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Uher O, Hadrava Vanova K, Taïeb D, Calsina B, Robledo M, Clifton-Bligh R, Pacak K. The Immune Landscape of Pheochromocytoma and Paraganglioma: Current Advances and Perspectives. Endocr Rev 2024; 45:521-552. [PMID: 38377172 PMCID: PMC11244254 DOI: 10.1210/endrev/bnae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/19/2023] [Accepted: 02/02/2024] [Indexed: 02/22/2024]
Abstract
Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumors derived from neural crest cells from adrenal medullary chromaffin tissues and extra-adrenal paraganglia, respectively. Although the current treatment for PPGLs is surgery, optimal treatment options for advanced and metastatic cases have been limited. Hence, understanding the role of the immune system in PPGL tumorigenesis can provide essential knowledge for the development of better therapeutic and tumor management strategies, especially for those with advanced and metastatic PPGLs. The first part of this review outlines the fundamental principles of the immune system and tumor microenvironment, and their role in cancer immunoediting, particularly emphasizing PPGLs. We focus on how the unique pathophysiology of PPGLs, such as their high molecular, biochemical, and imaging heterogeneity and production of several oncometabolites, creates a tumor-specific microenvironment and immunologically "cold" tumors. Thereafter, we discuss recently published studies related to the reclustering of PPGLs based on their immune signature. The second part of this review discusses future perspectives in PPGL management, including immunodiagnostic and promising immunotherapeutic approaches for converting "cold" tumors into immunologically active or "hot" tumors known for their better immunotherapy response and patient outcomes. Special emphasis is placed on potent immune-related imaging strategies and immune signatures that could be used for the reclassification, prognostication, and management of these tumors to improve patient care and prognosis. Furthermore, we introduce currently available immunotherapies and their possible combinations with other available therapies as an emerging treatment for PPGLs that targets hostile tumor environments.
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Affiliation(s)
- Ondrej Uher
- Section of Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-1109, USA
| | - Katerina Hadrava Vanova
- Section of Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-1109, USA
| | - David Taïeb
- Department of Nuclear Medicine, CHU de La Timone, Marseille 13005, France
| | - Bruna Calsina
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
- Familiar Cancer Clinical Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Institute of Health Carlos III (ISCIII), Madrid 28029, Spain
| | - Roderick Clifton-Bligh
- Department of Endocrinology, Royal North Shore Hospital, Sydney 2065, NSW, Australia
- Cancer Genetics Laboratory, Kolling Institute, University of Sydney, Sydney 2065, NSW, Australia
| | - Karel Pacak
- Section of Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-1109, USA
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2
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Martin MV, Aguilar-Rosas S, Franke K, Pieterse M, Langelaar JV, Schreurs R, Bijlsma MF, Besselink MG, Koster J, Timens W, Khasraw M, Ashley DM, Keir ST, Ottensmeier CH, King EV, Verheij J, Waasdorp C, Valk PJM, Engels SAG, Oostenbach E, van Dinter JT, Hofman DA, Mok JY, van Esch WJE, Wilmink H, Monkhorst K, Verheul HMW, Poel D, Hiltermann TJN, Kempen LCLTV, Groen HJM, Aerts JGJV, Heesch SV, Löwenberg B, Plasterk R, Kloosterman WP. The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy. Cancer Immunol Res 2024; 12:759-778. [PMID: 38573707 DOI: 10.1158/2326-6066.cir-23-0158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 09/22/2023] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
Identification of immunogenic cancer neoantigens as targets for therapy is challenging. Here, we integrate the whole-genome and long-read transcript sequencing of cancers to identify the collection of neo-open reading frame peptides (NOP) expressed in tumors. We termed this collection of NOPs the tumor framome. NOPs represent tumor-specific peptides that are different from wild-type proteins and may be strongly immunogenic. We describe a class of hidden NOPs that derive from structural genomic variants involving an upstream protein coding gene driving expression and translation of noncoding regions of the genome downstream of a rearrangement breakpoint, i.e., where no gene annotation or evidence for transcription exists. The entire collection of NOPs represents a vast number of possible neoantigens particularly in tumors with many structural genomic variants and a low number of missense mutations. We show that NOPs are immunogenic and epitopes derived from NOPs can bind to MHC class I molecules. Finally, we provide evidence for the presence of memory T cells specific for hidden NOPs in peripheral blood from a patient with lung cancer. This work highlights NOPs as a major source of possible neoantigens for personalized cancer immunotherapy and provides a rationale for analyzing the complete cancer genome and transcriptome as a basis for the detection of NOPs.
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Affiliation(s)
| | | | - Katka Franke
- CureVac Netherlands B.V., Amsterdam, the Netherlands
| | - Mark Pieterse
- CureVac Netherlands B.V., Amsterdam, the Netherlands
| | | | | | - Maarten F Bijlsma
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Marc G Besselink
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Surgery, Amsterdam, the Netherlands
| | - Jan Koster
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University, Medical Center Groningen, the Netherlands
| | - Mustafa Khasraw
- Duke University Medical Center, Duke University, Durham, North Carolina
| | - David M Ashley
- Preston Robert Tisch Brain Tumor Center, Department of Neurosurgery, Duke University, Durham, North Carolina
| | - Stephen T Keir
- Duke University Medical Center, Duke University, Durham, North Carolina
| | - Christian H Ottensmeier
- Liverpool Head and Neck Centre, Institute of Systems, Molecular and Integrative Biology, University of Liverpool and Clatterbridge Cancer Center NHS Foundation Trust, Liverpool, UK
| | - Emma V King
- Department of Otorhinolaryngology, Head and Neck Surgery, Poole Hospital, Poole, UK
| | - Joanne Verheij
- Amsterdam UMC, location University of Amsterdam, Department of Pathology, Amsterdam, the Netherlands
| | - Cynthia Waasdorp
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sem A G Engels
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ellen Oostenbach
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jip T van Dinter
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Damon A Hofman
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Juk Yee Mok
- Sanquin Reagents, Sanquin, Amsterdam, the Netherlands
| | | | - Hanneke Wilmink
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Medical Oncology, Amsterdam, the Netherlands
| | - Kim Monkhorst
- Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Dennis Poel
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the, Netherlands
| | - T Jeroen N Hiltermann
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Léon C L T van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University, Medical Center Groningen, the Netherlands
- University of Antwerp, Antwerp University Hospital, Edegem, Belgium
| | - Harry J M Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, the Netherlands
| | | | | | - Bob Löwenberg
- CureVac Netherlands B.V., Amsterdam, the Netherlands
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3
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Feola S, Chiaro J, Cerullo V. Integrating immunopeptidome analysis for the design and development of cancer vaccines. Semin Immunol 2023; 67:101750. [PMID: 37003057 DOI: 10.1016/j.smim.2023.101750] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 04/03/2023]
Abstract
The repertoire of naturally presented peptides within the MHC (major histocompatibility complex) or HLA (human leukocyte antigens) system on the cellular surface of every mammalian cell is referred to as ligandome or immunopeptidome. This later gained momentum upon the discovery of CD8 + T cells able to recognize and kill cancer cells in an MHC-I antigen-restricted manner. Indeed, cancer immune surveillance relies on T cell recognition of MHC-I-restricted peptides, making the identification of those peptides the core for designing T cell-based cancer vaccines. Moreover, the breakthrough of antibodies targeting immune checkpoint molecules has led to a new and strong interest in discovering suitable targets for CD8 +T cells. Therapeutic cancer vaccines are designed for the artificial generation and/or stimulation of CD8 +T cells; thus, their combination with ICIs to unleash the breaks of the immune system comes as a natural consequence to enhance anti-tumor efficacy. In this context, the identification and knowledge of peptide candidates take advantage of the fast technology updates in immunopeptidome and mass spectrometric methodologies, paying the way to the rational design of vaccines for immunotherapeutic approaches. In this review, we discuss mainly the role of immunopeptidome analysis and its application for the generation of therapeutic cancer vaccines with main focus on HLA-I peptides. Here, we review cancer vaccine platforms based on two different preparation methods: pathogens (viruses and bacteria) and not (VLPs, nanoparticles, subunits vaccines) that exploit discoveries in the ligandome field to generate and/or enhance anti-tumor specific response. Finally, we discuss possible drawbacks and future challenges in the field that remain still to be addressed.
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Affiliation(s)
- Sara Feola
- Drug Research Program (DRP) ImmunoViroTherapy Lab (IVT), Faculty of Pharmacy Helsinki University, Viikinkaari 5E, Finland; Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Fabianinkatu 33, Finland; Translational Immunology Program (TRIMM), Faculty of Medicine Helsinki University, Haartmaninkatu 8, Finland
| | - Jacopo Chiaro
- Drug Research Program (DRP) ImmunoViroTherapy Lab (IVT), Faculty of Pharmacy Helsinki University, Viikinkaari 5E, Finland; Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Fabianinkatu 33, Finland; Translational Immunology Program (TRIMM), Faculty of Medicine Helsinki University, Haartmaninkatu 8, Finland
| | - Vincenzo Cerullo
- Drug Research Program (DRP) ImmunoViroTherapy Lab (IVT), Faculty of Pharmacy Helsinki University, Viikinkaari 5E, Finland; Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Fabianinkatu 33, Finland; Translational Immunology Program (TRIMM), Faculty of Medicine Helsinki University, Haartmaninkatu 8, Finland; Department of Molecular Medicine and Medical Biotechnology, Naples University "Federico II", S. Pansini 5, Italy.
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4
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Borden ES, Ghafoor S, Buetow KH, LaFleur BJ, Wilson MA, Hastings KT. NeoScore Integrates Characteristics of the Neoantigen:MHC Class I Interaction and Expression to Accurately Prioritize Immunogenic Neoantigens. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1813-1827. [PMID: 35304420 DOI: 10.4049/jimmunol.2100700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/28/2022] [Indexed: 12/20/2022]
Abstract
Accurate prioritization of immunogenic neoantigens is key to developing personalized cancer vaccines and distinguishing those patients likely to respond to immune checkpoint inhibition. However, there is no consensus regarding which characteristics best predict neoantigen immunogenicity, and no model to date has both high sensitivity and specificity and a significant association with survival in response to immunotherapy. We address these challenges in the prioritization of immunogenic neoantigens by (1) identifying which neoantigen characteristics best predict immunogenicity; (2) integrating these characteristics into an immunogenicity score, the NeoScore; and (3) demonstrating a significant association of the NeoScore with survival in response to immune checkpoint inhibition. One thousand random and evenly split combinations of immunogenic and nonimmunogenic neoantigens from a validated dataset were analyzed using a regularized regression model for characteristic selection. The selected characteristics, the dissociation constant and binding stability of the neoantigen:MHC class I complex and expression of the mutated gene in the tumor, were integrated into the NeoScore. A web application is provided for calculation of the NeoScore. The NeoScore results in improved, or equivalent, performance in four test datasets as measured by sensitivity, specificity, and area under the receiver operator characteristics curve compared with previous models. Among cutaneous melanoma patients treated with immune checkpoint inhibition, a high maximum NeoScore was associated with improved survival. Overall, the NeoScore has the potential to improve neoantigen prioritization for the development of personalized vaccines and contribute to the determination of which patients are likely to respond to immunotherapy.
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Affiliation(s)
- Elizabeth S Borden
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ.,Phoenix Veterans Affairs Health Care System, Phoenix, AZ
| | - Suhail Ghafoor
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ
| | - Kenneth H Buetow
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ.,School of Life Sciences, Arizona State University, Tempe, AZ; and
| | | | - Melissa A Wilson
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ.,School of Life Sciences, Arizona State University, Tempe, AZ; and
| | - K Taraszka Hastings
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ; .,Phoenix Veterans Affairs Health Care System, Phoenix, AZ
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5
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Borden ES, Buetow KH, Wilson MA, Hastings KT. Cancer Neoantigens: Challenges and Future Directions for Prediction, Prioritization, and Validation. Front Oncol 2022; 12:836821. [PMID: 35311072 PMCID: PMC8929516 DOI: 10.3389/fonc.2022.836821] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/07/2022] [Indexed: 12/16/2022] Open
Abstract
Prioritization of immunogenic neoantigens is key to enhancing cancer immunotherapy through the development of personalized vaccines, adoptive T cell therapy, and the prediction of response to immune checkpoint inhibition. Neoantigens are tumor-specific proteins that allow the immune system to recognize and destroy a tumor. Cancer immunotherapies, such as personalized cancer vaccines, adoptive T cell therapy, and immune checkpoint inhibition, rely on an understanding of the patient-specific neoantigen profile in order to guide personalized therapeutic strategies. Genomic approaches to predicting and prioritizing immunogenic neoantigens are rapidly expanding, raising new opportunities to advance these tools and enhance their clinical relevance. Predicting neoantigens requires acquisition of high-quality samples and sequencing data, followed by variant calling and variant annotation. Subsequently, prioritizing which of these neoantigens may elicit a tumor-specific immune response requires application and integration of tools to predict the expression, processing, binding, and recognition potentials of the neoantigen. Finally, improvement of the computational tools is held in constant tension with the availability of datasets with validated immunogenic neoantigens. The goal of this review article is to summarize the current knowledge and limitations in neoantigen prediction, prioritization, and validation and propose future directions that will improve personalized cancer treatment.
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Affiliation(s)
- Elizabeth S Borden
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, United States.,Department of Research and Internal Medicine (Dermatology), Phoenix Veterans Affairs Health Care System, Phoenix, AZ, United States
| | - Kenneth H Buetow
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
| | - Karen Taraszka Hastings
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, United States.,Department of Research and Internal Medicine (Dermatology), Phoenix Veterans Affairs Health Care System, Phoenix, AZ, United States
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6
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Li W, Sun T, Li M, He Y, Li L, Wang L, Wang H, Li J, Wen H, Liu Y, Chen Y, Fan Y, Xin B, Zhang J. GNIFdb: a neoantigen intrinsic feature database for glioma. Database (Oxford) 2022; 2022:6527499. [PMID: 35150127 PMCID: PMC9216533 DOI: 10.1093/database/baac004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/06/2022] [Accepted: 01/29/2022] [Indexed: 12/24/2022]
Abstract
ABSTRACT Neoantigens are mutation-containing immunogenic peptides from tumor cells. Neoantigen intrinsic features are neoantigens' sequence-associated features characterized by different amino acid descriptors and physical-chemical properties, which have a crucial function in prioritization of neoantigens with immunogenic potentials and predicting patients with better survival. Different intrinsic features might have functions to varying degrees in evaluating neoantigens' potentials of immunogenicity. Identification and comparison of intrinsic features among neoantigens are particularly important for developing neoantigen-based personalized immunotherapy. However, there is still no public repository to host the intrinsic features of neoantigens. Therefore, we developed GNIFdb, a glioma neoantigen intrinsic feature database specifically designed for hosting, exploring and visualizing neoantigen and intrinsic features. The database provides a comprehensive repository of computationally predicted Human leukocyte antigen class I (HLA-I) restricted neoantigens and their intrinsic features; a systematic annotation of neoantigens including sequence, neoantigen-associated mutation, gene expression, glioma prognosis, HLA-I subtype and binding affinity between neoantigens and HLA-I; and a genome browser to visualize them in an interactive manner. It represents a valuable resource for the neoantigen research community and is publicly available at http://www.oncoimmunobank.cn/index.php. DATABASE URL http://www.oncoimmunobank.cn/index.php.
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Affiliation(s)
- Wendong Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
| | - Ting Sun
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
| | - Muyang Li
- Department of Plant Genetics and Breeding, State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing 100193, P. R. China
| | - Yufei He
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
| | - Lin Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
| | - Lu Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
| | - Haoyu Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
| | - Jing Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
| | - Hao Wen
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
| | - Yong Liu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
| | - Yifan Chen
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
| | - Yubo Fan
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
| | - Beibei Xin
- Department of Plant Genetics and Breeding, State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing 100193, P. R. China
| | - Jing Zhang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
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7
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Neoantigen Cancer Vaccines: Generation, Optimization, and Therapeutic Targeting Strategies. Vaccines (Basel) 2022; 10:vaccines10020196. [PMID: 35214655 PMCID: PMC8877108 DOI: 10.3390/vaccines10020196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 12/30/2022] Open
Abstract
Alternatives to conventional cancer treatments are highly sought after for high-risk malignancies that have a poor response to established treatment modalities. With research advancing rapidly in the past decade, neoantigen-based immunotherapeutic approaches represent an effective and highly tolerable therapeutic option. Neoantigens are tumor-specific antigens that are not expressed in normal cells and possess significant immunogenic potential. Several recent studies have described the conceptual framework and methodologies to generate neoantigen-based vaccines as well as the formulation of appropriate clinical trials to advance this approach for patient care. This review aims to describe some of the key studies in the recent literature in this rapidly evolving field and summarize the current advances in neoantigen identification and selection, vaccine generation and delivery, and the optimization of neoantigen-based therapeutic strategies, including the early data from pivotal clinical studies.
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8
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Identification of Immune Cell Infiltration in Murine Pheochromocytoma during Combined Mannan-BAM, TLR Ligand, and Anti-CD40 Antibody-Based Immunotherapy. Cancers (Basel) 2021; 13:cancers13163942. [PMID: 34439097 PMCID: PMC8393500 DOI: 10.3390/cancers13163942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/24/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
Immunotherapy has become an essential component in cancer treatment. However, the majority of solid metastatic cancers, such as pheochromocytoma, are resistant to this approach. Therefore, understanding immune cell composition in primary and distant metastatic tumors is important for therapeutic intervention and diagnostics. Combined mannan-BAM, TLR ligand, and anti-CD40 antibody-based intratumoral immunotherapy (MBTA therapy) previously resulted in the complete eradication of murine subcutaneous pheochromocytoma and demonstrated a systemic antitumor immune response in a metastatic model. Here, we further evaluated this systemic effect using a bilateral pheochromocytoma model, performing MBTA therapy through injection into the primary tumor and using distant (non-injected) tumors to monitor size changes and detailed immune cell infiltration. MBTA therapy suppressed the growth of not only injected but also distal tumors and prolonged MBTA-treated mice survival. Our flow cytometry analysis showed that MBTA therapy led to increased recruitment of innate and adaptive immune cells in both tumors and the spleen. Moreover, adoptive CD4+ T cell transfer from successfully MBTA-treated mice (i.e., subcutaneous pheochromocytoma) demonstrates the importance of these cells in long-term immunological memory. In summary, this study unravels further details on the systemic effect of MBTA therapy and its use for tumor and metastasis reduction or even elimination.
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9
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Sun T, He Y, Li W, Liu G, Li L, Wang L, Xiao Z, Han X, Wen H, Liu Y, Chen Y, Wang H, Li J, Fan Y, Zhang W, Zhang J. neoDL: a novel neoantigen intrinsic feature-based deep learning model identifies IDH wild-type glioblastomas with the longest survival. BMC Bioinformatics 2021; 22:382. [PMID: 34301201 PMCID: PMC8299600 DOI: 10.1186/s12859-021-04301-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/07/2021] [Indexed: 12/18/2022] Open
Abstract
Background Neoantigen based personalized immune therapies achieve promising results in melanoma and lung cancer, but few neoantigen based models perform well in IDH wild-type GBM, and the association between neoantigen intrinsic features and prognosis remain unclear in IDH wild-type GBM. We presented a novel neoantigen intrinsic feature-based deep learning model (neoDL) to stratify IDH wild-type GBMs into subgroups with different survivals. Results We first derived intrinsic features for each neoantigen associated with survival, followed by applying neoDL in TCGA data cohort(AUC = 0.988, p value < 0.0001). Leave one out cross validation (LOOCV) in TCGA demonstrated that neoDL successfully classified IDH wild-type GBMs into different prognostic subgroups, which was further validated in an independent data cohort from Asian population. Long-term survival IDH wild-type GBMs identified by neoDL were found characterized by 12 protective neoantigen intrinsic features and enriched in development and cell cycle. Conclusions The model can be therapeutically exploited to identify IDH wild-type GBM with good prognosis who will most likely benefit from neoantigen based personalized immunetherapy. Furthermore, the prognostic intrinsic features of the neoantigens inferred from this study can be used for identifying neoantigens with high potentials of immunogenicity. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04301-6.
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Affiliation(s)
- Ting Sun
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Yufei He
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Wendong Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Guang Liu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Lin Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Lu Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Zixuan Xiao
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Xiaohan Han
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Hao Wen
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Yong Liu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Yifan Chen
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Haoyu Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Jing Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Yubo Fan
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China.
| | - Wei Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, People's Republic of China. .,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 South Fourth Ring Road West, Fengtai District, Beijing, 100070, People's Republic of China.
| | - Jing Zhang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China.
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10
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Rollins MR, Spartz EJ, Stromnes IM. T Cell Receptor Engineered Lymphocytes for Cancer Therapy. ACTA ACUST UNITED AC 2020; 129:e97. [PMID: 32432843 DOI: 10.1002/cpim.97] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
T lymphocytes are capable of specific recognition and elimination of target cells. Physiological antigen recognition is mediated by the T cell receptor (TCR), which is an alpha beta heterodimer comprising the products of randomly rearranged V, D, and J genes. The exquisite specificity and functionality of T cells can be leveraged for cancer therapy: specifically, the adoptive transfer of T cells that express tumor-reactive TCRs can induce regression of solid tumors in patients with advanced cancer. However, the isolation and expression of a tumor antigen-specific TCRs is a highly involved process that requires identifying an immunogenic epitope, ensuring human cells are of the correct haplotype, performing a laborious T cell expansion process, and carrying out downstream TCR sequencing and cloning. Recent advances in single-cell sequencing have begun to streamline this process. This protocol synthesizes and expands upon methodologies to generate, isolate, and engineer human T cells with tumor-reactive TCRs for adoptive cell therapy. Though this process is perhaps more arduous than the alternative strategy of using chimeric antigen receptors (CARs) for engineering, the ability to target intracellular proteins using TCRs substantially increases the types of antigens that can be safely targeted. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Generation of human autologous dendritic cells from monocytes Basic Protocol 2: In vitro priming and expansion of human antigen-specific T cells Basic Protocol 3: Cloning of antigen-specific T cell receptors based on single-cell VDJ sequencing data Basic Protocol 4: Validation of T cell receptor expression and functionality in vitro Basic Protocol 5: Rapid expansion of T cell receptor-transduced T cells and human T cell clones.
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Affiliation(s)
- Meagan R Rollins
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Ellen J Spartz
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Ingunn M Stromnes
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota.,Center for Genome Engineering, University of Minnesota Medical School, Minneapolis, Minnesota.,Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, Minnesota
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11
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Sivanand A, Hennessey D, Iyer A, O'Keefe S, Surmanowicz P, Vaid G, Xiao Z, Gniadecki R. The Neoantigen Landscape of Mycosis Fungoides. Front Immunol 2020; 11:561234. [PMID: 33329522 PMCID: PMC7719792 DOI: 10.3389/fimmu.2020.561234] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/23/2020] [Indexed: 11/23/2022] Open
Abstract
Background Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma, for which there is no cure. Immune checkpoint inhibitors have been tried in MF but the results have been inconsistent. To gain insight into the immunogenicity of MF we characterized the neoantigen landscape of this lymphoma, focusing on the known predictors of responses to immunotherapy: the quantity, HLA-binding strength and subclonality of neoantigens. Methods Whole exome and whole transcriptome sequences were obtained from 24 MF samples (16 plaques, 8 tumors) from 13 patients. Bioinformatic pipelines (Mutect2, OptiType, MuPeXi) were used for mutation calling, HLA typing, and neoantigen prediction. PhyloWGS was used to subdivide malignant cells into stem and clades, to which neoantigens were matched to determine their clonality. Results MF has a high mutational load (median 3,217 non synonymous mutations), resulting in a significant number of total neoantigens (median 1,309 per sample) and high-affinity neoantigens (median 328). In stage I disease most neoantigens were clonal but with stage progression, 75% of lesions had >50% subclonal antigens and 53% lesions had CSiN scores <1. There was very little overlap in neoantigens across patients or between different lesions on the same patient, indicating a high degree of heterogeneity. Conclusions The neoantigen landscape of MF is characterized by high neoantigen load and significant subclonality which could indicate potential challenges for immunotherapy in patients with advanced-stage disease.
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Affiliation(s)
- Arunima Sivanand
- Division of Dermatology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Dylan Hennessey
- Division of Dermatology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Aishwarya Iyer
- Division of Dermatology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Sandra O'Keefe
- Division of Dermatology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Philip Surmanowicz
- Division of Dermatology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Gauravi Vaid
- Division of Dermatology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Zixuan Xiao
- Division of Dermatology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Robert Gniadecki
- Division of Dermatology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
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12
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Nguyen A, David JK, Maden SK, Wood MA, Weeder BR, Nellore A, Thompson RF. Human Leukocyte Antigen Susceptibility Map for Severe Acute Respiratory Syndrome Coronavirus 2. J Virol 2020; 94:e00510-20. [PMID: 32303592 PMCID: PMC7307149 DOI: 10.1128/jvi.00510-20] [Citation(s) in RCA: 350] [Impact Index Per Article: 87.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 04/14/2020] [Indexed: 02/07/2023] Open
Abstract
Genetic variability across the three major histocompatibility complex (MHC) class I genes (human leukocyte antigen A [HLA-A], -B, and -C genes) may affect susceptibility to and severity of the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19). We performed a comprehensive in silico analysis of viral peptide-MHC class I binding affinity across 145 HLA-A, -B, and -C genotypes for all SARS-CoV-2 peptides. We further explored the potential for cross-protective immunity conferred by prior exposure to four common human coronaviruses. The SARS-CoV-2 proteome was successfully sampled and was represented by a diversity of HLA alleles. However, we found that HLA-B*46:01 had the fewest predicted binding peptides for SARS-CoV-2, suggesting that individuals with this allele may be particularly vulnerable to COVID-19, as they were previously shown to be for SARS (M. Lin, H.-T. Tseng, J. A. Trejaut, H.-L. Lee, et al., BMC Med Genet 4:9, 2003, https://bmcmedgenet.biomedcentral.com/articles/10.1186/1471-2350-4-9). Conversely, we found that HLA-B*15:03 showed the greatest capacity to present highly conserved SARS-CoV-2 peptides that are shared among common human coronaviruses, suggesting that it could enable cross-protective T-cell-based immunity. Finally, we reported global distributions of HLA types with potential epidemiological ramifications in the setting of the current pandemic.IMPORTANCE Individual genetic variation may help to explain different immune responses to a virus across a population. In particular, understanding how variation in HLA may affect the course of COVID-19 could help identify individuals at higher risk from the disease. HLA typing can be fast and inexpensive. Pairing HLA typing with COVID-19 testing where feasible could improve assessment of severity of viral disease in the population. Following the development of a vaccine against SARS-CoV-2, the virus that causes COVID-19, individuals with high-risk HLA types could be prioritized for vaccination.
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Affiliation(s)
- Austin Nguyen
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
| | - Julianne K David
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
| | - Sean K Maden
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
| | - Mary A Wood
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon, USA
- Portland VA Research Foundation, Portland, Oregon, USA
| | - Benjamin R Weeder
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
| | - Abhinav Nellore
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
- Department of Surgery, Oregon Health & Science University, Portland, Oregon, USA
| | - Reid F Thompson
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
- Department of Radiation Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
- Division of Hospital and Specialty Medicine, VA Portland Healthcare System, Portland, Oregon, USA
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13
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Wood MA, Weeder BR, David JK, Nellore A, Thompson RF. Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival. Genome Med 2020; 12:33. [PMID: 32228719 PMCID: PMC7106909 DOI: 10.1186/s13073-020-00729-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/10/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Tumor mutational burden (TMB; the quantity of aberrant nucleotide sequences a given tumor may harbor) has been associated with response to immune checkpoint inhibitor therapy and is gaining broad acceptance as a result. However, TMB harbors intrinsic variability across cancer types, and its assessment and interpretation are poorly standardized. METHODS Using a standardized approach, we quantify the robustness of TMB as a metric and its potential as a predictor of immunotherapy response and survival among a diverse cohort of cancer patients. We also explore the additive predictive potential of RNA-derived variants and neoepitope burden, incorporating several novel metrics of immunogenic potential. RESULTS We find that TMB is a partial predictor of immunotherapy response in melanoma and non-small cell lung cancer, but not renal cell carcinoma. We find that TMB is predictive of overall survival in melanoma patients receiving immunotherapy, but not in an immunotherapy-naive population. We also find that it is an unstable metric with potentially problematic repercussions for clinical cohort classification. We finally note minimal additional predictive benefit to assessing neoepitope burden or its bulk derivatives, including RNA-derived sources of neoepitopes. CONCLUSIONS We find sufficient cause to suggest that the predictive clinical value of TMB should not be overstated or oversimplified. While it is readily quantified, TMB is at best a limited surrogate biomarker of immunotherapy response. The data do not support isolated use of TMB in renal cell carcinoma.
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Affiliation(s)
- Mary A Wood
- Computational Biology Program, Oregon Health & Science University, Portland, USA
- Portland VA Research Foundation, Portland, USA
| | - Benjamin R Weeder
- Computational Biology Program, Oregon Health & Science University, Portland, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, USA
| | - Julianne K David
- Computational Biology Program, Oregon Health & Science University, Portland, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, USA
| | - Abhinav Nellore
- Computational Biology Program, Oregon Health & Science University, Portland, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, USA
- Department of Surgery, Oregon Health & Science University, Portland, USA
| | - Reid F Thompson
- Computational Biology Program, Oregon Health & Science University, Portland, USA.
- Portland VA Research Foundation, Portland, USA.
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, USA.
- Department of Radiation Medicine, Oregon Health & Science University, Portland, USA.
- Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Portland, USA.
- VA Portland Healthcare System, Division of Hospital and Specialty Medicine, Portland, USA.
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14
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Bubie A, Gonzalez-Kozlova E, Akers N, Villanueva A, Losic B. Tumor fitness, immune exhaustion and clinical outcomes: impact of immune checkpoint inhibitors. Sci Rep 2020; 10:5062. [PMID: 32193450 PMCID: PMC7081289 DOI: 10.1038/s41598-020-61992-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/06/2020] [Indexed: 12/25/2022] Open
Abstract
Recently proposed tumor fitness measures, based on profiling neoepitopes for reactive viral epitope similarity, have been proposed to predict response to immune checkpoint inhibitors in melanoma and small-cell lung cancer. Here we applied these checkpoint based fitness measures to the matched checkpoint treatment naive Cancer Genome Atlas (TCGA) samples where cytolytic activity (CYT) imparts a known survival benefit. We observed no significant survival predictive power beyond that of overall patient tumor mutation burden, and furthermore, found no association between checkpoint based fitness and tumor T-cell infiltration, cytolytic activity, and abundance (tumor infiltrating lymphocyte, TIL, burden). In addition, we investigated the key assumption of viral epitope similarity driving immune response in the hepatitis B virally infected liver cancer TCGA cohort, and uncovered suggestive evidence that tumor neoepitopes actually dominate viral epitopes in putative immunogenicity and plausibly drive immune response and recruitment.
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Affiliation(s)
- Adrian Bubie
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Edgar Gonzalez-Kozlova
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nicholas Akers
- Adaptive biotechnologies, 1551 Eastlake Avenue E, Suite 200, Seattle, WA, 98102, USA
| | - Augusto Villanueva
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Tisch Cancer Institute, Cancer Immunology, Diabetes, Obesity and Metabolism Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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15
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Abstract
The remarkable success of cancer immunotherapies, especially the checkpoint blocking antibodies, in a subset of patients has reinvigorated the study of tumor-immune crosstalk and its role in heterogeneity of response. High-throughput sequencing and imaging technologies can help recapitulate various aspects of the tumor ecosystem. Computational approaches provide an arsenal of tools to efficiently analyze, quantify and integrate multiple parameters of tumor immunity mined from these diverse but complementary high-throughput datasets. This chapter describes numerous such computational approaches in tumor immunology that leverage high-throughput data from diverse sources (genomic, transcriptomics, epigenomics and digitized histopathology images) to systematically interrogate tumor immunity in context of its microenvironment, and to identify mechanisms that confer resistance or sensitivity to cancer therapies, in particular immunotherapy.
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16
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Roudko V, Greenbaum B, Bhardwaj N. Computational Prediction and Validation of Tumor-Associated Neoantigens. Front Immunol 2020; 11:27. [PMID: 32117226 PMCID: PMC7025577 DOI: 10.3389/fimmu.2020.00027] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/08/2020] [Indexed: 12/30/2022] Open
Abstract
Tumor progression is typically accompanied by an accumulation of driver and passenger somatic mutations. A handful of those mutations occur in protein coding genes which introduce non-synonymous polymorphisms. Certain substitutions may give rise to novel, tumor-associated antigens or neoantigens, presentable by cancer cells to the host adaptive immune system. As antigen recognition is the core of an effective immune response, the identification of patient tumor specific antigens derived from transformed cells is of importance for immunotherapeutic approaches. Recent technological advances in DNA sequencing of tumor genomes, advances in gene expression analysis, algorithm development for antigen predictions and methods for T-cell receptor (TCR) repertoire sequencing have facilitated the selection of candidate immunogenic neoantigens. In this regard, multiple research groups have reported encouraging results of neoantigen-based cancer vaccines that generate tumor antigen specific immune responses, both in mouse models and clinical trials. Additionally, both the quantity and quality of neoantigens has been shown to have predictive value for clinical outcomes in checkpoint-blockade immunotherapy in certain tumor types. Neoantigen recognition by vaccination or through adoptive T cell therapy may have unprecedented potential to advance cancer immunotherapy in combination with other approaches. In our review we discuss three parameters regarding neoantigens: computational methods for epitope prediction, experimental methods for epitope immunogenicity validation and future directions for improvement of those methods. Within each section, we will describe the advantages and limitations of existing methods as well as highlight pressing fundamental problems to be addressed.
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Affiliation(s)
- Vladimir Roudko
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
- Center for Computational Immunology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
| | - Benjamin Greenbaum
- Center for Computational Immunology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
- Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
| | - Nina Bhardwaj
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
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17
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Shao XM, Bhattacharya R, Huang J, Sivakumar IKA, Tokheim C, Zheng L, Hirsch D, Kaminow B, Omdahl A, Bonsack M, Riemer AB, Velculescu VE, Anagnostou V, Pagel KA, Karchin R. High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets. Cancer Immunol Res 2019; 8:396-408. [PMID: 31871119 DOI: 10.1158/2326-6066.cir-19-0464] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/08/2019] [Accepted: 12/20/2019] [Indexed: 02/04/2023]
Abstract
Computational prediction of binding between neoantigen peptides and major histocompatibility complex (MHC) proteins can be used to predict patient response to cancer immunotherapy. Current neoantigen predictors focus on in silico estimation of MHC binding affinity and are limited by low predictive value for actual peptide presentation, inadequate support for rare MHC alleles, and poor scalability to high-throughput data sets. To address these limitations, we developed MHCnuggets, a deep neural network method that predicts peptide-MHC binding. MHCnuggets can predict binding for common or rare alleles of MHC class I or II with a single neural network architecture. Using a long short-term memory network (LSTM), MHCnuggets accepts peptides of variable length and is faster than other methods. When compared with methods that integrate binding affinity and MHC-bound peptide (HLAp) data from mass spectrometry, MHCnuggets yields a 4-fold increase in positive predictive value on independent HLAp data. We applied MHCnuggets to 26 cancer types in The Cancer Genome Atlas, processing 26.3 million allele-peptide comparisons in under 2.3 hours, yielding 101,326 unique predicted immunogenic missense mutations (IMM). Predicted IMM hotspots occurred in 38 genes, including 24 driver genes. Predicted IMM load was significantly associated with increased immune cell infiltration (P < 2 × 10-16), including CD8+ T cells. Only 0.16% of predicted IMMs were observed in more than 2 patients, with 61.7% of these derived from driver mutations. Thus, we describe a method for neoantigen prediction and its performance characteristics and demonstrate its utility in data sets representing multiple human cancers.
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Affiliation(s)
- Xiaoshan M Shao
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Rohit Bhattacharya
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Computer Science, Johns Hopkins University, Baltimore, Maryland
| | - Justin Huang
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Computer Science, Johns Hopkins University, Baltimore, Maryland
| | - I K Ashok Sivakumar
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Computer Science, Johns Hopkins University, Baltimore, Maryland.,Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland
| | - Collin Tokheim
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Lily Zheng
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Dylan Hirsch
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Benjamin Kaminow
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Ashton Omdahl
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Maria Bonsack
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Angelika B Riemer
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany
| | - Victor E Velculescu
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kymberleigh A Pagel
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Rachel Karchin
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland. .,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland.,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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18
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Borden ES, Kang P, Natri HM, Phung TN, Wilson MA, Buetow KH, Hastings KT. Neoantigen Fitness Model Predicts Lower Immune Recognition of Cutaneous Squamous Cell Carcinomas Than Actinic Keratoses. Front Immunol 2019; 10:2799. [PMID: 31849976 PMCID: PMC6896054 DOI: 10.3389/fimmu.2019.02799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/14/2019] [Indexed: 12/17/2022] Open
Abstract
A low percentage of actinic keratoses progress to develop into cutaneous squamous cell carcinoma. The immune mechanisms that successfully control or eliminate the majority of actinic keratoses and the mechanisms of immune escape by invasive squamous cell carcinoma are not well-understood. Here, we took a systematic approach to evaluate the neoantigens present in actinic keratosis and cutaneous squamous cell carcinoma specimens. We compared the number of mutations, the number of neoantigens predicted to bind MHC class I, and the number of neoantigens that are predicted to bind MHC class I and be recognized by a T cell receptor in actinic keratoses and cutaneous squamous cell carcinomas. We also considered the relative binding strengths to both MHC class I and the T cell receptor in a fitness cost model that allows for a comparison of the immune recognition potential of the neoantigens in actinic keratosis and cutaneous squamous cell carcinoma samples. The fitness cost was subsequently adjusted by the expression rates of the neoantigens to examine the role of neoantigen expression in tumor immune evasion. Our analyses indicate that, while the number of mutations and neoantigens are not significantly different between actinic keratoses and cutaneous squamous cell carcinomas, the predicted immune recognition of the neoantigen with the highest expression-adjusted fitness cost is lower for cutaneous squamous cell carcinomas compared with actinic keratoses. These findings suggest a role for the down-regulation of expression of highly immunogenic neoantigens in the immune escape of cutaneous squamous cell carcinomas. Furthermore, these findings highlight the importance of incorporating additional factors, such as the quality and expression of the neoantigens, rather than focusing solely on tumor mutational burden, in assessing immune recognition potential.
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Affiliation(s)
- Elizabeth S. Borden
- Department of Basic Medical Sciences, College of Medicine Phoenix, University of Arizona, Phoenix, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Paul Kang
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Phoenix, AZ, United States
| | - Heini M. Natri
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Tanya N. Phung
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Kenneth H. Buetow
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Karen Taraszka Hastings
- Department of Basic Medical Sciences, College of Medicine Phoenix, University of Arizona, Phoenix, AZ, United States
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19
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Mösch A, Raffegerst S, Weis M, Schendel DJ, Frishman D. Machine Learning for Cancer Immunotherapies Based on Epitope Recognition by T Cell Receptors. Front Genet 2019; 10:1141. [PMID: 31798635 PMCID: PMC6878726 DOI: 10.3389/fgene.2019.01141] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022] Open
Abstract
In the last years, immunotherapies have shown tremendous success as treatments for multiple types of cancer. However, there are still many obstacles to overcome in order to increase response rates and identify effective therapies for every individual patient. Since there are many possibilities to boost a patient's immune response against a tumor and not all can be covered, this review is focused on T cell receptor-mediated therapies. CD8+ T cells can detect and destroy malignant cells by binding to peptides presented on cell surfaces by MHC (major histocompatibility complex) class I molecules. CD4+ T cells can also mediate powerful immune responses but their peptide recognition by MHC class II molecules is more complex, which is why the attention has been focused on CD8+ T cells. Therapies based on the power of T cells can, on the one hand, enhance T cell recognition by introducing TCRs that preferentially direct T cells to tumor sites (so called TCR-T therapy) or through vaccination to induce T cells in vivo. On the other hand, T cell activity can be improved by immune checkpoint inhibition or other means that help create a microenvironment favorable for cytotoxic T cell activity. The manifold ways in which the immune system and cancer interact with each other require not only the use of large omics datasets from gene, to transcript, to protein, and to peptide but also make the application of machine learning methods inevitable. Currently, discovering and selecting suitable TCRs is a very costly and work intensive in vitro process. To facilitate this process and to additionally allow for highly personalized therapies that can simultaneously target multiple patient-specific antigens, especially neoepitopes, breakthrough computational methods for predicting antigen presentation and TCR binding are urgently required. Particularly, potential cross-reactivity is a major consideration since off-target toxicity can pose a major threat to patient safety. The current speed at which not only datasets grow and are made available to the public, but also at which new machine learning methods evolve, is assuring that computational approaches will be able to help to solve problems that immunotherapies are still facing.
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Affiliation(s)
- Anja Mösch
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
- Medigene Immunotherapies GmbH, a subsidiary of Medigene AG, Planegg, Germany
| | - Silke Raffegerst
- Medigene Immunotherapies GmbH, a subsidiary of Medigene AG, Planegg, Germany
| | - Manon Weis
- Medigene Immunotherapies GmbH, a subsidiary of Medigene AG, Planegg, Germany
| | - Dolores J. Schendel
- Medigene Immunotherapies GmbH, a subsidiary of Medigene AG, Planegg, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
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Uher O, Caisova V, Hansen P, Kopecky J, Chmelar J, Zhuang Z, Zenka J, Pacak K. Coley's immunotherapy revived: Innate immunity as a link in priming cancer cells for an attack by adaptive immunity. Semin Oncol 2019; 46:385-392. [PMID: 31739997 DOI: 10.1053/j.seminoncol.2019.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022]
Abstract
There is no doubt that immunotherapy lies in the spotlight of current cancer research and clinical trials. However, there are still limitations in the treatment response in certain types of tumors largely due to the presence of the complex network of immunomodulatory and immunosuppressive pathways. These limitations are not likely to be overcome by current immunotherapeutic options, which often target isolated steps in immune pathways preferentially involved in adaptive immunity. Recently, we have developed an innovative anti-cancer immunotherapeutic strategy that initially elicits a strong innate immune response with subsequent activation of adaptive immunity in mouse models. Robust primary innate immune response against tumor cells is induced by toll-like receptor ligands and anti-CD40 agonistic antibodies combined with the phagocytosis-stimulating ligand mannan, anchored to a tumor cell membrane by biocompatible anchor for membrane. This immunotherapeutic approach results in a dramatic therapeutic response in large established murine subcutaneous tumors including melanoma, sarcoma, pancreatic adenocarcinoma, and pheochromocytoma. Additionally, eradication of metastases and/or long-lasting resistance to subsequent re-challenge with tumor cells was also accomplished. Current and future advantages of this immunotherapeutic approach and its possible combinations with other available therapies are discussed in this review.
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Affiliation(s)
- Ondrej Uher
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, MD 20814, USA; Department of Medical Biology, Faculty of Science, University of South Bohemia, Ceske Budejovice 37005, Czech Republic
| | - Veronika Caisova
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, MD 20814, USA
| | - Per Hansen
- Immunoaction LLC, Charlotte, Vermont, VT 05445, USA
| | - Jan Kopecky
- Department of Medical Biology, Faculty of Science, University of South Bohemia, Ceske Budejovice 37005, Czech Republic
| | - Jindrich Chmelar
- Department of Medical Biology, Faculty of Science, University of South Bohemia, Ceske Budejovice 37005, Czech Republic
| | - Zhengping Zhuang
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, MD 20814, USA
| | - Jan Zenka
- Department of Medical Biology, Faculty of Science, University of South Bohemia, Ceske Budejovice 37005, Czech Republic
| | - Karel Pacak
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, MD 20814, USA.
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21
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The Significant Reduction or Complete Eradication of Subcutaneous and Metastatic Lesions in a Pheochromocytoma Mouse Model after Immunotherapy Using Mannan-BAM, TLR Ligands, and Anti-CD40. Cancers (Basel) 2019; 11:cancers11050654. [PMID: 31083581 PMCID: PMC6562455 DOI: 10.3390/cancers11050654] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/04/2019] [Accepted: 05/06/2019] [Indexed: 12/16/2022] Open
Abstract
Therapeutic options for metastatic pheochromocytoma/paraganglioma (PHEO/PGL) are limited. Here, we tested an immunotherapeutic approach based on intratumoral injections of mannan-BAM with toll-like receptor ligands into subcutaneous PHEO in a mouse model. This therapy elicited a strong innate immunity-mediated antitumor response and resulted in a significantly lower PHEO volume compared to the phosphate buffered saline (PBS)-treated group and in a significant improvement in mice survival. The cytotoxic effect of neutrophils, as innate immune cells predominantly infiltrating treated tumors, was verified in vitro. Moreover, the combination of mannan-BAM and toll-like receptor ligands with agonistic anti-CD40 was associated with increased mice survival. Subsequent tumor re-challenge also supported adaptive immunity activation, reflected primarily by long-term tumor-specific memory. These results were further verified in metastatic PHEO, where the intratumoral injections of mannan-BAM, toll-like receptor ligands, and anti-CD40 into subcutaneous tumors resulted in significantly less intense bioluminescence signals of liver metastatic lesions induced by tail vein injection compared to the PBS-treated group. Subsequent experiments focusing on the depletion of T cell subpopulations confirmed the crucial role of CD8+ T cells in inhibition of bioluminescence signal intensity of liver metastatic lesions. These data call for a new therapeutic approach in patients with metastatic PHEO/PGL using immunotherapy that initially activates innate immunity followed by an adaptive immune response.
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Zhang J, Caruso FP, Sa JK, Justesen S, Nam DH, Sims P, Ceccarelli M, Lasorella A, Iavarone A. The combination of neoantigen quality and T lymphocyte infiltrates identifies glioblastomas with the longest survival. Commun Biol 2019; 2:135. [PMID: 31044160 PMCID: PMC6478916 DOI: 10.1038/s42003-019-0369-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/06/2019] [Indexed: 12/16/2022] Open
Abstract
Glioblastoma (GBM) is resistant to multimodality therapeutic approaches. A high burden of tumor-specific mutant peptides (neoantigens) correlates with better survival and response to immunotherapies in selected solid tumors but how neoantigens impact clinical outcome in GBM remains unclear. Here, we exploit the similarity between tumor neoantigens and infectious disease-derived immune epitopes and apply a neoantigen fitness model for identifying high-quality neoantigens in a human pan-glioma dataset. We find that the neoantigen quality fitness model stratifies GBM patients with more favorable clinical outcome and, together with CD8+ T lymphocytes tumor infiltration, identifies a GBM subgroup with the longest survival, which displays distinct genomic and transcriptomic features. Conversely, neither tumor neoantigen burden from a quantitative model nor the isolated enrichment of CD8+ T lymphocytes were able to predict survival of GBM patients. This approach may guide optimal stratification of GBM patients for maximum response to immunotherapy.
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Affiliation(s)
- Jing Zhang
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032 USA
| | - Francesca P. Caruso
- Department of Science and Technology, Universita’ degli Studi del Sannio, 82100 Benevento, Italy
- BIOGEM Istituto di Ricerche Genetiche ‘G. Salvatore’, Campo Reale, 83031 Ariano Irpino, Italy
| | - Jason K. Sa
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Republic of Korea
| | - Sune Justesen
- Immunitrack Aps, Rønnegade 4, 2100 Copenhagen East, Denmark
| | - Do-Hyun Nam
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Republic of Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Peter Sims
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - Michele Ceccarelli
- Department of Science and Technology, Universita’ degli Studi del Sannio, 82100 Benevento, Italy
- ABBVIE, Redwood City (CA), Redwood City, CA 94063 USA
| | - Anna Lasorella
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032 USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032 USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
- Department of Neurology, Columbia University Medical Center, New York, NY 10032 USA
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