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Pounraj S, Chen S, Ma L, Mazzieri R, Dolcetti R, Rehm BHA. Targeting Tumor Heterogeneity with Neoantigen-Based Cancer Vaccines. Cancer Res 2024; 84:353-363. [PMID: 38055891 DOI: 10.1158/0008-5472.can-23-2042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/24/2023] [Accepted: 12/04/2023] [Indexed: 12/08/2023]
Abstract
Neoantigen-based cancer vaccines have emerged as a promising immunotherapeutic approach to treat cancer. Nevertheless, the high degree of heterogeneity in tumors poses a significant hurdle for developing a vaccine that targets the therapeutically relevant neoantigens capable of effectively stimulating an immune response as each tumor contains numerous unique putative neoantigens. Understanding the complexities of tumor heterogeneity is crucial for the development of personalized neoantigen-based vaccines, which hold the potential to revolutionize cancer treatment and improve patient outcomes. In this review, we discuss recent advancements in the design of neoantigen-based cancer vaccines emphasizing the identification, validation, formulation, and targeting of neoantigens while addressing the challenges posed by tumor heterogeneity. The review highlights the application of cutting-edge approaches, such as single-cell sequencing and artificial intelligence to identify immunogenic neoantigens, while outlining current limitations and proposing future research directions to develop effective neoantigen-based vaccines.
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Affiliation(s)
- Saranya Pounraj
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
| | - Shuxiong Chen
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
| | - Linlin Ma
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
- School of Environment and Science, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
| | - Roberta Mazzieri
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Riccardo Dolcetti
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
- Menzies Health Institute Queensland (MHIQ), Griffith University (Gold Coast Campus), Queensland, Australia
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2
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De Groot AS, Khan S, Mattei AE, Lelias S, Martin WD. Does human homology reduce the potential immunogenicity of non-antibody scaffolds? Front Immunol 2023; 14:1215939. [PMID: 38022550 PMCID: PMC10664710 DOI: 10.3389/fimmu.2023.1215939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Biologics developers are moving beyond antibodies for delivery of a wide range of therapeutic interventions. These non-antibody modalities are often based on 'natural' protein scaffolds that are modified to deliver bioactive sequences. Both human-derived and non-human-sourced scaffold proteins have been developed. New types of "non-antibody" scaffolds are still being discovered, as they offer attractive alternatives to monoclonals due to their smaller size, improved stability, and ease of synthesis. They are believed to have low immunogenic potential. However, while several human-sourced protein scaffolds have not been immunogenic in clinical studies, this may not predict their overall performance in other therapeutic applications. A preliminary evaluation of their potential for immunogenicity is warranted. Immunogenicity risk potential has been clearly linked to the presence of T "helper" epitopes in the sequence of biologic therapeutics. In addition, tolerogenic epitopes are present in some human proteins and may decrease their immunogenic potential. While the detailed sequences of many non-antibody scaffold therapeutic candidates remain unpublished, their backbone sequences are available for review and analysis. We assessed 12 example non-antibody scaffold backbone sequences using our epitope-mapping tools (EpiMatrix) for this perspective. Based on EpiMatrix scoring, their HLA DRB1-restricted T cell epitope content appears to be lower than the average protein, and sequences that may act as tolerogenic epitopes are present in selected human-derived scaffolds. Assessing the potential immunogenicity of scaffold proteins regarding self and non-self T cell epitopes may be of use for drug developers and clinicians, as these exciting new non-antibody molecules begin to emerge from the preclinical pipeline into clinical use.
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Affiliation(s)
- Anne S. De Groot
- EpiVax, Providence, RI, United States
- University of Georgia, Center for Vaccines and Immunology, Athens, GA, United States
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3
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Wagner A, Mutschler H. Design principles and applications of synthetic self-replicating RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1803. [PMID: 37264531 DOI: 10.1002/wrna.1803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/24/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023]
Abstract
With the advent of ever more sophisticated methods for the in vitro synthesis and the in vivo delivery of RNAs, synthetic mRNAs have gained substantial interest both for medical applications, as well as for biotechnology. However, in most biological systems exogeneous mRNAs possess only a limited half-life, especially in fast dividing cells. In contrast, viral RNAs can extend their lifetime by actively replicating inside their host. As such they may serve as scaffolds for the design of synthetic self-replicating RNAs (srRNA), which can be used to increase both the half-life and intracellular concentration of coding RNAs. Synthetic srRNAs may be used to enhance recombinant protein expression or induce the reprogramming of differentiated cells into pluripotent stem cells but also to create cell-free systems for research based on experimental evolution. In this article, we discuss the applications and design principles of srRNAs used for cellular reprogramming, mRNA-based vaccines and tools for synthetic biology. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
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Affiliation(s)
- Alexander Wagner
- Biomimetic Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Hannes Mutschler
- Biomimetic Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
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4
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Dailey GP, Crosby EJ, Hartman ZC. Cancer vaccine strategies using self-replicating RNA viral platforms. Cancer Gene Ther 2023; 30:794-802. [PMID: 35821284 PMCID: PMC9275542 DOI: 10.1038/s41417-022-00499-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/21/2022] [Accepted: 06/23/2022] [Indexed: 11/09/2022]
Abstract
The development and success of RNA-based vaccines targeting SARS-CoV-2 has awakened new interest in utilizing RNA vaccines against cancer, particularly in the emerging use of self-replicating RNA (srRNA) viral vaccine platforms. These vaccines are based on different single-stranded RNA viruses, which encode RNA for target antigens in addition to replication genes that are capable of massively amplifying RNA messages after infection. The encoded replicase genes also stimulate innate immunity, making srRNA vectors ideal candidates for anti-tumor vaccination. In this review, we summarize different types of srRNA platforms that have emerged and review evidence for their efficacy in provoking anti-tumor immunity to different antigens. These srRNA platforms encompass the use of naked RNA, DNA-launched replicons, viral replicon particles (VRP), and most recently, synthetic srRNA replicon particles. Across these platforms, studies have demonstrated srRNA vaccine platforms to be potent inducers of anti-tumor immunity, which can be enhanced by homologous vaccine boosting and combining with chemotherapies, radiation, and immune checkpoint inhibition. As such, while this remains an active area of research, the past and present trajectory of srRNA vaccine development suggests immense potential for this platform in producing effective cancer vaccines.
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Affiliation(s)
| | | | - Zachary C Hartman
- Department of Surgery, Duke University, Durham, NC, USA.
- Department of Pathology, Duke University, Durham, NC, USA.
- Department of Immunology, Duke University, Durham, NC, USA.
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5
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Viborg N, Pavlidis MA, Barrio-Calvo M, Friis S, Trolle T, Sørensen AB, Thygesen CB, Kofoed SV, Kleine-Kohlbrecher D, Hadrup SR, Rønø B. DNA based neoepitope vaccination induces tumor control in syngeneic mouse models. NPJ Vaccines 2023; 8:77. [PMID: 37244905 DOI: 10.1038/s41541-023-00671-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/10/2023] [Indexed: 05/29/2023] Open
Abstract
Recent findings have positioned tumor mutation-derived neoepitopes as attractive targets for cancer immunotherapy. Cancer vaccines that deliver neoepitopes via various vaccine formulations have demonstrated promising preliminary results in patients and animal models. In the presented work, we assessed the ability of plasmid DNA to confer neoepitope immunogenicity and anti-tumor effect in two murine syngeneic cancer models. We demonstrated that neoepitope DNA vaccination led to anti-tumor immunity in the CT26 and B16F10 tumor models, with the long-lasting presence of neoepitope-specific T-cell responses in blood, spleen, and tumors after immunization. We further observed that engagement of both the CD4+ and CD8+ T cell compartments was essential to hamper tumor growth. Additionally, combination therapy with immune checkpoint inhibition provided an additive effect, superior to either monotherapy. DNA vaccination offers a versatile platform that allows the encoding of multiple neoepitopes in a single formulation and is thus a feasible strategy for personalized immunotherapy via neoepitope vaccination.
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Affiliation(s)
- Nadia Viborg
- Evaxion Biotech, Hørsholm, Denmark
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | | | | | | | | | | | | | | | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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6
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Daradoumis J, Ragonnaud E, Skandorff I, Nielsen KN, Bermejo AV, Andersson AM, Schroedel S, Thirion C, Neukirch L, Holst PJ. An Endogenous Retrovirus Vaccine Encoding an Envelope with a Mutated Immunosuppressive Domain in Combination with Anti-PD1 Treatment Eradicates Established Tumours in Mice. Viruses 2023; 15:v15040926. [PMID: 37112906 PMCID: PMC10141008 DOI: 10.3390/v15040926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Endogenous retroviruses (ERVs) account for 8% of our genome, and, although they are usually silent in healthy tissues, they become reactivated and expressed in pathological conditions such as cancer. Several studies support a functional role of ERVs in tumour development and progression, specifically through their envelope (Env) protein, which contains a region described as an immunosuppressive domain (ISD). We have previously shown that targeting of the murine ERV (MelARV) Env using virus-like vaccine (VLV) technology, consisting of an adenoviral vector encoding virus-like particles (VLPs), induces protection against small tumours in mice. Here, we investigate the potency and efficacy of a novel MelARV VLV with a mutated ISD (ISDmut) that can modify the properties of the adenoviral vaccine-encoded Env protein. We show that the modification of the vaccine's ISD significantly enhanced T-cell immunogenicity in both prime and prime-boost vaccination regimens. The modified VLV in combination with an α-PD1 checkpoint inhibitor (CPI) exhibited excellent curative efficacy against large established colorectal CT26 tumours in mice. Furthermore, only ISDmut-vaccinated mice that survived CT26 challenge were additionally protected against rechallenge with a triple-negative breast cancer cell line (4T1), showing that our modified VLV provides cross-protection against different tumour types expressing ERV-derived antigens. We envision that translating these findings and technology into human ERVs (HERVs) could provide new treatment opportunities for cancer patients with unmet medical needs.
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Affiliation(s)
- Joana Daradoumis
- Department of Immunology and Microbiology, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Emeline Ragonnaud
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
- Department of Biomedical Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Isabella Skandorff
- Department of Immunology and Microbiology, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | | | - Amaia Vergara Bermejo
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
- Department of Biomedical Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Anne-Marie Andersson
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | | | | | - Lasse Neukirch
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
- Department of Biomedical Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Peter Johannes Holst
- Department of Immunology and Microbiology, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
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Abstract
INTRODUCTION Prior to the emergence of SARS-CoV-2, the potential use of mRNA vaccines for a rapid pandemic response had been well described in the scientific literature, however during the SARS-CoV-2 outbreak we witnessed the large-scale deployment of the platform in a real pandemic setting. Of the three RNA platforms evaluated in clinical trials, including 1) conventional, non-amplifying mRNA (mRNA), 2) base-modified, non-amplifying mRNA (bmRNA), which incorporate chemically modified nucleotides, and 3) self-amplifying RNA (saRNA), the bmRNA technology emerged with superior clinical efficacy. AREAS COVERED This review describes the current state of these mRNA vaccine technologies, evaluates their strengths and limitations, and argues that saRNA may have significant advantages if the limitations of stability and complexities of manufacturing can be overcome. EXPERT OPINION The success of the SARS-CoV-2 mRNA vaccines has been remarkable. However, several challenges remain to be addressed before this technology can successfully be applied broadly to other disease targets. Innovation in the areas of mRNA engineering, novel delivery systems, antigen design, and high-quality manufacturing will be required to achieve the full potential of this disruptive technology.
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Affiliation(s)
| | - Zoltan Kis
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK.,Department of Chemical Engineering, Imperial College London, London, UK
| | - Jeffrey B Ulmer
- Immorna Biotherapeutics, Morrisville, North Carolina.,TechImmune LLC, Newport Beach, CA, USA
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8
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Shi W, Chen S, Chi F, Qiu Q, Zhong Y, Bian X, Zhang H, Xi J, Qian H. Advances in Tumor Antigen‐Based Anticancer Immunotherapy: Recent Progress, Prevailing Challenges, and Future Perspective. ADVANCED THERAPEUTICS 2022. [DOI: 10.1002/adtp.202200239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Wei Shi
- Center of Drug Discovery State Key Laboratory of Natural Medicines China Pharmaceutical University 24 Tongjiaxiang Nanjing 210009 P. R. China
| | - Shuang Chen
- Center of Drug Discovery State Key Laboratory of Natural Medicines China Pharmaceutical University 24 Tongjiaxiang Nanjing 210009 P. R. China
| | - Fanglian Chi
- Center of Drug Discovery State Key Laboratory of Natural Medicines China Pharmaceutical University 24 Tongjiaxiang Nanjing 210009 P. R. China
| | - Qianqian Qiu
- Center of Drug Discovery State Key Laboratory of Natural Medicines China Pharmaceutical University 24 Tongjiaxiang Nanjing 210009 P. R. China
| | - Yue Zhong
- Center of Drug Discovery State Key Laboratory of Natural Medicines China Pharmaceutical University 24 Tongjiaxiang Nanjing 210009 P. R. China
| | - Xiaojian Bian
- Center of Drug Discovery State Key Laboratory of Natural Medicines China Pharmaceutical University 24 Tongjiaxiang Nanjing 210009 P. R. China
| | - Hao Zhang
- School of Science China Pharmaceutical University 24 Tongjiaxiang Nanjing 210009 P. R. China
| | - Junting Xi
- School of Science China Pharmaceutical University 24 Tongjiaxiang Nanjing 210009 P. R. China
| | - Hai Qian
- Center of Drug Discovery State Key Laboratory of Natural Medicines China Pharmaceutical University 24 Tongjiaxiang Nanjing 210009 P. R. China
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease China Pharmaceutical University 24 Tongjiaxiang Nanjing 210009 P. R. China
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9
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Aliahmad P, Miyake-Stoner SJ, Geall AJ, Wang NS. Next generation self-replicating RNA vectors for vaccines and immunotherapies. Cancer Gene Ther 2022:10.1038/s41417-022-00435-8. [PMID: 35194198 PMCID: PMC8861484 DOI: 10.1038/s41417-022-00435-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/18/2022] [Accepted: 01/28/2022] [Indexed: 01/06/2023]
Abstract
RNA technology has recently come to the forefront of innovative medicines and is being explored for a wide range of therapies, including prophylactic and therapeutic vaccines, biotherapeutic protein expression and gene therapy. In addition to conventional mRNA platforms now approved for prophylactic SARS-CoV2 vaccines, synthetic self-replicating RNA vaccines are currently being evaluated in the clinic for infectious disease and oncology. The prototypical srRNA vectors in clinical development are derived from alphaviruses, specifically Venezuelan Equine Encephalitis Virus (VEEV). While non-VEEV alphaviral strains have been explored as single cycle viral particles, their use as synthetic vectors largely remains under-utilized in clinical applications. Here we describe the potential commonalities and differences in synthetic alphaviral srRNA vectors in host cell interactions, immunogenicity, cellular delivery, and cargo expression. Thus, unlike the current thinking that VEEV-based srRNA is a one-size-fits-all platform, we argue that a new drug development approach leveraging panels of customizable, synthetic srRNA vectors will be required for clinical success.
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10
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Neoantigen Cancer Vaccines: Generation, Optimization, and Therapeutic Targeting Strategies. Vaccines (Basel) 2022; 10:vaccines10020196. [PMID: 35214655 PMCID: PMC8877108 DOI: 10.3390/vaccines10020196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 12/30/2022] Open
Abstract
Alternatives to conventional cancer treatments are highly sought after for high-risk malignancies that have a poor response to established treatment modalities. With research advancing rapidly in the past decade, neoantigen-based immunotherapeutic approaches represent an effective and highly tolerable therapeutic option. Neoantigens are tumor-specific antigens that are not expressed in normal cells and possess significant immunogenic potential. Several recent studies have described the conceptual framework and methodologies to generate neoantigen-based vaccines as well as the formulation of appropriate clinical trials to advance this approach for patient care. This review aims to describe some of the key studies in the recent literature in this rapidly evolving field and summarize the current advances in neoantigen identification and selection, vaccine generation and delivery, and the optimization of neoantigen-based therapeutic strategies, including the early data from pivotal clinical studies.
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11
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Barazzone GC, Teixeira AF, Azevedo BOP, Damiano DK, Oliveira MP, Nascimento ALTO, Lopes APY. Revisiting the Development of Vaccines Against Pathogenic Leptospira: Innovative Approaches, Present Challenges, and Future Perspectives. Front Immunol 2022; 12:760291. [PMID: 35046936 PMCID: PMC8761801 DOI: 10.3389/fimmu.2021.760291] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022] Open
Abstract
Human vaccination against leptospirosis has been relatively unsuccessful in clinical applications despite an expressive amount of vaccine candidates has been tested over years of research. Pathogenic Leptospira encompass a great number of serovars, most of which do not cross-react, and there has been a lack of genetic tools for many years. These obstacles have hampered the understanding of the bacteria's biology and, consequently, the identification of an effective antigen. Thus far, many approaches have been used in an attempt to find a cost-effective and broad-spectrum protective antigen(s) against the disease. In this extensive review, we discuss several strategies that have been used to develop an effective vaccine against leptospirosis, starting with Leptospira-inactivated bacterin, proteins identified in the genome sequences of pathogenic Leptospira, including reverse vaccinology, plasmid DNA, live vaccines, chimeric multi-epitope, and toll- and nod-like receptors agonists. This overview should be able to guide scientists working in the field to select potential antigens and to choose the appropriate formulation to administer the candidates.
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Affiliation(s)
- Giovana C. Barazzone
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Aline F. Teixeira
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil
| | - Bruna O. P. Azevedo
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Deborah K. Damiano
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Marcos P. Oliveira
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Ana L. T. O. Nascimento
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Alexandre P. Y. Lopes
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo (USP), São Paulo, Brazil
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12
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Richard G, Princiotta MF, Bridon D, Martin WD, Steinberg GD, De Groot AS. Neoantigen-based personalized cancer vaccines: the emergence of precision cancer immunotherapy. Expert Rev Vaccines 2021; 21:173-184. [PMID: 34882038 DOI: 10.1080/14760584.2022.2012456] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION The field of cancer therapy has undergone a major transformation in less than a decade due to the introduction of checkpoint inhibitors, the advent of next generation sequencing and the discovery of neoantigens. The key observation that the breadth of each patient's immune response to the unique mutations or neoantigens present in their tumor is directly related to their survival has led oncologists to focus on driving immune responses to neoantigens through vaccination. Oncology has entered the era of precision immunotherapy, and cancer vaccine development is undergoing a paradigm shift. AREAS COVERED Neoantigens are short peptide sequences found in tumors, but not noncancerous tissues, the vast majority of which are unique to each patient. In addition to providing a description of the distinguishing features of neoantigen discovery platforms, this review will address cross-cutting personalized cancer vaccine design themes and developmental stumbling blocks. EXPERT OPINION Immunoinformatic pipelines that can rapidly scan cancer genomes and identify 'the best' neoantigens are in high demand. Despite the need for such tools, immunoinformatic methods for identifying neoepitopes in cancer genomes are diverse and have not been well-validated. Validation of 'personalized vaccine design pipelines' will bring about a revolution in neoantigen-based vaccine design and delivery.
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Affiliation(s)
| | | | | | | | - Gary D Steinberg
- EpiVax Therapeutics, Inc., Providence, RI, USA.,Perlmutter Cancer Center, Department of Urology at NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Anne S De Groot
- EpiVax, Inc., Providence, RI, USA.,Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
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13
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Multi-step screening of neoantigens' HLA- and TCR-interfaces improves prediction of survival. Sci Rep 2021; 11:9983. [PMID: 33976291 PMCID: PMC8113358 DOI: 10.1038/s41598-021-89016-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/19/2021] [Indexed: 12/21/2022] Open
Abstract
Improvement of risk stratification through prognostic biomarkers may enhance the personalization of cancer patient monitoring and treatment. We used Ancer, an immunoinformatic CD8, CD4, and regulatory T cell neoepitope screening system, to perform an advanced neoantigen analysis of genomic data derived from the urothelial cancer cohort of The Cancer Genome Atlas. Ancer demonstrated improved prognostic stratification and five-year survival prediction compared to standard analyses using tumor mutational burden or neoepitope identification using NetMHCpan and NetMHCIIpan. The superiority of Ancer, shown in both univariate and multivariate survival analyses, is attributed to the removal of neoepitopes that do not contribute to tumor immunogenicity based on their homology with self-epitopes. This analysis suggests that the presence of a higher number of unique, non-self CD8- and CD4-neoepitopes contributes to cancer survival, and that prospectively defining these neoepitopes using Ancer is a novel prognostic or predictive biomarker.
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