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Liu X, Jin W, Bao D, He T, Wang W, Li Z, Yang X, Tong Y, Shu M, Wang Y, Yuan J, Yang Y. DIPAN: Detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data. Comput Struct Biotechnol J 2024; 23:2057-2066. [PMID: 38783901 PMCID: PMC11112131 DOI: 10.1016/j.csbj.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Intronic polyadenylation (IPA) refers to a particular type of alternative polyadenylation where a gene makes use of a polyadenylation site located within its introns. Aberrant IPA events have been observed in various types of cancer. IPA can produce noncoding transcripts or truncated protein-coding transcripts with altered coding sequences in the resulting protein product. Therefore, IPA events hold the potential to act as a reservoir of tumor neoantigens. Here, we developed a computational method termed DIPAN, which incorporates IPA detection, protein fragmentation, and MHC binding prediction to predict IPA-derived neoantigens. Utilizing RNA-seq from breast cancer cell lines and ovarian cancer clinical samples, we demonstrated the significant contribution of IPA events to the neoantigen repertoire. Through mass spectrometry immunopeptidome analysis, we further illustrated the processing and presentation of IPA-derived neoantigens on the surface of cancer cells. While most IPA-derived neoantigens are sample-specific, shared neoantigens were identified in both cancer cell lines and clinical samples. Furthermore, we demonstrated an association between IPA-derived neoantigen burden and overall survival in cancer patients.
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Affiliation(s)
- Xiaochuan Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wen Jin
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Dengyi Bao
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tongxin He
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wenhui Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zekun Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiaoxiao Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yang Tong
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Meng Shu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuting Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jiapei Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yang Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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Hong N, Jiang D, Wang Z, Sun H, Luo H, Bao L, Song M, Kang Y, Hou T. TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides. J Chem Inf Model 2024; 64:5016-5027. [PMID: 38920330 DOI: 10.1021/acs.jcim.4c00678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
The intricate interaction between major histocompatibility complexes (MHCs) and antigen peptides with diverse amino acid sequences plays a pivotal role in immune responses and T cell activity. In recent years, deep learning (DL)-based models have emerged as promising tools for accelerating antigen peptide screening. However, most of these models solely rely on one-dimensional amino acid sequences, overlooking crucial information required for the three-dimensional (3-D) space binding process. In this study, we propose TransfIGN, a structure-based DL model that is inspired by our previously developed framework, Interaction Graph Network (IGN), and incorporates sequence information from transformers to predict the interactions between HLA-A*02:01 and antigen peptides. Our model, trained on a comprehensive data set containing 61,816 sequences with 9051 binding affinity labels and 56,848 eluted ligand labels, achieves an area under the curve (AUC) of 0.893 on the binary data set, better than state-of-the-art sequence-based models trained on larger data sets such as NetMHCpan4.1, ANN, and TransPHLA. Furthermore, when evaluated on the IEDB weekly benchmark data sets, our predictions (AUC = 0.816) are better than those of the recommended methods like the IEDB consensus (AUC = 0.795). Notably, the interaction weight matrices generated by our method highlight the strong interactions at specific positions within peptides, emphasizing the model's ability to provide physical interpretability. This capability to unveil binding mechanisms through intricate structural features holds promise for new immunotherapeutic avenues.
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Affiliation(s)
- Nanqi Hong
- College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang 310027, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dejun Jiang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhe Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Hao Luo
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lingjie Bao
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Mingli Song
- College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Yu Kang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Jurczak S, Druchok M. Cancer Immunotherapies Ignited by a Thorough Machine Learning-Based Selection of Neoantigens. Adv Biol (Weinh) 2024:e2400114. [PMID: 38971967 DOI: 10.1002/adbi.202400114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/02/2024] [Indexed: 07/08/2024]
Abstract
Identification of neoantigens, derived from somatic DNA alterations, emerges as a promising strategy for cancer immunotherapies. However, not all somatic mutations result in immunogenicity, hence, efficient tools to predict the immunogenicity of neoepitopes are needed. A pipeline is presented that provides a comprehensive solution for the identification of neoepitopes based on genomic sequencing data. The pipeline consists of a data pre-processing step and three machine learning predictive steps. The pre-processing step analyzes genomic data for different types of alterations, produces a list of all possible antigens, and determines the human leukocyte antigen (HLA) type and T-cell receptor (TCR) repertoire. The first predictive step performs a classification into antigens and neoantigens, selecting neoantigens for further consideration. The next step predicts the strength of binding between neoantigens and available major histocompatibility complexes of class I (MHC-I). The third step is engaged to predict the likelihood of inducing an immune response. Neoepitopes satisfying all three predictive stages are assumed to be potent candidates to ensure immunogenicity. The predictive pipeline is used in two regimes: selecting neoantigens from patients' sequencing data and generating novel neoantigen candidates. Two different techniques - Monte Carlo and Reinforcement Learning - are implemented to facilitate the generative regime.
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Affiliation(s)
- Sebastian Jurczak
- SoftServe Inc., 11/13 Building B, Jaworska St., Wroclaw, 53-612, Poland
| | - Maksym Druchok
- SoftServe Inc., 2d Sadova St., Lviv, 79021, Ukraine
- Institute for Condensed Matter Physics, 1 Svientsitskii St., Lviv, 79011, Ukraine
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4
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Ilangumaran S, Gui Y, Shukla A, Ramanathan S. SOCS1 expression in cancer cells: potential roles in promoting antitumor immunity. Front Immunol 2024; 15:1362224. [PMID: 38415248 PMCID: PMC10897024 DOI: 10.3389/fimmu.2024.1362224] [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: 12/27/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024] Open
Abstract
Suppressor of cytokine signaling 1 (SOCS1) is a potent regulator immune cell responses and a proven tumor suppressor. Inhibition of SOCS1 in T cells can boost antitumor immunity, whereas its loss in tumor cells increases tumor aggressivity. Investigations into the tumor suppression mechanisms so far focused on tumor cell-intrinsic functions of SOCS1. However, it is possible that SOCS1 expression in tumor cells also regulate antitumor immune responses in a cell-extrinsic manner via direct and indirect mechanisms. Here, we discuss the evidence supporting the latter, and its implications for antitumor immunity.
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Affiliation(s)
- Subburaj Ilangumaran
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
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5
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Ricker CA, Meli K, Van Allen EM. Historical perspective and future directions: computational science in immuno-oncology. J Immunother Cancer 2024; 12:e008306. [PMID: 38191244 PMCID: PMC10826578 DOI: 10.1136/jitc-2023-008306] [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] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Immuno-oncology holds promise for transforming patient care having achieved durable clinical response rates across a variety of advanced and metastatic cancers. Despite these achievements, only a minority of patients respond to immunotherapy, underscoring the importance of elucidating molecular mechanisms responsible for response and resistance to inform the development and selection of treatments. Breakthroughs in molecular sequencing technologies have led to the generation of an immense amount of genomic and transcriptomic sequencing data that can be mined to uncover complex tumor-immune interactions using computational tools. In this review, we discuss existing and emerging computational methods that contextualize the composition and functional state of the tumor microenvironment, infer the reactivity and clonal dynamics from reconstructed immune cell receptor repertoires, and predict the antigenic landscape for immune cell recognition. We further describe the advantage of multi-omics analyses for capturing multidimensional relationships and artificial intelligence techniques for integrating omics data with histopathological and radiological images to encapsulate patterns of treatment response and tumor-immune biology. Finally, we discuss key challenges impeding their widespread use and clinical application and conclude with future perspectives. We are hopeful that this review will both serve as a guide for prospective researchers seeking to use existing tools for scientific discoveries and inspire the optimization or development of novel tools to enhance precision, ultimately expediting advancements in immunotherapy that improve patient survival and quality of life.
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Affiliation(s)
- Cora A Ricker
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kevin Meli
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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6
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Türker F, Brennan A, Margolis SS. Neuronal membrane proteasome-derived peptides modulate NMDAR-dependent neuronal signaling to promote changes in gene expression. Mol Biol Cell 2024; 35:ar6. [PMID: 37910253 PMCID: PMC10881162 DOI: 10.1091/mbc.e23-06-0218] [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: 06/12/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023] Open
Abstract
The neuronal membrane proteasome (NMP) degrades intracellular proteins into peptides that are released directly into the extracellular space, whereby they stimulate neurons to promote signaling mechanisms that remain unknown. Here, we demonstrate that neuronal stimulation promotes NMP activity and, subsequently, enhanced production of NMP peptides. We show that these neuronal activity-dependent NMP peptides can rapidly promote N-methyl-D-aspartate receptor (NMDAR)-dependent calcium influx in neurons. This leads to sustained phosphorylation of the well-defined stimulus-induced transcription factor, cyclic AMP response element (CRE)-binding protein (CREB). Downstream of these events, we identified changes to neuronal target genes which included increased expression of immediate early genes (e.g., Fos, Npas4, Egr4) and other genes known to have critical neuroregulatory roles. Further observations led to the discovery that NMP peptide-induced changes in gene expression is dependent on NMDARs and independent of AMPA receptors or voltage-gated sodium channels. These data demonstrate that NMP peptides are endogenous and selective activators of NMDA receptors and act as sufficient and novel stimuli within the context of neuronal activity-dependent signaling. This novel pathway is parallel to classic neuronal activity-dependent programs and points to NMP and its resulting peptides as potential modulators of neuronal function.
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Affiliation(s)
- Fulya Türker
- Department of Biological Chemistry, The Johns Hopkins University, School of Medicine, Baltimore, MD 21205
| | - Anna Brennan
- Department of Biological Chemistry, The Johns Hopkins University, School of Medicine, Baltimore, MD 21205
| | - Seth S. Margolis
- Department of Biological Chemistry, The Johns Hopkins University, School of Medicine, Baltimore, MD 21205
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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7
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Prensner JR, Abelin JG, Kok LW, Clauser KR, Mudge JM, Ruiz-Orera J, Bassani-Sternberg M, Moritz RL, Deutsch EW, van Heesch S. What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome? Mol Cell Proteomics 2023; 22:100631. [PMID: 37572790 PMCID: PMC10506109 DOI: 10.1016/j.mcpro.2023.100631] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/21/2023] [Accepted: 08/08/2023] [Indexed: 08/14/2023] Open
Abstract
Ribosome profiling (Ribo-Seq) has proven transformative for our understanding of the human genome and proteome by illuminating thousands of noncanonical sites of ribosome translation outside the currently annotated coding sequences (CDSs). A conservative estimate suggests that at least 7000 noncanonical ORFs are translated, which, at first glance, has the potential to expand the number of human protein CDSs by 30%, from ∼19,500 annotated CDSs to over 26,000 annotated CDSs. Yet, additional scrutiny of these ORFs has raised numerous questions about what fraction of them truly produce a protein product and what fraction of those can be understood as proteins according to conventional understanding of the term. Adding further complication is the fact that published estimates of noncanonical ORFs vary widely by around 30-fold, from several thousand to several hundred thousand. The summation of this research has left the genomics and proteomics communities both excited by the prospect of new coding regions in the human genome but searching for guidance on how to proceed. Here, we discuss the current state of noncanonical ORF research, databases, and interpretation, focusing on how to assess whether a given ORF can be said to be "protein coding."
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Affiliation(s)
- John R Prensner
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA.
| | | | - Leron W Kok
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, Agora Center Bugnon 25A, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland; Agora Cancer Research Centre, Lausanne, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology (ISB), Seattle, Washington, USA
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington, USA
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8
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Ternette N, Adamopoulou E, Purcell AW. How mass spectrometric interrogation of MHC class I ligandomes has advanced our understanding of immune responses to viruses. Semin Immunol 2023; 68:101780. [PMID: 37276649 DOI: 10.1016/j.smim.2023.101780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023]
Affiliation(s)
- Nicola Ternette
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX37BN, UK.
| | - Eleni Adamopoulou
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX37BN, UK
| | - Anthony W Purcell
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
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9
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Li Q, Zhou L, Qin S, Huang Z, Li B, Liu R, Yang M, Nice EC, Zhu H, Huang C. Proteolysis-targeting chimeras in biotherapeutics: Current trends and future applications. Eur J Med Chem 2023; 257:115447. [PMID: 37229829 DOI: 10.1016/j.ejmech.2023.115447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023]
Abstract
The success of inhibitor-based therapeutics is largely constrained by the acquisition of therapeutic resistance, which is partially driven by the undruggable proteome. The emergence of proteolysis targeting chimera (PROTAC) technology, designed for degrading proteins involved in specific biological processes, might provide a novel framework for solving the above constraint. A heterobifunctional PROTAC molecule could structurally connect an E3 ubiquitin ligase ligand with a protein of interest (POI)-binding ligand by chemical linkers. Such technology would result in the degradation of the targeted protein via the ubiquitin-proteasome system (UPS), opening up a novel way of selectively inhibiting undruggable proteins. Herein, we will highlight the advantages of PROTAC technology and summarize the current understanding of the potential mechanisms involved in biotherapeutics, with a particular focus on its application and development where therapeutic benefits over classical small-molecule inhibitors have been achieved. Finally, we discuss how this technology can contribute to developing biotherapeutic drugs, such as antivirals against infectious diseases, for use in clinical practices.
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Affiliation(s)
- Qiong Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Li Zhou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, PR China
| | - Siyuan Qin
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Zhao Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Bowen Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Ruolan Liu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Mei Yang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Huili Zhu
- Department of Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, PR China.
| | - Canhua Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China; School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
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10
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Admon A. The biogenesis of the immunopeptidome. Semin Immunol 2023; 67:101766. [PMID: 37141766 DOI: 10.1016/j.smim.2023.101766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.
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Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Israel.
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11
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Geiger KM, Manoharan M, Coombs R, Arana K, Park CS, Lee AY, Shastri N, Robey EA, Coscoy L. Murine cytomegalovirus downregulates ERAAP and induces an unconventional T cell response to self. Cell Rep 2023; 42:112317. [PMID: 36995940 PMCID: PMC10539480 DOI: 10.1016/j.celrep.2023.112317] [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: 03/16/2022] [Revised: 01/02/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
The endoplasmic reticulum aminopeptidase associated with antigen processing (ERAAP) plays a crucial role in shaping the peptide-major histocompatibility complex (MHC) class I repertoire and maintaining immune surveillance. While murine cytomegalovirus (MCMV) has multiple strategies for manipulating the antigen processing pathway to evade immune responses, the host has also developed ways to counter viral immune evasion. In this study, we find that MCMV modulates ERAAP and induces an interferon γ (IFN-γ)-producing CD8+ T cell effector response that targets uninfected ERAAP-deficient cells. We observe that ERAAP downregulation during infection leads to the presentation of the self-peptide FL9 on non-classical Qa-1b, thereby eliciting Qa-1b-restricted QFL T cells to proliferate in the liver and spleen of infected mice. QFL T cells upregulate effector markers upon MCMV infection and are sufficient to reduce viral load after transfer to immunodeficient mice. Our study highlights the consequences of ERAAP dysfunction during viral infection and provides potential targets for anti-viral therapies.
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Affiliation(s)
- Kristina M Geiger
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael Manoharan
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel Coombs
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kathya Arana
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chan-Su Park
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Angus Y Lee
- Cancer Research Lab, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nilabh Shastri
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ellen A Robey
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Laurent Coscoy
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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12
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Santharam MA, Shukla A, Levesque D, Kufer TA, Boisvert FM, Ramanathan S, Ilangumaran S. NLRC5-CIITA Fusion Protein as an Effective Inducer of MHC-I Expression and Antitumor Immunity. Int J Mol Sci 2023; 24:ijms24087206. [PMID: 37108368 PMCID: PMC10138588 DOI: 10.3390/ijms24087206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Aggressive tumors evade cytotoxic T lymphocytes by suppressing MHC class-I (MHC-I) expression that also compromises tumor responsiveness to immunotherapy. MHC-I defects strongly correlate to defective expression of NLRC5, the transcriptional activator of MHC-I and antigen processing genes. In poorly immunogenic B16 melanoma cells, restoring NLRC5 expression induces MHC-I and elicits antitumor immunity, raising the possibility of using NLRC5 for tumor immunotherapy. As the clinical application of NLRC5 is constrained by its large size, we examined whether a smaller NLRC5-CIITA fusion protein, dubbed NLRC5-superactivator (NLRC5-SA) as it retains the ability to induce MHC-I, could be used for tumor growth control. We show that stable NLRC5-SA expression in mouse and human cancer cells upregulates MHC-I expression. B16 melanoma and EL4 lymphoma tumors expressing NLRC5-SA are controlled as efficiently as those expressing full-length NLRC5 (NLRC5-FL). Comparison of MHC-I-associated peptides (MAPs) eluted from EL4 cells expressing NLRC5-FL or NLRC5-SA and analyzed by mass spectrometry revealed that both NLRC5 constructs expanded the MAP repertoire, which showed considerable overlap but also included a substantial proportion of distinct peptides. Thus, we propose that NLRC5-SA, with its ability to increase tumor immunogenicity and promote tumor growth control, could overcome the limitations of NLRC5-FL for translational immunotherapy applications.
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Affiliation(s)
- Madanraj Appiya Santharam
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Akhil Shukla
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Dominique Levesque
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Thomas A Kufer
- Department of Immunology, Institute of Nutritional Medicine, University of Hohenheim, 70593 Stuttgart, Germany
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- CRCHUS, Centre Hospitalier de l'Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Sheela Ramanathan
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- CRCHUS, Centre Hospitalier de l'Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Subburaj Ilangumaran
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- CRCHUS, Centre Hospitalier de l'Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
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13
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Ahmad H, Zia B, Husain H, Husain A. Recent Advances in PROTAC-Based Antiviral Strategies. Vaccines (Basel) 2023; 11:vaccines11020270. [PMID: 36851148 PMCID: PMC9958553 DOI: 10.3390/vaccines11020270] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/15/2023] [Accepted: 01/20/2023] [Indexed: 02/03/2023] Open
Abstract
Numerous mysteries of cell and molecular biology have been resolved through extensive research into intracellular processes, which has also resulted in the development of innovative technologies for the treatment of infectious and non-infectious diseases. Some of the deadliest diseases, accounting for a staggering number of deaths, have been caused by viruses. Conventional antiviral therapies have been unable to achieve a feat in combating viral infections. As a result, the healthcare system has come under tremendous pressure globally. Therefore, there is an urgent need to discover and develop newer therapeutic approaches against viruses. One such innovative approach that has recently garnered attention in the research world and can be exploited for developing antiviral therapeutic strategies is the PROteolysis TArgeting Chimeras (PROTAC) technology, in which heterobifunctional compounds are employed for the selective degradation of target proteins by the intracellular protein degradation machinery. This review covers the most recent advancements in PROTAC technology, its diversity and mode of action, and how it can be applied to open up new possibilities for creating cutting-edge antiviral treatments and vaccines.
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Affiliation(s)
- Haleema Ahmad
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Bushra Zia
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Hashir Husain
- Department of Biosciences, Faculty of Science, Integral University, Lucknow 226026, India
| | - Afzal Husain
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
- Correspondence:
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14
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Wang Y, Yan K, Guo Y, Lu Y, Su H, Li H. IP-score correlated to endogenous tumour antigen peptide processing: A candidate clinical response score algorithm of immune checkpoint inhibitors therapy in multiple cohorts. Front Immunol 2023; 13:1085491. [PMID: 36700205 PMCID: PMC9868931 DOI: 10.3389/fimmu.2022.1085491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/13/2022] [Indexed: 01/11/2023] Open
Abstract
The processing of endogenous tumour antigen peptides was essential for anti-tumour immunity in the tumour microenvironment. A high degree of Endogenous tumour antigen peptide processing has been demonstrated to improve the prognosis of carcinoma patients. However, there is insufficient evidence to prove its effect on the clinical response to immune checkpoint inhibitor therapy. To undertake a more in-depth analysis of the effects of the aforementioned genes on immunotherapy, we constructed a gene set evaluation score system relevant to tumour endogenous antigen peptide therapy using the GSVA approach. This rating mechanism is known as IP score (IPs). Immediately afterwards, we used the TCGA pan-cancer cohorts to conduct a comprehensive analysis of 6 genes in the IPs, and the analysis results showed that these six genes were related to the proportion of CD8+ T lymphocytes in a variety of solid tumours. As a prognostic protective factor for solid tumours, patients had better prognosis outcomes in the group with high expression levels of the above genes. We analysed the differential expression of six genes between immune checkpoint inhibitor treatment response and disease progression groups using several treatment cohorts. The results revealed that after treatment with PD-1 or CTLA4 inhibitors, the expression levels of the above six genes were comparatively high in the effective group, but the expression of the signature genes was dramatically downregulated in the ICI-insensitive groups. This indicates that the 6 genes are related to the clinical response to ICI treatment. Finally, we used the GSVA method to evaluate the above signatures, and the results showed that PDCD1, CTAL4, CD274 and LAG3 were significantly higher expressed in the IPs high-expression group; therefore, based on the processing of endogenous antigenic peptides in tumours, a predictive score of clinical response to immune checkpoint inhibitor therapy composed of 6 genes(PSMB8/PSMB9/PSMB10/PSME1/PSME2/IRF1) was constructed, and the role of each independent variable in the signature in the solid tumour microenvironment and the impact on ICI treatment were comprehensively analysed. This study provides a candidate evaluation score for predicting clinical response to immune checkpoint inhibitor therapy.
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Affiliation(s)
- Yutao Wang
- Department of Urology, Chinese Academy of Medical Sciences, Peking Union Medical College, Peking Union Medical College Hospital, Beijing, China
| | - Kexin Yan
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Ye Guo
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yi Lu
- Department of Urology, Chinese Academy of Medical Sciences, Peking Union Medical College, Peking Union Medical College Hospital, Beijing, China
| | - Hao Su
- Department of Urology, Chinese Academy of Medical Sciences, Peking Union Medical College, Peking Union Medical College Hospital, Beijing, China
| | - Hongjun Li
- Department of Urology, Chinese Academy of Medical Sciences, Peking Union Medical College, Peking Union Medical College Hospital, Beijing, China,*Correspondence: Hongjun Li,
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15
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Arman I, Haus-Cohen M, Reiter Y. The Intracellular Proteome as a Source for Novel Targets in CAR-T and T-Cell Engagers-Based Immunotherapy. Cells 2022; 12:cells12010027. [PMID: 36611821 PMCID: PMC9818436 DOI: 10.3390/cells12010027] [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: 11/09/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
The impressive clinical success of cancer immunotherapy has motivated the continued search for new targets that may serve to guide potent effector functions in an attempt to efficiently kill malignant cells. The intracellular proteome is an interesting source for such new targets, such as neo-antigens and others, with growing interest in their application for cell-based immunotherapies. These intracellular-derived targets are peptides presented by MHC class I molecules on the cell surface of malignant cells. These disease-specific class I HLA-peptide complexes can be targeted by specific TCRs or by antibodies that mimic TCR-specificity, termed TCR-like (TCRL) antibodies. Adoptive cell transfer of TCR engineered T cells and T-cell-receptor-like based CAR-T cells, targeted against a peptide-MHC of interest, are currently tested as cancer therapeutic agents in pre-clinical and clinical trials, along with soluble TCR- and TCRL-based agents, such as immunotoxins and bi-specific T cell engagers. Targeting the intracellular proteome using TCRL- and TCR-based molecules shows promising results in cancer immunotherapy, as exemplified by the success of the anti-gp100/HLA-A2 TCR-based T cell engager, recently approved by the FDA for the treatment of unresectable or metastatic uveal melanoma. This review is focused on the selection and isolation processes of TCR- and TCRL-based targeting moieties, with a spotlight on pre-clinical and clinical studies, examining peptide-MHC targeting agents in cancer immunotherapy.
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16
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Li Z, Duan Y, Ke Q, Wang M, Cen H, Zhu X. Gene set-based identification of two immune subtypes of diffuse large B cell lymphoma for guiding immune checkpoint blocking therapy. Front Genet 2022; 13:1000460. [PMID: 36276947 PMCID: PMC9585251 DOI: 10.3389/fgene.2022.1000460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/22/2022] [Indexed: 12/01/2022] Open
Abstract
Background: Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma in adults. Tumour microenvironment is closely related to tumour prognosis and immune checkpoint blocking therapy (ICBT). This study aimed to investigate the immunological and prognostic characteristics of the tumour microenvironment (TME), as well as the regulatory mechanisms. Methods: Gene expression profiles and clinical data of patients with DLBCL were obtained from GEO database. ESTIMATE, CIBERSORT, and ssGSEA analyses were used to explore microenvironment characteristics and regulatory mechanism of the immune subtypes, which were identified by consistent clustering. The differences in enriched pathways were showed by GSEA. Hub genes associated with CD8+ T cells, which were identified by WCGNA, were exhibited biological functions through GO and KEGG. Immune-related gene scores (IRGSs) based on hub genes were used to evaluate the prediction of immune subtypes and ICBT, and retrospective analysis was used for validation. Finally, prognostic genes were screened to construct risk models. Results: Consensus clustering divided patients with DLBCL into two subtypes with significant heterogeneities in prognosis and immune microenvironment. Low immune infiltration was associated with poor prognosis. Subtype C1 with high immune infiltration was enriched in multiple immune pathways. We observed that two common mutated genes (B2M and EZH2) in DLBCL were closely related to MHC-I and microenvironment. Our further analysis manifested that MYD88L265P may be the main cause of TLR signalling pathway activation in subtype C1. Hub genes (SH2D1A, CD8A, GBP2, ITK, CD3D, RORA, IL1R2, CD28, CD247, CD3G, PRKCQ, CXCR6, and CD3E) in relation with CD8+ T cells were used to establish IRGS, which was proved an accurate predictor of immune subtypes, and patients in high-IRGS group were more likely to benefit from ICBT. Retrospective analysis showed that absolute lymphocyte count (ALC) was higher in the group that responded to the PD-1 inhibitor. Finally, the risk model was constructed based on two genes (CD3G and CD3D), and the low-risk group showed better prognosis. Conclusion: DLBCL immune classifications with highly heterogeneity are a powerful predictor of prognosis and ICBT. The IRGS is proved to be a reliable tool to distinguish immune subtypes as a substitute for gene expression profile.
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Affiliation(s)
- Zhe Li
- Department of Haematology/Oncology and Paediatric Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Ying Duan
- Department of Haematology/Oncology and Paediatric Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Qing Ke
- Department of Haematology/Oncology and Paediatric Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Mingyue Wang
- Department of Haematology/Oncology and Paediatric Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Hong Cen
- Department of Haematology/Oncology and Paediatric Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
- *Correspondence: Hong Cen, ; Xiaodong Zhu,
| | - Xiaodong Zhu
- Department of Oncology, Wuming Hospital of Guangxi Medical University, Nanning, China
- Department of Radiation Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
- *Correspondence: Hong Cen, ; Xiaodong Zhu,
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17
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Lawrence PJ, Ning X. Improving MHC class I antigen-processing predictions using representation learning and cleavage site-specific kernels. CELL REPORTS METHODS 2022; 2:100293. [PMID: 36160050 PMCID: PMC9499997 DOI: 10.1016/j.crmeth.2022.100293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/17/2022] [Accepted: 08/19/2022] [Indexed: 11/15/2022]
Abstract
In this work, we propose a new deep-learning model, MHCrank, to predict the probability that a peptide will be processed for presentation by MHC class I molecules. We find that the performance of our model is significantly higher than that of two previously published baseline methods: MHCflurry and netMHCpan. This improvement arises from utilizing both cleavage site-specific kernels and learned embeddings for amino acids. By visualizing site-specific amino acid enrichment patterns, we observe that MHCrank's top-ranked peptides exhibit enrichments at biologically relevant positions and are consistent with previous work. Furthermore, the cosine similarity matrix derived from MHCrank's learned embeddings for amino acids correlates highly with physiochemical properties that have been experimentally demonstrated to be instrumental in determining a peptide's favorability for processing. Altogether, the results reported in this work indicate that MHCrank demonstrates strong performance compared with existing methods and could have vast applicability in aiding drug and vaccine development.
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Affiliation(s)
- Patrick J. Lawrence
- Biomedical Informatics Department, The Ohio State University, 1800 Cannon Drive, Lincoln Tower 250, Columbus, OH 43210, USA
| | - Xia Ning
- Biomedical Informatics Department, The Ohio State University, 1800 Cannon Drive, Lincoln Tower 250, Columbus, OH 43210, USA
- Computer Science and Engineering Department, The Ohio State University, 2015 Neil Avenue, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, 1760 Neil Avenue, Columbus, OH 43210, USA
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18
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Sobecki M, Chen J, Krzywinska E, Nagarajan S, Fan Z, Nelius E, Monné Rodriguez JM, Seehusen F, Hussein A, Moschini G, Hajam EY, Kiran R, Gotthardt D, Debbache J, Badoual C, Sato T, Isagawa T, Takeda N, Tanchot C, Tartour E, Weber A, Werner S, Loffing J, Sommer L, Sexl V, Münz C, Feghali-Bostwick C, Pachera E, Distler O, Snedeker J, Jamora C, Stockmann C. Vaccination-based immunotherapy to target profibrotic cells in liver and lung. Cell Stem Cell 2022; 29:1459-1474.e9. [PMID: 36113462 DOI: 10.1016/j.stem.2022.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/19/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022]
Abstract
Fibrosis is the final path of nearly every form of chronic disease, regardless of the pathogenesis. Upon chronic injury, activated, fibrogenic fibroblasts deposit excess extracellular matrix, and severe tissue fibrosis can occur in virtually any organ. However, antifibrotic therapies that target fibrogenic cells, while sparing homeostatic fibroblasts in healthy tissues, are limited. We tested whether specific immunization against endogenous proteins, strongly expressed in fibrogenic cells but highly restricted in quiescent fibroblasts, can elicit an antigen-specific cytotoxic T cell response to ameliorate organ fibrosis. In silico epitope prediction revealed that activation of the genes Adam12 and Gli1 in profibrotic cells and the resulting "self-peptides" can be exploited for T cell vaccines to ablate fibrogenic cells. We demonstrate the efficacy of a vaccination approach to mount CD8+ T cell responses that reduce fibroblasts and fibrosis in the liver and lungs in mice. These results provide proof of principle for vaccination-based immunotherapies to treat fibrosis.
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Affiliation(s)
- Michal Sobecki
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jing Chen
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ewelina Krzywinska
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Shunmugam Nagarajan
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Zheng Fan
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Eric Nelius
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Josep M Monné Rodriguez
- Laboratory for Animal Model Pathology (LAMP), Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Frauke Seehusen
- Laboratory for Animal Model Pathology (LAMP), Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Amro Hussein
- Department of Orthopedics, Balgrist University Hospital, University of Zurich, Lengghalde 5, 8008 Zurich, Switzerland; Institute for Biomechanics, ETH Zurich, 8093 Zurich, Switzerland
| | - Greta Moschini
- Department of Orthopedics, Balgrist University Hospital, University of Zurich, Lengghalde 5, 8008 Zurich, Switzerland; Institute for Biomechanics, ETH Zurich, 8093 Zurich, Switzerland
| | - Edries Y Hajam
- IFOM-inStem Joint Research Laboratory, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka 560065, India
| | - Ravi Kiran
- IFOM-inStem Joint Research Laboratory, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka 560065, India
| | - Dagmar Gotthardt
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Julien Debbache
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Cécile Badoual
- Institut National de la Santé et de la Recherche Médicale (INSERM), Paris Cardiovascular Research Center, Unit 970, 56 Rue Leblanc, 75015 Paris, France; Pathology Department and PRB (Plateforme de ressources biologiques), AP-HP, Georges Pompidou European Hospital, 75015 Paris, France
| | - Tatsuyuki Sato
- Division of Cardiology and Metabolism, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke 329-0498, Japan
| | - Takayuki Isagawa
- Division of Cardiology and Metabolism, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke 329-0498, Japan
| | - Norihiko Takeda
- Division of Cardiology and Metabolism, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke 329-0498, Japan
| | - Corinne Tanchot
- Institut National de la Santé et de la Recherche Médicale (INSERM), Paris Cardiovascular Research Center, Unit 970, 56 Rue Leblanc, 75015 Paris, France
| | - Eric Tartour
- Institut National de la Santé et de la Recherche Médicale (INSERM), Paris Cardiovascular Research Center, Unit 970, 56 Rue Leblanc, 75015 Paris, France; Immunology, AP-HP, Hôpital Europeen Georges Pompidou, 75015 Paris, France
| | - Achim Weber
- Department for Pathology and Molecular Pathology, University of Zurich and Zurich University Hospital Zurich, 8091 Zurich, Switzerland; Comprehensive Cancer Center Zurich, 8091 Zurich, Switzerland; Institute of Molecular Cancer Research, 8091 Zurich, Switzerland
| | - Sabine Werner
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Johannes Loffing
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Lukas Sommer
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland
| | - Carol Feghali-Bostwick
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Elena Pachera
- Department of Rheumatology, University Hospital of Zurich, 8091 Zurich, Switzerland
| | - Oliver Distler
- Department of Rheumatology, University Hospital of Zurich, 8091 Zurich, Switzerland
| | - Jess Snedeker
- Department of Orthopedics, Balgrist University Hospital, University of Zurich, Lengghalde 5, 8008 Zurich, Switzerland; Institute for Biomechanics, ETH Zurich, 8093 Zurich, Switzerland
| | - Colin Jamora
- IFOM-inStem Joint Research Laboratory, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka 560065, India
| | - Christian Stockmann
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Comprehensive Cancer Center Zurich, 8091 Zurich, Switzerland.
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19
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Jackson KR, Antunes DA, Talukder AH, Maleki AR, Amagai K, Salmon A, Katailiha AS, Chiu Y, Fasoulis R, Rigo MM, Abella JR, Melendez BD, Li F, Sun Y, Sonnemann HM, Belousov V, Frenkel F, Justesen S, Makaju A, Liu Y, Horn D, Lopez-Ferrer D, Huhmer AF, Hwu P, Roszik J, Hawke D, Kavraki LE, Lizée G. Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules. PNAS NEXUS 2022; 1:pgac124. [PMID: 36003074 PMCID: PMC9391200 DOI: 10.1093/pnasnexus/pgac124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Human leukocyte antigen class I (HLA-I) molecules bind and present peptides at the cell surface to facilitate the induction of appropriate CD8+ T cell-mediated immune responses to pathogen- and self-derived proteins. The HLA-I peptide-binding cleft contains dominant anchor sites in the B and F pockets that interact primarily with amino acids at peptide position 2 and the C-terminus, respectively. Nonpocket peptide-HLA interactions also contribute to peptide binding and stability, but these secondary interactions are thought to be unique to individual HLA allotypes or to specific peptide antigens. Here, we show that two positively charged residues located near the top of peptide-binding cleft facilitate interactions with negatively charged residues at position 4 of presented peptides, which occur at elevated frequencies across most HLA-I allotypes. Loss of these interactions was shown to impair HLA-I/peptide binding and complex stability, as demonstrated by both in vitro and in silico experiments. Furthermore, mutation of these Arginine-65 (R65) and/or Lysine-66 (K66) residues in HLA-A*02:01 and A*24:02 significantly reduced HLA-I cell surface expression while also reducing the diversity of the presented peptide repertoire by up to 5-fold. The impact of the R65 mutation demonstrates that nonpocket HLA-I/peptide interactions can constitute anchor motifs that exert an unexpectedly broad influence on HLA-I-mediated antigen presentation. These findings provide fundamental insights into peptide antigen binding that could broadly inform epitope discovery in the context of viral vaccine development and cancer immunotherapy.
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Affiliation(s)
- Kyle R Jackson
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Dinler A Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Amjad H Talukder
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ariana R Maleki
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Kano Amagai
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Avery Salmon
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Arjun S Katailiha
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yulun Chiu
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Romanos Fasoulis
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | - Jayvee R Abella
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Brenda D Melendez
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Fenge Li
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yimo Sun
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Heather M Sonnemann
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | | | - Yang Liu
- ThermoFisher Scientific, San Jose, CA, USA
| | - David Horn
- ThermoFisher Scientific, San Jose, CA, USA
| | | | | | - Patrick Hwu
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Roszik
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - David Hawke
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Lydia E Kavraki
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Gregory Lizée
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, USA
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20
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Vijayasimha K, Leestemaker-Palmer AL, Gibbs JS, Yewdell JW, Dolan BP. MLN4924 Inhibits Defective Ribosomal Product Antigen Presentation Independently of Direct NEDDylation of Protein Antigens. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2273-2282. [PMID: 35428693 PMCID: PMC9288214 DOI: 10.4049/jimmunol.2100584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 03/01/2022] [Indexed: 05/17/2023]
Abstract
Successful direct MHC class I Ag presentation is dependent on the protein degradation machinery of the cell to generate antigenic peptides that can be loaded onto MHC class I molecules for surveillance by CD8+ T cells of the immune system. Most often this process involves the ubiquitin (Ub)-proteasome system; however, other Ub-like proteins have also been implicated in protein degradation and direct Ag presentation. In this article, we examine the role of neuronal precursor cell-expressed developmentally downregulated protein 8 (NEDD8) in direct Ag presentation in mouse cells. NEDD8 is the Ub-like protein with highest similarity to Ub, and fusion of NEDD8 to the N terminus of a target protein can lead to the degradation of target proteins. We find that appending NEDD8 to the N terminus of the model Ag OVA resulted in degradation by both the proteasome and the autophagy protein degradation pathways, but only proteasomal degradation, involving the proteasomal subunit NEDD8 ultimate buster 1, resulted in peptide presentation. When directly compared with Ub, NEDD8 fusion was less efficient at generating peptides. However, inactivation of the NEDD8-conugation machinery by treating cells with MLN4924 inhibited the presentation of peptides from the defective ribosomal product-derived form of a model Ag. These results demonstrate that NEDD8 activity in the cell is important for direct Ag presentation, but not by directly targeting proteins for degradation.
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Affiliation(s)
- Kartikeya Vijayasimha
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR; and
| | - Amy L Leestemaker-Palmer
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR; and
| | - James S Gibbs
- Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases, Bethesda, MD
| | - Jonathan W Yewdell
- Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases, Bethesda, MD
| | - Brian P Dolan
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR; and
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21
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DNA damage promotes HLA class I presentation by stimulating a pioneer round of translation-associated antigen production. Mol Cell 2022; 82:2557-2570.e7. [PMID: 35594857 DOI: 10.1016/j.molcel.2022.04.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 02/01/2022] [Accepted: 04/21/2022] [Indexed: 12/14/2022]
Abstract
Antigen presentation by the human leukocyte antigen (HLA) on the cell surface is critical for the transduction of the immune signal toward cytotoxic T lymphocytes. DNA damage upregulates HLA class I presentation; however, the mechanism is unclear. Here, we show that DNA-damage-induced HLA (di-HLA) presentation requires an immunoproteasome, PSMB8/9/10, and antigen-transporter, TAP1/2, demonstrating that antigen production is essential. Furthermore, we show that di-HLA presentation requires ATR, AKT, mTORC1, and p70-S6K signaling. Notably, the depletion of CBP20, a factor initiating the pioneer round of translation (PRT) that precedes nonsense-mediated mRNA decay (NMD), abolishes di-HLA presentation, suggesting that di-antigen production requires PRT. RNA-seq analysis demonstrates that DNA damage reduces NMD transcripts in an ATR-dependent manner, consistent with the requirement for ATR in the initiation of PRT/NMD. Finally, bioinformatics analysis identifies that PRT-derived 9-mer peptides bind to HLA and are potentially immunogenic. Therefore, DNA damage signaling produces immunogenic antigens by utilizing the machinery of PRT/NMD.
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22
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Reits E, Neefjes J. HLA
molecules in transplantation, autoimmunity and infection control. HLA 2022; 100:301-311. [PMID: 35429150 PMCID: PMC9545814 DOI: 10.1111/tan.14626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Eric Reits
- Department of Medical Biology Amsterdam UMC, location AMC, Meibergdreef 15 AZ Amsterdam The Netherlands
| | - Jacques Neefjes
- Department of Cell and Chemical Biology ONCODE Institute, Leiden University Medical Centre LUMC The Netherlands
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23
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Sengupta S, Board NL, Wu F, Moskovljevic M, Douglass J, Zhang J, Reinhold BR, Duke-Cohan J, Yu J, Reed MC, Tabdili Y, Azurmendi A, Fray EJ, Zhang H, Hsiue EHC, Jenike K, Ho YC, Gabelli SB, Kinzler KW, Vogelstein B, Zhou S, Siliciano JD, Sadegh-Nasseri S, Reinherz EL, Siliciano RF. TCR-mimic bispecific antibodies to target the HIV-1 reservoir. Proc Natl Acad Sci U S A 2022; 119:e2123406119. [PMID: 35394875 PMCID: PMC9169739 DOI: 10.1073/pnas.2123406119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/04/2022] [Indexed: 12/12/2022] Open
Abstract
HIV-1 infection is incurable due to the persistence of the virus in a latent reservoir of resting memory CD4+ T cells. “Shock-and-kill” approaches that seek to induce HIV-1 gene expression, protein production, and subsequent targeting by the host immune system have been unsuccessful due to a lack of effective latency-reversing agents (LRAs) and kill strategies. In an effort to develop reagents that could be used to promote killing of infected cells, we constructed T cell receptor (TCR)-mimic antibodies to HIV-1 peptide-major histocompatibility complexes (pMHC). Using phage display, we panned for phages expressing antibody-like variable sequences that bound HIV-1 pMHC generated using the common HLA-A*02:01 allele. We targeted three epitopes in Gag and reverse transcriptase identified and quantified via Poisson detection mass spectrometry from cells infected in vitro with a pseudotyped HIV-1 reporter virus (NL4.3 dEnv). Sequences isolated from phages that bound these pMHC were cloned into a single-chain diabody backbone (scDb) sequence, such that one fragment is specific for an HIV-1 pMHC and the other fragment binds to CD3ε, an essential signal transduction subunit of the TCR. Thus, these antibodies utilize the sensitivity of T cell signaling as readouts for antigen processing and as agents to promote killing of infected cells. Notably, these scDbs are exquisitely sensitive and specific for the peptide portion of the pMHC. Most importantly, one scDb caused killing of infected cells presenting a naturally processed target pMHC. This work lays the foundation for a novel therapeutic killing strategy toward elimination of the HIV-1 reservoir.
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Affiliation(s)
- Srona Sengupta
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Nathan L. Board
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Fengting Wu
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Milica Moskovljevic
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Josephine Zhang
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Bruce R. Reinhold
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Jonathan Duke-Cohan
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Jeanna Yu
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Madison C. Reed
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Yasmine Tabdili
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Aitana Azurmendi
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Emily J. Fray
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Emily Han-Chung Hsiue
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Katharine Jenike
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Kenneth W. Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
- HHMI, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
| | - Janet D. Siliciano
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | | | - Ellis L. Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Robert F. Siliciano
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- HHMI, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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24
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Sim MJW, Sun PD. T Cell Recognition of Tumor Neoantigens and Insights Into T Cell Immunotherapy. Front Immunol 2022; 13:833017. [PMID: 35222422 PMCID: PMC8867076 DOI: 10.3389/fimmu.2022.833017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/21/2022] [Indexed: 12/13/2022] Open
Abstract
In cancer, non-synonymous DNA base changes alter protein sequence and produce neoantigens that are detected by the immune system. For immune detection, neoantigens must first be presented on class I or II human leukocyte antigens (HLA) followed by recognition by peptide-specific receptors, exemplified by the T-cell receptor (TCR). Detection of neoantigens represents a unique challenge to the immune system due to their high similarity with endogenous ‘self’ proteins. Here, we review insights into how TCRs detect neoantigens from structural studies and delineate two broad mechanistic categories: 1) recognition of mutated ‘self’ peptides and 2) recognition of novel ‘non-self’ peptides generated through anchor residue modifications. While mutated ‘self’ peptides differ only by a single amino acid from an existing ‘self’ epitope, mutations that form anchor residues generate an entirely new epitope, hitherto unknown to the immune system. We review recent structural studies that highlight these structurally distinct mechanisms and discuss how they may lead to differential anti-tumor immune responses. We discuss how T cells specific for neoantigens derived from anchor mutations can be of high affinity and provide insights to their use in adoptive T cell transfer-based immunotherapy.
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Affiliation(s)
- Malcolm J W Sim
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Rockville, MD, United States
| | - Peter D Sun
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Rockville, MD, United States
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25
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Okada M, Shimizu K, Fujii SI. Identification of Neoantigens in Cancer Cells as Targets for Immunotherapy. Int J Mol Sci 2022; 23:ijms23052594. [PMID: 35269735 PMCID: PMC8910406 DOI: 10.3390/ijms23052594] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 02/06/2023] Open
Abstract
The clinical benefits of immune checkpoint blockage (ICB) therapy have been widely reported. In patients with cancer, researchers have demonstrated the clinical potential of antitumor cytotoxic T cells that can be reinvigorated or enhanced by ICB. Compared to self-antigens, neoantigens derived from tumor somatic mutations are believed to be ideal immune targets in tumors. Candidate tumor neoantigens can be identified through immunogenomic or immunopeptidomic approaches. Identification of neoantigens has revealed several points of the clinical relevance. For instance, tumor mutation burden (TMB) may be an indicator of immunotherapy. In various cancers, mutation rates accompanying neoantigen loads may be indicative of immunotherapy. Furthermore, mismatch repair-deficient tumors can be eradicated by T cells in ICB treatment. Hence, immunotherapies using vaccines or adoptive T-cell transfer targeting neoantigens are potential innovative strategies. However, significant efforts are required to identify the optimal epitopes. In this review, we summarize the recent progress in the identification of neoantigens and discussed preclinical and clinical studies based on neoantigens. We also discuss the issues remaining to be addressed before clinical applications of these new therapeutic strategies can be materialized.
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Affiliation(s)
- Masahiro Okada
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (M.O.); (K.S.)
| | - Kanako Shimizu
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (M.O.); (K.S.)
| | - Shin-ichiro Fujii
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (M.O.); (K.S.)
- Program for Drug Discovery and Medical Technology Platforms, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Correspondence: ; Tel.: +81-45-503-7062
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26
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Kubiniok P, Marcu A, Bichmann L, Kuchenbecker L, Schuster H, Hamelin DJ, Duquette JD, Kovalchik KA, Wessling L, Kohlbacher O, Rammensee HG, Neidert MC, Sirois I, Caron E. Understanding the constitutive presentation of MHC class I immunopeptidomes in primary tissues. iScience 2022; 25:103768. [PMID: 35141507 PMCID: PMC8810409 DOI: 10.1016/j.isci.2022.103768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/15/2021] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
Understanding the molecular principles that govern the composition of the MHC-I immunopeptidome across different primary tissues is fundamentally important to predict how T cells respond in different contexts in vivo. Here, we performed a global analysis of the MHC-I immunopeptidome from 29 to 19 primary human and mouse tissues, respectively. First, we observed that different HLA-A, HLA-B, and HLA-C allotypes do not contribute evenly to the global composition of the MHC-I immunopeptidome across multiple human tissues. Second, we found that tissue-specific and housekeeping MHC-I peptides share very distinct properties. Third, we discovered that proteins that are evolutionarily hyperconserved represent the primary source of the MHC-I immunopeptidome at the organism-wide scale. Fourth, we uncovered new components of the antigen processing and presentation network, including the carboxypeptidases CPE, CNDP1/2, and CPVL. Together, this study opens up new avenues toward a system-wide understanding of antigen presentation in vivo across mammalian species. Tissue-specific and housekeeping MHC class I peptides share distinct properties HLA-A, HLA-B, and HLA-C allotypes contribute very unevenly to the pool of class I peptides MHC-I immunopeptidomes are represented by evolutionarily conserved proteins An extended antigen processing and presentation pathway is uncovered
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Affiliation(s)
- Peter Kubiniok
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Ana Marcu
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- Cluster of Excellence iFIT (EXC 2180), “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
| | - Leon Bichmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72074 Tübingen, Baden-Württemberg, Germany
| | - Leon Kuchenbecker
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72074 Tübingen, Baden-Württemberg, Germany
| | - Heiko Schuster
- Immatics Biotechnologies GmbH, 72076 Tübingen, Baden-Württemberg, Germany
| | - David J. Hamelin
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | | | | | - Laura Wessling
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72074 Tübingen, Baden-Württemberg, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, 72076 Tübingen, Baden-Württemberg, Germany
- Cluster of Excellence Machine Learning in the Sciences (EXC 2064), University of Tübingen, 72074 Tübingen, Baden-Württemberg, Germany
- Translational Bioinformatics, University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- Cluster of Excellence iFIT (EXC 2180), “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), 72076 Tübingen, Baden-Württemberg, Germany
| | - Marian C. Neidert
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zürich, 8057&8091 Zürich, Switzerland
| | - Isabelle Sirois
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
- Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, QC H3T 1J4, Canada
- Corresponding author
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27
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Grohmann C, Marapana DS, Ebert G. Targeted protein degradation at the host-pathogen interface. Mol Microbiol 2021; 117:670-681. [PMID: 34816514 DOI: 10.1111/mmi.14849] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/24/2022]
Abstract
Infectious diseases remain a major burden to global health. Despite the implementation of successful vaccination campaigns and efficient drugs, the increasing emergence of pathogenic vaccine or treatment resistance demands novel therapeutic strategies. The development of traditional therapies using small-molecule drugs is based on modulating protein function and activity through the occupation of active sites such as enzyme inhibition or ligand-receptor binding. These prerequisites result in the majority of host and pathogenic disease-relevant, nonenzymatic and structural proteins being labeled "undruggable." Targeted protein degradation (TPD) emerged as a powerful strategy to eliminate proteins of interest including those of the undruggable variety. Proteolysis-targeting chimeras (PROTACs) are rationally designed heterobifunctional small molecules that exploit the cellular ubiquitin-proteasome system to specifically mediate the highly selective and effective degradation of target proteins. PROTACs have shown remarkable results in the degradation of various cancer-associated proteins, and several candidates are already in clinical development. Significantly, PROTAC-mediated TPD holds great potential for targeting and modulating pathogenic proteins, especially in the face of increasing drug resistance to the best-in-class treatments. In this review, we discuss advances in the development of TPD in the context of targeting the host-pathogen interface and speculate on their potential use to combat viral, bacterial, and parasitic infection.
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Affiliation(s)
- Christoph Grohmann
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Danushka S Marapana
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Gregor Ebert
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
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28
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Knolle PA, Huang LR, Kosinska A, Wohlleber D, Protzer U. Improving Therapeutic Vaccination against Hepatitis B-Insights from Preclinical Models of Immune Therapy against Persistent Hepatitis B Virus Infection. Vaccines (Basel) 2021; 9:1333. [PMID: 34835264 PMCID: PMC8623083 DOI: 10.3390/vaccines9111333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 12/02/2022] Open
Abstract
Chronic hepatitis B affects more than 250 million individuals worldwide, putting them at risk of developing liver cirrhosis and liver cancer. While antiviral immune responses are key to eliminating hepatitis B virus (HBV) infections, insufficient antiviral immunity characterized by failure to eliminate HBV-infected hepatocytes is associated with chronic hepatitis B. Prophylactic vaccination against hepatitis B successfully established protective immunity against infection with the hepatitis B virus and has been instrumental in controlling hepatitis B. However, prophylactic vaccination schemes have not been successful in mounting protective immunity to eliminate HBV infections in patients with chronic hepatitis B. Here, we discuss the current knowledge on the development and efficacy of therapeutic vaccination strategies against chronic hepatitis B with particular emphasis on the pathogenetic understanding of dysfunctional anti-viral immunity. We explore the development of additional immune stimulation measures within tissues, in particular activation of immunogenic myeloid cell populations, and their use for combination with therapeutic vaccination strategies to improve the efficacy of therapeutic vaccination against chronic hepatitis B.
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Affiliation(s)
- Percy A. Knolle
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, 81675 Munich, Germany;
- German Center for infection Research (DZIF), Munich Site, 81675 Munich, Germany;
| | - Li-Rung Huang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli City 350, Taiwan;
| | - Anna Kosinska
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany;
| | - Dirk Wohlleber
- Institute of Molecular Immunology and Experimental Oncology, School of Medicine, Technical University of Munich, 81675 Munich, Germany;
| | - Ulrike Protzer
- German Center for infection Research (DZIF), Munich Site, 81675 Munich, Germany;
- Institute of Virology, School of Medicine, Technical University of Munich, 81675 Munich, Germany;
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29
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Feola S, Haapala M, Peltonen K, Capasso C, Martins B, Antignani G, Federico A, Pietiäinen V, Chiaro J, Feodoroff M, Russo S, Rannikko A, Fusciello M, Koskela S, Partanen J, Hamdan F, Tähkä SM, Ylösmäki E, Greco D, Grönholm M, Kekarainen T, Eshaghi M, Gurvich OL, Ylä-Herttuala S, M. Branca RM, Lehtiö J, Sikanen TM, Cerullo V. PeptiCHIP: A Microfluidic Platform for Tumor Antigen Landscape Identification. ACS NANO 2021; 15:15992-16010. [PMID: 34605646 PMCID: PMC8552492 DOI: 10.1021/acsnano.1c04371] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Identification of HLA class I ligands from the tumor surface (ligandome or immunopeptidome) is essential for designing T-cell mediated cancer therapeutic approaches. However, the sensitivity of the process for isolating MHC-I restricted tumor-specific peptides has been the major limiting factor for reliable tumor antigen characterization, making clear the need for technical improvement. Here, we describe our work from the fabrication and development of a microfluidic-based chip (PeptiCHIP) and its use to identify and characterize tumor-specific ligands on clinically relevant human samples. Specifically, we assessed the potential of immobilizing a pan-HLA antibody on solid surfaces via well-characterized streptavidin-biotin chemistry, overcoming the limitations of the cross-linking chemistry used to prepare the affinity matrix with the desired antibodies in the immunopeptidomics workflow. Furthermore, to address the restrictions related to the handling and the limited availability of tumor samples, we further developed the concept toward the implementation of a microfluidic through-flow system. Thus, the biotinylated pan-HLA antibody was immobilized on streptavidin-functionalized surfaces, and immune-affinity purification (IP) was carried out on customized microfluidic pillar arrays made of thiol-ene polymer. Compared to the standard methods reported in the field, our methodology reduces the amount of antibody and the time required for peptide isolation. In this work, we carefully examined the specificity and robustness of our customized technology for immunopeptidomics workflows. We tested this platform by immunopurifying HLA-I complexes from 1 × 106 cells both in a widely studied B-cell line and in patients-derived ex vivo cell cultures, instead of 5 × 108 cells as required in the current technology. After the final elution in mild acid, HLA-I-presented peptides were identified by tandem mass spectrometry and further investigated by in vitro methods. These results highlight the potential to exploit microfluidics-based strategies in immunopeptidomics platforms and in personalized immunopeptidome analysis from cells isolated from individual tumor biopsies to design tailored cancer therapeutic vaccines. Moreover, the possibility to integrate multiple identical units on a single chip further improves the throughput and multiplexing of these assays with a view to clinical needs.
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Affiliation(s)
- Sara Feola
- Drug
Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University
of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
- Helsinki
Institute of Life Science (HiLIFE), University
of Helsinki, Fabianinkatu 33, 00710 Helsinki, Finland
- Translational
Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
| | - Markus Haapala
- Drug
Research Program, Division of Pharmaceutical Chemistry and Technology,
Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
| | - Karita Peltonen
- Drug
Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University
of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
- Helsinki
Institute of Life Science (HiLIFE), University
of Helsinki, Fabianinkatu 33, 00710 Helsinki, Finland
- Translational
Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
| | - Cristian Capasso
- Drug
Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University
of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
- Helsinki
Institute of Life Science (HiLIFE), University
of Helsinki, Fabianinkatu 33, 00710 Helsinki, Finland
- Translational
Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
| | - Beatriz Martins
- Drug
Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University
of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
- Helsinki
Institute of Life Science (HiLIFE), University
of Helsinki, Fabianinkatu 33, 00710 Helsinki, Finland
- Translational
Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
| | - Gabriella Antignani
- Drug
Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University
of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
- Helsinki
Institute of Life Science (HiLIFE), University
of Helsinki, Fabianinkatu 33, 00710 Helsinki, Finland
- Translational
Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
| | - Antonio Federico
- Faculty
of
Medicine and Health Technology, Tampere
University, Arvo Ylpön
katu 34, Tampere 33520, Finland
| | - Vilja Pietiäinen
- Helsinki
Institute of Life Science (HiLIFE), University
of Helsinki, Fabianinkatu 33, 00710 Helsinki, Finland
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
- Institute
for Molecular Medicine Finland, FIMM, Helsinki Institute of Life Science
(HiLIFE), University of Helsinki, Biomedicum 2U, Tukholmankatu 8, 00290 Helsinki, Finland
| | - Jacopo Chiaro
- Drug
Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University
of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
- Helsinki
Institute of Life Science (HiLIFE), University
of Helsinki, Fabianinkatu 33, 00710 Helsinki, Finland
- Translational
Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
| | - Michaela Feodoroff
- Drug
Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University
of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
- Helsinki
Institute of Life Science (HiLIFE), University
of Helsinki, Fabianinkatu 33, 00710 Helsinki, Finland
- Translational
Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
- Institute
for Molecular Medicine Finland, FIMM, Helsinki Institute of Life Science
(HiLIFE), University of Helsinki, Biomedicum 2U, Tukholmankatu 8, 00290 Helsinki, Finland
| | - Salvatore Russo
- Drug
Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University
of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
- Helsinki
Institute of Life Science (HiLIFE), University
of Helsinki, Fabianinkatu 33, 00710 Helsinki, Finland
- Translational
Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
| | - Antti Rannikko
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
- Department
of Urology, Helsinki University and Helsinki
University Hospital, Haartmaninkatu 8, 00029 Helsinki, Finland
- Research
Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, 00029 Helsinki, Finland
| | - Manlio Fusciello
- Drug
Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University
of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
- Helsinki
Institute of Life Science (HiLIFE), University
of Helsinki, Fabianinkatu 33, 00710 Helsinki, Finland
- Translational
Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
| | - Satu Koskela
- Research
& Development Finnish Red Cross Blood Service Helsinki, Kivihaantie 7, 00310 Helsinki, Finland
| | - Jukka Partanen
- Research
& Development Finnish Red Cross Blood Service Helsinki, Kivihaantie 7, 00310 Helsinki, Finland
| | - Firas Hamdan
- Drug
Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University
of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
- Helsinki
Institute of Life Science (HiLIFE), University
of Helsinki, Fabianinkatu 33, 00710 Helsinki, Finland
- Translational
Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
| | - Sari M. Tähkä
- Drug
Research Program, Division of Pharmaceutical Chemistry and Technology,
Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
| | - Erkko Ylösmäki
- Drug
Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University
of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
- Helsinki
Institute of Life Science (HiLIFE), University
of Helsinki, Fabianinkatu 33, 00710 Helsinki, Finland
- Translational
Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
| | - Dario Greco
- Faculty
of
Medicine and Health Technology, Tampere
University, Arvo Ylpön
katu 34, Tampere 33520, Finland
| | - Mikaela Grönholm
- Drug
Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University
of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
- Helsinki
Institute of Life Science (HiLIFE), University
of Helsinki, Fabianinkatu 33, 00710 Helsinki, Finland
- Translational
Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
| | - Tuija Kekarainen
- Kuopio
Center for Gene and Cell Therapy, Microkatu 1S, 70210 Kuopio, Finland
| | - Masoumeh Eshaghi
- Kuopio
Center for Gene and Cell Therapy, Microkatu 1S, 70210 Kuopio, Finland
| | - Olga L. Gurvich
- Kuopio
Center for Gene and Cell Therapy, Microkatu 1S, 70210 Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A.
I. Virtanen Institute, University of Eastern
Finland, Neulaniementie
2, 70211 Kuopio, Finland
| | - Rui M. M. Branca
- Science
for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Tomtebodavagen 23B, 171 21 Solna, Sweden
| | - Janne Lehtiö
- Science
for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Tomtebodavagen 23B, 171 21 Solna, Sweden
| | - Tiina M. Sikanen
- Drug
Research Program, Division of Pharmaceutical Chemistry and Technology,
Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
| | - Vincenzo Cerullo
- Drug
Research Program (DRP), ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical
Biosciences, Faculty of Pharmacy, University
of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
- Helsinki
Institute of Life Science (HiLIFE), University
of Helsinki, Fabianinkatu 33, 00710 Helsinki, Finland
- Translational
Immunology Program (TRIMM), Faculty of Medicine Helsinki University, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
- Digital
Precision Cancer Medicine Flagship (iCAN), University of Helsinki, 00014 Helsinki, Finland
- Department
of Molecular Medicine and Medical Biotechnology, Naples University “Federico II”, S. Pansini 5, 80131 Naples, Italy
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30
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Identification of tumor antigens with immunopeptidomics. Nat Biotechnol 2021; 40:175-188. [PMID: 34635837 DOI: 10.1038/s41587-021-01038-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 07/29/2021] [Indexed: 12/18/2022]
Abstract
The identification of actionable tumor antigens is indispensable for the development of several cancer immunotherapies, including T cell receptor-transduced T cells and patient-specific mRNA or peptide vaccines. Most known tumor antigens have been identified through extensive molecular characterization and are considered canonical if they derive from protein-coding regions of the genome. By eluting human leukocyte antigen-bound peptides from tumors and subjecting these to mass spectrometry analysis, the peptides can be identified by matching the resulting spectra against reference databases. Recently, mass-spectrometry-based immunopeptidomics has enabled the discovery of noncanonical antigens-antigens derived from sequences outside protein-coding regions or generated by noncanonical antigen-processing mechanisms. Coupled with transcriptomics and ribosome profiling, this method enables the identification of thousands of noncanonical peptides, of which a substantial fraction may be detected exclusively in tumors. Spectral matching against the immense noncanonical reference may generate false positives. However, sensitive mass spectrometry, analytical validation and advanced bioinformatics solutions are expected to uncover the full landscape of presented antigens and clinically relevant targets.
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31
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Charneau J, Suzuki T, Shimomura M, Fujinami N, Nakatsura T. Peptide-Based Vaccines for Hepatocellular Carcinoma: A Review of Recent Advances. J Hepatocell Carcinoma 2021; 8:1035-1054. [PMID: 34513746 PMCID: PMC8424432 DOI: 10.2147/jhc.s291558] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022] Open
Abstract
Primary liver cancer is the sixth most commonly diagnosed cancer and the third leading cause of cancer-related deaths worldwide. After surgery, up to 70% of patients experience relapses. The current first-line therapy for advanced cases of hepatocellular carcinoma (HCC) comprises sorafenib and lenvatinib administered as single-drug therapies. Regorafenib, cabozantinib, and ramucirumab are administered as second-line therapies. Recently, it has been reported that using the immune checkpoint inhibitors atezolizumab (anti-PDL1 antibody) and bevacizumab (anti-VEGF antibody) leads to longer overall survival of unresectable cases, when compared with the use of sorafenib. The role of cancer immunity against HCC has attracted the attention of clinicians. In this review, we describe our phase I/II clinical trials of peptide vaccines targeting GPC3 in HCC and discuss the potential of peptide vaccines targeting common cancer antigens that are highly expressed in HCC, such as WT-I, AFP, ROBO1, and FOXM1. Further, we introduce recent cancer vaccines targeting neoantigens, which have attracted attention in recent times, as well as present our preclinical studies, the results of which might aid to initiate a neoantigen vaccine clinical trial, which would be the first of its kind in Japan.
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Affiliation(s)
- Jimmy Charneau
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa City, Japan
| | - Toshihiro Suzuki
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa City, Japan.,Department of Pharmacology, School of Medicine, Teikyo University, Tokyo, Japan
| | - Manami Shimomura
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa City, Japan
| | - Norihiro Fujinami
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa City, Japan
| | - Tetsuya Nakatsura
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa City, Japan
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32
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Kikuchi Y, Tokita S, Hirama T, Kochin V, Nakatsugawa M, Shinkawa T, Hirohashi Y, Tsukahara T, Hata F, Takemasa I, Sato N, Kanaseki T, Torigoe T. CD8 + T-cell Immune Surveillance against a Tumor Antigen Encoded by the Oncogenic Long Noncoding RNA PVT1. Cancer Immunol Res 2021; 9:1342-1353. [PMID: 34433589 DOI: 10.1158/2326-6066.cir-20-0964] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 04/11/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022]
Abstract
CD8+ T cells recognize peptides displayed by HLA class I molecules on cell surfaces, monitoring pathologic conditions such as cancer. Advances in proteogenomic analysis of HLA ligandomes have demonstrated that cells present a subset of cryptic peptides derived from noncoding regions of the genome; however, the roles of cryptic HLA ligands in tumor immunity remain unknown. In the current study, we comprehensively and quantitatively investigated the HLA class I ligandome of a set of human colorectal cancer and matched normal tissues, showing that cryptic translation products accounted for approximately 5% of the HLA class I ligandome. We also found that a peptide encoded by the long noncoding RNA (lncRNA) PVT1 was predominantly enriched in multiple colorectal cancer tissues. The PVT1 gene is located downstream of the MYC gene in the genome and is aberrantly overexpressed across a variety of cancers, reflecting its oncogenic property. The PVT1 peptide was recognized by patient CD8+ tumor-infiltrating lymphocytes, as well as peripheral blood mononuclear cells, suggesting the presence of patient immune surveillance. Our findings show that peptides can be translated from lncRNAs and presented by HLA class I and that cancer patient T cells are capable of sensing aberrations in noncoding regions of the genome.
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Affiliation(s)
- Yasuhiro Kikuchi
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Serina Tokita
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Sapporo Dohto Hospital, Sapporo, Japan
| | - Tomomi Hirama
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Sapporo Dohto Hospital, Sapporo, Japan
| | - Vitaly Kochin
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Department of Immunology, Nagoya University, Nagoya, Japan
| | - Munehide Nakatsugawa
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Department of Pathology, Tokyo Medical University Hachioji Medical Center, Hachioji, Tokyo, Japan
| | - Tomoyo Shinkawa
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | | | | | | | - Ichiro Takemasa
- Department of Surgery, Surgical Oncology and Science, Sapporo Medical University, Sapporo, Japan
| | - Noriyuki Sato
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Sapporo Dohto Hospital, Sapporo, Japan
| | - Takayuki Kanaseki
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.
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33
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Bailey A, Nicholas B, Darley R, Parkinson E, Teo Y, Aleksic M, Maxwell G, Elliott T, Ardern-Jones M, Skipp P. Characterization of the Class I MHC Peptidome Resulting From DNCB Exposure of HaCaT Cells. Toxicol Sci 2021; 180:136-147. [PMID: 33372950 PMCID: PMC7916740 DOI: 10.1093/toxsci/kfaa184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Skin sensitization following the covalent modification of proteins by low molecular weight chemicals (haptenation) is mediated by cytotoxic T lymphocyte (CTL) recognition of human leukocyte antigen (HLA) molecules presented on the surface of almost all nucleated cells. There exist 3 nonmutually exclusive hypotheses for how haptens mediate CTL recognition: direct stimulation by haptenated peptides, hapten modification of HLA leading to an altered HLA-peptide repertoire, or a hapten altered proteome leading to an altered HLA-peptide repertoire. To shed light on the mechanism underpinning skin sensitization, we set out to utilize proteomic analysis of keratinocyte presented antigens following exposure to 2,4-dinitrochlorobenzene (DNCB). We show that the following DNCB exposure, cultured keratinocytes present cysteine haptenated (dinitrophenylated) peptides in multiple HLA molecules. In addition, we find that one of the DNCB modified peptides derives from the active site of cytosolic glutathione-S transferase-ω. These results support the current view that a key mechanism of skin sensitization is stimulation of CTLs by haptenated peptides. Data are available via ProteomeXchange with identifier PXD021373.
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Affiliation(s)
- Alistair Bailey
- Centre for Proteomic Research, Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Centre for Cancer Immunology and Institute for Life Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Ben Nicholas
- Centre for Proteomic Research, Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Centre for Cancer Immunology and Institute for Life Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Rachel Darley
- Centre for Cancer Immunology and Institute for Life Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Erika Parkinson
- Centre for Proteomic Research, Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Ying Teo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Maja Aleksic
- Safety & Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook MK44 1LQ, UK
| | - Gavin Maxwell
- Safety & Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook MK44 1LQ, UK
| | - Tim Elliott
- Centre for Cancer Immunology and Institute for Life Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Michael Ardern-Jones
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Paul Skipp
- Centre for Proteomic Research, Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
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34
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Hui C, Chau B, Gan G, Stokes W, Karam SD, Amini A. Overcoming Resistance to Immunotherapy in Head and Neck Cancer Using Radiation: A Review. Front Oncol 2021; 11:592319. [PMID: 34277390 PMCID: PMC8280353 DOI: 10.3389/fonc.2021.592319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 06/21/2021] [Indexed: 12/19/2022] Open
Abstract
Radiation therapy remains at the center of head and neck cancer treatment. With improvements in treatment delivery, radiation therapy has become an affective ablative modality for head and neck cancers. Immune checkpoint inhibitors are now also playing a more active role both in the locally advanced and metastatic setting. With improved systemic options, local noninvasive modalities including radiation therapy are playing a critical role in overcoming resistance in head and neck cancer. The aim of this review is to describe the role of radiation therapy in modulating the tumor microenvironment and how radiation dose, fractionation and treatment field can impact the immune system and potentially effect outcomes when combined with immunotherapy. The review will encompass several common scenarios where radiation is used to improve outcomes and overcome potential resistance that may develop with immunotherapy in head and neck squamous cell carcinoma (HNSCC), including upfront locally advanced disease receiving definitive radiation and recurrent disease undergoing re-irradiation. Lastly, we will review the potential toxicities of combined therapy and future directions of their role in the management of HNSCC.
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Affiliation(s)
- Caressa Hui
- Department of Radiation Oncology, Stanford University, Palo Alto, CA, United States
| | - Brittney Chau
- School of Medicine, New York Medical College, Valhalla, NY, United States
| | - Greg Gan
- Department of Radiation Oncology, University of Kansas, Kansas City, KA, United States
| | - William Stokes
- Department of Radiation Oncology, Emory University, Atlanta, GA, United States
| | - Sana D. Karam
- Department of Radiation Oncology, University of Colorado, Aurora, CO, United States
| | - Arya Amini
- Department of Radiation Oncology, City of Hope National Medical Center, Duarte, CA, United States
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35
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Aflalo A, Boyle LH. Polymorphisms in MHC class I molecules influence their interactions with components of the antigen processing and presentation pathway. Int J Immunogenet 2021; 48:317-325. [PMID: 34176210 DOI: 10.1111/iji.12546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
MHC class I (MHC-I) molecules undergo an intricate folding process in order to pick up antigenic peptide to present to the immune system. In recent years, the discovery of a new peptide editor for MHC-I has added an extra level of complexity in our understanding of how peptide presentation is regulated. On top of this, the incredible diversity in MHC-I molecules leads to significant variation in the interaction between MHC-I and components of the antigen processing and presentation pathway. Here, we review our current understanding regarding how polymorphisms in human leukocyte antigen class I molecules influence their interactions with key components of the antigen processing and presentation pathway. A deeper understanding of this may offer new insights regarding how apparently subtle variation in MHC-I can have a significant impact on susceptibility to disease.
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Affiliation(s)
- Aure Aflalo
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Cambridge, UK
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36
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Özer O, Lenz TL. Unique pathogen peptidomes facilitate pathogen-specific selection and specialization of MHC alleles. Mol Biol Evol 2021; 38:4376-4387. [PMID: 34110412 PMCID: PMC8476153 DOI: 10.1093/molbev/msab176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A key component of pathogen-specific adaptive immunity in vertebrates is the presentation of pathogen-derived antigenic peptides by major histocompatibility complex (MHC) molecules. The excessive polymorphism observed at MHC genes is widely presumed to result from the need to recognize diverse pathogens, a process called pathogen-driven balancing selection. This process assumes that pathogens differ in their peptidomes—the pool of short peptides derived from the pathogen’s proteome—so that different pathogens select for different MHC variants with distinct peptide-binding properties. Here, we tested this assumption in a comprehensive data set of 51.9 Mio peptides, derived from the peptidomes of 36 representative human pathogens. Strikingly, we found that 39.7% of the 630 pairwise comparisons among pathogens yielded not a single shared peptide and only 1.8% of pathogen pairs shared more than 1% of their peptides. Indeed, 98.8% of all peptides were unique to a single pathogen species. Using computational binding prediction to characterize the binding specificities of 321 common human MHC class-I variants, we investigated quantitative differences among MHC variants with regard to binding peptides from distinct pathogens. Our analysis showed signatures of specialization toward specific pathogens especially by MHC variants with narrow peptide-binding repertoires. This supports the hypothesis that such fastidious MHC variants might be maintained in the population because they provide an advantage against particular pathogens. Overall, our results establish a key selection factor for the excessive allelic diversity at MHC genes observed in natural populations and illuminate the evolution of variable peptide-binding repertoires among MHC variants.
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Affiliation(s)
- Onur Özer
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.,Research Unit for Evolutionary Immunogenomics, Department of Biology, Universität Hamburg, 20146 Hamburg, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.,Research Unit for Evolutionary Immunogenomics, Department of Biology, Universität Hamburg, 20146 Hamburg, Germany
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37
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Pappalardo JS, Salmaso S, Levchenko TS, Mastrotto F, Bersani S, Langellotti CA, Vermeulen M, Ghersa F, Quattrocchi V, Zamorano PI, Hartner WC, Toniutti M, Musacchio T, Torchilin VP. Characterization of a Nanovaccine Platform Based on an α1,2-Mannobiose Derivative Shows Species-non-specific Targeting to Human, Bovine, Mouse, and Teleost Fish Dendritic Cells. Mol Pharm 2021; 18:2540-2555. [PMID: 34106726 DOI: 10.1021/acs.molpharmaceut.1c00048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Dendritic cells serve as the main immune cells that trigger the immune response. We developed a simple and cost-effective nanovaccine platform based on the α1',2-mannobiose derivative for dendritic cell targeting. In previous work, we have formulated the α1,2-mannobiose-based nanovaccine platform with plasmid DNA and tested it in cattle against BoHV-1 infection. There, we have shown that the dendritic cell targeting using this nanovaccine platform in vivo can boost the immunogenicity, resulting in a long-lasting immunity. In this work, we aim to characterize the α1',2-mannobiose derivative, which is key in the nanovaccine platform. This DC-targeting strategy takes advantage of the specific receptor known as DC-SIGN and exploits its capacity to bind α1,2-mannobiose that is present at terminal ends of oligosaccharides in certain viruses, bacteria, and other pathogens. The oxidative conjugation of α1',2-mannobiose to NH2-PEG2kDa-DSPE allowed us to preserve the chemical structure of the non-reducing mannose of the disaccharide and the OH groups and the stereochemistry of all carbons of the reducing mannose involved in the binding to DC-SIGN. Here, we show specific targeting to DC-SIGN of decorated micelles incubated with the Raji/DC-SIGN cell line and uptake of targeted liposomes that took place in human, bovine, mouse, and teleost fish DCs in vitro, by flow cytometry. Specific targeting was found in all cultures, demonstrating a species-non-specific avidity for this ligand, which opens up the possibility of using this nanoplatform to develop new vaccines for various species, including humans.
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Affiliation(s)
- Juan Sebastian Pappalardo
- Veterinary Nanomedicine Group, Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB, INTA-CONICET), EEA Bariloche, Instituto Nacional de Tecnología Agropecuaria, Bote Modesta Victoria 4450, San Carlos de Bariloche, Río Negro R8403DVZ, Argentina.,Immunology and Immunomodulators Group, Instituto de Virología e Innovaciones Tecnológicas (IVIT, INTA-CONICET), IV, Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto 2799, William Morris, Buenos Aires B1681FUU, Argentina.,Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Stefano Salmaso
- Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via F. Marzolo, 5, Padova 35121, Padova, Italy
| | - Tatyana S Levchenko
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Francesca Mastrotto
- Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via F. Marzolo, 5, Padova 35121, Padova, Italy
| | - Sara Bersani
- Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via F. Marzolo, 5, Padova 35121, Padova, Italy
| | - Cecilia A Langellotti
- Immunology and Immunomodulators Group, Instituto de Virología e Innovaciones Tecnológicas (IVIT, INTA-CONICET), IV, Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto 2799, William Morris, Buenos Aires B1681FUU, Argentina.,National Council of Scientific and Technical Research (CONICET), Avenida Rivadavia 1917, Ciudad de Buenos Aires C1033AAJ, Argentina
| | - Monica Vermeulen
- National Council of Scientific and Technical Research (CONICET), Avenida Rivadavia 1917, Ciudad de Buenos Aires C1033AAJ, Argentina.,Institute of Experimental Medicine (IMEX, ANM-CONICET), Academia Nacional de Medicina, Pacheco de Melo 3081, Ciudad de Buenos Aires C1425AUM, Argentina
| | - Federica Ghersa
- Veterinary Nanomedicine Group, Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB, INTA-CONICET), EEA Bariloche, Instituto Nacional de Tecnología Agropecuaria, Bote Modesta Victoria 4450, San Carlos de Bariloche, Río Negro R8403DVZ, Argentina.,Parasitology Laboratory, Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA, UNCo-CONICET) Universidad Nacional del Comahue, Quintral 1250, San Carlos de Bariloche, Río Negro R8400FRF, Argentina
| | - Valeria Quattrocchi
- Immunology and Immunomodulators Group, Instituto de Virología e Innovaciones Tecnológicas (IVIT, INTA-CONICET), IV, Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto 2799, William Morris, Buenos Aires B1681FUU, Argentina
| | - Patricia I Zamorano
- Immunology and Immunomodulators Group, Instituto de Virología e Innovaciones Tecnológicas (IVIT, INTA-CONICET), IV, Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto 2799, William Morris, Buenos Aires B1681FUU, Argentina.,National Council of Scientific and Technical Research (CONICET), Avenida Rivadavia 1917, Ciudad de Buenos Aires C1033AAJ, Argentina
| | - William C Hartner
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Micaela Toniutti
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Tiziana Musacchio
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Vladimir P Torchilin
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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Komov L, Melamed Kadosh D, Barnea E, Admon A. The Effect of Interferons on Presentation of Defective Ribosomal Products as HLA Peptides. Mol Cell Proteomics 2021; 20:100105. [PMID: 34087483 PMCID: PMC8724922 DOI: 10.1016/j.mcpro.2021.100105] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/15/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
A subset of class I major histocompatibility complex (MHC)-bound peptides is produced from immature proteins that are rapidly degraded after synthesis. These defective ribosomal products (DRiPs) have been implicated in early alert of the immune system about impending infections. Interferons are important cytokines, produced in response to viral infection, that modulate cellular metabolism and gene expression patterns, increase the presentation of MHC molecules, and induce rapid degradation of proteins and cell-surface presentation of their derived MHC peptides, thereby contributing to the battle against pathogen infections. This study evaluated the role of interferons in the induction of rapid degradation of DRiPs to modulate the repertoire of DRiP-derived MHC peptides. Cultured human breast cancer cells were treated with interferons, and the rates of synthesis and degradation of cellular protein and their degradation products were determined by LC-MS/MS analysis, following the rates of incorporation of heavy stable isotope–labeled amino acids (dynamic stable isotope labeling by amino acids in cell culture, dynamic SILAC) at several time points after the interferon application. Large numbers of MHC peptides that incorporated the heavy amino acids faster than their source proteins indicated that DRiP peptides were abundant in the MHC peptidome; interferon treatment increased by about twofold their relative proportions in the peptidome. Such typical DRiP-derived MHC peptides were from the surplus subunits of the proteasome and ribosome, which are degraded because of the transition to immunoproteasomes and a new composition of ribosomes incorporating protein subunits that are induced by the interferon. We conclude that degradation of surplus subunits induced by the interferon is a major source for DRiP–MHC peptides, a phenomenon relevant to coping with viral infections, where a rapid presentation of MHC peptides derived from excess viral proteins may help alert the immune system about the impending infection. Degradation products of surplus subunits are often presented as HLA peptides. Interferons increase degradation and presentation of such defective products. Dynamic SILAC facilitates identification of such HLA peptides. This cellular pathway provides alert to the immune system about viral infections.
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Affiliation(s)
- Liran Komov
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Eilon Barnea
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
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39
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Fangazio M, Ladewig E, Gomez K, Garcia-Ibanez L, Kumar R, Teruya-Feldstein J, Rossi D, Filip I, Pan-Hammarström Q, Inghirami G, Boldorini R, Ott G, Staiger AM, Chapuy B, Gaidano G, Bhagat G, Basso K, Rabadan R, Pasqualucci L, Dalla-Favera R. Genetic mechanisms of HLA-I loss and immune escape in diffuse large B cell lymphoma. Proc Natl Acad Sci U S A 2021; 118:e2104504118. [PMID: 34050029 PMCID: PMC8179151 DOI: 10.1073/pnas.2104504118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Fifty percent of diffuse large B cell lymphoma (DLBCL) cases lack cell-surface expression of the class I major histocompatibility complex (MHC-I), thus escaping recognition by cytotoxic T cells. Here we show that, across B cell lymphomas, loss of MHC-I, but not MHC-II, is preferentially restricted to DLBCL. To identify the involved mechanisms, we performed whole exome and targeted HLA deep-sequencing in 74 DLBCL samples, and found somatic inactivation of B2M and the HLA-I loci in 80% (34 of 42) of MHC-INEG tumors. Furthermore, 70% (22 of 32) of MHC-IPOS DLBCLs harbored monoallelic HLA-I genetic alterations (MHC-IPOS/mono), indicating allele-specific inactivation. MHC-INEG and MHC-IPOS/mono cases harbored significantly higher mutational burden and inferred neoantigen load, suggesting potential coselection of HLA-I loss and sustained neoantigen production. Notably, the analysis of >500,000 individuals across different cancer types revealed common germline HLA-I homozygosity, preferentially in DLBCL. In mice, germinal-center B cells lacking HLA-I expression did not progress to lymphoma and were counterselected in the context of oncogene-driven lymphomagenesis, suggesting that additional events are needed to license immune evasion. These results suggest a multistep process of HLA-I loss in DLBCL development including both germline and somatic events, and have direct implications for the pathogenesis and immunotherapeutic targeting of this disease.
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Affiliation(s)
- Marco Fangazio
- Institute for Cancer Genetics, Columbia University, New York, NY 10032
| | - Erik Ladewig
- Department of Systems Biology, Columbia University, New York, NY 10032
- Department of Biomedical Informatics, Columbia University, New York, NY 10032
| | - Karen Gomez
- Department of Systems Biology, Columbia University, New York, NY 10032
- Department of Biomedical Informatics, Columbia University, New York, NY 10032
| | | | - Rahul Kumar
- Institute for Cancer Genetics, Columbia University, New York, NY 10032
| | | | - Davide Rossi
- Laboratory of Experimental Hematology, Institute of Oncology Research, 6500 Bellinzona, Switzerland
- Clinic of Hematology, Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland
- Faculty of Biomedical Science, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Ioan Filip
- Department of Systems Biology, Columbia University, New York, NY 10032
- Department of Biomedical Informatics, Columbia University, New York, NY 10032
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, SE14183 Huddinge, Sweden
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065
| | - Renzo Boldorini
- Department of Health Sciences, Division of Pathology, Amedeo Avogadro University of Eastern Piedmont, 28100 Novara, Italy
| | - German Ott
- Department of Clinical Pathology, Robert Bosch Krankenhaus, 70376 Stuttgart, Germany
| | - Annette M Staiger
- Department of Clinical Pathology, Robert Bosch Krankenhaus, 70376 Stuttgart, Germany
- Institute of Clinical Pharmacology, Stuttgart and University of Tuebingen, 72074 Tuebingen, Germany
| | - Björn Chapuy
- Department of Hematology and Oncology, University of Göttingen, 37073 Göttingen, Germany
| | - Gianluca Gaidano
- Department of Translational Medicine, Division of Hematology, Amedeo Avogadro University of Eastern Piedmont, 28100 Novara, Italy
| | - Govind Bhagat
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY 10032
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032
| | - Raul Rabadan
- Department of Systems Biology, Columbia University, New York, NY 10032
- Department of Biomedical Informatics, Columbia University, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032
- Program for Mathematical Genomics, Columbia University, New York, NY 10032
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY 10032;
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY 10032;
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032
- Department of Microbiology and Immunology, Columbia University, New York, NY 10032
- Department of Genetics and Development, Columbia University, New York, NY 10032
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40
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Nikoobakht MR, Khalili M, Dialameh H, A Pishkuhi M, Karimi A, Ramezani-Binabaj M, Jelveh-Moghaddam E. Evaluation of circulating β2-microglobulin as a prognostic factor for biochemical recurrence after radical prostatectomy. JOURNAL OF CLINICAL UROLOGY 2021. [DOI: 10.1177/20514158211010656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Objectives: One of the most challenging issues after radical prostatectomy (RP) is biochemical recurrence (BCR). The prediction of BCR can determine the selection of modality and its continuation. Currently, preoperative PSA level, Gleason score, and stage of tumor are used for prediction of BCR. The association of β2-microglobulin (B2MG) with hematologic and solid tumors, such as prostate cancer, was suggested in previous studies. The circulating B2MG, as a risk factor for BCR, has been applied for the first time in the current study. Circulating B2MG likely provides a good environment for the growth of cancer cells due to its angiogenesis and tumorigenesis properties. Methods and materials: A cohort study of 59 patients who underwent RP from 2012 to 2013 was carried out. B2MG was measured in the stored serum samples taken from the patients who underwent biopsy. Patients were monitored for BCR and metastasis caused by prostate cancer over a five-year period. The association of B2MG level with the PSA rising were investigated using multivariate models by adjustment for age, PSA, and Gleason's score effects. Results: Mean concentration of B2MG varied significantly according to patient age, PSA, and Gleason's score. One unit increase in the B2MG may significantly increase the hazard of PSA rising (HR=2.528; 95% CI 1.101–5.319; p-value=0.015). Hazard of PSA rising in high-risk groups was a 2.543-fold increase with a unit increase in B2MG. Conclusion: B2MG could help identify those who would derive the greatest benefit from additional systemic or local treatment. Level of evidence: Not applicable for this multicentre audit.
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Affiliation(s)
| | - Masoud Khalili
- Department of Urology, Sina Hospital, Tehran University of Medical Sciences, Iran
| | - Hossein Dialameh
- Department of Urology, Sina Hospital, Tehran University of Medical Sciences, Iran
| | - Mahin A Pishkuhi
- Pars Advanced and Minimally Invasive Medical Manners Research Center, Pars Hospital, Iran University of Medical Sciences, Iran
| | - Arash Karimi
- Department of Urology, Sina Hospital, Tehran University of Medical Sciences, Iran
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41
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Story CM, Wang T, Bhatt VR, Battiwalla M, Badawy SM, Kamoun M, Gragert L, Brown V, Baxter-Lowe LA, Marsh SGE, Gadalla SM, Schetelig J, Mytilineos J, Miklos D, Waller EK, Kuxhausen M, Spellman S, Lee S, Paczesny S, Lansford JL, Vincent BG, Riches ML, Armistead PM. Genetics of HLA Peptide Presentation and Impact on Outcomes in HLA-Matched Allogeneic Hematopoietic Cell Transplantation. Transplant Cell Ther 2021; 27:591-599. [PMID: 33882342 DOI: 10.1016/j.jtct.2021.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 01/06/2023]
Abstract
Minor histocompatibility antigens (mHAs), recipient-derived peptide epitopes presented on the cell surface, are known to mediate graft-versus-host disease (GVHD); however, there are no current methods to associate mHA features with GVHD risk. This deficiency is due in part to the lack of technological means to accurately predict, let alone confirm, the tremendous number of potential mHAs in each individual transplant. Previous studies have shown that different HLA molecules present varying fractions of candidate peptide epitopes; however, the genetic "distance" between HLA-matched donors and recipients is relatively constrained. From these 2 observations, it is possible that the HLA type for a donor-recipient pair (DRP) would provide a surrogate measurement of the number of predicted mHAs, which could be related to GVHD risk. Because different HLA molecules present variable numbers of peptide antigens, a predicted cumulative peptide-binding efficiency can be calculated for individual DRP based on the pair's HLA type. The purpose of this study was to test whether cumulative peptide-binding efficiency is associated with the risk of acute GVHD (aGVHD) or relapse. In this retrospective Center for International Blood and Marrow Transplant Research study, a total of 3242 HLA-matched DRPs were analyzed for predicted cumulative peptide-binding efficiency using their HLA types and were divided into tertiles based on their scores. Univariable and multivariable analyses was performed to test for associations between cumulative peptide-binding efficiency for DRPs, divided into the HLA-matched related donor (MRD) and HLA-matched unrelated donor (MUD) cohorts, and the primary outcomes of aGVHD and relapse. Secondary outcomes investigated included overall survival, disease-free survival, and transplantation-related mortality. Using a computationally generated peptidome as a test dataset, the tested series of HLA class I displayed peptide-binding frequencies ranging from 0.1% to 3.8% of the full peptidome, and HLA class II molecules had peptide-binding frequencies of 12% to 77% across the HLA-DRB1 allotypes. By increasing binding efficiency tertile, the cumulative incidence of aGVHD at 6 months for MUD patients was 41%, 41%, and 45% for HLA class I (P = .336) and 44%, 41%, and 42% for HLA class II (P = .452). The cumulative incidences of relapse at 3 years for MUD transplant recipients were 36%, 38%, and 38% for HLA class I (P = .533) and 37%, 37%, and 38% for HLA class II (P = .896). The findings were similar for MRD transplant recipients. Multivariable analysis did not identify any impact of peptide-binding efficiency on aGVHD or relapse in MUD or MRD transplant recipients. Whereas GVHD is mediated by minor antigen mismatches in the context of HLA-matched allo-HCT, peptide-binding efficiency, which was used as a surrogate measurement for predicted number of binding antigens, did not provide additional clinical information for GVHD risk assessment. The negative result may be due to the limitations of this surrogate marker, or it is possible that GVHD is driven by a subset of immunogenic mHAs. Further research should be directed at direct mHA epitope and immunogenicity prediction.
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Affiliation(s)
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Vijaya Raj Bhatt
- The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Minoo Battiwalla
- Director of Outcomes Research, Sarah Cannon Blood Cancer Network, Nashville, Tennessee
| | - Sherif M Badawy
- Division of Hematology, Oncology and Stem Cell Transplant, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Malek Kamoun
- Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Loren Gragert
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Valerie Brown
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, Penn State Hershey Children's Hospital and College of Medicine, Hershey, Pennsylvania
| | - Lee Ann Baxter-Lowe
- Director of HLA Laboratory, Children's Hospital of Los Angeles, Los Angeles, California
| | - Steven G E Marsh
- Anthony Nolan Research Institute & University College London Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Shahinaz M Gadalla
- Division of Cancer Epidemiology & Genetics, NIH-NCI Clinical Genetics Branch, Rockville, Maryland
| | - Johannes Schetelig
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, TU Dresden, and DKMS, Clinical Trials Unit, Dresden, Germany
| | | | - David Miklos
- BMT and Cell Therapy Division, Department of Medicine, Stanford Health Care, Stanford, California
| | - Edmund K Waller
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Michelle Kuxhausen
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Stephen Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Stephanie Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina
| | - Jefferson L Lansford
- Orthopedic Surgery, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Benjamin G Vincent
- BMTCT Program, Division of Hematology, University of North Carolina, Chapel Hill, North Carolina; BMTCT Program, Division of Hematology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Marcie L Riches
- BMTCT Program, Division of Hematology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Paul M Armistead
- Internal Medicine, University of North Carolina, Chapel Hill, North Carolina; BMTCT Program, Division of Hematology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.
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42
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Nagamine BS, Godil J, Dolan BP. The Unfolded Protein Response Reveals eIF2α Phosphorylation as a Critical Factor for Direct MHC Class I Antigen Presentation. Immunohorizons 2021; 5:135-146. [PMID: 33685907 DOI: 10.4049/immunohorizons.2100012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 11/19/2022] Open
Abstract
The ability to modulate direct MHC class I (MHC I) Ag presentation is a desirable goal for the treatment of a variety of conditions, including autoimmune diseases, chronic viral infections, and cancers. It is therefore necessary to understand how changes in the cellular environment alter the cells' ability to present peptides to T cells. The unfolded protein response (UPR) is a signaling pathway activated by the presence of excess unfolded proteins in the endoplasmic reticulum. Previous studies have indicated that chemical induction of the UPR decreases direct MHC I Ag presentation, but the precise mechanisms are unknown. In this study, we used a variety of small molecule modulators of different UPR signaling pathways to query which UPR signaling pathways can alter Ag presentation in both murine and human cells. When signaling through the PERK pathway, and subsequent eIF2α phosphorylation, was blocked by treatment with GSK2656157, MHC I Ag presentation remain unchanged, whereas treatment with salubrinal, which has the opposite effect of GSK2656157, decreases both Ag presentation and overall cell-surface MHC I levels. Treatment with 4μ8C, an inhibitor of the IRE1α UPR activation pathway that blocks splicing of Xbp1 mRNA, also diminished MHC I Ag presentation. However, 4μ8C treatment unexpectedly led to an increase in eIF2α phosphorylation in addition to blocking IRE1α signaling. Given that salubrinal and 4μ8C lead to eIF2α phosphorylation and similar decreases in Ag presentation, we conclude that UPR signaling through PERK, leading to eIF2α phosphorylation, results in a modest decrease in direct MHC I Ag presentation.
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Affiliation(s)
- Brandy S Nagamine
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331
| | - Jamila Godil
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331
| | - Brian P Dolan
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331
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43
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Padariya M, Kalathiya U, Mikac S, Dziubek K, Tovar Fernandez MC, Sroka E, Fahraeus R, Sznarkowska A. Viruses, cancer and non-self recognition. Open Biol 2021; 11:200348. [PMID: 33784856 PMCID: PMC8061760 DOI: 10.1098/rsob.200348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/04/2021] [Indexed: 12/11/2022] Open
Abstract
Virus-host interactions form an essential part of every aspect of life, and this review is aimed at looking at the balance between the host and persistent viruses with a focus on the immune system. The virus-host interaction is like a cat-and-mouse game and viruses have developed ingenious mechanisms to manipulate cellular pathways, most notably the major histocompatibility (MHC) class I pathway, to reside within infected cell while evading detection and destruction by the immune system. However, some of the signals sensing and responding to viral infection are derived from viruses and the fact that certain viruses can prevent the infection of others, highlights a more complex coexistence between the host and the viral microbiota. Viral immune evasion strategies also illustrate that processes whereby cells detect and present non-self genetic material to the immune system are interlinked with other cellular pathways. Immune evasion is a target also for cancer cells and a more detailed look at the interfaces between viral factors and components of the MHC class I peptide-loading complex indicates that these interfaces are also targets for cancer mutations. In terms of the immune checkpoint, however, viral and cancer strategies appear different.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Sara Mikac
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Katarzyna Dziubek
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Maria C. Tovar Fernandez
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Ewa Sroka
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 65653 Brno, Czech Republic
- Department of Medical Biosciences, Umeå University, Building 6M, 901 85 Umeå, Sweden
| | - Alicja Sznarkowska
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
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44
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Lhuillier C, Rudqvist NP, Yamazaki T, Zhang T, Charpentier M, Galluzzi L, Dephoure N, Clement CC, Santambrogio L, Zhou XK, Formenti SC, Demaria S. Radiotherapy-exposed CD8+ and CD4+ neoantigens enhance tumor control. J Clin Invest 2021; 131:138740. [PMID: 33476307 DOI: 10.1172/jci138740] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 01/13/2021] [Indexed: 12/23/2022] Open
Abstract
Neoantigens generated by somatic nonsynonymous mutations are key targets of tumor-specific T cells, but only a small number of mutations predicted to be immunogenic are presented by MHC molecules on cancer cells. Vaccination studies in mice and patients have shown that the majority of neoepitopes that elicit T cell responses fail to induce significant antitumor activity, for incompletely understood reasons. We report that radiotherapy upregulates the expression of genes containing immunogenic mutations in a poorly immunogenic mouse model of triple-negative breast cancer. Vaccination with neoepitopes encoded by these genes elicited CD8+ and CD4+ T cells that, whereas ineffective in preventing tumor growth, improved the therapeutic efficacy of radiotherapy. Mechanistically, neoantigen-specific CD8+ T cells preferentially killed irradiated tumor cells. Neoantigen-specific CD4+ T cells were required for the therapeutic efficacy of vaccination and acted by producing Th1 cytokines, killing irradiated tumor cells, and promoting epitope spread. Such a cytotoxic activity relied on the ability of radiation to upregulate class II MHC molecules as well as the death receptors FAS/CD95 and DR5 on the surface of tumor cells. These results provide proof-of-principle evidence that radiotherapy works in concert with neoantigen vaccination to improve tumor control.
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Affiliation(s)
| | | | | | - Tuo Zhang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, USA
| | | | - Lorenzo Galluzzi
- Department of Radiation Oncology and.,Sandra and Edward Meyer Cancer Center, New York, New York, USA.,Caryl and Israel Englander Institute for Precision Medicine, New York, New York, USA
| | - Noah Dephoure
- Sandra and Edward Meyer Cancer Center, New York, New York, USA.,Department of Biochemistry
| | | | - Laura Santambrogio
- Department of Radiation Oncology and.,Caryl and Israel Englander Institute for Precision Medicine, New York, New York, USA
| | - Xi Kathy Zhou
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, and
| | - Silvia C Formenti
- Department of Radiation Oncology and.,Sandra and Edward Meyer Cancer Center, New York, New York, USA.,Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Sandra Demaria
- Department of Radiation Oncology and.,Sandra and Edward Meyer Cancer Center, New York, New York, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
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45
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Shukla A, Cloutier M, Appiya Santharam M, Ramanathan S, Ilangumaran S. The MHC Class-I Transactivator NLRC5: Implications to Cancer Immunology and Potential Applications to Cancer Immunotherapy. Int J Mol Sci 2021; 22:ijms22041964. [PMID: 33671123 PMCID: PMC7922096 DOI: 10.3390/ijms22041964] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
The immune system constantly monitors the emergence of cancerous cells and eliminates them. CD8+ cytotoxic T lymphocytes (CTLs), which kill tumor cells and provide antitumor immunity, select their targets by recognizing tumor antigenic peptides presented by MHC class-I (MHC-I) molecules. Cancer cells circumvent immune surveillance using diverse strategies. A key mechanism of cancer immune evasion is downregulation of MHC-I and key proteins of the antigen processing and presentation machinery (APM). Even though impaired MHC-I expression in cancers is well-known, reversing the MHC-I defects remains the least advanced area of tumor immunology. The discoveries that NLRC5 is the key transcriptional activator of MHC-I and APM genes, and genetic lesions and epigenetic modifications of NLRC5 are the most common cause of MHC-I defects in cancers, have raised the hopes for restoring MHC-I expression. Here, we provide an overview of cancer immunity mediated by CD8+ T cells and the functions of NLRC5 in MHC-I antigen presentation pathways. We describe the impressive advances made in understanding the regulation of NLRC5 expression, the data supporting the antitumor functions of NLRC5 and a few reports that argue for a pro-tumorigenic role. Finally, we explore the possible avenues of exploiting NLRC5 for cancer immunotherapy.
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Affiliation(s)
- Akhil Shukla
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
| | - Maryse Cloutier
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
| | - Madanraj Appiya Santharam
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
| | - Sheela Ramanathan
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
- CRCHUS, Centre Hospitalier de l’Université de Sherbrooke, Sherbrooke, QC J1H5N4, Canada
| | - Subburaj Ilangumaran
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
- CRCHUS, Centre Hospitalier de l’Université de Sherbrooke, Sherbrooke, QC J1H5N4, Canada
- Correspondence: ; Tel.: +1-819-346-1110 (ext. 14834)
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46
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Çetin G, Klafack S, Studencka-Turski M, Krüger E, Ebstein F. The Ubiquitin-Proteasome System in Immune Cells. Biomolecules 2021; 11:biom11010060. [PMID: 33466553 PMCID: PMC7824874 DOI: 10.3390/biom11010060] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 12/11/2022] Open
Abstract
The ubiquitin–proteasome system (UPS) is the major intracellular and non-lysosomal protein degradation system. Thanks to its unique capacity of eliminating old, damaged, misfolded, and/or regulatory proteins in a highly specific manner, the UPS is virtually involved in almost all aspects of eukaryotic life. The critical importance of the UPS is particularly visible in immune cells which undergo a rapid and profound functional remodelling upon pathogen recognition. Innate and/or adaptive immune activation is indeed characterized by a number of substantial changes impacting various cellular processes including protein homeostasis, signal transduction, cell proliferation, and antigen processing which are all tightly regulated by the UPS. In this review, we summarize and discuss recent progress in our understanding of the molecular mechanisms by which the UPS contributes to the generation of an adequate immune response. In this regard, we also discuss the consequences of UPS dysfunction and its role in the pathogenesis of recently described immune disorders including cancer and auto-inflammatory diseases.
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47
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Jappe EC, Garde C, Ramarathinam SH, Passantino E, Illing PT, Mifsud NA, Trolle T, Kringelum JV, Croft NP, Purcell AW. Thermostability profiling of MHC-bound peptides: a new dimension in immunopeptidomics and aid for immunotherapy design. Nat Commun 2020; 11:6305. [PMID: 33298915 PMCID: PMC7726561 DOI: 10.1038/s41467-020-20166-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
The features of peptide antigens that contribute to their immunogenicity are not well understood. Although the stability of peptide-MHC (pMHC) is known to be important, current assays assess this interaction only for peptides in isolation and not in the context of natural antigen processing and presentation. Here, we present a method that provides a comprehensive and unbiased measure of pMHC stability for thousands of individual ligands detected simultaneously by mass spectrometry (MS). The method allows rapid assessment of intra-allelic and inter-allelic differences in pMHC stability and reveals profiles of stability that are broader than previously appreciated. The additional dimensionality of the data facilitated the training of a model which improves the prediction of peptide immunogenicity, specifically of cancer neoepitopes. This assay can be applied to any cells bearing MHC or MHC-like molecules, offering insight into not only the endogenous immunopeptidome, but also that of neoepitopes and pathogen-derived sequences.
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Affiliation(s)
- Emma C Jappe
- Evaxion Biotech, Bredgade 34E, 1260, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | | | - Sri H Ramarathinam
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ethan Passantino
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Patricia T Illing
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Nicole A Mifsud
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Thomas Trolle
- Evaxion Biotech, Bredgade 34E, 1260, Copenhagen, Denmark
| | | | - Nathan P Croft
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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48
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Tan X, Li D, Huang P, Jian X, Wan H, Wang G, Li Y, Ouyang J, Lin Y, Xie L. dbPepNeo: a manually curated database for human tumor neoantigen peptides. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5747759. [PMID: 32090262 PMCID: PMC7043295 DOI: 10.1093/database/baaa004] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/24/2019] [Accepted: 01/09/2020] [Indexed: 12/20/2022]
Abstract
Neoantigens can function as actual antigens to facilitate tumor rejection, which play a crucial role in cancer immunology and immunotherapy. Emerging evidence revealed that neoantigens can be used to develop personalized, cancer-specific vaccines. To date, large numbers of immunogenomic peptides have been computationally predicted to be potential neoantigens. However, experimental validation remains the gold standard for potential clinical application. Experimentally validated neoantigens are rare and mostly appear scattered among scientific papers and various databases. Here, we constructed dbPepNeo, a specific database for human leukocyte antigen class I (HLA-I) binding neoantigen peptides based on mass spectrometry (MS) validation or immunoassay in human tumors. According to the verification methods of these neoantigens, the collection of peptides was classified as 295 high confidence, 247 medium confidence and 407 794 low confidence neoantigens, respectively. This can serve as a valuable resource to aid further screening for effective neoantigens, optimize a neoantigen prediction pipeline and study T-cell receptor (TCR) recognition. Three applications of dbPepNeo are shown. In summary, this work resulted in a platform to promote the screening and confirmation of potential neoantigens in cancer immunotherapy. Database URL: www.biostatistics.online/dbPepNeo/.
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Affiliation(s)
- Xiaoxiu Tan
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China
| | - Daixi Li
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, China
| | - Pengjie Huang
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China
| | - Xingxing Jian
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education; Key Laboratory of Carcinogenesis, National Health and Family Planning Commission, Xiangya Hospital, Central South University, Central South University, No. 932, South Lushan Road, Yuelu District, Changsha 410083, China
| | - Huihui Wan
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China
| | - Guangzhi Wang
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China.,College of Food Science and Technology, Shanghai Ocean University, No. 999, Hucheng Ring Road, Pudong New District, Shanghai 201306, China
| | - Yuyu Li
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China.,College of Food Science and Technology, Shanghai Ocean University, No. 999, Hucheng Ring Road, Pudong New District, Shanghai 201306, China
| | - Jian Ouyang
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China
| | - Yong Lin
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China
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49
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Yang Y, Liu W, Hu D, Su R, Ji M, Huang Y, Shereen MA, Xu X, Luo Z, Zhang Q, Liu F, Wu K, Liu Y, Wu J. HIV-1 Nef Interacts with LMP7 To Attenuate Immunoproteasome Formation and Major Histocompatibility Complex Class I Antigen Presentation. mBio 2020; 11:e02221-19. [PMID: 33109760 PMCID: PMC7593969 DOI: 10.1128/mbio.02221-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/21/2020] [Indexed: 01/03/2023] Open
Abstract
The proteasome is a major protein degradation machinery with essential and diverse biological functions. Upon induction by cytokines, proteasome subunits β1, β2, and β5 are replaced by β1i/LMP2, β2i/MECL-1, and β5i/LMP7, resulting in the formation of an immunoproteasome (iProteasome). iProteasome-degraded products are loaded onto the major histocompatibility complex class I (MHC-I), regulating immune responses and inducing cytotoxic T lymphocytes (CTLs). Human immunodeficiency virus type 1 (HIV-1) is the causal agent of AIDS. HIV-1-specific CTLs represent a critical immune mechanism limiting viral replication. HIV-1 negative regulatory factor (Nef) counteracts host immunity, particularly the response involving MHC-I/CTL. This study identifies a distinct mechanism by which Nef facilitates immune evasion via suppressing the function of iProteasome and MHC-I. Nef interacts with LMP7 on the endoplasmic reticulum (ER), downregulating the incorporation of LMP7 into iProteasome and thereby attenuating its formation. Moreover, Nef represses the iProteasome function of protein degradation, MHC-I trafficking, and antigen presentation.IMPORTANCE The ubiquitin-proteasome system (UPS) is essential for the degradation of damaged proteins, which takes place in the proteasome. Upon activation by cytokines, the catalytic subunits of the proteasome are replaced by distinct isoforms resulting in the formation of an immunoproteasome (iProteasome). iProteasome generates peptides used by major histocompatibility complex class I (MHC-I) for antigen presentation and is essential for immune responses. HIV-1 is the causative agent of AIDS, and HIV-1-specific cytotoxic T lymphocytes (CTLs) provide immune responses limiting viral replication. This study identifies a distinct mechanism by which HIV-1 promotes immune evasion. The viral protein negative regulatory factor (Nef) interacts with a component of iProteasome, LMP7, attenuating iProteasome formation and protein degradation function, and thus repressing the MHC-I antigen presentation activity of MHC-I. Therefore, HIV-1 targets LMP7 to inhibit iProteasome activation, and LMP7 may be used as the target for the development of anti-HIV-1/AIDS therapy.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Weiyong Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Dan Hu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Rui Su
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Man Ji
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yuqing Huang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Muhammad Adnan Shereen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaodi Xu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhen Luo
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Qi Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fang Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Kailang Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yingle Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Jianguo Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
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50
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Gopanenko AV, Kosobokova EN, Kosorukov VS. Main Strategies for the Identification of Neoantigens. Cancers (Basel) 2020; 12:E2879. [PMID: 33036391 PMCID: PMC7600129 DOI: 10.3390/cancers12102879] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/24/2022] Open
Abstract
Genetic instability of tumors leads to the appearance of numerous tumor-specific somatic mutations that could potentially result in the production of mutated peptides that are presented on the cell surface by the MHC molecules. Peptides of this kind are commonly called neoantigens. Their presence on the cell surface specifically distinguishes tumors from healthy tissues. This feature makes neoantigens a promising target for immunotherapy. The rapid evolution of high-throughput genomics and proteomics makes it possible to implement these techniques in clinical practice. In particular, they provide useful tools for the investigation of neoantigens. The most valuable genomic approach to this problem is whole-exome sequencing coupled with RNA-seq. High-throughput mass-spectrometry is another option for direct identification of MHC-bound peptides, which is capable of revealing the entire MHC-bound peptidome. Finally, structure-based predictions could significantly improve the understanding of physicochemical and structural features that affect the immunogenicity of peptides. The development of pipelines combining such tools could improve the accuracy of the peptide selection process and decrease the required time. Here we present a review of the main existing approaches to investigating the neoantigens and suggest a possible ideal pipeline that takes into account all modern trends in the context of neoantigen discovery.
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Affiliation(s)
| | | | - Vyacheslav S. Kosorukov
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, 115478 Moscow, Russia; (A.V.G.); (E.N.K.)
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