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Zhang Y, Jiang L, Huang S, Lian C, Liang H, Xing Y, Liu J, Tian X, Liu Z, Wang R, An Y, Lu F, Pan Y, Han W, Li Z, Yin F. Sulfonium-Stapled Peptides-Based Neoantigen Delivery System for Personalized Tumor Immunotherapy and Prevention. Adv Sci (Weinh) 2024:e2307754. [PMID: 38605600 DOI: 10.1002/advs.202307754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/22/2024] [Indexed: 04/13/2024]
Abstract
Neoantigen peptides hold great potential as vaccine candidates for tumor immunotherapy. However, due to the limitation of antigen cellular uptake and cross-presentation, the progress with neoantigen peptide-based vaccines has obviously lagged in clinical trials. Here, a stapling peptide-based nano-vaccine is developed, comprising a self-assembly nanoparticle driven by the nucleic acid adjuvant-antigen conjugate. This nano-vaccine stimulates a strong tumor-specific T cell response by activating antigen presentation and toll-like receptor signaling pathways. By markedly improving the efficiency of antigen/adjuvant co-delivery to the draining lymph nodes, the nano-vaccine leads to 100% tumor prevention for up to 11 months and without tumor recurrence, heralding the generation of long-term anti-tumor memory. Moreover, the injection of nano-vaccine with signal neoantigen eliminates the established MC-38 tumor (a cell line of murine carcinoma of the colon without exogenous OVA protein expression) in 40% of the mice by inducing potent cytotoxic T lymphocyte infiltration in the tumor microenvironment without substantial systemic toxicity. These findings represent that stapling peptide-based nano-vaccine may serve as a facile, general, and safe strategy to stimulate a strong anti-tumor immune response for the neoantigen peptide-based personalized tumor immunotherapy.
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Affiliation(s)
- Yaping Zhang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, P. R. China
| | - Leying Jiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Siyong Huang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Chenshan Lian
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, P. R. China
| | - Huiting Liang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, P. R. China
| | - Yun Xing
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, P. R. China
| | - Jianbo Liu
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, P. R. China
| | - Xiaojing Tian
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Zhihong Liu
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, P. R. China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, P. R. China
| | - Yuhao An
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, P. R. China
| | - Fei Lu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Youdong Pan
- NeoCura Bio-Medical Technology Co. Ltd., Shenzhen, 518055, P. R. China
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Zigang Li
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, P. R. China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, P. R. China
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2
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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. Mol Ther Oncol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Mikhaylov V, Brambley CA, Keller GLJ, Arbuiso AG, Weiss LI, Baker BM, Levine AJ. Accurate modeling of peptide-MHC structures with AlphaFold. Structure 2024; 32:228-241.e4. [PMID: 38113889 PMCID: PMC10872456 DOI: 10.1016/j.str.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/17/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023]
Abstract
Major histocompatibility complex (MHC) proteins present peptides on the cell surface for T cell surveillance. Reliable in silico prediction of which peptides would be presented and which T cell receptors would recognize them is an important problem in structural immunology. Here, we introduce an AlphaFold-based pipeline for predicting the three-dimensional structures of peptide-MHC complexes for class I and class II MHC molecules. Our method demonstrates high accuracy, outperforming existing tools in class I modeling accuracy and class II peptide register prediction. We validate its performance and utility with new experimental data on a recently described cancer neoantigen/wild-type peptide pair and explore applications toward improving peptide-MHC binding prediction.
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Affiliation(s)
- Victor Mikhaylov
- The Simons Center for Systems Biology, Institute for Advanced Study, 1 Einstein Drive, Princeton, NJ 08540, USA.
| | - Chad A Brambley
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Grant L J Keller
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Alyssa G Arbuiso
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Laura I Weiss
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Arnold J Levine
- The Simons Center for Systems Biology, Institute for Advanced Study, 1 Einstein Drive, Princeton, NJ 08540, USA
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4
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Ponomarev AV, Shubina IZ, Sokolova ZA, Baryshnikova MA, Kosorukov VS. Transplantable Murine Tumors in the Studies of Peptide Antitumor Vaccines. Oncol Rev 2024; 17:12189. [PMID: 38260723 PMCID: PMC10800450 DOI: 10.3389/or.2023.12189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Numerous studies have shown that antitumor vaccines based on synthetic peptides are safe and can induce both CD8+ and CD4+ tumor-specific T cell responses. However, clinical results are still scarce, and such approach to antitumor treatment has not gained a wide implication, yet. Recently, particular advances have been achieved due to tumor sequencing and the search for immunogenic neoantigens caused by mutations. One of the most important issues for peptide vaccines, along with the choice of optimal adjuvants and vaccination regimens, is the search for effective target antigens. Extensive studies of peptide vaccines, including those on murine models, are required to reveal the effective vaccine constructs. The review presents transplantable murine tumors with the detected peptides that showed antitumor efficacy as a vaccine compound.
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5
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Pulakuntla S, Syed K, Reddy VD. Analysis of Somatic Mutations in the TCGA-LIHC Whole Exome Sequence to Identify the Neoantigen for Immunotherapy in Hepatocellular Carcinoma. Curr Issues Mol Biol 2023; 46:106-120. [PMID: 38248311 PMCID: PMC10813969 DOI: 10.3390/cimb46010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/08/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
There are numerous clinically proven methods for treating cancer worldwide. Immunotherapy has been used to treat cancer with significant success in the current studies. The purpose of this work is to identify somatically altered target gene neoantigens and investigate liver cancer-related immune cell interaction and functional changes for potential immunotherapy in future clinical trials. Clinical patient data from the Cancer Genome Atlas (TCGA) database were used in this investigation. The R maf utility package was used to perform somatic analysis. The 17-mer peptide neoantigens were extracted using an in-house Python software called Peptide.py. Additionally, the epitope analysis was conducted using NetMHCpan4.1 program. Neopeptide immunogenicity was assessed using DeepCNN-Ineo, and tumor immune interaction, association with immune cells, correlation, and survival analysis were assessed using the TIMER web server. Based on somatic mutation analysis, we have identified the top 10 driver genes (TP53, TNN, CTNNB1, MUC16, ALB, PCLO, MUC4, ABCA13, APOB, and RYR2). From the superfamily of 20 HLA (Human leukocyte antigens) allele epitopes, we discovered 5653 neopeptides. Based on T cell receptor face hydrophobic analysis, these neopeptides were subjected to immunogenicity investigation. A mutation linked to tumor growth may have an impact on immune cells. According to this study's correlation and survival analysis, all driver genes may function as immune targets for liver cancer. These genes are recognized to be immune targets. In the future, immune checkpoint inhibitors may be developed to prolong patient survival times and prevent hepatocellular carcinoma (HCC) through immunotherapy.
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Affiliation(s)
- Swetha Pulakuntla
- School of Applied Sciences, REVA University, Bangalore 560064, Karnataka, India;
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Vaddi Damodara Reddy
- School of Applied Sciences, REVA University, Bangalore 560064, Karnataka, India;
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa 3886, South Africa
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6
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Shah RK, Cygan E, Kozlik T, Colina A, Zamora AE. Utilizing immunogenomic approaches to prioritize targetable neoantigens for personalized cancer immunotherapy. Front Immunol 2023; 14:1301100. [PMID: 38149253 PMCID: PMC10749952 DOI: 10.3389/fimmu.2023.1301100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Advancements in sequencing technologies and bioinformatics algorithms have expanded our ability to identify tumor-specific somatic mutation-derived antigens (neoantigens). While recent studies have shown neoantigens to be compelling targets for cancer immunotherapy due to their foreign nature and high immunogenicity, the need for increasingly accurate and cost-effective approaches to rapidly identify neoantigens remains a challenging task, but essential for successful cancer immunotherapy. Currently, gene expression analysis and algorithms for variant calling can be used to generate lists of mutational profiles across patients, but more care is needed to curate these lists and prioritize the candidate neoantigens most capable of inducing an immune response. A growing amount of evidence suggests that only a handful of somatic mutations predicted by mutational profiling approaches act as immunogenic neoantigens. Hence, unbiased screening of all candidate neoantigens predicted by Whole Genome Sequencing/Whole Exome Sequencing may be necessary to more comprehensively access the full spectrum of immunogenic neoepitopes. Once putative cancer neoantigens are identified, one of the largest bottlenecks in translating these neoantigens into actionable targets for cell-based therapies is identifying the cognate T cell receptors (TCRs) capable of recognizing these neoantigens. While many TCR-directed screening and validation assays have utilized bulk samples in the past, there has been a recent surge in the number of single-cell assays that provide a more granular understanding of the factors governing TCR-pMHC interactions. The goal of this review is to provide an overview of existing strategies to identify candidate neoantigens using genomics-based approaches and methods for assessing neoantigen immunogenicity. Additionally, applications, prospects, and limitations of some of the current single-cell technologies will be discussed. Finally, we will briefly summarize some of the recent models that have been used to predict TCR antigen specificity and analyze the TCR receptor repertoire.
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Affiliation(s)
- Ravi K. Shah
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Erin Cygan
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Tanya Kozlik
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Alfredo Colina
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Anthony E. Zamora
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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7
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Yossef R, Krishna S, Sindiri S, Lowery FJ, Copeland AR, Gartner JJ, Parkhurst MR, Parikh NB, Hitscherich KJ, Levi ST, Chatani PD, Zacharakis N, Levin N, Vale NR, Nah SK, Dinerman A, Hill VK, Ray S, Bera A, Levy L, Jia L, Kelly MC, Goff SL, Robbins PF, Rosenberg SA. Phenotypic signatures of circulating neoantigen-reactive CD8 + T cells in patients with metastatic cancers. Cancer Cell 2023; 41:2154-2165.e5. [PMID: 38039963 PMCID: PMC10843665 DOI: 10.1016/j.ccell.2023.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 08/07/2023] [Accepted: 11/07/2023] [Indexed: 12/03/2023]
Abstract
Circulating T cells from peripheral blood (PBL) can provide a rich and noninvasive source for antitumor T cells. By single-cell transcriptomic profiling of 36 neoantigen-specific T cell clones from 6 metastatic cancer patients, we report the transcriptional and cell surface signatures of antitumor PBL-derived CD8+ T cells (NeoTCRPBL). Comparison of tumor-infiltrating lymphocyte (TIL)- and PBL-neoantigen-specific T cells revealed that NeoTCRPBL T cells are low in frequency and display less-dysfunctional memory phenotypes relative to their TIL counterparts. Analysis of 100 antitumor TCR clonotypes indicates that most NeoTCRPBL populations target the same neoantigens as TILs. However, NeoTCRPBL TCR repertoire is only partially shared with TIL. Prediction and testing of NeoTCRPBL signature-derived TCRs from PBL of 6 prospective patients demonstrate high enrichment of clonotypes targeting tumor mutations, a viral oncogene, and patient-derived tumor. Thus, the NeoTCRPBL signature provides an alternative source for identifying antitumor T cells from PBL of cancer patients, enabling immune monitoring and immunotherapies.
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Affiliation(s)
- Rami Yossef
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sri Krishna
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sivasish Sindiri
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank J Lowery
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R Copeland
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jared J Gartner
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria R Parkhurst
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neilesh B Parikh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyle J Hitscherich
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shoshana T Levi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Praveen D Chatani
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nikolaos Zacharakis
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noam Levin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nolan R Vale
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shirley K Nah
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aaron Dinerman
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Victoria K Hill
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Satyajit Ray
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alakesh Bera
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lior Levy
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Jia
- National Institutes of Health Library, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael C Kelly
- Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory, Bethesda, MD 20892, USA
| | - Stephanie L Goff
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul F Robbins
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven A Rosenberg
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [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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9
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Zhu Y, Li X, Chen T, Wang J, Zhou Y, Mu X, Du Y, Wang J, Tang J, Liu J. Personalised neoantigen-based therapy in colorectal cancer. Clin Transl Med 2023; 13:e1461. [PMID: 37921274 PMCID: PMC10623652 DOI: 10.1002/ctm2.1461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023] Open
Abstract
Colorectal cancer (CRC) has become one of the most common tumours with high morbidity, mortality and distinctive evolution mechanism. The neoantigens arising from the somatic mutations have become considerable treatment targets in the management of CRC. As cancer-specific aberrant peptides, neoantigens can trigger the robust host immune response and exert anti-tumour effects while minimising the emergence of adverse events commonly associated with alternative therapeutic regimens. In this review, we summarised the mechanism, generation, identification and prognostic significance of neoantigens, as well as therapeutic strategies challenges of neoantigen-based therapy in CRC. The evidence suggests that the establishment of personalised neoantigen-based therapy holds great promise as an effective treatment approach for patients with CRC.
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Affiliation(s)
- Ya‐Juan Zhu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiong Li
- Department of GastroenterologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Ting‐Ting Chen
- The Second Clinical Medical College of Lanzhou UniversityLanzhouChina
| | - Jia‐Xiang Wang
- Department of Renal Cancer and MelanomaPeking University Cancer Hospital & InstituteBeijingChina
| | - Yi‐Xin Zhou
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiao‐Li Mu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yang Du
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jia‐Ling Wang
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jie Tang
- Clinical Trial CenterWest China HospitalSichuan UniversityChengduChina
| | - Ji‐Yan Liu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
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10
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Jia M, Liang J, Li Z, Qin Y, Li Q, Wang J, Lu X. Screening tumor stage-specific candidate neoantigens in thyroid adenocarcinoma using integrated exome and transcriptome sequencing. Front Immunol 2023; 14:1187160. [PMID: 37854594 PMCID: PMC10579579 DOI: 10.3389/fimmu.2023.1187160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023] Open
Abstract
Background The incidence of thyroid carcinoma (THCA), the most common endocrine tumor, is continuously increasing worldwide. Although the overall prognosis of THCA is good, patients with distant metastases exhibit a mortality rate of 5-20%. Methods To improve the diagnosis and overall prognosis of patients with thyroid cancer, we screened specific candidate neoantigen genes in early- and late-stage THCA by analyzing the transcriptome and somatic cell mutations in this study. Results The top five early-stage neoantigen-related genes (NRGs) were G protein-coupled receptor 4 [GPR4], chondroitin sulfate proteoglycan 4 [CSPG4], teneurin transmembrane protein 1 [TENM1], protein S 1 [PROS1], and thymidine kinase 1 [TK1], whereas the top five late-stage NRGs were cadherin 6 [CDH6], semaphorin 6B [SEMA6B], dysferlin [DYSF], xenotropic and polytropic retrovirus receptor 1 [XPR1], and ABR activator of RhoGEF and GTPase [ABR]. Subsequently, we used machine learning models to verify their ability to screen NRGs and analyze the correlations among NRGs, immune cell types, and immune checkpoint regulators. The use of candidate antigen genes resulted in a better diagnostic model (the area under the curve [AUC] value of the early-stage group [0.979] was higher than that of the late-stage group [0.959]). Then, a prognostic model was constructed to predict NRG survival, and the 1-, 3- and 5-year AUC values were 0.83, 0.87, and 0.86, respectively, which were closely related to different immune cell types. Comparison of the expression trends and mutation frequencies of NRGs in multiple tumors revealed their potential for the development of broad spectrum therapeutic drugs. Conclusion In conclusion, the candidate NRGs identified in this study could potentially be used as therapeutic targets and diagnostic biomarkers for the development of novel broad spectrum therapeutic agents.
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Affiliation(s)
- Meng Jia
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiawen Liang
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Zhuyao Li
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ye Qin
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qianqian Li
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianwei Wang
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou, China
| | - Xiubo Lu
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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11
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Jaton F. Groundwork for AI: Enforcing a benchmark for neoantigen prediction in personalized cancer immunotherapy. Soc Stud Sci 2023; 53:787-810. [PMID: 37650579 PMCID: PMC10543129 DOI: 10.1177/03063127231192857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
This article expands on recent studies of machine learning or artificial intelligence (AI) algorithms that crucially depend on benchmark datasets, often called 'ground truths.' These ground-truth datasets gather input-data and output-targets, thereby establishing what can be retrieved computationally and evaluated statistically. I explore the case of the Tumor nEoantigen SeLection Alliance (TESLA), a consortium-based ground-truthing project in personalized cancer immunotherapy, where the 'truth' of the targets-immunogenic neoantigens-to be retrieved by the would-be AI algorithms depended on a broad technoscientific network whose setting up implied important organizational and material infrastructures. The study shows that instead of grounding an undisputable 'truth', the TESLA endeavor ended up establishing a contestable reference, the biology of neoantigens and how to measure their immunogenicity having slightly evolved alongside this four-year project. However, even if this controversy played down the scope of the TESLA ground truth, it did not discredit the whole undertaking. The magnitude of the technoscientific efforts that the TESLA project set into motion and the needs it ultimately succeeded in filling for the scientific and industrial community counterbalanced its metrological uncertainties, effectively instituting its contestable representation of 'true' neoantigens within the field of personalized cancer immunotherapy (at least temporarily). More generally, this case study indicates that the enforcement of ground truths, and what it leaves out, is a necessary condition to enable AI technologies in personalized medicine.
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Affiliation(s)
- Florian Jaton
- Graduate Institute of International and Development Studies, Geneva, Switzerland
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12
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Ratajska M, Sette C, Cunliffe HE. Editorial: 365 days of progress in cancer genetics. Front Oncol 2023; 13:1270902. [PMID: 37823056 PMCID: PMC10562717 DOI: 10.3389/fonc.2023.1270902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 10/13/2023] Open
Affiliation(s)
- Magdalena Ratajska
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, University of the Sacred Hearth, Rome, Italy
- Gemelli Science and Technology Park (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Heather E. Cunliffe
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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13
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Anzar I, Malone B, Samarakoon P, Vardaxis I, Simovski B, Fontenelle H, Meza-Zepeda LA, Stratford R, Keung EZ, Burgess M, Tawbi HA, Myklebost O, Clancy T. The interplay between neoantigens and immune cells in sarcomas treated with checkpoint inhibition. Front Immunol 2023; 14:1226445. [PMID: 37799721 PMCID: PMC10548483 DOI: 10.3389/fimmu.2023.1226445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 07/10/2023] [Indexed: 10/07/2023] Open
Abstract
Introduction Sarcomas are comprised of diverse bone and connective tissue tumors with few effective therapeutic options for locally advanced unresectable and/or metastatic disease. Recent advances in immunotherapy, in particular immune checkpoint inhibition (ICI), have shown promising outcomes in several cancer indications. Unfortunately, ICI therapy has provided only modest clinical responses and seems moderately effective in a subset of the diverse subtypes. Methods To explore the immune parameters governing ICI therapy resistance or immune escape, we performed whole exome sequencing (WES) on tumors and their matched normal blood, in addition to RNA-seq from tumors of 31 sarcoma patients treated with pembrolizumab. We used advanced computational methods to investigate key immune properties, such as neoantigens and immune cell composition in the tumor microenvironment (TME). Results A multifactorial analysis suggested that expression of high quality neoantigens in the context of specific immune cells in the TME are key prognostic markers of progression-free survival (PFS). The presence of several types of immune cells, including T cells, B cells and macrophages, in the TME were associated with improved PFS. Importantly, we also found the presence of both CD8+ T cells and neoantigens together was associated with improved survival compared to the presence of CD8+ T cells or neoantigens alone. Interestingly, this trend was not identified with the combined presence of CD8+ T cells and TMB; suggesting that a combined CD8+ T cell and neoantigen effect on PFS was important. Discussion The outcome of this study may inform future trials that may lead to improved outcomes for sarcoma patients treated with ICI.
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Affiliation(s)
- Irantzu Anzar
- Oslo Cancer Cluster, NEC OncoImmunity AS, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | | | | | | | - Leonardo A. Meza-Zepeda
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Genomics Core Facility, Department of Core Facilities, Oslo University Hospital, Oslo, Norway
| | | | - Emily Z. Keung
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Melissa Burgess
- Department of Medical Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Hussein A. Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ola Myklebost
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Trevor Clancy
- Oslo Cancer Cluster, NEC OncoImmunity AS, Oslo, Norway
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14
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Barrio-Calvo M, Kofoed SV, Holste SC, Sørensen AB, Viborg N, Kringelum JV, Kleine-Kohlbrecher D, Steenmans CS, Thygesen CB, Rønø B, Friis S. Corrigendum: Targeting neoantigens to APC-surface molecules improves the immunogenicity and anti-tumor efficacy of a DNA cancer vaccine. Front Immunol 2023; 14:1290431. [PMID: 37781410 PMCID: PMC10539896 DOI: 10.3389/fimmu.2023.1290431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 10/03/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fimmu.2023.1234912.].
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15
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Mistretta B, Rankothgedera S, Castillo M, Rao M, Holloway K, Bhardwaj A, El Noafal M, Albarracin C, El-Zein R, Rezaei H, Su X, Akbani R, Shao XM, Czerniecki BJ, Karchin R, Bedrosian I, Gunaratne PH. Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer. Front Immunol 2023; 14:1188831. [PMID: 37744342 PMCID: PMC10512078 DOI: 10.3389/fimmu.2023.1188831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/27/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction We present here a strategy to identify immunogenic neoantigen candidates from unique amino acid sequences at the junctions of fusion proteins which can serve as targets in the development of tumor vaccines for the treatment of breastcancer. Method We mined the sequence reads of breast tumor tissue that are usually discarded as discordant paired-end reads and discovered cancer specific fusion transcripts using tissue from cancer free controls as reference. Binding affinity predictions of novel peptide sequences crossing the fusion junction were analyzed by the MHC Class I binding predictor, MHCnuggets. CD8+ T cell responses against the 15 peptides were assessed through in vitro Enzyme Linked Immunospot (ELISpot). Results We uncovered 20 novel fusion transcripts from 75 breast tumors of 3 subtypes: TNBC, HER2+, and HR+. Of these, the NSFP1-LRRC37A2 fusion transcript was selected for further study. The 3833 bp chimeric RNA predicted by the consensus fusion junction sequence is consistent with a read-through transcription of the 5'-gene NSFP1-Pseudo gene NSFP1 (NSFtruncation at exon 12/13) followed by trans-splicing to connect withLRRC37A2 located immediately 3' through exon 1/2. A total of 15 different 8-mer neoantigen peptides discovered from the NSFP1 and LRRC37A2 truncations were predicted to bind to a total of 35 unique MHC class I alleles with a binding affinity of IC50<500nM.); 1 of which elicited a robust immune response. Conclusion Our data provides a framework to identify immunogenic neoantigen candidates from fusion transcripts and suggests a potential vaccine strategy to target the immunogenic neopeptides in patients with tumors carrying the NSFP1-LRRC37A2 fusion.
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Affiliation(s)
- Brandon Mistretta
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Sakuni Rankothgedera
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Micah Castillo
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Mitchell Rao
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Kimberly Holloway
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Anjana Bhardwaj
- Department of Breast Surgical Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Maha El Noafal
- Department of Medicine, Houston Methodist Research Institute, Houston, TX, United States
| | - Constance Albarracin
- Department of Pathology, The UT MD Anderson Cancer Center, Houston, TX, United States
| | - Randa El-Zein
- Department of Medicine, Houston Methodist Research Institute, Houston, TX, United States
| | - Hengameh Rezaei
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
| | - Xiaoping Su
- Department of Bioinformatics & Computational Biology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Rehan Akbani
- Department of Bioinformatics & Computational Biology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Xiaoshan M. Shao
- Biomedical Engineering Department, Institute for Computational Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Brian J. Czerniecki
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Rachel Karchin
- Biomedical Engineering Department, Institute for Computational Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Isabelle Bedrosian
- Department of Breast Surgical Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Preethi H. Gunaratne
- Department of Biology & Biochemistry, University of Houston, Houston, TX, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
- Department of Breast Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, United States
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16
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Zhou LY, Zou F, Sun W. Prioritizing candidate peptides for cancer vaccines through predicting peptide presentation by HLA-I proteins. Biometrics 2023; 79:2664-2676. [PMID: 35833513 PMCID: PMC10548401 DOI: 10.1111/biom.13717] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 07/01/2022] [Indexed: 11/02/2022]
Abstract
Cancer (treatment) vaccines that are made of neoantigens, or peptides unique to tumor cells due to somatic mutations, have emerged as a promising method to reinvigorate the immune response against cancer. A key step to prioritizing neoantigens for cancer vaccines is computationally predicting which neoantigens are presented on the cell surface by a human leukocyte antigen (HLA). We propose to address this challenge by training a neural network using mass spectrometry (MS) data composed of peptides presented by at least one of several HLAs of a subject. We embed the neural network within a mixture model and train the neural network by maximizing the likelihood of the mixture model. After evaluating our method using data sets where the peptide presentation status was known, we applied it to analyze somatic mutations of 60 melanoma patients and identified a group of neoantigens more immunogenic in tumor cells than in normal cells. Moreover, neoantigen burden estimated by our method was significantly associated with a measurement of the immune system activity, suggesting these neoantigens could induce an immune response.
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Affiliation(s)
- Laura Y. Zhou
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Fei Zou
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Wei Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Biostatistics Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle, Washington
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17
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Barrio-Calvo M, Kofoed SV, Holste SC, Sørensen AB, Viborg N, Kringelum JV, Kleine-Kohlbrecher D, Steenmans CS, Thygesen CB, Rønø B, Friis S. Targeting neoantigens to APC-surface molecules improves the immunogenicity and anti-tumor efficacy of a DNA cancer vaccine. Front Immunol 2023; 14:1234912. [PMID: 37720215 PMCID: PMC10499626 DOI: 10.3389/fimmu.2023.1234912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
Introduction Tumor-specific mutations generate neoepitopes unique to the cancer that can be recognized by the immune system, making them appealing targets for therapeutic cancer vaccines. Since the vast majority of tumor mutations are patient-specific, it is crucial for cancer vaccine designs to be compatible with individualized treatment strategies. Plasmid DNA vaccines have substantiated the immunogenicity and tumor eradication capacity of cancer neoepitopes in preclinical models. Moreover, early clinical trials evaluating personalized neoepitope vaccines have indicated favorable safety profiles and demonstrated their ability to elicit specific immune responses toward the vaccine neoepitopes. Methods By fusing in silico predicted neoepitopes to molecules with affinity for receptors on the surface of APCs, such as chemokine (C-C motif) ligand 19 (CCL19), we designed an APC-targeting cancer vaccine and evaluated their ability to induce T-cell responses and anti-tumor efficacy in the BALB/c syngeneic preclinical tumor model. Results In this study, we demonstrate how the addition of an antigen-presenting cell (APC) binding molecule to DNA-encoded cancer neoepitopes improves neoepitope-specific T-cell responses and the anti-tumor efficacy of plasmid DNA vaccines. Dose-response evaluation and longitudinal analysis of neoepitope-specific T-cell responses indicate that combining APC-binding molecules with the delivery of personalized tumor antigens holds the potential to improve the clinical efficacy of therapeutic DNA cancer vaccines. Discussion Our findings indicate the potential of the APC-targeting strategy to enhance personalized DNA cancer vaccines while acknowledging the need for further research to investigate its molecular mechanism of action and to translate the preclinical results into effective treatments for cancer patients.
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18
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Goldberger Z, Hauert S, Chang K, Kurtanich T, Alpar AT, Repond G, Wang Y, Gomes S, Krishnakumar R, Siddarth P, Swartz MA, Hubbell JA, Briquez PS. Membrane-localized neoantigens predict the efficacy of cancer immunotherapy. Cell Rep Med 2023; 4:101145. [PMID: 37552990 PMCID: PMC10439248 DOI: 10.1016/j.xcrm.2023.101145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 12/24/2022] [Accepted: 07/13/2023] [Indexed: 08/10/2023]
Abstract
Immune checkpoint immunotherapy (ICI) can re-activate immune reactions against neoantigens, leading to remarkable remission in cancer patients. Nevertheless, only a minority of patients are responsive to ICI, and approaches for prediction of responsiveness are needed to improve the success of cancer treatments. While the tumor mutational burden (TMB) correlates positively with responsiveness and survival of patients undergoing ICI, the influence of the subcellular localizations of the neoantigens remains unclear. Here, we demonstrate in both a mouse melanoma model and human clinical datasets of 1,722 ICI-treated patients that a high proportion of membrane-localized neoantigens, particularly at the plasma membrane, correlate with responsiveness to ICI therapy and improved overall survival across multiple cancer types. We further show that combining membrane localization and TMB analyses can enhance the predictability of cancer patient response to ICI. Our results may have important implications for establishing future clinical guidelines to direct the choice of treatment toward ICI.
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Affiliation(s)
- Zoe Goldberger
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA; Department of Bioengineering, McGill University, Montreal, QC, Canada
| | - Sylvie Hauert
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Kevin Chang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Trevin Kurtanich
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Aaron T Alpar
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Grégoire Repond
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Yue Wang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Suzana Gomes
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | | | - Prabha Siddarth
- Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
| | - Melody A Swartz
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA; Ben May Department of Cancer Research, University of Chicago, Chicago, IL, USA; Committee on Immunology, University of Chicago, Chicago, IL, USA; Committee on Cancer Biology, University of Chicago, Chicago, IL, USA
| | - Jeffrey A Hubbell
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA; Committee on Immunology, University of Chicago, Chicago, IL, USA; Committee on Cancer Biology, University of Chicago, Chicago, IL, USA.
| | - Priscilla S Briquez
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA; Department of General and Visceral Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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Nguyen KB, Roerden M, Copeland CJ, Backlund CM, Klop-Packel NG, Remba T, Kim B, Singh NK, Birnbaum ME, Irvine DJ, Spranger S. Decoupled neoantigen cross-presentation by dendritic cells limits anti-tumor immunity against tumors with heterogeneous neoantigen expression. eLife 2023; 12:e85263. [PMID: 37548358 PMCID: PMC10425174 DOI: 10.7554/elife.85263] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 08/06/2023] [Indexed: 08/08/2023] Open
Abstract
Cancer immunotherapies, in particular checkpoint blockade immunotherapy (CBT), can induce control of cancer growth, with a fraction of patients experiencing durable responses. However, the majority of patients currently do not respond to CBT and the molecular determinants of resistance have not been fully elucidated. Mounting clinical evidence suggests that the clonal status of neoantigens (NeoAg) impacts the anti-tumor T cell response. High intratumor heterogeneity (ITH), where the majority of NeoAgs are expressed subclonally, is correlated with poor clinical response to CBT and poor infiltration with tumor-reactive T cells. However, the mechanism by which ITH blunts tumor-reactive T cells is unclear. We developed a transplantable murine lung cancer model to characterize the immune response against a defined set of NeoAgs expressed either clonally or subclonally to model low or high ITH, respectively. Here we show that clonal expression of a weakly immunogenic NeoAg with a relatively strong NeoAg increased the immunogenicity of tumors with low but not high ITH. Mechanistically we determined that clonal NeoAg expression allowed cross-presenting dendritic cells to acquire and present both NeoAgs. Dual NeoAg presentation by dendritic cells was associated with a more mature DC phenotype and a higher stimulatory capacity. These data suggest that clonal NeoAg expression can induce more potent anti-tumor responses due to more stimulatory dendritic cell:T cell interactions. Therapeutic vaccination targeting subclonally expressed NeoAgs could be used to boost anti-tumor T cell responses.
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Affiliation(s)
- Kim Bich Nguyen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Malte Roerden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
| | | | - Coralie M Backlund
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering, MITCambridgeUnited States
| | - Nory G Klop-Packel
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Tanaka Remba
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Byungji Kim
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Nishant K Singh
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Michael E Birnbaum
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering, MITCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | - Darrell J Irvine
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering, MITCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | - Stefani Spranger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Ludwig Center at MIT’s Koch Institute for Integrative Cancer ResearchCambridgeUnited States
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20
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Casiraghi F, Perico N, Remuzzi G. Editorial: Global excellence in translational immunology: Europe. Front Immunol 2023; 14:1250624. [PMID: 37554325 PMCID: PMC10406128 DOI: 10.3389/fimmu.2023.1250624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/12/2023] [Indexed: 08/10/2023] Open
Affiliation(s)
- Federica Casiraghi
- Istituto di Ricerche Farmacologiche Mario Negri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Bergamo, Italy
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21
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Wolf Y, Sameuls Y. Neoantigens in Cancer Immunotherapy: Quantity vs. Quality. Mol Oncol 2023. [PMID: 37370255 PMCID: PMC10399717 DOI: 10.1002/1878-0261.13483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Traditional immunotherapies provide clinical benefits to only a few patients with solid tumors, highlighting the urgent need for more effective approaches. Traditional immunotherapies rely on the presence of cancer antigens, with neoantigens being highly important in this context as they are specific to malignant tissue but not healthy tissue. The quantity of neoantigens is often associated with clinical benefit, but it cannot fully explain or predict patient response. In this Viewpoint, we highlight several qualitative aspects that should be considered in neoantigen-based therapy. We emphasize the distinction between private and recurrent neoantigens, discuss the importance of neoantigen clonality, and describe new subtypes of neopeptides that further diversify the potential of neoantigens in immunotherapy.
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Affiliation(s)
- Yochai Wolf
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Ramat Gan, 5265601, Israel
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Israel
| | - Yardena Sameuls
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 761000, Israel
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22
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Alturki NA. Review of the Immune Checkpoint Inhibitors in the Context of Cancer Treatment. J Clin Med 2023; 12:4301. [PMID: 37445336 DOI: 10.3390/jcm12134301] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Checkpoint proteins are an integral part of the immune system and are used by the tumor cells to evade immune response, which helps them grow uncontrollably. By blocking these proteins, immune checkpoint inhibitors can restore the capability of the immune system to attack cancer cells and stop their growth. These findings are backed by adequate clinical trial data and presently, several FDA-approved immune checkpoint inhibitors exist in the market for treating various types of cancers, including melanoma, hepatocellular, endometrial, lung, kidney and others. Their mode of action is inhibition by targeting the checkpoint proteins CTLA-4, PD-1, PD-L1, etc. They can be used alone as well as in amalgamation with other cancer treatments, like surgery, radiation or chemotherapy. Since these drugs target only specific immune system proteins, their side effects are reduced in comparison with the traditional chemotherapy drugs, but may still cause a few affects like fatigue, skin rashes, and fever. In rare cases, these inhibitors are known to have caused more serious side effects, such as cardiotoxicity, and inflammation in the intestines or lungs. Herein, we provide an overview of these inhibitors and their role as biomarkers, immune-related adverse outcomes and clinical studies in the treatment of various cancers, as well as present some future perspectives.
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Affiliation(s)
- Norah A Alturki
- Clinical Laboratory Science Department, College of Applied Medical Sciences, King Saud University, Riyadh 11433, Saudi Arabia
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23
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Okada M, Shimizu K, Nakazato H, Yamasaki S, Fujii SI. Detection of mutant antigen-specific T cell receptors against multiple myeloma for T cell engineering. Mol Ther Methods Clin Dev 2023; 29:541-555. [PMID: 37359417 PMCID: PMC10285226 DOI: 10.1016/j.omtm.2023.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/12/2023] [Indexed: 06/28/2023]
Abstract
Multiple myeloma (MM) remains an incurable hematological neoplasm. Neoantigen-specific T cell receptor (TCR)-engineered T (TCR-T) cell therapy is a potential alternative treatment. Particularly, TCRs derived from a third-party donor may cover broad ranges of neoantigens, whereas TCRs in patients suffering from immune disorders are limited. However, the efficacy and feasibility of treating MM have not been evaluated thoroughly. In this study, we established a system for identifying immunogenic mutant antigens on MM cells and their corresponding TCRs using healthy donor-derived peripheral blood mononuclear cells (PBMCs). Initially, the immune responses to 35 candidate peptides predicted by the immunogenomic analysis were investigated. Peptide-reactive T lymphocytes were enriched, and subsequently, TCR repertoires were determined by single-cell TCR sequencing. Eleven reconstituted TCRs showed mutation-specific responses against 4 peptides. Particularly, we verified the HLA-A∗24:02-binding QYSPVQATF peptide derived from COASY S55Y as the naturally processed epitope across MM cells, making it a promising immune target. Corresponding TCRs specifically recognized COASY S55Y+HLA-A∗24:02+ MM cells and augmented tumoricidal activity. Finally, adoptive cell transfer of TCR-T cells showed objective responses in the xenograft model. We initiatively proposed the utility of tumor mutated antigen-specific TCR genes to suppress MM. Our unique strategy will facilitate further identification of neoantigen-specific TCRs.
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Affiliation(s)
- Masahiro Okada
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kanako Shimizu
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroshi Nakazato
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Satoru Yamasaki
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shin-ichiro Fujii
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Program for Drug Discovery and Medical Technology Platforms, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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24
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Diao L, Liu M. Rethinking Antigen Source: Cancer Vaccines Based on Whole Tumor Cell/tissue Lysate or Whole Tumor Cell. Adv Sci (Weinh) 2023:e2300121. [PMID: 37254712 PMCID: PMC10401146 DOI: 10.1002/advs.202300121] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/29/2023] [Indexed: 06/01/2023]
Abstract
Cancer immunotherapies have improved human health, and one among the important technologies for cancer immunotherapy is cancer vaccine. Antigens are the most important components in cancer vaccines. Generally, antigens in cancer vaccines can be divided into two categories: pre-defined antigens and unidentified antigens. Although, cancer vaccines loaded with predefined antigens are commonly used, cancer vaccine loaded with mixed unidentified antigens, especially whole cancer cells or cancer cell lysates, is a very promising approach, and such vaccine can obviate some limitations in cancer vaccines. Their advantages include, but are not limited to, the inclusion of pan-spectra (all or most kinds of) antigens, inducing pan-clones specific T cells, and overcoming the heterogeneity of cancer cells. In this review, the recent advances in cancer vaccines based on whole-tumor antigens, either based on whole cancer cells or whole cancer cell lysates, are summarized. In terms of whole cancer cell lysates, the focus is on applying whole water-soluble cell lysates as antigens. Recently, utilizing the whole cancer cell lysates as antigens in cancer vaccines has become feasible. Considering that pre-determined antigen-based cancer vaccines (mainly peptide-based or mRNA-based) have various limitations, developing cancer vaccines based on whole-tumor antigens is a promising alternative.
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Affiliation(s)
- Lu Diao
- Department of Pharmaceutics, College of Pharmaceutical Sciences, Soochow University, 199 of Ren ai Road, Suzhou, Jiangsu, 215123, P. R. China
- Kunshan Hospital of Traditional Chinese Medicine, Kunshan, Jiangsu, 215300, P. R. China
- Suzhou Ersheng Biopharmaceutical Co., Ltd., Suzhou, 215123, P. R. China
| | - Mi Liu
- Department of Pharmaceutics, College of Pharmaceutical Sciences, Soochow University, 199 of Ren ai Road, Suzhou, Jiangsu, 215123, P. R. China
- Kunshan Hospital of Traditional Chinese Medicine, Kunshan, Jiangsu, 215300, P. R. China
- Suzhou Ersheng Biopharmaceutical Co., Ltd., Suzhou, 215123, P. R. China
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25
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Georgopoulos AP, James LM, Charonis SA, Sanders M. Melanoma and Human Leukocyte Antigen (HLA): Immunogenicity of 69 HLA Class I Alleles With 11 Antigens Expressed in Melanoma Tumors. Cancer Inform 2023; 22:11769351231172604. [PMID: 37251656 PMCID: PMC10214068 DOI: 10.1177/11769351231172604] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 04/12/2023] [Indexed: 05/31/2023] Open
Abstract
Host immunogenetics play a critical role in the human immune response to melanoma, influencing both melanoma prevalence and immunotherapy outcomes. Beneficial outcomes that stimulate T cell response hinge on binding affinity and immunogenicity of human leukocyte antigen (HLA) with melanoma antigen epitopes. Here, we use an in silico approach to characterize binding affinity and immunogenicity of 69 HLA Class I human leukocyte antigen alleles to epitopes of 11 known melanoma antigens. The findings document a significant proportion of positively immunogenic epitope-allele combinations, with the highest proportions of positive immunogenicity found for the Q13072/BAGE1 melanoma antigen and alleles of the HLA B and C genes. The findings are discussed in terms of a personalized precision HLA-mediated adjunct to immune checkpoint blockade immunotherapy to maximize tumor elimination.
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Affiliation(s)
- Apostolos P Georgopoulos
- The HLA Research Group, Brain Sciences
Center, Department of Veterans Affairs Health Care System, Minneapolis, MN,
USA
- Department of Neuroscience, University
of Minnesota Medical School, Minneapolis, MN, USA
- Department of Psychiatry, University of
Minnesota Medical School, Minneapolis, MN, USA
- Department of Neurology, University of
Minnesota Medical School, Minneapolis, MN, USA
| | - Lisa M James
- The HLA Research Group, Brain Sciences
Center, Department of Veterans Affairs Health Care System, Minneapolis, MN,
USA
- Department of Neuroscience, University
of Minnesota Medical School, Minneapolis, MN, USA
- Department of Psychiatry, University of
Minnesota Medical School, Minneapolis, MN, USA
| | - Spyros A Charonis
- The HLA Research Group, Brain Sciences
Center, Department of Veterans Affairs Health Care System, Minneapolis, MN,
USA
- Department of Neuroscience, University
of Minnesota Medical School, Minneapolis, MN, USA
| | - Matthew Sanders
- The HLA Research Group, Brain Sciences
Center, Department of Veterans Affairs Health Care System, Minneapolis, MN,
USA
- Department of Neuroscience, University
of Minnesota Medical School, Minneapolis, MN, USA
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26
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Abdel Mouti M, Pauklin S. Chemically modified neoantigen-based immunotherapy for targeting KRAS G12C-driven tumors. Trends Pharmacol Sci 2023; 44:255-257. [PMID: 36934024 DOI: 10.1016/j.tips.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/19/2023]
Abstract
The clinical efficacy and durability of KRASG12C-targeted therapies are limited by the development of resistance mechanisms. Here, we provide a review of recent KRASG12C-targeted therapy and immunotherapy-unifying strategies that utilize covalently modified peptide/MHC class I complexes as tumor-specific neoantigens to tag drug-resistant cancer cells for destruction with hapten-based immunotherapeutics.
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Affiliation(s)
- Mai Abdel Mouti
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK.
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27
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Brancati VU, Minutoli L, Marini HR, Puzzolo D, Allegra A. Identification and Targeting of Mutant Neoantigens in Multiple Myeloma Treatment. Curr Oncol 2023; 30:4603-4617. [PMID: 37232806 PMCID: PMC10217221 DOI: 10.3390/curroncol30050348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/11/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
Multiple myeloma (MM) is malignant disease characterized by the clonal proliferation of plasma cells in the bone marrow, leading to anemia, immunosuppression, and other symptoms, that is generally hard to treat. In MM, the immune system is likely exposed to neoplasia-associated neoantigens for several years before the tumor onset. Different types of neoantigens have been identified. Public or shared neoantigens derive from tumor-specific modifications often reported in several patients or across diverse tumors. They are intriguing therapeutic targets because they are frequently observed, and they have an oncogenic effect. Only a small number of public neoantigens have been recognized. Most of the neoantigens that have been identified are patient-specific or "private", necessitating a personalized approach for adaptive cell treatment. It was demonstrated that the targeting of a single greatly immunogenic neoantigen may be appropriate for tumor control. The purpose of this review was to analyze the neoantigens present in patients with MM, and to evaluate the possibility of using their presence as a prognostic factor or as a therapeutic target. We reviewed the most recent literature on neoantigen treatment strategies and on the use of bispecific, trispecific, and conjugated antibodies for the treatment of MM. Finally, a section was dedicated to the use of CAR-T in relapsed and refractory patients.
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Affiliation(s)
- Valentina Urzì Brancati
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (V.U.B.); (H.R.M.)
| | - Letteria Minutoli
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (V.U.B.); (H.R.M.)
| | - Herbert Ryan Marini
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (V.U.B.); (H.R.M.)
| | - Domenico Puzzolo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98125 Messina, Italy;
| | - Alessandro Allegra
- Division of Haematology, Department of Human Pathology in Adulthood and Childhood, University of Messina, 98125 Messina, Italy;
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Tu SM, Aydin AM, Maraboyina S, Chen Z, Singh S, Gokden N, Langford T. Stem Cell Origin of Cancer: Implications of Oncogenesis Recapitulating Embryogenesis in Cancer Care. Cancers (Basel) 2023; 15:cancers15092516. [PMID: 37173982 PMCID: PMC10177345 DOI: 10.3390/cancers15092516] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/18/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
From this perspective, we wonder about the clinical implications of oncology recapturing ontogeny in the contexts of neoantigens, tumor biomarkers, and cancer targets. We ponder about the biological ramifications of finding remnants of mini-organs and residuals of tiny embryos in some tumors. We reminisce about classical experiments showing that the embryonic microenvironment possesses antitumorigenic properties. Ironically, a stem-ness niche-in the wrong place at the wrong time-is also an onco-niche. We marvel at the paradox of TGF-beta both as a tumor suppressor and a tumor promoter. We query about the dualism of EMT as a stem-ness trait engaged in both normal development and abnormal disease states, including various cancers. It is uncanny that during fetal development, proto-oncogenes wax, while tumor-suppressor genes wane. Similarly, during cancer development, proto-oncogenes awaken, while tumor-suppressor genes slumber. Importantly, targeting stem-like pathways has therapeutic implications because stem-ness may be the true driver, if not engine, of the malignant process. Furthermore, anti-stem-like activity elicits anti-cancer effects for a variety of cancers because stem-ness features may be a universal property of cancer. When a fetus survives and thrives despite immune surveillance and all the restraints of nature and the constraints of its niche, it is a perfect baby. Similarly, when a neoplasm survives and thrives in an otherwise healthy and immune-competent host, is it a perfect tumor? Therefore, a pertinent narrative of cancer depends on a proper perspective of cancer. If malignant cells are derived from stem cells, and both cells are intrinsically RB1 negative and TP53 null, do the absence of RB1 and loss of TP53 really matter in this whole narrative and an entirely different perspective of cancer?
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Affiliation(s)
- Shi-Ming Tu
- Division of Hematology and Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Ahmet Murat Aydin
- Department of Urology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Sanjay Maraboyina
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Zhongning Chen
- Division of Hematology and Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Sunny Singh
- Division of Hematology and Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Neriman Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Timothy Langford
- Department of Urology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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29
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D’Alise AM, Nocchi L, Garzia I, Seclì L, Infante L, Troise F, Cotugno G, Allocca S, Romano G, Lahm A, Leoni G, Sasso E, Scarselli E, Nicosia A. Adenovirus Encoded Adjuvant (AdEnA) anti-CTLA-4, a novel strategy to improve Adenovirus based vaccines against infectious diseases and cancer. Front Immunol 2023; 14:1156714. [PMID: 37180141 PMCID: PMC10169702 DOI: 10.3389/fimmu.2023.1156714] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/13/2023] [Indexed: 05/15/2023] Open
Abstract
Introduction Virus vectored genetic vaccines (Vvgv) represent a promising approach for eliciting immune protection against infectious diseases and cancer. However, at variance with classical vaccines to date, no adjuvant has been combined with clinically approved genetic vaccines, possibly due to the detrimental effect of the adjuvant-induced innate response on the expression driven by the genetic vaccine vector. We reasoned that a potential novel approach to develop adjuvants for genetic vaccines would be to "synchronize" in time and space the activity of the adjuvant with that of the vaccine. Methods To this aim, we generated an Adenovirus vector encoding a murine anti-CTLA-4 monoclonal antibody (Ad-9D9) as a genetic adjuvant for Adenovirus based vaccines. Results The co-delivery of Ad-9D9 with an Adeno-based COVID-19 vaccine encoding the Spike protein resulted in stronger cellular and humoral immune responses. In contrast, only a modest adjuvant effect was achieved when combining the vaccine with the same anti-CTLA-4 in its proteinaceous form. Importantly, the administration of the adjuvant vector at different sites of the vaccine vector abrogates the immunostimulatory effect. We showed that the adjuvant activity of Ad-α-CTLA-4 is independent from the vaccine antigen as it improved the immune response and efficacy of an Adenovirus based polyepitope vaccine encoding tumor neoantigens. Discussion Our study demonstrated that the combination of Adenovirus Encoded Adjuvant (AdEnA) with an Adeno-encoded antigen vaccine enhances immune responses to viral and tumor antigens, representing a potent approach to develop more effective genetic vaccines.
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Affiliation(s)
| | | | | | | | - Luigia Infante
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | | | | | | | | | | | | | - Emanuele Sasso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- CEINGE-Advanced Biotechnologies s.c. a.r.l., Naples, Italy
| | | | - Alfredo Nicosia
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- CEINGE-Advanced Biotechnologies s.c. a.r.l., Naples, Italy
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30
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Deng EZ, Fleishman RH, Xie Z, Marino GB, Clarke DJB, Ma'ayan A. Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells. Aging Cell 2023:e13809. [PMID: 37082798 DOI: 10.1111/acel.13809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 04/22/2023] Open
Abstract
To prioritize gene and protein candidates that may enable the selective identification and removal of senescent cells, we compared gene expression signatures from replicative senescent cells to transcriptomics and proteomics atlases of normal human tissues and cell types. RNA-seq samples from in vitro senescent cells (6 studies, 13 conditions) were analyzed for identifying targets at the gene and transcript levels that are highly expressed in senescent cells compared to their expression in normal human tissues and cell types. A gene set made of 301 genes called SenoRanger was established based on consensus analysis across studies and backgrounds. Of the identified senescence-associated targets, 29% of the genes in SenoRanger are also highly differentially expressed in aged tissues from GTEx. The SenoRanger gene set includes previously known as well as novel senescence-associated genes. Pathway analysis that connected the SenoRanger genes to their functional annotations confirms their potential role in several aging and senescence-related processes. Overall, SenoRanger provides solid hypotheses about potentially useful targets for identifying and removing senescence cells.
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Affiliation(s)
- Eden Z Deng
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Reid H Fleishman
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zhuorui Xie
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Giacomo B Marino
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Daniel J B Clarke
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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31
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Want MY, Bashir Z, Najar RA. T Cell Based Immunotherapy for Cancer: Approaches and Strategies. Vaccines (Basel) 2023; 11:vaccines11040835. [PMID: 37112747 PMCID: PMC10142387 DOI: 10.3390/vaccines11040835] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
T cells are critical in destroying cancer cells by recognizing antigens presented by MHC molecules on cancer cells or antigen-presenting cells. Identifying and targeting cancer-specific or overexpressed self-antigens is essential for redirecting T cells against tumors, leading to tumor regression. This is achieved through the identification of mutated or overexpressed self-proteins in cancer cells, which guide the recognition of cancer cells by T-cell receptors. There are two main approaches to T cell-based immunotherapy: HLA-restricted and HLA-non-restricted Immunotherapy. Significant progress has been made in T cell-based immunotherapy over the past decade, using naturally occurring or genetically engineered T cells to target cancer antigens in hematological malignancies and solid tumors. However, limited specificity, longevity, and toxicity have limited success rates. This review provides an overview of T cells as a therapeutic tool for cancer, highlighting the advantages and future strategies for developing effective T cell cancer immunotherapy. The challenges associated with identifying T cells and their corresponding antigens, such as their low frequency, are also discussed. The review further examines the current state of T cell-based immunotherapy and potential future strategies, such as the use of combination therapy and the optimization of T cell properties, to overcome current limitations and improve clinical outcomes.
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Affiliation(s)
- Muzamil Y Want
- Department of Immunology, Division of Translational Immuno-Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Zeenat Bashir
- Department of Chemistry and Biochemistry, Canisius College, Buffalo, NY 14208, USA
| | - Rauf A Najar
- Department of Pediatrics, Lung Biology and Disease Program, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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Gabbia D, De Martin S. Tumor Mutational Burden for Predicting Prognosis and Therapy Outcome of Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:ijms24043441. [PMID: 36834851 PMCID: PMC9960420 DOI: 10.3390/ijms24043441] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
Hepatocellular carcinoma (HCC), the primary hepatic malignancy, represents the second-highest cause of cancer-related death worldwide. Many efforts have been devoted to finding novel biomarkers for predicting both patients' survival and the outcome of pharmacological treatments, with a particular focus on immunotherapy. In this regard, recent studies have focused on unravelling the role of tumor mutational burden (TMB), i.e., the total number of mutations per coding area of a tumor genome, to ascertain whether it can be considered a reliable biomarker to be used either for the stratification of HCC patients in subgroups with different responsiveness to immunotherapy, or for the prediction of disease progression, particularly in relation to the different HCC etiologies. In this review, we summarize the recent advances on the study of TMB and TMB-related biomarkers in the HCC landscape, focusing on their feasibility as guides for therapy decisions and/or predictors of clinical outcome.
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33
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Chambuso R, Mthembu M, Kaambo E, Robertson B, Ramesar R. Immunogenomic Biomarkers and Validation in Lynch Syndrome. Cells 2023; 12. [PMID: 36766832 DOI: 10.3390/cells12030491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/15/2023] [Accepted: 01/22/2023] [Indexed: 02/05/2023] Open
Abstract
Lynch syndrome (LS) is an inherited disorder in which affected individuals have a significantly higher-than-average risk of developing colorectal and non-colorectal cancers, often before the age of 50 years. In LS, mutations in DNA repair genes lead to a dysfunctional post-replication repair system. As a result, the unrepaired errors in coding regions of the genome produce novel proteins, called neoantigens. Neoantigens are recognised by the immune system as foreign and trigger an immune response. Due to the invasive nature of cancer screening tests, universal cancer screening guidelines unique for LS (primarily colonoscopy) are poorly adhered to by LS variant heterozygotes (LSVH). Currently, it is unclear whether immunogenomic components produced as a result of neoantigen formation can be used as novel biomarkers in LS. We hypothesise that: (i) LSVH produce measurable and dynamic immunogenomic components in blood, and (ii) these quantifiable immunogenomic components correlate with cancer onset and stage. Here, we discuss the feasibility to: (a) identify personalised novel immunogenomic biomarkers and (b) validate these biomarkers in various clinical scenarios in LSVH.
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34
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Hannani D, Leplus E, Laulagnier K, Chaperot L, Plumas J. Leveraging a powerful allogeneic dendritic cell line towards neoantigen-based cancer vaccines. Genes Cancer 2023; 14:3-11. [PMID: 36726965 PMCID: PMC9886307 DOI: 10.18632/genesandcancer.229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
In recent years, immunotherapy has finally found its place in the anti-cancer therapeutic arsenal, even becoming standard of care as first line treatment for metastatic forms. The clinical benefit provided by checkpoint blockers such as anti-PD-1/PD-L1 in many cancers revolutionized the field. However, too many patients remain refractory to these treatments due to weak baseline anti-cancer immunity. There is therefore a need to boost the frequency and function of patients' cytotoxic CD8+ cellular effectors by targeting immunogenic and tumor-restricted antigens, such as neoantigens using an efficient vaccination platform. Dendritic cells (DC) are the most powerful immune cell subset for triggering cellular immune response. However, autologous DC-based vaccines display several limitations, such as the lack of reproducibility and the limited number of cells that can be manufactured. Here we discuss the advantages of a new therapeutic vaccine based on an allogeneic Plasmacytoid DC cell line, which is easy to produce and represents a powerful platform for priming and expanding anti-neoantigen cytotoxic CD8+ T-cells.
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Affiliation(s)
| | | | | | - Laurence Chaperot
- 2R&D Laboratory, Etablissement Français du Sang Auvergne Rhône-Alpes (EFS AURA), Grenoble, France
| | - Joël Plumas
- 1PDC*line Pharma, Grenoble, France,2R&D Laboratory, Etablissement Français du Sang Auvergne Rhône-Alpes (EFS AURA), Grenoble, France,Correspondence to:Joël Plumas, email:
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35
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Abstract
This review provides an overview covering mRNA from its use in the COVID-19 pandemic to cancer immunotherapy, starting from the selection of appropriate antigens, tumor-associated and tumor-specific antigens, neoantigens, the basics of optimizing the mRNA molecule in terms of stability, efficacy, and tolerability, choosing the best formulation and the optimal route of administration, to summarizing current clinical trials of mRNA vaccines in tumor therapy.
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Abstract
Cancer immunotherapies have reshaped the paradigm for cancer treatment over the past decade. Among them, therapeutic cancer vaccines that aim to modulate antigen-presenting cells and subsequent T cell priming processes are among the first FDA-approved cancer immunotherapies. However, despite showing benign safety profiles and the capability to generate antigen-specific humoral and cellular responses, cancer vaccines have been limited by the modest therapeutic efficacy, especially for immunologically cold solid tumors. One key challenge lies in the identification of tumor-specific antigens, which involves a costly and lengthy process of tumor cell isolation, DNA/RNA extraction, sequencing, mutation analysis, epitope prediction, peptide synthesis, and antigen screening. To address these issues, in situ cancer vaccines have been actively pursued to generate endogenous antigens directly from tumors and utilize the generated tumor antigens to elicit potent cytotoxic T lymphocyte (CTL) response. Biomaterials-based in situ cancer vaccines, in particular, have achieved significant progress by taking advantage of biomaterials that can synergize antigens and adjuvants, troubleshoot delivery issues, home, and manipulate immune cells in situ. This review will provide an overview of biomaterials-based in situ cancer vaccines, either living or artificial materials, under development or in the clinic, and discuss the design criteria for in situ cancer vaccines.
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Affiliation(s)
- Yang Bo
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hua Wang
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Cancer Center at Illinois (CCIL), Urbana, IL, 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carle College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Dror Levinsky M, Brenner B, Yalon M, Levi Z, Livneh Z, Cohen Z, Paz-Elizur T, Grossman R, Ram Z, Volovitz I. A Highly Sensitive Flow Cytometric Approach to Detect Rare Antigen-Specific T Cells: Development and Comparison to Standard Monitoring Tools. Cancers (Basel) 2023; 15. [PMID: 36765532 DOI: 10.3390/cancers15030574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
Personalized vaccines against patient-unique tumor-associated antigens represent a promising new approach for cancer immunotherapy. Vaccine efficacy is assessed by quantification of changes in the frequency and/or the activity of antigen-specific T cells. Enzyme-linked immunosorbent spot (ELISpot) and flow cytometry (FCM) are methodologies frequently used for assessing vaccine efficacy. We tested these methodologies and found that both ELISpot and standard FCM [monitoring CD3/CD4/CD8/IFNγ/Viability+CD14+CD19 (dump)] demonstrate background IFNγ secretion, which, in many cases, was higher than the antigen-specific signal measured by the respective methodology (frequently ranging around 0.05-0.2%). To detect such weak T-cell responses, we developed an FCM panel that included two early activation markers, 4-1BB (CD137) and CD40L (CD154), in addition to the above-cited markers. These two activation markers have a close to zero background expression and are rapidly upregulated following antigen-specific activation. They enabled the quantification of rare T cells responding to antigens within the assay well. Background IFNγ-positive CD4 T cell frequencies decreased to 0.019% ± 0.028% and CD8 T cells to 0.009% ± 0.013%, which are 19 and 13 times lower, respectively, than without the use of these markers. The presented methodology enables highly sensitive monitoring of T-cell responses to tumor-associated antigens in the very low, but clinically relevant, frequencies.
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Salnikov M, Prusinkiewicz MA, Lin S, Ghasemi F, Cecchini MJ, Mymryk JS. Tumor-Infiltrating T Cells in EBV-Associated Gastric Carcinomas Exhibit High Levels of Multiple Markers of Activation, Effector Gene Expression, and Exhaustion. Viruses 2023; 15:176. [PMID: 36680216 PMCID: PMC9860965 DOI: 10.3390/v15010176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Epstein-Barr virus (EBV) is a gamma-herpesvirus associated with 10% of all gastric cancers (GCs) and 1.5% of all human cancers. EBV-associated GCs (EBVaGCs) are pathologically and clinically distinct entities from EBV-negative GCs (EBVnGCs), with EBVaGCs exhibiting differential molecular pathology, treatment response, and patient prognosis. However, the tumor immune landscape of EBVaGC has not been well explored. In this study, a systemic and comprehensive analysis of gene expression and immune landscape features was performed for both EBVaGC and EBVnGC. EBVaGCs exhibited many aspects of a T cell-inflamed phenotype, with greater T and NK cell infiltration, increased expression of immune checkpoint markers (BTLA, CD96, CTLA4, LAG3, PD1, TIGIT, and TIM3), and multiple T cell effector molecules in comparison with EBVnGCs. EBVaGCs also displayed a higher expression of anti-tumor immunity factors (PDL1, CD155, CEACAM1, galectin-9, and IDO1). Six EBV-encoded miRNAs (miR-BARTs 8-3p, 9-5p, 10-3p, 22, 5-5p, and 14-3p) were strongly negatively correlated with the expression of immune checkpoint receptors and multiple markers of anti-tumor immunity. These profound differences in the tumor immune landscape between EBVaGCs and EBVnGCs may help explain some of the observed differences in pathological and clinical outcomes, with an EBV-positive status possibly being a potential biomarker for the application of immunotherapy in GC.
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Affiliation(s)
- Mikhail Salnikov
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada
| | - Martin A Prusinkiewicz
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada
| | - Sherman Lin
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Farhad Ghasemi
- Department of General Surgery, Western University, London, ON N6A 3K7, Canada
| | - Matthew J Cecchini
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
- Department of Oncology, Western University, London, ON N6A 3K7, Canada
| | - Joe S Mymryk
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada
- Department of Oncology, Western University, London, ON N6A 3K7, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6A 5W9, Canada
- Department of Otolaryngology, Western University, London, ON N6A 5W9, Canada
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Schrörs B, Hos BJ, Yildiz IG, Löwer M, Lang F, Holtsträter C, Becker J, Vormehr M, Sahin U, Ossendorp F, Diken M. MC38 colorectal tumor cell lines from two different sources display substantial differences in transcriptome, mutanome and neoantigen expression. Front Immunol 2023; 14:1102282. [PMID: 36969213 PMCID: PMC10030996 DOI: 10.3389/fimmu.2023.1102282] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/23/2023] [Indexed: 03/29/2023] Open
Abstract
Introduction The cell line MC38 is a commonly used murine model for colorectal carcinoma. It has a high mutational burden, is sensitive to immune checkpoint immunotherapy and endogenous CD8+ T cell responses against neoantigens have been reported. Methods Here, we re-sequenced exomes and transcriptomes of MC38 cells from two different sources, namely Kerafast (originating from NCI/NIH, MC38-K) and the Leiden University Medical Center cell line collection (MC38-L), comparing the cell lines on the genomic and transcriptomic level and analyzing their recognition by CD8+ T cells with known neo-epitope specificity. Results The data reveals a distinct structural composition of MC38-K and MC38-L cell line genomes and different ploidies. Further, the MC38-L cell line harbored about 1.3-fold more single nucleotide variations and small insertions and deletions than the MC38-K cell line. In addition, the observed mutational signatures differed; only 35.3% of the non-synonymous variants and 5.4% of the fusion gene events were shared. Transcript expression values of both cell lines correlated strongly (p = 0.919), but we found different pathways enriched in the genes that were differentially upregulated in the MC38-L or MC38-K cells, respectively. Our data show that previously described neoantigens in the MC38 model such as Rpl18mut and Adpgkmut were absent in the MC38-K cell line resulting that such neoantigen-specific CD8+ T cells recognizing and killing MC38-L cells did not recognize or kill MC38-K cells. Conclusion This strongly indicates that at least two sub-cell lines of MC38 exist in the field and underlines the importance of meticulous tracking of investigated cell lines to obtain reproducible results, and for correct interpretation of the immunological data without artifacts. We present our analyses as a reference for researchers to select the appropriate sub-cell line for their own studies.
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Affiliation(s)
- Barbara Schrörs
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany
| | - Brett J. Hos
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Ikra G. Yildiz
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany
| | - Martin Löwer
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany
| | - Franziska Lang
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany
| | - Christoph Holtsträter
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany
| | - Julia Becker
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany
| | | | - Ugur Sahin
- BioNTech SE, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Ferry Ossendorp
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- *Correspondence: Ferry Ossendorp, ; Mustafa Diken,
| | - Mustafa Diken
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz gGmbH, Mainz, Germany
- BioNTech SE, Mainz, Germany
- *Correspondence: Ferry Ossendorp, ; Mustafa Diken,
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Besson S, Boucher E, Laurin D, Manches O, Aspord C, Hannani D, Fender P. Stimulation of the immune system by a tumor antigen-bearing adenovirus-inspired VLP allows control of melanoma growth. Mol Ther Methods Clin Dev 2023; 28:76-89. [PMID: 36620074 DOI: 10.1016/j.omtm.2022.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Virus-like particles (VLPs) are versatile protein-based platforms that can be used as a vaccine platform mainly in infectiology. In the present work, we compared a previously designed, non-infectious, adenovirus-inspired 60-mer dodecahedric VLP to display short epitopes or a large tumor model antigen. To validate these two kinds of platforms as a potential immuno-stimulating approach, we evaluated their ability to control melanoma B16-ovalbumin (OVA) growth in mice. A set of adjuvants was screened, showing that polyinosinic-polycytidylic acid (poly(I:C)) was well suited to generate a homogeneous cellular and humoral response against the desired epitopes. In a prophylactic setting, vaccination with the VLP displaying these epitopes resulted in total inhibition of tumor growth 1 month after vaccination. A therapeutic vaccination strategy showed a delay in grafted tumor growth or its total rejection. If the "simple" epitope display on the VLP is sufficient to prevent tumor growth, then an improved engineered platform enabling display of a large antigen is a tool to overcome the barrier of immune allele restriction, broadening the immune response, and paving the way for its potential utilization in humans as an off-the-shelf vaccine.
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Chen Y, Zhao H, Luo J, Liao Y, Dan X, Hu G, Gu W. A phase I dose-escalation study of neoantigen-activated haploidentical T cell therapy for the treatment of relapsed or refractory peripheral T-cell lymphoma. Front Oncol 2022; 12:944511. [PMID: 36439517 PMCID: PMC9684663 DOI: 10.3389/fonc.2022.944511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 10/10/2022] [Indexed: 01/25/2023] Open
Abstract
UNLABELLED Peripheral T-cell lymphoma (PTCL) is a type of highly heterogeneous non-Hodgkin lymphoma with a poor prognosis and lack of effective targeted therapies. Adoptive T-cell therapy has been successfully used in the treatment of B-cell malignancies. We first used adoptive transfer of haploidentical T cells activated by patient-specific neoantigens in vitro to treat an elderly patient with refractory angioimmunoblastic T-cell lymphoma (AITL) in 2017, and the patient achieved long-term complete remission (CR). Here we report on early results from this first-in-human phase 1 clinical trial that aims to assess the safety and tolerability of neoantigen-activated haploidentical T cell therapy (NAHTC) for relapsed/refractory PTCL. CLINICAL TRIAL REGISTRATION http://www.chictr.org.cn/index.aspx, identifier [ChiCTR1800017440].
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Affiliation(s)
- Yuan Chen
- Department of Hematology, The Affiliated Zhuzhou Hospital Xiangya Medical College CSU, Zhuzhou, Hunan, China
| | - Hu Zhao
- Department of Hematology, The Affiliated Zhuzhou Hospital Xiangya Medical College CSU, Zhuzhou, Hunan, China
| | - Jing Luo
- Department of Hematology, The Affiliated Zhuzhou Hospital Xiangya Medical College CSU, Zhuzhou, Hunan, China
| | - Youping Liao
- Department of Hematology, The Affiliated Zhuzhou Hospital Xiangya Medical College CSU, Zhuzhou, Hunan, China
| | - Xu Dan
- YuceBio Medical Technology Co., Ltd, Shenzhen, Guangdong, China
| | - Guoyu Hu
- Department of Hematology, The Affiliated Zhuzhou Hospital Xiangya Medical College CSU, Zhuzhou, Hunan, China,*Correspondence: Guoyu Hu, ; Weiyue Gu,
| | - Weiyue Gu
- Chineo Medical Technology Co., Ltd, Beijing, China,*Correspondence: Guoyu Hu, ; Weiyue Gu,
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Liu Q, Chu Y, Shao J, Qian H, Yang J, Sha H, Cen L, Tian M, Xu Q, Chen F, Yang Y, Wang W, Wang K, Yu L, Wei J, Liu B. Benefits of an Immunogenic Personalized Neoantigen Nanovaccine in Patients with High-Risk Gastric/Gastroesophageal Junction Cancer. Adv Sci (Weinh) 2022; 10:e2203298. [PMID: 36351249 PMCID: PMC9811442 DOI: 10.1002/advs.202203298] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Personalized neoantigen vaccines have shown strong immunogenicity in clinical trial, but still face various challenges in facilitating an efficient antitumor immune response. Here, a personalized neoantigen nanovaccine (PNVAC) platform for adjuvant cancer immunotherapy is generated. PNVAC triggers superior protective efficacy against tumor recurrence and promotes longer survival than free neoantigens, especially when combined with anti-PD-1 treatment in a murine tumor model. A phase I clinical trial (ChiCTR1800017319) is initiated to evaluate the safety, immunogenicity, and prophylactic effect of PNVAC on preventing tumor recurrence in patients with high-risk gastric/gastroesophageal junction cancer after adjuvant chemotherapy of postsurgical resection. The one- and two-year disease-free survival rates are significantly higher than historical record. PNVAC induces both CD4+ and CD8+ T cell responses as well as antigen-experienced memory T cell phenotype. Furthermore, the immune response is persistent and remains evident one year after the vaccination. This work provides a safe and feasible strategy for developing neoantigen vaccines to delay gastric cancer recurrence after surgery.
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Affiliation(s)
- Qin Liu
- The Comprehensive Cancer Centre of Drum Tower HospitalMedical School of Nanjing University and Clinical Cancer Institute of Nanjing UniversityNanjing210008China
| | - Yanhong Chu
- The Comprehensive Cancer Centre of Drum Tower HospitalMedical School of Nanjing University and Clinical Cancer Institute of Nanjing UniversityNanjing210008China
| | - Jie Shao
- The Comprehensive Cancer Centre of Drum Tower HospitalMedical School of Nanjing University and Clinical Cancer Institute of Nanjing UniversityNanjing210008China
| | - Hanqing Qian
- The Comprehensive Cancer Centre of Drum Tower HospitalMedical School of Nanjing University and Clinical Cancer Institute of Nanjing UniversityNanjing210008China
| | - Ju Yang
- The Comprehensive Cancer Centre of Drum Tower HospitalMedical School of Nanjing University and Clinical Cancer Institute of Nanjing UniversityNanjing210008China
| | - Huizi Sha
- The Comprehensive Cancer Centre of Drum Tower HospitalMedical School of Nanjing University and Clinical Cancer Institute of Nanjing UniversityNanjing210008China
| | - Lanqi Cen
- The Comprehensive Cancer Centre of Drum Tower HospitalMedical School of Nanjing University and Clinical Cancer Institute of Nanjing UniversityNanjing210008China
| | - Manman Tian
- The Comprehensive Cancer Centre of Drum Tower HospitalMedical School of Nanjing University and Clinical Cancer Institute of Nanjing UniversityNanjing210008China
| | - Qiuping Xu
- The Comprehensive Cancer Centre of Drum Tower HospitalMedical School of Nanjing University and Clinical Cancer Institute of Nanjing UniversityNanjing210008China
| | - Fangjun Chen
- The Comprehensive Cancer Centre of Drum Tower HospitalMedical School of Nanjing University and Clinical Cancer Institute of Nanjing UniversityNanjing210008China
| | - Yang Yang
- The Comprehensive Cancer Centre of Drum Tower HospitalMedical School of Nanjing University and Clinical Cancer Institute of Nanjing UniversityNanjing210008China
| | | | | | - Lixia Yu
- The Comprehensive Cancer Centre of Drum Tower HospitalMedical School of Nanjing University and Clinical Cancer Institute of Nanjing UniversityNanjing210008China
| | - Jia Wei
- The Comprehensive Cancer Centre of Drum Tower HospitalMedical School of Nanjing University and Clinical Cancer Institute of Nanjing UniversityNanjing210008China
| | - Baorui Liu
- The Comprehensive Cancer Centre of Drum Tower HospitalMedical School of Nanjing University and Clinical Cancer Institute of Nanjing UniversityNanjing210008China
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Aparicio B, Repáraz D, Ruiz M, Llopiz D, Silva L, Vercher E, Theunissen P, Tamayo I, Smerdou C, Igea A, Santisteban M, Gónzalez-Deza C, Lasarte JJ, Hervás-Stubbs S, Sarobe P. Identification of HLA class I-restricted immunogenic neoantigens in triple negative breast cancer. Front Immunol 2022; 13:985886. [PMID: 36405725 PMCID: PMC9666480 DOI: 10.3389/fimmu.2022.985886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/14/2022] [Indexed: 07/20/2023] Open
Abstract
Immune checkpoint inhibitor (ICI)-based immunotherapy in triple negative breast cancer (TNBC) is achieving limited therapeutic results, requiring the development of more potent strategies. Combination of ICI with vaccination strategies would enhance antitumor immunity and response rates to ICI in patients having poorly infiltrated tumors. In heavily mutated tumors, neoantigens (neoAgs) resulting from tumor mutations have induced potent responses when used as vaccines. Thus, our aim was the identification of immunogenic neoAgs suitable as vaccines in TNBC patients. By using whole exome sequencing, RNAseq and HLA binding algorithms of tumor samples from a cohort of eight TNBC patients, we identified a median of 60 mutations/patient, which originated a putative median number of 98 HLA class I-restricted neoAgs. Considering a group of 27 predicted neoAgs presented by HLA-A*02:01 allele in two patients, peptide binding to HLA was experimentally confirmed in 63% of them, whereas 55% were immunogenic in vivo in HLA-A*02:01+ transgenic mice, inducing T-cells against the mutated but not the wild-type peptide sequence. Vaccination with peptide pools or DNA plasmids expressing these neoAgs induced polyepitopic T-cell responses, which recognized neoAg-expressing tumor cells. These results suggest that TNBC tumors harbor neoAgs potentially useful in therapeutic vaccines, opening the way for new combined immunotherapies.
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Affiliation(s)
- Belén Aparicio
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - David Repáraz
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Marta Ruiz
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Diana Llopiz
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Leyre Silva
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Enric Vercher
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Patrick Theunissen
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Ibon Tamayo
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Cristian Smerdou
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Ana Igea
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Marta Santisteban
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
- Oncología Médica, Clínica Universidad de Navarra, Pamplona, Spain
| | | | - Juan J. Lasarte
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Sandra Hervás-Stubbs
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Pablo Sarobe
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
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Velaga R, Koo KM, Mainwaring PN. Harnessing gene fusion-derived neoantigens for 'cold' breast and prostate tumor immunotherapy. Immunotherapy 2022; 14:1165-1179. [PMID: 36043380 DOI: 10.2217/imt-2022-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Breast and prostate cancers are generally considered immunologically 'cold' tumors due to multiple mechanisms rendering them unresponsive to immune checkpoint blockade therapies. With little success in garnering positive outcomes in modern immunotherapeutic clinical trials, it is prudent to re-examine the role of immunogenic neoantigens in these cold tumors. Gene fusions are driver mutations in hormone-driven cancers that can result in alternative mutation-specific neoantigens to promote immunotherapy sensitivity. This review focuses on 1) gene fusion formation mechanisms in neoantigen generation; 2) gene fusion neoantigens in cancer immunotherapeutic strategies and associated clinical trials; and 3) challenges and opportunities in computational and liquid biopsy technologies. This review is anticipated to initiate further research into gene fusion neoantigens of cold tumors for further experimental validation.
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Affiliation(s)
- Ravi Velaga
- Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Kevin M Koo
- XING Technologies Pty Ltd, Brisbane, QLD 4073, Australia.,The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, QLD 4029, Australia
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Irajizad E, Fahrmann JF, Long JP, Vykoukal J, Kobayashi M, Capello M, Yu CY, Cai Y, Hsiao FC, Patel N, Park S, Peng Q, Dennison JB, Kato T, Tai MC, Taguchi A, Kadara H, Wistuba II, Katayama H, Do KA, Hanash SM, Ostrin EJ. A Comprehensive Search of Non-Canonical Proteins in Non-Small Cell Lung Cancer and Their Impact on the Immune Response. Int J Mol Sci 2022; 23:ijms23168933. [PMID: 36012199 PMCID: PMC9409146 DOI: 10.3390/ijms23168933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 12/02/2022] Open
Abstract
There is substantial interest in mining neoantigens for cancer applications. Non-canonical proteins resulting from frameshift mutations have been identified as neoantigens in cancer. We investigated the landscape of non-canonical proteins in non-small cell lung cancer (NSCLC) and their induced immune response in the form of autoantibodies. A database of cryptoproteins was computationally constructed and comprised all alternate open reading frames (altORFs) and ORFs identified in pseudogenes, noncoding RNAs, and untranslated regions of mRNAs that did not align with known canonical proteins. Proteomic profiles of seventeen lung adenocarcinoma (LUAD) cell lines were searched to evaluate the occurrence of cryptoproteins. To assess the immunogenicity, immunoglobulin (Ig)-bound cryptoproteins in plasmas were profiled by mass spectrometry. The specimen set consisted of plasmas from 30 newly diagnosed NSCLC cases, pre-diagnostic plasmas from 51 NSCLC cases, and 102 control plasmas. An analysis of LUAD cell lines identified 420 cryptoproteins. Plasma Ig-bound analyses revealed 90 cryptoproteins uniquely found in cases and 14 cryptoproteins that had a fold-change >2 compared to controls. In pre-diagnostic samples, 17 Ig-bound cryptoproteins yielded an odds ratio ≥2. Eight Ig-bound cryptoproteins were elevated in both pre-diagnostic and newly diagnosed cases compared to controls. Cryptoproteins represent a class of neoantigens that induce an autoantibody response in NSCLC.
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Affiliation(s)
- Ehsan Irajizad
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Johannes F. Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - James P. Long
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Jody Vykoukal
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Makoto Kobayashi
- Department of Basic Pathology, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima 960-1247, Japan
| | - Michela Capello
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Chuan-Yih Yu
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Yining Cai
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Fu Chung Hsiao
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Nikul Patel
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Soyoung Park
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Qian Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Jennifer B. Dennison
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Taketo Kato
- Department of Thoracic Surgery, Nagoya University, Nagoya 464-8601, Japan
| | - Mei Chee Tai
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Ayumu Taguchi
- Division of Molecular Diagnostics, Aichi Cancer Center, Nagoya 464-8601, Japan
- Division of Advanced Cancer Diagnostics, Nagoya University Graduate School of Medicine, Nagoya 464-8601, Japan
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - Kim-Anh Do
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
- Correspondence: (K.-A.D.); (S.M.H.); (E.J.O.); Tel.: +1-713-745-5242 (S.M.H.)
| | - Samir M. Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
- Correspondence: (K.-A.D.); (S.M.H.); (E.J.O.); Tel.: +1-713-745-5242 (S.M.H.)
| | - Edwin J. Ostrin
- Departments of General Internal Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
- Correspondence: (K.-A.D.); (S.M.H.); (E.J.O.); Tel.: +1-713-745-5242 (S.M.H.)
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46
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Hanada KI, Zhao C, Gil-Hoyos R, Gartner JJ, Chow-Parmer C, Lowery FJ, Krishna S, Prickett TD, Kivitz S, Parkhurst MR, Wong N, Rae Z, Kelly MC, Goff SL, Robbins PF, Rosenberg SA, Yang JC. A phenotypic signature that identifies neoantigen-reactive T cells in fresh human lung cancers. Cancer Cell 2022; 40:479-493.e6. [PMID: 35452604 PMCID: PMC9196205 DOI: 10.1016/j.ccell.2022.03.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 02/08/2022] [Accepted: 03/29/2022] [Indexed: 02/07/2023]
Abstract
A common theme across multiple successful immunotherapies for cancer is the recognition of tumor-specific mutations (neoantigens) by T cells. The rapid discovery of such antigen responses could lead to improved therapies through the adoptive transfer of T cells engineered to express neoantigen-reactive T cell receptors (TCRs). Here, through CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) and TCR-seq of non-small cell lung cancer (NSCLC) tumor-infiltrating lymphocytes (TILs), we develop a neoantigen-reactive T cell signature based on clonotype frequency and CD39 protein and CXCL13 mRNA expression. Screening of TCRs selected by the signature allows us to identify neoantigen-reactive TCRs with a success rate of 45% for CD8+ and 66% for CD4+ T cells. Because of the small number of samples analyzed (4 patients), generalizability remains to be tested. However, this approach can enable the quick identification of neoantigen-reactive TCRs and expedite the engineering of personalized neoantigen-reactive T cells for therapy.
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Affiliation(s)
- Ken-Ichi Hanada
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Chihao Zhao
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raul Gil-Hoyos
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jared J Gartner
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher Chow-Parmer
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank J Lowery
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sri Krishna
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Todd D Prickett
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scott Kivitz
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria R Parkhurst
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nathan Wong
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21701, USA
| | - Zachary Rae
- Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Michael C Kelly
- Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Stephanie L Goff
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul F Robbins
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven A Rosenberg
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James C Yang
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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47
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Zhou JG, Ding Z, Shi H, Cheng M. Editorial: The Clinical Application of Neoantigens. Front Immunol 2022; 13:842633. [PMID: 35309343 PMCID: PMC8930198 DOI: 10.3389/fimmu.2022.842633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/07/2022] [Indexed: 02/05/2023] Open
Affiliation(s)
- Jian-Guo Zhou
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China.,Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany.,Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany.,Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (EMN), Erlangen, Germany
| | - Zhenyu Ding
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Huashan Shi
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Min Cheng
- Department of Physiology, Weifang Medical University, Weifang, China
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48
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Guelman S, Zhou Y, Brady A, Peng K. A Fit-for-Purpose Method to Measure Circulating Levels of the mRNA Component of a Liposomal-Formulated Individualized Neoantigen-Specific Therapy for Cancer. AAPS J 2022; 24:64. [PMID: 35501406 DOI: 10.1208/s12248-022-00709-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022] Open
Abstract
Autogene cevumeran is an individualized neoantigen-specific therapy (iNeST) under development for the treatment of various solid tumors. It consists of an RNA-Lipoplex (RNA-LPX) in which the encapsulated mRNA molecule encodes up to ten neoepitopes identified from each individual patient. In association with major histocompatibility complex (MHC) class I and MHC class II, these neoantigens can potentially stimulate and expand neoantigen-specific CD4+ and CD8+ T cells, leading to antitumor responses. As part of the pharmacokinetic (PK) property assessment of Autogene cevumeran in patients, both the lipid and mRNA content in circulation are measured. This work focused on our efforts to establish a sensitive and robust method for the measurement of mRNA levels of RNA-LPX in plasma. Due to the chemical characteristics of mRNA, extra precautions are required in order to effectively preserve mRNA integrity in human plasma during sample collection, handling and storage. To this end, a number of sample collection tubes and storage conditions were evaluated in order to inform the most optimal and operationally feasible conditions by which to preserve mRNA integrity during sample collection and upon freeze-thaw. PAXgene Blood ccfDNA tubes successfully prevented mRNA degradation and were subsequently selected for patient sample collection in the clinical trial. A branched DNA (bDNA)-based mRNA PK assay was developed to achieve the desired assay performance. Here, we discuss the evaluation of various sample collection and processing conditions as well as the optimization of the work flow during bDNA PK method development.
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Affiliation(s)
- Sebastian Guelman
- Department of BioAnalytical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, California, 94080-4990, USA.
| | - Ying Zhou
- Department of BioAnalytical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, California, 94080-4990, USA
| | - Ann Brady
- Department of BioAnalytical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, California, 94080-4990, USA
| | - Kun Peng
- Department of BioAnalytical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, California, 94080-4990, USA
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49
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Pao SC, Chu MT, Hung SI. Therapeutic Vaccines Targeting Neoantigens to Induce T-Cell Immunity against Cancers. Pharmaceutics 2022; 14:867. [PMID: 35456701 DOI: 10.3390/pharmaceutics14040867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 12/12/2022] Open
Abstract
Cancer immunotherapy has achieved multiple clinical benefits and has become an indispensable component of cancer treatment. Targeting tumor-specific antigens, also known as neoantigens, plays a crucial role in cancer immunotherapy. T cells of adaptive immunity that recognize neoantigens, but do not induce unwanted off-target effects, have demonstrated high efficacy and low side effects in cancer immunotherapy. Tumor neoantigens derived from accumulated genetic instability can be characterized using emerging technologies, such as high-throughput sequencing, bioinformatics, predictive algorithms, mass-spectrometry analyses, and immunogenicity validation. Neoepitopes with a higher affinity for major histocompatibility complexes can be identified and further applied to the field of cancer vaccines. Therapeutic vaccines composed of tumor lysates or cells and DNA, mRNA, or peptides of neoantigens have revoked adaptive immunity to kill cancer cells in clinical trials. Broad clinical applicability of these therapeutic cancer vaccines has emerged. In this review, we discuss recent progress in neoantigen identification and applications for cancer vaccines and the results of ongoing trials.
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50
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Liang H, Xu Y, Chen M, Zhao J, Zhong W, Liu X, Gao X, Li S, Li J, Guo C, Jia H, Wang M. Characterization of Somatic Mutations That Affect Neoantigens in Non-Small Cell Lung Cancer. Front Immunol 2022; 12:749461. [PMID: 35356154 PMCID: PMC8959482 DOI: 10.3389/fimmu.2021.749461] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/27/2021] [Indexed: 12/17/2022] Open
Abstract
Purpose Immune checkpoint inhibitors (ICIs) have recently emerged as an important option for treating patients with advanced non-small cell lung cancer (NSCLC). Neoantigens are important biomarkers and potential immunotherapy targets that play important roles in the prognosis and treatment of patients with NSCLC. This study aimed to evaluate and characterize the relationships between somatic mutations and potential neoantigens in specimens from patients who underwent surgical treatment for NSCLC. Patients and Methods This prospective study evaluated specimens from patients with NSCLC who underwent surgical treatment at the Peking Union Medical College, China, from June 2019 to September 2019. Whole-exome sequencing was performed for tumor tissues and corresponding normal tissues. Candidate neoantigens were predicted using generative software, and the relationships between various mutation characteristics and number of neoantigens were evaluated. Results Neoantigen-related gene mutations were less frequent than mutations affecting the whole genome. Genes with high neoantigen burden had more types and higher frequencies of mutations. The number of candidate neoantigens was positively correlated with missense mutations, code shift insertions/deletions, split-site variations, and nonsense mutations. However, in the multiple linear regression analysis, only missense mutations were positively correlated with the number of neoantigens. The number of neoantigens was also positively correlated with base transversions (A>C/C>A, T>G/G>T, and C>G/G>C) and negatively correlated with base transitions (A>G/G>A and C>T/T>C). Conclusion The number of candidate neoantigens in NSCLC specimens was associated with mutation frequency, type of mutation, and type of base substitution.
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Affiliation(s)
- Hongge Liang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yan Xu
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Minjiang Chen
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Zhao
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Zhong
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyan Liu
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoxing Gao
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shanqing Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ji Li
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chao Guo
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - He Jia
- Department of Biological Information, Beijing Neoantigen Biotechnology Co., Ltd., Beijing, China
| | - Mengzhao Wang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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