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Pounraj S, Chen S, Ma L, Mazzieri R, Dolcetti R, Rehm BHA. Targeting Tumor Heterogeneity with Neoantigen-Based Cancer Vaccines. Cancer Res 2024; 84:353-363. [PMID: 38055891 DOI: 10.1158/0008-5472.can-23-2042] [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: 07/10/2023] [Revised: 10/24/2023] [Accepted: 12/04/2023] [Indexed: 12/08/2023]
Abstract
Neoantigen-based cancer vaccines have emerged as a promising immunotherapeutic approach to treat cancer. Nevertheless, the high degree of heterogeneity in tumors poses a significant hurdle for developing a vaccine that targets the therapeutically relevant neoantigens capable of effectively stimulating an immune response as each tumor contains numerous unique putative neoantigens. Understanding the complexities of tumor heterogeneity is crucial for the development of personalized neoantigen-based vaccines, which hold the potential to revolutionize cancer treatment and improve patient outcomes. In this review, we discuss recent advancements in the design of neoantigen-based cancer vaccines emphasizing the identification, validation, formulation, and targeting of neoantigens while addressing the challenges posed by tumor heterogeneity. The review highlights the application of cutting-edge approaches, such as single-cell sequencing and artificial intelligence to identify immunogenic neoantigens, while outlining current limitations and proposing future research directions to develop effective neoantigen-based vaccines.
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Affiliation(s)
- Saranya Pounraj
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
| | - Shuxiong Chen
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
| | - Linlin Ma
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
- School of Environment and Science, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
| | - Roberta Mazzieri
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Riccardo Dolcetti
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
- Menzies Health Institute Queensland (MHIQ), Griffith University (Gold Coast Campus), Queensland, Australia
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2
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Kozak M, Hu J. DNA Vaccines: Their Formulations, Engineering and Delivery. Vaccines (Basel) 2024; 12:71. [PMID: 38250884 PMCID: PMC10820593 DOI: 10.3390/vaccines12010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
The concept of DNA vaccination was introduced in the early 1990s. Since then, advancements in the augmentation of the immunogenicity of DNA vaccines have brought this technology to the market, especially in veterinary medicine, to prevent many diseases. Along with the successful COVID mRNA vaccines, the first DNA vaccine for human use, the Indian ZyCovD vaccine against SARS-CoV-2, was approved in 2021. In the current review, we first give an overview of the DNA vaccine focusing on the science, including adjuvants and delivery methods. We then cover some of the emerging science in the field of DNA vaccines, notably efforts to optimize delivery systems, better engineer delivery apparatuses, identify optimal delivery sites, personalize cancer immunotherapy through DNA vaccination, enhance adjuvant science through gene adjuvants, enhance off-target and heritable immunity through epigenetic modification, and predict epitopes with bioinformatic approaches. We also discuss the major limitations of DNA vaccines and we aim to address many theoretical concerns.
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Affiliation(s)
- Michael Kozak
- The Jake Gittlen Laboratories for Cancer Research, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
- The Department of Pathology and Laboratory Medicine, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Jiafen Hu
- The Jake Gittlen Laboratories for Cancer Research, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
- The Department of Pathology and Laboratory Medicine, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
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3
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Prognostic Significance of mRNA Expression RBBP8 or Its Methylation in Gliomas. Cell Mol Neurobiol 2023; 43:409-422. [PMID: 35106666 DOI: 10.1007/s10571-022-01198-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 01/21/2022] [Indexed: 01/07/2023]
Abstract
Retinoblastoma-binding protein 8 (RBBP8) affects the prognosis of patients with malignancies through various mechanisms. However, its function in gliomas is unknown. Our study explored the effects of RBBP8 on the prognosis of glioma patients, as well as its regulatory role in the glioma immune microenvironment. We used various bioinformatics methods to analyze the transcriptional profiles and methylation data of RBBP8 in gliomas from multiple databases. Our results showed that the mRNA and protein expression of RBBP8 in gliomas was higher than that in normal tissues and positively correlated with malignant clinical features such as age and WHO grade. A Kaplan-Meier analysis showed that patients with high RBBP8 expression had a poor prognosis. Cox regression demonstrated that RBBP8 was an independent risk indicator and had good diagnostic value for the poor prognosis of glioma. Importantly, RBBP8 was positively correlated with many well-known immune checkpoints (e.g., CTLA4 and PDL-1). Finally, a gene set enrichment analysis revealed that RBBP8 was remarkably enriched in cancer-related pathways such as cell cycle, DNA replication and so on. In conclusion, this study is the first to elaborate on the value of RBBP8 in the pathological process of glioma for anti-tumor immunotherapy. In addition, the expression of RBBP8 and its methylation site, cg05513509, may provide potential targets for glioma therapy.
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Neoantigen Vaccines; Clinical Trials, Classes, Indications, Adjuvants and Combinatorial Treatments. Cancers (Basel) 2022; 14:cancers14205163. [PMID: 36291947 PMCID: PMC9600771 DOI: 10.3390/cancers14205163] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/02/2022] [Accepted: 10/18/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Personalized neoantigen vaccines are a diverse group of personally tailored cancer vaccines that strengthen patients´ own immune reaction against cancer antigens. We analyzed 147 neoantigen vaccine clinical trials from ClinicalTrials.gov database and showed that peptide vaccines were the dominating vaccine type, while there were multiple new neoantigen vaccine types in the field. We also showed that neoantigen vaccines were mostly used in the treatment of small cell lung cancer, non-small cell lung cancer, melanoma, and glioma. According to our results neoantigen vaccines work at their best when combined with other treatments such as immune checkpoint inhibitors, chemotherapy, and radiation therapy. The effect of some neoantigen vaccine types were also often promoted with adjuvant therapy where poly-ICLC were the most recurrent adjuvant choice. Abstract Personalized neoantigen vaccines are a highly specific cancer treatment designed to induce a robust cytotoxic T-cell attack against a patient’s cancer antigens. In this study, we searched ClinicalTrials.gov for neoantigen vaccine clinical trials and systematically analyzed them, a total of 147 trials. Peptide vaccines are the largest neoantigen vaccine type, comprising up to 41% of the clinical trials. However, mRNA vaccines are a growing neoantigen vaccine group, especially in the most recent clinical trials. The most common cancer types in the clinical trials are glioma, lung cancer, and malignant melanoma, being seen in more than half of the clinical trials. Small-cell lung cancer and non-small-cell lung cancer are the largest individual cancer types. According to the results from the clinical trials, neoantigen vaccines work best when combined with other cancer treatments, and popular combination treatments include immune checkpoint inhibitors, chemotherapy, and radiation therapy. Additionally, half of the clinical trials combined neoantigen vaccines with an adjuvant to boost the immune effects, with poly-ICLC being the most recurrent adjuvant choice. This study clarifies the rapid clinical trial development of personalized neoantigen vaccines as an emerging class of cancer treatment with increasingly diversified opportunities in classes, indications, and combinatorial treatments.
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de Mey W, De Schrijver P, Autaers D, Pfitzer L, Fant B, Locy H, Esprit A, Lybaert L, Bogaert C, Verdonck M, Thielemans K, Breckpot K, Franceschini L. A synthetic DNA template for fast manufacturing of versatile single epitope mRNA. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:943-954. [PMID: 36159589 PMCID: PMC9464653 DOI: 10.1016/j.omtn.2022.08.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/14/2022] [Indexed: 11/30/2022]
Abstract
A flexible, affordable, and rapid vaccine platform is necessary to unlock the potential of personalized cancer vaccines in order to achieve full clinical efficiency. mRNA cancer vaccine manufacture relies on the rigid sequence design of multiepitope constructs produced by laborious bacterial cloning and time-consuming plasmid preparation. Here, we introduce a synthetic DNA template (SDT) assembly process, which allows cost- and time-efficient manufacturing of single (neo)epitope mRNA. We benchmarked SDT-derived mRNA against mRNA derived from a plasmid DNA template (PDT), showing that monocyte-derived dendritic cells (moDCs) electroporated with SDT-mRNA or PDT-mRNA, encoding HLA-I- or HLA-II-restricted (neo)epitopes, equally activated T cells that were modified to express the cognate T cell receptors. Furthermore, we validated the SDT-mRNA platform for neoepitope immunogenicity screening using the characterized HLA-A2-restricted neoepitope DHX40B and four new candidate HLA-A2-restricted melanoma neoepitopes. Finally, we compared SDT-mRNA with PDT-mRNA for vaccine development purposes. moDCs electroporated with mRNA encoding the HLA-A2-restricted, mutated Melan-A/Mart-1 epitope together with TriMix mRNA-generated high levels of functional Melan-A/Mart-1-specific CD8+ T cells. In conclusion, SDT single epitope mRNA can be manufactured in a more flexible, cost-efficient, and time-efficient way compared with PDT-mRNA, allowing prompt neoepitope immunogenicity screening, and might be exploited for the development of personalized cancer vaccines.
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Affiliation(s)
- Wout de Mey
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Phaedra De Schrijver
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Dorien Autaers
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Lena Pfitzer
- myNEO, Ottergemsesteenweg-Zuid 808, 9000 Ghent, Belgium
| | - Bruno Fant
- myNEO, Ottergemsesteenweg-Zuid 808, 9000 Ghent, Belgium
| | - Hanne Locy
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Arthur Esprit
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Lien Lybaert
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
- myNEO, Ottergemsesteenweg-Zuid 808, 9000 Ghent, Belgium
| | | | - Magali Verdonck
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Kris Thielemans
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Karine Breckpot
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Lorenzo Franceschini
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
- Corresponding author Lorenzo Franceschini, Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium.
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Chen Y, He J, Chen R, Wang Z, Dai Z, Liang X, Wu W, Luo P, Zhang J, Peng Y, Zhang N, Liu Z, Zhang L, Zhang H, Cheng Q. Pan-Cancer Analysis of the Immunological Role of PDIA5: A Potential Target for Immunotherapy. Front Immunol 2022; 13:881722. [PMID: 36003400 PMCID: PMC9393377 DOI: 10.3389/fimmu.2022.881722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/23/2022] [Indexed: 01/27/2023] Open
Abstract
The aberrant protein disulfide isomerase A5 (PDIA5) expression was relevant to the poor prognosis of patients with human cancers. However, its relationship with the epigenetic and genetic alterations and its effect on tumor immunity is still lacking. In the present study, we comprehensively analyzed the immune infiltration role of PDIA5 in human cancers based on large-scale bioinformatics analyses and in vitro experiments. Obvious DNA methylation and moderate alteration frequency of PDIA5 were observed in human cancers. The expression level of PDIA5 was significantly correlated with infiltrated immune cells, immune pathways, and other immune signatures. We found that cancer cells and macrophages exhibited high PDIA5 expression in human cancers using the single-cell RNA sequencing analysis. We also demonstrated the interaction between PDIA5 and immune cells in glioblastoma multiforme (GBM). Multiplex immunofluorescence staining showed the upregulated expression level of PDIA5 and the increased number of M2 macrophage markers-CD163 positive cells in pan-cancer samples. Notably, PDIA5 silencing resulted in upregulated expression of PD-L1 and SPP1 in U251 cells. Silencing of PDIA5 in hepG2 cells, U251 cells, and PC3 cells contributed to a decline in their ability of proliferation, clone formation, and invasion and inhibited the migration of cocultured M2 macrophages. Additionally, PDIA5 also displayed predictive value in the immunotherapy response of both murine and human cancer cohorts. Overall, our findings indicated that PDIA5 might be a potential target for immunotherapies in cancers.
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Affiliation(s)
- Yu Chen
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jialin He
- Department of Neurology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Rui Chen
- Department of Neurosurgery, Affiliated Nanhua Hospital, University of South China, Changsha, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xisong Liang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wantao Wu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Oncology, Xiangya Hospital, Central South University, Guangzhou, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Changsha, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Changsha, China
| | - Yun Peng
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
- Teaching and Research Section of Clinical Nursing, Xiangya Hospital of Central South University, Changsha, China
| | - Nan Zhang
- One-third Lab, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou, Changsha, China
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Quan Cheng, ; Hao Zhang, ; Liyang Zhang,
| | - Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- *Correspondence: Quan Cheng, ; Hao Zhang, ; Liyang Zhang,
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Quan Cheng, ; Hao Zhang, ; Liyang Zhang,
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Lv D, Khawar MB, Liang Z, Gao Y, Sun H. Neoantigens and NK Cells: “Trick or Treat” the Cancers? Front Immunol 2022; 13:931862. [PMID: 35874694 PMCID: PMC9302773 DOI: 10.3389/fimmu.2022.931862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/14/2022] [Indexed: 12/15/2022] Open
Abstract
Immunotherapy has become an important treatment strategy for cancer patients nowadays. Targeting cancer neoantigens presented by major histocompatibility complex (MHC) molecules, which emerge as a result of non-synonymous somatic mutations with high immunogenicity, is one of the most promising cancer immunotherapy strategies. Currently, several therapeutic options based on the personalized or shared neoantigens have been developed, including neoantigen vaccine and adoptive T-cell therapy, both of which are now being tested in clinical trials for various malignancies. The goal of this review is to outline the use of neoantigens as cancer therapy targets, with an emphasis on neoantigen identification, clinical usage of personalized neoantigen-based cancer therapy agents, and the development of off-the-shelf products based on shared neoantigens. In addition, we introduce and discuss the potential impact of the neoantigen–MHC complex on natural killer (NK) cell antitumor function, which could be a novel way to boost immune response-induced cytotoxicity against malignancies.
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Affiliation(s)
- Dan Lv
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- School of Life Sciences, Anqing Normal University, Anqing, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research Yangzhou, Yangzhou, China
| | - Muhammad Babar Khawar
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research Yangzhou, Yangzhou, China
- Applied Molecular Biology and Biomedicine Lab, Department of Zoology, University of Narowal, Narowal, Pakistan
| | - Zhengyan Liang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research Yangzhou, Yangzhou, China
| | - Yu Gao
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research Yangzhou, Yangzhou, China
| | - Haibo Sun
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research Yangzhou, Yangzhou, China
- *Correspondence: Haibo Sun,
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Starzer AM, Preusser M, Berghoff AS. Immune escape mechanisms and therapeutic approaches in cancer: the cancer-immunity cycle. Ther Adv Med Oncol 2022; 14:17588359221096219. [PMID: 35510032 PMCID: PMC9058458 DOI: 10.1177/17588359221096219] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/04/2022] [Indexed: 12/31/2022] Open
Abstract
The introduction of immune checkpoint inhibitors has changed the therapeutic possibilities for various cancer types. However, despite the success in some entities, a significant fraction of patients does not respond to immune checkpoint inhibitors. A functioning cancer-immunity cycle is needed as the precondition for a clinically meaningful response to immune checkpoint inhibitors. It is assumed that only if each step of the cycle is activated and functioning properly, immune checkpoint inhibitors induce a meaningful immune response. However, an activated cancer-immunity cycle might not be present equally in each patient and cancer type. Ideally, treatment concepts should consider each single step of the cancer-immunity cycle and provide personalized treatment approaches, allowing the adaption to functioning and malfunctioning steps of the individual patient’s specific cancer-immunity cycle. In the following review, we provide an overview of the single steps of the cancer-immunity cycle as well as the impact of malfunctioning steps on the generation of an effective tumor-specific immune response.
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Affiliation(s)
- Angelika M. Starzer
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- Christian Doppler Laboratory for Personalized Immunotherapy, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Matthias Preusser
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- Christian Doppler Laboratory for Personalized Immunotherapy, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Anna S. Berghoff
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
- Christian Doppler Laboratory for Personalized Immunotherapy, Department of Medicine I, Medical University of Vienna, Vienna, Austria
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McCann K, von Witzleben A, Thomas J, Wang C, Wood O, Singh D, Boukas K, Bendjama K, Silvestre N, Nielsen FC, Thomas G, Sanchez-Elsner T, Greenbaum J, Schoenberger S, Peters B, Vijayanand P, Savelyeva N, Ottensmeier C. Targeting the tumor mutanome for personalized vaccination in a TMB low non-small cell lung cancer. J Immunother Cancer 2022; 10:e003821. [PMID: 35361728 PMCID: PMC8971766 DOI: 10.1136/jitc-2021-003821] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Cancer is characterized by an accumulation of somatic mutations, of which a significant subset can generate cancer-specific neoepitopes that are recognized by autologous T cells. Such neoepitopes are emerging as important targets for cancer immunotherapy, including personalized cancer vaccination strategies. METHODS We used whole-exome and RNA sequencing analysis to identify potential neoantigens for a patient with non-small cell lung cancer. Thereafter, we assessed the autologous T-cell reactivity to the candidate neoantigens using a long peptide approach in a cultured interferon gamma ELISpot and tracked the neoantigen-specific T-cells in the tumor by T-cell receptor (TCR) sequencing. In parallel, identified gene variants were incorporated into a Modified Vaccinia Ankara-based vaccine, which was evaluated in the human leucocyte antigen A*0201 transgenic mouse model (HHD). RESULTS Sequencing revealed a tumor with a low mutational burden: 2219 sequence variants were identified from the primary tumor, of which 23 were expressed in the transcriptome, involving 18 gene products. We could demonstrate spontaneous T-cell responses to 5/18 (28%) mutated gene variants, and further analysis of the TCR repertoire of neoantigen-specific CD4+ and CD8+ T cells revealed TCR clonotypes that were expanded in both blood and tumor tissue. Following vaccination of HHD mice, de novo T-cell responses were generated to 4/18 (22%) mutated gene variants; T cells reactive against two variants were also evident in the autologous setting. Subsequently, we determined the major histocompatibility complex restriction of the T-cell responses and used in silico prediction tools to determine the likely neoepitopes. CONCLUSIONS Our study demonstrates the feasibility of efficiently identifying tumor-specific neoantigens that can be targeted by vaccination in tumors with a low mutational burden, promising successful clinical exploitation, with trials currently underway.
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Affiliation(s)
- Katy McCann
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
| | - Adrian von Witzleben
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Ulm, Ulm, Germany
| | - Jaya Thomas
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
| | - Chuan Wang
- Head and Neck Centre, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Oliver Wood
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
| | - Divya Singh
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
| | - Konstantinos Boukas
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
| | - Kaidre Bendjama
- Research and Development Department, Transgene, Illkirch-Graffenstaden, France
| | - Nathalie Silvestre
- Research and Development Department, Transgene, Illkirch-Graffenstaden, France
| | | | - Gareth Thomas
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Tilman Sanchez-Elsner
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | - Jason Greenbaum
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Stephen Schoenberger
- Laboratory of Cellular Immunology, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | | | - Natalia Savelyeva
- Head and Neck Centre, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Christian Ottensmeier
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
- Head and Neck Centre, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- La Jolla Institute for Immunology, La Jolla, California, USA
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10
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Landscape of Immunotherapy Options for Colorectal Cancer: Current Knowledge and Future Perspectives beyond Immune Checkpoint Blockade. Life (Basel) 2022; 12:life12020229. [PMID: 35207516 PMCID: PMC8878674 DOI: 10.3390/life12020229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/21/2022] [Accepted: 01/31/2022] [Indexed: 11/24/2022] Open
Abstract
Colorectal cancer is the third most prevalent malignancy in Western countries and a major cause of death despite recent improvements in screening programs and early detection methods. In the last decade, a growing effort has been put into better understanding how the immune system interacts with cancer cells. Even if treatments with immune checkpoint inhibitors (anti-PD1, anti-PD-L1, anti-CTLA4) were proven effective for several cancer types, the benefit for colorectal cancer patients is still limited. However, a subset of patients with deficient mismatch repair (dMMR)/microsatellite-instability-high (MSI-H) metastatic colorectal cancer has been observed to have a prolonged benefit to immune checkpoint inhibitors. As a result, pembrolizumab and nivolumab +/− ipilimumab recently obtained the Food and Drug Administration approval. This review aims to highlight the body of knowledge on immunotherapy in the colorectal cancer setting, discussing the potential mechanisms of resistance and future strategies to extend its use.
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11
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Shen C, He Y, Chen Q, Feng H, Williams TM, Lu Y, He Z. Narrative review of emerging roles for AKT-mTOR signaling in cancer radioimmunotherapy. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1596. [PMID: 34790802 PMCID: PMC8576660 DOI: 10.21037/atm-21-4544] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/27/2021] [Indexed: 12/20/2022]
Abstract
Objective To summarize the roles of AKT-mTOR signaling in the regulation of the DNA damage response and PD-L1 expression in cancer cells, and propose a novel strategy of targeting AKT-mTOR signaling in combination with radioimmunotherapy in the era of cancer immunotherapy Background Immunotherapy has greatly improved the clinical outcomes of many cancer patients and has changed the landscape of cancer patient management. However, only a small subgroup of cancer patients (~20–30%) benefit from immune checkpoint blockade-based immunotherapy. The current challenge is to find biomarkers to predict the response of patients to immunotherapy and strategies to sensitize patients to immunotherapy. Methods Search and review the literature which were published in PUBMED from 2000–2021 with the key words mTOR, AKT, drug resistance, DNA damage response, immunotherapy, PD-L1, DNA repair, radioimmunotherapy. Conclusions More than 50% of cancer patients receive radiotherapy during their course of treatment. Radiotherapy has been shown to reduce the growth of locally irradiated tumors as well as metastatic non-irradiated tumors (abscopal effects) by affecting systemic immunity. Consistently, immunotherapy has been demonstrated to enhance radiotherapy with more than one hundred clinical trials of radiation in combination with immunotherapy (radioimmunotherapy) across cancer types. Nevertheless, current available data have shown limited efficacy of trials testing radioimmunotherapy. AKT-mTOR signaling is a major tumor growth-promoting pathway and is upregulated in most cancers. AKT-mTOR signaling is activated by growth factors as well as genotoxic stresses including radiotherapy. Importantly, recent advances have shown that AKT-mTOR is one of the main signaling pathways that regulate DNA damage repair as well as PD-L1 levels in cancers. These recent advances clearly suggest a novel cancer therapy strategy by targeting AKT-mTOR signaling in combination with radioimmunotherapy.
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Affiliation(s)
- Changxian Shen
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Yuqi He
- Monash School of Medicine, Monash University, Clayton, VIC, Australia
| | - Qiang Chen
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Haihua Feng
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Terence M Williams
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Yuanzhi Lu
- Department of Clinical Pathology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Zhengfu He
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, College of Medicine Zhejiang University, Hangzhou, China
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12
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Zhu Y, Liu J. The Role of Neoantigens in Cancer Immunotherapy. Front Oncol 2021; 11:682325. [PMID: 34513673 PMCID: PMC8429900 DOI: 10.3389/fonc.2021.682325] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/10/2021] [Indexed: 02/05/2023] Open
Abstract
Somatic mutation-derived neoantigens, expressed only on tumor cells, may elicit antitumor T-cell responses in cancer immunotherapies with minimal immune tolerance. Neoantigens can be identified by multiple bioinformatics technologies, mainly based on whole-exome sequencing. Personalized cancer vaccines and adoptive T cell therapies are two primary treatment modalities targeting neoantigens, and both of them have shown promising therapeutic effects. This review, summarizes the history of neoantigen-related tumor control, introduces recent neoantigen screening and identification methods, and discusses the role of neoantigen in cancer immunotherapies. Moreover, we propose the challenges of targeting neoantigens for cancer treatment.
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Affiliation(s)
- Yueting Zhu
- Department of Biotherapy, Cancer Center, and National Clinical Research Center for Geriatrics, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Jiyan Liu
- Department of Biotherapy, Cancer Center, and National Clinical Research Center for Geriatrics, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.,Department of Oncology, The First People's Hospital of Ziyang, Ziyang, China
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13
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Tagliamento M, Agostinetto E, Borea R, Brandão M, Poggio F, Addeo A, Lambertini M. VISTA: A Promising Target for Cancer Immunotherapy? Immunotargets Ther 2021; 10:185-200. [PMID: 34189130 PMCID: PMC8235942 DOI: 10.2147/itt.s260429] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/19/2021] [Indexed: 12/16/2022] Open
Abstract
Agents targeting the B7 family co-inhibitory receptors cytotoxic T-lymphocyte antigen-4 (CTLA-4) and programmed cell death protein-1 (PD-1), or its ligand (PD-L1), have a pivotal role in clinical practice. V-domain Ig suppressor of T-cell activation (VISTA) is a protein highly conserved between species, with a similar amino acid sequence to the B7 family members, characterized by a particularly structural homology to PD-1. It has been counted as an emerging target within the list of novel targetable immune checkpoints in oncology. Physiologically, VISTA exerts a regulatory function on the immune system at several levels, particularly by modulating T cells activation. Its altered activity plays a role in many autoimmune diseases, and its expression has been found to be prognostically implicated in different cancer types in preclinical models. We hereby present the main evidence on the value of VISTA as an immune checkpoint in solid and hematological malignancies. We also review its value as a potential target for cancer immunotherapy, by reporting the results of Phase I and II clinical trials assessing the use of drugs targeting VISTA. The complexity of its pathway, along with some unclear biological aspects concerning its molecular interactions, currently represent a limit to the applicability of VISTA as an effective biomarker for immunotherapy in oncology. A deeper characterization of this immune checkpoint may help defining its value within immune signatures of solid and hematological malignancies, and to design future therapeutic strategies.
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Affiliation(s)
- Marco Tagliamento
- Department of Medical Oncology, Medical Oncology 2, IRCCS Ospedale Policlinico San Martino, Genova, Italy.,Department of Internal Medicine and Medical Specialties (Di.M.I.), University of Genova, Genova, Italy
| | - Elisa Agostinetto
- Institut Jules Bordet and Université Libre de Bruxelles (U.L.B), Brussels, Belgium.,Medical Oncology and Hematology Unit, IRCCS Humanitas Clinical and Research Center and Humanitas University, Milan, Italy
| | - Roberto Borea
- Department of Internal Medicine and Medical Specialties (Di.M.I.), University of Genova, Genova, Italy.,Department of Medical Oncology, Medical Oncology 1, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Mariana Brandão
- Institut Jules Bordet and Université Libre de Bruxelles (U.L.B), Brussels, Belgium
| | - Francesca Poggio
- Breast Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Alfredo Addeo
- Oncology Department, University Hospital of Geneva, Geneva, Switzerland
| | - Matteo Lambertini
- Department of Internal Medicine and Medical Specialties (Di.M.I.), University of Genova, Genova, Italy.,Department of Medical Oncology, UOC Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova, Italy
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14
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Li W, Amei A, Bui F, Norouzifar S, Lu L, Wang Z. Impact of Neoantigen Expression and T-Cell Activation on Breast Cancer Survival. Cancers (Basel) 2021; 13:cancers13122879. [PMID: 34207556 PMCID: PMC8228363 DOI: 10.3390/cancers13122879] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Neoantigens are novel proteins presented on the cell surface and derived from the accumulation of somatic mutations in tumor cells. They can be recognized by the immune system and may play a crucial role in boosting immune responses against tumor cells. The impact of neoantigen expression and T-cell activation status on overall survival was investigated in a breast cancer cohort. We found that high neoantigen expression and T-cell activation status was correlated with improved patient survival in the study population. This result supports that neoantigens are promising to serve as immunogenic agents for immunotherapy in breast cancer. Abstract Neoantigens are derived from tumor-specific somatic mutations. Neoantigen-based synthesized peptides have been under clinical investigation to boost cancer immunotherapy efficacy. The promising results prompt us to further elucidate the effect of neoantigen expression on patient survival in breast cancer. We applied Kaplan–Meier survival and multivariable Cox regression models to evaluate the effect of neoantigen expression and its interaction with T-cell activation on overall survival in a cohort of 729 breast cancer patients. Pearson’s chi-squared tests were used to assess the relationships between neoantigen expression and clinical pathological variables. Spearman correlation analysis was conducted to identify correlations between neoantigen expression, mutation load, and DNA repair gene expression. ERCC1, XPA, and XPC were negatively associated with neoantigen expression, while BLM, BRCA2, MSH2, XRCC2, RAD51, CHEK1, and CHEK2 were positively associated with neoantigen expression. Based on the multivariable Cox proportional hazard model, patients with a high level of neoantigen expression and activated T-cell status showed improved overall survival. Similarly, in the T-cell exhaustion and progesterone receptor (PR) positive subgroups, patients with a high level of neoantigen expression showed prolonged survival. In contrast, there was no significant difference in the T-cell activation and PR negative subgroups. In conclusion, neoantigens may serve as immunogenic agents for immunotherapy in breast cancer.
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Affiliation(s)
- Wenjing Li
- Department of Mathematical Sciences, University of Nevada, Las Vegas, NV 89154, USA;
| | - Amei Amei
- Department of Mathematical Sciences, University of Nevada, Las Vegas, NV 89154, USA;
- Correspondence: (A.A.); (Z.W.)
| | - Francis Bui
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA; (F.B.); (S.N.)
| | - Saba Norouzifar
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA; (F.B.); (S.N.)
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06520, USA;
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA
- Correspondence: (A.A.); (Z.W.)
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15
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De Mattos-Arruda L, Cortes J, Blanco-Heredia J, Tiezzi DG, Villacampa G, Gonçalves-Ribeiro S, Paré L, Souza CA, Ortega V, Sammut SJ, Cusco P, Fasani R, Chin SF, Perez-Garcia J, Dienstmann R, Nuciforo P, Villagrasa P, Rubio IT, Prat A, Caldas C. The temporal mutational and immune tumour microenvironment remodelling of HER2-negative primary breast cancers. NPJ Breast Cancer 2021; 7:73. [PMID: 34099718 PMCID: PMC8185105 DOI: 10.1038/s41523-021-00282-0] [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: 09/24/2020] [Accepted: 05/03/2021] [Indexed: 12/30/2022] Open
Abstract
The biology of breast cancer response to neoadjuvant therapy is underrepresented in the literature and provides a window-of-opportunity to explore the genomic and microenvironment modulation of tumours exposed to therapy. Here, we characterised the mutational, gene expression, pathway enrichment and tumour-infiltrating lymphocytes (TILs) dynamics across different timepoints of 35 HER2-negative primary breast cancer patients receiving neoadjuvant eribulin therapy (SOLTI-1007 NEOERIBULIN-NCT01669252). Whole-exome data (N = 88 samples) generated mutational profiles and candidate neoantigens and were analysed along with RNA-Nanostring 545-gene expression (N = 96 samples) and stromal TILs (N = 105 samples). Tumour mutation burden varied across patients at baseline but not across the sampling timepoints for each patient. Mutational signatures were not always conserved across tumours. There was a trend towards higher odds of response and less hazard to relapse when the percentage of subclonal mutations was low, suggesting that more homogenous tumours might have better responses to neoadjuvant therapy. Few driver mutations (5.1%) generated putative neoantigens. Mutation and neoantigen load were positively correlated (R2 = 0.94, p = <0.001); neoantigen load was weakly correlated with stromal TILs (R2 = 0.16, p = 0.02). An enrichment in pathways linked to immune infiltration and reduced programmed cell death expression were seen after 12 weeks of eribulin in good responders. VEGF was downregulated over time in the good responder group and FABP5, an inductor of epithelial mesenchymal transition (EMT), was upregulated in cases that recurred (p < 0.05). Mutational heterogeneity, subclonal architecture and the improvement of immune microenvironment along with remodelling of hypoxia and EMT may influence the response to neoadjuvant treatment.
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Affiliation(s)
- Leticia De Mattos-Arruda
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain.
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK.
| | - Javier Cortes
- Oncology Department International Breast Cancer Center (IBCC), Quiron Group, Barcelona, Spain
- Medica Scientia Innovation Research (MedSIR), Barcelona, Spain
- Medica Scientia Innovation Research (MedSIR), Ridgewood, NJ, USA
- Breast Cancer Research program, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Universidad Europea de Madrid, Faculty of Biomedical and Health Sciences, Department of Medicine, Madrid, Spain
| | - Juan Blanco-Heredia
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Daniel G Tiezzi
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
- Breast Disease Division, Ribeirão Preto School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Guillermo Villacampa
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Laia Paré
- Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain
- SOLTI Breast Cancer Research Group, Barcelona, Spain
- Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain
| | - Carla Anjos Souza
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Vanesa Ortega
- Breast Cancer Research program, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Stephen-John Sammut
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Pol Cusco
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Roberta Fasani
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Jose Perez-Garcia
- Oncology Department International Breast Cancer Center (IBCC), Quiron Group, Barcelona, Spain
- Medica Scientia Innovation Research (MedSIR), Barcelona, Spain
- Medica Scientia Innovation Research (MedSIR), Ridgewood, NJ, USA
| | - Rodrigo Dienstmann
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Isabel T Rubio
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Aleix Prat
- Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain
- SOLTI Breast Cancer Research Group, Barcelona, Spain
- Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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16
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Esprit A, de Mey W, Bahadur Shahi R, Thielemans K, Franceschini L, Breckpot K. Neo-Antigen mRNA Vaccines. Vaccines (Basel) 2020; 8:E776. [PMID: 33353155 PMCID: PMC7766040 DOI: 10.3390/vaccines8040776] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
The interest in therapeutic cancer vaccines has caught enormous attention in recent years due to several breakthroughs in cancer research, among which the finding that successful checkpoint blockade treatments reinvigorate neo-antigen-specific T cells and that successful adoptive cell therapies are directed towards neo-antigens. Neo-antigens are cancer-specific antigens, which develop from somatic mutations in the cancer cell genome that can be highly immunogenic and are not subjected to central tolerance. As the majority of neo-antigens are unique to each patient's cancer, a vaccine technology that is flexible and potent is required to develop personalized neo-antigen vaccines. In vitro transcribed mRNA is such a technology platform and has been evaluated for delivery of neo-antigens to professional antigen-presenting cells both ex vivo and in vivo. In addition, strategies that support the activity of T cells in the tumor microenvironment have been developed. These represent a unique opportunity to ensure durable T cell activity upon vaccination. Here, we comprehensively review recent progress in mRNA-based neo-antigen vaccines, summarizing critical milestones that made it possible to bring the promise of therapeutic cancer vaccines within reach.
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Affiliation(s)
| | | | | | | | | | - Karine Breckpot
- Laboratory for Molecular and Cellular Therapy (LMCT), Department of Biomedical Sciences, Vrije Universiteit Brussel, B-1090 Brussels, Belgium; (A.E.); (W.d.M.); (R.B.S.); (K.T.); (L.F.)
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17
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De Mattos-Arruda L, Vazquez M, Finotello F, Lepore R, Porta E, Hundal J, Amengual-Rigo P, Ng CKY, Valencia A, Carrillo J, Chan TA, Guallar V, McGranahan N, Blanco J, Griffith M. Neoantigen prediction and computational perspectives towards clinical benefit: recommendations from the ESMO Precision Medicine Working Group. Ann Oncol 2020; 31:978-990. [PMID: 32610166 PMCID: PMC7885309 DOI: 10.1016/j.annonc.2020.05.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/01/2020] [Accepted: 05/07/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The use of next-generation sequencing technologies has enabled the rapid identification of non-synonymous somatic mutations in cancer cells. Neoantigens are mutated peptides derived from somatic mutations not present in normal tissues that may result in the presentation of tumour-specific peptides capable of eliciting antitumour T-cell responses. Personalised neoantigen-based cancer vaccines and adoptive T-cell therapies have been shown to prime host immunity against tumour cells and are under clinical trial development. However, the optimisation and standardisation of neoantigen identification, as well as its delivery as immunotherapy are needed to increase tumour-specific T-cell responses and, thus, the clinical efficacy of current cancer immunotherapies. METHODS In this recommendation article, launched by the European Society for Medical Oncology (ESMO), we outline and discuss the available framework for neoantigen prediction and present a systematic review of the current scientific evidence. RESULTS A number of computational pipelines for neoantigen prediction are available. Most of them provide peptide major histocompatibility complex (MHC) binding affinity predictions, but more recent approaches incorporate additional features like variant allele fraction, gene expression, and clonality of mutations. Neoantigens can be predicted in all cancer types with high and low tumour mutation burden, in part by exploiting tumour-specific aberrations derived from mutational frameshifts, splice variants, gene fusions, endogenous retroelements and other tumour-specific processes that could yield more potently immunogenic tumour neoantigens. Ongoing clinical trials will highlight those cancer types and combinations of immune therapies that would derive the most benefit from neoantigen-based immunotherapies. CONCLUSIONS Improved identification, selection and prioritisation of tumour-specific neoantigens are needed to increase the scope of benefit from cancer vaccines and adoptive T-cell therapies. Novel pipelines are being developed to resolve the challenges posed by high-throughput sequencing and to predict immunogenic neoantigens.
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Affiliation(s)
- L De Mattos-Arruda
- IrsiCaixa, Hospital Universitari Trias i Pujol, Badalona, Spain; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
| | - M Vazquez
- Barcelona Supercomputing Center, Barcelona, Spain
| | - F Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - R Lepore
- Barcelona Supercomputing Center, Barcelona, Spain
| | - E Porta
- Barcelona Supercomputing Center, Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - J Hundal
- The McDonnell Genome Institute, Washington University in St Louis, USA
| | | | - C K Y Ng
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - A Valencia
- Barcelona Supercomputing Center, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - J Carrillo
- IrsiCaixa, Hospital Universitari Trias i Pujol, Badalona, Spain; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - T A Chan
- Center for Immunotherapy and Precision-Immuno-Oncology, Cleveland Clinic, Cleveland, USA
| | - V Guallar
- Barcelona Supercomputing Center, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - N McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College, London, UK; Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
| | - J Blanco
- IrsiCaixa, Hospital Universitari Trias i Pujol, Badalona, Spain; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain; Universitat de Vic-Universitat Central de Catalunya (UVic-UCC), Vic, Spain
| | - M Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, USA
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