1
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Weerakoon H, Mohamed A, Wong Y, Chen J, Senadheera B, Haigh O, Watkins TS, Kazakoff S, Mukhopadhyay P, Mulvenna J, Miles JJ, Hill MM, Lepletier A. Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation. NPJ Syst Biol Appl 2024; 10:21. [PMID: 38418561 PMCID: PMC10901835 DOI: 10.1038/s41540-024-00346-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/25/2024] [Indexed: 03/01/2024] Open
Abstract
Engagement of the T cell receptor (TCR) triggers molecular reprogramming leading to the acquisition of specialized effector functions by CD4 helper and CD8 cytotoxic T cells. While transcription factors, chemokines, and cytokines are known drivers in this process, the temporal proteomic and transcriptomic changes that regulate different stages of human primary T cell activation remain to be elucidated. Here, we report an integrative temporal proteomic and transcriptomic analysis of primary human CD4 and CD8 T cells following ex vivo stimulation with anti-CD3/CD28 beads, which revealed major transcriptome-proteome uncoupling. The early activation phase in both CD4 and CD8 T cells was associated with transient downregulation of the mRNA transcripts and protein of the central glucose transport GLUT1. In the proliferation phase, CD4 and CD8 T cells became transcriptionally more divergent while their proteome became more similar. In addition to the kinetics of proteome-transcriptome correlation, this study unveils selective transcriptional and translational metabolic reprogramming governing CD4 and CD8 T cell responses to TCR stimulation. This temporal transcriptome/proteome map of human T cell activation provides a reference map exploitable for future discovery of biomarkers and candidates targeting T cell responses.
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Affiliation(s)
- Harshi Weerakoon
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
- Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Ahmed Mohamed
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Yide Wong
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Jinjin Chen
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | | | - Oscar Haigh
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Thomas S Watkins
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Stephen Kazakoff
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | - Jason Mulvenna
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - John J Miles
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Ailin Lepletier
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.
- Institute for Glycomics, Griffith Univeristy, Gold Coast, QLD, Australia.
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2
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Hewavisenti RV, Ferguson AL, Gasparini G, Ohashi T, Braun A, Watkins TS, Miles JJ, Elliott M, Sierro F, Feng CG, Britton WJ, Gebhardt T, Tangye S, Palendira U. Tissue-resident regulatory T cells accumulate at human barrier lymphoid organs. Immunol Cell Biol 2021; 99:894-906. [PMID: 34080230 DOI: 10.1111/imcb.12481] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/19/2021] [Accepted: 05/31/2021] [Indexed: 12/17/2022]
Abstract
Regulatory T cells (Tregs) play a critical role in immune regulation and peripheral tolerance. While different types of Tregs have been identified in both mice and humans, much of our understanding about how these cells maintain immune homeostasis is derived from animal models. In this study, we examined two distinct human lymphoid organs to understand how repeated exposure to infections at the mucosal surface influences the phenotype and tissue localization of Tregs. We show that while Tregs in both tonsils and spleen express a tissue-resident phenotype, they accumulate in greater numbers in tonsils. Tonsillar-resident Tregs exhibit a highly suppressive phenotype with significantly increased expression of CD39, ICOS and CTLA-4 compared with their counterparts in circulation or in the spleen. Functionally, resident Tregs are able effectively to suppress T cell proliferation. We further demonstrate that tonsillar-resident Tregs share key features of T follicular helper cells. Spatial analysis reveals that the vast majority of resident Tregs are localized at the border of the T-zone and B cell follicle, as well as within the lymphocyte pockets enriched with resident memory T cells. Together our findings suggest that resident Tregs are strategically co-localized to maintain immune homeostasis at sites of recurrent inflammation.
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Affiliation(s)
- Rehana V Hewavisenti
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| | - Angela L Ferguson
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Centenary Institute, The University of Sydney, Sydney, NSW, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Georgia Gasparini
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Tomoki Ohashi
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Asolina Braun
- Department of Immunology and Microbiology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Thomas S Watkins
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - John J Miles
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Michael Elliott
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.,Chris O'Brien Lifehouse Cancer Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Frederic Sierro
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Australian Nuclear Science and Technology Organisation, Sydney, NSW, Australia
| | - Carl G Feng
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Centenary Institute, The University of Sydney, Sydney, NSW, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Warwick J Britton
- Centenary Institute, The University of Sydney, Sydney, NSW, Australia.,Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Thomas Gebhardt
- Department of Immunology and Microbiology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Stuart Tangye
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Umaimainthan Palendira
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Centenary Institute, The University of Sydney, Sydney, NSW, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
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3
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Smallwood TB, Navarro S, Cristofori-Armstrong B, Watkins TS, Tungatt K, Ryan RYM, Haigh OL, Lutzky VP, Mulvenna JP, Rosengren KJ, Loukas A, Miles JJ, Clark RJ. Synthetic hookworm-derived peptides are potent modulators of primary human immune cell function that protect against experimental colitis in vivo. J Biol Chem 2021; 297:100834. [PMID: 34051231 PMCID: PMC8239465 DOI: 10.1016/j.jbc.2021.100834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
The prevalence of autoimmune diseases is on the rise globally. Currently, autoimmunity presents in over 100 different forms and affects around 9% of the world's population. Current treatments available for autoimmune diseases are inadequate, expensive, and tend to focus on symptom management rather than cure. Clinical trials have shown that live helminthic therapy can decrease chronic inflammation associated with inflammatory bowel disease and other gastrointestinal autoimmune inflammatory conditions. As an alternative and better controlled approach to live infection, we have identified and characterized two peptides, Acan1 and Nak1, from the excretory/secretory component of parasitic hookworms for their therapeutic activity on experimental colitis. We synthesized Acan1 and Nak1 peptides from the Ancylostoma caninum and Necator americanus hookworms and assessed their structures and protective properties in human cell-based assays and in a mouse model of acute colitis. Acan1 and Nak1 displayed anticolitic properties via significantly reducing weight loss and colon atrophy, edema, ulceration, and necrosis in 2,4,6-trinitrobenzene sulfonic acid-exposed mice. These hookworm peptides prevented mucosal loss of goblet cells and preserved intestinal architecture. Acan1 upregulated genes responsible for the repair and restitution of ulcerated epithelium, whereas Nak1 downregulated genes responsible for epithelial cell migration and apoptotic cell signaling within the colon. These peptides were nontoxic and displayed key immunomodulatory functions in human peripheral blood mononuclear cells by suppressing CD4+ T cell proliferation and inhibiting IL-2 and TNF production. We conclude that Acan1 and Nak1 warrant further development as therapeutics for the treatment of autoimmunity, particularly gastrointestinal inflammatory conditions.
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Affiliation(s)
- Taylor B Smallwood
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, QLD, Australia
| | - Severine Navarro
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; The Australian Institute of Tropical Health and Medicine, James Cook University, QLD, Australia; Woolworths Centre for Child Nutrition Research, Institute of Health and Biomedical Innovation, Queensland University of Technology, QLD, Australia
| | - Ben Cristofori-Armstrong
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, QLD, Australia
| | - Thomas S Watkins
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; Centre for Molecular Therapeutics, The Australian Institute of Tropical Health and Medicine, James Cook University, QLD, Australia
| | - Katie Tungatt
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; Centre for Molecular Therapeutics, The Australian Institute of Tropical Health and Medicine, James Cook University, QLD, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, QLD, Australia
| | - Rachael Y M Ryan
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; The Australian Institute of Tropical Health and Medicine, James Cook University, QLD, Australia; Centre for Molecular Therapeutics, The Australian Institute of Tropical Health and Medicine, James Cook University, QLD, Australia
| | - Oscar L Haigh
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Viviana P Lutzky
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jason P Mulvenna
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - K Johan Rosengren
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, QLD, Australia
| | - Alex Loukas
- Centre for Molecular Therapeutics, The Australian Institute of Tropical Health and Medicine, James Cook University, QLD, Australia
| | - John J Miles
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; The Australian Institute of Tropical Health and Medicine, James Cook University, QLD, Australia; Centre for Molecular Therapeutics, The Australian Institute of Tropical Health and Medicine, James Cook University, QLD, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, QLD, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, University Hospital, Cardiff, Wales, United Kingdom.
| | - Richard J Clark
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, QLD, Australia.
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4
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Watkins TS, Miles JJ. The human T-cell receptor repertoire in health and disease and potential for omics integration. Immunol Cell Biol 2020; 99:135-145. [PMID: 32677130 DOI: 10.1111/imcb.12377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/07/2020] [Accepted: 07/12/2020] [Indexed: 12/11/2022]
Abstract
The adaptive immune system arose 600 million years ago in a cold-blooded fish. Over countless generations, our antecedents tuned the function of the T-cell receptor (TCR). The TCR system is arguably the most complex known to science. The TCR evolved hypervariability to fight the hypervariability of pathogens and cancers that look to consume our resources. This review describes the genetics and architecture of the human TCR and highlights surprising new discoveries over the past years that have disproved very old dogmas. The standardization of TCR sequencing data is discussed in preparation for big data bioinformatics and predictive analysis. We next catalogue new signatures and phenomenon discovered by TCR next generation sequencing (NGS) in health and disease and work that remain to be done in this space. Finally, we discuss how TCR NGS can add to immunodiagnostics and integrate with other omics platforms for both a deeper understanding of TCR biology and its use in the clinical setting.
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Affiliation(s)
- Thomas S Watkins
- The Australian Institute of Tropical Health and Medicine (AITHM), James Cook University, Cairns, QLD, Australia.,Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD, Australia
| | - John J Miles
- The Australian Institute of Tropical Health and Medicine (AITHM), James Cook University, Cairns, QLD, Australia.,Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD, Australia
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5
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Vuckovic S, Minnie SA, Smith D, Gartlan KH, Watkins TS, Markey KA, Mukhopadhyay P, Guillerey C, Kuns RD, Locke KR, Pritchard AL, Johansson PA, Varelias A, Zhang P, Huntington ND, Waddell N, Chesi M, Miles JJ, Smyth MJ, Hill GR. Bone marrow transplantation generates T cell-dependent control of myeloma in mice. J Clin Invest 2018; 129:106-121. [PMID: 30300141 DOI: 10.1172/jci98888] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 10/02/2018] [Indexed: 12/14/2022] Open
Abstract
Transplantation with autologous hematopoietic progenitors remains an important consolidation treatment for patients with multiple myeloma (MM) and is thought to prolong the disease plateau phase by providing intensive cytoreduction. However, transplantation induces inflammation in the context of profound lymphodepletion that may cause hitherto unexpected immunological effects. We developed preclinical models of bone marrow transplantation (BMT) for MM using Vk*MYC myeloma-bearing recipient mice and donor mice that were myeloma naive or myeloma experienced to simulate autologous transplantation. Surprisingly, we demonstrated broad induction of T cell-dependent myeloma control, most efficiently from memory T cells within myeloma-experienced grafts, but also through priming of naive T cells after BMT. CD8+ T cells from mice with controlled myeloma had a distinct T cell receptor (TCR) repertoire and higher clonotype overlap relative to myeloma-free BMT recipients. Furthermore, T cell-dependent myeloma control could be adoptively transferred to secondary recipients and was myeloma cell clone specific. Interestingly, donor-derived IL-17A acted directly on myeloma cells expressing the IL-17 receptor to induce a transcriptional landscape that promoted tumor growth and immune escape. Conversely, donor IFN-γ secretion and signaling were critical to protective immunity and were profoundly augmented by CD137 agonists. These data provide new insights into the mechanisms of action of transplantation in myeloma and provide rational approaches to improving clinical outcomes.
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Affiliation(s)
- Slavica Vuckovic
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Faculty of Medicine, The University of Queensland, Herston, Australia.,Multiple Myeloma Research Group, Institute of Haematology, Royal Prince Alfred Hospital, Camperdown, Australia
| | - Simone A Minnie
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Faculty of Medicine, The University of Queensland, Herston, Australia
| | - David Smith
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kate H Gartlan
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Faculty of Medicine, The University of Queensland, Herston, Australia.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Kate A Markey
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Faculty of Medicine, The University of Queensland, Herston, Australia.,Division of Immunology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Camille Guillerey
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Faculty of Medicine, The University of Queensland, Herston, Australia
| | - Rachel D Kuns
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kelly R Locke
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Antonia L Pritchard
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Genetics and Immunology, University of the Highlands and Islands, Inverness, United Kingdom
| | | | - Antiopi Varelias
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Faculty of Medicine, The University of Queensland, Herston, Australia
| | - Ping Zhang
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Nicholas D Huntington
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology and.,Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Marta Chesi
- Comprehensive Cancer Center, Mayo Clinic, Scottsdale, Arizona, USA
| | - John J Miles
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine (AITHM), James Cook University, Cairns, Australia
| | - Mark J Smyth
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Geoffrey R Hill
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Haematology, The Royal Brisbane and Women's Hospital, Brisbane, Australia.,Division of Medical Oncology, University of Washington, Seattle, Washington, USA
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6
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Lepletier A, Lutzky VP, Mittal D, Stannard K, Watkins TS, Ratnatunga CN, Smith C, McGuire HM, Kemp RA, Mukhopadhyay P, Waddell N, Smyth MJ, Dougall WC, Miles JJ. The immune checkpoint CD96 defines a distinct lymphocyte phenotype and is highly expressed on tumor-infiltrating T cells. Immunol Cell Biol 2018; 97:152-164. [PMID: 30222899 DOI: 10.1111/imcb.12205] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 09/13/2018] [Accepted: 09/13/2018] [Indexed: 12/01/2022]
Abstract
CD96 has recently been shown to be a potent immune checkpoint molecule in mice, but a similar role in humans is not known. In this study, we provide a detailed map of CD96 expression across human lymphocyte lineages, the kinetics of CD96 regulation on T-cell activation and co-expression with other conventional and emerging immune checkpoint molecules. We show that CD96 is predominantly expressed by T cells and has a unique lymphocyte expression profile. CD96high T cells exhibited distinct effector functions on activation. Of note, CD96 expression was highly correlated with T-cell markers in primary and metastatic human tumors and was elevated on antigen-experienced T cells and tumor-infiltrating lymphocytes. Collectively, these data demonstrate that CD96 may be a promising immune checkpoint to enhance T-cell function against human cancer and infectious disease.
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Affiliation(s)
- Ailin Lepletier
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Viviana P Lutzky
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Deepak Mittal
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kimberley Stannard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Thomas S Watkins
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia
| | - Champa N Ratnatunga
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia.,Centre for Biodiscovery and Molecular Development of Therapeutics, AITHM, James Cook University, Cairns, QLD 4870, Australia
| | - Corey Smith
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Helen M McGuire
- Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.,Ramaciotti Facility for Human Systems Biology, University of Sydney, Sydney, NSW 2006, Australia
| | - Roslyn A Kemp
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand
| | | | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Mark J Smyth
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - William C Dougall
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - John J Miles
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia.,Centre for Biodiscovery and Molecular Development of Therapeutics, AITHM, James Cook University, Cairns, QLD 4870, Australia.,Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK.,Medicine, Dentistry and Health, Griffith University, Brisbane, QLD 4111, Australia
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7
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Minnie S, Vuckovic S, Smith D, Gartlan KH, Watkins TS, Kuns RD, Guillerey C, Chesi M, Markey KA, Miles JJ, Smyth MJ, Hill GR. Syngeneic stem cell transplantation generates antigen-specific T cells that maintain myeloma-immune equilibrium. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.55.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Multiple myeloma (MM) is a largely incurable hematological malignancy characterized by clonal expansion of plasma cells in bone marrow (BM). Autologous stem cell transplantation (ASCT) remains a standard treatment for MM, allows intensive cytoreduction and induces inflammation in the context of lymphodepletion. We hypothesized that SCT may overcome myeloma-induced immune defects to restore immune-equilibrium. To address this, we developed a model of ASCT for MM using Vk*MYC myeloma. Surprisingly, we demonstrate the induction of T cell-dependent MM control after SCT as recipients of syngeneic BM grafts containing T cells had prolonged survival and reduced tumor burden compared to BM alone. This anti-myeloma activity was independent of γδ T, natural killer (NK) and NK T cells and was dependent on CD4+and CD8+ T cells. MM-primed T cells, harvested from SCT recipients with controlled MM, protected against relapse in secondary recipients and were Vk*MYC clone-specific. Recipients of MM-primed T cells had increased central memory CD8+ T cells and transfer of MM-primed CD8+ T cells was sufficient to prevent relapse. Furthermore, TCR sequencing of CD8+ T cells from mice with controlled MM revealed a higher clonotype overlap relative to MM-free SCT recipients, consistent with MM-specific T cells. Donor IFNγ secretion and signaling was critical to protective immunity and CD8+ T cells from mice with relapsed MM had impaired IFNγ production compared to those with controlled disease. Importantly, IFNγ production was profoundly augmented by CD137 agonist treatment such that majority of mice controlled disease. These data provide new insights into the mechanisms of action of SCT in myeloma and suggest the use of CD137 agonists to prevent relapse.
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Affiliation(s)
- Simone Minnie
- 1QIMR Berghofer Med. Res. Inst., Australia
- 2Faculty of Medicine, The University of Queensland, Australia
| | | | | | - Kate H. Gartlan
- 1QIMR Berghofer Med. Res. Inst., Australia
- 2Faculty of Medicine, The University of Queensland, Australia
| | - Thomas S. Watkins
- 1QIMR Berghofer Med. Res. Inst., Australia
- 3Centre for Biodiscovery and Molecular Development of Therapeutics, AITHM, James Cook University, Australia
| | | | | | | | - Kate A. Markey
- 1QIMR Berghofer Med. Res. Inst., Australia
- 2Faculty of Medicine, The University of Queensland, Australia
- 5Department of Haematology and Bone Marrow Transplantation, The Royal Brisbane and Women’s Hospital, Australia
| | - John J. Miles
- 3Centre for Biodiscovery and Molecular Development of Therapeutics, AITHM, James Cook University, Australia
| | | | - Geoffrey R. Hill
- 1QIMR Berghofer Med. Res. Inst., Australia
- 5Department of Haematology and Bone Marrow Transplantation, The Royal Brisbane and Women’s Hospital, Australia
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8
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Miles JJ, Tan MP, Dolton G, Edwards ES, Galloway SA, Laugel B, Clement M, Makinde J, Ladell K, Matthews KK, Watkins TS, Tungatt K, Wong Y, Lee HS, Clark RJ, Pentier JM, Attaf M, Lissina A, Ager A, Gallimore A, Rizkallah PJ, Gras S, Rossjohn J, Burrows SR, Cole DK, Price DA, Sewell AK. Peptide mimic for influenza vaccination using nonnatural combinatorial chemistry. J Clin Invest 2018; 128:1569-1580. [PMID: 29528337 PMCID: PMC5873848 DOI: 10.1172/jci91512] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/18/2018] [Indexed: 01/11/2023] Open
Abstract
Polypeptide vaccines effectively activate human T cells but suffer from poor biological stability, which confines both transport logistics and in vivo therapeutic activity. Synthetic biology has the potential to address these limitations through the generation of highly stable antigenic "mimics" using subunits that do not exist in the natural world. We developed a platform based on D-amino acid combinatorial chemistry and used this platform to reverse engineer a fully artificial CD8+ T cell agonist that mirrored the immunogenicity profile of a native epitope blueprint from influenza virus. This nonnatural peptide was highly stable in human serum and gastric acid, reflecting an intrinsic resistance to physical and enzymatic degradation. In vitro, the synthetic agonist stimulated and expanded an archetypal repertoire of polyfunctional human influenza virus-specific CD8+ T cells. In vivo, specific responses were elicited in naive humanized mice by subcutaneous vaccination, conferring protection from subsequent lethal influenza challenge. Moreover, the synthetic agonist was immunogenic after oral administration. This proof-of-concept study highlights the power of synthetic biology to expand the horizons of vaccine design and therapeutic delivery.
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Affiliation(s)
- John J. Miles
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Griffith University, Brisbane, Queensland, Australia
| | - Mai Ping Tan
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Garry Dolton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Emily S.J. Edwards
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Sarah A.E. Galloway
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Bruno Laugel
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Mathew Clement
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Julia Makinde
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | | | - Thomas S. Watkins
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Katie Tungatt
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Yide Wong
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Han Siean Lee
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Richard J. Clark
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Johanne M. Pentier
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Meriem Attaf
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Anya Lissina
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Ann Ager
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Awen Gallimore
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Pierre J. Rizkallah
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Stephanie Gras
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Scott R. Burrows
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - David K. Cole
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - David A. Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Andrew K. Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
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9
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McGuire HM, Watkins TS, Field M, Taylor S, Yasuyama N, Farmer A, Miles JJ, Fazekas de St. Groth B. TCR deep sequencing of transgenic RAG-1-deficient mice reveals endogenous TCR recombination: a cause for caution. Immunol Cell Biol 2018; 96:642-645. [DOI: 10.1111/imcb.12033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/27/2018] [Accepted: 02/27/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Helen M McGuire
- Centenary Institute; Camperdown NSW Australia
- Discipline of Pathology; School of Medical Sciences; Charles Perkins Centre; University of Sydney; NSW Australia
- Ramaciotti Facility for Human Systems Biology; Charles Perkins Centre; University of Sydney; NSW Australia
| | - Thomas S Watkins
- Centre for Biodiscovery and Molecular Development of Therapeutics; AITHM; James Cook University; Cairns QLD Australia
- QIMR Berghofer Medical Research Institute; Brisbane QLD Australia
- Faculty of Medicine; The University of Queensland; Brisbane QLD Australia
| | - Matthew Field
- Centre for Biodiscovery and Molecular Development of Therapeutics; AITHM; James Cook University; Cairns QLD Australia
| | - Sarah Taylor
- Takara Bio USA, Inc.; 1290 Terra Bella Ave, Mountain View CA USA
| | - Nao Yasuyama
- Takara Bio USA, Inc.; 1290 Terra Bella Ave, Mountain View CA USA
| | - Andrew Farmer
- Takara Bio USA, Inc.; 1290 Terra Bella Ave, Mountain View CA USA
| | - John J Miles
- Centre for Biodiscovery and Molecular Development of Therapeutics; AITHM; James Cook University; Cairns QLD Australia
- QIMR Berghofer Medical Research Institute; Brisbane QLD Australia
- Faculty of Medicine; The University of Queensland; Brisbane QLD Australia
- Institute of Infection and Immunity; Cardiff University School of Medicine; Heath Park Cardiff UK
| | - Barbara Fazekas de St. Groth
- Discipline of Pathology; School of Medical Sciences; Charles Perkins Centre; University of Sydney; NSW Australia
- Ramaciotti Facility for Human Systems Biology; Charles Perkins Centre; University of Sydney; NSW Australia
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10
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Watkins TS, Miles JJ. Erratum: Tracking the T-cell repertoire after adoptive therapy. Clin Transl Immunology 2017; 6:e146. [PMID: 28695922 PMCID: PMC5493591 DOI: 10.1038/cti.2017.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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11
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Affiliation(s)
- Thomas S Watkins
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia.,School of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John J Miles
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia.,School of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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12
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Proietti C, Zakrzewski M, Watkins TS, Berger B, Hasan S, Ratnatunga CN, Brion MJ, Crompton PD, Miles JJ, Doolan DL, Krause L. Mining, visualizing and comparing multidimensional biomolecular data using the Genomics Data Miner (GMine) Web-Server. Sci Rep 2016; 6:38178. [PMID: 27922118 PMCID: PMC5138638 DOI: 10.1038/srep38178] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/04/2016] [Indexed: 12/21/2022] Open
Abstract
Genomics Data Miner (GMine) is a user-friendly online software that allows non-experts to mine, cluster and compare multidimensional biomolecular datasets. Various powerful visualization techniques are provided, generating high quality figures that can be directly incorporated into scientific publications. Robust and comprehensive analyses are provided via a broad range of data-mining techniques, including univariate and multivariate statistical analysis, supervised learning, correlation networks, clustering and multivariable regression. The software has a focus on multivariate techniques, which can attribute variance in the measurements to multiple explanatory variables and confounders. Various normalization methods are provided. Extensive help pages and a tutorial are available via a wiki server. Using GMine we reanalyzed proteome microarray data of host antibody response against Plasmodium falciparum. Our results support the hypothesis that immunity to malaria is a higher-order phenomenon related to a pattern of responses and not attributable to any single antigen. We also analyzed gene expression across resting and activated T cells, identifying many immune-related genes with differential expression. This highlights both the plasticity of T cells and the operation of a hardwired activation program. These application examples demonstrate that GMine facilitates an accurate and in-depth analysis of complex molecular datasets, including genomics, transcriptomics and proteomics data.
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Affiliation(s)
- Carla Proietti
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Thomas S Watkins
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Bernard Berger
- Nestlé Research Centre, Vers-chez-les-Blanc, Lausanne, Switzerland
| | - Shihab Hasan
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | | | - Marie-Jo Brion
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA
| | - John J Miles
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Centre for Biosecurity and Tropical Infectious Diseases, Australian Institute of Tropical Health &Medicine, James Cook University, Cairns, QLD, Australia
| | - Denise L Doolan
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Centre for Biosecurity and Tropical Infectious Diseases, Australian Institute of Tropical Health &Medicine, James Cook University, Cairns, QLD, Australia
| | - Lutz Krause
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
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13
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Karunarathne DS, Horne-Debets JM, Huang JX, Faleiro R, Leow CY, Amante F, Watkins TS, Miles JJ, Dwyer PJ, Stacey KJ, Yarski M, Poh CM, Lee JS, Cooper MA, Rénia L, Richard D, McCarthy JS, Sharpe AH, Wykes MN. Programmed Death-1 Ligand 2-Mediated Regulation of the PD-L1 to PD-1 Axis Is Essential for Establishing CD4 + T Cell Immunity. Immunity 2016; 45:333-45. [DOI: 10.1016/j.immuni.2016.07.017] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/28/2016] [Accepted: 05/19/2016] [Indexed: 12/31/2022]
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14
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Neller MA, Ladell K, McLaren JE, Matthews KK, Gostick E, Pentier JM, Dolton G, Schauenburg AJA, Koning D, Fontaine Costa AICA, Watkins TS, Venturi V, Smith C, Khanna R, Miners K, Clement M, Wooldridge L, Cole DK, van Baarle D, Sewell AK, Burrows SR, Price DA, Miles JJ. Naive CD8⁺ T-cell precursors display structured TCR repertoires and composite antigen-driven selection dynamics. Immunol Cell Biol 2015; 93:625-33. [PMID: 25801351 PMCID: PMC4533101 DOI: 10.1038/icb.2015.17] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 01/04/2015] [Accepted: 01/22/2015] [Indexed: 02/07/2023]
Abstract
Basic parameters of the naive antigen (Ag)-specific T-cell repertoire in humans remain poorly defined. Systematic characterization of this ‘ground state' immunity in comparison with memory will allow a better understanding of clonal selection during immune challenge. Here, we used high-definition cell isolation from umbilical cord blood samples to establish the baseline frequency, phenotype and T-cell antigen receptor (TCR) repertoire of CD8+ T-cell precursor populations specific for a range of viral and self-derived Ags. Across the board, these precursor populations were phenotypically naive and occurred with hierarchical frequencies clustered by Ag specificity. The corresponding patterns of TCR architecture were highly ordered and displayed partial overlap with adult memory, indicating biased structuring of the T-cell repertoire during Ag-driven selection. Collectively, these results provide new insights into the complex nature and dynamics of the naive T-cell compartment.
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Affiliation(s)
- Michelle A Neller
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Kristin Ladell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - James E McLaren
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Katherine K Matthews
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Emma Gostick
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Johanne M Pentier
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Garry Dolton
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Andrea J A Schauenburg
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Dan Koning
- Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Thomas S Watkins
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Vanessa Venturi
- Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW, Australia
| | - Corey Smith
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Rajiv Khanna
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Kelly Miners
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Mathew Clement
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Linda Wooldridge
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - David K Cole
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Debbie van Baarle
- Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Andrew K Sewell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Scott R Burrows
- 1] Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia [2] School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - David A Price
- 1] Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK [2] Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John J Miles
- 1] Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia [2] Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK [3] School of Medicine, The University of Queensland, Brisbane, QLD, Australia
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