PMC8695127 DOI: 10.1016/j.cell.2021.12.026] [Citation(s) in RCA: 199] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/12/2021] [Accepted: 12/17/2021] [Indexed: 01/06/2023]
Abstract
SARS-CoV-2 mRNA vaccines induce robust anti-spike (S) antibody and CD4+ T cell responses. It is not yet clear whether vaccine-induced follicular helper CD4+ T (TFH) cell responses contribute to this outstanding immunogenicity. Using fine-needle aspiration of draining axillary lymph nodes from individuals who received the BNT162b2 mRNA vaccine, we evaluated the T cell receptor sequences and phenotype of lymph node TFH. Mining of the responding TFH T cell receptor repertoire revealed a strikingly immunodominant HLA-DPB1∗04-restricted response to S167-180 in individuals with this allele, which is among the most common HLA alleles in humans. Paired blood and lymph node specimens show that while circulating S-specific TFH cells peak one week after the second immunization, S-specific TFH persist at nearly constant frequencies for at least six months. Collectively, our results underscore the key role that robust TFH cell responses play in establishing long-term immunity by this efficacious human vaccine.
Collapse
Affiliation(s)
- Philip A Mudd
- Department of Emergency Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Anastasia A Minervina
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jackson S Turner
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Wooseob Kim
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Elizaveta Kalaidina
- Division of Allergy and Immunology, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jan Petersen
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Aaron J Schmitz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Tingting Lei
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Alem Haile
- Clinical Trials Unit, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Allison M Kirk
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3052, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3052, Australia
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel 24105, Germany
| | - Katherine A Richards
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Andrea J Sant
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Michael K Klebert
- Clinical Trials Unit, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Teresa Suessen
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - William D Middleton
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sharlene A Teefey
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jane A O'Halloran
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Rachel M Presti
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO 63110, USA; Clinical Trials Unit, Washington University School of Medicine, Saint Louis, MO 63110, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3052, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Ali H Ellebedy
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, USA.
| |
Collapse
|
35
|
Patel S, Ramnoruth N, Wehr P, Rossjohn J, Reid HH, Campbell K, Nel HJ, Thomas R. Evaluation of a fit-for-purpose assay to monitor antigen-specific functional CD4+ T-cell subpopulations in rheumatoid arthritis using flow cytometry-based peptide-MHC class-II tetramer staining. Clin Exp Immunol 2022; 207:72-83. [PMID: 35020859 PMCID: PMC8802177 DOI: 10.1093/cei/uxab008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/13/2021] [Accepted: 12/01/2021] [Indexed: 12/11/2022] Open
Abstract
Antigen-specific T cells can serve as a response biomarker in non-clinical or clinical immunotherapy studies in autoimmune disease. There are protocols with optimized multimer staining methods to detect peptide (p)MHCII+ CD4+ T cells, and some qualified and validated protocols for pMHCI+ CD8+ T cells. However, no protocol is fully or partially qualified to enumerate and characterize antigen-specific pMHCII+ CD4+ T cells from patient samples. Implementing such an assay requires a desired level of specificity and precision, in terms of assay repeatability and reproducibility. In transgenic type II collagen (CII)-immunized HLA-DR1/DR4 humanized mouse models of collagen-induced arthritis (CIA), CII259-273-specific T cells dominantly expand. Therefore antigen-specific T cells recognizing this epitope presented by rheumatoid arthritis (RA)-associated risk HLA-DR allomorphs are of interest to understand disease progression and responses to immunotherapy in RA patients. Using HLA-DRB1∗04:01 or ∗01:01-collagen type II (CII)259-273 tetramers, we evaluated parameters influencing precision and reproducibility of an optimized flow cytometry-based method for antigen-specific CD4+ T cells and eight specific subpopulations with and without tetramer positivity. We evaluated specificity, precision, and reproducibility for research environments and non-regulated laboratories. The assay has excellent overall precision with %CV<25% for intra-assay repeatability, inter-analyst precision, and inter-assay reproducibility. The precision of the assay correlated negatively with the cell viability after thawing, indicating that post-thaw viability is a critical parameter for reproducibility. This assay is suitable for longitudinal analysis of treatment response and disease activity outcome in RA patients, and adaptable for translational or immunotherapy clinical trial settings.
Collapse
Affiliation(s)
- Swati Patel
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Nishta Ramnoruth
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Pascale Wehr
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Hugh H Reid
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Kim Campbell
- Janssen Research & Development, LLC, Spring House, PA, USA
- Janssen Research & Development, LLC, La Jolla, CA, USA
| | - Hendrik J Nel
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Ranjeny Thomas
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
36
|
TIL expansion with high dose IL-2 or low dose IL-2 with anti-CD3/anti-CD28 stimulation provides different quality of TIL-expanded T cell clones. J Immunol Methods 2022; 503:113229. [DOI: 10.1016/j.jim.2022.113229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/02/2021] [Accepted: 01/24/2022] [Indexed: 11/18/2022]
|
37
|
Ben-Skowronek I, Sieniawska J, Pach E, Wrobel W, Skowronek A, Tomczyk Z, Rosolowska I. Potential Therapeutic Application of Regulatory T Cells in Diabetes Mellitus Type 1. Int J Mol Sci 2021; 23:ijms23010390. [PMID: 35008819 PMCID: PMC8745590 DOI: 10.3390/ijms23010390] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/18/2021] [Accepted: 12/28/2021] [Indexed: 01/02/2023] Open
Abstract
The autoimmune reaction against the beta cells of the pancreatic islets in type 1 diabetes mellitus (T1DM) patients is active in prediabetes and during the development of the clinical manifestation of T1DM, but it decreases within a few years of the clinical manifestation of this disease. A key role in the pathogenesis of T1DM is played by regulatory T cell (Treg) deficiency or dysfunction. Immune interventions, such as potential therapeutic applications or the induction of the Treg-cell population in T1DM, will be important in the development of new types of treatment. The aim of this study was to evaluate innovative immune interventions as treatments for T1DM. After an evaluation of full-length papers from the PubMed database from 2010 to 2021, 20 trials were included for the final analysis. The analysis led to the following conclusions: Treg cells play an important role in the limitation of the development of T1DM, the activation or application of Tregs may be more effective in the early stages of T1DM development, and the therapeutic use of Treg cells in T1DM is promising but requires long-term observation in a large group of patients.
Collapse
|
38
|
Tran MT, Faridi P, Lim JJ, Ting YT, Onwukwe G, Bhattacharjee P, Jones CM, Tresoldi E, Cameron FJ, La Gruta NL, Purcell AW, Mannering SI, Rossjohn J, Reid HH. T cell receptor recognition of hybrid insulin peptides bound to HLA-DQ8. Nat Commun 2021; 12:5110. [PMID: 34433824 PMCID: PMC8387461 DOI: 10.1038/s41467-021-25404-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/05/2021] [Indexed: 12/20/2022] Open
Abstract
HLA-DQ8, a genetic risk factor in type I diabetes (T1D), presents hybrid insulin peptides (HIPs) to autoreactive CD4+ T cells. The abundance of spliced peptides binding to HLA-DQ8 and how they are subsequently recognised by the autoreactive T cell repertoire is unknown. Here we report, the HIP (GQVELGGGNAVEVLK), derived from splicing of insulin and islet amyloid polypeptides, generates a preferred peptide-binding motif for HLA-DQ8. HLA-DQ8-HIP tetramer+ T cells from the peripheral blood of a T1D patient are characterised by repeated TRBV5 usage, which matches the TCR bias of CD4+ T cells reactive to the HIP peptide isolated from the pancreatic islets of a patient with T1D. The crystal structure of three TRBV5+ TCR-HLA-DQ8-HIP complexes shows that the TRBV5-encoded TCR β-chain forms a common landing pad on the HLA-DQ8 molecule. The N- and C-termini of the HIP is recognised predominantly by the TCR α-chain and TCR β-chain, respectively, in all three TCR ternary complexes. Accordingly, TRBV5 + TCR recognition of HIP peptides might occur via a 'polarised' mechanism, whereby each chain within the αβTCR heterodimer recognises distinct origins of the spliced peptide presented by HLA-DQ8.
Collapse
Affiliation(s)
- Mai T Tran
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Pouya Faridi
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jia Jia Lim
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Yi Tian Ting
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Goodluck Onwukwe
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Pushpak Bhattacharjee
- Immunology and Diabetes Unit, St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Claerwen M Jones
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Eleonora Tresoldi
- Immunology and Diabetes Unit, St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Fergus J Cameron
- Department of Endocrinology and Diabetes, Royal Children's Hospital, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Nicole L La Gruta
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Anthony W Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Stuart I Mannering
- Immunology and Diabetes Unit, St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia. .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia. .,Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK.
| | - Hugh H Reid
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia. .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia.
| |
Collapse
|
39
|
Zhang Y, Zhu Y, Wang J, Xu Y, Wang Z, Liu Y, Di X, Feng L, Zhang Y. A comprehensive model based on temporal dynamics of peripheral T cell repertoire for predicting post-treatment distant metastasis of nasopharyngeal carcinoma. Cancer Immunol Immunother 2021; 71:675-688. [PMID: 34342668 DOI: 10.1007/s00262-021-03016-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023]
Abstract
Many nasopharyngeal carcinoma (NPC) patients develop distant metastases after treatment, leading to poor outcomes. To date, there are no peripheral biomarkers suitable for all NPC patients to predict distant metastasis. Hence, we purposed to develop a noninvasive comprehensive model for predicting post-treatment distant metastasis of all NPC. Since T-cell receptor β chain (TCRB) repertoire has achieved prognostic prediction in many cancers, the clinical characteristics and parameters of TCRB repertoire of 71 cases of peripheral blood samples (pairwise pre-treatment and post-treatment samples from 40 NPC patients who without (nM, n = 21) or with (M, n = 19) post-treatment distant metastasis) were collected. The least absolute shrinkage and selection operator algorithm was used to construct a distant metastasis prediction model. In terms of TCRB repertoire parameters, the diversity of TCRB repertoire was significantly decreased in M group after treatment but not in nM group. Ascending TCRB diversity and higher similarity between pre- and post-treatment samples showed better distant metastasis-free survival (DMFS). The similarity still had robust DMFS prediction in patients with reduced TCRB diversity. More importantly, the 5-factor comprehensive model consisting of basic clinical characteristics and TCRB repertoire indices showed a higher prognostic accuracy than any one individual factor in DMFS predicting. In conclusion, treatment had different effects on the composition of TCRB repertoire in patients without and with post-treatment distant metastasis. The dynamics of TCRB diversity, the similarity of TCRB repertoires, and combinations of these factors with basic clinical characteristics could serve as noninvasive DMFS predictors for all NPC patients.
Collapse
Affiliation(s)
- Yajing Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yujie Zhu
- Department of Blood Transfusion, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jiaqi Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi Xu
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing, China
| | - Zekun Wang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing, China
| | - Yang Liu
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing, China
| | - Xuebing Di
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Ye Zhang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing, China.
| |
Collapse
|
40
|
Pai JA, Satpathy AT. High-throughput and single-cell T cell receptor sequencing technologies. Nat Methods 2021; 18:881-892. [PMID: 34282327 PMCID: PMC9345561 DOI: 10.1038/s41592-021-01201-8] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
T cells express T cell receptors (TCRs) composed of somatically recombined TCRα and TCRβ chains, which mediate recognition of major histocompatibility complex (MHC)-antigen complexes and drive the antigen-specific adaptive immune response to pathogens and cancer. The TCR repertoire in each individual is highly diverse, which allows for recognition of a wide array of foreign antigens, but also presents a challenge in analyzing this response using conventional methods. Recent studies have developed high-throughput sequencing technologies to identify TCR sequences, analyze their antigen specificities using experimental and computational tools, and pair TCRs with transcriptional and epigenetic cell state phenotypes in single cells. In this Review, we highlight these technological advances and describe how they have been applied to discover fundamental insights into T cell-mediated immunity.
Collapse
Affiliation(s)
- Joy A Pai
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
41
|
Shevyrev D, Tereshchenko V, Kozlov V. Immune Equilibrium Depends on the Interaction Between Recognition and Presentation Landscapes. Front Immunol 2021; 12:706136. [PMID: 34394106 PMCID: PMC8362327 DOI: 10.3389/fimmu.2021.706136] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/12/2021] [Indexed: 12/15/2022] Open
Abstract
In this review, we described the structure and organization of antigen-recognizing repertoires of B and T cells from the standpoint of modern immunology. We summarized the latest advances in bioinformatics analysis of sequencing data from T and B cell repertoires and also presented contemporary ideas about the mechanisms of clonal diversity formation at different stages of organism development. At the same time, we focused on the importance of the allelic variants of the HLA genes and spectra of presented antigens for the formation of T-cell receptors (TCR) landscapes. The main idea of this review is that immune equilibrium and proper functioning of immunity are highly dependent on the interaction between the recognition and the presentation landscapes of antigens. Certain changes in these landscapes can occur during life, which can affect the protective function of adaptive immunity. We described some mechanisms associated with these changes, for example, the conversion of effector cells into regulatory cells and vice versa due to the trans-differentiation or bystander effect, changes in the clonal organization of the general TCR repertoire due to homeostatic proliferation or aging, and the background for the altered presentation of some antigens due to SNP mutations of MHC, or the alteration of the presenting antigens due to post-translational modifications. The authors suggest that such alterations can lead to an increase in the risk of the development of oncological and autoimmune diseases and influence the sensitivity of the organism to different infectious agents.
Collapse
Affiliation(s)
- Daniil Shevyrev
- Laboratory of Clinical Immunopathology, Research Institute for Fundamental and Clinical Immunology, Novosibirsk, Russia
| | - Valeriy Tereshchenko
- Laboratory of Molecular Immunology, Research Institute for Fundamental and Clinical Immunology, Novosibirsk, Russia
| | - Vladimir Kozlov
- Laboratory of Clinical Immunopathology, Research Institute for Fundamental and Clinical Immunology, Novosibirsk, Russia
| |
Collapse
|
42
|
Gherardin NA, Redmond SJ, McWilliam HEG, Almeida CF, Gourley KHA, Seneviratna R, Li S, De Rose R, Ross FJ, Nguyen-Robertson CV, Su S, Ritchie ME, Villadangos JA, Moody DB, Pellicci DG, Uldrich AP, Godfrey DI. CD36 family members are TCR-independent ligands for CD1 antigen-presenting molecules. Sci Immunol 2021; 6:6/60/eabg4176. [PMID: 34172588 DOI: 10.1126/sciimmunol.abg4176] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/01/2021] [Accepted: 05/18/2021] [Indexed: 12/22/2022]
Abstract
CD1c presents lipid-based antigens to CD1c-restricted T cells, which are thought to be a major component of the human T cell pool. However, the study of CD1c-restricted T cells is hampered by the presence of an abundantly expressed, non-T cell receptor (TCR) ligand for CD1c on blood cells, confounding analysis of TCR-mediated CD1c tetramer staining. Here, we identified the CD36 family (CD36, SR-B1, and LIMP-2) as ligands for CD1c, CD1b, and CD1d proteins and showed that CD36 is the receptor responsible for non-TCR-mediated CD1c tetramer staining of blood cells. Moreover, CD36 blockade clarified tetramer-based identification of CD1c-restricted T cells and improved identification of CD1b- and CD1d-restricted T cells. We used this technique to characterize CD1c-restricted T cells ex vivo and showed diverse phenotypic features, TCR repertoire, and antigen-specific subsets. Accordingly, this work will enable further studies into the biology of CD1 and human CD1-restricted T cells.
Collapse
Affiliation(s)
- Nicholas A Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3000, Australia. .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Samuel J Redmond
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hamish E G McWilliam
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3000, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Catarina F Almeida
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Katherine H A Gourley
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rebecca Seneviratna
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robert De Rose
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Fiona J Ross
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Catriona V Nguyen-Robertson
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shian Su
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3053, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Matthew E Ritchie
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3053, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jose A Villadangos
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3000, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - D Branch Moody
- Division of Rheumatology, Immunity, and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniel G Pellicci
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia.,Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia
| | - Adam P Uldrich
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3000, Australia. .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| |
Collapse
|
43
|
Miron M, Meng W, Rosenfeld AM, Dvorkin S, Poon MML, Lam N, Kumar BV, Louzoun Y, Luning Prak ET, Farber DL. Maintenance of the human memory T cell repertoire by subset and tissue site. Genome Med 2021; 13:100. [PMID: 34127056 PMCID: PMC8204429 DOI: 10.1186/s13073-021-00918-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 06/01/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Immune-mediated protection is mediated by T cells expressing pathogen-specific T cell antigen receptors (TCR) that are maintained at diverse sites of infection as tissue-resident memory T cells (TRM) or that disseminate as circulating effector-memory (TEM), central memory (TCM), or terminal effector (TEMRA) subsets in blood and tissues. The relationship between circulating and tissue resident T cell subsets in humans remains elusive, and is important for promoting site-specific protective immunity. METHODS We analyzed the TCR repertoire of the major memory CD4+ and CD8+T cell subsets (TEM, TCM, TEMRA, and TRM) isolated from blood and/or lymphoid organs (spleen, lymph nodes, bone marrow) and lungs of nine organ donors, and blood of three living individuals spanning five decades of life. High-throughput sequencing of the variable (V) portion of individual TCR genes for each subset, tissue, and individual were analyzed for clonal diversity, expansion and overlap between lineage, T cell subsets, and anatomic sites. TCR repertoires were further analyzed for TRBV gene usage and CDR3 edit distance. RESULTS Across blood, lymphoid organs, and lungs, human memory, and effector CD8+T cells exhibit greater clonal expansion and distinct TRBV usage compared to CD4+T cell subsets. Extensive sharing of clones between tissues was observed for CD8+T cells; large clones specific to TEMRA cells were present in all sites, while TEM cells contained clones shared between sites and with TRM. For CD4+T cells, TEM clones exhibited the most sharing between sites, followed by TRM, while TCM clones were diverse with minimal sharing between sites and subsets. Within sites, TRM clones exhibited tissue-specific expansions, and maintained clonal diversity with age, compared to age-associated clonal expansions in circulating memory subsets. Edit distance analysis revealed tissue-specific biases in clonal similarity. CONCLUSIONS Our results show that the human memory T cell repertoire comprises clones which persist across sites and subsets, along with clones that are more restricted to certain subsets and/or tissue sites. We also provide evidence that the tissue plays a key role in maintaining memory T cells over age, bolstering the rationale for site-specific targeting of memory reservoirs in vaccines and immunotherapies.
Collapse
Affiliation(s)
- Michelle Miron
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shirit Dvorkin
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| | - Maya Meimei Li Poon
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Nora Lam
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Brahma V Kumar
- Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Yoram Louzoun
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Donna L Farber
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA.
- Department of Surgery, Columbia University, New York, NY, USA.
| |
Collapse
|
44
|
Lineburg KE, Grant EJ, Swaminathan S, Chatzileontiadou DSM, Szeto C, Sloane H, Panikkar A, Raju J, Crooks P, Rehan S, Nguyen AT, Lekieffre L, Neller MA, Tong ZWM, Jayasinghe D, Chew KY, Lobos CA, Halim H, Burrows JM, Riboldi-Tunnicliffe A, Chen W, D'Orsogna L, Khanna R, Short KR, Smith C, Gras S. CD8 + T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses. Immunity 2021; 54:1055-1065.e5. [PMID: 33945786 PMCID: PMC8043652 DOI: 10.1016/j.immuni.2021.04.006] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/26/2021] [Accepted: 04/09/2021] [Indexed: 01/16/2023]
Abstract
Efforts are being made worldwide to understand the immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic, including the impact of T cell immunity and cross-recognition with seasonal coronaviruses. Screening of SARS-CoV-2 peptide pools revealed that the nucleocapsid (N) protein induced an immunodominant response in HLA-B7+ COVID-19-recovered individuals that was also detectable in unexposed donors. A single N-encoded epitope that was highly conserved across circulating coronaviruses drove this immunodominant response. In vitro peptide stimulation and crystal structure analyses revealed T cell-mediated cross-reactivity toward circulating OC43 and HKU-1 betacoronaviruses but not 229E or NL63 alphacoronaviruses because of different peptide conformations. T cell receptor (TCR) sequencing indicated that cross-reactivity was driven by private TCR repertoires with a bias for TRBV27 and a long CDR3β loop. Our findings demonstrate the basis of selective T cell cross-reactivity for an immunodominant SARS-CoV-2 epitope and its homologs from seasonal coronaviruses, suggesting long-lasting protective immunity.
Collapse
Affiliation(s)
- Katie E Lineburg
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Emma J Grant
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Srividhya Swaminathan
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Demetra S M Chatzileontiadou
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Christopher Szeto
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Hannah Sloane
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Archana Panikkar
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Jyothy Raju
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Pauline Crooks
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Sweera Rehan
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Andrea T Nguyen
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Lea Lekieffre
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Michelle A Neller
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Zhen Wei Marcus Tong
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Dhilshan Jayasinghe
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Keng Yih Chew
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Christian A Lobos
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Hanim Halim
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Jacqueline M Burrows
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Lloyd D'Orsogna
- Department of Clinical Immunology, PathWest Laboratory Medicine, Fiona Stanley Hospital, Murdoch, WA 6150, Australia; School of Medicine, University of Western Australia, Nedlands, WA 6009, Australia
| | - Rajiv Khanna
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Corey Smith
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.
| |
Collapse
|
45
|
Sullivan LC, Nguyen THO, Harpur CM, Stankovic S, Kanagarajah AR, Koutsakos M, Saunders PM, Cai Z, Gray JA, Widjaja JML, Lin J, Pietra G, Mingari MC, Moretta L, Samir J, Luciani F, Westall GP, Malmberg KJ, Kedzierska K, Brooks AG. Natural killer cell receptors regulate responses of HLA-E-restricted T cells. Sci Immunol 2021; 6:eabe9057. [PMID: 33893172 DOI: 10.1126/sciimmunol.abe9057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/25/2021] [Indexed: 12/11/2022]
Abstract
Human cytomegalovirus (CMV) infection can stimulate robust human leukocyte antigen (HLA)-E-restricted CD8+ T cell responses. These T cells recognize a peptide from UL40, which differs by as little as a single methyl group from self-peptides that also bind HLA-E, challenging their capacity to avoid self-reactivity. Unexpectedly, we showed that the UL40/HLA-E T cell receptor (TCR) repertoire included TCRs that had high affinities for HLA-E/self-peptide. However, paradoxically, lower cytokine responses were observed from UL40/HLA-E T cells bearing TCRs with high affinity for HLA-E. RNA sequencing and flow cytometric analysis revealed that these T cells were marked by the expression of inhibitory natural killer cell receptors (NKRs) KIR2DL1 and KIR2DL2/L3. On the other hand, UL40/HLA-E T cells bearing lower-affinity TCRs expressed the activating receptor NKG2C. Activation of T cells bearing higher-affinity TCRs was regulated by the interaction between KIR2D receptors and HLA-C. These findings identify a role for NKR signaling in regulating self/non-self discrimination by HLA-E-restricted T cells, allowing for antiviral responses while avoiding contemporaneous self-reactivity.
Collapse
Affiliation(s)
- Lucy C Sullivan
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia.
- Lung Transplant Service, The Alfred Hospital and Monash University Melbourne, Victoria 3000, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Christopher M Harpur
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Sanda Stankovic
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Abbie R Kanagarajah
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Philippa M Saunders
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Zhangying Cai
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - James A Gray
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Jacqueline M L Widjaja
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Jie Lin
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Gabriella Pietra
- Department of Experimental Medicine (DiMES). University of Genoa, Genoa 16132, Italy
- Unità Operativa Complessa Immunologia, Ospedale Policlinico San Martino, Genoa 16132, Italy
| | - Maria Cristina Mingari
- Department of Experimental Medicine (DiMES). University of Genoa, Genoa 16132, Italy
- Unità Operativa Complessa Immunologia, Ospedale Policlinico San Martino, Genoa 16132, Italy
- Center of Excellence for Biomedical Research, University of Genoa, Genoa 16132, Italy
| | - Lorenzo Moretta
- Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Pediatrico Bambino Gesù, 00165 Roma, Italy
| | - Jerome Samir
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Fabio Luciani
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Glen P Westall
- Lung Transplant Service, The Alfred Hospital and Monash University Melbourne, Victoria 3000, Australia
| | - Karl J Malmberg
- KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Oslo 0318, Norway
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo 0310, Norway
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14186 Stockholm, Sweden
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Andrew G Brooks
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia.
| |
Collapse
|
46
|
Lim JJ, Jones CM, Loh TJ, Ting YT, Zareie P, Loh KL, Felix NJ, Suri A, McKinnon M, Stevenaert F, Sharma RK, Klareskog L, Malmström V, Baker DG, Purcell AW, Reid HH, La Gruta NL, Rossjohn J. The shared susceptibility epitope of HLA-DR4 binds citrullinated self-antigens and the TCR. Sci Immunol 2021; 6:6/58/eabe0896. [PMID: 33863750 DOI: 10.1126/sciimmunol.abe0896] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 03/18/2021] [Indexed: 12/11/2022]
Abstract
Individuals expressing HLA-DR4 bearing the shared susceptibility epitope (SE) have an increased risk of developing rheumatoid arthritis (RA). Posttranslational modification of self-proteins via citrullination leads to the formation of neoantigens that can be presented by HLA-DR4 SE allomorphs. However, in T cell-mediated autoimmunity, the interplay between the HLA molecule, posttranslationally modified epitope(s), and the responding T cell repertoire remains unclear. In HLA-DR4 transgenic mice, we show that immunization with a Fibβ-74cit69-81 peptide led to a population of HLA-DR4Fibβ-74cit69-81 tetramer+ T cells that exhibited biased T cell receptor (TCR) β chain usage, which was attributable to selective clonal expansion from the preimmune repertoire. Crystal structures of pre- and postimmune TCRs showed that the SE of HLA-DR4 represented a main TCR contact zone. Immunization with a double citrullinated epitope (Fibβ-72,74cit69-81) altered the responding HLA-DR4 tetramer+ T cell repertoire, which was due to the P2-citrulline residue interacting with the TCR itself. We show that the SE of HLA-DR4 has dual functionality, namely, presentation and a direct TCR recognition determinant. Analogous biased TCR β chain usage toward the Fibβ-74cit69-81 peptide was observed in healthy HLA-DR4+ individuals and patients with HLA-DR4+ RA, thereby suggesting a link to human RA.
Collapse
Affiliation(s)
- Jia Jia Lim
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Claerwen M Jones
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Tiing Jen Loh
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Yi Tian Ting
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Pirooz Zareie
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Khai L Loh
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Nathan J Felix
- Janssen Research & Development LLC, Horsham, Philadelphia, PA, USA
| | - Anish Suri
- Janssen Research & Development, Turnhoutseweg 30, BE-2340, Beerse, Belgium
| | - Murray McKinnon
- Janssen Research & Development LLC, Horsham, Philadelphia, PA, USA
| | | | - Ravi K Sharma
- Rheumatology Division, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 17177 Stockholm, Sweden
| | - Lars Klareskog
- Rheumatology Division, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 17177 Stockholm, Sweden
| | - Vivianne Malmström
- Rheumatology Division, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 17177 Stockholm, Sweden
| | - Daniel G Baker
- Janssen Research & Development LLC, Horsham, Philadelphia, PA, USA
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Hugh H Reid
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia. .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Nicole L La Gruta
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia. .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| |
Collapse
|
47
|
Mifsud NA, Illing PT, Lai JW, Fettke H, Hensen L, Huang Z, Rossjohn J, Vivian JP, Kwan P, Purcell AW. Carbamazepine Induces Focused T Cell Responses in Resolved Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis Cases But Does Not Perturb the Immunopeptidome for T Cell Recognition. Front Immunol 2021; 12:653710. [PMID: 33912179 PMCID: PMC8071863 DOI: 10.3389/fimmu.2021.653710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Antiseizure medications (ASMs) are frequently implicated in T cell-mediated drug hypersensitivity reactions and cause skin tropic pathologies that range in severity from mild rashes to life-threatening systemic syndromes. During the acute stages of the more severe manifestations of these reactions, drug responsive proinflammatory CD8+ T cells display classical features of Th1 cytokine production (e.g. IFNγ) and cytolysis (e.g. granzyme B, perforin). These T cells may be found locally at the site of pathology (e.g. blister cells/fluid), as well as systemically (e.g. blood, organs). What is less understood are the long-lived immunological effects of the memory T cell pool following T cell-mediated drug hypersensitivity reactions. In this study, we examine the ASM carbamazepine (CBZ) and the CBZ-reactive memory T cell pool in patients who have a history of either Stevens-Johnson syndrome (SJS) or toxic epidermal necrolysis (TEN) from 3-to-20 years following their initial adverse reaction. We show that in vitro drug restimulation of CBZ-reactive CD8+ T cells results in a proinflammatory profile and produces a mainly focused, yet private, T cell receptor (TCR) usage amongst human leukocyte antigen (HLA)-B*15:02-positive SJS or TEN patients. Additionally, we show that expression of these CBZ-reactive TCRs in a reporter cell line, lacking endogenous αβTCR, recapitulates the features of TCR activation reported for ASM-treated T cell lines/clones, providing a useful tool for further functional validations. Finally, we conduct a comprehensive evaluation of the HLA-B*15:02 immunopeptidome following ASM (or a metabolite) treatment of a HLA-B*15:02-positive B-lymphoblastoid cell line (C1R.B*15:02) and minor perturbation of the peptide repertoire. Collectively, this study shows that the CBZ-reactive T cells characterized require both the drug and HLA-B*15:02 for activation and that reactivation of memory T cells from blood results in a focused private TCR profile in patients with resolved disease.
Collapse
Affiliation(s)
- Nicole A Mifsud
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Patricia T Illing
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jeffrey W Lai
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Heidi Fettke
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Luca Hensen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Ziyi Huang
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Julian P Vivian
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Alfred Hospital, Monash University, Melbourne, VIC, Australia.,Departments of Medicine and Neurology, Royal Melbourne Hospital, University of Melbourne, Parkville, VIC, Australia.,Department of Medicine and Therapeutics, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Anthony W Purcell
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| |
Collapse
|
48
|
Gohil SH, Iorgulescu JB, Braun DA, Keskin DB, Livak KJ. Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy. Nat Rev Clin Oncol 2021; 18:244-256. [PMID: 33277626 PMCID: PMC8415132 DOI: 10.1038/s41571-020-00449-x] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2020] [Indexed: 02/07/2023]
Abstract
Advances in molecular biology, microfluidics and bioinformatics have empowered the study of thousands or even millions of individual cells from malignant tumours at the single-cell level of resolution. This high-dimensional, multi-faceted characterization of the genomic, transcriptomic, epigenomic and proteomic features of the tumour and/or the associated immune and stromal cells enables the dissection of tumour heterogeneity, the complex interactions between tumour cells and their microenvironment, and the details of the evolutionary trajectory of each tumour. Single-cell transcriptomics, the ability to track individual T cell clones through paired sequencing of the T cell receptor genes and high-dimensional single-cell spatial analysis are all areas of particular relevance to immuno-oncology. Multidimensional biomarker signatures will increasingly be crucial to guiding clinical decision-making in each patient with cancer. High-dimensional single-cell technologies are likely to provide the resolution and richness of data required to generate such clinically relevant signatures in immuno-oncology. In this Perspective, we describe advances made using transformative single-cell analysis technologies, especially in relation to clinical response and resistance to immunotherapy, and discuss the growing utility of single-cell approaches for answering important research questions.
Collapse
Affiliation(s)
- Satyen H Gohil
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Academic Haematology, University College London Cancer Institute, London, UK
| | - J Bryan Iorgulescu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David A Braun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Derin B Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA.
| |
Collapse
|
49
|
DeepTCR is a deep learning framework for revealing sequence concepts within T-cell repertoires. Nat Commun 2021; 12:1605. [PMID: 33707415 PMCID: PMC7952906 DOI: 10.1038/s41467-021-21879-w] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/15/2021] [Indexed: 01/31/2023] Open
Abstract
Deep learning algorithms have been utilized to achieve enhanced performance in pattern-recognition tasks. The ability to learn complex patterns in data has tremendous implications in immunogenomics. T-cell receptor (TCR) sequencing assesses the diversity of the adaptive immune system and allows for modeling its sequence determinants of antigenicity. We present DeepTCR, a suite of unsupervised and supervised deep learning methods able to model highly complex TCR sequencing data by learning a joint representation of a TCR by its CDR3 sequences and V/D/J gene usage. We demonstrate the utility of deep learning to provide an improved 'featurization' of the TCR across multiple human and murine datasets, including improved classification of antigen-specific TCRs and extraction of antigen-specific TCRs from noisy single-cell RNA-Seq and T-cell culture-based assays. Our results highlight the flexibility and capacity for deep neural networks to extract meaningful information from complex immunogenomic data for both descriptive and predictive purposes.
Collapse
|
50
|
Kedzierska K, Koutsakos M. The ABC of Major Histocompatibility Complexes and T Cell Receptors in Health and Disease. Viral Immunol 2021; 33:160-178. [PMID: 32286182 PMCID: PMC7185345 DOI: 10.1089/vim.2019.0184] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A seminal discovery of major histocompatibility complex (MHC) restriction in T cell recognition by Peter Doherty and Rolf Zinkernagel has led to 45 years of exciting research on the mechanisms governing peptide MHC (pMHC) recognition by T cell receptors (TCRs) and their importance in health and disease. T cells provide a significant level of protection against viral, bacterial, and parasitic infections, as well as tumors, hence, the generation of protective T cell responses is a primary goal for cell-mediated vaccines and immunotherapies. Understanding the mechanisms underlying generation of optimal high-avidity effector T cell responses, memory development, maintenance, and recall is of major importance for the rational design of preventative and therapeutic vaccines/immunotherapies. In this review, we summarize the lessons learned over the last four decades and outline our current understanding of the basis and consequences of pMHC/TCR interactions on T cell development and function, and TCR diversity and composition, driving better clinical outcomes and prevention of viral escape. We also discuss the current models of T cell memory formation and determinants of immunodominant T cell responses in animal models and humans. As TCR composition and diversity can affect both the protective capacity of T cells and protection against viral escape, defining the spectrum of TCR selection has implications for improving the functional efficacy of effector T cell responsiveness and memory formation.
Collapse
Affiliation(s)
- Katherine Kedzierska
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| |
Collapse
|