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Zhu B, Ouda R, An N, Tanaka T, Kobayashi KS. The balance between nuclear import and export of NLRC5 regulates MHC class I transactivation. J Biol Chem 2024; 300:107205. [PMID: 38519032 PMCID: PMC11044055 DOI: 10.1016/j.jbc.2024.107205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 02/08/2024] [Accepted: 03/06/2024] [Indexed: 03/24/2024] Open
Abstract
Major histocompatibility complex (MHC) class I molecules play an essential role in regulating the adaptive immune system by presenting antigens to CD8 T cells. CITA (MHC class I transactivator), also known as NLRC5 (NLR family, CARD domain-containing 5), regulates the expression of MHC class I and essential components involved in the MHC class I antigen presentation pathway. While the critical role of the nuclear distribution of NLRC5 in its transactivation activity has been known, the regulatory mechanism to determine the nuclear localization of NLRC5 remains poorly understood. In this study, a comprehensive analysis of all domains in NLRC5 revealed that the regulatory mechanisms for nuclear import and export of NLRC5 coexist and counterbalance each other. Moreover, GCN5 (general control non-repressed 5 protein), a member of HATs (histone acetyltransferases), was found to be a key player to retain NLRC5 in the nucleus, thereby contributing to the expression of MHC class I. Therefore, the balance between import and export of NLRC5 has emerged as an additional regulatory mechanism for MHC class I transactivation, which would be a potential therapeutic target for the treatment of cancer and virus-infected diseases.
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Affiliation(s)
- Baohui Zhu
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Ryota Ouda
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Ning An
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Tsutomu Tanaka
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Japan; Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Koichi S Kobayashi
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Japan; Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan; Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas, USA.
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2
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Zhou L, Liu Y, Wu Y, Yang X, Spring Kong FM, Lu Y, Xue J. Low-dose radiation therapy mobilizes antitumor immunity: New findings and future perspectives. Int J Cancer 2024; 154:1143-1157. [PMID: 38059788 DOI: 10.1002/ijc.34801] [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: 08/09/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 12/08/2023]
Abstract
Radiotherapy has unique immunostimulatory and immunosuppressive effects. Although high-dose radiotherapy has been found to have systemic antitumor effects, clinically significant abscopal effects were uncommon on the basis of irradiating single lesion. Low-dose radiation therapy (LDRT) emerges as a novel approach to enhance the antitumor immune response due to its role as a leverage to reshape the tumor immune microenvironment (TIME). In this article, from bench to bedside, we reviewed the possible immunomodulatory role of LDRT on TIME and systemic tumor immune environment, and outlined preclinical evidence and clinical application. We also discussed the current challenges when LDRT is used as a combination therapy, including the optimal dose, fraction, frequency, and combination of drugs. The advantage of low toxicity makes LDRT potential to be applied in multiple lesions to amplify antitumor immune response in polymetastatic disease, and its intersection with other disciplines might also make it a direction for radiotherapy-combined modalities.
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Affiliation(s)
- Laiyan Zhou
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- Disaster Medical Center, Sichuan University, Chengdu, China
| | - Yuanxin Liu
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuanjun Wu
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xue Yang
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Feng-Ming Spring Kong
- Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - You Lu
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Clinical Cell Therapy, West China Hospital, Sichuan University, Chengdu, China
| | - Jianxin Xue
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Clinical Cell Therapy, West China Hospital, Sichuan University, Chengdu, China
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3
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Guan J, Peske JD, Manoharan Valerio M, Park C, Robey EA, Sadegh-Nasseri S. Commensal bacteria maintain a Qa-1 b-restricted unconventional CD8 + T population in gut epithelium. eLife 2023; 12:RP90466. [PMID: 38127067 PMCID: PMC10735220 DOI: 10.7554/elife.90466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Intestinal intraepithelial lymphocytes (IELs) are characterized by an unusual phenotype and developmental pathway, yet their specific ligands and functions remain largely unknown. Here by analysis of QFL T cells, a population of CD8+ T cells critical for monitoring the MHC I antigen processing pathway, we established that unconventional Qa-1b-restricted CD8+ T cells are abundant in intestinal epithelium. We found that QFL T cells showed a Qa-1b-dependent unconventional phenotype in the spleen and small intestine of naïve wild-type mice. The splenic QFL T cells showed innate-like functionality exemplified by rapid response to cytokines or antigens, while the gut population was refractory to stimuli. Microbiota was required for the maintenance, but not the initial gut homing of QFL T cells. Moreover, monocolonization with Pediococcus pentosaceus, which expresses a peptide that cross-activated QFL T cells, was sufficient to maintain QFL T cells in the intestine. Thus, microbiota is critical for shaping the Qa-1b-restricted IEL landscape.
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Affiliation(s)
- Jian Guan
- Department of Pathology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Institute of Cell Engineering, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - J David Peske
- Department of Pathology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Institute of Cell Engineering, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Michael Manoharan Valerio
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Chansu Park
- Department of Pathology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Institute of Cell Engineering, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Ellen A Robey
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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4
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Kormos J, Veres AJ, Imre L, Mátyus L, Benkő S, Szöllősi J, Jenei A. HLA DQ protein changes the cell surface distribution pattern of HLA proteins as monitored by Förster resonance energy transfer and high-resolution electron microscopy. Cytometry A 2023; 103:978-991. [PMID: 37605541 DOI: 10.1002/cyto.a.24787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 08/03/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Peptide presentation by MHC class I and MHC class II molecules plays important roles in the regulation of the immune response. One factor in these displays is the density of antigen, which must exceed a critical threshold for the effective activation of T cells. Nonrandom distribution of MHC class I and class II has already been detected at the nanometer level and at higher hierarchical levels. It is not clear how the absence and reappearance of some protein molecules can influence the nonrandom distribution. Therefore, we performed experiments on HLA II-deficient bare lymphocyte syndrome (BLS1) cells: we created a stable transfected cell line, tDQ6-BLS-1, and were able to detect the effect of the appearance of HLA-DQ6 molecules on the homo and heteroassociation of different cell surface molecules by comparing Förster resonance energy transfer (FRET) efficiency on transfected cells to that on nontransfected BLS-1 and JY human B-cell lines. Our FRET results show a decrease in homoassociation FRET between HLA I chains in HLA-DQ6-transfected tDQ6-BLS-1 cells compared with the parent BLS-1 cell line and an increase in heteroassociation FRET between HLA I and HLA II (compared with JY cells), suggesting a similar pattern of antigen presentation by the HLA-DQ6 allele. Transmission electron microscopy (TEM) revealed that both HLA class I and class II molecules formed clusters at higher hierarchical levels on the tDQ6-BLS-1 cells, and the de novo synthesized HLA DQ molecules did not intersperse with HLA class I islands. These observations could be important in understanding the fine tuning of the immune response.
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Affiliation(s)
- József Kormos
- Department of Biophysics and Cell Biology, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - Adrienn J Veres
- Department of Biophysics and Cell Biology, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - László Imre
- Department of Biophysics and Cell Biology, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - László Mátyus
- Department of Biophysics and Cell Biology, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - Szilvia Benkő
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - János Szöllősi
- Department of Biophysics and Cell Biology, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
- ELKH-DE Cell Biology and Signaling Research Group (Eötvös Loránd Research Network-University of Debrecen), Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Jenei
- Department of Biophysics and Cell Biology, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
- Department of Basic Medical Sciences, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
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5
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Guan J, Peske JD, Valerio MM, Park C, Robey EA, Sadegh-Nasseri S. Commensal Bacteria Maintain a Qa-1 b -restricted Unconventional CD8 + T Population in Gut Epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530600. [PMID: 36909616 PMCID: PMC10002720 DOI: 10.1101/2023.03.01.530600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Intestinal intraepithelial lymphocytes (IELs) are characterized by an unusual phenotype and developmental pathway, yet their specific ligands and functions remain largely unknown. Here by analysis of QFL T cells, a population of CD8 + T cells critical for monitoring the MHC I antigen processing pathway, we established that unconventional Qa-1 b -restricted CD8 + T cells are abundant in intestinal epithelium. We found that QFL T cells showed a Qa-1 b -dependent unconventional phenotype in the spleen and small intestine of naïve wild-type mice. The splenic QFL T cells showed innate-like functionality exemplified by rapid response to cytokines or antigen, while the gut population was refractory to stimuli. Microbiota was required for the maintenance, but not the initial gut homing of QFL T cells. Moreover, monocolonization with Pediococcus pentosaceus, which expresses a peptide that cross-activated QFL T cells, was sufficient to maintain QFL T cells in the intestine. Thus, microbiota is critical for shaping the Qa-1 b -restricted IEL landscape.
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6
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Aldea M, Friboulet L, Apcher S, Jaulin F, Mosele F, Sourisseau T, Soria JC, Nikolaev S, André F. Precision medicine in the era of multi-omics: can the data tsunami guide rational treatment decision? ESMO Open 2023; 8:101642. [PMID: 37769400 PMCID: PMC10539962 DOI: 10.1016/j.esmoop.2023.101642] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/30/2023] Open
Abstract
Precision medicine for cancer is rapidly moving to an approach that integrates multiple dimensions of the biology in order to model mechanisms of cancer progression in each patient. The discovery of multiple drivers per tumor challenges medical decision that faces several treatment options. Drug sensitivity depends on the actionability of the target, its clonal or subclonal origin and coexisting genomic alterations. Sequencing has revealed a large diversity of drivers emerging at treatment failure, which are potential targets for clinical trials or drug repurposing. To effectively prioritize therapies, it is essential to rank genomic alterations based on their proven actionability. Moving beyond primary drivers, the future of precision medicine necessitates acknowledging the intricate spatial and temporal heterogeneity inherent in cancer. The advent of abundant complex biological data will make artificial intelligence algorithms indispensable for thorough analysis. Here, we will discuss the advancements brought by the use of high-throughput genomics, the advantages and limitations of precision medicine studies and future perspectives in this field.
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Affiliation(s)
- M Aldea
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif.
| | | | - S Apcher
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F Jaulin
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F Mosele
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif
| | | | - J-C Soria
- Paris Saclay University, Orsay; Drug Development Department, Gustave Roussy, Villejuif, France
| | - S Nikolaev
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F André
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif; Paris Saclay University, Orsay
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7
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Truex NL, Mohapatra S, Melo M, Rodriguez J, Li N, Abraham W, Sementa D, Touti F, Keskin DB, Wu CJ, Irvine DJ, Gómez-Bombarelli R, Pentelute BL. Design of Cytotoxic T Cell Epitopes by Machine Learning of Human Degrons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554289. [PMID: 37662211 PMCID: PMC10473641 DOI: 10.1101/2023.08.22.554289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Antigen processing is critical for producing epitope peptides that are presented by HLA molecules for T cell recognition. Therapeutic vaccines aim to harness these epitopes for priming cytotoxic T cell responses against cancer and pathogens, but insufficient processing often reduces vaccine efficacy through limiting the quantity of epitopes released. Here, we set out to improve antigen processing by harnessing protein degradation signals called degrons from the ubiquitin-proteasome system. We used machine learning to generate a computational model that ascribes a proteasomal degradation score between 0 and 100. Epitope peptides with varying degron activities were synthesized and translocated into cells using nontoxic anthrax proteins: protective antigen (PA) and the N-terminus of lethal factor (LFN). Immunogenicity studies revealed epitope sequences with a low score (<25) show pronounced T-cell activation but epitope sequences with a higher score (>75) provide limited activation. This work sheds light on the sequence-activity relationships between proteasomal degradation and epitope immunogenicity, through conserving the epitope region but varying the flanking sequence. We anticipate that future efforts to incorporate proteasomal degradation signals into vaccine designs will lead to enhanced cytotoxic T cell priming by vaccine therapeutics in clinical settings.
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Affiliation(s)
- Nicholas L. Truex
- Department of Chemistry, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Department of Chemistry and Biochemistry, University of South Carolina; 631 Sumter St., Columbia, South Carolina, 29208, USA
| | - Somesh Mohapatra
- Department of Materials Science and Engineering, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Machine Intelligence and Manufacturing Operations Group, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Mariane Melo
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; 500 Main Street, Cambridge, Massachusetts 02142, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology; 400 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Jacob Rodriguez
- Department of Chemistry, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Na Li
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; 500 Main Street, Cambridge, Massachusetts 02142, USA
| | - Wuhbet Abraham
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; 500 Main Street, Cambridge, Massachusetts 02142, USA
| | - Deborah Sementa
- Department of Chemistry, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Faycal Touti
- Department of Chemistry, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Derin B. Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, Massachusetts, 02215, USA
- Harvard Medical School; Boston, Massachusetts, 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, Massachusetts, USA
- Translational Immunogenomics Laboratory (TIGL), Dana-Farber Cancer Institute; Boston, Massachusetts, 02215, USA
- Department of Computer Science, Metropolitan College, Boston University; Boston, Massachusetts, USA
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark; Lyngby, DK
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, Massachusetts, 02215, USA
- Harvard Medical School; Boston, Massachusetts, 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital; Boston, MA 02215, USA
| | - Darrell J. Irvine
- Department of Materials Science and Engineering, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; 500 Main Street, Cambridge, Massachusetts 02142, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology; 400 Technology Square, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Howard Hughes Medical Institute; 4000 Jones Bridge Rd, Chevy Chase, Maryland 20815, USA
| | - Rafael Gómez-Bombarelli
- Department of Materials Science and Engineering, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Bradley L. Pentelute
- Department of Chemistry, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; 500 Main Street, Cambridge, Massachusetts 02142, USA
- Broad Institute of MIT and Harvard; Cambridge, Massachusetts, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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8
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Biochemical detection system for intermediates of endogenous antigen and elucidation of the role of molecular chaperones. Cell Immunol 2023; 385:104685. [PMID: 36806381 DOI: 10.1016/j.cellimm.2023.104685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 12/16/2022] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Cytotoxic T lymphocytes recognize antigen-derived peptides (epitopes) bound to MHC class I presented on the cell surface of virus-infected cells and cancer cells. To date, numerous pathogen-derived epitopes and cancer cell-specific epitopes have been identified and used in the development of mRNA and peptide vaccines, but much remains unknown regarding the intracellular mechanisms that generate these antigen epitopes. These mechanisms are essential for cytotoxic T cell immunity. In this paper, I outline an innovation pioneered by Professor Nilabh Shastri and me, in which we developed a biochemical system to detect antigen intermediates and illuminated the role of molecular chaperones in antigen processing.
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9
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Tang F, Pan Z, Wang Y, Lan T, Wang M, Li F, Quan W, Liu Z, Wang Z, Li Z. Advances in the Immunotherapeutic Potential of Isocitrate Dehydrogenase Mutations in Glioma. Neurosci Bull 2022; 38:1069-1084. [PMID: 35670952 PMCID: PMC9468211 DOI: 10.1007/s12264-022-00866-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/16/2022] [Indexed: 11/26/2022] Open
Abstract
Isocitrate dehydrogenase (IDH) is an essential metabolic enzyme in the tricarboxylic acid cycle (TAC). The high mutation frequency of the IDH gene plays a complicated role in gliomas. In addition to affecting gliomas directly, mutations in IDH can also alter their immune microenvironment and can change immune-cell function in direct and indirect ways. IDH mutations mediate immune-cell infiltration and function by modulating immune-checkpoint gene expression and chemokine secretion. In addition, IDH mutation-derived D2-hydroxyglutarate can be absorbed by surrounding immune cells, also affecting their functioning. In this review, we summarize current knowledge about the effects of IDH mutations as well as other gene mutations on the immune microenvironment of gliomas. We also describe recent preclinical and clinical data related to IDH-mutant inhibitors for the treatment of gliomas. Finally, we discuss different types of immunotherapy and the immunotherapeutic potential of IDH mutations in gliomas.
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Affiliation(s)
- Feng Tang
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Zhiyong Pan
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Yi Wang
- Department of Physiology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Tian Lan
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Mengyue Wang
- Department of Physiology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Fengping Li
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Wei Quan
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Zhenyuan Liu
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Zefen Wang
- Department of Physiology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China.
| | - Zhiqiang Li
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China.
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Pastor Y, Ghazzaui N, Hammoudi A, Centlivre M, Cardinaud S, Levy Y. Refining the DC-targeting vaccination for preventing emerging infectious diseases. Front Immunol 2022; 13:949779. [PMID: 36016929 PMCID: PMC9396646 DOI: 10.3389/fimmu.2022.949779] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 07/14/2022] [Indexed: 11/26/2022] Open
Abstract
The development of safe, long-term, effective vaccines is still a challenge for many infectious diseases. Thus, the search of new vaccine strategies and production platforms that allow rapidly and effectively responding against emerging or reemerging pathogens has become a priority in the last years. Targeting the antigens directly to dendritic cells (DCs) has emerged as a new approach to enhance the immune response after vaccination. This strategy is based on the fusion of the antigens of choice to monoclonal antibodies directed against specific DC surface receptors such as CD40. Since time is essential, in silico approaches are of high interest to select the most immunogenic and conserved epitopes to improve the T- and B-cells responses. The purpose of this review is to present the advances in DC vaccination, with special focus on DC targeting vaccines and epitope mapping strategies and provide a new framework for improving vaccine responses against infectious diseases.
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Affiliation(s)
- Yadira Pastor
- Vaccine Research Institute, Université Paris-Est Créteil, Institut Mondor de Recherche Biomédicale, Inserm U955, Team 16, Créteil, France
| | - Nour Ghazzaui
- Vaccine Research Institute, Université Paris-Est Créteil, Institut Mondor de Recherche Biomédicale, Inserm U955, Team 16, Créteil, France
| | - Adele Hammoudi
- Vaccine Research Institute, Université Paris-Est Créteil, Institut Mondor de Recherche Biomédicale, Inserm U955, Team 16, Créteil, France
| | - Mireille Centlivre
- Vaccine Research Institute, Université Paris-Est Créteil, Institut Mondor de Recherche Biomédicale, Inserm U955, Team 16, Créteil, France
| | - Sylvain Cardinaud
- Vaccine Research Institute, Université Paris-Est Créteil, Institut Mondor de Recherche Biomédicale, Inserm U955, Team 16, Créteil, France
| | - Yves Levy
- Vaccine Research Institute, Université Paris-Est Créteil, Institut Mondor de Recherche Biomédicale, Inserm U955, Team 16, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Groupe Henri-Mondor Albert-Chenevier, Service Immunologie Clinique, Créteil, France
- *Correspondence: Yves Levy,
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11
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Morani F, Doccini S, Galatolo D, Pezzini F, Soliymani R, Simonati A, Lalowski MM, Gemignani F, Santorelli FM. Integrative Organelle-Based Functional Proteomics: In Silico Prediction of Impaired Functional Annotations in SACS KO Cell Model. Biomolecules 2022; 12:biom12081024. [PMID: 35892334 PMCID: PMC9331974 DOI: 10.3390/biom12081024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 02/07/2023] Open
Abstract
Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is an inherited neurodegenerative disease characterized by early-onset spasticity in the lower limbs, axonal-demyelinating sensorimotor peripheral neuropathy, and cerebellar ataxia. Our understanding of ARSACS (genetic basis, protein function, and disease mechanisms) remains partial. The integrative use of organelle-based quantitative proteomics and whole-genome analysis proposed in the present study allowed identifying the affected disease-specific pathways, upstream regulators, and biological functions related to ARSACS, which exemplify a rationale for the development of improved early diagnostic strategies and alternative treatment options in this rare condition that currently lacks a cure. Our integrated results strengthen the evidence for disease-specific defects related to bioenergetics and protein quality control systems and reinforce the role of dysregulated cytoskeletal organization in the pathogenesis of ARSACS.
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Affiliation(s)
- Federica Morani
- Department of Biology, University of Pisa, 56126 Pisa, Italy; (F.M.); (F.G.)
| | - Stefano Doccini
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit—IRCCS Stella Maris, 56128 Pisa, Italy; (S.D.); (D.G.)
| | - Daniele Galatolo
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit—IRCCS Stella Maris, 56128 Pisa, Italy; (S.D.); (D.G.)
| | - Francesco Pezzini
- Department of Surgery, Dentistry, Paediatrics and Gynaecology, University of Verona, 37129 Verona, Italy; (F.P.); (A.S.)
| | - Rabah Soliymani
- HiLIFE, Meilahti Clinical Proteomics Core Facility, Faculty of Medicine, University of Helsinki, FI-00014 Helsinki, Finland; (R.S.); (M.M.L.)
| | - Alessandro Simonati
- Department of Surgery, Dentistry, Paediatrics and Gynaecology, University of Verona, 37129 Verona, Italy; (F.P.); (A.S.)
| | - Maciej M. Lalowski
- HiLIFE, Meilahti Clinical Proteomics Core Facility, Faculty of Medicine, University of Helsinki, FI-00014 Helsinki, Finland; (R.S.); (M.M.L.)
- Institute of Bioorganic Chemistry, PAS, Department of Biomedical Proteomics, 61-704 Poznań, Poland
| | - Federica Gemignani
- Department of Biology, University of Pisa, 56126 Pisa, Italy; (F.M.); (F.G.)
| | - Filippo M. Santorelli
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit—IRCCS Stella Maris, 56128 Pisa, Italy; (S.D.); (D.G.)
- Correspondence: ; Tel.: +39-050-886311
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12
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Mahmud S, Rafi MO, Paul GK, Promi MM, Shimu MSS, Biswas S, Emran TB, Dhama K, Alyami SA, Moni MA, Saleh MA. Designing a multi-epitope vaccine candidate to combat MERS-CoV by employing an immunoinformatics approach. Sci Rep 2021; 11:15431. [PMID: 34326355 PMCID: PMC8322212 DOI: 10.1038/s41598-021-92176-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/21/2021] [Indexed: 01/26/2023] Open
Abstract
Currently, no approved vaccine is available against the Middle East respiratory syndrome coronavirus (MERS-CoV), which causes severe respiratory disease. The spike glycoprotein is typically considered a suitable target for MERS-CoV vaccine candidates. A computational strategy can be used to design an antigenic vaccine against a pathogen. Therefore, we used immunoinformatics and computational approaches to design a multi-epitope vaccine that targets the spike glycoprotein of MERS-CoV. After using numerous immunoinformatics tools and applying several immune filters, a poly-epitope vaccine was constructed comprising cytotoxic T-cell lymphocyte (CTL)-, helper T-cell lymphocyte (HTL)-, and interferon-gamma (IFN-γ)-inducing epitopes. In addition, various physicochemical, allergenic, and antigenic profiles were evaluated to confirm the immunogenicity and safety of the vaccine. Molecular interactions, binding affinities, and the thermodynamic stability of the vaccine were examined through molecular docking and dynamic simulation approaches, during which we identified a stable and strong interaction with Toll-like receptors (TLRs). In silico immune simulations were performed to assess the immune-response triggering capabilities of the vaccine. This computational analysis suggested that the proposed vaccine candidate would be structurally stable and capable of generating an effective immune response to combat viral infections; however, experimental evaluations remain necessary to verify the exact safety and immunogenicity profile of this vaccine.
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Affiliation(s)
- Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Maria Meha Promi
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Mst Sharmin Sultana Shimu
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Salem A Alyami
- Department of Mathematics and Statistics, Imam Mohammad Ibn Saud Islamic University, Riyadh, 11432, Saudi Arabia
| | - Mohammad Ali Moni
- Faculty of Medicine, WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia.
| | - Md Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6505, Bangladesh.
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13
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In silico designing of vaccine candidate against Clostridium difficile. Sci Rep 2021; 11:14215. [PMID: 34244557 PMCID: PMC8271013 DOI: 10.1038/s41598-021-93305-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/21/2021] [Indexed: 12/19/2022] Open
Abstract
Clostridium difficile is a spore-forming gram-positive bacterium, recognized as the primary cause of antibiotic-associated nosocomial diarrhoea. Clostridium difficile infection (CDI) has emerged as a major health-associated infection with increased incidence and hospitalization over the years with high mortality rates. Contamination and infection occur after ingestion of vegetative spores, which germinate in the gastro-intestinal tract. The surface layer protein and flagellar proteins are responsible for the bacterial colonization while the spore coat protein, is associated with spore colonization. Both these factors are the main concern of the recurrence of CDI in hospitalized patients. In this study, the CotE, SlpA and FliC proteins are chosen to form a multivalent, multi-epitopic, chimeric vaccine candidate using the immunoinformatics approach. The overall reliability of the candidate vaccine was validated in silico and the molecular dynamics simulation verified the stability of the vaccine designed. Docking studies showed stable vaccine interactions with Toll‐Like Receptors of innate immune cells and MHC receptors. In silico codon optimization of the vaccine and its insertion in the cloning vector indicates a competent expression of the modelled vaccine in E. coli expression system. An in silico immune simulation system evaluated the effectiveness of the candidate vaccine to trigger a protective immune response.
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14
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Guerra-Almeida D, Tschoeke DA, da-Fonseca RN. Understanding small ORF diversity through a comprehensive transcription feature classification. DNA Res 2021; 28:6317669. [PMID: 34240112 PMCID: PMC8435553 DOI: 10.1093/dnares/dsab007] [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] [Received: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Small open reading frames (small ORFs/sORFs/smORFs) are potentially coding sequences smaller than 100 codons that have historically been considered junk DNA by gene prediction software and in annotation screening; however, the advent of next-generation sequencing has contributed to the deeper investigation of junk DNA regions and their transcription products, resulting in the emergence of smORFs as a new focus of interest in systems biology. Several smORF peptides were recently reported in noncanonical mRNAs as new players in numerous biological contexts; however, their relevance is still overlooked in coding potential analysis. Hence, this review proposes a smORF classification based on transcriptional features, discussing the most promising approaches to investigate smORFs based on their different characteristics. First, smORFs were divided into nonexpressed (intergenic) and expressed (genic) smORFs. Second, genic smORFs were classified as smORFs located in noncoding RNAs (ncRNAs) or canonical mRNAs. Finally, smORFs in ncRNAs were further subdivided into sequences located in small or long RNAs, whereas smORFs located in canonical mRNAs were subdivided into several specific classes depending on their localization along the gene. We hope that this review provides new insights into large-scale annotations and reinforces the role of smORFs as essential components of a hidden coding DNA world.
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Affiliation(s)
- Diego Guerra-Almeida
- Institute of Biodiversity and Sustainability, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Diogo Antonio Tschoeke
- Alberto Luiz Coimbra Institute of Graduate Studies and Engineering Research (COPPE), Biomedical Engineering Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodrigo Nunes- da-Fonseca
- Institute of Biodiversity and Sustainability, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Institute of Science and Technology in Molecular Entomology, Rio de Janeiro, Brazil
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15
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The nonclassical immune surveillance for ERAAP function. Curr Opin Immunol 2021; 70:105-111. [PMID: 34098489 DOI: 10.1016/j.coi.2021.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 01/04/2023]
Abstract
The peptide repertoire presented by MHC class I molecules on the cell surface is essential for the immune surveillance of intracellular pathogens and transformed cells. The generation of this peptide repertoire is critically dependent on the endoplasmic reticulum aminopeptidase associated with antigen processing (ERAAP). Loss of ERAAP function leads to the generation of a profoundly disrupted peptide repertoire including many novel and immunogenic peptides. Strikingly, a large fraction of these novel peptides on ERAAP-KO cells are presented by the nonclassical MHC Ib molecule, Qa-1b. One immunodominant Qa-1b-restricted novel peptide is recognized by a unique CD8+ T cell population showing features of both conventional cytotoxic T cells and unconventional innate-like T cells. While much remains to be uncovered, here we summarize the latest discoveries of our lab on the important immune surveillance of ERAAP function mediated by nonclassical MHC Ib molecules and their unusual cognate T cells.
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16
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Li T, Wu B, Yang T, Zhang L, Jin K. The outstanding antitumor capacity of CD4 + T helper lymphocytes. Biochim Biophys Acta Rev Cancer 2020; 1874:188439. [PMID: 32980465 DOI: 10.1016/j.bbcan.2020.188439] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/10/2020] [Accepted: 09/21/2020] [Indexed: 02/05/2023]
Abstract
Over the past decades, tumor-resident immune cells have been extensively studied to dissect their biological functions and clinical roles. Tumor-infiltrating CD8+ T cells, because of their cytotoxic and killing ability, have been under the spotlight for a long time, whereas CD4+ T cells are considered just a supporting actor in the field of cancer immunotherapy. Until recently, accumulating evidence has demonstrated the ability of CD4+ T cells in eradicating solid tumors, and their functions in mediating antitumor immunity have been investigated in various orientations. In this review, we highlight the pivotal role of CD4+ T cells in eliciting vigorous antitumor immune responses, summarize key signaling axes and molecular networks behind these antitumor functions, and also propose possible targets and promising strategies which might translate into more efficient immunotherapies against human cancers.
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Affiliation(s)
- Tong Li
- Laboratory of Human Diseases and Immunotherapies, West China Hospital, Sichuan University, Chengdu 610041, China; State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Bowen Wu
- School of Medicine, Stanford University, Stanford, CA 94304, USA
| | - Tao Yang
- Laboratory of Human Diseases and Immunotherapies, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Long Zhang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ke Jin
- Laboratory of Human Diseases and Immunotherapies, West China Hospital, Sichuan University, Chengdu 610041, China.
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17
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Kar T, Narsaria U, Basak S, Deb D, Castiglione F, Mueller DM, Srivastava AP. A candidate multi-epitope vaccine against SARS-CoV-2. Sci Rep 2020; 10:10895. [PMID: 32616763 PMCID: PMC7331818 DOI: 10.1038/s41598-020-67749-1] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/12/2020] [Indexed: 12/17/2022] Open
Abstract
In the past two decades, 7 coronaviruses have infected the human population, with two major outbreaks caused by SARS-CoV and MERS-CoV in the year 2002 and 2012, respectively. Currently, the entire world is facing a pandemic of another coronavirus, SARS-CoV-2, with a high fatality rate. The spike glycoprotein of SARS-CoV-2 mediates entry of virus into the host cell and is one of the most important antigenic determinants, making it a potential candidate for a vaccine. In this study, we have computationally designed a multi-epitope vaccine using spike glycoprotein of SARS-CoV-2. The overall quality of the candidate vaccine was validated in silico and Molecular Dynamics Simulation confirmed the stability of the designed vaccine. Docking studies revealed stable interactions of the vaccine with Toll-Like Receptors and MHC Receptors. The in silico cloning and codon optimization supported the proficient expression of the designed vaccine in E. coli expression system. The efficiency of the candidate vaccine to trigger an effective immune response was assessed by an in silico immune simulation. The computational analyses suggest that the designed multi-epitope vaccine is structurally stable which can induce specific immune responses and thus, can be a potential vaccine candidate against SARS-CoV-2.
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Affiliation(s)
- Tamalika Kar
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Utkarsh Narsaria
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Srijita Basak
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Debashrito Deb
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Filippo Castiglione
- Institute for Applied Computing, National Research Council of Italy, Via dei Taurini, Rome, Italy
| | - David M Mueller
- Center for Genetic Diseases, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, USA
| | - Anurag P Srivastava
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India.
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18
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Boulpicante M, Darrigrand R, Pierson A, Salgues V, Rouillon M, Gaudineau B, Khaled M, Cattaneo A, Bachi A, Cascio P, Apcher S. Tumors escape immunosurveillance by overexpressing the proteasome activator PSME3. Oncoimmunology 2020; 9:1761205. [PMID: 32923122 PMCID: PMC7458623 DOI: 10.1080/2162402x.2020.1761205] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The success of CD8+ T cell-based cancer immunotherapy emphasizes the importance of understanding the mechanisms of generation of MHC-I peptide ligands and the possible pathways of tumor cell escape from immunosurveillance. Recently, we showed that peptides generated in the nucleus during a pioneer round of mRNA translation (pioneer translation products, or PTPs) are an important source of tumor specific peptides which correlates with the aberrant splicing and transcription events associated with oncogenesis. Here we show that up-regulation of PSME3 proteasome activator in cancer cells results in increased destruction of PTP-derived peptides in the nucleus thus enabling cancer cell to subvert immunosurveillance. These findings unveil a previously unexpected role for PSME3 in antigen processing and identify PSME3 as a druggable target to improve the efficacy of cancer immunotherapy.
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Affiliation(s)
- Mathilde Boulpicante
- Immunologie des Tumeurs et Immunothérapie, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
| | - Romain Darrigrand
- Immunologie des Tumeurs et Immunothérapie, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
| | - Alison Pierson
- Immunologie des Tumeurs et Immunothérapie, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
| | - Valérie Salgues
- Immunologie des Tumeurs et Immunothérapie, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
| | - Marine Rouillon
- Immunologie des Tumeurs et Immunothérapie, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
| | - Benoit Gaudineau
- Dynamique des Cellules Tumorales, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
| | - Mehdi Khaled
- Dynamique des Cellules Tumorales, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
| | - Angela Cattaneo
- IFOM, The FIRC Institute of Molecular Oncology, Milano, Italy
| | - Angela Bachi
- IFOM, The FIRC Institute of Molecular Oncology, Milano, Italy
| | - Paolo Cascio
- Department of Veterinary Sciences, University of Turin, 10095, Grugliasco, Turin, Italy
| | - Sébastien Apcher
- Immunologie des Tumeurs et Immunothérapie, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
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19
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Padariya M, Kalathiya U, Houston DR, Alfaro JA. Recognition Dynamics of Cancer Mutations on the ERp57-Tapasin Interface. Cancers (Basel) 2020; 12:cancers12030737. [PMID: 32244998 PMCID: PMC7140079 DOI: 10.3390/cancers12030737] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/05/2020] [Accepted: 03/18/2020] [Indexed: 01/16/2023] Open
Abstract
Down regulation of the major histocompatibility class (MHC) I pathway plays an important role in tumour development, and can be achieved by suppression of HLA expression or mutations in the MHC peptide-binding pocket. The peptide-loading complex (PLC) loads peptides on the MHC-I molecule in a dynamic multi-step assembly process. The effects of cancer variants on ERp57 and tapasin components from the MHC-I pathway is less known, and they could have an impact on antigen presentation. Applying computational approaches, we analysed whether the ERp57-tapasin binding might be altered by missense mutations. The variants H408R(ERp57) and P96L, D100A, G183R(tapasin) at the protein–protein interface improved protein stability (ΔΔG) during the initial screen of 14 different variants. The H408R(ERp57) and P96L(tapasin) variants, located close to disulphide bonds, were further studied by molecular dynamics (MD). Identifying intramolecular a-a’ domain interactions, MD revealed open and closed conformations of ERp57 in the presence and absence of tapasin. In wild-type and mutant ERp57-tapasin complexes, residues Val97, Ser98, Tyr100, Trp405, Gly407(ERp57) and Asn94, Cys95, Arg97, Asp100(tapasin) formed common H-bond interactions. Moreover, comparing the H-bond networks for P96L and H408R with each other, suggests that P96L(tapasin) improved ERp57-tapasin binding more than the H408R(ERp57) mutant. During MD, the C-terminus domain (that binds MHC-I) in tapasin from the ERp57(H408R)-tapasin complex moved away from the PLC, whereas in the ERp57-tapasin(P96L) system was oppositely displaced. These findings can have implications for the function of PLC and, ultimately, for the presentation of MHC-I peptide complex on the tumour cell surface.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland;
- Correspondence: (M.P.); (J.A.A.)
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland;
| | - Douglas R. Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, Scotland EH9 3BF, UK;
| | - Javier Antonio Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland;
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
- Correspondence: (M.P.); (J.A.A.)
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20
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Abstract
Recent decades, there is significant progress in understanding the mechanisms of tumor progression and immune evasion. The newly discovered protein NLRC5 is demonstrated to participate in regulating cancer immune escape through enhancing MHC class I genes expression in certain tumors. Nevertheless, increasing evidence has revealed that NLRC5 is up-regulated in some other tumors and promote tumor development and progression. The purpose of this review is to describe the role of NLRC5 in tumors and discuss whether NLRC5 can be a potential target in cancer treatment.
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Affiliation(s)
- Feng Tang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China.
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China.
| | - Yadi Xu
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China.
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China.
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21
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D’Alicandro V, Romania P, Melaiu O, Fruci D. Role of genetic variations on MHC class I antigen-processing genes in human cancer and viral-mediated diseases. Mol Immunol 2019; 113:11-15. [DOI: 10.1016/j.molimm.2018.03.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/11/2018] [Accepted: 03/29/2018] [Indexed: 01/09/2023]
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22
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Biochemical Analysis of Naturally Processed Antigenic Peptides Presented by MHC Class I Molecules. Methods Mol Biol 2019. [PMID: 31147935 DOI: 10.1007/978-1-4939-9450-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Immune surveillance of infected or tumor cells by CD8+ T cells requires that MHC class I molecules present a diverse repertoire of peptides on the cell surface. Even a few copies of individual peptides among this mixture are sufficient for recognition by the antigen receptors of appropriate CD8 T cells. Here we describe methods for biochemical analysis of the naturally processed peptides and their precursors in living cells. The peptides are fractionated using reverse phase high performance liquid chromatography and detected by the activation of CD8+ T cell hybridomas. The results provide information on the structure and amount of the peptides and yield insights into the mechanisms that generate the naturally processed peptides.
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23
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Yeon Yeon S, Jung SH, Jo YS, Choi EJ, Kim MS, Chung YJ, Lee SH. Immune checkpoint blockade resistance-related B2M hotspot mutations in microsatellite-unstable colorectal carcinoma. Pathol Res Pract 2018; 215:209-214. [PMID: 30503610 DOI: 10.1016/j.prp.2018.11.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/07/2018] [Accepted: 11/23/2018] [Indexed: 12/30/2022]
Abstract
β2-microglobulin (B2M), a component of major histocompatibility complex class I, plays an important role in host immune reaction to tumor, and inactivation of B2M is known to contribute to resistance to immune checkpoint blockade (ICB) treatment. To further characterize the B2M alterations in tumors, we analyzed B2M hotspot mutations in 2765 benign and malignant tumor tissues by Sanger sequencing and found B2M mutations in 9 (7.5%) microsatellite-unstable (MSU) colorectal cancers (CRCs) and 3 leukemias (0.6-1.3%), but not in other tumors. Targeted sequencing panel analysis for MSU CRCs showed that B2M-mutated MSU CRCs harbored more driver mutations including TP53 than B2M-wild-type MSU CRCs. Of note, bi-allelic B2M alterations, which had been known to be accumulated during ICB treatment, were frequently found (3/9) in ICB treatment-naive CRCs. Clinicopathologic parameters including CD8 + T cell numbers, cancer stages and patients' survival, however, were not significantly different between B2M-mutated and B2M-wild-type MSU CRCs. Our results indicate that B2M mutation abundance is tissue type-specific (e.g., MSU CRCs) and that genetic makeup of B2M mutation might possibly shape the MSU CRC genomes even before the ICB therapies. Our results show that B2M mutation is common in MSU CRCs, which is one of the main targets for ICB treatment, suggesting that frequent B2M mutation status should be reminded for MSU CRCs in patient selection of ICB.
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Affiliation(s)
- Su Yeon Yeon
- Departments of Pathology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea; Departments of Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea
| | - Seung-Hyun Jung
- Departments of Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea; Departments of Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea
| | - Yun Sol Jo
- Departments of Pathology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea
| | - Eun Ji Choi
- Departments of Pathology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea
| | - Min Sung Kim
- Departments of Pathology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea; Departments of Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea
| | - Yeun-Jun Chung
- Departments of Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea; Departments of Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea; Departments of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea.
| | - Sug Hyung Lee
- Departments of Pathology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea; Departments of Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul 137-701, Republic of Korea.
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López de Castro JA. How ERAP1 and ERAP2 Shape the Peptidomes of Disease-Associated MHC-I Proteins. Front Immunol 2018; 9:2463. [PMID: 30425713 PMCID: PMC6219399 DOI: 10.3389/fimmu.2018.02463] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/04/2018] [Indexed: 12/28/2022] Open
Abstract
Four inflammatory diseases are strongly associated with Major Histocompatibility Complex class I (MHC-I) molecules: birdshot chorioretinopathy (HLA-A*29:02), ankylosing spondylitis (HLA-B*27), Behçet's disease (HLA-B*51), and psoriasis (HLA-C*06:02). The endoplasmic reticulum aminopeptidases (ERAP) 1 and 2 are also risk factors for these diseases. Since both enzymes are involved in the final processing steps of MHC-I ligands it is reasonable to assume that MHC-I-bound peptides play a significant pathogenetic role. This review will mainly focus on recent studies concerning the effects of ERAP1 and ERAP2 polymorphism and expression on shaping the peptidome of disease-associated MHC-I molecules in live cells. These studies will be discussed in the context of the distinct mechanisms and substrate preferences of both enzymes, their different patterns of genetic association with various diseases, the role of polymorphisms determining changes in enzymatic activity or expression levels, and the distinct peptidomes of disease-associated MHC-I allotypes. ERAP1 and ERAP2 polymorphism and expression induce significant changes in multiple MHC-I-bound peptidomes. These changes are MHC allotype-specific and, without excluding a degree of functional inter-dependence between both enzymes, reflect largely separate roles in their processing of MHC-I ligands. The studies reviewed here provide a molecular basis for the distinct patterns of genetic association of ERAP1 and ERAP2 with disease and for the pathogenetic role of peptides. The allotype-dependent alterations induced on distinct peptidomes may explain that the joint association of both enzymes and unrelated MHC-I alleles influence different pathological outcomes.
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Swartz AM, Shen SH, Salgado MA, Congdon KL, Sanchez-Perez L. Promising vaccines for treating glioblastoma. Expert Opin Biol Ther 2018; 18:1159-1170. [PMID: 30281978 DOI: 10.1080/14712598.2018.1531846] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Conventional therapies for glioblastoma (GBM) typically fail to provide lasting antitumor benefits, owing to their inability to specifically eliminate all malignant cells. Cancer vaccines are currently being evaluated as a means to direct the adaptive immune system to target residual GBM cells that remain following standard-of-care treatment. AREAS COVERED In this review, we provide an overview of the more noteworthy cancer vaccines that are under investigation for the treatment of GBM, as well as potential future directions that may enhance GBM-vaccine effectiveness. EXPERT OPINION To date, no cancer vaccines have been proven effective against GBM; however, only a few have reached phase III clinical testing. Clinical immunological monitoring data suggest that GBM vaccines are capable of stimulating immune responses reactive to GBM antigens, but whether these responses have an appreciable antitumor effect on GBM is still uncertain. Nevertheless, there have been several promising outcomes in early phase clinical trials, which lend encouragement to this area of study. Further studies with GBM vaccines are, therefore, warranted.
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Affiliation(s)
- Adam M Swartz
- a Duke Brain Tumor Immunotherapy Program, Department of Neurosurgery , Duke University Medical Center , Durham , NC , USA.,b The Preston Robert Tisch Brain Tumor Center , Duke University Medical Center , Durham , NC , USA.,c Department of Pathology , Duke University Medical Center , Durham , NC , USA
| | - Steven H Shen
- a Duke Brain Tumor Immunotherapy Program, Department of Neurosurgery , Duke University Medical Center , Durham , NC , USA.,b The Preston Robert Tisch Brain Tumor Center , Duke University Medical Center , Durham , NC , USA.,c Department of Pathology , Duke University Medical Center , Durham , NC , USA
| | - Miguel A Salgado
- a Duke Brain Tumor Immunotherapy Program, Department of Neurosurgery , Duke University Medical Center , Durham , NC , USA.,b The Preston Robert Tisch Brain Tumor Center , Duke University Medical Center , Durham , NC , USA.,d Department of Neurosurgery , Duke University Medical Center , Durham , NC , USA
| | - Kendra L Congdon
- a Duke Brain Tumor Immunotherapy Program, Department of Neurosurgery , Duke University Medical Center , Durham , NC , USA.,b The Preston Robert Tisch Brain Tumor Center , Duke University Medical Center , Durham , NC , USA.,d Department of Neurosurgery , Duke University Medical Center , Durham , NC , USA
| | - Luis Sanchez-Perez
- a Duke Brain Tumor Immunotherapy Program, Department of Neurosurgery , Duke University Medical Center , Durham , NC , USA.,b The Preston Robert Tisch Brain Tumor Center , Duke University Medical Center , Durham , NC , USA.,d Department of Neurosurgery , Duke University Medical Center , Durham , NC , USA
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26
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Lanoix J, Durette C, Courcelles M, Cossette É, Comtois-Marotte S, Hardy MP, Côté C, Perreault C, Thibault P. Comparison of the MHC I Immunopeptidome Repertoire of B-Cell Lymphoblasts Using Two Isolation Methods. Proteomics 2018; 18:e1700251. [PMID: 29508533 DOI: 10.1002/pmic.201700251] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/19/2018] [Indexed: 11/10/2022]
Abstract
Significant technological advances in both affinity chromatography and mass spectrometry have facilitated the identification of peptides associated with the major histocompatibility complex class I (MHC I) molecules, and enabled a greater understanding of the dynamic nature of the immunopeptidome of normal and neoplastic cells. While the isolation of MHC I-associated peptides (MIPs) typically used mild acid elution (MAE) or immunoprecipitation (IP), limited information currently exists regarding their respective analytical merits. Here, a comparison of these approaches for the isolation of two different B-cell lymphoblast cell models is presented, and it is reported on the recovery, reproducibility, scalability, and complementarity of identification from each method. Both approaches yielded reproducible datasets for peptide extracts obtained from 2 to 100 million cells, with 2016 to 5093 MIPs, respectively. The IP typically provides up to 6.4-fold increase in MIPs compared to the MAE. The comprehensiveness of these immunopeptidome analyses is extended using personalized genomic database of B-cell lymphoblasts, and it is discovered that 0.4% of their respective MIP repertoire harbored nonsynonymous single nucleotide variations (also known as minor histocompatibility antigens, MiHAs).
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Affiliation(s)
- Joël Lanoix
- Institute for Research in Immunology and Cancer
| | | | | | | | | | | | | | - Claude Perreault
- Institute for Research in Immunology and Cancer.,Department of Medicine.,Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer.,Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
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Immunoribosomes: Where's there's fire, there's fire. Mol Immunol 2018; 113:38-42. [PMID: 29361306 DOI: 10.1016/j.molimm.2017.12.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/31/2017] [Indexed: 01/13/2023]
Abstract
The MHC class I antigen presentation pathway enables T cell immunosurveillance of cancer cells, viruses and other intracellular pathogens. Rapidly degraded newly synthesized proteins (DRiPs) are a major source of self-, and particularly, viral antigenic peptides. A number of findings support the idea that a substantial fraction of antigenic peptides are synthesized by "immunoribosomes", a subset of translating ribosomes that generate class I peptides with enhanced efficiency. Here, we review the evidence for the immunoribosome hypothesis.
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28
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Abram QH, Dixon B, Katzenback BA. Impacts of Low Temperature on the Teleost Immune System. BIOLOGY 2017; 6:E39. [PMID: 29165340 PMCID: PMC5745444 DOI: 10.3390/biology6040039] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/14/2017] [Accepted: 11/14/2017] [Indexed: 12/17/2022]
Abstract
As poikilothermic vertebrates, fish can experience changes in water temperature, and hence body temperature, as a result of seasonal changes, migration, or efflux of large quantities of effluent into a body of water. Temperature shifts outside of the optimal temperature range for an individual fish species can have negative impacts on the physiology of the animal, including the immune system. As a result, acute or chronic exposure to suboptimal temperatures can impair an organisms' ability to defend against pathogens and thus compromise the overall health of the animal. This review focuses on the advances made towards understanding the impacts of suboptimal temperature on the soluble and cellular mediators of the innate and adaptive immune systems of fishes. Although cold stress can result in varying effects in different fish species, acute and chronic suboptimal temperature exposure generally yield suppressive effects, particularly on adaptive immunity. Knowledge of the effects of environmental temperature on fish species is critical for both the optimal management of wild species and the best management practices for aquaculture species.
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Affiliation(s)
- Quinn H Abram
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada.
| | - Brian Dixon
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada.
| | - Barbara A Katzenback
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada.
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29
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Shi B, Thomas AJ, Benninghoff AD, Sessions BR, Meng Q, Parasar P, Rutigliano HM, White KL, Davies CJ. Genetic and epigenetic regulation of major histocompatibility complex class I gene expression in bovine trophoblast cells. Am J Reprod Immunol 2017; 79. [PMID: 29131441 PMCID: PMC5728445 DOI: 10.1111/aji.12779] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 10/10/2017] [Indexed: 11/28/2022] Open
Abstract
Problem The regulatory mechanisms governing differential expression of classical major histocompatibility complex (MHC) class I (MHC‐Ia) and non‐classical MHC class I (MHC‐Ib) genes are poorly understood. Method of study Quantitative reverse transcription‐ polymerase chain reaction (PCR) was used to compare the abundance of MHC‐I transcripts and related transcription factors in peripheral blood mononuclear cells (PBMC) and placental trophoblast cells (PTC). Methylation of MHC‐I CpG islands was detected by bisulfite treatment and next‐generation sequencing. Demethylation of PBMC and PTC with 5′‐aza‐deoxycytidine was used to assess the role of methylation in gene regulation. Results MHC‐I expression was higher in PBMC than PTC and was correlated with expression of IRF1, class II MHC transactivator (CIITA), and STAT1. The MHC‐Ia genes and BoLA‐NC1 were devoid of CpG methylation in PBMC and PTC. In contrast, CpG sites in the gene body of BoLA‐NC2, ‐NC3, and ‐NC4 were highly methylated in PBMC but largely unmethylated in normal PTC and moderately methylated in somatic cell nuclear transfer PTC. In PBMC, demethylation resulted in upregulation of MHC‐Ib by 2.8‐ to 6‐fold, whereas MHC‐Ia transcripts were elevated less than 2‐fold. Conclusion DNA methylation regulates bovine MHC‐Ib expression and is likely responsible for the different relative levels of MHC‐Ib to MHC‐Ia transcripts in PBMC and PTC.
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Affiliation(s)
- Bi Shi
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Aaron J Thomas
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Abby D Benninghoff
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,School of Veterinary Medicine, Utah State University, Logan, UT, USA
| | - Benjamin R Sessions
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Qinggang Meng
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Parveen Parasar
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA
| | - Heloisa M Rutigliano
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,School of Veterinary Medicine, Utah State University, Logan, UT, USA
| | - Kenneth L White
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA.,School of Veterinary Medicine, Utah State University, Logan, UT, USA
| | - Christopher J Davies
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.,Center for Integrated BioSystems, Utah State University, Logan, UT, USA.,School of Veterinary Medicine, Utah State University, Logan, UT, USA
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30
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Starck SR, Shastri N. Nowhere to hide: unconventional translation yields cryptic peptides for immune surveillance. Immunol Rev 2017; 272:8-16. [PMID: 27319338 DOI: 10.1111/imr.12434] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Effective immune surveillance by CD8(+) cytotoxic T cells of intracellular microbes and cancer depends on the antigen presentation pathway. This pathway produces an optimal peptide repertoire for presentation by major histocompatibility (MHC) class I molecules (pMHCs I) on the cell surface. We have known for years that the pMHC I repertoire is a reflection of the intracellular protein pool. However, many studies have revealed that pMHCs I present peptides not only from precursors encoded in open-reading frames of mRNA transcripts but also cryptic peptides encoded in apparently 'untranslated' regions. These sources vastly increase the availability of peptides for presentation and immune evasion. Here, we review studies on the composition of the cryptic pMHC I repertoire, the immunological significance of these pMHC I, and the novel translational mechanisms that generate cryptic peptides from unusual sources.
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Affiliation(s)
- Shelley R Starck
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,NGM Biopharmaceuticals Inc., South San Francisco, CA, USA
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
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31
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Balar AV, Weber JS. PD-1 and PD-L1 antibodies in cancer: current status and future directions. Cancer Immunol Immunother 2017; 66:551-564. [PMID: 28213726 PMCID: PMC11028560 DOI: 10.1007/s00262-017-1954-6] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/06/2017] [Indexed: 12/20/2022]
Abstract
Immunotherapy has moved to the center stage of cancer treatment with the recent success of trials in solid tumors with PD-1/PD-L1 axis blockade. Programmed death-1 or PD-1 is a checkpoint molecule on T cells that plays a vital role in limiting adaptive immune responses and preventing autoimmune and auto-inflammatory reactivity in the normal host. In cancer patients, PD-1 expression is very high on T cells in the tumor microenvironment, and PD-L1, its primary ligand, is variably expressed on tumor cells and antigen-presenting cells within tumors, providing a potent inhibitory influence within the tumor microenvironment. While PD-L1 expression on tumors is often regarded as a negative prognostic factor, it is clearly associated with a positive outcome for treatment with PD-1/PD-L1 blocking antibodies, and has been used to select patients for this therapy. Responses of long duration, a minority of patients with atypical responses in which progression may precede tumor shrinkage, and a pattern of autoimmune side effects often seen with this class of drugs characterize therapy with PD-1/PD-L1 blocking drugs. While excellent efficacy has been seen with a limited number of tumor types, most epithelial cancers do not show responses of long duration with these agents. In the current review, we will briefly summarize the scientific background data supporting the development of PD-1/PD-L1 blockade, and then describe the track record of these antibodies in multiple different histologies ranging from melanoma and lung cancer to less common tumor types as well as discuss biomarkers that may assist in patient selection.
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Affiliation(s)
- Arjun Vasant Balar
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, 522 First Avenue, 1310 Smilow Research Building, New York, NY, 10016, USA
| | - Jeffrey S Weber
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, 522 First Avenue, 1310 Smilow Research Building, New York, NY, 10016, USA.
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32
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Ding Y, Zheng H, Feng C, Wang B, Liu C, Mi K, Cao H, Meng S. Heat-Shock Protein gp96 Enhances T Cell Responses and Protective Potential to Bacillus Calmette-Guérin Vaccine. Scand J Immunol 2017; 84:222-8. [PMID: 27417661 DOI: 10.1111/sji.12463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/12/2016] [Indexed: 01/28/2023]
Abstract
The commonly used Bacillus Calmette-Guérin (BCG) vaccine only induces moderate T cell responses and is less effective in protecting against pulmonary tuberculosis (TB) in adults and ageing populations. Thus, developing new TB vaccine candidates is an important strategy against the spread of Mycobacterium tuberculosis. Here, we demonstrated that immunization with heat-shock protein gp96 as an adjuvant led to a significantly increased CD4(+) and CD8(+) T cell response to a BCG vaccine. Secretion of the Th1-type cytokines was increased by splenocytes from gp96-immunized mice. In addition, adding gp96 as an adjuvant effectively improved the protection against intravenous challenge with Mycobacterium bovis BCG in mice. Our study reveals the novel property of gp96 in boosting the vaccine-specific T cell response and its potential use as an adjuvant for BCG vaccines against mycobacterial infection.
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Affiliation(s)
- Y Ding
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - H Zheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - C Feng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - B Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - C Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - K Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - H Cao
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China.
| | - S Meng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
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33
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Guan J, Yang SJ, Gonzalez F, Yin Y, Shastri N. Antigen Processing in the Endoplasmic Reticulum Is Monitored by Semi-Invariant αβ TCRs Specific for a Conserved Peptide-Qa-1 b MHC Class Ib Ligand. THE JOURNAL OF IMMUNOLOGY 2017; 198:2017-2027. [PMID: 28108559 DOI: 10.4049/jimmunol.1600764] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 12/19/2016] [Indexed: 12/11/2022]
Abstract
Ag processing in the endoplasmic reticulum (ER) by the ER aminopeptidase associated with Ag processing (ERAAP) is central to presentation of a normal peptide-MHC class I (MHC I) repertoire. Alternations in ERAAP function cause dramatic changes in the MHC I-presented peptides, which elicit potent immune responses. An unusual subset of CD8+ T cells monitor normal Ag processing by responding to a highly conserved FL9 peptide that is presented by Qa-1b, a nonclassical MHC Ib molecule (QFL) in ERAAP-deficient cells. To understand the structural basis for recognition of the conserved ligand, we analyzed the αβ TCRs of QFL-specific T cells. Individual cells in normal wild-type and TCRβ-transgenic mice were assessed for QFL-specific TCR α- and β-chains. The QFL-specific cells expressed a predominant semi-invariant TCR generated by DNA rearrangement of TRAV9d-3-TRAJ21 α-chain and TRBV5-TRBD1-TRBJ2-7 β-chain gene segments. Furthermore, the CDR3 regions of the α- as well as β-chains were required for QFL ligand recognition. Thus, the αβ TCRs used to recognize the peptide-Qa-1 ligand presented by ERAAP-deficient cells are semi-invariant and likely reflect a conserved mechanism for monitoring the fidelity of Ag processing in the ER.
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Affiliation(s)
- Jian Guan
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, People's Republic of China; and.,Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Soo Jung Yang
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Federico Gonzalez
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, People's Republic of China; and
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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Topalian SL, Taube JM, Anders RA, Pardoll DM. Mechanism-driven biomarkers to guide immune checkpoint blockade in cancer therapy. Nat Rev Cancer 2016; 16:275-87. [PMID: 27079802 PMCID: PMC5381938 DOI: 10.1038/nrc.2016.36] [Citation(s) in RCA: 1879] [Impact Index Per Article: 234.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With recent approvals for multiple therapeutic antibodies that block cytotoxic T lymphocyte associated antigen 4 (CTLA4) and programmed cell death protein 1 (PD1) in melanoma, non-small-cell lung cancer and kidney cancer, and additional immune checkpoints being targeted clinically, many questions still remain regarding the optimal use of drugs that block these checkpoint pathways. Defining biomarkers that predict therapeutic effects and adverse events is a crucial mandate, highlighted by recent approvals for two PDL1 diagnostic tests. Here, we discuss biomarkers for anti-PD1 therapy based on immunological, genetic and virological criteria. The unique biology of the CTLA4 immune checkpoint, compared with PD1, requires a different approach to biomarker development. Mechanism-based insights from such studies may guide the design of synergistic treatment combinations based on immune checkpoint blockade.
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Affiliation(s)
- Suzanne L Topalian
- Department of Surgery, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center and Bloomberg-Kimmel Institute for Cancer Immunotherapy, 1550 Orleans Street, CRB2 Room 508, Baltimore, Maryland 21287, USA
| | - Janis M Taube
- Department of Dermatology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center and Bloomberg-Kimmel Institute for Cancer Immunotherapy, 1550 Orleans Street, CRB2 Room 508, Baltimore, Maryland 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center and Bloomberg-Kimmel Institute for Cancer Immunotherapy, 1550 Orleans Street, CRB2 Room 508, Baltimore, Maryland 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center and Bloomberg-Kimmel Institute for Cancer Immunotherapy, 1550 Orleans Street, CRB2 Room 508, Baltimore, Maryland 21287, USA
| | - Robert A Anders
- Department of Pathology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center and Bloomberg-Kimmel Institute for Cancer Immunotherapy, 1550 Orleans Street, CRB2 Room 508, Baltimore, Maryland 21287, USA
| | - Drew M Pardoll
- Department of Oncology, Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center and Bloomberg-Kimmel Institute for Cancer Immunotherapy, 1550 Orleans Street, CRB2 Room 508, Baltimore, Maryland 21287, USA
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35
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Sasaki T, Kanaseki T, Shionoya Y, Tokita S, Miyamoto S, Saka E, Kochin V, Takasawa A, Hirohashi Y, Tamura Y, Miyazaki A, Torigoe T, Hiratsuka H, Sato N. Microenvironmental stresses induce HLA-E/Qa-1 surface expression and thereby reduce CD8(+) T-cell recognition of stressed cells. Eur J Immunol 2016; 46:929-40. [PMID: 26711740 DOI: 10.1002/eji.201545835] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 11/29/2015] [Accepted: 12/23/2015] [Indexed: 02/04/2023]
Abstract
Hypoxia and glucose deprivation are often observed in the microenvironment surrounding solid tumors in vivo. However, how they interfere with MHC class I antigen processing and CD8(+) T-cell responses remains unclear. In this study, we analyzed the production of antigenic peptides presented by classical MHC class I in mice, and showed that it is quantitatively decreased in the cells exposed to either hypoxia or glucose deprivation. In addition, we unexpectedly found increased surface expression of HLA-E in human and Qa-1 in mouse tumor cells exposed to combined oxygen and glucose deprivation. The induced Qa-1 on the stressed tumor model interacted with an inhibitory NKG2/CD94 receptor on activated CD8(+) T cells and attenuated their specific response to the antigen. Our results thus suggest that microenvironmental stresses modulate not only classical but also nonclassical MHC class I presentation, and confer the stressed cells the capability to escape from the CD8(+) T-cell recognition.
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Affiliation(s)
- Takanori Sasaki
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
- Department of Oral Surgery, Sapporo Medical University, Sapporo, Japan
| | | | - Yosuke Shionoya
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
- Department of Respiratory Medicine and Allergology, Sapporo Medical University, Sapporo, Japan
| | - Serina Tokita
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Sho Miyamoto
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
- Department of Oral Surgery, Sapporo Medical University, Sapporo, Japan
| | - Eri Saka
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Vitaly Kochin
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Akira Takasawa
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | | | - Yasuaki Tamura
- Department of Molecular Therapeutics, Center for Food and Medical Innovation, Hokkaido University, Sapporo, Japan
| | - Akihiro Miyazaki
- Department of Oral Surgery, Sapporo Medical University, Sapporo, Japan
| | | | | | - Noriyuki Sato
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
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Joyce S. Immunoproteasomes edit tumors, which then escapes immune recognition. Eur J Immunol 2015; 45:3241-5. [PMID: 26527367 PMCID: PMC4695966 DOI: 10.1002/eji.201546100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 10/27/2015] [Accepted: 10/30/2015] [Indexed: 01/23/2023]
Abstract
In 1985, John Monaco--the discoverer of LMP-2 and -7, the inducible components of the immunoproteasome--asked his advanced immunology class as to why the MHC region contained not only structural genes, but several others as well, whose functions were then unknown. As we drew a blank, he quipped: perchance because many of the MHC genes are induced by IFN-γ! The ensuing three decades have witnessed the unveiling of the profound fundamental and clinical implications of that classroom tête-à-tête. Amongst its multitudinous effects, IFN-γ induces genes enhancing antigen processing and presentation to T cells; such as those encoding cellular proteases and activators of proteases. In this issue, Keller et al. [Eur. J. Immunol. 2015. 45: 3257-3268] demonstrate that the limited success of MART-1/Melan-A-targeted immunotherapy in melanoma patients could be due to inefficient MART-1(26-35) presentation, owing to the proteolytic activities of IFN-γ-inducible β2i/MECL-1, proteasome activator 28 (PA28), and endoplasmic reticulum-associated aminopeptidase-associated with antigen processing (ERAP). Specifically, whilst β2i and PA28 impede MART-1(26-35) liberation from its precursor protein, ERAP-1 degrades this epitope. Hence, critical to effective cancer immunotherapy is deep knowledge of T-cell-targeted tumor antigens and how cellular proteases generate protective epitope(s) from them, or destroy them.
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Affiliation(s)
- Sebastian Joyce
- Veterans Administration Tennessee Valley Healthcare System and the Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
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37
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Steers NJ, Currier JR, Jobe O, Tovanabutra S, Ratto-Kim S, Marovich MA, Kim JH, Michael NL, Alving CR, Rao M. Designing the epitope flanking regions for optimal generation of CTL epitopes. Vaccine 2014; 32:3509-16. [DOI: 10.1016/j.vaccine.2014.04.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 01/15/2014] [Accepted: 04/17/2014] [Indexed: 12/25/2022]
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38
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Hsu HT, Janßen L, Lawand M, Kim J, Perez-Arroyo A, Culina S, Gdoura A, Burgevin A, Cumenal D, Fourneau Y, Moser A, Kratzer R, Wong FS, Springer S, van Endert P. Endoplasmic reticulum targeting alters regulation of expression and antigen presentation of proinsulin. THE JOURNAL OF IMMUNOLOGY 2014; 192:4957-66. [PMID: 24778449 DOI: 10.4049/jimmunol.1300631] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Peptide ligands presented by MHC class I (MHC-I) molecules are produced by degradation of cytosolic and nuclear, but also endoplasmic reticulum (ER)-resident, proteins by the proteasome. However, Ag processing of ER proteins remains little characterized. Studying processing and presentation of proinsulin, which plays a pivotal role in autoimmune diabetes, we found that targeting to the ER has profound effects not only on how proinsulin is degraded, but also on regulation of its cellular levels. While proteasome inhibition inhibited degradation and presentation of cytosolic proinsulin, as expected, it reduced the abundance of ER-targeted proinsulin. This targeting and protein modifications modifying protein half-life also had profound effects on MHC-I presentation and proteolytic processing of proinsulin. Thus, presentation of stable luminal forms was inefficient but enhanced by proteasome inhibition, whereas that of unstable luminal forms and of a cytosolic form were more efficient and compromised by proteasome inhibitors. Distinct stability of peptide MHC complexes produced from cytosolic and luminal proinsulin suggests that different proteolytic activities process the two Ag forms. Thus, both structural features and subcellular targeting of Ags can have strong effects on the processing pathways engaged by MHC-I-restricted Ags, and on the efficiency and regulation of their presentation.
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Affiliation(s)
- Hsiang-Ting Hsu
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Linda Janßen
- Biochemistry and Cell Biology, Molecular Life Science Center, Jacobs University Bremen, 28759 Bremen, Germany; and
| | - Myriam Lawand
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Jessica Kim
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Alicia Perez-Arroyo
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Slobodan Culina
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Abdel Gdoura
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Anne Burgevin
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Delphine Cumenal
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Yousra Fourneau
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Anna Moser
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Roland Kratzer
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - F Susan Wong
- Centre for Endocrine and Diabetes Science, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Sebastian Springer
- Biochemistry and Cell Biology, Molecular Life Science Center, Jacobs University Bremen, 28759 Bremen, Germany; and
| | - Peter van Endert
- INSERM, Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France;
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Shastri N, Nagarajan N, Lind KC, Kanaseki T. Monitoring peptide processing for MHC class I molecules in the endoplasmic reticulum. Curr Opin Immunol 2013; 26:123-7. [PMID: 24556408 DOI: 10.1016/j.coi.2013.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 11/18/2013] [Indexed: 01/22/2023]
Abstract
Classical MHC class I molecules open a window into the cell by presenting intracellular peptides (pMHC I) on the surface. The peptides are used for immune surveillance by circulating CD8+ T and NK cells to detect and eliminate infected or tumor cells. Not surprisingly, viruses and tumor cells have evolved immune evasion mechanisms to keep the window shades down and the cytotoxic cells oblivious to their presence. Here, we review counter mechanisms that nevertheless allow the immune system to detect and eliminate cells unable to properly process antigenic peptides in the endoplasmic reticulum.
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Affiliation(s)
- Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
| | - Niranjana Nagarajan
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Kristin C Lind
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Takayuki Kanaseki
- Department of Pathology, School of Medicine, Sapporo Medical University, Sapporo, Japan
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40
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Kanaseki T, Lind KC, Escobar H, Nagarajan N, Reyes-Vargas E, Rudd B, Rockwood AL, Van Kaer L, Sato N, Delgado JC, Shastri N. ERAAP and tapasin independently edit the amino and carboxyl termini of MHC class I peptides. THE JOURNAL OF IMMUNOLOGY 2013; 191:1547-55. [PMID: 23863903 DOI: 10.4049/jimmunol.1301043] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Effective CD8(+) T cell responses depend on presentation of a stable peptide repertoire by MHC class I (MHC I) molecules on the cell surface. The overall quality of peptide-MHC I complexes (pMHC I) is determined by poorly understood mechanisms that generate and load peptides with appropriate consensus motifs onto MHC I. In this article, we show that both tapasin (Tpn), a key component of the peptide loading complex, and the endoplasmic reticulum aminopeptidase associated with Ag processing (ERAAP) are quintessential editors of distinct structural features of the peptide repertoire. We carried out reciprocal immunization of wild-type mice with cells from Tpn- or ERAAP-deficient mice. Specificity analysis of T cell responses showed that absence of Tpn or ERAAP independently altered the peptide repertoire by causing loss as well as gain of new pMHC I. Changes in amino acid sequences of MHC-bound peptides revealed that ERAAP and Tpn, respectively, defined the characteristic amino and carboxy termini of canonical MHC I peptides. Thus, the optimal pMHC I repertoire is produced by two distinct peptide editing steps in the endoplasmic reticulum.
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Affiliation(s)
- Takayuki Kanaseki
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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41
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Wu W, Qiu HJ, Liu ZJ. Immunoregulatory effects of intraepithelial lymphocytes in inflammatory bowel disease. Shijie Huaren Xiaohua Zazhi 2013; 21:568-573. [DOI: 10.11569/wcjd.v21.i7.568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Intraepithelial lymphocytes (IELs) are found in a wide variety of sites, especially in the mucosa of the intestine, respiratory tract, and genital tract. Intestinal IELs are located between intestinal epithelial cells (IECs) and the basement membrane. The ratio between IECs and IELs in the small intestine is 4-10:1, but is slightly lower in the large intestine. As the first guard of the intestine, IELs play a significant role in maintaining the integrity of the mucosa, immune surveillance and regulating the homeostasis on the intestinal mucosal surface. Recent studies have demonstrated that IELs are also involved in the pathogenesis of inflammatory bowel disease (IBD).
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42
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Kanaseki T, Shastri N. Biochemical analysis of naturally processed antigenic peptides presented by MHC class I molecules. Methods Mol Biol 2013; 960:179-185. [PMID: 23329488 DOI: 10.1007/978-1-62703-218-6_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Immune surveillance of infected or tumor cells by CD8(+) T cells requires that MHC class I molecules present a diverse repertoire of peptides on the cell surface. Even a few copies of individual peptides among this mixture are sufficient for recognition by the antigen receptors of appropriate CD8(+) T cells. Here we describe a method for biochemical analysis of the naturally processed peptides in living cells. The peptide mixture in cell extracts is fractionated using reverse phase high performance liquid chromatography and detected by the activation of CD8(+) T cell hybridomas. The results provide information on the structure and amount of the peptides and yield insights into the mechanisms that generate the naturally processed peptides.
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Affiliation(s)
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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44
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Census of cytosolic aminopeptidase activity reveals two novel cytosolic aminopeptidases. Med Microbiol Immunol 2012; 201:463-73. [DOI: 10.1007/s00430-012-0266-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 08/24/2012] [Indexed: 01/27/2023]
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45
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Meissner TB, Liu YJ, Lee KH, Li A, Biswas A, van Eggermond MCJA, van den Elsen PJ, Kobayashi KS. NLRC5 cooperates with the RFX transcription factor complex to induce MHC class I gene expression. THE JOURNAL OF IMMUNOLOGY 2012; 188:4951-8. [PMID: 22490869 DOI: 10.4049/jimmunol.1103160] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Tight regulation of MHC class I gene expression is critical for CD8 T cell activation and host adaptive-immune responses. The promoters of MHC class I genes contain a well-conserved core module, the W/S-X-Y motif, which assembles a nucleoprotein complex termed MHC enhanceosome. A member of the nucleotide-binding domain, leucine-rich repeat (NLR) protein family, NLRC5, is a newly identified transcriptional regulator of MHC class I genes. NLRC5 associates with and transactivates the proximal promoters of MHC class I genes, although the molecular mechanism of transactivation has not been understood. In this article, we show that NLRC5-mediated MHC class I gene induction requires the W/S and X1, X2 cis-regulatory elements. The transcription factors RFX5, RFXAP, and RFXANK/B, which compose the RFX protein complex and associate with the X1 box, cooperate with NLRC5 for MHC class I expression. Coimmunoprecipitation experiments revealed that NLRC5 specifically interacts with the RFX subunit RFXANK/B via its ankyrin repeats. In addition, we show that NLRC5 can cooperate with ATF1 and the transcriptional coactivators CBP/p300 and general control nonderepressible 5, which display histone acetyltransferase activity. Taken together, our data suggest that NLRC5 participates in an MHC class I-specific enhanceosome, which assembles on the conserved W/S-X-Y core module of the MHC class I proximal promoters, including the RFX factor components and CREB/ATF1 family transcription factors, to promote MHC class I gene expression.
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Affiliation(s)
- Torsten B Meissner
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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46
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Meissner TB, Li A, Kobayashi KS. NLRC5: a newly discovered MHC class I transactivator (CITA). Microbes Infect 2011; 14:477-84. [PMID: 22209772 DOI: 10.1016/j.micinf.2011.12.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Revised: 12/09/2011] [Accepted: 12/12/2011] [Indexed: 02/07/2023]
Abstract
Major histocompatibility complex (MHC) class I and class II are crucial for the function of the human adaptive immune system. An NLR protein, CIITA (MHC class II transactivator), is a master regulator of MHC class II gene expression as well as of some of the genes involved in MHC class II antigen presentation. It has recently been discovered that another member of the NLR protein family, NLRC5, transcriptionally activates MHC class I genes, and thus acts as "CITA" (MHC class I transactivator), a counterpart to CIITA. In addition to MHC class I genes, NLRC5 can induce the expression of β2M, TAP1 and LMP2, essential components of MHC class I antigen presentation. These findings indicate that NLRC5 and CIITA are transcriptional regulators that orchestrate the concerted expression of critical components in the MHC class I and MHC class II pathways, respectively.
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Affiliation(s)
- Torsten B Meissner
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Dana 1420A, Boston, MA 02215, United States
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47
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Oliveira CC, Querido B, Sluijter M, Derbinski J, van der Burg SH, van Hall T. Peptide transporter TAP mediates between competing antigen sources generating distinct surface MHC class I peptide repertoires. Eur J Immunol 2011; 41:3114-24. [PMID: 21898382 DOI: 10.1002/eji.201141836] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 08/10/2011] [Accepted: 08/30/2011] [Indexed: 01/28/2023]
Abstract
We recently described a category of TAP-independent peptide-epitopes that are selectively presented by cells with processing defects in the classical MHC class I (MHC-I) pathway. Here, we studied the ER-resident ceramide synthase Trh4 as a prototypic example of these neo-antigens and found that moderate inhibition of TAP permits cell surface presentation of the Trh4 peptide. The absence of this peptide from WT cells was not related to the binding or stability of the Trh4/D(b) complexes, or to the availability of MHC-I heavy chains, but rather to the limited expression of the antigen. Strongly elevated antigen levels were needed to reach comparable peptide display on WT as on TAP-deficient cells. Our data suggest that the normal influx of TAP-transported peptides in the ER during routine processing creates an efficient barrier for peptides from alternative processing routes. Impairment of TAP function, as commonly found in cancers and virus-infected cells, lowers this resistance allowing for MHC-I presentation of other peptide sources.
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Affiliation(s)
- Cláudia C Oliveira
- Department of Clinical Oncology, Leiden University Medical Center, Leiden, The Netherlands
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48
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Brezar V, Carel JC, Boitard C, Mallone R. Beyond the hormone: insulin as an autoimmune target in type 1 diabetes. Endocr Rev 2011; 32:623-69. [PMID: 21700723 DOI: 10.1210/er.2011-0010] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Insulin is not only the hormone produced by pancreatic β-cells but also a key target antigen of the autoimmune islet destruction leading to type 1 diabetes. Despite cultural biases between the fields of endocrinology and immunology, these two facets should not be regarded separately, but rather harmonized in a unifying picture of diabetes pathogenesis. There is increasing evidence suggesting that metabolic factors (β-cell dysfunction, insulin resistance) and immunological components (inflammation and β-cell-directed adaptive immune responses) may synergize toward islet destruction, with insulin standing at the crossroad of these pathways. This concept further calls for a revision of the classical dichotomy between type 1 and type 2 diabetes because metabolic and immune mechanisms may both contribute to different extents to the development of different forms of diabetes. After providing a background on the mechanisms of β-cell autoimmunity, we will explain the role of insulin and its precursors as target antigens expressed not only by β-cells but also in the thymus. Available knowledge on the autoimmune antibody and T-cell responses against insulin will be summarized. A unifying scheme will be proposed to show how different aspects of insulin biology may lead to β-cell destruction and may be therapeutically exploited. We will argue about possible reasons why insulin remains the mainstay of metabolic control in type 1 diabetes but has so far failed to prevent or halt β-cell autoimmunity as an immune modulatory reagent.
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Affiliation(s)
- Vedran Brezar
- Institut National de la Santé et de la Recherche Médicale, Unité 986, DeAR Lab Avenir, Saint Vincent de Paul Hospital, and Paris Descartes University, 82 avenue Denfert Rochereau, 75674 Paris Cedex 14, France
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49
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Kotsiou E, Brzostek J, Lenart I, Antoniou AN, Dyson J, Gould KG. Dimerization of soluble disulfide trap single-chain major histocompatibility complex class I molecules dependent on peptide binding affinity. Antioxid Redox Signal 2011; 15:635-44. [PMID: 21050141 DOI: 10.1089/ars.2010.3691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Stable presentation of peptide epitope by major histocompatibility complex (MHC) class I molecules is a prerequisite for the efficient expansion of CD8(+) T cells. The construction of single-chain MHC class I molecules in which the peptide, β(2)-microglobulin, and MHC heavy chain are all joined together via flexible linkers increases peptide-MHC stability. We have expressed two T cell epitopes that may be useful in leukemia treatment as single-chain MHC class I molecules, aiming to develop a system for the expansion of antigen-specific CD8(+) T cells in vitro. Disulfide trap versions of these single-chain MHC molecules were also created to improve anchoring of the peptides in the MHC molecule. Unexpectedly, we observed that soluble disulfide trap single-chain molecules expressed in eukaryotic cells were prone to homodimerization, depending on the binding affinity of the peptide epitope. The dimers were remarkably stable and efficiently recognized by conformation-specific antibodies, suggesting that they consisted of largely correctly folded molecules. However, dimerization was not observed when the disulfide trap molecules were expressed as full-length, transmembrane-anchored molecules. Our results further emphasize the importance of peptide binding affinity for the efficient folding of MHC class I molecules.
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Affiliation(s)
- Eleni Kotsiou
- Department of Immunology, Wright-Fleming Institute, Imperial College London, London, United Kingdom
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50
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Major source of antigenic peptides for the MHC class I pathway is produced during the pioneer round of mRNA translation. Proc Natl Acad Sci U S A 2011; 108:11572-7. [PMID: 21709220 DOI: 10.1073/pnas.1104104108] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The MHC class I antigen presentation pathway allows the immune system to distinguish between self and nonself. Despite extensive research on the processing of antigenic peptides, little is known about their origin. Here, we show that mRNAs carrying premature stop codons that prevent the production of full-length proteins via the nonsense-mediated decay pathway still produce a majority of peptide substrates for the MHC class I pathway by a noncanonical mRNA translation process. Blocking the interaction of the translation initiation factor eIF4E with the cap structure suppresses the synthesis of full-length proteins but has only a limited effect on the production of antigenic peptides. These results reveal an essential cell biological function for a class of translation products derived during the pioneer round of mRNA translation and will have important implications for understanding how the immune system detects cells harboring pathogens and generates tolerance.
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