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D'Alise AM, Leoni G, Cotugno G, Siani L, Vitale R, Ruzza V, Garzia I, Antonucci L, Micarelli E, Venafra V, Gogov S, Capone A, Runswick S, Martin‐Liberal J, Calvo E, Moreno V, Symeonides SN, Scarselli E, Bechter O. Phase I Trial of Viral Vector-Based Personalized Vaccination Elicits Robust Neoantigen-Specific Antitumor T-Cell Responses. Clin Cancer Res 2024; 30:2412-2423. [PMID: 38506710 PMCID: PMC11145154 DOI: 10.1158/1078-0432.ccr-23-3940] [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: 12/15/2023] [Revised: 02/13/2024] [Accepted: 03/18/2024] [Indexed: 03/21/2024]
Abstract
PURPOSE Personalized vaccines targeting multiple neoantigens (nAgs) are a promising strategy for eliciting a diversified antitumor T-cell response to overcome tumor heterogeneity. NOUS-PEV is a vector-based personalized vaccine, expressing 60 nAgs and consists of priming with a nonhuman Great Ape Adenoviral vector (GAd20) followed by boosts with Modified Vaccinia Ankara. Here, we report data of a phase Ib trial of NOUS-PEV in combination with pembrolizumab in treatment-naïve patients with metastatic melanoma (NCT04990479). PATIENTS AND METHODS The feasibility of this approach was demonstrated by producing, releasing, and administering to 6 patients 11 of 12 vaccines within 8 weeks from biopsy collection to GAd20 administration. RESULTS The regimen was safe, with no treatment-related serious adverse events observed and mild vaccine-related reactions. Vaccine immunogenicity was demonstrated in all evaluable patients receiving the prime/boost regimen, with detection of robust neoantigen-specific immune responses to multiple neoantigens comprising both CD4 and CD8 T cells. Expansion and diversification of vaccine-induced T-cell receptor (TCR) clonotypes was observed in the posttreatment biopsies of patients with clinical response, providing evidence of tumor infiltration by vaccine-induced neoantigen-specific T cells. CONCLUSIONS These findings indicate the ability of NOUS-PEV to amplify and broaden the repertoire of tumor-reactive T cells to empower a diverse, potent, and durable antitumor immune response. Finally, a gene signature indicative of the reduced presence of activated T cells together with very poor expression of the antigen-processing machinery genes has been identified in pretreatment biopsies as a potential biomarker of resistance to the treatment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Veronica Venafra
- Department of Biology, University of Rome “Tor Vergata,” Rome, Italy
| | | | | | | | | | - Emiliano Calvo
- START Madrid‐CIOCC, Centro Integral Oncológico Clara Campal, Madrid, Spain
| | - Victor Moreno
- START Madrid‐FJD, Hospital Fundacion Jimenez Díaz, Madrid, Spain
| | - Stefan N. Symeonides
- Edinburgh Experimental Cancer Medicine Centre, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Oliver Bechter
- Leuven Cancer Institute, Department of General Medical Oncology, University Hospitals Leuven, Leuven, Belgium
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Troise F, Leoni G, Sasso E, Del Sorbo M, Esposito M, Romano G, Allocca S, Froechlich G, Cotugno G, Capone S, Folgori A, Scarselli E, D’Alise AM, Nicosia A. Prime and pull of T cell responses against cancer-exogenous antigens is effective against CPI-resistant tumors. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200760. [PMID: 38596303 PMCID: PMC10869775 DOI: 10.1016/j.omton.2024.200760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/25/2023] [Accepted: 01/05/2024] [Indexed: 04/11/2024]
Abstract
Neoantigen (neoAg)-based cancer vaccines expand preexisting antitumor immunity and elicit novel cancer-specific T cells. However, at odds with prophylactic vaccines, therapeutic antitumor immunity must be induced when the tumor is present and has already established an immunosuppressive environment capable of rapidly impairing the function of anticancer neoAg T cells, thereby leading to lack of efficacy. To overcome tumor-induced immunosuppression, we first vaccinated mice bearing immune checkpoint inhibitor (CPI)-resistant tumors with an adenovirus vector encoding a set of potent cancer-exogenous CD8 and CD4 T cell epitopes (Ad-CAP1), and then "taught" cancer cells to express the same epitopes by using a tumor-retargeted herpesvirus vector (THV-CAP1). Potent CD8 effector T lymphocytes were elicited by Ad-CAP1, and subsequent THV-CAP1 delivery led to a significant delay in tumor growth and even cure.
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Affiliation(s)
- Fulvia Troise
- Nouscom S.r.l, Via di Castel Romano 100, 00128 Rome, Italy
| | - Guido Leoni
- Nouscom S.r.l, Via di Castel Romano 100, 00128 Rome, Italy
| | - Emanuele Sasso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
- CEINGE-Advanced Biotechnologies S.c. a.r.l, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | | | | | | | - Simona Allocca
- Nouscom S.r.l, Via di Castel Romano 100, 00128 Rome, Italy
| | - Guendalina Froechlich
- CEINGE-Advanced Biotechnologies S.c. a.r.l, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | | | | | | | | | | | - Alfredo Nicosia
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
- CEINGE-Advanced Biotechnologies S.c. a.r.l, Via Gaetano Salvatore 486, 80145 Naples, Italy
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Seclì L, Leoni G, Ruzza V, Siani L, Cotugno G, Scarselli E, D’Alise AM. Personalized Cancer Vaccines Go Viral: Viral Vectors in the Era of Personalized Immunotherapy of Cancer. Int J Mol Sci 2023; 24:16591. [PMID: 38068911 PMCID: PMC10706435 DOI: 10.3390/ijms242316591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The aim of personalized cancer vaccines is to elicit potent and tumor-specific immune responses against neoantigens specific to each patient and to establish durable immunity, while minimizing the adverse events. Over recent years, there has been a renewed interest in personalized cancer vaccines, primarily due to the advancement of innovative technologies for the identification of neoantigens and novel vaccine delivery platforms. Here, we review the emerging field of personalized cancer vaccination, with a focus on the use of viral vectors as a vaccine platform. The recent advancements in viral vector technology have led to the development of efficient production processes, positioning personalized viral vaccines as one of the preferred technologies. Many clinical trials have shown the feasibility, safety, immunogenicity and, more recently, preliminary evidence of the anti-tumor activity of personalized vaccination, fostering active research in the field, including further clinical trials for different tumor types and in different clinical settings.
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Affiliation(s)
| | | | | | | | | | | | - Anna Morena D’Alise
- Nouscom, Via di Castel Romano 100, 00128 Rome, Italy; (L.S.); (G.L.); (V.R.); (L.S.); (G.C.); (E.S.)
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Systems Biology Approaches for the Improvement of Oncolytic Virus-Based Immunotherapies. Cancers (Basel) 2023; 15:cancers15041297. [PMID: 36831638 PMCID: PMC9954314 DOI: 10.3390/cancers15041297] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
Oncolytic virus (OV)-based immunotherapy is mainly dependent on establishing an efficient cell-mediated antitumor immunity. OV-mediated antitumor immunity elicits a renewed antitumor reactivity, stimulating a T-cell response against tumor-associated antigens (TAAs) and recruiting natural killer cells within the tumor microenvironment (TME). Despite the fact that OVs are unspecific cancer vaccine platforms, to further enhance antitumor immunity, it is crucial to identify the potentially immunogenic T-cell restricted TAAs, the main key orchestrators in evoking a specific and durable cytotoxic T-cell response. Today, innovative approaches derived from systems biology are exploited to improve target discovery in several types of cancer and to identify the MHC-I and II restricted peptide repertoire recognized by T-cells. Using specific computation pipelines, it is possible to select the best tumor peptide candidates that can be efficiently vectorized and delivered by numerous OV-based platforms, in order to reinforce anticancer immune responses. Beyond the identification of TAAs, system biology can also support the engineering of OVs with improved oncotropism to reduce toxicity and maintain a sufficient portion of the wild-type virus virulence. Finally, these technologies can also pave the way towards a more rational design of armed OVs where a transgene of interest can be delivered to TME to develop an intratumoral gene therapy to enhance specific immune stimuli.
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Cai Y, Chen R, Gao S, Li W, Liu Y, Su G, Song M, Jiang M, Jiang C, Zhang X. Artificial intelligence applied in neoantigen identification facilitates personalized cancer immunotherapy. Front Oncol 2023; 12:1054231. [PMID: 36698417 PMCID: PMC9868469 DOI: 10.3389/fonc.2022.1054231] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/16/2022] [Indexed: 01/10/2023] Open
Abstract
The field of cancer neoantigen investigation has developed swiftly in the past decade. Predicting novel and true neoantigens derived from large multi-omics data became difficult but critical challenges. The rise of Artificial Intelligence (AI) or Machine Learning (ML) in biomedicine application has brought benefits to strengthen the current computational pipeline for neoantigen prediction. ML algorithms offer powerful tools to recognize the multidimensional nature of the omics data and therefore extract the key neoantigen features enabling a successful discovery of new neoantigens. The present review aims to outline the significant technology progress of machine learning approaches, especially the newly deep learning tools and pipelines, that were recently applied in neoantigen prediction. In this review article, we summarize the current state-of-the-art tools developed to predict neoantigens. The standard workflow includes calling genetic variants in paired tumor and blood samples, and rating the binding affinity between mutated peptide, MHC (I and II) and T cell receptor (TCR), followed by characterizing the immunogenicity of tumor epitopes. More specifically, we highlight the outstanding feature extraction tools and multi-layer neural network architectures in typical ML models. It is noted that more integrated neoantigen-predicting pipelines are constructed with hybrid or combined ML algorithms instead of conventional machine learning models. In addition, the trends and challenges in further optimizing and integrating the existing pipelines are discussed.
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Affiliation(s)
- Yu Cai
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Rui Chen
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Shenghan Gao
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Wenqing Li
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Yuru Liu
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Guodong Su
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Mingming Song
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Mengju Jiang
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Chao Jiang
- Department of Neurology, The Second Affiliated Hospital of Xi’an Medical University, Xi’an, Shaanxi, China,*Correspondence: Chao Jiang, ; Xi Zhang,
| | - Xi Zhang
- School of Medicine, Northwest University, Xi’an, Shaanxi, China,*Correspondence: Chao Jiang, ; Xi Zhang,
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Gu W, Xu Y, Chen X, Jiang H. Characteristics of clinical trials for non-small cell lung cancer therapeutic vaccines registered on ClinicalTrials.gov. Front Immunol 2022; 13:936667. [PMID: 36341464 PMCID: PMC9627174 DOI: 10.3389/fimmu.2022.936667] [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: 05/05/2022] [Accepted: 09/26/2022] [Indexed: 11/26/2022] Open
Abstract
Background Even after complete surgical treatment or chemotherapy, Non-Small Cell Lung Cancer (NSCLC) patients are also at substantial risk for recurrence and spread trend. Therapeutic cancer vaccination could increase the anti-tumor immune response and prevent tumor relapse. This study aimed to assess the characteristics of NSCLC therapeutic vaccines registered on ClinicalTrials.gov. Methods We conducted a cross-sectional, descriptive study of clinical trials for Non-Small Cell Lung Cancer Therapeutic Vaccines Registered on ClinicalTrials.gov (https://clinicaltrials.gov/) through March 17, 2022. Results This study encompassed 117 registered trials included for data analysis. The number of trials was significantly correlated with a beginning year (r = 0.504, P < 0.010). Of these trials, 45.30% were completed, 12.82% were terminated, and 8.55% were withdrawn. More than half of trials (52.99%) were funded by industry, and more than half of trials (52.14%) were located in economically developed North America. Regarding study designs of these trials, 27.35% were randomized, 52.14% were single group assignment, 83.76% were without masking, 35.90% were phase 1, and more than half of the trials (56.41%) recruited less than 50 participants. The highest proportion of vaccine types was protein/peptide vaccines (41.88%). Regarding TNM staging, the highest proportion of the trials is stage III-IV (26.50%). Conclusion The number of clinical trials about the cancer therapeutic vaccines was sustained an increase in recent years. The main characteristic of clinical trials for NSCLC therapeutic vaccines is lack of randomized control, lack of mask, and recruiting less than 50 participants. In recent years, the protein/peptide vaccines for NSCLC active immunotherapy have been well studied.
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Affiliation(s)
- Wenyue Gu
- Department of Pathology, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng Third People's Hospital, Yancheng, China
| | - Yangjie Xu
- Department of Oncology, Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, China
| | - Xiaohong Chen
- Intensive Care Unit, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng Third People's Hospital, Yancheng, China
| | - Hao Jiang
- Department of Oncology, Zhejiang Hospital, Hangzhou, China
- *Correspondence: Hao Jiang,
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Diao K, Chen J, Wu T, Wang X, Wang G, Sun X, Zhao X, Wu C, Wang J, Yao H, Gerarduzzi C, Liu XS. Seq2Neo: A Comprehensive Pipeline for Cancer Neoantigen Immunogenicity Prediction. Int J Mol Sci 2022; 23:ijms231911624. [PMID: 36232923 PMCID: PMC9569519 DOI: 10.3390/ijms231911624] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Neoantigens derived from somatic DNA alterations are ideal cancer-specific targets. In recent years, the combination therapy of PD-1/PD-L1 blockers and neoantigen vaccines has shown clinical efficacy in original PD-1/PD-L1 blocker non-responders. However, not all somatic DNA mutations result in immunogenicity among cancer cells and efficient tools to predict the immunogenicity of neoepitopes are still urgently needed. Here, we present the Seq2Neo pipeline, which provides a one-stop solution for neoepitope feature prediction using raw sequencing data. Neoantigens derived from different types of genome DNA alterations, including point mutations, insertion deletions and gene fusions, are all supported. Importantly, a convolutional neural network (CNN)-based model was trained to predict the immunogenicity of neoepitopes and this model showed an improved performance compared to the currently available tools in immunogenicity prediction using independent datasets. We anticipate that the Seq2Neo pipeline could become a useful tool in the prediction of neoantigen immunogenicity and cancer immunotherapy. Seq2Neo is open-source software under an academic free license (AFL) v3.0 and is freely available at Github.
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Affiliation(s)
- Kaixuan Diao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Xuan Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Guangshuai Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Xiaoqin Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Xiangyu Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Chenxu Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Jinyu Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Huizi Yao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Casimiro Gerarduzzi
- Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, QC H4T 1G2, Canada
| | - Xue-Song Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
- Correspondence:
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