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Martínez-Cortés F, Domínguez-Romero AN, Pérez-Hernández EG, Orozco-Delgado DL, Avila S, Odales J, Guzman Valle J, Gevorkian G, Manoutcharian K. Tumor antigen-unbiased variable epitope library contains mimotopes with antitumor effect in a mouse model of breast cancer. Mol Immunol 2023; 157:91-100. [PMID: 37002957 DOI: 10.1016/j.molimm.2023.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/23/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023]
Abstract
Breast cancer is one of the leading causes of death that affects the female population worldwide. Despite advances in treatments and a greater understanding of the disease, there are still difficulties in successfully treating patients. Currently, the main challenge in the field of cancer vaccines is antigenic variability which can reduce antigen-specific T- cell response efficacy. The search for and validation of immunogenic antigen targets increased dramatically over the past few decades and, with the advent of modern sequencing techniques, permitting the fast and accurate identification of the neoantigen landscape of tumor cells, will undoubtedly continue to grow exponentially for years to come. We have previously implemented Variable Epitope Libraries (VEL) as an unconventional vaccine strategy in preclinical models and for identifying and selecting mutant epitope variants. Here, we used an alanine-based sequence to generate a 9-mer VEL-like combinatorial mimotope library G3d as a new class of vaccine immunogen. An in silico analysis of the 16,000 G3d-derived sequences revealed potential MHC-I binders and immunogenic mimotopes. We demonstrated the antitumor effect of treatment with G3d in the 4T1 murine model of breast cancer. Moreover, two different T cell proliferation screening assays against a panel of randomly selected G3d-derived mimotopes allowed the isolation of both stimulatory and inhibitory mimotopes showing differential therapeutic vaccine efficacy. Thus, the mimotope library is a promising vaccine immunogen and a reliable source for isolating molecular cancer vaccine components.
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Affiliation(s)
- Fernando Martínez-Cortés
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, AP 70228, México City 04510, Mexico
| | - Allan Noé Domínguez-Romero
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, AP 70228, México City 04510, Mexico
| | - Eréndira G Pérez-Hernández
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, AP 70228, México City 04510, Mexico
| | - Diana L Orozco-Delgado
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, AP 70228, México City 04510, Mexico
| | - Sandra Avila
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, AP 70228, México City 04510, Mexico
| | - Josué Odales
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, AP 70228, México City 04510, Mexico
| | - Jesus Guzman Valle
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, AP 70228, México City 04510, Mexico
| | - Goar Gevorkian
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, AP 70228, México City 04510, Mexico
| | - Karen Manoutcharian
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, AP 70228, México City 04510, Mexico.
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Abstract
T cells respond to threats in an antigen-specific manner using T cell receptors (TCRs) that recognize short peptide antigens presented on major histocompatibility complex (MHC) proteins. The TCR-peptide-MHC interaction mediated between a T cell and its target cell dictates its function and thereby influences its role in disease. A lack of approaches for antigen discovery has limited the fundamental understanding of the antigenic landscape of the overall T cell response. Recent advances in high-throughput sequencing, mass cytometry, microfluidics and computational biology have led to a surge in approaches to address the challenge of T cell antigen discovery. Here, we summarize the scope of this challenge, discuss in depth the recent exciting work and highlight the outstanding questions and remaining technical hurdles in this field.
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Kubrycht J, Sigler K, Souček P. Virtual interactomics of proteins from biochemical standpoint. Mol Biol Int 2012; 2012:976385. [PMID: 22928109 PMCID: PMC3423939 DOI: 10.1155/2012/976385] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/18/2012] [Accepted: 05/18/2012] [Indexed: 12/24/2022] Open
Abstract
Virtual interactomics represents a rapidly developing scientific area on the boundary line of bioinformatics and interactomics. Protein-related virtual interactomics then comprises instrumental tools for prediction, simulation, and networking of the majority of interactions important for structural and individual reproduction, differentiation, recognition, signaling, regulation, and metabolic pathways of cells and organisms. Here, we describe the main areas of virtual protein interactomics, that is, structurally based comparative analysis and prediction of functionally important interacting sites, mimotope-assisted and combined epitope prediction, molecular (protein) docking studies, and investigation of protein interaction networks. Detailed information about some interesting methodological approaches and online accessible programs or databases is displayed in our tables. Considerable part of the text deals with the searches for common conserved or functionally convergent protein regions and subgraphs of conserved interaction networks, new outstanding trends and clinically interesting results. In agreement with the presented data and relationships, virtual interactomic tools improve our scientific knowledge, help us to formulate working hypotheses, and they frequently also mediate variously important in silico simulations.
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Affiliation(s)
- Jaroslav Kubrycht
- Department of Physiology, Second Medical School, Charles University, 150 00 Prague, Czech Republic
| | - Karel Sigler
- Laboratory of Cell Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic
| | - Pavel Souček
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
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Zhao L, Liu Z, Fan D. Overview of mimotopes and related strategies in tumor vaccine development. Expert Rev Vaccines 2009; 7:1547-55. [PMID: 19053210 DOI: 10.1586/14760584.7.10.1547] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Tumor vaccine has been studied extensively as an alternative or adjuvant therapy in the treatment of malignant tumors in the hope of prolonging the overall survival rates of cancer patients. The efficacy largely relies on the specificity of the target. In the last decade, many antibody epitopes, called mimotopes, have been revealed as candidates through phage-display technology. These mimotopes do not necessarily consist of amino acid sequences that are identical to the native antigen but they do mimic their structure. Tumor vaccines based on these mimotopes have been proposed as an important developing strategy. Some peptide mimotopes have produced encouraging clinical outcomes. Although most studies are still in the preclinical phase, these findings will possibly pave the way for the development of novel mimotope-based tumor vaccines.
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Affiliation(s)
- Lina Zhao
- State Key Laboratory of Cancer Biology, Institute of Digestive Disease, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China.
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Abstract
Cancer vaccines need to be designed to effectively induce tumor-specific CD8(+) T cells, the key effector cells in immune responses against tumors. These T cells recognize peptides generated from cellular proteins by limited proteolysis, and bound and presented at cell surfaces by MHC class I molecules. Mimotopes, mimetics of T cell epitopes, have been derived from known epitopes by sequence modification, or developed de novo using combinatorial peptide libraries to scan the entire sequence space for peptides that induce the desired T cell responses. Mimotopes of both types have been tested in clinical vaccination trials for treatment of cancer.
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Affiliation(s)
- Tumenjargal Sharav
- Department of Dermatology, Venerology and Allergy, Clinical Research Group Tumor Immunology, Charité - Universitätsmedizin Berlin, Humboldt University, D-10098 Berlin, Germany
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Abstract
With increasing knowledge of tumor-associated antigens and T cell epitopes, and the mechanisms of induction and regulation of T-cellular immune responses, therapeutic vaccination is increasingly being explored as a treatment option for cancer. Several clinical cancer vaccination trials, the majority of them with melanoma patients, have demonstrated efficient induction of tumor-specific cellular immune responses in patients. However, these immune responses, in most cases, do not translate into clinical responses. The clinical response rates in these trials are relatively low. The most likely causes for the lack of correlation of immunological and clinical responsiveness are loss of antigenicity and immune suppression. Nonetheless, many patients in the vaccination trials have experienced extended survival compared to clinical experience. Therapeutic vaccination thus appears suited for maintenance therapy where cure is not possible and is an interesting option for adjuvant therapy after surgical tumor resection. While the clinical efficacy of vaccination is expected to be better for early-stage cancer, advancement of the treatment of advanced-stage disease will require combination with other therapeutic principles.
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Affiliation(s)
- Peter Walden
- Department of Dermatology, Venerology and Allergy, Clinical Research Group Tumor Immunology, Berlin, Germany
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Bredenbeck A, Losch FO, Sharav T, Eichler-Mertens M, Filter M, Givehchi A, Sterry W, Wrede P, Walden P. Identification of Noncanonical Melanoma-Associated T Cell Epitopes for Cancer Immunotherapy. THE JOURNAL OF IMMUNOLOGY 2005; 174:6716-24. [PMID: 15905511 DOI: 10.4049/jimmunol.174.11.6716] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The identification of tumor-associated T cell epitopes has contributed significantly to the understanding of the interrelationship of tumor and immune system and is instrumental in the development of therapeutic vaccines for the treatment of cancer. Most of the known epitopes have been identified with prediction algorithms that compute the potential capacity of a peptide to bind to HLA class I molecules. However, naturally expressed T cell epitopes need not necessarily be strong HLA binders. To overcome this limitation of the available prediction algorithms we established a strategy for the identification of T cell epitopes that include suboptimal HLA binders. To this end, an artificial neural network was developed that predicts HLA-binding peptides in protein sequences by taking the entire sequence context into consideration rather than computing the sum of the contribution of the individual amino acids. Using this algorithm, we predicted seven HLA A*0201-restricted potential T cell epitopes from known melanoma-associated Ags that do not conform to the canonical anchor motif for this HLA molecule. All seven epitopes were validated as T cell epitopes and three as naturally processed by melanoma tumor cells. T cells for four of the new epitopes were found at elevated frequencies in the peripheral blood of melanoma patients. Modification of the peptides to the canonical sequence motifs led to improved HLA binding and to improved capacity to stimulate T cells.
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Affiliation(s)
- Anne Bredenbeck
- Department of Dermatology, Clinical Research Group Tumor Immunology, Charité-Universitätsmedizin Berlin, Germany
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Deocaris CC, Taira K, Kaul SC, Wadhwa R. Mimotope-hormesis and mortalin/grp75/mthsp70: a new hypothesis on how infectious disease-associated epitope mimicry may explain low cancer burden in developing nations. FEBS Lett 2004; 579:586-90. [PMID: 15670812 DOI: 10.1016/j.febslet.2004.11.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2004] [Revised: 11/25/2004] [Accepted: 11/29/2004] [Indexed: 01/13/2023]
Abstract
It is generally observed that countries with heavy infectious burden show lower cancer incidence as compared to more affluent nations. With the emerging paradigm on microbial heat shock proteins (hsps) as molecular link between infections and autoimmune diseases, we posit a new hypothesis, the "mimotope-hormesis", on the immunologic impact of infections on regional cancer prevention. According to this, assaults of infection during early adulthood could fortify the immune system to evoke more potent defenses against late-onset diseases, such as cancer, via autoimmunity. Interestingly, both experimental and clinical data support the beneficial role of autoimmunity in long-term cancer survivors. We illustrate this by a comprehensive in silico mimotope (epitope mimicry) analysis of human infectious pathogens against mortalin (mthsp70/PB74/GRP75), a type of hsp70 protein involved in control of cell proliferation, immortalization and tumorigenesis.
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Affiliation(s)
- Custer C Deocaris
- Cell Proliferation Research Team, Gene Function Research Center, National Institute of Advanced Industrial Science & Technology (AIST), 1-1-1 Higashi, Tsukuba Science City 305-8562, Japan
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