1
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Zhang Y, Yan H, Wei Y, Wei X. Decoding mitochondria's role in immunity and cancer therapy. Biochim Biophys Acta Rev Cancer 2024; 1879:189107. [PMID: 38734035 DOI: 10.1016/j.bbcan.2024.189107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/22/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024]
Abstract
The functions of mitochondria, including energy production and biomolecule synthesis, have been known for a long time. Given the rising incidence of cancer, the role of mitochondria in cancer has become increasingly popular. Activated by components released by mitochondria, various pathways interact with each other to induce immune responses to protect organisms from attack. However, mitochondria play dual roles in the progression of cancer. Abnormalities in proteins, which are the elementary structures of mitochondria, are closely linked with oncogenesis. Both the aberrant accumulation of intermediates and mutations in enzymes result in the generation and progression of cancer. Therefore, targeting mitochondria to treat cancer may be a new strategy. Several drugs aimed at inhibiting mutated enzymes and accumulated intermediates have been tested clinically. Here, we discuss the current understanding of mitochondria in cancer and the interactions between mitochondrial functions, immune responses, and oncogenesis. Furthermore, we discuss mitochondria as hopeful targets for cancer therapy, providing insights into the progression of future therapeutic strategies.
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Affiliation(s)
- Yu Zhang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan, PR China
| | - Hong Yan
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan, PR China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan, PR China.
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041 Chengdu, Sichuan, PR China.
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2
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Koncz B, Balogh GM, Manczinger M. A journey to your self: The vague definition of immune self and its practical implications. Proc Natl Acad Sci U S A 2024; 121:e2309674121. [PMID: 38722806 PMCID: PMC11161755 DOI: 10.1073/pnas.2309674121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2024] Open
Abstract
The identification of immunogenic peptides has become essential in an increasing number of fields in immunology, ranging from tumor immunotherapy to vaccine development. The nature of the adaptive immune response is shaped by the similarity between foreign and self-protein sequences, a concept extensively applied in numerous studies. Can we precisely define the degree of similarity to self? Furthermore, do we accurately define immune self? In the current work, we aim to unravel the conceptual and mechanistic vagueness hindering the assessment of self-similarity. Accordingly, we demonstrate the remarkably low consistency among commonly employed measures and highlight potential avenues for future research.
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Affiliation(s)
- Balázs Koncz
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Hungarian Research Network (HUN-REN) Biological Research Centre, Szeged6726, Hungary
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre (HCEMM-BRC) Systems Immunology Research Group, Szeged6726, Hungary
- Department of Dermatology and Allergology, University of Szeged, Szeged6720, Hungary
| | - Gergő Mihály Balogh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Hungarian Research Network (HUN-REN) Biological Research Centre, Szeged6726, Hungary
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre (HCEMM-BRC) Systems Immunology Research Group, Szeged6726, Hungary
- Department of Dermatology and Allergology, University of Szeged, Szeged6720, Hungary
| | - Máté Manczinger
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Hungarian Research Network (HUN-REN) Biological Research Centre, Szeged6726, Hungary
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre (HCEMM-BRC) Systems Immunology Research Group, Szeged6726, Hungary
- Department of Dermatology and Allergology, University of Szeged, Szeged6720, Hungary
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3
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Hamid MHBA, Cespedes PF, Jin C, Chen JL, Gileadi U, Antoun E, Liang Z, Gao F, Teague R, Manoharan N, Maldonado-Perez D, Khalid-Alham N, Cerundolo L, Ciaoca R, Hester SS, Pinto-Fernández A, Draganov SD, Vendrell I, Liu G, Yao X, Kvalvaag A, Dominey-Foy DCC, Nanayakkara C, Kanellakis N, Chen YL, Waugh C, Clark SA, Clark K, Sopp P, Rahman NM, Verrill C, Kessler BM, Ogg G, Fernandes RA, Fisher R, Peng Y, Dustin ML, Dong T. Unconventional human CD61 pairing with CD103 promotes TCR signaling and antigen-specific T cell cytotoxicity. Nat Immunol 2024; 25:834-846. [PMID: 38561495 PMCID: PMC11065694 DOI: 10.1038/s41590-024-01802-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 02/29/2024] [Indexed: 04/04/2024]
Abstract
Cancer remains one of the leading causes of mortality worldwide, leading to increased interest in utilizing immunotherapy strategies for better cancer treatments. In the past decade, CD103+ T cells have been associated with better clinical prognosis in patients with cancer. However, the specific immune mechanisms contributing toward CD103-mediated protective immunity remain unclear. Here, we show an unexpected and transient CD61 expression, which is paired with CD103 at the synaptic microclusters of T cells. CD61 colocalization with the T cell antigen receptor further modulates downstream T cell antigen receptor signaling, improving antitumor cytotoxicity and promoting physiological control of tumor growth. Clinically, the presence of CD61+ tumor-infiltrating T lymphocytes is associated with improved clinical outcomes, mediated through enhanced effector functions and phenotype with limited evidence of cellular exhaustion. In conclusion, this study identified an unconventional and transient CD61 expression and pairing with CD103 on human immune cells, which potentiates a new target for immune-based cellular therapies.
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MESH Headings
- Animals
- Humans
- Mice
- Antigens, CD/metabolism
- Antigens, CD/immunology
- Apyrase
- Cell Line, Tumor
- Cytotoxicity, Immunologic
- Integrin alpha Chains/metabolism
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Neoplasms/immunology
- Neoplasms/therapy
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/immunology
- Signal Transduction/immunology
- T-Lymphocytes, Cytotoxic/immunology
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Affiliation(s)
- Megat H B A Hamid
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Pablo F Cespedes
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Chen Jin
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ji-Li Chen
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Uzi Gileadi
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Elie Antoun
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Zhu Liang
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Fei Gao
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Renuka Teague
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Nikita Manoharan
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Maldonado-Perez
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Nasullah Khalid-Alham
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
- Oxford National Institute of Health Research (NIHR) Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Lucia Cerundolo
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Raul Ciaoca
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Svenja S Hester
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Adán Pinto-Fernández
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Simeon D Draganov
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Iolanda Vendrell
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Guihai Liu
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Xuan Yao
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Audun Kvalvaag
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Department of Molecular Cell Biology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Charunya Nanayakkara
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nikolaos Kanellakis
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford National Institute of Health Research (NIHR) Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Laboratory of Pleural and Lung Cancer Translational Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Respiratory Medicine, Churchill Hospital, Oxford University Hospitals, Oxford, UK
| | - Yi-Ling Chen
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Craig Waugh
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sally-Ann Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Kevin Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Sopp
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Najib M Rahman
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford National Institute of Health Research (NIHR) Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Laboratory of Pleural and Lung Cancer Translational Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Respiratory Medicine, Churchill Hospital, Oxford University Hospitals, Oxford, UK
| | - Clare Verrill
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Oxford National Institute of Health Research (NIHR) Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Benedikt M Kessler
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Graham Ogg
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ricardo A Fernandes
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roman Fisher
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Yanchun Peng
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Michael L Dustin
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Tao Dong
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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4
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Feng Z, Zhang X, Zhou J, Li Q, Chu L, Di G, Xu Z, Chen Q, Wang M, Jiang X, Xia H, Chen X. An in vitro-transcribed circular RNA targets the mitochondrial inner membrane cardiolipin to ablate EIF4G2 +/PTBP1 + pan-adenocarcinoma. NATURE CANCER 2024; 5:30-46. [PMID: 37845485 DOI: 10.1038/s43018-023-00650-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 09/07/2023] [Indexed: 10/18/2023]
Abstract
In vitro-transcribed (IVT) mRNA has arisen as a rapid method for the production of nucleic acid drugs. Here, we have constructed an oncolytic IVT mRNA that utilizes human rhinovirus type 2 (HRV2) internal ribosomal entry sites (IRESs) to selectively trigger translation in cancer cells with high expression of EIF4G2 and PTBP1. The oncolytic effect was provided by a long hGSDMDc .825 T>A/c.884 A>G-F1LCT mutant mRNA sequence with mitochondrial inner membrane cardiolipin targeting toxicity that triggers mitophagy. Utilizing the permuted intron-exon (PIE) splicing circularization strategy and lipid nanoparticle (LNP) encapsulation reduced immunogenicity of the mRNA and enabled delivery to eukaryotic cells in vivo. Engineered HRV2 IRESs-GSDMDp.D275E/E295G-F1LCT circRNA-LNPs (GSDMDENG circRNA) successfully inhibited EIF4G2+/PTBP1+ pan-adenocarcinoma xenografts growth. Importantly, in a spontaneous tumor model with abnormal EIF4G2 and PTBP1 caused by KRAS G12D mutation, GSDMDENG circRNA significantly prevented the occurrence of pancreatic, lung and colon adenocarcinoma, improved the survival rate and induced persistent KRAS G12D tumor antigen-specific cytotoxic T lymphocyte responses.
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Affiliation(s)
- Zunyong Feng
- The Translational Research Institute for Neurological Disorders & Interdisciplinary Research Center of Neuromedicine and Chemical Biology of Wannan Medical College, Department of Neurosurgery, Department of Intensive Care Medicine, the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Zhongda Hospital, School of Medicine & School of Biological Sciences and Medical Engineering, Advanced Institute for Life and Health & Interdisciplinary Innovation Institute for Medicine and Engineering, Southeast University, Nanjing, China
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore, Singapore
| | - Xuanbo Zhang
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore, Singapore
| | - Jing Zhou
- Department of Anatomy, School of Basic Medicine & School of Medical Imageology, Anhui Province Key laboratory of Active Biological Macro-molecules Research, Wannan Medical College, Wuhu, China
| | - Qiang Li
- Department of Anatomy, School of Basic Medicine & School of Medical Imageology, Anhui Province Key laboratory of Active Biological Macro-molecules Research, Wannan Medical College, Wuhu, China
| | - Liuxi Chu
- Zhongda Hospital, School of Medicine & School of Biological Sciences and Medical Engineering, Advanced Institute for Life and Health & Interdisciplinary Innovation Institute for Medicine and Engineering, Southeast University, Nanjing, China
| | - Guangfu Di
- The Translational Research Institute for Neurological Disorders & Interdisciplinary Research Center of Neuromedicine and Chemical Biology of Wannan Medical College, Department of Neurosurgery, Department of Intensive Care Medicine, the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
| | - Zhengyuan Xu
- Department of Anatomy, School of Basic Medicine & School of Medical Imageology, Anhui Province Key laboratory of Active Biological Macro-molecules Research, Wannan Medical College, Wuhu, China
| | - Qun Chen
- The Translational Research Institute for Neurological Disorders & Interdisciplinary Research Center of Neuromedicine and Chemical Biology of Wannan Medical College, Department of Neurosurgery, Department of Intensive Care Medicine, the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
| | - Ming Wang
- Department of Neurosurgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiaochun Jiang
- The Translational Research Institute for Neurological Disorders & Interdisciplinary Research Center of Neuromedicine and Chemical Biology of Wannan Medical College, Department of Neurosurgery, Department of Intensive Care Medicine, the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China.
| | - Hongping Xia
- Zhongda Hospital, School of Medicine & School of Biological Sciences and Medical Engineering, Advanced Institute for Life and Health & Interdisciplinary Innovation Institute for Medicine and Engineering, Southeast University, Nanjing, China.
- Department of Pathology, Nanjing Drum Tower Hospital Clinical College & Key Laboratory of Antibody Technique of National Health Commission & Jiangsu Antibody Drug Engineering Research Center, Nanjing Medical University, Nanjing, China.
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore, Singapore.
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5
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Li CY, Chou TF, Lo YL. An innovative nanoformulation utilizing tumor microenvironment-responsive PEG-polyglutamic coating and dynamic charge adjustment for specific targeting of ER stress inducer, microRNA, and immunoadjuvant in pancreatic cancer: In vitro investigations. Int J Biol Macromol 2024; 254:127905. [PMID: 37939778 DOI: 10.1016/j.ijbiomac.2023.127905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a significant obstacle to lowering global cancer deaths. CB-5083, a novel valosin-containing protein (VCP)/p97 inhibitor that disrupts proteasomal degradation and induces endoplasmic reticulum stress (ERS) accumulation, was evaluated as an inducer of immunogenic cell death (ICD) in PDAC treatment. Furthermore, miR-142 enhances checkpoint blockade and promotes M1 repolarization, while Toll-like receptor 7/8 agonist resiquimod (R) acts as an immunoadjuvant to amplify the immune response to miR-142. This research signifies the first integration of CB, miR-142, and R in solid lipid nanoparticles (SLNs) modified with peptides targeting PD-L1, EGFR, and ER, which were shelled by the PEG-polyglutamic (PGA) coating that detaches in response to the acidic pH values in the tumor microenvironment (TME). The modified SLNs exhibited pH-sensitive cytotoxicity against Panc-02 cells, preserving normal cells and preventing hemolysis. The innovative approach simultaneously modulated pathways, including VCP/Bip/K48-Ub/ATF6, IRE1α/XBPs/LC3II, PD-L1/TGF-β/IL-10/CD206/MSR1/Arg1, and TNF-α/IFN-γ/IL-6/iNOS/COX-2. Combined treatment blocked VCP, arrested the cell cycle, inhibited EMT, triggered ERS-mediated autophagy/apoptosis, and stimulated robust ICD via the release of damage-associated molecular patterns. This adaptable nanoformulation, displaying pH-sensitive PEG-PGA de-coating and precisely targeting EGFR, PD-L1, and ER, serves to hinder EMT and immune evasion, subsequently amplifying ICD in PDAC cells and the TME.
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Affiliation(s)
- Ching-Yao Li
- Department and Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, United States
| | - Yu-Li Lo
- Department and Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan; Faculty of Pharmacy, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan.
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6
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Karnaukhov V, Paes W, Woodhouse IB, Partridge T, Nicastri A, Brackenridge S, Shcherbinin D, Chudakov DM, Zvyagin IV, Ternette N, Koohy H, Borrow P, Shugay M. HLA variants have different preferences to present proteins with specific molecular functions which are complemented in frequent haplotypes. Front Immunol 2022; 13:1067463. [PMID: 36605212 PMCID: PMC9808399 DOI: 10.3389/fimmu.2022.1067463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Human leukocyte antigen (HLA) genes are the most polymorphic loci in the human genome and code for proteins that play a key role in guiding adaptive immune responses by presenting foreign and self peptides (ligands) to T cells. Each person carries up to 6 HLA class I variants (maternal and paternal copies of HLA-A, HLA-B and HLA-C genes) and also multiple HLA class II variants, which cumulatively define the landscape of peptides presented to T cells. Each HLA variant has its own repertoire of presented peptides with a certain sequence motif which is mainly defined by peptide anchor residues (typically the second and the last positions for HLA class I ligands) forming key interactions with the peptide-binding groove of HLA. In this study, we aimed to characterize HLA binding preferences in terms of molecular functions of presented proteins. To focus on the ligand presentation bias introduced specifically by HLA-peptide interaction we performed large-scale in silico predictions of binding of all peptides from human proteome for a wide range of HLA variants and established which functions are characteristic for proteins that are more or less preferentially presented by different HLA variants using statistical calculations and gene ontology (GO) analysis. We demonstrated marked distinctions between HLA variants in molecular functions of preferentially presented proteins (e.g. some HLA variants preferentially present membrane and receptor proteins, while others - ribosomal and DNA-binding proteins) and reduced presentation of extracellular matrix and collagen proteins by the majority of HLA variants. To explain these observations we demonstrated that HLA preferentially presents proteins enriched in amino acids which are required as anchor residues for the particular HLA variant. Our observations can be extrapolated to explain the protective effect of certain HLA alleles in infectious diseases, and we hypothesize that they can also explain susceptibility to certain autoimmune diseases and cancers. We demonstrate that these differences lead to differential presentation of HIV, influenza virus, SARS-CoV-1 and SARS-CoV-2 proteins by various HLA alleles. Taking into consideration that HLA alleles are inherited in haplotypes, we hypothesized that haplotypes composed of a combination of HLA variants with different presentation preferences should be more advantageous as they allow presenting a larger repertoire of peptides and avoiding holes in immunopeptidome. Indeed, we demonstrated that HLA-A/HLA-B and HLA-A/HLA-C haplotypes which have a high frequency in the human population are comprised of HLA variants that are more distinct in terms of functions of preferentially presented proteins than the control pairs.
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Affiliation(s)
- Vadim Karnaukhov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Isaac B. Woodhouse
- Medical Research Council (MRC) Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM) Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, Oxford, United Kingdom
| | - Thomas Partridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon Brackenridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Dmitrii Shcherbinin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry M. Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan V. Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Hashem Koohy
- Medical Research Council (MRC) Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM) Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, Oxford, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia,*Correspondence: Mikhail Shugay,
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7
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Mitochondrial Proteins as Source of Cancer Neoantigens. Int J Mol Sci 2022; 23:ijms23052627. [PMID: 35269772 PMCID: PMC8909979 DOI: 10.3390/ijms23052627] [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: 01/28/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 01/27/2023] Open
Abstract
In the past decade, anti-tumour immune responses have been successfully exploited to improve the outcome of patients with different cancers. Significant progress has been made in taking advantage of different types of T cell functions for therapeutic purposes. Despite these achievements, only a subset of patients respond favorably to immunotherapy. Therefore, there is a need of novel approaches to improve the effector functions of immune cells and to recognize the major targets of anti-tumour immunity. A major hallmark of cancer is metabolic rewiring associated with switch of mitochondrial functions. These changes are a consequence of high energy demand and increased macromolecular synthesis in cancer cells. Such adaptations in tumour cells might generate novel targets of tumour therapy, including the generation of neoantigens. Here, we review the most recent advances in research on the immune response to mitochondrial proteins in different cellular conditions.
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Morotti M, Albukhari A, Alsaadi A, Artibani M, Brenton JD, Curbishley SM, Dong T, Dustin ML, Hu Z, McGranahan N, Miller ML, Santana-Gonzalez L, Seymour LW, Shi T, Van Loo P, Yau C, White H, Wietek N, Church DN, Wedge DC, Ahmed AA. Promises and challenges of adoptive T-cell therapies for solid tumours. Br J Cancer 2021; 124:1759-1776. [PMID: 33782566 PMCID: PMC8144577 DOI: 10.1038/s41416-021-01353-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/22/2021] [Accepted: 03/04/2021] [Indexed: 12/11/2022] Open
Abstract
Cancer is a leading cause of death worldwide and, despite new targeted therapies and immunotherapies, many patients with advanced-stage- or high-risk cancers still die, owing to metastatic disease. Adoptive T-cell therapy, involving the autologous or allogeneic transplant of tumour-infiltrating lymphocytes or genetically modified T cells expressing novel T-cell receptors or chimeric antigen receptors, has shown promise in the treatment of cancer patients, leading to durable responses and, in some cases, cure. Technological advances in genomics, computational biology, immunology and cell manufacturing have brought the aspiration of individualised therapies for cancer patients closer to reality. This new era of cell-based individualised therapeutics challenges the traditional standards of therapeutic interventions and provides opportunities for a paradigm shift in our approach to cancer therapy. Invited speakers at a 2020 symposium discussed three areas-cancer genomics, cancer immunology and cell-therapy manufacturing-that are essential to the effective translation of T-cell therapies in the treatment of solid malignancies. Key advances have been made in understanding genetic intratumour heterogeneity, and strategies to accurately identify neoantigens, overcome T-cell exhaustion and circumvent tumour immunosuppression after cell-therapy infusion are being developed. Advances are being made in cell-manufacturing approaches that have the potential to establish cell-therapies as credible therapeutic options. T-cell therapies face many challenges but hold great promise for improving clinical outcomes for patients with solid tumours.
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Affiliation(s)
- Matteo Morotti
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Ashwag Albukhari
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulkhaliq Alsaadi
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mara Artibani
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James D Brenton
- Functional Genomics of Ovarian Cancer Laboratory, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Stuart M Curbishley
- Advanced Therapies Facility and National Institute for Health Research (NIHR) Biomedical Research Centre, University of Birmingham, Birmingham, UK
| | - Tao Dong
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, University of Oxford, Oxford, UK
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Zhiyuan Hu
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
| | - Martin L Miller
- Cancer System Biology Group, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Laura Santana-Gonzalez
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Leonard W Seymour
- Gene Therapy Group, Department of Oncology, University of Oxford, Oxford, UK
| | - Tingyan Shi
- Department of Gynecological Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Christopher Yau
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
- The Alan Turing Institute, London, UK
| | - Helen White
- Patient Representative, Endometrial Cancer Genomics England Clinical Interpretation Partnership (GeCIP) Domain, London, UK
| | - Nina Wietek
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - David N Church
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
| | - David C Wedge
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK.
| | - Ahmed A Ahmed
- Ovarian Cancer Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK.
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Karnaukhov V, Paes W, Woodhouse IB, Partridge T, Nicastri A, Brackenridge S, Scherbinin D, Chudakov DM, Zvyagin IV, Ternette N, Koohy H, Borrow P, Shugay M. HLA binding of self-peptides is biased towards proteins with specific molecular functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.16.431395. [PMID: 33619495 PMCID: PMC7899460 DOI: 10.1101/2021.02.16.431395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Human leukocyte antigen (HLA) is highly polymorphic and plays a key role in guiding adaptive immune responses by presenting foreign and self peptides to T cells. Each HLA variant selects a minor fraction of peptides that match a certain motif required for optimal interaction with the peptide-binding groove. These restriction rules define the landscape of peptides presented to T cells. Given these limitations, one might suggest that the choice of peptides presented by HLA is non-random and there is preferential presentation of an array of peptides that is optimal for distinguishing self and foreign proteins. In this study we explore these preferences with a comparative analysis of self peptides enriched and depleted in HLA ligands. We show that HLAs exhibit preferences towards presenting peptides from certain proteins while disfavoring others with specific functions, and highlight differences between various HLA genes and alleles in those preferences. We link those differences to HLA anchor residue propensities and amino acid composition of preferentially presented proteins. The set of proteins that peptides presented by a given HLA are most likely to be derived from can be used to distinguish between class I and class II HLAs and HLA alleles. Our observations can be extrapolated to explain the protective effect of certain HLA alleles in infectious diseases, and we hypothesize that they can also explain susceptibility to certain autoimmune diseases and cancers. We demonstrate that these differences lead to differential presentation of HIV, influenza virus, SARS-CoV-1 and SARS-CoV-2 proteins by various HLA alleles. Finally, we show that the reported self peptidome preferences of distinct HLA variants can be compensated by combinations of HLA-A/HLA-B and HLA-A/HLA-C alleles in frequent haplotypes.
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Affiliation(s)
- Vadim Karnaukhov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Isaac B. Woodhouse
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Thomas Partridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Simon Brackenridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Dmitrii Scherbinin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry M. Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan V. Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hashem Koohy
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
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