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Epstein M, Pike R, Leire E, Middleton J, Wileman M, Ouboussad L, Manning L, Oakes T, Pekle E, Baker A, Brown M, Melandri D, Becker P, Ramirez A, Hadjistephanou N, Turaljic S, Jamal-Hanjani M, Forster M, Ali I, Robertson J, Peggs K, Quezada S. Abstract 1508: Characterization of a novel clonal neoantigen reactive T cell (cNeT) product through a comprehensive translational research program. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-1508] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Adoptive cell therapy (ACT) using ex vivo expanded tumor infiltrating lymphocytes (TIL) has shown great promise as a treatment for metastatic melanoma and has the potential to deliver durable responses in other solid tumors. Clonal neoantigens, which are derived from mutations occurring very early in the tumor development, are present in all cancer cells within a patient and therefore could be the optimal targets for TIL-based therapies. Recently it was shown that the number of clonal neoantigens within a tumor is associated with improved clinical outcomes following checkpoint inhibition in patients with non-small cell lung cancer (NSCLC) and melanoma. An approach that targets multiple clonal neoantigens with specific T cells has the potential to demonstrate high specificity and efficacy whilst mitigating the risk of immune escape.
Achilles Therapeutics is developing a personalized ACT product, ATL001, to target clonal neoantigens, which are identified using tumor exome sequencing and the PELEUS™ bioinformatics platform. Clonal neoantigen reactive T cells (cNeTs) are then manufactured from TIL using the VELOS™ manufacturing process. Two Phase I/IIa clinical trials of ATL001 are ongoing in patients with advanced NSCLC and metastatic or recurrent melanoma.
In common with the development of other ACT products, the key to characterizing and improving cNeT products relies on evaluating a diverse set of exploratory endpoints in early clinical trials, including understanding the procedural, clinical and biological factors that influence cNeT manufacturing rate and product reactivity; monitoring the expansion, persistence and phenotype of the infused cells in vivo and identifying potential biomarkers of clinical activity or safety of cNeTs in treated patients. These insights may suggest further improvements to cNeT product development in ensuing iterations.
The evaluation of these endpoints requires the collection of a rich longitudinal dataset that traces each patient's journey from tissue procurement and cNeT manufacture, to final product infusion and follow up. The data collected will include clinical and disease characteristics, tumor microenvironment insights from exome sequencing and immunohistochemistry of procured tumor, and metrics from the VELOS™ manufacturing process, along with a comprehensive immune-monitoring programme comprising immuno-sequencing, immunophenotyping, bespoke ctDNA panels and reactivity assays at specified timepoints, all to be evaluated against clinical outcomes data. The amalgamation of diverse streams of data requires the development of robust processes and systems for data collection, processing and storage. Furthermore, the evaluation of multiple exploratory endpoints will require integration and modelling of baseline covariates, time-series immune-monitoring and efficacy data, all of which will be described
Citation Format: Michael Epstein, Rebecca Pike, Emma Leire, Jen Middleton, Megan Wileman, Lylia Ouboussad, Leah Manning, Theres Oakes, Eva Pekle, Amy Baker, Mark Brown, Daisy Melandri, Pablo Becker, Anabel Ramirez, Natasa Hadjistephanou, Samra Turaljic, Mariam Jamal-Hanjani, Martin Forster, Iraj Ali, Jane Robertson, Karl Peggs, Sergio Quezada. Characterization of a novel clonal neoantigen reactive T cell (cNeT) product through a comprehensive translational research program [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1508.
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Affiliation(s)
| | | | - Emma Leire
- 1Achilles Therapeutics, London, United Kingdom
| | | | | | | | | | | | - Eva Pekle
- 1Achilles Therapeutics, London, United Kingdom
| | - Amy Baker
- 1Achilles Therapeutics, London, United Kingdom
| | - Mark Brown
- 1Achilles Therapeutics, London, United Kingdom
| | | | | | | | | | | | | | | | - Iraj Ali
- 1Achilles Therapeutics, London, United Kingdom
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2
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Barennes P, Quiniou V, Shugay M, Egorov ES, Davydov AN, Chudakov DM, Uddin I, Ismail M, Oakes T, Chain B, Eugster A, Kashofer K, Rainer PP, Darko S, Ransier A, Douek DC, Klatzmann D, Mariotti-Ferrandiz E. Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases. Nat Biotechnol 2021; 39:236-245. [PMID: 32895550 DOI: 10.1038/s41587-020-0656-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/28/2020] [Indexed: 12/13/2022]
Abstract
Monitoring the T cell receptor (TCR) repertoire in health and disease can provide key insights into adaptive immune responses, but the accuracy of current TCR sequencing (TCRseq) methods is unclear. In this study, we systematically compared the results of nine commercial and academic TCRseq methods, including six rapid amplification of complementary DNA ends (RACE)-polymerase chain reaction (PCR) and three multiplex-PCR approaches, when applied to the same T cell sample. We found marked differences in accuracy and intra- and inter-method reproducibility for T cell receptor α (TRA) and T cell receptor β (TRB) TCR chains. Most methods showed a lower ability to capture TRA than TRB diversity. Low RNA input generated non-representative repertoires. Results from the 5' RACE-PCR methods were consistent among themselves but differed from the RNA-based multiplex-PCR results. Using an in silico meta-repertoire generated from 108 replicates, we found that one genomic DNA-based method and two non-unique molecular identifier (UMI) RNA-based methods were more sensitive than UMI methods in detecting rare clonotypes, despite the better clonotype quantification accuracy of the latter.
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Affiliation(s)
- Pierre Barennes
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Valentin Quiniou
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Mikhail Shugay
- Center of Life Sciences, Skoltech, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Evgeniy S Egorov
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Alexey N Davydov
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czechia
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skoltech, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czechia
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK
| | - Anne Eugster
- DFG-Centre for Regenerative Therapies Dresden, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Karl Kashofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Peter P Rainer
- Division of Cardiology, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Samuel Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy Ransier
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Klatzmann
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Encarnita Mariotti-Ferrandiz
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France.
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3
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Ronel T, Harries M, Wicks K, Oakes T, Singleton H, Dearman R, Maxwell G, Chain B. The clonal structure and dynamics of the human T cell response to an organic chemical hapten. eLife 2021; 10:54747. [PMID: 33432924 PMCID: PMC7880692 DOI: 10.7554/elife.54747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 01/12/2021] [Indexed: 12/27/2022] Open
Abstract
Diphenylcyclopropenone (DPC) is an organic chemical hapten which induces allergic contact dermatitis and is used in the treatment of warts, melanoma, and alopecia areata. This therapeutic setting therefore provided an opportunity to study T cell receptor (TCR) repertoire changes in response to hapten sensitization in humans. Repeated exposure to DPC induced highly dynamic transient expansions of a polyclonal diverse T cell population. The number of TCRs expanded early after sensitization varies between individuals and predicts the magnitude of the allergic reaction. The expanded TCRs show preferential TCR V and J gene usage and consist of clusters of TCRs with similar sequences, two characteristic features of antigen-driven responses. The expanded TCRs share subtle sequence motifs that can be captured using a dynamic Bayesian network. These observations suggest the response to DPC is mediated by a polyclonal population of T cells recognizing a small number of dominant antigens.
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Affiliation(s)
- Tahel Ronel
- Division of Infection and Immunity, University College London, London, United Kingdom.,Cancer Institute, University College London, London, United Kingdom
| | - Matthew Harries
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.,Salford Royal NHS Foundation Trust (Dermatology Centre), Salford, United Kingdom
| | - Kate Wicks
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Helen Singleton
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Rebecca Dearman
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Gavin Maxwell
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Bedford, United Kingdom
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom.,Department of Computer Science, University College London, London, United Kingdom
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4
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Kotsiou E, Hou TZ, Robinson J, Varsani S, Oakes T, Becker PD, Patel S, Mootien J, Craig A, Robertson J, Samuel E, Reading J, Rosario LD, Haynes A, Turajlic S, Islam F, Lawrence D, Jamal-Hanjani M, Foster M, Quezada SA, Newton K. Abstract 875: Next generation clonal neoantigen targeting T cells, generated using the PELEUSTM bioinformatics platform and the VELOSTM manufacturing method show superior reactivity and phenotypic characteristics than classical TIL products. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-875] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Adoptive transfer of tumor infiltrating lymphocytes (TIL) has generated objective clinical responses in patients with advanced metastatic cancers. Therapeutic exploitation of neoantigens as targets can potentially lead to safer and more effective treatment modalities with reduced toxicities. The Achilles Therapeutics trial NCT03517917 enabled the acquisition of matched tumor specimens and peripheral blood samples from patients undergoing routine surgery and facilitated the development of the proprietary VELOSTM manufacturing process, generating a personalized clonal neoantigen specific T cell product. An in-depth characterization of T cells expanded with the VELOSTM process was performed and compared to a standard TIL product. Samples were obtained from patients with primary NSCLC or metastatic melanoma. TIL were expanded from tumor fragments after dissection in the presence of IL-2. Peptide pools corresponding to the clonal mutations that were identified using the PELEUSTM bioinformatics platform were used to pulse dendritic cells (DC) generated from peripheral blood monocytes from each patient. Clonal neoantigen specific T cells (cNeT) were expanded using the VELOSTM process by co-culture of TIL with the peptide-pulsed autologous DC. As a comparison, TIL were expanded with a rapid expansion protocol (REP-TIL) in the presence of allogeneic feeders, anti-CD3 antibody and high-dose IL-2. Intracellular cytokine staining was performed following rechallenge with individual peptide pools encoding the clonal mutations. Single peptide reactivities were identified using ELISPOT and extended flow cytometric analysis of markers associated with T cell fitness or dysfunction was performed to phenotypically characterize the cNeT, TIL and REP-TIL. Analysis of the immune cell composition showed that cNeT, TIL and REP-TIL have similar CD3+ T cell content (median cNeT 90.2%, TIL 87.3%, REP-TIL 95%, n=6) and are composed of CD4+ and CD8+ T cells (median CD4:CD8 ratio- cNeT 11.1, TIL 2.03 and REP-TIL 4.7, n=6). cNeT showed superior clonal neoantigen specificity compared to TIL or REP-TIL. The proportion of CD3+ T cells responding to clonal neoantigen rechallenge was increased in cNeT (median 24.3%) compared to TIL (median 0.6%) and REP-TIL (median 1.8%) (n=5). The VELOSTM process incorporating the PELEUSTM platform for prediction of clonal neoantigens generates T cell products enriched for clonal neoantigen reactivities and superior phenotypic characteristics compared to conventional TIL. The VELOSTM process is currently being used to manufacture cNeT for two first-in-human studies including NSCLC and melanoma patients (NCT04032847, NCT03997474). Ethical approval: The samples for the study were collected under an ethically approved protocol (NCT03517917).
Citation Format: Eleni Kotsiou, Tie Zheng Hou, Joseph Robinson, Sonal Varsani, Theres Oakes, Pablo D. Becker, Shreenal Patel, Jennine Mootien, Andrew Craig, Jane Robertson, Edward Samuel, James Reading, Lyra Del Rosario, Andrew Haynes, Samra Turajlic, Farah Islam, David Lawrence, Mariam Jamal-Hanjani, Martin Foster, Sergio A. Quezada, Katy Newton. Next generation clonal neoantigen targeting T cells, generated using the PELEUSTM bioinformatics platform and the VELOSTM manufacturing method show superior reactivity and phenotypic characteristics than classical TIL products [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 875.
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Affiliation(s)
- Eleni Kotsiou
- 1Achilles Therapeutics Limited, Stevenage, United Kingdom
| | - Tie Zheng Hou
- 1Achilles Therapeutics Limited, Stevenage, United Kingdom
| | | | - Sonal Varsani
- 1Achilles Therapeutics Limited, Stevenage, United Kingdom
| | - Theres Oakes
- 1Achilles Therapeutics Limited, Stevenage, United Kingdom
| | | | - Shreenal Patel
- 1Achilles Therapeutics Limited, Stevenage, United Kingdom
| | | | - Andrew Craig
- 1Achilles Therapeutics Limited, Stevenage, United Kingdom
| | - Jane Robertson
- 1Achilles Therapeutics Limited, Stevenage, United Kingdom
| | - Edward Samuel
- 1Achilles Therapeutics Limited, Stevenage, United Kingdom
| | - James Reading
- 2University College London Cancer Institute, London, United Kingdom
| | | | - Andrew Haynes
- 3Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Samra Turajlic
- 3Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Farah Islam
- 2University College London Cancer Institute, London, United Kingdom
| | | | | | - Martin Foster
- 2University College London Cancer Institute, London, United Kingdom
| | | | - Katy Newton
- 1Achilles Therapeutics Limited, Stevenage, United Kingdom
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5
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Joshi K, de Massy MR, Ismail M, Reading JL, Uddin I, Woolston A, Hatipoglu E, Oakes T, Rosenthal R, Peacock T, Ronel T, Noursadeghi M, Turati V, Furness AJS, Georgiou A, Wong YNS, Ben Aissa A, Sunderland MW, Jamal-Hanjani M, Veeriah S, Birkbak NJ, Wilson GA, Hiley CT, Ghorani E, Guerra-Assunção JA, Herrero J, Enver T, Hadrup SR, Hackshaw A, Peggs KS, McGranahan N, Swanton C, Quezada SA, Chain B. Publisher Correction: Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer. Nat Med 2020; 26:1148. [PMID: 32494063 DOI: 10.1038/s41591-020-0866-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Kroopa Joshi
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Marc Robert de Massy
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, UK
| | - Annemarie Woolston
- Division of Infection and Immunity, University College London, London, UK
| | - Emine Hatipoglu
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Thomas Peacock
- Division of Infection and Immunity, University College London, London, UK
- Computation, Mathematics and Physics in the Life Sciences and Experimental Biology, Department of Computer Science, University College London, London, UK
| | - Tahel Ronel
- Division of Infection and Immunity, University College London, London, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Virginia Turati
- Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Andrew J S Furness
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Andrew Georgiou
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Yien Ning Sophia Wong
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Assma Ben Aissa
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Ehsan Ghorani
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | | | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Tariq Enver
- University College London Cancer Institute, London, UK
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Allan Hackshaw
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Karl S Peggs
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK.
- Department of Computer Sciences, University College London, London, UK.
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6
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Ghorani E, Reading JL, Henry JY, Massy MRD, Rosenthal R, Turati V, Joshi K, Furness AJS, Ben Aissa A, Saini SK, Ramskov S, Georgiou A, Sunderland MW, Wong YNS, Mucha MVD, Day W, Galvez-Cancino F, Becker PD, Uddin I, Oakes T, Ismail M, Ronel T, Woolston A, Jamal-Hanjani M, Veeriah S, Birkbak NJ, Wilson GA, Litchfield K, Conde L, Guerra-Assunção JA, Blighe K, Biswas D, Salgado R, Lund T, Bakir MA, Moore DA, Hiley CT, Loi S, Sun Y, Yuan Y, AbdulJabbar K, Turajilic S, Herrero J, Enver T, Hadrup SR, Hackshaw A, Peggs KS, McGranahan N, Chain B, Swanton C, Quezada SA. The T cell differentiation landscape is shaped by tumour mutations in lung cancer. Nat Cancer 2020; 1:546-561. [PMID: 32803172 PMCID: PMC7115931 DOI: 10.1038/s43018-020-0066-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/20/2020] [Indexed: 01/06/2023]
Abstract
Tumour mutational burden (TMB) predicts immunotherapy outcome in non-small cell lung cancer (NSCLC), consistent with immune recognition of tumour neoantigens. However, persistent antigen exposure is detrimental for T cell function. How TMB affects CD4 and CD8 T cell differentiation in untreated tumours, and whether this affects patient outcomes is unknown. Here we paired high-dimensional flow cytometry, exome, single-cell and bulk RNA sequencing from patients with resected, untreated NSCLC to examine these relationships. TMB was associated with compartment-wide T cell differentiation skewing, characterized by loss of TCF7-expressing progenitor-like CD4 T cells, and an increased abundance of dysfunctional CD8 and CD4 T cell subsets, with significant phenotypic and transcriptional similarity to neoantigen-reactive CD8 T cells. A gene signature of redistribution from progenitor-like to dysfunctional states associated with poor survival in lung and other cancer cohorts. Single-cell characterization of these populations informs potential strategies for therapeutic manipulation in NSCLC.
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Affiliation(s)
- Ehsan Ghorani
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Jake Y Henry
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Marc Robert de Massy
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Virginia Turati
- Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Kroopa Joshi
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Andrew J S Furness
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Assma Ben Aissa
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sunil Kumar Saini
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Sofie Ramskov
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Andrew Georgiou
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Yien Ning Sophia Wong
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Maria Vila De Mucha
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - William Day
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Felipe Galvez-Cancino
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Pablo D Becker
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, UK
| | - Tahel Ronel
- Division of Infection and Immunity, University College London, London, UK
| | - Annemarie Woolston
- Division of Infection and Immunity, University College London, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Lucia Conde
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | | | - Kevin Blighe
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Dhruva Biswas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Tom Lund
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - David A Moore
- Department of Pathology, University College London Cancer Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Yuxin Sun
- Division of Infection and Immunity, University College London, London, UK
| | - Yinyin Yuan
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Khalid AbdulJabbar
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Samra Turajilic
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Tariq Enver
- Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Allan Hackshaw
- Cancer Research UK and University College London Cancer Trials Centre, London, UK
| | - Karl S Peggs
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK
- Department of Computer Sciences, University College London, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- University College London Hospitals, London, UK.
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
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7
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de Greef PC, Oakes T, Gerritsen B, Ismail M, Heather JM, Hermsen R, Chain B, de Boer RJ. The naive T-cell receptor repertoire has an extremely broad distribution of clone sizes. eLife 2020; 9:e49900. [PMID: 32187010 PMCID: PMC7080410 DOI: 10.7554/elife.49900] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [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: 07/03/2019] [Accepted: 03/03/2020] [Indexed: 12/24/2022] Open
Abstract
The clone size distribution of the human naive T-cell receptor (TCR) repertoire is an important determinant of adaptive immunity. We estimated the abundance of TCR sequences in samples of naive T cells from blood using an accurate quantitative sequencing protocol. We observe most TCR sequences only once, consistent with the enormous diversity of the repertoire. However, a substantial number of sequences were observed multiple times. We detect abundant TCR sequences even after exclusion of methodological confounders such as sort contamination, and multiple mRNA sampling from the same cell. By combining experimental data with predictions from models we describe two mechanisms contributing to TCR sequence abundance. TCRα abundant sequences can be primarily attributed to many identical recombination events in different cells, while abundant TCRβ sequences are primarily derived from large clones, which make up a small percentage of the naive repertoire, and could be established early in the development of the T-cell repertoire.
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MESH Headings
- Adaptive Immunity
- Algorithms
- Antigens/immunology
- Clonal Evolution/genetics
- Computational Biology/methods
- High-Throughput Nucleotide Sequencing
- Humans
- Immunologic Memory
- Models, Biological
- Organ Specificity/genetics
- Organ Specificity/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- V(D)J Recombination
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Affiliation(s)
- Peter C de Greef
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
| | - Theres Oakes
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Bram Gerritsen
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
- Department of Pathology, Yale School of MedicineNew HavenUnited States
| | - Mazlina Ismail
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - James M Heather
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Rutger Hermsen
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
| | - Benjamin Chain
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
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8
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Lanteri-Minet M, Kalidas K, Oakes T, Bardos J, Zhou C, Wenzel R, Yang J, Aurora S. Acute and preventive treatment use in a phase-3 randomized trial of galcanezumab in chronic cluster headache. J Neurol Sci 2019. [DOI: 10.1016/j.jns.2019.10.334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Joshi K, de Massy MR, Ismail M, Reading JL, Uddin I, Woolston A, Hatipoglu E, Oakes T, Rosenthal R, Peacock T, Ronel T, Noursadeghi M, Turati V, Furness AJS, Georgiou A, Wong YNS, Ben Aissa A, Sunderland MW, Jamal-Hanjani M, Veeriah S, Birkbak NJ, Wilson GA, Hiley CT, Ghorani E, Guerra-Assunção JA, Herrero J, Enver T, Hadrup SR, Hackshaw A, Peggs KS, McGranahan N, Swanton C, Quezada SA, Chain B. Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer. Nat Med 2019; 25:1549-1559. [PMID: 31591606 PMCID: PMC6890490 DOI: 10.1038/s41591-019-0592-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
Abstract
Somatic mutations together with immunoediting drive extensive heterogeneity within non-small-cell lung cancer (NSCLC). Herein we examine heterogeneity of the T cell antigen receptor (TCR) repertoire. The number of TCR sequences selectively expanded in tumors varies within and between tumors and correlates with the number of nonsynonymous mutations. Expanded TCRs can be subdivided into TCRs found in all tumor regions (ubiquitous) and those present in a subset of regions (regional). The number of ubiquitous and regional TCRs correlates with the number of ubiquitous and regional nonsynonymous mutations, respectively. Expanded TCRs form part of clusters of TCRs of similar sequence, suggestive of a spatially constrained antigen-driven process. CD8+ tumor-infiltrating lymphocytes harboring ubiquitous TCRs display a dysfunctional tissue-resident phenotype. Ubiquitous TCRs are preferentially detected in the blood at the time of tumor resection as compared to routine follow-up. These findings highlight a noninvasive method to identify and track relevant tumor-reactive TCRs for use in adoptive T cell immunotherapy.
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MESH Headings
- Aged
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/pathology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/therapy
- Female
- Genetic Heterogeneity
- Humans
- Immunotherapy, Adoptive
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/pathology
- Male
- Middle Aged
- Mutation
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
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Affiliation(s)
- Kroopa Joshi
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Marc Robert de Massy
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, UK
| | - Annemarie Woolston
- Division of Infection and Immunity, University College London, London, UK
| | - Emine Hatipoglu
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Thomas Peacock
- Division of Infection and Immunity, University College London, London, UK
- Computation, Mathematics and Physics in the Life Sciences and Experimental Biology, Department of Computer Science, University College London, London, UK
| | - Tahel Ronel
- Division of Infection and Immunity, University College London, London, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Virginia Turati
- Department of Cancer Biology, University College London Cancer Institute, London, UK
| | - Andrew J S Furness
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Andrew Georgiou
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Yien Ning Sophia Wong
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Assma Ben Aissa
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Ehsan Ghorani
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | | | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Tariq Enver
- University College London Cancer Institute, London, UK
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Allan Hackshaw
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Karl S Peggs
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK.
- Department of Computer Sciences, University College London, London, UK.
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10
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Uddin I, Joshi K, Oakes T, Heather JM, Swanton C, Chain B. An Economical, Quantitative, and Robust Protocol for High-Throughput T Cell Receptor Sequencing from Tumor or Blood. Methods Mol Biol 2019; 1884:15-42. [PMID: 30465193 DOI: 10.1007/978-1-4939-8885-3_2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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] [Indexed: 12/23/2022]
Abstract
The T cell receptor repertoire provides a window to the cellular adaptive immune response within a tumor, and has the potential to identify specific and personalized biomarkers for tracking host responses during cancer therapy, including immunotherapy. We describe a protocol for amplifying, sequencing, and analyzing T cell receptors which is economical, robust, sensitive, and versatile. The key experimental step is the ligation of a single-stranded oligonucleotide to the 3' end of the T cell receptor cDNA, which allows easy amplification of all possible rearrangements using only a single set of primers per locus, while simultaneously introducing a unique molecular identifier to label each starting cDNA molecule. After sequencing, this molecular identifier can be used to correct both sequence errors and the effects of differential PCR amplification efficiency, thus producing a more accurate measure of the true T cell receptor frequency within the sample. This method has been applied to the analysis of unfractionated human tumor lysates, subpopulations of tumor-infiltrating lymphocytes, and peripheral blood samples from patients with a variety of solid tumors.
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MESH Headings
- Antineoplastic Agents, Immunological/therapeutic use
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/immunology
- Biomarkers, Tumor/metabolism
- High-Throughput Nucleotide Sequencing/economics
- High-Throughput Nucleotide Sequencing/instrumentation
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Neoplasms/blood
- Neoplasms/drug therapy
- Neoplasms/immunology
- Neoplasms/pathology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Treatment Outcome
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Affiliation(s)
- Imran Uddin
- Division of Infection and Immunity, UCL, London, UK
| | - Kroopa Joshi
- Cancer Immunology Unit, UCL Cancer Institute, UCL, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, UCL, London, UK
| | | | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, UCL, London, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK
| | - Benny Chain
- Division of Infection and Immunity, UCL, London, UK.
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11
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Wong YNS, Joshi K, Khetrapal P, Ismail M, Reading JL, Sunderland MW, Georgiou A, Furness AJS, Ben Aissa A, Ghorani E, Oakes T, Uddin I, Tan WS, Feber A, McGovern U, Swanton C, Freeman A, Marafioti T, Briggs TP, Kelly JD, Powles T, Peggs KS, Chain BM, Linch MD, Quezada SA. Urine-derived lymphocytes as a non-invasive measure of the bladder tumor immune microenvironment. J Exp Med 2018; 215:2748-2759. [PMID: 30257862 PMCID: PMC6219732 DOI: 10.1084/jem.20181003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/03/2018] [Accepted: 09/05/2018] [Indexed: 12/19/2022] Open
Abstract
Despite the advances in cancer immunotherapy, only a fraction of patients with bladder cancer exhibit responses to checkpoint blockade, highlighting a need to better understand drug resistance and identify rational immunotherapy combinations. However, accessibility to the tumor prior and during therapy is a major limitation in understanding the immune tumor microenvironment (TME). Herein, we identified urine-derived lymphocytes (UDLs) as a readily accessible source of T cells in 32 patients with muscle invasive bladder cancer (MIBC). We observed that effector CD8+ and CD4+ cells and regulatory T cells within the urine accurately map the immune checkpoint landscape and T cell receptor repertoire of the TME. Finally, an increased UDL count, specifically high expression of PD-1 (PD-1hi) on CD8+ at the time of cystectomy, was associated with a shorter recurrence-free survival. UDL analysis represents a dynamic liquid biopsy that is representative of the bladder immune TME that may be used to identify actionable immuno-oncology (IO) targets with potential prognostic value in MIBC.
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Affiliation(s)
- Yien Ning Sophia Wong
- Cancer Immunology Unit, University College London (UCL) Cancer Institute, London, England, UK
- Research Department of Haematology, UCL Cancer Institute, London, England, UK
- Department of Oncology, UCL Cancer Institute, London, England, UK
- Department of Oncology, University College London Hospital, London, England, UK
| | - Kroopa Joshi
- Cancer Immunology Unit, University College London (UCL) Cancer Institute, London, England, UK
- Research Department of Haematology, UCL Cancer Institute, London, England, UK
- Division of Infection and Immunity, University College London, London, England, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, England, UK
| | - Pramit Khetrapal
- Department of Urology, University College London Hospital at Westmoreland Street, London, England, UK
- Division of Surgical and Interventional Sciences, University College London, London, England, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, England, UK
| | - James L Reading
- Cancer Immunology Unit, University College London (UCL) Cancer Institute, London, England, UK
- Research Department of Haematology, UCL Cancer Institute, London, England, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, University College London (UCL) Cancer Institute, London, England, UK
- Research Department of Haematology, UCL Cancer Institute, London, England, UK
| | - Andrew Georgiou
- Cancer Immunology Unit, University College London (UCL) Cancer Institute, London, England, UK
- Research Department of Haematology, UCL Cancer Institute, London, England, UK
| | - Andrew J S Furness
- Cancer Immunology Unit, University College London (UCL) Cancer Institute, London, England, UK
- Research Department of Haematology, UCL Cancer Institute, London, England, UK
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, England, UK
| | - Assma Ben Aissa
- Cancer Immunology Unit, University College London (UCL) Cancer Institute, London, England, UK
- Research Department of Haematology, UCL Cancer Institute, London, England, UK
| | - Ehsan Ghorani
- Cancer Immunology Unit, University College London (UCL) Cancer Institute, London, England, UK
- Research Department of Haematology, UCL Cancer Institute, London, England, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, England, UK
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, England, UK
| | - Wei Shen Tan
- Department of Urology, University College London Hospital at Westmoreland Street, London, England, UK
- Division of Surgical and Interventional Sciences, University College London, London, England, UK
| | - Andrew Feber
- Division of Surgical and Interventional Sciences, University College London, London, England, UK
| | - Ursula McGovern
- Department of Oncology, University College London Hospital, London, England, UK
| | | | - Alex Freeman
- Department of Cellular Pathology, University College London Hospital, London, England, UK
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospital, London, England, UK
| | - Timothy P Briggs
- Department of Urology, University College London Hospital at Westmoreland Street, London, England, UK
| | - John D Kelly
- Department of Urology, University College London Hospital at Westmoreland Street, London, England, UK
- Division of Surgical and Interventional Sciences, University College London, London, England, UK
| | - Thomas Powles
- Centre for Experimental Cancer Medicine, Barts Cancer Institute, Queen Mary University of London, London, England, UK
| | - Karl S Peggs
- Cancer Immunology Unit, University College London (UCL) Cancer Institute, London, England, UK
- Research Department of Haematology, UCL Cancer Institute, London, England, UK
| | - Benjamin M Chain
- Division of Infection and Immunity, University College London, London, England, UK
| | - Mark D Linch
- Department of Oncology, UCL Cancer Institute, London, England, UK
- Department of Oncology, University College London Hospital, London, England, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, University College London (UCL) Cancer Institute, London, England, UK
- Research Department of Haematology, UCL Cancer Institute, London, England, UK
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12
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Gkazi AS, Margetts BK, Attenborough T, Mhaldien L, Standing JF, Oakes T, Heather JM, Booth J, Pasquet M, Chiesa R, Veys P, Klein N, Chain B, Callard R, Adams SP. Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation. Front Immunol 2018; 9:2547. [PMID: 30455696 PMCID: PMC6231291 DOI: 10.3389/fimmu.2018.02547] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 06/18/2018] [Accepted: 10/16/2018] [Indexed: 12/21/2022] Open
Abstract
Spectratyping assays are well recognized as the clinical gold standard for assessing the T cell receptor (TCR) repertoire in haematopoietic stem cell transplant (HSCT) recipients. These assays use length distributions of the hyper variable complementarity-determining region 3 (CDR3) to characterize a patient's T cell immune reconstitution post-transplant. However, whilst useful, TCR spectratyping is notably limited by its resolution, with the technique unable to provide data on the individual clonotypes present in a sample. High-resolution clonotype data are necessary to provide quantitative clinical TCR assessments and to better understand clonotype dynamics during clinically relevant events such as viral infections or GvHD. In this study we developed and applied a CDR3 Next Generation Sequencing (NGS) methodology to assess the TCR repertoire in cord blood transplant (CBT) recipients. Using this, we obtained comprehensive TCR data from 16 CBT patients and 5 control cord samples at Great Ormond Street Hospital (GOSH). These were analyzed to provide a quantitative measurement of the TCR repertoire and its constituents in patients post-CBT. We were able to both recreate and quantify inferences typically drawn from spectratyping data. Additionally, we demonstrate that an NGS approach to TCR assessment can provide novel insights into the recovery of the immune system in these patients. We show that NGS can be used to accurately quantify TCR repertoire diversity and to provide valuable inference on clonotypes detected in a sample. We serially assessed the progress of T cell immune reconstitution demonstrating that there is dramatic variation in TCR diversity immediately following transplantation and that the dynamics of T cell immune reconstitution is perturbed by the presence of GvHD. These findings provide a proof of concept for the adoption of NGS TCR sequencing in clinical practice.
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Affiliation(s)
- Athina Soragia Gkazi
- Infection, Immunity and Inflammation Section, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Ben K Margetts
- Infection, Immunity and Inflammation Section, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- Digital Research Environment, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- Centre for Computation, Mathematics, and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, United Kingdom
| | - Teresa Attenborough
- Infection, Immunity and Inflammation Section, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- Centre for Computation, Mathematics, and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, United Kingdom
| | - Lana Mhaldien
- SIHMDS-Haematology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Joseph F. Standing
- Infection, Immunity and Inflammation Section, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- Pharmacy Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - James M. Heather
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - John Booth
- Digital Research Environment, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Marlene Pasquet
- Le Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Robert Chiesa
- Department of Blood and Marrow Transplantation, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Paul Veys
- Department of Blood and Marrow Transplantation, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Nigel Klein
- Infection, Immunity and Inflammation Section, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- Infectious Diseases Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Robin Callard
- Infection, Immunity and Inflammation Section, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- Centre for Computation, Mathematics, and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, United Kingdom
| | - Stuart P. Adams
- Infection, Immunity and Inflammation Section, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- SIHMDS-Haematology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
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13
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Heather JM, Ismail M, Oakes T, Chain B. High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities. Brief Bioinform 2018; 19:554-565. [PMID: 28077404 PMCID: PMC6054146 DOI: 10.1093/bib/bbw138] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [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: 09/08/2016] [Revised: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
T-cell specificity is determined by the T-cell receptor, a heterodimeric protein coded for by an extremely diverse set of genes produced by imprecise somatic gene recombination. Massively parallel high-throughput sequencing allows millions of different T-cell receptor genes to be characterized from a single sample of blood or tissue. However, the extraordinary heterogeneity of the immune repertoire poses significant challenges for subsequent analysis of the data. We outline the major steps in processing of repertoire data, considering low-level processing of raw sequence files and high-level algorithms, which seek to extract biological or pathological information. The latest generation of bioinformatics tools allows millions of DNA sequences to be accurately and rapidly assigned to their respective variable V and J gene segments, and to reconstruct an almost error-free representation of the non-templated additions and deletions that occur. High-level processing can measure the diversity of the repertoire in different samples, quantify V and J usage and identify private and public T-cell receptors. Finally, we discuss the major challenge of linking T-cell receptor sequence to function, and specifically to antigen recognition. Sophisticated machine learning algorithms are being developed that can combine the paradoxical degeneracy and cross-reactivity of individual T-cell receptors with the specificity of the overall T-cell immune response. Computational analysis will provide the key to unlock the potential of the T-cell receptor repertoire to give insight into the fundamental biology of the adaptive immune system and to provide powerful biomarkers of disease.
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Affiliation(s)
| | | | | | - Benny Chain
- Division of Infection and Immunity, University College of London, Bloomsbury, UK
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14
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Joshi K, Ismail M, Reading JL, Robert De Massy M, Uddin I, Jamal-Hanjani M, Veeriah S, Oakes T, Wong YNS, Furness AJS, Ghorani E, Georgiou A, Beastall C, Mangal N, Ben Aissa A, Werner Sunderland M, Peggs K, Swanton C, Chain B, Quezada SA. Characterisation of the TCR repertoire in NSCLC to reveal the relationship between TCR heterogeneity and genetic heterogeneity that is influenced by mutational load and is associated with disease recurrence. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.12009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Kroopa Joshi
- Cancer Immunology Unit, University College London Cancer Institute, London, United Kingdom
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - James L Reading
- Cancer Immunology Unit, University College London Cancer Institute, London, United Kingdom
| | - Marc Robert De Massy
- Cancer Immunology Unit, University College London Cancer Institute, London, United Kingdom
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Mariam Jamal-Hanjani
- Translational Cancer Therapeutics Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Selvaraju Veeriah
- Translational Cancer Therapeutics Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Yien Ning Sophia Wong
- Cancer Immunology Unit, University College London Cancer Institute, London, United Kingdom
| | | | - Ehsan Ghorani
- Cancer Immunology Unit, University College London Cancer Institute, London, United Kingdom
| | - Andrew Georgiou
- Cancer Immunology Unit, University College London Cancer Institute, London, United Kingdom
| | - Carmella Beastall
- Cancer Immunology Unit, University College London Cancer Institute, London, United Kingdom
| | - Nagina Mangal
- Cancer Immunology Unit, University College London Cancer Institute, London, United Kingdom
| | - Assma Ben Aissa
- Cancer Immunology Unit, University College London Cancer Institute, London, United Kingdom
| | | | - Karl Peggs
- University College London Cancer Institute, London, United Kingdom
| | - Charles Swanton
- Translation Cancer Therapeutics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Benjamin Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Sergio A Quezada
- Cancer Immunology Unit, University College London Cancer Institute, London, United Kingdom
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15
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Joshi K, Reading J, Ismail M, Oakes T, Rosenthal R, Uddin I, Jamal-Hanjani M, McGranahan N, Wong Y, Furness A, Aissa A, Werner Sunderland M, Georgiou A, Veeriah S, Czyzewska-Khan J, Marafioti T, Peggs K, Swanton C, Chain B, Quezada S. Deciphering the intra-tumoural T cell receptor repertoire in patients with NSCLC within the lung TRACERx study. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx712.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Oakes T, Heather JM, Best K, Byng-Maddick R, Husovsky C, Ismail M, Joshi K, Maxwell G, Noursadeghi M, Riddell N, Ruehl T, Turner CT, Uddin I, Chain B. Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile. Front Immunol 2017; 8:1267. [PMID: 29075258 PMCID: PMC5643411 DOI: 10.3389/fimmu.2017.01267] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/22/2017] [Indexed: 11/13/2022] Open
Abstract
The T cell receptor (TCR) repertoire can provide a personalized biomarker for infectious and non-infectious diseases. We describe a protocol for amplifying, sequencing, and analyzing TCRs which is robust, sensitive, and versatile. The key experimental step is ligation of a single-stranded oligonucleotide to the 3' end of the TCR cDNA. This allows amplification of all possible rearrangements using a single set of primers per locus. It also introduces a unique molecular identifier to label each starting cDNA molecule. This molecular identifier is used to correct for sequence errors and for effects of differential PCR amplification efficiency, thus producing more accurate measures of the true TCR frequency within the sample. This integrated experimental and computational pipeline is applied to the analysis of human memory and naive subpopulations, and results in consistent measures of diversity and inequality. After error correction, the distribution of TCR sequence abundance in all subpopulations followed a power law over a wide range of values. The power law exponent differed between naïve and memory populations, but was consistent between individuals. The integrated experimental and analysis pipeline we describe is appropriate to studies of T cell responses in a broad range of physiological and pathological contexts.
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Affiliation(s)
- Theres Oakes
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - James M. Heather
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Katharine Best
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Rachel Byng-Maddick
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Connor Husovsky
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Kroopa Joshi
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Gavin Maxwell
- Unilever Safety and Environmental Assurance Centre, Unilever, Sharnbrook, United Kingdom
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Natalie Riddell
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Tabea Ruehl
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Carolin T. Turner
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
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17
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Lippa S, Chaplin A, French L, Yeh P, Oakes T, Brickell T, Lange R. B-59The Relationship Between White Matter Hyperintensities, Neurocognitive Performance, and White Matter Integrity Following Mild Traumatic Brain Injury. Arch Clin Neuropsychol 2017. [DOI: 10.1093/arclin/acx076.144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Oakes T, Popple AL, Williams J, Best K, Heather JM, Ismail M, Maxwell G, Gellatly N, Dearman RJ, Kimber I, Chain B. The T Cell Response to the Contact Sensitizer Paraphenylenediamine Is Characterized by a Polyclonal Diverse Repertoire of Antigen-Specific Receptors. Front Immunol 2017; 8:162. [PMID: 28261218 PMCID: PMC5311069 DOI: 10.3389/fimmu.2017.00162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 01/31/2017] [Indexed: 01/07/2023] Open
Abstract
Paraphenylenediamine (PPD) is a common component of hair dyes and black henna tattoos and can cause skin sensitization and allergic contact dermatitis (ACD). The cutaneous inflammatory reaction associated with ACD is driven by both CD4+ and CD8+ T cells. However, the characteristics of such responses with respect to clonal breadth and magnitude are poorly defined. In this study, we have characterized the in vitro recall response of peripheral blood T cells prepared from PPD-allergic individuals to a PPD–human serum albumin (HSA) conjugate (PPD–HSA). Quantitative high throughput sequencing was used to characterize the changes in the repertoire of T cell receptor (TCR) α and β genes after exposure to antigen in vitro. The PPD conjugate induced expansion of T cells carrying selected TCRs, with around 800 sequences (around 1%) being 8 or more times as abundant after culture than before. The expanded sequences showed strong skewing of V and J usage, consistent with an antigen-driven clonal expansion. The complementarity-determining region 3 sequences of the expanded TCRs could be grouped into several families of related amino acid sequence, but the overall diversity of the expanded sample was not much less than that of a random sample of the same size. The results suggest a model in which PPD–HSA conjugate stimulates a broad diversity of TCRs, with a wide range of stimulation strengths, which manifest as different degrees of in vitro expansion.
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Affiliation(s)
- Theres Oakes
- Division of Infection and Immunity, UCL , London , UK
| | - Amy Lee Popple
- Faculty of Life Sciences, University of Manchester , Manchester , UK
| | - Jason Williams
- Contact Dermatitis Investigation Unit, Salford Royal NHS Foundation Trust , Manchester , UK
| | | | | | | | - Gavin Maxwell
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park , Sharnbrook , UK
| | - Nichola Gellatly
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park , Sharnbrook , UK
| | - Rebecca J Dearman
- Faculty of Life Sciences, University of Manchester , Manchester , UK
| | - Ian Kimber
- Faculty of Life Sciences, University of Manchester , Manchester , UK
| | - Benny Chain
- Division of Infection and Immunity, UCL , London , UK
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19
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Joshi K, Furness AJ, Oakes T, Heather J, Spain LA, Wong YNS, Ben Aissa A, Stares M, Smith MJF, Strauss DC, Hayes AJ, Marafioti T, Turajlic S, Gore ME, Peggs K, Chain B, Quezada S, Larkin JMG. Defining the mechanisms of response and resistance to anti-PD-1 therapy: An exploratory phase II study of pembrolizumab in advanced melanoma (ADAPTeM). J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.tps9599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Kroopa Joshi
- University College London Cancer Institute, London, United Kingdom
| | | | - Theres Oakes
- Department of Infection and Immunity, University College London, London, United Kingdom
| | - James Heather
- Department of Infection and Immunity, University College London, London, United Kingdom
| | | | | | - Assma Ben Aissa
- University College London Cancer Institute, London, United Kingdom
| | - Mark Stares
- The Francis Crick Institute, London, United Kingdom
| | - Myles JF Smith
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Dirk C Strauss
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Andrew J Hayes
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Teresa Marafioti
- University College London Cancer Institute, London, United Kingdom
| | | | | | - Karl Peggs
- University College London Cancer Institute, London, United Kingdom
| | - Benjamin Chain
- Department of Infection and Immunity, University College London, London, United Kingdom
| | - Sergio Quezada
- University College London Cancer Institute, London, United Kingdom
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20
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Heather JM, Best K, Oakes T, Gray ER, Roe JK, Thomas N, Friedman N, Noursadeghi M, Chain B. Dynamic Perturbations of the T-Cell Receptor Repertoire in Chronic HIV Infection and following Antiretroviral Therapy. Front Immunol 2016; 6:644. [PMID: 26793190 PMCID: PMC4707277 DOI: 10.3389/fimmu.2015.00644] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/10/2015] [Indexed: 01/23/2023] Open
Abstract
HIV infection profoundly affects many parameters of the immune system and ultimately leads to AIDS, yet which factors are most important for determining resistance, pathology, and response to antiretroviral treatment – and how best to monitor them – remain unclear. We develop a quantitative high-throughput sequencing pipeline to characterize the TCR repertoires of HIV-infected individuals before and after antiretroviral therapy, working from small, unfractionated samples of peripheral blood. This reveals the TCR repertoires of HIV+ individuals to be highly perturbed, with considerably reduced diversity as a small proportion of sequences are highly overrepresented. HIV also causes specific qualitative changes to the repertoire including an altered distribution of V gene usage, depletion of public TCR sequences, and disruption of TCR networks. Short-term antiretroviral therapy has little impact on most of the global damage to repertoire structure, but is accompanied by rapid changes in the abundance of many individual TCR sequences, decreases in abundance of the most common sequences, and decreases in the majority of HIV-associated CDR3 sequences. Thus, high-throughput repertoire sequencing of small blood samples that are easy to take, store, and process can shed light on various aspects of the T-cell immune compartment and stands to offer insights into patient stratification and immune reconstitution.
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Affiliation(s)
- James M Heather
- Division of Infection and Immunity, University College London , London , UK
| | - Katharine Best
- Division of Infection and Immunity, University College London, London, UK; Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London , London , UK
| | - Eleanor R Gray
- Division of Infection and Immunity, University College London , London , UK
| | - Jennifer K Roe
- Division of Infection and Immunity, University College London , London , UK
| | - Niclas Thomas
- Division of Infection and Immunity, University College London , London , UK
| | - Nir Friedman
- Department of Immunology, Weizmann Institute , Rehovot , Israel
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London , London , UK
| | - Benjamin Chain
- Division of Infection and Immunity, University College London , London , UK
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Lange R, Yeh P, Oakes T, Riedy G, Ollinger J, French L. A-65Diffusion Tensor Imaging and Postconcussion Symptom Reporting in US Military Service Members Following Mild to Moderate Traumatic Brain Injury. Arch Clin Neuropsychol 2015. [DOI: 10.1093/arclin/acv047.65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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22
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Abstract
AIMS The objectives of the present review were to summarise the key findings from the clinical literature regarding the neurobiology of major depressive disorder (MDD) and their implications for maximising treatment outcomes. Several neuroanatomical structures in the prefrontal and limbic areas of the brain are involved in affective regulation. In patients with MDD, alterations in the dynamic patterns of activity among these structures have profound implications for the pathogenesis of this illness. DISCUSSION The present work reviews the evidence for the progressive nature of MDD along with associated changes in neuroanatomical structure and function, especially for the hippocampus. The role of glucocorticoids, inflammatory cytokines and brain-derived growth factors are discussed as mediators of these pathological alterations. From this integrated model, the role of antidepressant therapy in restoring normative processes is examined along with additional treatment guidelines. CONCLUSION Major depressive disorder is an illness with significant neurobiological consequences involving structural, functional and molecular alterations in several areas of the brain. Antidepressant pharmacotherapy is associated with restoration of the underlying physiology. Clinicians are advised to intervene with MDD using an early, comprehensive treatment approach that has remission as the goal.
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Affiliation(s)
- V Maletic
- School of Medicine, University of South Carolina, Greer, SC 29650, USA.
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