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Zareian N, Eremin O, Pandha H, Baird R, Kwatra V, Funingana G, Verma C, Choy D, Hargreaves S, Moghimi P, Shepherd A, Lobo DN, Eremin J, Farzaneh F, Kordasti S, Spicer J. A phase 1 trial of human telomerase reverse transcriptase (hTERT) vaccination combined with therapeutic strategies to control immune-suppressor mechanisms. Exp Biol Med (Maywood) 2024; 249:10021. [PMID: 38463391 PMCID: PMC10911124 DOI: 10.3389/ebm.2024.10021] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/04/2024] [Indexed: 03/12/2024] Open
Abstract
The presence of inhibitory immune cells and difficulty in generating activated effector T cells remain obstacles to development of effective cancer vaccines. We designed a vaccine regimen combining human telomerase reverse transcriptase (hTERT) peptides with concomitant therapies targeting regulatory T cells (Tregs) and cyclooxygenase-2 (COX2)-mediated immunosuppression. This Phase 1 trial combined an hTERT-derived 7-peptide library, selected to ensure presentation by both HLA class-I and class-II in 90% of patients, with oral low-dose cyclophosphamide (to modulate Tregs) and the COX2 inhibitor celecoxib. Adjuvants were Montanide and topical TLR-7 agonist, to optimise antigen presentation. The primary objective was determination of the safety and tolerability of this combination therapy, with anti-cancer activity, immune response and detection of antigen-specific T cells as additional endpoints. Twenty-nine patients with advanced solid tumours were treated. All were multiply-pretreated, and the majority had either colorectal or prostate cancer. The most common adverse events were injection-site reactions, fatigue and nausea. Median progression-free survival was 9 weeks, with no complete or partial responses, but 24% remained progression-free for ≥6 months. Immunophenotyping showed post-vaccination expansion of CD4+ and CD8+ T cells with effector phenotypes. The in vitro re-challenge of T cells with hTERT peptides, TCR sequencing, and TCR similarity index analysis demonstrated the expansion following vaccination of oligoclonal T cells with specificity for hTERT. However, a population of exhausted PD-1+ cytotoxic T cells was also expanded in vaccinated patients. This vaccine combination regimen was safe and associated with antigen-specific immunological responses. Clinical activity could be improved in future by combination with anti-PD1 checkpoint inhibition to address the emergence of an exhausted T cell population.
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Affiliation(s)
- Nahid Zareian
- School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Oleg Eremin
- Nottingham Digestive Diseases Centre, NIHR Nottingham Biomedical Research Centre, Queen's Medical Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Hardev Pandha
- Department of Microbiology and Cellular Sciences, University of Surrey, Guildford, United Kingdom
| | - Richard Baird
- Cancer Research UK Cambridge Centre, Cambridge, United Kingdom
| | - Vineet Kwatra
- School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | | | - Chandan Verma
- Nottingham Digestive Diseases Centre, NIHR Nottingham Biomedical Research Centre, Queen's Medical Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Desmond Choy
- School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Steven Hargreaves
- Research Department of Pathology, UCL Cancer Institute, Faculty of Medical Sciences, University College London (UCL), London, United Kingdom
| | - Pejvak Moghimi
- The Institute of Structural and Molecular Biology (ISMB), Birkbeck, University of London, London, United Kingdom
| | - Adrian Shepherd
- The Institute of Structural and Molecular Biology (ISMB), Birkbeck, University of London, London, United Kingdom
| | - Dileep N Lobo
- Nottingham Digestive Diseases Centre, NIHR Nottingham Biomedical Research Centre, Queen's Medical Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jennifer Eremin
- Nottingham Digestive Diseases Centre, NIHR Nottingham Biomedical Research Centre, Queen's Medical Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Farzin Farzaneh
- School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Shahram Kordasti
- School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - James Spicer
- School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
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Olson BJ, Moghimi P, Schramm CA, Obraztsova A, Ralph D, Vander Heiden JA, Shugay M, Shepherd AJ, Lees W, Matsen FA. sumrep: A Summary Statistic Framework for Immune Receptor Repertoire Comparison and Model Validation. Front Immunol 2019; 10:2533. [PMID: 31736960 PMCID: PMC6838214 DOI: 10.3389/fimmu.2019.02533] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 07/19/2019] [Accepted: 10/11/2019] [Indexed: 12/28/2022] Open
Abstract
The adaptive immune system generates an incredible diversity of antigen receptors for B and T cells to keep dangerous pathogens at bay. The DNA sequences coding for these receptors arise by a complex recombination process followed by a series of productivity-based filters, as well as affinity maturation for B cells, giving considerable diversity to the circulating pool of receptor sequences. Although these datasets hold considerable promise for medical and public health applications, the complex structure of the resulting adaptive immune receptor repertoire sequencing (AIRR-seq) datasets makes analysis difficult. In this paper we introduce sumrep, an R package that efficiently performs a wide variety of repertoire summaries and comparisons, and show how sumrep can be used to perform model validation. We find that summaries vary in their ability to differentiate between datasets, although many are able to distinguish between covariates such as donor, timepoint, and cell type for BCR and TCR repertoires. We show that deletion and insertion lengths resulting from V(D)J recombination tend to be more discriminative characterizations of a repertoire than summaries that describe the amino acid composition of the CDR3 region. We also find that state-of-the-art generative models excel at recapitulating gene usage and recombination statistics in a given experimental repertoire, but struggle to capture many physiochemical properties of real repertoires.
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Affiliation(s)
- Branden J Olson
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Statistics, University of Washington, Seattle, WA, United States
| | - Pejvak Moghimi
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Anna Obraztsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Duncan Ralph
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Jason A Vander Heiden
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, United States
| | - Mikhail Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Adrian J Shepherd
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - William Lees
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
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