1
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Aparicio B, Theunissen P, Hervas-Stubbs S, Fortes P, Sarobe P. Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies. Hum Vaccin Immunother 2024; 20:2303799. [PMID: 38346926 PMCID: PMC10863374 DOI: 10.1080/21645515.2024.2303799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024] Open
Abstract
Efficacy of cancer immunotherapies relies on correct recognition of tumor antigens by lymphocytes, eliciting thus functional responses capable of eliminating tumor cells. Therefore, important efforts have been carried out in antigen identification, with the aim of understanding mechanisms of response to immunotherapy and to design safer and more efficient strategies. In addition to classical tumor-associated antigens identified during the last decades, implementation of next-generation sequencing methodologies is enabling the identification of neoantigens (neoAgs) arising from mutations, leading to the development of new neoAg-directed therapies. Moreover, there are numerous non-classical tumor antigens originated from other sources and identified by new methodologies. Here, we review the relevance of neoAgs in different immunotherapies and the results obtained by applying neoAg-based strategies. In addition, the different types of non-classical tumor antigens and the best approaches for their identification are described. This will help to increase the spectrum of targetable molecules useful in cancer immunotherapies.
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Affiliation(s)
- Belen Aparicio
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Patrick Theunissen
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Sandra Hervas-Stubbs
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Puri Fortes
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Spain
| | - Pablo Sarobe
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
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2
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Faghfuri E. Recent advances in personalized cancer immunotherapy with immune checkpoint inhibitors, T cells and vaccines. Per Med 2024; 21:45-57. [PMID: 38088165 DOI: 10.2217/pme-2023-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
The results of genomic and molecular profiling of cancer patients can be effectively applied to immunotherapy agents, including immune checkpoint inhibitors, to select the most appropriate treatment. In addition, accurate prediction of neoantigens facilitates the development of individualized cancer vaccines and T-cell therapy. This review summarizes the biomarker(s) predicting responses to immune checkpoint inhibitors and focuses on current strategies to identify and isolate neoantigen-reactive T cells as well as the clinical development of neoantigen-based therapeutics. The results suggest that maximal T-cell stimulation and expansion can be achieved with combination therapies that enhance antigen-presenting cells' function and optimal T-cell priming in lymph nodes.
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Affiliation(s)
- Elnaz Faghfuri
- Digestive Disease Research Center, Ardabil University of Medical Sciences, Ardabil, 5613658115, Iran
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3
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Shah RK, Cygan E, Kozlik T, Colina A, Zamora AE. Utilizing immunogenomic approaches to prioritize targetable neoantigens for personalized cancer immunotherapy. Front Immunol 2023; 14:1301100. [PMID: 38149253 PMCID: PMC10749952 DOI: 10.3389/fimmu.2023.1301100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Advancements in sequencing technologies and bioinformatics algorithms have expanded our ability to identify tumor-specific somatic mutation-derived antigens (neoantigens). While recent studies have shown neoantigens to be compelling targets for cancer immunotherapy due to their foreign nature and high immunogenicity, the need for increasingly accurate and cost-effective approaches to rapidly identify neoantigens remains a challenging task, but essential for successful cancer immunotherapy. Currently, gene expression analysis and algorithms for variant calling can be used to generate lists of mutational profiles across patients, but more care is needed to curate these lists and prioritize the candidate neoantigens most capable of inducing an immune response. A growing amount of evidence suggests that only a handful of somatic mutations predicted by mutational profiling approaches act as immunogenic neoantigens. Hence, unbiased screening of all candidate neoantigens predicted by Whole Genome Sequencing/Whole Exome Sequencing may be necessary to more comprehensively access the full spectrum of immunogenic neoepitopes. Once putative cancer neoantigens are identified, one of the largest bottlenecks in translating these neoantigens into actionable targets for cell-based therapies is identifying the cognate T cell receptors (TCRs) capable of recognizing these neoantigens. While many TCR-directed screening and validation assays have utilized bulk samples in the past, there has been a recent surge in the number of single-cell assays that provide a more granular understanding of the factors governing TCR-pMHC interactions. The goal of this review is to provide an overview of existing strategies to identify candidate neoantigens using genomics-based approaches and methods for assessing neoantigen immunogenicity. Additionally, applications, prospects, and limitations of some of the current single-cell technologies will be discussed. Finally, we will briefly summarize some of the recent models that have been used to predict TCR antigen specificity and analyze the TCR receptor repertoire.
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Affiliation(s)
- Ravi K. Shah
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Erin Cygan
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Tanya Kozlik
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Alfredo Colina
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Anthony E. Zamora
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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4
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Osei-Hwedieh DO, Sedlacek AL, Hernandez LM, Yamoah AA, Iyer SG, Weiss KR, Binder RJ. Immunosurveillance shapes the emergence of neo-epitope landscapes of sarcomas, revealing prime targets for immunotherapy. JCI Insight 2023; 8:e170324. [PMID: 37427594 PMCID: PMC10371341 DOI: 10.1172/jci.insight.170324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/25/2023] [Indexed: 07/11/2023] Open
Abstract
T cells recognize tumor-derived mutated peptides presented on MHC by tumors. The recognition of these neo-epitopes leads to rejection of tumors, an event that is critical for successful cancer immunosurveillance. Determination of tumor-rejecting neo-epitopes in human tumors has proved difficult, though recently developed systems approaches are becoming increasingly useful at evaluating their immunogenicity. We have used the differential aggretope index to determine the neo-epitope burden of sarcomas and observed a conspicuously titrated antigenic landscape, ranging from the highly antigenic osteosarcomas to the low antigenic leiomyosarcomas and liposarcomas. We showed that the antigenic landscape of the tumors inversely reflected the historical T cell responses in the tumor-bearing patients. We predicted that highly antigenic tumors with poor antitumor T cell responses, such as osteosarcomas, would be responsive to T cell-based immunotherapy regimens and demonstrated this in a murine osteosarcoma model. Our study presents a potentially novel pipeline for determining antigenicity of human tumors, provides an accurate predictor of potential neo-epitopes, and will be an important indicator of which cancers to target with T cell-enhancing immunotherapy.
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Affiliation(s)
| | | | | | | | | | - Kurt R. Weiss
- Department of Orthopaedic Surgery, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
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5
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Das A, Ghose A, Naicker K, Sanchez E, Chargari C, Rassy E, Boussios S. Advances in adoptive T-cell therapy for metastatic melanoma. Curr Res Transl Med 2023; 71:103404. [PMID: 37478776 DOI: 10.1016/j.retram.2023.103404] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/30/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023]
Abstract
Adoptive T cell therapy (ACT) is a fast developing, niche area of immunotherapy (IO), which is revolutionising the therapeutic landscape of solid tumour oncology, especially metastatic melanoma (MM). Identifying tumour antigens (TAs) as potential targets, the ACT response is mediated by either Tumour Infiltrating Lymphocytes (TILs) or genetically modified T cells with specific receptors - T cell receptors (TCRs) or chimeric antigen receptors (CARs) or more prospectively, natural killer (NK) cells. Clinical trials involving ACT in MM from 2006 to present have shown promising results. Yet it is not without its drawbacks which include significant auto-immune toxicity and need for pre-conditioning lymphodepletion. Although immune-modulation is underway using various combination therapies in the hope of enhancing efficacy and reducing toxicity. Our review article explores the role of ACT in MM, including the various modalities - their safety, efficacy, risks and their development in the trial and the real world setting.
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Affiliation(s)
- Aparimita Das
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, ME7 5NY, Gillingham, Kent, United Kingdom; Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chennai, India
| | - Aruni Ghose
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, ME7 5NY, Gillingham, Kent, United Kingdom; Department of Medical Oncology, Barts Cancer Centre, St. Bartholomew's Hospital, Barts Health NHS Trust, London, United Kingdom; Department of Medical Oncology, Mount Vernon Cancer Centre, East and North Hertfordshire NHS Trust, London, United Kingdom
| | - Kevin Naicker
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, ME7 5NY, Gillingham, Kent, United Kingdom
| | - Elisabet Sanchez
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, ME7 5NY, Gillingham, Kent, United Kingdom
| | - Cyrus Chargari
- Department of Radiation Oncology, Pitié Salpêtrière University Hospital, Paris, France
| | - Elie Rassy
- Department of Medical Oncology, Gustave Roussy Institut, 94805, Villejuif, France
| | - Stergios Boussios
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, ME7 5NY, Gillingham, Kent, United Kingdom; Kent and Medway Medical School, University of Kent, Canterbury, United Kingdom; Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, King's College London, SE1 9RT, London, United Kingdom; AELIA Organization, 9th Km Thessaloniki, Thermi 57001, Thessaloniki, Greece.
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6
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Abstract
The long-term benefits demonstrated by immunotherapy in select tumors have failed to generalize to most nonhematologic solid tumors. Adoptive cell therapy (ACT)-a treatment on the basis of the isolation and engineering of living T cells and other immune cells-has shown early clinical advances. ACT, through tumor-infiltrating lymphocyte therapy, has shown activity in traditionally immunogenic tumors such as melanoma and cervical cancers, and has the potential to improve immune reactivity in these tumor types where traditional therapies have failed. Engineered T-cell receptor and chimeric antigen receptor T-cell therapies have also shown activity in select nonhematologic solid tumors. Through receptor engineering, and improved understanding of tumor antigens, these therapies have the potential to target poorly immunogenic tumors to deliver long-lasting responses. Additionally, non-T-cell therapies such as natural killer-cell therapy may allow for allogeneic forms of ACT. Each form of ACT has trade-offs that will likely limit their application to specific clinical settings. Key challenges with ACT include the logistical challenges of manufacturing, accurate antigen identification, and the risk of on-target, off-tumor toxicity. The successes of ACT are built on decades of advances in cancer immunology, antigen identification, and cell engineering. With continued refinements in these processes, ACT may extend the benefits of immunotherapy to more patients with advanced nonhematologic solid tumors. Herein, we review the major forms of ACT, their successes, and strategies to overcome the trade-offs of current ACTs.
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Affiliation(s)
- Daniel J Olson
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL
| | - Kunle Odunsi
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL
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7
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Millar DG, Yang SYC, Sayad A, Zhao Q, Nguyen LT, Warner K, Sangster AG, Nakatsugawa M, Murata K, Wang BX, Shaw P, Clarke B, Bernardini MQ, Pugh T, Thibault P, Hirano N, Perreault C, Ohashi PS. Identification of antigenic epitopes recognized by tumor infiltrating lymphocytes in high grade serous ovarian cancer by multi-omics profiling of the auto-antigen repertoire. Cancer Immunol Immunother 2023:10.1007/s00262-023-03413-7. [PMID: 36943460 DOI: 10.1007/s00262-023-03413-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/16/2023] [Indexed: 03/23/2023]
Abstract
Immunotherapeutic strategies aimed at enhancing tumor cell killing by tumor-specific T cells hold great potential for reducing tumor burden and prolonging survival of cancer patients. Although many potential tumor antigens have been described, identifying relevant targets when designing anti-cancer vaccines or targeted cell therapies remains a challenge. To identify novel, potentially immunogenic candidate tumor antigens, we performed integrated tumor transcriptomic, seromic, and proteomic analyses of high grade serous ovarian cancer (HGSC) patient tumor samples. We identified tumor neo-antigens and over-expressed antigens using whole exome and RNA sequencing and examined these in relation to patient-matched auto-antibody repertoires. Focusing on MHC class I epitopes recognized by CD8+ T cells, HLA-binding epitopes were identified or predicted from the highly expressed, mutated, or auto-antibody target antigen, or MHC-associated peptides (MAPs). Recognition of candidate antigenic peptides was assessed within the tumor-infiltrating T lymphocyte (TIL) population expanded from each patient. Known tumor-associated antigens (TAA) and cancer/testis antigens (CTA) were commonly found in the auto-antibody and MAP repertoires and CD8+ TILs recognizing epitopes from these antigens were detected, although neither expression level nor the presence of auto-antibodies correlated with TIL recognition. Auto-antibodies against tumor-mutated antigens were found in most patients, however, no TIL recognition of the highest predicted affinity neo-epitopes was detected. Using high expression level, auto-antibody recognition, and epitope prediction algorithms, we identified epitopes in 5 novel antigens (MOB1A, SOCS3, TUBB, PRKAR1A, CCDC6) recognized by HGSC patient TILs. Furthermore, selection of epitopes from the MAP repertoire identified 5 additional targets commonly recognized by multiple patient TILs. We find that the repertoire of TIL specificities includes recognition of highly expressed and immunogenic self-antigens that are processed and presented by tumors. These results indicate an ongoing autoimmune response against a range of self-antigens targeted by HGSC TILs.
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Affiliation(s)
- Douglas G Millar
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - S Y Cindy Yang
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Azin Sayad
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Qingchuan Zhao
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Linh T Nguyen
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Kathrin Warner
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Ami G Sangster
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Munehide Nakatsugawa
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Kenji Murata
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Ben X Wang
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Patricia Shaw
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Blaise Clarke
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Marcus Q Bernardini
- Division of Gynecologic Oncology, Cancer Clinical Research Unit (CCRU), Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Trevor Pugh
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Naoto Hirano
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Pamela S Ohashi
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada.
- Department of Immunology, University of Toronto, Toronto, ON, Canada.
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8
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Norberg SM, Hinrichs CS. Engineered T cell therapy for viral and non-viral epithelial cancers. Cancer Cell 2023; 41:58-69. [PMID: 36400016 PMCID: PMC9839504 DOI: 10.1016/j.ccell.2022.10.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/13/2022] [Accepted: 10/17/2022] [Indexed: 11/18/2022]
Abstract
Engineered T cell therapy has shown remarkable efficacy in hematologic malignancies and has the potential for application to common epithelial cancers. Diverse T cell therapy strategies including adoptive transfer of tumor-infiltrating lymphocytes, chimeric antigen receptor (CAR)-T cells, and T cell receptor (TCR)-T cells have been studied in clinical trials. Recent research has established treatment of human papillomavirus (HPV)-associated cancers with TCR-T cells as a model for proof-of-principle studies in epithelial cancers. These studies and others have provided critical insight into mechanisms of tumor regression, therapeutic targets, treatment safety, treatment design, and barriers to curative cell therapies for common types of cancer. This perspective will review and consolidate understanding gained from clinical trials to treat viral and non-viral epithelial cancers with cell and gene therapy and will examine how past experience may guide future strategy in treatment and biomarker discovery.
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Affiliation(s)
- Scott M Norberg
- National Cancer Institute, Center for Immuno-Oncology, Bethesda, MD 20892, USA
| | - Christian S Hinrichs
- Rutgers Cancer Institute of New Jersey, Duncan and Nancy MacMillan Cancer Immunology and Metabolism Center of Excellence, New Brunswick, NJ 08901, USA.
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9
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Mirza S, Bhadresha K, Mughal MJ, McCabe M, Shahbazi R, Ruff P, Penny C. Liquid biopsy approaches and immunotherapy in colorectal cancer for precision medicine: Are we there yet? Front Oncol 2023; 12:1023565. [PMID: 36686736 PMCID: PMC9853908 DOI: 10.3389/fonc.2022.1023565] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer-related deaths globally, with nearly half of patients detected in the advanced stages. This is due to the fact that symptoms associated with CRC often do not appear until the cancer has reached an advanced stage. This suggests that CRC is a cancer with a slow progression, making it curable and preventive if detected in its early stage. Therefore, there is an urgent clinical need to improve CRC early detection and personalize therapy for patients with this cancer. Recently, liquid biopsy as a non-invasive or nominally invasive approach has attracted considerable interest for its real-time disease monitoring capability through repeated sample analysis. Several studies in CRC have revealed the potential for liquid biopsy application in a real clinical setting using circulating RNA/miRNA, circulating tumor cells (CTCs), exosomes, etc. However, Liquid biopsy still remains a challenge since there are currently no promising results with high specificity and specificity that might be employed as optimal circulatory biomarkers. Therefore, in this review, we conferred the plausible role of less explored liquid biopsy components like mitochondrial DNA (mtDNA), organoid model of CTCs, and circulating cancer-associated fibroblasts (cCAFs); which may allow researchers to develop improved strategies to unravel unfulfilled clinical requirements in CRC patients. Moreover, we have also discussed immunotherapy approaches to improve the prognosis of MSI (Microsatellite Instability) CRC patients using neoantigens and immune cells in the tumor microenvironment (TME) as a liquid biopsy approach in detail.
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Affiliation(s)
- Sheefa Mirza
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Department of Internal Medicine, Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kinjal Bhadresha
- Hematology/Oncology Division, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Muhammed Jameel Mughal
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Science, The George Washington University, Washington, DC, United States
| | - Michelle McCabe
- Department of Anatomical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown, Johannesburg, South Africa
| | - Reza Shahbazi
- Hematology/Oncology Division, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Paul Ruff
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Department of Internal Medicine, Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Clement Penny
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Department of Internal Medicine, Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,*Correspondence: Clement Penny,
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10
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Long GV, Ferrucci PF, Khattak A, Meniawy TM, Ott PA, Chisamore M, Trolle T, Hyseni A, Heegaard E. KEYNOTE - D36: personalized immunotherapy with a neoepitope vaccine, EVX-01 and pembrolizumab in advanced melanoma. Future Oncol 2022; 18:3473-3480. [PMID: 36047545 DOI: 10.2217/fon-2022-0694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Despite improvements made with checkpoint inhibitor (CPI) therapy, a need for new approaches to improve outcomes for patients with unresectable or metastatic melanoma remains. EVX-01, a personalized neoepitope vaccine, combined with pembrolizumab treatment, holds the potential to fulfill this need. Here we present the rationale and novel design behind the KEYNOTE - D36 trial: an open label, single arm, phase II trial aiming to establish the clinical proof of concept and evaluate the safety of EVX-01 in combination with pembrolizumab in CPI naive patients with unresectable or metastatic melanoma. The primary objective is to evaluate if EVX-01 improves best overall response after initial stable disease or partial response to pembrolizumab treatment, in patients with advanced melanoma. The novel end points ensure a decisive readout which may prove helpful before making major investments in phase III trials with limited phase I data. Clinical Trial Registration: NCT05309421 (ClinicalTrials.gov).
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Affiliation(s)
- Georgina V Long
- Melanoma Institute Australia, The University of Sydney, & Royal North Shore & Mater Hospitals, Sydney, New South Wales, 2065, Australia
| | - Pier Francesco Ferrucci
- Cancer Biotherapy Unit, Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, 20139, Italy
| | - Adnan Khattak
- Hollywood Private Hospital & Edith Cowan University, Perth, 6009, Australia
| | | | | | | | - Thomas Trolle
- Evaxion Biotech A/S, Dr. Neergaards Vej 5F, Hørsholm, 2970, Denmark
| | - Agon Hyseni
- Evaxion Biotech A/S, Dr. Neergaards Vej 5F, Hørsholm, 2970, Denmark
| | - Erik Heegaard
- Evaxion Biotech A/S, Dr. Neergaards Vej 5F, Hørsholm, 2970, Denmark
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11
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Shen Y, Yu L, Xu X, Yu S, Yu Z. Neoantigen vaccine and neoantigen-specific cell adoptive transfer therapy in solid tumors: Challenges and future directions. CANCER INNOVATION 2022; 1:168-182. [PMID: 38090649 PMCID: PMC10686129 DOI: 10.1002/cai2.26] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/26/2022] [Accepted: 08/01/2022] [Indexed: 06/11/2024]
Abstract
The phenomenon of tumor hierarchy and genetic instability can be explained by the "two-hits theory" and results in the occurrence of many somatic mutations. The expression of nonsynonymous mutations results in the production of mutant proteins from tumor cells, namely tumor-specific antigens called neoantigens. Because neoantigens do not exist in healthy cells, they have the potential to stimulate antitumor immune responses by CD4+ and CD8+ T-cell activation without jeopardizing normal tissues. Immunotherapy has reshaped the cancer treatment paradigm in recent decades with the introduction of immune-checkpoint blockade therapy and transgenic T-cell receptor/chimeric antigen receptor T cells. However, these strategies performed poorly in solid tumors because of the obstacles of the immunosuppressive microenvironment caused by regulatory T cells and other suppressor cells. Therefore, other immunotherapeutic strategies are under development, such as personalized vaccines, to trigger de novo T-cell responses against neoantigens and lead to the amplification of tumor-specific T-cell subclones. Neoantigen epitope prediction algorithms have enabled the detection of neoantigens and the creation of tailored neoantigen vaccines as a result of the fast development of next-generation sequencing and cancer bioinformatics. Here we provide an overview of the current neoantigen cancer vaccines and adoptive T-cell transfer therapy with neoantigen-specific lymphocytes. We also discuss the challenges in developing neoantigen-targeted immunotherapeutic strategies for cancer.
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Affiliation(s)
- Yanwei Shen
- Shanghai Jianshan Medical Tech Co LtdShanghaiChina
| | - Lu Yu
- Shanghai Jianshan Medical Tech Co LtdShanghaiChina
| | - Xiaoli Xu
- Shanghai Jianshan Medical Tech Co LtdShanghaiChina
| | - Shaojun Yu
- Department of Surgery, The Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Zhuo Yu
- Department of Medical Oncology, Beijing Tsinghua Changgung Hospital, School of Clinical MedicineTsinghua UniversityBeijingChina
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12
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Abstract
ABSTRACT The holy grail of cancer therapeutics is the destruction of cancer cells while avoiding harm to normal cells. Cancer is unique from normal tissues because of the presence of somatic mutations that accumulate during tumorigenesis. Some nonsynonymous mutations can give rise to mutated peptide antigens (hereafter referred to as neoantigens) that can be specifically recognized by T cells. Thus, the immunological targeting of neoantigens represents a safe and promising strategy to treat patients with cancer. This article reviews the clinical application of adoptive cell therapy targeting neoantigens in patients with epithelial cancers.
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13
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Diaz-Cano I, Paz-Ares L, Otano I. Adoptive tumor infiltrating lymphocyte transfer as personalized immunotherapy. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2022; 370:163-192. [PMID: 35798505 DOI: 10.1016/bs.ircmb.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cancer is a leading cause of death worldwide and, despite new targeted therapies and immunotherapies, a large group of patients fail to respond to therapy or progress after initial response, which brings the need for additional treatment options. Manipulating the immune system using a variety of approaches has been explored for the past years with successful results. Sustained progress has been made to understand the T cell-mediated anti-tumor responses counteracting the tumorigenesis process. The T-lymphocyte pool, especially its capacity for antigen-directed cytotoxicity, has become a central focus for engaging the immune system in defeating cancer. The adoptive cell transfer of autologous tumor-infiltrating lymphocytes has been used in humans for over 30 years to treat metastatic melanoma. In this review, we provide a brief history of ACT-TIL and discuss the current state of ACT-TIL clinical development in solid tumors. We also discuss how key advances in understanding genetic intratumor heterogeneity, to accurately identify neoantigens, and new strategies designed to overcome T-cell exhaustion and tumor immunosuppression have improved the efficacy of the TIL-therapy infusion. Characteristics of the TIL products will be discussed, as well as new strategies, including the selective expansion of specific fractions from the cell product or the genetic manipulation of T cells for improving the in-vivo survival and functionality. In summary, this review outlines the potential of ACT-TIL as a personalized approach for epithelial tumors and continued discoveries are making it increasingly more effective against other types of cancers.
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Affiliation(s)
- Ines Diaz-Cano
- H12O-CNIO Lung Cancer Clinical Research Unit, Health Research Institute Hospital 12 de Octubre/Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Luis Paz-Ares
- H12O-CNIO Lung Cancer Clinical Research Unit, Health Research Institute Hospital 12 de Octubre/Spanish National Cancer Research Center (CNIO), Madrid, Spain; Spanish Center for Biomedical Research Network in Oncology (CIBERONC), Madrid, Spain; Medicine and Physiology Department, School of Medicine, Complutense University of Madrid, Madrid, Spain
| | - Itziar Otano
- H12O-CNIO Lung Cancer Clinical Research Unit, Health Research Institute Hospital 12 de Octubre/Spanish National Cancer Research Center (CNIO), Madrid, Spain; Spanish Center for Biomedical Research Network in Oncology (CIBERONC), Madrid, Spain.
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14
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Creasy CA, Meng YJ, Forget MA, Karpinets T, Tomczak K, Stewart C, Torres-Cabala CA, Pilon-Thomas S, Sarnaik AA, Mulé JJ, Garraway L, Bustos M, Zhang J, Patel SP, Diab A, Glitza IC, Yee C, Tawbi H, Wong MK, McQuade J, Hoon DSB, Davies MA, Hwu P, Amaria RN, Haymaker C, Beroukhim R, Bernatchez C. Genomic Correlates of Outcome in Tumor-Infiltrating Lymphocyte Therapy for Metastatic Melanoma. Clin Cancer Res 2022; 28:1911-1924. [PMID: 35190823 DOI: 10.1158/1078-0432.ccr-21-1060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/01/2021] [Accepted: 02/16/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Adoptive cell therapy (ACT) of tumor-infiltrating lymphocytes (TIL) historically yields a 40%-50% response rate in metastatic melanoma. However, the determinants of outcome are largely unknown. EXPERIMENTAL DESIGN We investigated tumor-based genomic correlates of overall survival (OS), progression-free survival (PFS), and response to therapy by interrogating tumor samples initially collected to generate TIL infusion products. RESULTS Whole-exome sequencing (WES) data from 64 samples indicated a positive correlation between neoantigen load and OS, but not PFS or response to therapy. RNA sequencing analysis of 34 samples showed that expression of PDE1C, RTKN2, and NGFR was enriched in responders who had improved PFS and OS. In contrast, the expression of ELFN1 was enriched in patients with unfavorable response, poor PFS and OS, whereas enhanced methylation of ELFN1 was observed in patients with favorable outcomes. Expression of ELFN1, NGFR, and PDE1C was mainly found in cancer-associated fibroblasts and endothelial cells in tumor tissues across different cancer types in publicly available single-cell RNA sequencing datasets, suggesting a role for elements of the tumor microenvironment in defining the outcome of TIL therapy. CONCLUSIONS Our findings suggest that transcriptional features of melanomas correlate with outcomes after TIL therapy and may provide candidates to guide patient selection.
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Affiliation(s)
- Caitlin A Creasy
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Yuzhong Jeff Meng
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Tatiana Karpinets
- Department of Genomic Medicine, The University of Texas MDACC, Houston, Texas
| | - Katarzyna Tomczak
- Department of Translational Molecular Pathology, The University of Texas MDACC, Houston, Texas
| | - Chip Stewart
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Shari Pilon-Thomas
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Amod A Sarnaik
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - James J Mulé
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Levi Garraway
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matias Bustos
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Saint John's Health Center, Santa Monica, California
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MDACC, Houston, Texas
| | - Sapna P Patel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Adi Diab
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Isabella C Glitza
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Cassian Yee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Hussein Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Michael K Wong
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Jennifer McQuade
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Saint John's Health Center, Santa Monica, California
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MDACC, Houston, Texas
| | - Rameen Beroukhim
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas.,Department of Translational Molecular Pathology, The University of Texas MDACC, Houston, Texas
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15
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Wei F, Cheng XX, Xue JZ, Xue SA. Emerging Strategies in TCR-Engineered T Cells. Front Immunol 2022; 13:850358. [PMID: 35432319 PMCID: PMC9006933 DOI: 10.3389/fimmu.2022.850358] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/03/2022] [Indexed: 12/12/2022] Open
Abstract
Immunotherapy of cancer has made tremendous progress in recent years, as demonstrated by the remarkable clinical responses obtained from adoptive cell transfer (ACT) of patient-derived tumor infiltrating lymphocytes, chimeric antigen receptor (CAR)-modified T cells (CAR-T) and T cell receptor (TCR)-engineered T cells (TCR-T). TCR-T uses specific TCRS optimized for tumor engagement and can recognize epitopes derived from both cell-surface and intracellular targets, including tumor-associated antigens, cancer germline antigens, viral oncoproteins, and tumor-specific neoantigens (neoAgs) that are largely sequestered in the cytoplasm and nucleus of tumor cells. Moreover, as TCRS are naturally developed for sensitive antigen detection, they are able to recognize epitopes at far lower concentrations than required for CAR-T activation. Therefore, TCR-T holds great promise for the treatment of human cancers. In this focused review, we summarize basic, translational, and clinical insights into the challenges and opportunities of TCR-T. We review emerging strategies used in current ACT, point out limitations, and propose possible solutions. We highlight the importance of targeting tumor-specific neoAgs and outline a strategy of combining neoAg vaccines, checkpoint blockade therapy, and adoptive transfer of neoAg-specific TCR-T to produce a truly tumor-specific therapy, which is able to penetrate into solid tumors and resist the immunosuppressive tumor microenvironment. We believe such a combination approach should lead to a significant improvement in cancer immunotherapies, especially for solid tumors, and may provide a general strategy for the eradication of multiple cancers.
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Affiliation(s)
- Fang Wei
- Genetic Engineering Laboratory, School of Biological & Environmental Engineering, Xi'An University, Xi'An, China
| | - Xiao-Xia Cheng
- Genetic Engineering Laboratory, School of Biological & Environmental Engineering, Xi'An University, Xi'An, China
| | - John Zhao Xue
- Genetic Engineering Laboratory, School of Biological & Environmental Engineering, Xi'An University, Xi'An, China
| | - Shao-An Xue
- Genetic Engineering Laboratory, School of Biological & Environmental Engineering, Xi'An University, Xi'An, China
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16
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Lang F, Schrörs B, Löwer M, Türeci Ö, Sahin U. Identification of neoantigens for individualized therapeutic cancer vaccines. Nat Rev Drug Discov 2022; 21:261-282. [PMID: 35105974 PMCID: PMC7612664 DOI: 10.1038/s41573-021-00387-y] [Citation(s) in RCA: 172] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2021] [Indexed: 02/07/2023]
Abstract
Somatic mutations in cancer cells can generate tumour-specific neoepitopes, which are recognized by autologous T cells in the host. As neoepitopes are not subject to central immune tolerance and are not expressed in healthy tissues, they are attractive targets for therapeutic cancer vaccines. Because the vast majority of cancer mutations are unique to the individual patient, harnessing the full potential of this rich source of targets requires individualized treatment approaches. Many computational algorithms and machine-learning tools have been developed to identify mutations in sequence data, to prioritize those that are more likely to be recognized by T cells and to design tailored vaccines for every patient. In this Review, we fill the gaps between the understanding of basic mechanisms of T cell recognition of neoantigens and the computational approaches for discovery of somatic mutations and neoantigen prediction for cancer immunotherapy. We present a new classification of neoantigens, distinguishing between guarding, restrained and ignored neoantigens, based on how they confer proficient antitumour immunity in a given clinical context. Such context-based differentiation will contribute to a framework that connects neoantigen biology to the clinical setting and medical peculiarities of cancer, and will enable future neoantigen-based therapies to provide greater clinical benefit.
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Affiliation(s)
- Franziska Lang
- TRON Translational Oncology, Mainz, Germany
- Faculty of Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | | | | | | | - Ugur Sahin
- BioNTech, Mainz, Germany.
- University Medical Center, Johannes Gutenberg University, Mainz, Germany.
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17
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Kalaora S, Nagler A, Wargo JA, Samuels Y. Mechanisms of immune activation and regulation: lessons from melanoma. Nat Rev Cancer 2022; 22:195-207. [PMID: 35105962 DOI: 10.1038/s41568-022-00442-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 12/14/2022]
Abstract
Melanoma, a skin cancer that develops from pigment cells, has been studied intensively, particularly in terms of the immune response to tumours, and has been used as a model for the development of immunotherapy. This is due, in part, to the high mutational burden observed in melanomas, which increases both their immunogenicity and the infiltration of immune cells into the tumours, compared with other types of cancers. The immune response to melanomas involves a complex set of components and interactions. As the tumour evolves, it accumulates an increasing number of genetic and epigenetic alterations, some of which contribute to the immunogenicity of the tumour cells and the infiltration of immune cells. However, tumour evolution also enables the development of resistance mechanisms, which, in turn, lead to tumour immune escape. Understanding the interactions between melanoma tumour cells and the immune system, and the evolving changes within the melanoma tumour cells, the immune system and the microenvironment, is essential for the development of new cancer therapies. However, current research suggests that other extrinsic factors, such as the microbiome, may play a role in the immune response to melanomas. Here, we review the mechanisms underlying the immune response in the tumour and discuss recent advances as well as strategies for treatment development.
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Affiliation(s)
- Shelly Kalaora
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Nagler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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18
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A decade of checkpoint blockade immunotherapy in melanoma: understanding the molecular basis for immune sensitivity and resistance. Nat Immunol 2022; 23:660-670. [PMID: 35241833 DOI: 10.1038/s41590-022-01141-1] [Citation(s) in RCA: 209] [Impact Index Per Article: 104.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/18/2022] [Indexed: 12/30/2022]
Abstract
Ten years since the immune checkpoint inhibitor ipilimumab was approved for advanced melanoma, it is time to reflect on the lessons learned regarding modulation of the immune system to treat cancer and on novel approaches to further extend the efficacy of current and emerging immunotherapies. Here, we review the studies that led to our current understanding of the melanoma immune microenvironment in humans and the mechanistic work supporting these observations. We discuss how this information is guiding more precise analyses of the mechanisms of action of immune checkpoint blockade and novel immunotherapeutic approaches. Lastly, we review emerging evidence supporting the negative impact of melanoma metabolic adaptation on anti-tumor immunity and discuss how to counteract such mechanisms for more successful use of immunotherapy.
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19
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Shakiba M, Zumbo P, Espinosa-Carrasco G, Menocal L, Dündar F, Carson SE, Bruno EM, Sanchez-Rivera FJ, Lowe SW, Camara S, Koche RP, Reuter VP, Socci ND, Whitlock B, Tamzalit F, Huse M, Hellmann MD, Wells DK, Defranoux NA, Betel D, Philip M, Schietinger A. TCR signal strength defines distinct mechanisms of T cell dysfunction and cancer evasion. J Exp Med 2022; 219:212936. [PMID: 34935874 PMCID: PMC8704919 DOI: 10.1084/jem.20201966] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 07/07/2021] [Accepted: 11/12/2021] [Indexed: 12/26/2022] Open
Abstract
T cell receptor (TCR) signal strength is a key determinant of T cell responses. We developed a cancer mouse model in which tumor-specific CD8 T cells (TST cells) encounter tumor antigens with varying TCR signal strength. High-signal-strength interactions caused TST cells to up-regulate inhibitory receptors (IRs), lose effector function, and establish a dysfunction-associated molecular program. TST cells undergoing low-signal-strength interactions also up-regulated IRs, including PD1, but retained a cell-intrinsic functional state. Surprisingly, neither high- nor low-signal-strength interactions led to tumor control in vivo, revealing two distinct mechanisms by which PD1hi TST cells permit tumor escape; high signal strength drives dysfunction, while low signal strength results in functional inertness, where the signal strength is too low to mediate effective cancer cell killing by functional TST cells. CRISPR-Cas9-mediated fine-tuning of signal strength to an intermediate range improved anti-tumor activity in vivo. Our study defines the role of TCR signal strength in TST cell function, with important implications for T cell-based cancer immunotherapies.
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Affiliation(s)
- Mojdeh Shakiba
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY.,Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY
| | | | - Laura Menocal
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Friederike Dündar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY.,Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY
| | - Sandra E Carson
- Department of Biochemistry, Cell and Molecular Biology, Weill Cornell Medicine, New York, NY
| | - Emmanuel M Bruno
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Scott W Lowe
- Cancer Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Steven Camara
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vincent P Reuter
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nicholas D Socci
- Bioinformatics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Benjamin Whitlock
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Fella Tamzalit
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Morgan Huse
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | - Matthew D Hellmann
- Parker Institute for Cancer Immunotherapy, San Francisco, CA.,Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, Cornell University, New York, NY
| | - Daniel K Wells
- Parker Institute for Cancer Immunotherapy, San Francisco, CA
| | | | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY.,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Mary Philip
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
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20
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Gartner JJ, Parkhurst MR, Gros A, Tran E, Jafferji MS, Copeland A, Hanada KI, Zacharakis N, Lalani A, Krishna S, Sachs A, Prickett TD, Li YF, Florentin M, Kivitz S, Chatmon SC, Rosenberg SA, Robbins PF. A machine learning model for ranking candidate HLA class I neoantigens based on known neoepitopes from multiple human tumor types. NATURE CANCER 2021; 2:563-574. [PMID: 34927080 DOI: 10.1038/s43018-021-00197-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Tumor neoepitopes presented by major histocompatibility complex (MHC) class I are recognized by tumor-infiltrating lymphocytes (TIL) and are targeted by adoptive T-cell therapies. Identifying which mutant neoepitopes from tumor cells are capable of recognition by T cells can assist in the development of tumor-specific, cell-based therapies and can shed light on antitumor responses. Here, we generate a ranking algorithm for class I candidate neoepitopes by using next-generation sequencing data and a dataset of 185 neoepitopes that are recognized by HLA class I-restricted TIL from individuals with metastatic cancer. Random forest model analysis showed that the inclusion of multiple factors impacting epitope presentation and recognition increased output sensitivity and specificity compared to the use of predicted HLA binding alone. The ranking score output provides a set of class I candidate neoantigens that may serve as therapeutic targets and provides a tool to facilitate in vitro and in vivo studies aimed at the development of more effective immunotherapies.
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Affiliation(s)
- Jared J Gartner
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria R Parkhurst
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alena Gros
- Vall d'Hebron Institute of Oncology (VHIO), Cellex Center, Barcelona, Spain
| | - Eric Tran
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | | | - Amy Copeland
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ken-Ichi Hanada
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nikolaos Zacharakis
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Almin Lalani
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sri Krishna
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Abraham Sachs
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Todd D Prickett
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yong F Li
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria Florentin
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Scott Kivitz
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samuel C Chatmon
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Steven A Rosenberg
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul F Robbins
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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21
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Transcriptional and Epigenetic Bioinformatic Analysis of Claudin-9 Regulation in Gastric Cancer. JOURNAL OF ONCOLOGY 2021. [DOI: 10.1155/2021/5936905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Gastric cancer is a heterogeneous disease that represents 5% to 10% of all new cancer cases worldwide. Advances in histological diagnosis and the discovery of new genes have admitted new genomic classifications. Nevertheless, the bioinformatic analysis of gastric cancer databases has favored the detection of specific differentially expressed genes with biological significance. Claudins, a family of proteins involved in tight junction physiology, have emerged as the key regulators of cellular processes, such as growth, proliferation, and migration, associated with cancer progression. The expression of Claudin-9 in the gastric cancer tissue has been linked to poor prognosis, however, its transcriptional and epigenetic regulations demand a more comprehensive analysis. Using the neural network promoter prediction, TransFact, Uniprot-KB, Expasy-SOPMA, protein data bank, proteomics DB, Interpro, BioGRID, String, and the FASTA protein sequence databases and software, we found the following: (1) the promoter sequence has an unconventional structure, including different transcriptional regulation elements distributed throughout it, (2) GATA 4, GATA 6, and KLF5 are the key regulators of Claudin-9 expression, (3) Oct1, NF-κB, AP-1, c-Ets-1, and HNF-3β have the higher binding affinity to the CLDN9 promoter, (4) Claudin-9 interacts with cell differentiation and development proteins, (5) CLDN9 is highly methylated, and (6) Claudin-9 expression is associated with poor survival. In conclusion, Claudin-9 is a protein that should be considered a diagnostic marker as its gene promoter region binds to the transcription factors associated with the deregulation of cell control, enhanced cell proliferation, and metastasis.
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22
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Von Rueden SK, Fan TM. Cancer-Immunity Cycle and Therapeutic Interventions- Opportunities for Including Pet Dogs With Cancer. Front Oncol 2021; 11:773420. [PMID: 34869014 PMCID: PMC8639699 DOI: 10.3389/fonc.2021.773420] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/01/2021] [Indexed: 12/22/2022] Open
Abstract
The tumor-immune interplay represents a dynamic series of events executed by cellular and soluble participants that either promote or inhibit successful tumor formation and growth. Throughout a tumor’s development and progression, the host organism’s immune system reacts by generating anti-cancer defenses through various incremental and combinatorial mechanisms, and this reactive orchestration is termed the cancer-immunity cycle. Success or failure of the cancer-immunity cycle dictates the fate of both host and tumor as winner or loser. Insights into how the tumor and host immune system continuously adapt to each other throughout the lifecycle of the tumor is necessary to rationally develop new effective immunotherapies. Additionally, the evolving nature of the cancer-immunity cycle necessitates therapeutic agility, requiring real-time serial assessment of immunobiologic markers that permits tailoring of therapies to the everchanging tumor immune microenvironment. In order to accelerate advances in the field of immuno-oncology, this review summarizes the steps comprising the cancer-immunity cycle, and underscores key breakpoints in the cycle that either favor cancer regression or progression, as well as shaping of the tumor microenvironment and associated immune phenotypes. Furthermore, specific large animal models of spontaneous cancers that are deemed immunogenic will be reviewed and proposed as unique resources for validating investigational immunotherapeutic protocols that are informed by the cancer-immunity cycle. Collectively, this review will provide a progressive look into the dynamic interplay between tumor and host immune responses and raise awareness for how large animal models can be included for developing combinatorial and sequenced immunotherapies to maximizing favorable treatment outcomes.
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Affiliation(s)
- Samantha K Von Rueden
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Timothy M Fan
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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23
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Davis L, Tarduno A, Lu YC. Neoantigen-Reactive T Cells: The Driving Force behind Successful Melanoma Immunotherapy. Cancers (Basel) 2021; 13:cancers13236061. [PMID: 34885172 PMCID: PMC8657037 DOI: 10.3390/cancers13236061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Cancer immunotherapy is a revolutionary type of cancer therapy. It uses the patient’s own immune system to fight and potentially cure cancer. The first major breakthrough of immunotherapy came from successful clinical trials for melanoma treatments. Since then, researchers have focused on understanding the science behind immunotherapy, so that patients with other types of cancer may also benefit. One of the major findings is that the T cells in melanoma patients may recognize a specific type of tumor antigen, called neoantigens, and then kill tumor cells that present these neoantigens. The neoantigens mainly arise from the DNA mutations found in tumor cells. These mutations are translated into mutated proteins that are then distinguished by T cells. In this article, we discuss the critical role of T cells in immunotherapy, as well as the clinical trials that shaped the treatments for melanoma. Abstract Patients with metastatic cutaneous melanoma have experienced significant clinical responses after checkpoint blockade immunotherapy or adoptive cell therapy. Neoantigens are mutated proteins that arise from tumor-specific mutations. It is hypothesized that the neoantigen recognition by T cells is the critical step for T-cell-mediated anti-tumor responses and subsequent tumor regressions. In addition to describing neoantigens, we review the sentinel and ongoing clinical trials that are helping to shape the current treatments for patients with cutaneous melanoma. We also present the existing evidence that establishes the correlations between neoantigen-reactive T cells and clinical responses in melanoma immunotherapy.
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Affiliation(s)
- Lindy Davis
- Department of Surgery, Albany Medical Center, Albany, NY 12208, USA; (L.D.); (A.T.)
| | - Ashley Tarduno
- Department of Surgery, Albany Medical Center, Albany, NY 12208, USA; (L.D.); (A.T.)
| | - Yong-Chen Lu
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence:
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24
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Kristensen NP, Heeke C, Tvingsholm SA, Borch A, Draghi A, Crowther MD, Carri I, Munk KK, Holm JS, Bjerregaard AM, Bentzen AK, Marquard AM, Szallasi Z, McGranahan N, Andersen R, Nielsen M, Jönsson GB, Donia M, Svane IM, Hadrup SR. Neoantigen-reactive CD8+ T cells affect clinical outcome of adoptive transfer with tumor-infiltrating lymphocytes in melanoma. J Clin Invest 2021; 132:150535. [PMID: 34813506 PMCID: PMC8759789 DOI: 10.1172/jci150535] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/18/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Neoantigen-driven recognition and T cell-mediated killing contribute to tumor clearance following adoptive cell therapy (ACT) with Tumor-Infiltrating Lymphocytes (TILs). Yet, how diversity, frequency, and persistence of expanded neoepitope-specific CD8+ T cells derived from TIL infusion products affect patient outcome is not fully determined. METHODS Using barcoded pMHC multimers, we provide a comprehensive mapping of CD8+ T cells recognizing neoepitopes in TIL infusion products and blood samples from 26 metastatic mela-noma patients who received ACT. RESULTS We identified 106 neoepitopes within TIL infusion products corresponding to 1.8% of all predicted neoepitopes. We observed neoepitope-specific recognition to be virtually devoid in TIL infusion products given to patients with progressive disease outcome. Moreover, we found that the frequency of neoepitope-specific CD8+ T cells in TIL infusion products correlated with in-creased survival, and that detection of engrafted CD8+ T cells in post-treatment (i.e. originating from the TIL infusion product) were unique to responders of TIL-ACT. Finally, we found that a transcriptional signature for lymphocyte activity within the tumor microenvironment was associated with a higher frequency of neoepitope-specific CD8+ T cells in the infusion product. CONCLUSIONS These data support previous case studies of neoepitope-specific CD8+ T cells in melanoma, and indicate that successful TIL-ACT is associated with an expansion of neoepitope-specific CD8+ T cells. FUNDING NEYE Foundation; European Research Council; Lundbeck Foundation Fellowship; Carlsberg Foundation.
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Affiliation(s)
- Nikolaj Pagh Kristensen
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Christina Heeke
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Siri A Tvingsholm
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Annie Borch
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Arianna Draghi
- Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | | | - Ibel Carri
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Kamilla K Munk
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Jeppe Sejerø Holm
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Anne-Mette Bjerregaard
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Amalie Kai Bentzen
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Andrea M Marquard
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
| | | | - Rikke Andersen
- Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Morten Nielsen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
| | - Göran B Jönsson
- Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Marco Donia
- Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Inge Marie Svane
- Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark (DTU), Kgs. Lyngby, Denmark
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25
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Peri A, Greenstein E, Alon M, Pai JA, Dingjan T, Reich-Zeliger S, Barnea E, Barbolin C, Levy R, Arnedo-Pac C, Kalaora S, Dassa B, Feldmesser E, Shang P, Greenberg P, Levin Y, Benedek G, Levesque MP, Adams DJ, Lotem M, Wilmott JS, Scolyer RA, Jönsson GB, Admon A, Rosenberg SA, Cohen CJ, Niv MY, Lopez-Bigas N, Satpathy AT, Friedman N, Samuels Y. Combined presentation and immunogenicity analysis reveals a recurrent RAS.Q61K neoantigen in melanoma. J Clin Invest 2021; 131:129466. [PMID: 34651586 DOI: 10.1172/jci129466] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/02/2021] [Indexed: 12/30/2022] Open
Abstract
Neoantigens are now recognized drivers of the antitumor immune response. Recurrent neoantigens, shared among groups of patients, have thus become increasingly coveted therapeutic targets. Here, we report on the data-driven identification of a robustly presented, immunogenic neoantigen that is derived from the combination of HLA-A*01:01 and RAS.Q61K. Analysis of large patient cohorts indicated that this combination applies to 3% of patients with melanoma. Using HLA peptidomics, we were able to demonstrate robust endogenous presentation of the neoantigen in 10 tumor samples. We detected specific reactivity to the mutated peptide within tumor-infiltrating lymphocytes (TILs) from 2 unrelated patients, thus confirming its natural immunogenicity. We further investigated the neoantigen-specific clones and their T cell receptors (TCRs) via a combination of TCR sequencing, TCR overexpression, functional assays, and single-cell transcriptomics. Our analysis revealed a diverse repertoire of neoantigen-specific clones with both intra- and interpatient TCR similarities. Moreover, 1 dominant clone proved to cross-react with the highly prevalent RAS.Q61R variant. Transcriptome analysis revealed a high association of TCR clones with specific T cell phenotypes in response to cognate melanoma, with neoantigen-specific cells showing an activated and dysfunctional phenotype. Identification of recurrent neoantigens and their reactive TCRs can promote "off-the-shelf" precision immunotherapies, alleviating limitations of personalized treatments.
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Affiliation(s)
| | - Erez Greenstein
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Joy A Pai
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Tamir Dingjan
- The Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Eilon Barnea
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | | | - Ronen Levy
- Department of Molecular Cell Biology and
| | - Claudia Arnedo-Pac
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Bareket Dassa
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ester Feldmesser
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ping Shang
- Melanoma Institute Australia and.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Yishai Levin
- The de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Benedek
- Tissue Typing and Immunogenetics Unit, Hadassah Medical Center, Jerusalem, Israel
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Michal Lotem
- Sharett Institute of Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - James S Wilmott
- Melanoma Institute Australia and.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia and.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, Australia
| | - Göran B Jönsson
- Lund University Cancer Center, Lund University, Lund, Sweden
| | - Arie Admon
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Steven A Rosenberg
- Surgery Branch, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Cyrille J Cohen
- Laboratory of Tumor Immunotherapy, The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Masha Y Niv
- The Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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26
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van den Berg JH, Heemskerk B, van Rooij N, Gomez-Eerland R, Michels S, van Zon M, de Boer R, Bakker NAM, Jorritsma-Smit A, van Buuren MM, Kvistborg P, Spits H, Schotte R, Mallo H, Karger M, van der Hage JA, Wouters MWJM, Pronk LM, Geukes Foppen MH, Blank CU, Beijnen JH, Nuijen B, Schumacher TN, Haanen JBAG. Tumor infiltrating lymphocytes (TIL) therapy in metastatic melanoma: boosting of neoantigen-specific T cell reactivity and long-term follow-up. J Immunother Cancer 2021; 8:jitc-2020-000848. [PMID: 32753545 PMCID: PMC7406109 DOI: 10.1136/jitc-2020-000848] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2020] [Indexed: 12/18/2022] Open
Abstract
Treatment of metastatic melanoma with autologous tumor infiltrating lymphocytes (TILs) is currently applied in several centers. Robust and remarkably consistent overall response rates, of around 50% of treated patients, have been observed across hospitals, including a substantial fraction of durable, complete responses. PURPOSE Execute a phase I/II feasibility study with TIL therapy in metastatic melanoma at the Netherlands Cancer Institute, with the goal to assess feasibility and potential value of a randomized phase III trial. EXPERIMENTAL Ten patients were treated with TIL therapy. Infusion products and peripheral blood samples were phenotypically characterized and neoantigen reactivity was assessed. Here, we present long-term clinical outcome and translational data on neoantigen reactivity of the T cell products. RESULTS Five out of 10 patients, who were all anti-PD-1 naïve at time of treatment, showed an objective clinical response, including two patients with a complete response that are both ongoing for more than 7 years. Immune monitoring demonstrated that neoantigen-specific T cells were detectable in TIL infusion products from three out of three patients analyzed. For six out of the nine neoantigen-specific T cell responses detected in these TIL products, T cell response magnitude increased significantly in the peripheral blood compartment after therapy, and neoantigen-specific T cells were detectable for up to 3 years after TIL infusion. CONCLUSION The clinical results from this study confirm the robustness of TIL therapy in metastatic melanoma and the potential role of neoantigen-specific T cell reactivity. In addition, the data from this study supported the rationale to initiate an ongoing multicenter phase III TIL trial.
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Affiliation(s)
| | - Bianca Heemskerk
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nienke van Rooij
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Raquel Gomez-Eerland
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Samira Michels
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maaike van Zon
- BioTherapeutics Unit, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Renate de Boer
- BioTherapeutics Unit, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Noor A M Bakker
- BioTherapeutics Unit, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Annelies Jorritsma-Smit
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marit M van Buuren
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Pia Kvistborg
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hergen Spits
- AIMM Therapeutics, Amsterdam, The Netherlands.,Experimental Immunology, Amsterdam University Medical Centres, Amsterdam, Noord-Holland, The Netherlands
| | | | - Henk Mallo
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Matthias Karger
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joris A van der Hage
- Department of Surgery, Leiden Universitair Medisch Centrum, Leiden, Zuid-Holland, The Netherlands
| | - Michel W J M Wouters
- Surgical Oncology, Antoni van Leeuwenhoek Nederlands Kanker Instituut, Amsterdam, The Netherlands.,Dutch Institute for Clinical Auditing, Leiden, The Netherlands
| | - Loes M Pronk
- Department of Biometrics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marnix H Geukes Foppen
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christian U Blank
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Noord-Holland, The Netherlands
| | - Jos H Beijnen
- Department of Pharmacy & Pharmacology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht University Department of Pharmaceutical Sciences, Utrecht, Utrecht, The Netherlands
| | - Bastiaan Nuijen
- Department of Pharmacy & Pharmacology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ton N Schumacher
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - John B A G Haanen
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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27
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Lu YC, Zheng Z, Lowery FJ, Gartner JJ, Prickett TD, Robbins PF, Rosenberg SA. Direct identification of neoantigen-specific TCRs from tumor specimens by high-throughput single-cell sequencing. J Immunother Cancer 2021; 9:jitc-2021-002595. [PMID: 34321276 PMCID: PMC8320258 DOI: 10.1136/jitc-2021-002595] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2021] [Indexed: 01/22/2023] Open
Abstract
Background Recognition of neoantigens by T cells plays a major role in cancer immunotherapy. Identification of neoantigen-specific T-cell receptors (TCRs) has become a critical research tool for studying T cell-mediated responses after immunotherapy. In addition, neoantigen-specific TCRs can be used to modify the specificity of T cells for T cell-based therapies targeting tumor-specific mutations. Although several techniques have been developed to identify TCR sequences, these techniques still require a significant amount of labor, making them impractical in the clinical setting. Methods Thanks to the availability of high-throughput single-cell sequencing, we developed a new process to isolate neoantigen-specific TCR sequences. This process included the isolation of tumor-infiltrating T cells from a tumor specimen and the stimulation of T cells by neoantigen-loaded dendritic cells, followed by single-cell sequencing for TCR and T-cell activation markers, interferon-γ and interleukin-2. Results In this study, potential neoantigen-specific TCRs were isolated from three melanoma and three colorectal tumor specimens. These TCRs were then synthesized and transduced into autologous T cells, followed by testing the recognition of neoantigens. A total of 28 neoantigen-specific TCRs were identified by this process. If identical TCR sequences were detected from two or more single cells, this approach was highly reliable (100%, 19 out of 19 TCRs). Conclusion This single-cell approach provides an efficient process to isolate antigen-specific TCRs for research and clinical applications.
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Affiliation(s)
- Yong-Chen Lu
- Surgery Branch, National Institutes of Health, Bethesda, Maryland, USA
- Department of Pathology and Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Zhili Zheng
- Surgery Branch, National Institutes of Health, Bethesda, Maryland, USA
| | - Frank J Lowery
- Surgery Branch, National Institutes of Health, Bethesda, Maryland, USA
| | - Jared J Gartner
- Surgery Branch, National Institutes of Health, Bethesda, Maryland, USA
| | - Todd D Prickett
- Surgery Branch, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul F Robbins
- Surgery Branch, National Institutes of Health, Bethesda, Maryland, USA
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28
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Kumar A, Watkins R, Vilgelm AE. Cell Therapy With TILs: Training and Taming T Cells to Fight Cancer. Front Immunol 2021; 12:690499. [PMID: 34140957 PMCID: PMC8204054 DOI: 10.3389/fimmu.2021.690499] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 05/06/2021] [Indexed: 01/16/2023] Open
Abstract
The rationale behind cancer immunotherapy is based on the unequivocal demonstration that the immune system plays an important role in limiting cancer initiation and progression. Adoptive cell therapy (ACT) is a form of cancer immunotherapy that utilizes a patient’s own immune cells to find and eliminate tumor cells, however, donor immune cells can also be employed in some cases. Here, we focus on T lymphocyte (T cell)-based cancer immunotherapies that have gained significant attention after initial discoveries that graft-versus-tumor responses were mediated by T cells. Accumulating knowledge of T cell development and function coupled with advancements in genetics and data science has enabled the use of a patient’s own (autologous) T cells for ACT (TIL ACTs). In TIL ACT, tumor-infiltrating lymphocytes (TILs) are collected from resected tumor material, enhanced and expanded ex-vivo, and delivered back to the patient as therapeutic agents. ACT with TILs has been shown to cause objective tumor regression in several types of cancers including melanoma, cervical squamous cell carcinoma, and cholangiocarcinoma. In this review, we provide a brief history of TIL ACT and discuss the current state of TIL ACT clinical development in solid tumors. We also discuss the niche of TIL ACT in the current cancer therapy landscape and potential strategies for patient selection.
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Affiliation(s)
- Amrendra Kumar
- Department of Pathology, The Ohio State University, Columbus, OH, United States.,The Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, United States
| | - Reese Watkins
- Department of Pathology, The Ohio State University, Columbus, OH, United States.,The Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, United States
| | - Anna E Vilgelm
- Department of Pathology, The Ohio State University, Columbus, OH, United States.,The Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, United States
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29
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Morotti M, Albukhari A, Alsaadi A, Artibani M, Brenton JD, Curbishley SM, Dong T, Dustin ML, Hu Z, McGranahan N, Miller ML, Santana-Gonzalez L, Seymour LW, Shi T, Van Loo P, Yau C, White H, Wietek N, Church DN, Wedge DC, Ahmed AA. Promises and challenges of adoptive T-cell therapies for solid tumours. Br J Cancer 2021; 124:1759-1776. [PMID: 33782566 PMCID: PMC8144577 DOI: 10.1038/s41416-021-01353-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/22/2021] [Accepted: 03/04/2021] [Indexed: 12/11/2022] Open
Abstract
Cancer is a leading cause of death worldwide and, despite new targeted therapies and immunotherapies, many patients with advanced-stage- or high-risk cancers still die, owing to metastatic disease. Adoptive T-cell therapy, involving the autologous or allogeneic transplant of tumour-infiltrating lymphocytes or genetically modified T cells expressing novel T-cell receptors or chimeric antigen receptors, has shown promise in the treatment of cancer patients, leading to durable responses and, in some cases, cure. Technological advances in genomics, computational biology, immunology and cell manufacturing have brought the aspiration of individualised therapies for cancer patients closer to reality. This new era of cell-based individualised therapeutics challenges the traditional standards of therapeutic interventions and provides opportunities for a paradigm shift in our approach to cancer therapy. Invited speakers at a 2020 symposium discussed three areas-cancer genomics, cancer immunology and cell-therapy manufacturing-that are essential to the effective translation of T-cell therapies in the treatment of solid malignancies. Key advances have been made in understanding genetic intratumour heterogeneity, and strategies to accurately identify neoantigens, overcome T-cell exhaustion and circumvent tumour immunosuppression after cell-therapy infusion are being developed. Advances are being made in cell-manufacturing approaches that have the potential to establish cell-therapies as credible therapeutic options. T-cell therapies face many challenges but hold great promise for improving clinical outcomes for patients with solid tumours.
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Affiliation(s)
- Matteo Morotti
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Ashwag Albukhari
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulkhaliq Alsaadi
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mara Artibani
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James D Brenton
- Functional Genomics of Ovarian Cancer Laboratory, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Stuart M Curbishley
- Advanced Therapies Facility and National Institute for Health Research (NIHR) Biomedical Research Centre, University of Birmingham, Birmingham, UK
| | - Tao Dong
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, University of Oxford, Oxford, UK
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Zhiyuan Hu
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
| | - Martin L Miller
- Cancer System Biology Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Laura Santana-Gonzalez
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Leonard W Seymour
- Gene Therapy Group, Department of Oncology, University of Oxford, Oxford, UK
| | - Tingyan Shi
- Department of Gynecological Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Christopher Yau
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
- The Alan Turing Institute, London, UK
| | - Helen White
- Patient Representative, Endometrial Cancer Genomics England Clinical Interpretation Partnership (GeCIP) Domain, London, UK
| | - Nina Wietek
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - David N Church
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
| | - David C Wedge
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK.
| | - Ahmed A Ahmed
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK.
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30
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Kast F, Klein C, Umaña P, Gros A, Gasser S. Advances in identification and selection of personalized neoantigen/T-cell pairs for autologous adoptive T cell therapies. Oncoimmunology 2021; 10:1869389. [PMID: 33520408 PMCID: PMC7808433 DOI: 10.1080/2162402x.2020.1869389] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Based on the success of tumor-infiltrating lymphocytes (TIL)-based therapies, personalized adoptive cell therapies (ACT) targeting neoantigens have the potential to become a disruptive technology and lead to highly effective treatments for cancer patients for whom no other options exist. ACT of TIL, peripheral blood or gene-engineered peripheral blood lymphocytes (PBLs) targeting neoantigens is a highly personalized intervention that requires three discrete steps: i) Identification of suitable personal targets (neoantigens), ii) selection of T cells or their T cell receptors (TCRs) that are specific for the identified neoantigens and iii) expansion of the selected T cell population or generation of sufficient number of TCR modified T cells. In this review, we provide an introduction into challenges and approaches to identify neoantigens and to select the Adoptive Cell Therapy, ACT, Neoantigen, T cell, Cancer respective neoantigen-reactive T cells for use in ACT.
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Affiliation(s)
- Florian Kast
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Christian Klein
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Pablo Umaña
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Alena Gros
- Vall d'Hebron Institute of Oncology, Cellex Center, Barcelona, Spain
| | - Stephan Gasser
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
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31
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Elsharkawy SS, Elrheem MA, Elrheem SA. The Tumor Infiltrating Lymphocytes (TILs): Did We Find the Missed Piece of the Huge Puzzle? OPEN JOURNAL OF OBSTETRICS AND GYNECOLOGY 2021; 11:146-161. [DOI: 10.4236/ojog.2021.112017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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32
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Lazdun Y, Si H, Creasy T, Ranade K, Higgs BW, Streicher K, Durham NM. A New Pipeline to Predict and Confirm Tumor Neoantigens Predict Better Response to Immune Checkpoint Blockade. Mol Cancer Res 2020; 19:498-506. [PMID: 33257508 DOI: 10.1158/1541-7786.mcr-19-1118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 06/04/2020] [Accepted: 11/20/2020] [Indexed: 11/16/2022]
Abstract
Mutations that drive oncogenesis in cancer can generate neoantigens that may be recognized by the immune system. Identification of these neoantigens remains challenging due to the complexity of the MHC antigen and T-cell receptor interaction. Here, we describe the development of a systematic approach to efficiently identify and validate immunogenic neoantigens. Whole-exome sequencing of tissue from a patient with melanoma was used to identify nonsynonymous mutations, followed by MHC binding prediction and identification of tumor clonal architecture. The top 18 putative class I neoantigens were selected for immunogenicity testing via a novel in vitro pipeline in HLA-A201 healthy donor blood. Naïve CD8 T cells from donors were stimulated with allogeneic dendritic cells pulsed with peptide pools and then with individual peptides. The presence of antigen-specific T cells was determined via functional assays. We identified one putative neoantigen that expanded T cells specific to the mutant form of the peptide and validated this pipeline in a subset of patients with bladder tumors treated with durvalumab (n = 5). Within this cohort, the top predicted neoantigens from all patients were immunogenic in vitro. Finally, we looked at overall survival in the whole durvalumab-treated bladder cohort (N = 37) by stratifying patients by tertile measure of tumor mutation burden (TMB) or neoantigen load. Patients with higher neoantigen and TMB load tended to show better overall survival. IMPLICATIONS: This pipeline can enable accurate and rapid identification of personalized neoantigens that may help to identify patients who will survive longer on durvalumab.
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Affiliation(s)
- Yelena Lazdun
- Translational Functional Genomics, AstraZeneca, Gaithersburg, Maryland
| | - Han Si
- Translational Bioinformatics, AstraZeneca, Gaithersburg, Maryland
| | - Todd Creasy
- Translational Bioinformatics, AstraZeneca, Gaithersburg, Maryland
| | - Koustubh Ranade
- Translational Medicine, Oncology R&D, AstraZeneca, Gaithersburg, Maryland
| | - Brandon W Higgs
- Translational Bioinformatics, AstraZeneca, Gaithersburg, Maryland
| | - Katie Streicher
- Translational Medicine, Oncology R&D, AstraZeneca, Gaithersburg, Maryland
| | - Nicholas M Durham
- Translational Functional Genomics, AstraZeneca, Gaithersburg, Maryland.
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33
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Leko V, Rosenberg SA. Identifying and Targeting Human Tumor Antigens for T Cell-Based Immunotherapy of Solid Tumors. Cancer Cell 2020; 38:454-472. [PMID: 32822573 PMCID: PMC7737225 DOI: 10.1016/j.ccell.2020.07.013] [Citation(s) in RCA: 202] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/24/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
Abstract
Cancer elimination in humans can be achieved with immunotherapy that relies on T lymphocyte-mediated recognition of tumor antigens. Several types of these antigens have been recognized based on their cellular origins and expression patterns, while their detection has been greatly facilitated by recent achievements in next-generation sequencing and immunopeptidomics. Some of them have been targeted in clinical trials with various immunotherapy approaches, while many others remain untested. Here, we discuss molecular identification of different tumor antigen types, and the clinical safety and efficacy of targeting them with immunotherapy. Additionally, we suggest strategies to increase the efficacy and availability of antigen-directed immunotherapies for treatment of patients with metastatic cancer.
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Affiliation(s)
- Vid Leko
- Surgery Branch, National Cancer Institute, National Institutes of Health, Building 10-CRC, Room 3-3942, 10 Center Drive, Bethesda, MD 20892, USA.
| | - Steven A Rosenberg
- Surgery Branch, National Cancer Institute, National Institutes of Health, Building 10-CRC, Room 3-3942, 10 Center Drive, Bethesda, MD 20892, USA.
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34
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Han X, Alu A, Xiao Y, Wei Y, Wei X. Hyperprogression: A novel response pattern under immunotherapy. Clin Transl Med 2020; 10:e167. [PMID: 32997401 PMCID: PMC7510779 DOI: 10.1002/ctm2.167] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 02/05/2023] Open
Abstract
Checkpoint blockade therapy has shown significant therapeutic benefits and resulted in durable responses in patients with various tumors. However, accumulating evidence has demonstrated that 4-29% of all patients with cancers with various histologies may suffer from tumor flare following such therapy. This novel tumor response pattern, termed hyperprogression, is a potentially deleterious side effect of checkpoint blockade therapy that accelerates disease progression in a subset of patients. In this review, we describe possible immune checkpoint blockade biomarkers and the epidemiology, different definitions, and predictors of hyperprogression based on the research findings and further present the available evidence supporting pathophysiological hypotheses that might explain hyperprogression during checkpoint blockade therapy. We also compare hyperprogression and pseudoprogression. Finally, we discuss areas requiring further study.
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Affiliation(s)
- Xue‐jiao Han
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduChina
| | - Aqu Alu
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduChina
| | - Yi‐nan Xiao
- West China School of MedicineWest China HospitalSichuan UniversityChengduChina
| | - Yu‐quan Wei
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduChina
| | - Xia‐wei Wei
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduChina
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35
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Li Q, Ding ZY. The Ways of Isolating Neoantigen-Specific T Cells. Front Oncol 2020; 10:1347. [PMID: 32850430 PMCID: PMC7431921 DOI: 10.3389/fonc.2020.01347] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 06/26/2020] [Indexed: 02/05/2023] Open
Abstract
Immunotherapy has revolutionized the standard of care for a range of malignancies. Accumulating evidence suggests that the success of immunotherapy is likely attributable to neoantigen-specific T cells. Thus, adoptive cell therapy with these neoantigen-specific T cells is highly promising. This strategy has proven to successfully elicit tumor regression or even complete remission in metastatic cancer patients. However, a fundamental challenge is to effectively identify and isolate neoantigen-specific T cells or their T cell receptors (TCRs), from either tumor-infiltrating lymphocytes (TILs) or peripheral blood lymphocytes (PBLs), and many methods have been developed to this end. In this review, we focus on the current proposed strategies for identifying and isolating neoantigen-specific T cells.
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Affiliation(s)
- Qing Li
- Department of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Zhen-Yu Ding
- Department of Biotherapy, Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
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36
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Bianchi V, Harari A, Coukos G. Neoantigen-Specific Adoptive Cell Therapies for Cancer: Making T-Cell Products More Personal. Front Immunol 2020; 11:1215. [PMID: 32695101 PMCID: PMC7333784 DOI: 10.3389/fimmu.2020.01215] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Mutation-derived neoantigens are taking central stage as a determinant in eliciting effective antitumor immune responses following adoptive T-cell therapies. These mutations are patient-specific, and their targeting calls for highly personalized pipelines. The promising clinical outcomes of tumor-infiltrating lymphocyte (TIL) therapy have spurred interest in generating T-cell infusion products that have been selectively enriched in neoantigen (or autologous tumor) reactivity. The implementation of an isolation step, prior to T-cell in vitro expansion and reinfusion, may provide a way to improve the overall response rates achieved to date by adoptive T-cell therapies in metastatic cancer patients. Here we provide an overview of the main technologies [i.e., peptide major histocompatibility complex (pMHC) multimers, cytokine capture, and activation markers] to enrich infiltrating or circulating T-cells in predefined neoantigen specificities (or tumor reactivity). The unique technical and regulatory challenges faced by such highly specialized and patient-specific manufacturing T-cell platforms are also discussed.
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Affiliation(s)
- Valentina Bianchi
- Department of Oncology, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Center of Experimental Therapeutics, Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Alexandre Harari
- Department of Oncology, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Center of Experimental Therapeutics, Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - George Coukos
- Department of Oncology, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
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37
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Akazawa Y, Saito Y, Yoshikawa T, Saito K, Nosaka K, Shimomura M, Mizuno S, Nakamoto Y, Nakatsura T. Efficacy of immunotherapy targeting the neoantigen derived from epidermal growth factor receptor T790M/C797S mutation in non-small cell lung cancer. Cancer Sci 2020; 111:2736-2746. [PMID: 32391625 PMCID: PMC7419036 DOI: 10.1111/cas.14451] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 12/11/2022] Open
Abstract
Lung cancer is the leading cause of cancer‐related deaths worldwide. Epidermal growth factor receptor‐tyrosine kinase inhibitors (EGFR‐TKI) often have good clinical activity against non–small cell lung cancer (NSCLC) with activating EGFR mutations. Osimertinib, which is a third‐generation EGFR‐TKI, has a clinical effect even on NSCLC harboring the threonine to methionine change at codon 790 of EGFR (EGFR T790M) mutation that causes TKI resistance. However, most NSCLC patients develop acquired resistance to osimertinib within approximately 1 year, and 40% of these patients have the EGFR T790M and cysteine to serine change at codon 797 (C797S) mutations. Therefore, there is an urgent need for the development of novel treatment strategies for NSCLC patients with the EGFR T790M/C797S mutation. In this study, we identified the EGFR T790M/C797S mutation‐derived peptide (790‐799) (MQLMPFGSLL) that binds the human leukocyte antigen (HLA)‐A*02:01, and successfully established EGFR T790M/C797S‐peptide‐specific CTL clones from human PBMC of HLA‐A2 healthy donors. One established CTL clone demonstrated adequate cytotoxicity against T2 cells pulsed with the EGFR T790M/C797S peptide. This CTL clone also had high reactivity against cancer cells that expressed an endogenous EGFR T790M/C797S peptide using an interferon‐γ (IFN‐γ) enzyme‐linked immunospot (ELISPOT) assay. In addition, we demonstrated using a mouse model that EGFR T790M/C797S peptide‐specific CTL were induced by EGFR T790M/C797S peptide vaccine in vivo. These findings suggest that an immunotherapy targeting a neoantigen derived from EGFR T790M/C797S mutation could be a useful novel therapeutic strategy for NSCLC patients with EGFR‐TKI resistance, especially those resistant to osimertinib.
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Affiliation(s)
- Yu Akazawa
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan.,Second Department of Internal Medicine, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Yuki Saito
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Toshiaki Yoshikawa
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Keigo Saito
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Kazuto Nosaka
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan.,Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Manami Shimomura
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Shoichi Mizuno
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Yasunari Nakamoto
- Second Department of Internal Medicine, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Tetsuya Nakatsura
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
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38
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Gros A, Tran E, Parkhurst MR, Ilyas S, Pasetto A, Groh EM, Robbins PF, Yossef R, Garcia-Garijo A, Fajardo CA, Prickett TD, Jia L, Gartner JJ, Ray S, Ngo L, Wunderllich JR, Yang JC, Rosenberg SA. Recognition of human gastrointestinal cancer neoantigens by circulating PD-1+ lymphocytes. J Clin Invest 2020; 129:4992-5004. [PMID: 31609250 DOI: 10.1172/jci127967] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 08/13/2019] [Indexed: 12/17/2022] Open
Abstract
Tumor-resident lymphocytes can mount a response against neoantigens expressed in microsatellite-stable gastrointestinal (GI) cancers, and adoptive transfer of neoantigen-specific lymphocytes has demonstrated antitumor activity in selected patients. However, whether peripheral blood could be used as an alternative minimally invasive source to identify lymphocytes targeting neoantigens in patients with GI cancer with relatively low mutation burden is unclear. We used a personalized high-throughput screening strategy to investigate whether PD-1 expression in peripheral blood could be used to identify CD8+ or CD4+ lymphocytes recognizing neoantigens identified by whole-exome sequencing in 7 patients with GI cancer. We found that neoantigen-specific lymphocytes were preferentially enriched in the CD8+PD-1+/hi or CD4+PD-1+/hi subsets, but not in the corresponding bulk or PD-1- fractions. In 6 of 7 individuals analyzed we identified circulating CD8+ and CD4+ lymphocytes targeting 6 and 4 neoantigens, respectively. Moreover, neoantigen-reactive T cells and a T cell receptor (TCR) isolated from the CD8+PD-1+ subsets recognized autologous tumor, albeit at reduced levels, in 2 patients with available cell lines. These data demonstrate the existence of circulating T cells targeting neoantigens in GI cancer patients and provide an approach to generate enriched populations of personalized neoantigen-specific lymphocytes and isolate TCRs that could be exploited therapeutically to treat cancer.
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Affiliation(s)
- Alena Gros
- Vall d'Hebron Institute of Oncology, Cellex Center, Barcelona, Spain
| | - Eric Tran
- Surgery Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA.,Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Cancer Institute, Portland, Oregon, USA
| | - Maria R Parkhurst
- Surgery Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Sadia Ilyas
- Surgery Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Anna Pasetto
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Eric M Groh
- Surgery Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Paul F Robbins
- Surgery Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Rami Yossef
- Surgery Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | | | - Carlos A Fajardo
- Vall d'Hebron Institute of Oncology, Cellex Center, Barcelona, Spain
| | - Todd D Prickett
- Surgery Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Li Jia
- Surgery Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Jared J Gartner
- Surgery Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Satyajit Ray
- Surgery Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Lien Ngo
- Surgery Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | | | - James C Yang
- Surgery Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
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39
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Li Y, Wang G, Tan X, Ouyang J, Zhang M, Song X, Liu Q, Leng Q, Chen L, Xie L. ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection. BMC Med Genomics 2020; 13:52. [PMID: 32241270 PMCID: PMC7118832 DOI: 10.1186/s12920-020-0683-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Neoantigens can be differentially recognized by T cell receptor (TCR) as these sequences are derived from mutant proteins and are unique to the tumor. The discovery of neoantigens is the first key step for tumor-specific antigen (TSA) based immunotherapy. Based on high-throughput tumor genomic analysis, each missense mutation can potentially give rise to multiple neopeptides, resulting in a vast total number, but only a small percentage of these peptides may achieve immune-dominant status with a given major histocompatibility complex (MHC) class I allele. Specific identification of immunogenic candidate neoantigens is consequently a major challenge. Currently almost all neoantigen prediction tools are based on genomics data. RESULTS Here we report the construction of proteogenomics prediction of neoantigen (ProGeo-neo) pipeline, which incorporates the following modules: mining tumor specific antigens from next-generation sequencing genomic and mRNA expression data, predicting the binding mutant peptides to class I MHC molecules by latest netMHCpan (v.4.0), verifying MHC-peptides by MaxQuant with mass spectrometry proteomics data searched against customized protein database, and checking potential immunogenicity of T-cell-recognization by additional screening methods. ProGeo-neo pipeline achieves proteogenomics strategy and the neopeptides identified were of much higher quality as compared to those identified using genomic data only. CONCLUSIONS The pipeline was constructed based on the genomics and proteomics data of Jurkat leukemia cell line but is generally applicable to other solid cancer research. With massively parallel sequencing and proteomics profiling increasing, this proteogenomics workflow should be useful for neoantigen oriented research and immunotherapy.
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Affiliation(s)
- Yuyu Li
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Keyuan Road, Shanghai, 201203, China
| | - Guangzhi Wang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Keyuan Road, Shanghai, 201203, China
| | - Xiaoxiu Tan
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Keyuan Road, Shanghai, 201203, China
| | - Jian Ouyang
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Keyuan Road, Shanghai, 201203, China
| | - Menghuan Zhang
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Keyuan Road, Shanghai, 201203, China
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Qi Liu
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Qibin Leng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, 78 Heng Zhi Gang, Lu Hu Road, Guangzhou, 510095, China
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, China.
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Keyuan Road, Shanghai, 201203, China.
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40
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Chruściel E, Urban-Wójciuk Z, Arcimowicz Ł, Kurkowiak M, Kowalski J, Gliwiński M, Marjański T, Rzyman W, Biernat W, Dziadziuszko R, Montesano C, Bernardini R, Marek-Trzonkowska N. Adoptive Cell Therapy-Harnessing Antigen-Specific T Cells to Target Solid Tumours. Cancers (Basel) 2020; 12:E683. [PMID: 32183246 PMCID: PMC7140076 DOI: 10.3390/cancers12030683] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 12/26/2022] Open
Abstract
In recent years, much research has been focused on the field of adoptive cell therapies (ACT) that use native or genetically modified T cells as therapeutic tools. Immunotherapy with T cells expressing chimeric antigen receptors (CARs) demonstrated great success in the treatment of haematologic malignancies, whereas adoptive transfer of autologous tumour infiltrating lymphocytes (TILs) proved to be highly effective in metastatic melanoma. These encouraging results initiated many studies where ACT was tested as a treatment for various solid tumours. In this review, we provide an overview of the challenges of T cell-based immunotherapies of solid tumours. We describe alternative approaches for choosing the most efficient T cells for cancer treatment in terms of their tumour-specificity and phenotype. Finally, we present strategies for improvement of anti-tumour potential of T cells, including combination therapies.
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Affiliation(s)
- Elżbieta Chruściel
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-309 Gdańsk, Poland; (E.C.); (Z.U.-W.); (M.K.); (J.K.)
| | - Zuzanna Urban-Wójciuk
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-309 Gdańsk, Poland; (E.C.); (Z.U.-W.); (M.K.); (J.K.)
| | - Łukasz Arcimowicz
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-309 Gdańsk, Poland; (E.C.); (Z.U.-W.); (M.K.); (J.K.)
| | - Małgorzata Kurkowiak
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-309 Gdańsk, Poland; (E.C.); (Z.U.-W.); (M.K.); (J.K.)
| | - Jacek Kowalski
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-309 Gdańsk, Poland; (E.C.); (Z.U.-W.); (M.K.); (J.K.)
- Department of Pathomorphology, Medical University of Gdańsk, 80-210 Gdańsk, Poland;
| | - Mateusz Gliwiński
- Department of Medical Immunology, Medical University of Gdańsk, 80-210 Gdańsk, Poland;
| | - Tomasz Marjański
- Department of Thoracic Surgery, Medical University of Gdańsk, 80-210 Gdańsk, Poland; (T.M.); (W.R.)
| | - Witold Rzyman
- Department of Thoracic Surgery, Medical University of Gdańsk, 80-210 Gdańsk, Poland; (T.M.); (W.R.)
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdańsk, 80-210 Gdańsk, Poland;
| | - Rafał Dziadziuszko
- Department of Oncology and Radiology, Medical University of Gdańsk, 80-210 Gdańsk, Poland;
| | - Carla Montesano
- Department of Biology, University of Rome "Tor Vergata", 00133 Rome, Italy;
| | - Roberta Bernardini
- Department of Biology and Interdepartmental Center CIMETA, University of Rome "Tor Vergata", 00133 Rome, Italy;
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-309 Gdańsk, Poland; (E.C.); (Z.U.-W.); (M.K.); (J.K.)
- Laboratory of Immunoregulation and Cellular Therapies, Department of Family Medicine, Medical University of Gdańsk, 80-210 Gdańsk, Poland
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41
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Benvenuto M, Focaccetti C, Izzi V, Masuelli L, Modesti A, Bei R. Tumor antigens heterogeneity and immune response-targeting neoantigens in breast cancer. Semin Cancer Biol 2019; 72:65-75. [PMID: 31698088 DOI: 10.1016/j.semcancer.2019.10.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/30/2019] [Indexed: 12/25/2022]
Abstract
Breast cancer is both the most common type of cancer and the most frequent cause of cancer mortality in women, mainly because of its heterogeneity and limited immunogenicity. The aim of specific active cancer immunotherapy is to stimulate the host's immune response against cancer cells directly using a vaccine platform carrying one or more tumor antigens. In particular, the ideal tumor antigen should be able to elicit T cell and B cell responses, be specific for the tumor and be expressed at high levels on cancer cells. Neoantigens are ideal targets for immunotherapy because they are exclusive to individual patient's tumors, are absent in healthy tissues and are not subject to immune tolerance mechanisms. Thus, neoantigens should generate a specific reaction towards tumors since they constitute the largest fraction of targets of tumor-infiltrating T cells. In this review, we describe the technologies used for neoantigen discovery, the heterogeneity of neoantigens in breast cancer and recent studies of breast cancer immunotherapy targeting neoantigens.
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Affiliation(s)
- Monica Benvenuto
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy; Saint Camillus International University of Health and Medical Sciences, via di Sant'Alessandro 8, 00131, Rome, Italy.
| | - Chiara Focaccetti
- Department of Human Science and Promotion of the Quality of Life, University San Raffaele Rome, Via di Val Cannuta 247, 00166, Rome, Italy.
| | - Valerio Izzi
- Center for Cell-Matrix Research, Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7C, FI-90230, Oulu, Finland.
| | - Laura Masuelli
- Department of Experimental Medicine, University of Rome "Sapienza", Viale Regina Elena 324, 00161 Rome, Italy.
| | - Andrea Modesti
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.
| | - Roberto Bei
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.
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42
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Lu YC, Jia L, Zheng Z, Tran E, Robbins PF, Rosenberg SA. Single-Cell Transcriptome Analysis Reveals Gene Signatures Associated with T-cell Persistence Following Adoptive Cell Therapy. Cancer Immunol Res 2019; 7:1824-1836. [PMID: 31484655 PMCID: PMC6825592 DOI: 10.1158/2326-6066.cir-19-0299] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/24/2019] [Accepted: 08/28/2019] [Indexed: 12/28/2022]
Abstract
Adoptive cell therapy (ACT) using tumor-infiltrating lymphocytes (TIL) can mediate responses in some patients with metastatic epithelial cancer. Identifying gene signatures associated with successful ACT might enable the development of improved therapeutic approaches. The persistence of transferred T cells in the peripheral blood is one indication of clinical effectiveness, but many T-cell and host factors may influence T-cell persistence. To limit these variables, we previously studied a patient with metastatic colorectal cancer treated with polyclonal TILs targeting the KRAS(G12D) hotspot mutation, who experienced a partial response for 9 months. Three dominant clonotypes specifically recognizing KRAS(G12D) epitopes were identified, but we found that only two clonotypes persisted 40 days after ACT. Because of these findings, in this study, we performed the single-cell transcriptome analysis of the infused TILs. The analysis revealed a total of 472 genes that were differentially expressed between clonotypes 9.1-NP and 9.2-P single cells, and 528 genes between 9.1-NP and 10-P. Following these clonotypes in the peripheral blood after ACT, the gene expression patterns changed, but IL7R, ITGB1, KLF2, and ZNF683 remained expressed in the persistent 9.2-P and 10-P cells, compared with the nonpersistent 9.1-NP cells. In addition, four autologous TILs, which were used for treatment but persisted poorly 1 month after ACT, did not express the gene profiles associated with persistence. These results suggest that certain TIL populations possess a unique gene expression profile that can lead to the persistence of T cells. Thus, this single-patient study provides insight into how to improve ACT for solid cancer.
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Affiliation(s)
- Yong-Chen Lu
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
| | - Li Jia
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Zhili Zheng
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Eric Tran
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Paul F Robbins
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Steven A Rosenberg
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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43
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Gorabi AM, Hajighasemi S, Sathyapalan T, Sahebkar A. Cell transfer-based immunotherapies in cancer: A review. IUBMB Life 2019; 72:790-800. [PMID: 31633881 DOI: 10.1002/iub.2180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/21/2019] [Indexed: 12/17/2022]
Abstract
In cell transfer therapy (CTT), immune cells such as innate immune-derived natural killer cells and dendritic cells as well as acquired immune-related T lymphocytes such as tumor-infiltrating lymphocytes and cytokine-activated or genetically modified peripheral blood T cells are used in the management of cancer. These therapies are increasingly becoming the most used treatment modality in cancer after tumor resection, chemotherapy, and radiotherapy. In adoptive cell transfer, the lymphocytes isolated from either a donor or the patient are modified ex vivo and reinfused to target malignant cells. Transferring in vitro-manipulated immune cells produces a continuous antitumor immune response. In this review, we evaluate the recent advances in CTT for the management of various malignancies.
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Affiliation(s)
- Armita M Gorabi
- Research Center for Advanced Technologies in Cardiovascular Medicine, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeideh Hajighasemi
- Faculty of Paramedicine, Department of Medical Biotechnology, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Thozhukat Sathyapalan
- Department of Academic Diabetes, Endocrinology and Metabolism, Hull York Medical School, University of Hull, Hull, UK
| | - Amirhossein Sahebkar
- Halal Research Center of IRI, FDA, Tehran, Iran.,Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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44
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A novel small RNA contributes to restrain cellular chain length and anti-phagocytic ability in Streptococcus suis 2. Microb Pathog 2019; 137:103730. [PMID: 31499182 DOI: 10.1016/j.micpath.2019.103730] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 02/04/2023]
Abstract
Streptococcus suis serotype 2 (SS2) is an important porcine and human pathogen. Regulatory small non-coding RNAs (sRNAs) play an essential role in diverse physiological processes, although they remain poorly understood in SS2. In this study, we identified eight novel sRNAs through a combination of computational strategies and experimental identification. To explore roles of these novel sRNAs, sRNA34 was preferentially selected to assess phenotypes of the deletion strain in vitro and in vivo. The inactivation of sRNA34 significantly elongated the cellular chain, remarkably increased sensitivity to phagocytosis by RAW264.7, and attenuated virulence in a mouse infection model. Transcriptomic analysis revealed that inactivation of sRNA34 altered expression of multiple genes contributing to cellular chain formation and elongation, indicating a potential mechanism of sRNA34 in maintaining proper bacterial chain length to resist phagocytosis by the host cell. In summary, sRNA34 is a novel sRNA that contributes to cellular chain regulation and the anti-phagocytosis ability of SS2.
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45
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Shen H, Yang ESH, Conry M, Fiveash J, Contreras C, Bonner JA, Shi LZ. Predictive biomarkers for immune checkpoint blockade and opportunities for combination therapies. Genes Dis 2019; 6:232-246. [PMID: 32042863 PMCID: PMC6997608 DOI: 10.1016/j.gendis.2019.06.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/07/2019] [Accepted: 06/16/2019] [Indexed: 12/30/2022] Open
Abstract
Immune checkpoint blockade therapies (ICBs) are a prominent breakthrough in cancer immunotherapy in recent years (named the 2013 “Breakthrough of the Year” by the Science magazine). Thus far, FDA-approved ICBs primarily target immune checkpoints CTLA-4, PD-1, and PD-L1. Notwithstanding their impressive long-term therapeutic benefits, their efficacy is limited to a small subset of cancer patients. In addition, ICBs induce inadvertent immune-related adverse events (irAEs) and can be costly for long-term use. To overcome these limitations, two strategies are actively being pursued: identification of predictive biomarkers for clinical response to ICBs and multi-pronged combination therapies. Biomarkers will allow clinicians to practice a precision medicine approach in ICBs (biomarker-based patient selection) such as treating triple-negative breast cancer patients that exhibit PD-L1 staining of tumor-infiltrating immune cells in ≥1% of the tumor area with nanoparticle albumin-bound (nab)–paclitaxel plus anti-PD-L1 and treating patients of MSI-H or MMR deficient unresectable or metastatic solid tumors with pembrolizumab (anti-PD-1). Importantly, the insights gained from these biomarker studies can guide rational combinatorial strategies such as CDK4/6 inhibitor/fractionated radiotherapy/HDACi in conjunction with ICBs to maximize therapeutic benefits. Further, with the rapid technological advents (e.g., ATCT-Seq), we predict more reliable biomarkers will be identified, which in turn will inspire more promising combination therapies.
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Affiliation(s)
- Hongxing Shen
- Department of Radiation Oncology, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA.,O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA
| | - Eddy Shih-Hsin Yang
- Department of Radiation Oncology, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA.,O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA
| | - Marty Conry
- O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA.,Department of Medical Oncology, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA
| | - John Fiveash
- Department of Radiation Oncology, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA.,O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA
| | - Carlo Contreras
- O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA.,Department of Surgical Oncology, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA
| | - James A Bonner
- Department of Radiation Oncology, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA.,O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA
| | - Lewis Zhichang Shi
- Department of Radiation Oncology, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA.,O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA.,Department of Microbiology, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA.,Program in Immunology, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA
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46
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Garcia-Garijo A, Fajardo CA, Gros A. Determinants for Neoantigen Identification. Front Immunol 2019; 10:1392. [PMID: 31293573 PMCID: PMC6601353 DOI: 10.3389/fimmu.2019.01392] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/03/2019] [Indexed: 12/22/2022] Open
Abstract
All tumors accumulate genetic alterations, some of which can give rise to mutated, non-self peptides presented by human leukocyte antigen (HLA) molecules and elicit T-cell responses. These immunogenic mutated peptides, or neoantigens, are foreign in nature and display exquisite tumor specificity. The correlative evidence suggesting they play an important role in the effectiveness of various cancer immunotherapies has triggered the development of vaccines and adoptive T-cell therapies targeting them. However, the systematic identification of personalized neoantigens in cancer patients, a critical requisite for the success of these therapies, remains challenging. A growing amount of evidence supports that only a small fraction of all tumor somatic non-synonymous mutations (NSM) identified represent bona fide neoantigens; mutated peptides that are processed, presented on the cell surface HLA molecules of cancer cells and are capable of triggering immune responses in patients. Here, we provide an overview of the existing strategies to identify candidate neoantigens and to evaluate their immunogenicity, two factors that impact on neoantigen identification. We will focus on their strengths and limitations to allow readers to rationally select and apply the most suitable method for their specific laboratory setting.
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Affiliation(s)
| | | | - Alena Gros
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
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Parkhurst MR, Robbins PF, Tran E, Prickett TD, Gartner JJ, Jia L, Ivey G, Li YF, El-Gamil M, Lalani A, Crystal JS, Sachs A, Groh E, Ray S, Ngo LT, Kivitz S, Pasetto A, Yossef R, Lowery FJ, Goff SL, Lo W, Cafri G, Deniger DC, Malekzadeh P, Ahmadzadeh M, Wunderlich JR, Somerville RPT, Rosenberg SA. Unique Neoantigens Arise from Somatic Mutations in Patients with Gastrointestinal Cancers. Cancer Discov 2019; 9:1022-1035. [PMID: 31164343 DOI: 10.1158/2159-8290.cd-18-1494] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/12/2019] [Accepted: 05/30/2019] [Indexed: 12/21/2022]
Abstract
Immunotherapies can mediate regression of human tumors with high mutation rates, but responses are rarely observed in patients with common epithelial cancers. This raises the question of whether patients with these common cancers harbor T lymphocytes that recognize mutant proteins expressed by autologous tumors that may represent ideal targets for immunotherapy. Using high-throughput immunologic screening of mutant gene products identified via whole-exome sequencing, we identified neoantigen-reactive tumor-infiltrating lymphocytes (TIL) from 62 of 75 (83%) patients with common gastrointestinal cancers. In total, 124 neoantigen-reactive TIL populations were identified, and all but one of the neoantigenic determinants were unique. The results of in vitro T-cell recognition assays demonstrated that 1.6% of the gene products encoded by somatic nonsynonymous mutations were immunogenic. These findings demonstrate that the majority of common epithelial cancers elicit immune recognition and open possibilities for cell-based immunotherapies for patients bearing these cancers. SIGNIFICANCE: TILs cultured from 62 of 75 (83%) patients with gastrointestinal cancers recognized neoantigens encoded by 1.6% of somatic mutations expressed by autologous tumor cells, and 99% of the neoantigenic determinants appeared to be unique and not shared between patients.This article is highlighted in the In This Issue feature, p. 983.
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Affiliation(s)
| | | | - Eric Tran
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Cancer Institute, Portland, Oregon
| | | | | | - Li Jia
- NIH, NCI, Bethesda, Maryland
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48
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Chen Q, Li JY, Du SD. Application of neoantigens in malignant tumor treatment and prognosis evaluation. Shijie Huaren Xiaohua Zazhi 2019; 27:287-292. [DOI: 10.11569/wcjd.v27.i5.287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In the last decade, there have been an endless number of cancer therapy strategies, and the study of tumor neoantigens provides a new direction for cancer immune therapy. With the development of deep sequencing, especially whole-exome sequencing, great opportunities have been provided to precise immune therapy of malignant tumors. This article systematically summarizes the research on tumor neoantigens in the past ten years and the challenges most likely to be encountered, describes the role of neoantigens in the treatment of malignant tumors, and discusses their possible clinical applications.
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Affiliation(s)
- Qiao Chen
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Jia-Yi Li
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Shun-Da Du
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
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49
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Chen F, Zou Z, Du J, Su S, Shao J, Meng F, Yang J, Xu Q, Ding N, Yang Y, Liu Q, Wang Q, Sun Z, Zhou S, Du S, Wei J, Liu B. Neoantigen identification strategies enable personalized immunotherapy in refractory solid tumors. J Clin Invest 2019; 129:2056-2070. [PMID: 30835255 DOI: 10.1172/jci99538] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Recent genomic and bioinformatic technological advances have made it possible to dissect the immune response to personalized neoantigens encoded by tumor-specific mutations. However, timely and efficient identification of neoantigens is still one of the major obstacles to using personalized neoantigen-based cancer immunotherapy. METHODS Two different pipelines of neoantigens identification were established in this study: (1) Clinical grade targeted sequencing was performed in patients with refractory solid tumor, and mutant peptides with high variant allele frequency and predicted high HLA-binding affinity were de novo synthesized. (2) An inventory-shared neoantigen peptide library of common solid tumors was constructed, and patients' hotspot mutations were matched to the neoantigen peptide library. The candidate neoepitopes were identified by recalling memory T-cell responses in vitro. Subsequently, neoantigen-loaded dendritic cell vaccines and neoantigen-reactive T cells were generated for personalized immunotherapy in six patients. RESULTS Immunogenic neo-epitopes were recognized by autologous T cells in 3 of 4 patients who utilized the de novo synthesis mode and in 6 of 13 patients who performed shared neoantigen peptide library, respectively. A metastatic thymoma patient achieved a complete and durable response beyond 29 months after treatment. Immune-related partial response was observed in another patient with metastatic pancreatic cancer. The remaining four patients achieved the prolonged stabilization of disease with a median PFS of 8.6 months. CONCLUSIONS The current study provided feasible pipelines for neoantigen identification. Implementing these strategies to individually tailor neoantigens could facilitate the neoantigen-based translational immunotherapy research.TRIAL REGSITRATION. ChiCTR.org ChiCTR-OIC-16010092, ChiCTR-OIC-17011275, ChiCTR-OIC-17011913; ClinicalTrials.gov NCT03171220. FUNDING This work was funded by grants from the National Key Research and Development Program of China (Grant No. 2017YFC1308900), the National Major Projects for "Major New Drugs Innovation and Development" (Grant No.2018ZX09301048-003), the National Natural Science Foundation of China (Grant No. 81672367, 81572329, 81572601), and the Key Research and Development Program of Jiangsu Province (No. BE2017607).
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50
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Brown SD, Holt RA. Neoantigen characteristics in the context of the complete predicted MHC class I self-immunopeptidome. Oncoimmunology 2018; 8:1556080. [PMID: 30723589 PMCID: PMC6350689 DOI: 10.1080/2162402x.2018.1556080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 01/21/2023] Open
Abstract
The self-immunopeptidome is the repertoire of all self-peptides that can be presented by the combination of MHC variants carried by an individual, defined by their HLA genotype. Each MHC variant presents a distinct set of self-peptides, and the number of peptides in a set is variable. Subjects carrying MHC variants that present fewer self-peptides should also present fewer mutated peptides, resulting in decreased immune pressure on tumor cells. To explore this, we predicted peptide-MHC binding values using all unique 8-11mer human peptides in the human proteome and all available HLA class I allelic variants, for a total of 134 billion unique peptide--MHC binding predictions. From these predictions, we observe that most peptides are able to be presented by relatively few (< 250) MHC, while some can be presented by upwards of 1,500 different MHC. There is substantial overlap among the repertoires of peptides presented by different MHC and no relationship between the number of peptides presented and HLA population frequency. Nearly 30% of self-peptides are presentable by at least one MHC, leaving 70% of the human peptidome unsurveyed by T cells. We observed similar distributions of predicted self-immunopeptidome sizes in cancer subjects compared to controls, and within the pan-cancer population, predicted self-immunopeptidome size combined with mutational load to predict survival. Self-immunopeptidome analysis revealed evidence for tumor immunoediting and identified specific peptide positions that most influence immunogenicity. Because self-immunopeptidome size is defined by HLA genotypes and approximates neoantigen load, HLA genotyping could offer a rapid predictive biomarker for response to immunotherapy.
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Affiliation(s)
- Scott D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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