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Ito M, Koido S, Iwamoto T, Morimoto S, Fujiki F, Sugiyama H, Matsumoto S, Effenberger C, Kiyotani K, Shiba K. Enhancing the immunogenicity of Wilms tumor 1 epitope in mesothelioma cells with immunoproteasome inhibitors. PLoS One 2024; 19:e0308330. [PMID: 39116074 PMCID: PMC11309442 DOI: 10.1371/journal.pone.0308330] [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: 10/17/2023] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
The immunogenicity of cancer cells is influenced by several factors, including the expression of the major histocompatibility complex class I (MHC-I), antigen expression, and the repertoire of proteasome-produced epitope peptides. The malignant pleural mesothelioma cell line ACC-MEOS-4 (MESO-4) expresses high levels of MHC-I and Wilms tumor 1 (WT1) tumor antigens. Using a functional T cell reporter assay specific for the HLA-A*24:02 restricted WT1 epitope (WT1235, CMTWNQMNL), we searched for factors that augmented the immunogenicity of MESO-4, focusing on proteasomes, which have a central role in the antigen processing machinery. ONX-0914, a selective inhibitor of the immunoproteasome subunit β5i, enhanced immunogenicity dose-dependently at low concentrations without cytotoxicity. In addition, CD8+ T lymphocytes recognizing WT1 showed greater cytotoxicity against MESO-4 pre-treated with ONX-0914. MESO-4 expresses a standard proteasome (SP) and immunoproteasome (IP). Notably, IP has distinct catalytic activity from SP, favoring the generation of antigenic peptides with high affinity for MHC-I in antigen-presenting cells and cancer cells. In vitro, immunoproteasome digestion assay and mass spectrometry analysis showed that IP cleaved WT1235 internally after the hydrophobic residues. Importantly, this internal cleavage of the WT1235 epitope was mitigated by ONX-0914. These results suggest that ONX-0914 prevents the internal destructive cleavage of WT1235 by IP, thereby promoting the specific presentation of the WT1 epitope by MESO-4. In conclusion, selective IP inhibitors might offer a means to modulate cancer cell immunogenicity by directing the presentation of particular tumor epitopes.
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Affiliation(s)
- Masaki Ito
- Institute of Clinical Medicine and Research, Research Center for Medical Sciences, The Jikei University School of Medicine, Chiba, Japan
- Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Shigeo Koido
- The Division of Gastroenterology and Hepatology, Department of Internal Medicine, The Jikei University School of Medicine, Kashiwa Hospital, Chiba, Japan
| | - Takeo Iwamoto
- Core Research Facilities, The Jikei University School of Medicine, Tokyo, Japan
| | - Soyoko Morimoto
- Department of Cancer Stem Cell Biology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Fumihiro Fujiki
- Department of Cancer Stem Cell Biology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Haruo Sugiyama
- Department of Cancer Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Saki Matsumoto
- Project for Immunogenomics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Clara Effenberger
- Project for Immunogenomics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kazuma Kiyotani
- Project for Immunogenomics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kiyotaka Shiba
- Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
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Weeder BR, Wood MA, Li E, Nellore A, Thompson RF. pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification. Bioinformatics 2021; 37:3723-3733. [PMID: 34478497 DOI: 10.1093/bioinformatics/btab628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/21/2021] [Accepted: 08/31/2021] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION Proteasomal cleavage is a key component in protein turnover, as well as antigen processing and presentation. Although tools for proteasomal cleavage prediction are available, they vary widely in their performance, options, and availability. RESULTS Herein we present pepsickle, an open-source tool for proteasomal cleavage prediction with better in vivo prediction performance (AUC) and computational speed than current models available in the field and with the ability to predict sites based on both constitutive and immunoproteasome profiles. Post-hoc filtering of predicted patient neoepitopes using pepsickle significantly enriches for immune-responsive epitopes and may improve current epitope prediction and vaccine development pipelines. AVAILABILITY pepsickle is open source and available at https://github.com/pdxgx/pepsickle. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Benjamin R Weeder
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon, USA.,Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
| | | | - Ellysia Li
- Pacific University, Forest Grove, OR, USA
| | - Abhinav Nellore
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon, USA.,Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA.,Department of Surgery, Oregon Health & Science University, Portland, Oregon, USA
| | - Reid F Thompson
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon, USA.,Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA.,Department of Radiation Medicine, Oregon Health & Science University, Portland, Oregon, USA.,Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA.,Division of Hospital and Specialty Medicine, VA Portland Healthcare System, Portland, Oregon, USA
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TAS0314, a novel multi-epitope long peptide vaccine, showed synergistic antitumor immunity with PD-1/PD-L1 blockade in HLA-A*2402 mice. Sci Rep 2020; 10:17284. [PMID: 33057061 PMCID: PMC7560884 DOI: 10.1038/s41598-020-74187-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 09/28/2020] [Indexed: 01/05/2023] Open
Abstract
Cancer peptide vaccines are a promising cancer immunotherapy that can induce cancer-specific cytotoxic T lymphocytes (CTLs) in tumors. However, recent clinical trials of cancer vaccines have revealed that the efficacy of the vaccines is limited. Targeting single antigens and vaccination with short peptides are partly the cause of the poor clinical outcomes. We synthesized a novel multi-epitope long peptide, TAS0314, which induced multiple epitope-specific CTLs in HLA knock-in mice. It also showed superior epitope-specific CTL induction and antitumor activity. We also established a combination treatment model of vaccination with PD-1/PD-L1 blockade in HLA-A*2402 knock-in mice, and it showed a synergistic antitumor effect with TAS0314. Thus, our data indicated that TAS0314 treatment, especially in combination with PD-1/PD-L1 blockade, is a promising therapeutic candidate for cancer immunotherapy.
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Wada H, Shimizu A, Osada T, Tanaka Y, Fukaya S, Sasaki E. Correction: Development of a novel immunoproteasome digestion assay for synthetic long peptide vaccine design. PLoS One 2018; 13:e0205567. [PMID: 30286206 PMCID: PMC6171946 DOI: 10.1371/journal.pone.0205567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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