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Oshima S, Sinha R, Ohno M, Nishi K, Eto K, Takaori-Kondo A, Nishi E, Yamamoto R. Nardilysin determines hematopoietic stem cell fitness by regulating protein synthesis. Biochem Biophys Res Commun 2024; 693:149355. [PMID: 38096617 DOI: 10.1016/j.bbrc.2023.149355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 10/31/2023] [Accepted: 12/03/2023] [Indexed: 01/10/2024]
Abstract
Nardilysin (NRDC) is a multifunctional protein required for maintaining homeostasis in various cellular and tissue contexts. However, its role in hematopoietic stem cells (HSCs) remains unclear. Here, through the conditional deletion of NRDC in hematopoietic cells, we demonstrate that NRDC is required for HSCs expansion in vitro and the reconstitution of hematopoiesis in vivo after transplantation. We found NRDC-deficient HSCs lose their self-renewal ability and display a preferential bias to myeloid differentiation in response to replication stress. Transcriptome data analysis revealed the upregulation of heat shock response-related genes in NRDC-deficient HSCs. Additionally, we observed increased protein synthesis in cultured NRDC-deficient HSCs. Thus, loss of NRDC may cause the inability to control protein synthesis in response to replication induced protein stress, leading to the impaired HSC self-renewal ability. This highlights a novel model of action of NRDC specifically in HSCs.
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Affiliation(s)
- Shinichiro Oshima
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8507, Japan; Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford Medicine, Stanford, CA, 94305, USA
| | - Mikiko Ohno
- Department of Pharmacology, Shiga University of Medical Sciences, Seta Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
| | - Kiyoto Nishi
- Department of Pharmacology, Shiga University of Medical Sciences, Seta Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
| | - Koji Eto
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8507, Japan
| | - Eiichiro Nishi
- Department of Pharmacology, Shiga University of Medical Sciences, Seta Tsukinowa-cho, Otsu, Shiga, 520-2192, Japan
| | - Ryo Yamamoto
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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2
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Neves RL, Marem A, Carmona B, Arata JG, Cyrillo Ramos MP, Justo GZ, Machado de Melo FH, Oliveira V, Icimoto MY. Expression of thimet oligopeptidase (THOP) modulated by oxidative stress in human multidrug resistant (MDR) leukemia cells. Biochimie 2023; 212:21-30. [PMID: 36997147 DOI: 10.1016/j.biochi.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 03/03/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023]
Abstract
Thimet oligopeptidase (THOP) is a cytosolic metallopeptidase known to regulate the fate of post-proteasomal peptides, protein turnover and peptide selection in the antigen presentation machinery (APM) system. Oxidative stress influences THOP expression and regulates its proteolytic activity, generating variable cytosolic peptide levels, possibly affecting the immune evasion of tumor cells. In the present work, we examined the association between THOP expression/activity and stress oxidative resistance in human leukemia cells using the K562 cell line, a chronic myeloid leukemia (CML), and the multidrug-resistant (MDR) Lucena 1 (K562-derived MDR cell line) as model. The Lucena 1 phenotype was validated under vincristine treatment and the relative THOP1 mRNA levels and protein expression compared to K562 cell line. Our data demonstrated increased THOP1 gene and protein levels in K562 cells in contrast to the oxidative-resistant Lucena 1, even after H2O2 treatment, suggesting an oxidative stress dependence in THOP regulation. Further, it was observed higher basal levels of reactive oxygen species (ROS) in K562 compared to Lucena 1 cell line using DHE fluorescent probe. Since THOP activity is dependent on its oligomeric state, we also compared its proteolytic activity under reducing agent treatment, which demonstrated that its function modulation with respect to changes in redox state. Finally, the mRNA expression and FACS analyses demonstrated a reduced expression of MHC I only in K562 cell line. In conclusion, our results highlight THOP redox modulation, which could influence antigen presentation in multidrug resistant leukemia cells.
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Affiliation(s)
- Raquel Leão Neves
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Alyne Marem
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Bruno Carmona
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Júlia Galanakis Arata
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Giselle Zenker Justo
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil; Departamento de Ciências Farmacêuticas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | | | - Vitor Oliveira
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil.
| | - Marcelo Yudi Icimoto
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil; Division of Biomaterials and Biomechanics, Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR, United States.
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3
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Schmalen A, Kammerl IE, Meiners S, Noessner E, Deeg CA, Hauck SM. A Lysine Residue at the C-Terminus of MHC Class I Ligands Correlates with Low C-Terminal Proteasomal Cleavage Probability. Biomolecules 2023; 13:1300. [PMID: 37759700 PMCID: PMC10527444 DOI: 10.3390/biom13091300] [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: 03/16/2023] [Revised: 08/10/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The majority of peptides presented by MHC class I result from proteasomal protein turnover. The specialized immunoproteasome, which is induced during inflammation, plays a major role in antigenic peptide generation. However, other cellular proteases can, either alone or together with the proteasome, contribute peptides to MHC class I loading non-canonically. We used an immunopeptidomics workflow combined with prediction software for proteasomal cleavage probabilities to analyze how inflammatory conditions affect the proteasomal processing of immune epitopes presented by A549 cells. The treatment of A549 cells with IFNγ enhanced the proteasomal cleavage probability of MHC class I ligands for both the constitutive proteasome and the immunoproteasome. Furthermore, IFNγ alters the contribution of the different HLA allotypes to the immunopeptidome. When we calculated the HLA allotype-specific proteasomal cleavage probabilities for MHC class I ligands, the peptides presented by HLA-A*30:01 showed characteristics hinting at a reduced C-terminal proteasomal cleavage probability independently of the type of proteasome. This was confirmed by HLA-A*30:01 ligands from the immune epitope database, which also showed this effect. Furthermore, two additional HLA allotypes, namely, HLA-A*03:01 and HLA-A*11:01, presented peptides with a markedly reduced C-terminal proteasomal cleavage probability. The peptides eluted from all three HLA allotypes shared a peptide binding motif with a C-terminal lysine residue, suggesting that this lysine residue impairs proteasome-dependent HLA ligand production and might, in turn, favor peptide generation by other cellular proteases.
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Affiliation(s)
- Adrian Schmalen
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, Martinsried, 82152 Planegg, Germany
- Core Facility—Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), 80939 Munich, Germany
| | - Ilona E. Kammerl
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians-University, Helmholtz Center Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Silke Meiners
- Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), 23845 Borstel, Germany
- Institute of Experimental Medicine, Christian-Albrechts University Kiel, 24118 Kiel, Germany
| | - Elfriede Noessner
- Immunoanalytics Research Group—Tissue Control of Immunocytes, Helmholtz Center Munich, 81377 Munich, Germany
| | - Cornelia A. Deeg
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, Martinsried, 82152 Planegg, Germany
| | - Stefanie M. Hauck
- Core Facility—Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), 80939 Munich, Germany
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4
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Leddy O, White FM, Bryson BD. Immunopeptidomics reveals determinants of Mycobacterium tuberculosis antigen presentation on MHC class I. eLife 2023; 12:e84070. [PMID: 37073954 PMCID: PMC10159623 DOI: 10.7554/elife.84070] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/17/2023] [Indexed: 04/20/2023] Open
Abstract
CD8+ T cell recognition of Mycobacterium tuberculosis (Mtb)-specific peptides presented on major histocompatibility complex class I (MHC-I) contributes to immunity to tuberculosis (TB), but the principles that govern presentation of Mtb antigens on MHC-I are incompletely understood. In this study, mass spectrometry (MS) analysis of the MHC-I repertoire of Mtb-infected primary human macrophages reveals that substrates of Mtb's type VII secretion systems (T7SS) are overrepresented among Mtb-derived peptides presented on MHC-I. Quantitative, targeted MS shows that ESX-1 activity is required for presentation of Mtb peptides derived from both ESX-1 substrates and ESX-5 substrates on MHC-I, consistent with a model in which proteins secreted by multiple T7SSs access a cytosolic antigen processing pathway via ESX-1-mediated phagosome permeabilization. Chemical inhibition of proteasome activity, lysosomal acidification, or cysteine cathepsin activity did not block presentation of Mtb antigens on MHC-I, suggesting involvement of other proteolytic pathways or redundancy among multiple pathways. Our study identifies Mtb antigens presented on MHC-I that could serve as targets for TB vaccines, and reveals how the activity of multiple T7SSs interacts to contribute to presentation of Mtb antigens on MHC-I.
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Affiliation(s)
- Owen Leddy
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of Massachusetts General Hospital, Harvard, and MITCambridgeUnited States
- Koch Institute for Integrative Cancer ResearchCambridgeUnited States
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Koch Institute for Integrative Cancer ResearchCambridgeUnited States
- Center for Precision Cancer MedicineCambridgeUnited States
| | - Bryan D Bryson
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of Massachusetts General Hospital, Harvard, and MITCambridgeUnited States
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5
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Molinero M, Gómez S, Benítez ID, Vengoechea JJ, González J, Polanco D, Gort-Paniello C, Moncusí-Moix A, García-Hidalgo MC, Perez-Pons M, Belmonte T, Torres G, Caballero J, Barberà C, Ayestarán Rota JI, Socías Crespí L, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Lorente-Balanza JÁ, Menéndez R, Motos A, Peñuelas O, Riera J, Torres A, Barbé F, de Gonzalo-Calvo D. Multiplex protein profiling of bronchial aspirates reveals disease-, mortality- and respiratory sequelae-associated signatures in critically ill patients with ARDS secondary to SARS-CoV-2 infection. Front Immunol 2022; 13:942443. [PMID: 35967328 PMCID: PMC9373836 DOI: 10.3389/fimmu.2022.942443] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction Bronchial aspirates (BAS) obtained during invasive mechanical ventilation (IMV) constitutes a useful tool for molecular phenotyping and decision making. Aim To identify the proteomic determinants associated with disease pathogenesis, all-cause mortality and respiratory sequelae in BAS samples from critically ill patients with SARS-CoV-2-induced ARDS. Methods Multicenter study including 74 critically ill patients with COVID-19 and non-COVID-19 ARDS. BAS were obtained by bronchoaspiration after IMV initiation. Three hundred sixty-four proteins were quantified using proximity extension assay (PEA) technology. Random forest models were used to assess predictor importance. Results After adjusting for confounding factors, CST5, NADK, SRPK2 and TGF-α were differentially detected in COVID-19 and non-COVID-19 patients. In random forest models for COVID-19, CST5, DPP7, NADK, KYAT1 and TYMP showed the highest variable importance. In COVID-19 patients, reduced levels of ENTPD2 and PTN were observed in nonsurvivors of ICU stay, even after adjustment. AGR2, NQO2, IL-1α, OSM and TRAIL showed the strongest associations with in-ICU mortality and were used to construct a protein-based prediction model. Kaplan-Meier curves revealed a clear separation in mortality risk between subgroups of PTN, ENTPD2 and the prediction model. Cox regression models supported these findings. In survivors, the levels of FCRL1, NTF4 and THOP1 in BAS samples obtained during the ICU stay correlated with lung function (i.e., DLCO levels) 3 months after hospital discharge. Similarly, Flt3L and THOP1 levels were correlated with radiological features (i.e., TSS). These proteins are expressed in immune and nonimmune lung cells. Poor host response to viral infectivity and an inappropriate reparative mechanism seem to be linked with the pathogenesis of the disease and fatal outcomes, respectively. Conclusion BAS proteomics identified novel factors associated with the pathology of SARS-CoV-2-induced ARDS and its adverse outcomes. BAS-based protein testing emerges as a novel tool for risk assessment in the ICU.
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Affiliation(s)
- Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Silvia Gómez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Iván D Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - J J Vengoechea
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Dinora Polanco
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - María C García-Hidalgo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Manel Perez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Thalía Belmonte
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jesús Caballero
- Intensive Care Department, University Hospital Arnau de Vilanova, IRBLleida, Lleida, Spain
| | - Carme Barberà
- Intensive Care Department, University Hospital Santa María, IRBLleida, Lleida, Spain
| | - Jose Ignacio Ayestarán Rota
- Intensive Care Unit, Son Espases University Hospital, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | | | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Intensive Care Department, Vall d'Hebron Hospital Universitari. SODIR Research Group, Vall d'Hebron Institut de Recerca VHIR), Barcelona, Spain
| | | | - Jose Ángel Lorente-Balanza
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario de Getafe, Madrid, Spain
| | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario de Getafe, Madrid, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Intensive Care Department, Vall d'Hebron Hospital Universitari. SODIR Research Group, Vall d'Hebron Institut de Recerca VHIR), Barcelona, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
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6
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Vaishnav J, Jadeja SD, Singh M, Khan F, Yadav M, Begum R. Altered Levels of Negative Costimulatory Molecule V-Set Domain-Containing T-Cell Activation Inhibitor-1 (VTCN1) and Metalloprotease Nardilysin (NRD1) are Associated with Generalized Active Vitiligo. Immunol Invest 2022; 51:2035-2052. [PMID: 35815687 DOI: 10.1080/08820139.2022.2097091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Vitiligo is characterized by depigmented macules on the skin caused due to autoimmune destruction of melanocytes. V-set domain-containing T-cell activation inhibitor-1 (VTCN1) is a negative costimulatory molecule that plays a vital role in suppressing autoimmunity and tuning immune response. Nardilysin (NRD1), a metalloproteinase, cleaves membrane-tethered VTCN1 resulting in the shedding of soluble-VTCN1 (sVTCN1). However, the role of VTCN1 and NRD1 in vitiligo pathogenesis is unexplored. OBJECTIVES AND METHODS This study was aimed to (i) Investigate the association of VTCN1 intronic polymorphisms (rs10923223 T/C and rs12046117 C/T) with vitiligo susceptibility in Gujarat population by using Polymerase Chain Reaction- Restriction Fragment Length Polymorphism (PCR-RFLP) (ii) Estimate VTCN1 & NRD1 transcript levels from peripheral blood mononuclear cells (PBMCs) and skin samples of vitiligo patients by real-time PCR, (iii) Estimate sVTCN1 and NRD1 protein levels from plasma by ELISA and (iv) Estimate VTCN1 protein levels in the skin samples of vitiligo patients by immunofluorescence. RESULTS The analysis revealed increased VTCN1 and NRD1 transcript levels in the skin (p = .039, p = .021 respectively), increased sVTCN1 and NRD1 levels (p = .026, p = .015 respectively) in the plasma, and decreased VTCN1 protein levels (p = .0002) in the skin of vitiligo patients as compared to healthy controls. The genetic analysis revealed no significant association of VTCN1 intronic polymorphisms rs10923223 T/C and rs12046117 C/T with vitiligo susceptibility in Gujarat population (p = .359, p = .937, respectively). CONCLUSIONS The present study revealed altered VTCN1 and NRD1 expressions in the blood and skin of vitiligo patients, suggesting their potential role in the development and progression of Vitiligo.
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Affiliation(s)
- Jayvadan Vaishnav
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Shahnawaz D Jadeja
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Mala Singh
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Farheen Khan
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Madhu Yadav
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Rasheedunnisa Begum
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, India
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7
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Probing the Conformational States of Thimet Oligopeptidase in Solution. Int J Mol Sci 2022; 23:ijms23137297. [PMID: 35806299 PMCID: PMC9266445 DOI: 10.3390/ijms23137297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 02/06/2023] Open
Abstract
Thimet oligopeptidase (TOP) is a metallopeptidase involved in the metabolism of oligopeptides inside and outside cells of various tissues. It has been proposed that substrate or inhibitor binding in the TOP active site induces a large hinge-bending movement leading to a closed structure, in which the bound ligand is enclosed. The main goal of the present work was to study this conformational change, and fluorescence techniques were used. Four active TOP mutants were created, each equipped with a single-Trp residue (fluorescence donor) and a p-nitro-phenylalanine (pNF) residue as fluorescence acceptor at opposite sides of the active site. pNF was biosynthetically incorporated with high efficiency using the amber codon suppression technology. Inhibitor binding induced shorter Donor-Acceptor (D-A) distances in all mutants, supporting the view that a hinge-like movement is operative in TOP. The activity of TOP is known to be dependent on the ionic strength of the assay buffer and D-A distances were measured at different ionic strengths. Interestingly, a correlation between the D-A distance and the catalytic activity of TOP was observed: the highest activities corresponded to the shortest D-A distances. In this study for the first time the hinge-bending motion of a metallopeptidase in solution could be studied, yielding insight about the position of the equilibrium between the open and closed conformation. This information will contribute to a more detailed understanding of the mode of action of these enzymes, including therapeutic targets like neurolysin and angiotensin-converting enzyme 2 (ACE2).
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8
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Pymm P, Tenzer S, Wee E, Weimershaus M, Burgevin A, Kollnberger S, Gerstoft J, Josephs TM, Ladell K, McLaren JE, Appay V, Price DA, Fugger L, Bell JI, Schild H, van Endert P, Harkiolaki M, Iversen AKN. Epitope length variants balance protective immune responses and viral escape in HIV-1 infection. Cell Rep 2022; 38:110449. [PMID: 35235807 PMCID: PMC9631117 DOI: 10.1016/j.celrep.2022.110449] [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: 04/23/2020] [Revised: 10/31/2021] [Accepted: 02/07/2022] [Indexed: 11/21/2022] Open
Abstract
Cytotoxic T lymphocyte (CTL) and natural killer (NK) cell responses to a single optimal 10-mer epitope (KK10) in the human immunodeficiency virus type-1 (HIV-1) protein p24Gag are associated with enhanced immune control in patients expressing human leukocyte antigen (HLA)-B∗27:05. We find that proteasomal activity generates multiple length variants of KK10 (4-14 amino acids), which bind TAP and HLA-B∗27:05. However, only epitope forms ≥8 amino acids evoke peptide length-specific and cross-reactive CTL responses. Structural analyses reveal that all epitope forms bind HLA-B∗27:05 via a conserved N-terminal motif, and competition experiments show that the truncated epitope forms outcompete immunogenic epitope forms for binding to HLA-B∗27:05. Common viral escape mutations abolish (L136M) or impair (R132K) production of KK10 and longer epitope forms. Peptide length influences how well the inhibitory NK cell receptor KIR3DL1 binds HLA-B∗27:05 peptide complexes and how intraepitope mutations affect this interaction. These results identify a viral escape mechanism from CTL and NK responses based on differential antigen processing and peptide competition.
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Affiliation(s)
- Phillip Pymm
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK; Walter and Eliza Hall Institute of Medical Research, University of Melbourne, 1G Royalparade, Parkville, VIC 3052, Australia
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University of Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany
| | - Edmund Wee
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Mirjana Weimershaus
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France
| | - Anne Burgevin
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France
| | - Simon Kollnberger
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, CF14 4XN Cardiff, UK
| | - Jan Gerstoft
- Department of Infectious Diseases, Rigshospitalet, The National University Hospital, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Tracy M Josephs
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, CF14 4XN Cardiff, UK
| | - James E McLaren
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, CF14 4XN Cardiff, UK
| | - Victor Appay
- Institut National de la Santé et de la Recherche Médicale, Unité 1135, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Université, Boulevard de l'Hopital, 75013 Paris, France; International Research Center of Medical Sciences, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto City 860-0811, Japan
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, CF14 4XN Cardiff, UK; Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Tenovus Building, CF14 4XN Cardiff, UK
| | - Lars Fugger
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK; Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, OX3 9DS Oxford, UK
| | - John I Bell
- Office of the Regius Professor of Medicine, The Richard Doll Building, University of Oxford, Old Road Campus, OX3 7LF Oxford, UK
| | - Hansjörg Schild
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University of Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany
| | - Peter van Endert
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France
| | - Maria Harkiolaki
- Structural Biology Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Old Road Campus, OX3 7LF Oxford, UK; Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, OX11 0DE Didcot, UK
| | - Astrid K N Iversen
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK.
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9
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Wellington D, Yin Z, Kessler BM, Dong T. Immunodominance complexity: lessons yet to be learned from dominant T cell responses to SARS-COV-2. Curr Opin Virol 2021; 50:183-191. [PMID: 34534732 PMCID: PMC8424056 DOI: 10.1016/j.coviro.2021.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 11/14/2022]
Abstract
Immunodominance is a complex and highly debated topic of T cell biology. The current SARS-CoV-2 pandemic has provided the opportunity to profile adaptive immune responses and determine molecular factors contributing to emerging responses towards immunodominant viral epitopes. Here, we discuss parameters that alter the dynamics of CD8 viral epitope processing, generation and T-cell responses, and how immunodominance counteracts viral immune escape mechanisms that develop in the context of emerging SARS-CoV-2 variants.
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Affiliation(s)
- Dannielle Wellington
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK.
| | - Zixi Yin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK
| | - Benedikt M Kessler
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Target Discovery Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK.
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10
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Abstract
Peptidases generate bioactive peptides that can regulate cell signaling and mediate intercellular communication. While the processing of peptide precursors is initiated intracellularly, some modifications by peptidases may be conducted extracellularly. Thimet oligopeptidase (TOP) is a peptidase that processes neuroendocrine peptides with roles in mood, metabolism, and immune responses, among other functions. TOP also hydrolyzes angiotensin I to angiotensin 1–7, which may be involved in the pathophysiology of COVID-19 infection. Although TOP is primarily cytosolic, it can also be associated with the cell plasma membrane or secreted to the extracellular space. Recent work indicates that membrane-associated TOP can be released with extracellular vesicles (EVs) to the extracellular space. Here we briefly summarize the enzyme’s classical function in extracellular processing of neuroendocrine peptides, as well as its more recently understood role in intracellular processing of various peptides that impact human diseases. Finally, we discuss new findings of EV-associated TOP in the extracellular space.
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11
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Iannetta AA, Rogers HT, Al-Mohanna T, O'Brien JN, Wommack AJ, Popescu SC, Hicks LM. Profiling thimet oligopeptidase-mediated proteolysis in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:336-350. [PMID: 33481299 DOI: 10.1111/tpj.15165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Protein homeostasis (proteostasis) is crucial for proper cellular function, including the production of peptides with biological functions through controlled proteolysis. Proteostasis has roles in maintenance of cellular functions and plant interactions with the environment under physiological conditions. Plant stress continues to reduce agricultural yields causing substantial economic losses; thus, it is critical to understand how plants perceive stress signals to elicit responses for survival. As previously shown in Arabidopsis thaliana, thimet oligopeptidases (TOPs) TOP1 (also referred to as organellar oligopeptidase) and TOP2 (also referred to as cytosolic oligopeptidase) are essential components in plant response to pathogens, but further characterization of TOPs and their peptide substrates is required to understand their contributions to stress perception and defense signaling. Herein, label-free peptidomics via liquid chromatography-tandem mass spectrometry was used to differentially quantify 1111 peptides, originating from 369 proteins, between the Arabidopsis Col-0 wild type and top1top2 knock-out mutant. This revealed 350 peptides as significantly more abundant in the mutant, representing accumulation of these potential TOP substrates. Ten direct substrates were validated using in vitro enzyme assays with recombinant TOPs and synthetic candidate peptides. These TOP substrates are derived from proteins involved in photosynthesis, glycolysis, protein folding, biogenesis, and antioxidant defense, implicating TOP involvement in processes aside from defense signaling. Sequence motif analysis revealed TOP cleavage preference for non-polar residues in the positions surrounding the cleavage site. Identification of these substrates provides a framework for TOP signaling networks, through which the interplay between proteolytic pathways and defense signaling can be further characterized.
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Affiliation(s)
- Anthony A Iannetta
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Holden T Rogers
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thualfeqar Al-Mohanna
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi, MS, USA
| | | | - Andrew J Wommack
- Department of Chemistry, High Point University, High Point, NC, USA
| | - Sorina C Popescu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi, MS, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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12
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Thimet Oligopeptidase Biochemical and Biological Significances: Past, Present, and Future Directions. Biomolecules 2020; 10:biom10091229. [PMID: 32847123 PMCID: PMC7565970 DOI: 10.3390/biom10091229] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/15/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022] Open
Abstract
Thimet oligopeptidase (EC 3.4.24.15; EP24.15, THOP1) is a metallopeptidase ubiquitously distributed in mammalian tissues. Beyond its previously well characterized role in major histocompatibility class I (MHC-I) antigen presentation, the recent characterization of the THOP1 C57BL6/N null mice (THOP1−/−) phenotype suggests new key functions for THOP1 in hyperlipidic diet-induced obesity, insulin resistance and non-alcoholic liver steatosis. Distinctive levels of specific intracellular peptides (InPeps), genes and microRNAs were observed when comparing wild type C57BL6/N to THOP1−/− fed either standard or hyperlipidic diets. A possible novel mechanism of action was suggested for InPeps processed by THOP1, which could be modulating protein-protein interactions and microRNA processing, thus affecting the phenotype. Together, research into the biochemical and biomedical significance of THOP1 suggests that degradation by the proteasome is a step in the processing of various proteins, not merely for ending their existence. This allows many functional peptides to be generated by proteasomal degradation in order to, for example, control mRNA translation and the formation of protein complexes.
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13
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The Relevance of Thimet Oligopeptidase in the Regulation of Energy Metabolism and Diet-Induced Obesity. Biomolecules 2020; 10:biom10020321. [PMID: 32079362 PMCID: PMC7072564 DOI: 10.3390/biom10020321] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/11/2022] Open
Abstract
Thimet oligopeptidase (EC 3.4.24.15; EP24.15; THOP1) is a potential therapeutic target, as it plays key biological functions in processing biologically functional peptides. The structural conformation of THOP1 provides a unique restriction regarding substrate size, in that it only hydrolyzes peptides (optimally, those ranging from eight to 12 amino acids) and not proteins. The proteasome activity of hydrolyzing proteins releases a large number of intracellular peptides, providing THOP1 substrates within cells. The present study aimed to investigate the possible function of THOP1 in the development of diet-induced obesity (DIO) and insulin resistance by utilizing a murine model of hyperlipidic DIO with both C57BL6 wild-type (WT) and THOP1 null (THOP1−/−) mice. After 24 weeks of being fed a hyperlipidic diet (HD), THOP1−/− and WT mice ingested similar chow and calories; however, the THOP1−/− mice gained 75% less body weight and showed neither insulin resistance nor non-alcoholic fatty liver steatosis when compared to WT mice. THOP1−/− mice had increased adrenergic-stimulated adipose tissue lipolysis as well as a balanced level of expression of genes and microRNAs associated with energy metabolism, adipogenesis, or inflammation. Altogether, these differences converge to a healthy phenotype of THOP1−/− fed a HD. The molecular mechanism that links THOP1 to energy metabolism is suggested herein to involve intracellular peptides, of which the relative levels were identified to change in the adipose tissue of WT and THOP1−/− mice. Intracellular peptides were observed by molecular modeling to interact with both pre-miR-143 and pre-miR-222, suggesting a possible novel regulatory mechanism for gene expression. Therefore, we successfully demonstrated the previously anticipated relevance of THOP1 in energy metabolism regulation. It was suggested that intracellular peptides were responsible for mediating the phenotypic differences that are described herein by a yet unknown mechanism of action.
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14
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Kemps PG, Zondag TC, Steenwijk EC, Andriessen Q, Borst J, Vloemans S, Roelen DL, Voortman LM, Verdijk RM, van Noesel CJM, Cleven AHG, Hawkins C, Lang V, de Ru AH, Janssen GMC, Haasnoot GW, Franken KLMC, van Eijk R, Solleveld-Westerink N, van Wezel T, Egeler RM, Beishuizen A, van Laar JAM, Abla O, van den Bos C, van Veelen PA, van Halteren AGS. Apparent Lack of BRAF V600E Derived HLA Class I Presented Neoantigens Hampers Neoplastic Cell Targeting by CD8 + T Cells in Langerhans Cell Histiocytosis. Front Immunol 2020; 10:3045. [PMID: 31998317 PMCID: PMC6967030 DOI: 10.3389/fimmu.2019.03045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022] Open
Abstract
Langerhans Cell Histiocytosis (LCH) is a neoplastic disorder of hematopoietic origin characterized by inflammatory lesions containing clonal histiocytes (LCH-cells) intermixed with various immune cells, including T cells. In 50-60% of LCH-patients, the somatic BRAF V600E driver mutation, which is common in many cancers, is detected in these LCH-cells in an otherwise quiet genomic landscape. Non-synonymous mutations like BRAF V600E can be a source of neoantigens capable of eliciting effective antitumor CD8+ T cell responses. This requires neopeptides to be stably presented by Human Leukocyte Antigen (HLA) class I molecules and sufficient numbers of CD8+ T cells at tumor sites. Here, we demonstrate substantial heterogeneity in CD8+ T cell density in n = 101 LCH-lesions, with BRAF V600E mutated lesions displaying significantly lower CD8+ T cell:CD1a+ LCH-cell ratios (p = 0.01) than BRAF wildtype lesions. Because LCH-lesional CD8+ T cell density had no significant impact on event-free survival, we investigated whether the intracellularly expressed BRAF V600E protein is degraded into neopeptides that are naturally processed and presented by cell surface HLA class I molecules. Epitope prediction tools revealed a single HLA class I binding BRAF V600E derived neopeptide (KIGDFGLATEK), which indeed displayed strong to intermediate binding capacity to HLA-A*03:01 and HLA-A*11:01 in an in vitro peptide-HLA binding assay. Mass spectrometry-based targeted peptidomics was used to investigate the presence of this neopeptide in HLA class I presented peptides isolated from several BRAF V600E expressing cell lines with various HLA genotypes. While the HLA-A*02:01 binding BRAF wildtype peptide KIGDFGLATV was traced in peptides isolated from all five cell lines expressing this HLA subtype, KIGDFGLATEK was not detected in the HLA class I peptidomes of two distinct BRAF V600E transduced cell lines with confirmed expression of HLA-A*03:01 or HLA-A*11:01. These data indicate that the in silico predicted HLA class I binding and proteasome-generated neopeptides derived from the BRAF V600E protein are not presented by HLA class I molecules. Given that the BRAF V600E mutation is highly prevalent in chemotherapy refractory LCH-patients who may qualify for immunotherapy, this study therefore questions the efficacy of immune checkpoint inhibitor therapy in LCH.
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Affiliation(s)
- Paul G Kemps
- Immunology Laboratory Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Timo C Zondag
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Eline C Steenwijk
- Immunology Laboratory Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Quirine Andriessen
- Immunology Laboratory Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Jelske Borst
- Immunology Laboratory Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Sandra Vloemans
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Dave L Roelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Robert M Verdijk
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Carel J M van Noesel
- Department of Pathology, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Arjen H G Cleven
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | - Cynthia Hawkins
- Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Veronica Lang
- Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Geert W Haasnoot
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Kees L M C Franken
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | - R Maarten Egeler
- Immunology Laboratory Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands.,Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Auke Beishuizen
- Department of Pediatric Oncology, Sophia Children's Hospital, Erasmus University Medical Center, Rotterdam, Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Jan A M van Laar
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Oussama Abla
- Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Cor van den Bos
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Department of Pediatric Oncology, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Astrid G S van Halteren
- Immunology Laboratory Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
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15
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Covarrubias-Zambrano O, Yu J, Bossmann SH. Nano-Inspired Technologies for Peptide Delivery. Curr Protein Pept Sci 2019; 21:379-400. [PMID: 31793426 DOI: 10.2174/1389203720666191202112429] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/26/2019] [Accepted: 10/02/2019] [Indexed: 12/15/2022]
Abstract
Nano-inspired technologies offer unique opportunities to treat numerous diseases by using therapeutic peptides. Therapeutic peptides have attractive pharmacological profiles and can be manufactured at relatively low costs. The major advantages of using a nanodelivery approach comprises significantly lower required dosages compared to systemic delivery, and thus reduced toxicity and immunogenicity. The combination of therapeutic peptides with delivery peptides and nanoparticles or small molecule drugs offers systemic treatment approaches, instead of aiming for single biological targets or pathways. This review article discusses exemplary state-of-the-art nanosized delivery systems for therapeutic peptides and antibodies, as well as their biochemical and biophysical foundations and emphasizes still remaining challenges. The competition between using different nanoplatforms, such as liposome-, hydrogel-, polymer-, silica nanosphere-, or nanosponge-based delivery systems is still "on" and no clear frontrunner has emerged to date.
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Affiliation(s)
| | - Jing Yu
- Department of Chemistry, Kansas State University, 419 CBC Building, Manhattan, KS 66506-0401, United States.,Johns Hopkins University, Department of Radiology, Baltimore, MD, United States
| | - Stefan H Bossmann
- Department of Chemistry, Kansas State University, 419 CBC Building, Manhattan, KS 66506-0401, United States
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16
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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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17
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Thimet Oligopeptidase (EC 3.4.24.15) Key Functions Suggested by Knockout Mice Phenotype Characterization. Biomolecules 2019; 9:biom9080382. [PMID: 31431000 PMCID: PMC6722639 DOI: 10.3390/biom9080382] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/29/2019] [Accepted: 07/29/2019] [Indexed: 12/14/2022] Open
Abstract
Thimet oligopeptidase (THOP1) is thought to be involved in neuropeptide metabolism, antigen presentation, neurodegeneration, and cancer. Herein, the generation of THOP1 C57BL/6 knockout mice (THOP1−/−) is described showing that they are viable, have estrus cycle, fertility, and a number of puppies per litter similar to C57BL/6 wild type mice (WT). In specific brain regions, THOP1-/- exhibit altered mRNA expression of proteasome beta5, serotonin 5HT2a receptor and dopamine D2 receptor, but not of neurolysin (NLN). Peptidomic analysis identifies differences in intracellular peptide ratios between THOP1-/- and WT mice, which may affect normal cellular functioning. In an experimental model of multiple sclerosis THOP1-/- mice present worse clinical behavior scores compared to WT mice, corroborating its possible involvement in neurodegenerative diseases. THOP1-/- mice also exhibit better survival and improved behavior in a sepsis model, but also a greater peripheral pain sensitivity measured in the hot plate test after bradykinin administration in the paw. THOP1-/- mice show depressive-like behavior, as well as attention and memory retention deficits. Altogether, these results reveal a role of THOP1 on specific behaviors, immune-stimulated neurodegeneration, and infection-induced inflammation.
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18
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Leclerc M, Mezquita L, Guillebot De Nerville G, Tihy I, Malenica I, Chouaib S, Mami-Chouaib F. Recent Advances in Lung Cancer Immunotherapy: Input of T-Cell Epitopes Associated With Impaired Peptide Processing. Front Immunol 2019; 10:1505. [PMID: 31333652 PMCID: PMC6616108 DOI: 10.3389/fimmu.2019.01505] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/17/2019] [Indexed: 12/26/2022] Open
Abstract
Recent advances in lung cancer treatment are emerging from new immunotherapies that target T-cell inhibitory receptors, such as programmed cell death-1 (PD-1). However, responses to anti-PD-1 antibodies as single agents are observed in fewer than 20% of non-small-cell lung cancer (NSCLC) patients, and immune mechanisms involved in the response to these therapeutic interventions remain poorly elucidated. Accumulating evidence indicates that effective anti-tumor immunity is associated with the presence of T cells directed toward cancer neoepitopes, a class of major histocompatibility complex (MHC)-bound peptides that arise from tumor-specific mutations. Nevertheless, tumors frequently use multiple pathways to escape T-cell recognition and destruction. In this regard, primary and acquired resistance to immune checkpoint blockade (ICB) therapy was associated with alterations in genes relevant to antigen presentation by MHC-class I/beta-2-microglobulin (MHC-I/β2m) complexes to CD8 T lymphocytes. Among additional known mechanisms involved in tumor resistance to CD8 T-cell immunity, alterations in transporter associated with antigen processing (TAP) play a major role by inducing a sharp decrease in surface expression of MHC-I/β2m-peptide complexes, enabling malignant cells to evade cytotoxic T lymphocyte (CTL)-mediated killing. Therefore, development of novel immunotherapies based on tumor neoantigens, that are selectively presented by cancer cells carrying defects in antigen processing and presentation, and that are capable of inducing destruction of such transformed cells, is a major challenge in translational research for application in treatment of lung cancer. In this context, we previously identified a non-mutant tumor neoepitope, ppCT16−25, derived from the preprocalcitonin (ppCT) leader sequence and processed independently of proteasomes/TAP by a mechanism involving signal peptidase (SP) and signal peptide peptidase (SPP). We also provided in vitro and in vivo proof of the concept of active immunotherapy based on ppCT-derived peptides capable of controlling growth of immune-escaped tumors expressing low levels of MHC-I molecules. Thus, non-mutant and mutant neoepitopes are promising T-cell targets for therapeutic cancer vaccines in combination with ICB. In this review, we summarize current treatments for lung cancer and discuss the promises that conserved neoantigens offer for more effective immunotherapies targeting immune-escaped tumor variants.
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Affiliation(s)
- Marine Leclerc
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, PSL, Faculté de Médecine - Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Laura Mezquita
- Department of Medical Oncology, Gustave Roussy Cancer Campus, Institut d'Oncologie Thoracique, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Guillaume Guillebot De Nerville
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, PSL, Faculté de Médecine - Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Isabelle Tihy
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, PSL, Faculté de Médecine - Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Ines Malenica
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, PSL, Faculté de Médecine - Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Salem Chouaib
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, PSL, Faculté de Médecine - Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Fathia Mami-Chouaib
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, PSL, Faculté de Médecine - Université Paris-Sud, Université Paris-Saclay, Villejuif, France
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19
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Basler M, Groettrup M. Testing the Impact of Protease Inhibitors in Antigen Presentation Assays. Methods Mol Biol 2019; 1988:59-69. [PMID: 31147932 DOI: 10.1007/978-1-4939-9450-2_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The major histocompatibility complex (MHC) class I restricted pathway of antigen processing allows the presentation of intracellular antigens to cytotoxic T lymphocytes. The proteasome is the main protease in the cytoplasm and the nucleus, which is responsible for the generation of most peptide ligands of MHC-I molecules. Peptides produced by the proteasome can be further trimmed or destroyed by numerous cytosolic or endoplasmic reticulum (ER) luminal proteases. Small molecule inhibitors are useful tools for probing the role of proteases in MHC class I antigen processing. Here, we describe different methods to test the impact of protease inhibitors in antigen presentation assays.
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Affiliation(s)
- Michael Basler
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland. .,Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Marcus Groettrup
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland.,Division of Immunology, Department of Biology, University of Konstanz, Konstanz, Germany
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20
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Tibúrcio R, Nunes S, Nunes I, Rosa Ampuero M, Silva IB, Lima R, Machado Tavares N, Brodskyn C. Molecular Aspects of Dendritic Cell Activation in Leishmaniasis: An Immunobiological View. Front Immunol 2019; 10:227. [PMID: 30873156 PMCID: PMC6401646 DOI: 10.3389/fimmu.2019.00227] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/28/2019] [Indexed: 12/11/2022] Open
Abstract
Dendritic cells (DC) are a diverse group of leukocytes responsible for bridging innate and adaptive immunity. Despite their functional versatility, DCs exist primarily in two basic functional states: immature and mature. A large body of evidence suggests that upon interactions with pathogens, DCs undergo intricate cellular processes that culminate in their activation, which is paramount to the orchestration of effective immune responses against Leishmania parasites. Herein we offer a concise review of the emerging hallmarks of DCs activation in leishmaniasis as well as a comprehensive discussion of the following underlying molecular events: DC-Leishmania interaction, antigen uptake, costimulatory molecule expression, parasite ability to affect DC migration, antigen presentation, metabolic reprogramming, and epigenetic alterations.
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Affiliation(s)
- Rafael Tibúrcio
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Sara Nunes
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Ivanéia Nunes
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Mariana Rosa Ampuero
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Icaro Bonyek Silva
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Reinan Lima
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Natalia Machado Tavares
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil.,Instituto Nacional de Ciência e Tecnologia (INCT) iii Instituto de Investigação em Imunologia, São Paulo, Brazil
| | - Cláudia Brodskyn
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil.,Instituto Nacional de Ciência e Tecnologia (INCT) iii Instituto de Investigação em Imunologia, São Paulo, Brazil
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21
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Boucau J, Le Gall S. Antigen processing and presentation in HIV infection. Mol Immunol 2018; 113:67-74. [PMID: 29636181 DOI: 10.1016/j.molimm.2018.03.027] [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] [Received: 09/11/2017] [Revised: 01/09/2018] [Accepted: 03/29/2018] [Indexed: 12/11/2022]
Abstract
The presentation of virus-derived peptides by MHC molecules constitutes the earliest signals for immune recognition by T cells. In HIV infection, immune responses elicited during infection do not enable to clear infection and correlates of immune protection are not well defined. Here we review features of antigen processing and presentation specific to HIV, analyze how HIV has adapted to the antigen processing machinery and discuss how advances in biochemical and computational protein degradation analyses and in immunopeptidome definition may help identify targets for efficient immune clearance and vaccine immunogen design.
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Affiliation(s)
- Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, United States
| | - Sylvie Le Gall
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, United States.
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22
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Durgeau A, Virk Y, Corgnac S, Mami-Chouaib F. Recent Advances in Targeting CD8 T-Cell Immunity for More Effective Cancer Immunotherapy. Front Immunol 2018; 9:14. [PMID: 29403496 PMCID: PMC5786548 DOI: 10.3389/fimmu.2018.00014] [Citation(s) in RCA: 311] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/04/2018] [Indexed: 12/18/2022] Open
Abstract
Recent advances in cancer treatment have emerged from new immunotherapies targeting T-cell inhibitory receptors, including cytotoxic T-lymphocyte associated antigen (CTLA)-4 and programmed cell death (PD)-1. In this context, anti-CTLA-4 and anti-PD-1 monoclonal antibodies have demonstrated survival benefits in numerous cancers, including melanoma and non-small-cell lung carcinoma. PD-1-expressing CD8+ T lymphocytes appear to play a major role in the response to these immune checkpoint inhibitors (ICI). Cytotoxic T lymphocytes (CTL) eliminate malignant cells through recognition by the T-cell receptor (TCR) of specific antigenic peptides presented on the surface of cancer cells by major histocompatibility complex class I/beta-2-microglobulin complexes, and through killing of target cells, mainly by releasing the content of secretory lysosomes containing perforin and granzyme B. T-cell adhesion molecules and, in particular, lymphocyte-function-associated antigen-1 and CD103 integrins, and their cognate ligands, respectively, intercellular adhesion molecule 1 and E-cadherin, on target cells, are involved in strengthening the interaction between CTL and tumor cells. Tumor-specific CTL have been isolated from tumor-infiltrating lymphocytes and peripheral blood lymphocytes (PBL) of patients with varied cancers. TCRβ-chain gene usage indicated that CTL identified in vitro selectively expanded in vivo at the tumor site compared to autologous PBL. Moreover, functional studies indicated that these CTL mediate human leukocyte antigen class I-restricted cytotoxic activity toward autologous tumor cells. Several of them recognize truly tumor-specific antigens encoded by mutated genes, also known as neoantigens, which likely play a key role in antitumor CD8 T-cell immunity. Accordingly, it has been shown that the presence of T lymphocytes directed toward tumor neoantigens is associated with patient response to immunotherapies, including ICI, adoptive cell transfer, and dendritic cell-based vaccines. These tumor-specific mutation-derived antigens open up new perspectives for development of effective second-generation therapeutic cancer vaccines.
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Affiliation(s)
- Aurélie Durgeau
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, Fac. de Médecine - Univ. Paris-Sud, Université Paris-Saclay, Villejuif, France.,ElyssaMed, Paris Biotech Santé, Paris, France
| | - Yasemin Virk
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, Fac. de Médecine - Univ. Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Stéphanie Corgnac
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, Fac. de Médecine - Univ. Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Fathia Mami-Chouaib
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, Fac. de Médecine - Univ. Paris-Sud, Université Paris-Saclay, Villejuif, France
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23
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Chang AY, Dao T, Gejman RS, Jarvis CA, Scott A, Dubrovsky L, Mathias MD, Korontsvit T, Zakhaleva V, Curcio M, Hendrickson RC, Liu C, Scheinberg DA. A therapeutic T cell receptor mimic antibody targets tumor-associated PRAME peptide/HLA-I antigens. J Clin Invest 2017; 127:2705-2718. [PMID: 28628042 PMCID: PMC5490756 DOI: 10.1172/jci92335] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/27/2017] [Indexed: 12/18/2022] Open
Abstract
Preferentially expressed antigen in melanoma (PRAME) is a cancer-testis antigen that is expressed in many cancers and leukemias. In healthy tissue, PRAME expression is limited to the testes and ovaries, making it a highly attractive cancer target. PRAME is an intracellular protein that cannot currently be drugged. After proteasomal processing, the PRAME300-309 peptide ALYVDSLFFL (ALY) is presented in the context of human leukocyte antigen HLA-A*02:01 molecules for recognition by the T cell receptor (TCR) of cytotoxic T cells. Here, we have described Pr20, a TCR mimic (TCRm) human IgG1 antibody that recognizes the cell-surface ALY peptide/HLA-A2 complex. Pr20 is an immunological tool and potential therapeutic agent. Pr20 bound to PRAME+HLA-A2+ cancers. An afucosylated Fc form (Pr20M) directed antibody-dependent cellular cytotoxicity against PRAME+HLA-A2+ leukemia cells and was therapeutically effective against mouse xenograft models of human leukemia. In some tumors, Pr20 binding markedly increased upon IFN-γ treatment, mediated by induction of the immunoproteasome catalytic subunit β5i. The immunoproteasome reduced internal destructive cleavages within the ALY epitope compared with the constitutive proteasome. The data provide rationale for developing TCRm antibodies as therapeutic agents for cancer, offer mechanistic insight on proteasomal regulation of tumor-associated peptide/HLA antigen complexes, and yield possible therapeutic solutions to target antigens with ultra-low surface presentation.
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Affiliation(s)
- Aaron Y. Chang
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
- Biochemistry Cell and Molecular Biology Program
| | - Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Ron S. Gejman
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
- Pharmacology Program, and
| | - Casey A. Jarvis
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Andrew Scott
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, Cornell University, New York, New York, USA
| | - Leonid Dubrovsky
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Melissa D. Mathias
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Tatyana Korontsvit
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Victoriya Zakhaleva
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Michael Curcio
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Ronald C. Hendrickson
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Cheng Liu
- Eureka Therapeutics, Emeryville, California, USA
| | - David A. Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
- Pharmacology Program, and
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24
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Icimoto MY, Ferreira JC, Yokomizo CH, Bim LV, Marem A, Gilio JM, Oliveira V, Nantes IL. Redox modulation of thimet oligopeptidase activity by hydrogen peroxide. FEBS Open Bio 2017; 7:1037-1050. [PMID: 28680816 PMCID: PMC5494303 DOI: 10.1002/2211-5463.12245] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 05/15/2017] [Indexed: 11/09/2022] Open
Abstract
Thimet oligopeptidase (EC 3.4.24.15, TOP) is a cytosolic mammalian zinc protease that can process a diversity of bioactive peptides. TOP has been pointed out as one of the main postproteasomal enzymes that process peptide antigens in the MHC class I presentation route. In the present study, we describe a fine regulation of TOP activity by hydrogen peroxide (H2O2). Cells from a human embryonic kidney cell line (HEK293) underwent an ischemia/reoxygenation-like condition known to increase H2O2 production. Immediately after reoxygenation, HEK293 cells exhibited a 32% increase in TOP activity, but no TOP activity was observed 2 h after reoxygenation. In another model, recombinant rat TOP (rTOP) was challenged by H2O2 produced by rat liver mitoplasts (RLMt) alone, and in combination with antimycin A, succinate, and antimycin A plus succinate. In these conditions, rTOP activity increased 17, 30, 32 and 38%, respectively. Determination of H2O2 concentration generated in reoxygenated cells and mitoplasts suggested a possible modulation of rTOP activity dependent on the concentration of H2O2. The measure of pure rTOP activity as a function of H2O2 concentration corroborated this hypothesis. The data fitted to an asymmetrical bell-shaped curve in which the optimal activating H2O2 concentration was 1.2 nM, and the maximal inhibition (75% about the control) was 1 μm. Contrary to the oxidation produced by aging associated with enzyme oligomerization and inhibition, H2O2 oxidation produced sulfenic acid and maintained rTOP in the monomeric form. Consistent with the involvement of rTOP in a signaling redox cascade, the H2O2-oxidized rTOP reacted with dimeric thioredoxin-1 (TRx-1) and remained covalently bound to one subunit of TRx-1.
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Affiliation(s)
| | - Juliana C Ferreira
- Laboratório de Nanoestruturas para Biologia e Materiais Avançados Centro de Ciências Naturais e Humanas Universidade Federal do ABC Santo André Brazil.,Present address: Structural Biology and Biophysical Chemistry Lab New York University Abu Dhabi Saadiyat Marina District, Abu Dhabi United Arab Emirates
| | - César H Yokomizo
- Laboratório de Nanoestruturas para Biologia e Materiais Avançados Centro de Ciências Naturais e Humanas Universidade Federal do ABC Santo André Brazil
| | - Larissa V Bim
- Departamento de Biofísica Universidade Federal de São Paulo Brazil
| | - Alyne Marem
- Departamento de Biofísica Universidade Federal de São Paulo Brazil
| | - Joyce M Gilio
- Departamento de Biofísica Universidade Federal de São Paulo Brazil.,Present address: Departamento de Neurologia Centro de Degeneração Universidade de São Paulo - Escola de Medicina São Paulo SP Brazil
| | - Vitor Oliveira
- Departamento de Biofísica Universidade Federal de São Paulo Brazil
| | - Iseli L Nantes
- Laboratório de Nanoestruturas para Biologia e Materiais Avançados Centro de Ciências Naturais e Humanas Universidade Federal do ABC Santo André Brazil
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25
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Kasai Y, Toriguchi K, Hatano E, Nishi K, Ohno M, Yoh T, Fukuyama K, Nishio T, Okuno M, Iwaisako K, Seo S, Taura K, Kurokawa M, Kunichika M, Uemoto S, Nishi E. Nardilysin promotes hepatocellular carcinoma through activation of signal transducer and activator of transcription 3. Cancer Sci 2017; 108:910-917. [PMID: 28207963 PMCID: PMC5448622 DOI: 10.1111/cas.13204] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/06/2017] [Accepted: 02/12/2017] [Indexed: 12/13/2022] Open
Abstract
Nardilysin (NRDC) is a metalloendopeptidase of the M16 family. We previously showed that NRDC activates inflammatory cytokine signaling, including interleukin‐6‐signal transducer and activator of transcription 3 (STAT3) signaling. NRDC has been implicated in the promotion of breast, gastric and esophageal cancer, as well as the development of liver fibrosis. In this study, we investigated the role of NRDC in the promotion of hepatocellular carcinoma (HCC), both clinically and experimentally. We found that NRDC expression was upregulated threefold in HCC tissue compared to the adjacent non‐tumor liver tissue, which was confirmed by immunohistochemistry and western blotting. We also found that high serum NRDC was associated with large tumor size (>3 cm, P = 0.016) and poor prognosis after hepatectomy (median survival time 32.0 vs 73.9 months, P = 0.003) in patients with hepatitis C (n = 120). Diethylnitrosamine‐induced hepatocarcinogenesis was suppressed in heterozygous NRDC‐deficient mice compared to their wild‐type littermates. Gene silencing of NRDC with miRNA diminished the growth of Huh‐7 and Hep3B spheroids in vitro. Notably, phosphorylation of STAT3 was decreased in NRDC‐depleted Huh‐7 spheroids compared to control spheroids. The effect of a STAT3 inhibitor (S3I‐201) on the growth of Huh‐7 spheroids was reduced in NRDC‐depleted cells relative to controls. Our results show that NRDC is a promising prognostic marker for HCC in patients with hepatitis C, and that NRDC promotes tumor growth through activation of STAT3.
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Affiliation(s)
- Yosuke Kasai
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kan Toriguchi
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Etsuro Hatano
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Surgery, Hyogo College of Medicine, Nishinomiya, Japan
| | - Kiyoto Nishi
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mikiko Ohno
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoaki Yoh
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keita Fukuyama
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takahiro Nishio
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masayuki Okuno
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keiko Iwaisako
- Department of Target Therapy and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoru Seo
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kojiro Taura
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | | | - Shinji Uemoto
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Eiichiro Nishi
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Pharmacology, Shiga University of Medical Science, Otsu, Japan
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26
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Kmiec B, Teixeira PF, Murcha MW, Glaser E. Divergent evolution of the M3A family of metallopeptidases in plants. PHYSIOLOGIA PLANTARUM 2016; 157:380-388. [PMID: 27100569 DOI: 10.1111/ppl.12457] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/06/2016] [Accepted: 04/18/2016] [Indexed: 06/05/2023]
Abstract
Plants, as stationary organisms, have developed mechanisms allowing them efficient resource reallocation and a response to changing environmental conditions. One of these mechanisms is proteome remodeling via a broad peptidase network present in various cellular compartments including mitochondria and chloroplasts. The genome of the model plant Arabidopsis thaliana encodes as many as 616 putative peptidase-coding genes organized in 55 peptidase families. In this study, we describe the M3A family of peptidases, which comprises four members: mitochondrial and chloroplastic oligopeptidase (OOP), cytosolic oligopeptidase (CyOP), mitochondrial octapeptidyl aminopeptidase 1 (Oct1) and plant-specific protein of M3 family (PSPM3) of unknown function. We have analyzed the evolutionary conservation of M3A peptidases across plant species and the functional specialization of the three distinct subfamilies. We found that the subfamily-containing OOP and CyOP-like peptidases, responsible for oligopeptide degradation in the endosymbiotic organelles (OOP) or in the cytosol (CyOP), are highly conserved in all kingdoms of life. The Oct1-like peptidase subfamily involved in pre-protein maturation in mitochondria is conserved in all eukaryotes, whereas the PSPM3-like protein subfamily is strictly conserved in higher plants only and is of unknown function. Specific characteristics within PSPM3 sequences, i.e. occurrence of a N-terminal transmembrane domain and amino acid changes in distal substrate-binding motif, distinguish PSPM3 proteins from other members of M3A family. We performed peptidase activity measurements to analyze the role of substrate-binding residues in the different Arabidopsis M3A paralogs.
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Affiliation(s)
- Beata Kmiec
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Pedro F Teixeira
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Monika W Murcha
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia, Australia
| | - Elzbieta Glaser
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
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27
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Radichev IA, Maneva-Radicheva LV, Amatya C, Salehi M, Parker C, Ellefson J, Burn P, Savinov AY. Loss of Peripheral Protection in Pancreatic Islets by Proteolysis-Driven Impairment of VTCN1 (B7-H4) Presentation Is Associated with the Development of Autoimmune Diabetes. THE JOURNAL OF IMMUNOLOGY 2016; 196:1495-506. [PMID: 26773144 DOI: 10.4049/jimmunol.1403251] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 12/05/2015] [Indexed: 12/28/2022]
Abstract
Ag-specific activation of T cells is an essential process in the control of effector immune responses. Defects in T cell activation, particularly in the costimulation step, have been associated with many autoimmune conditions, including type 1 diabetes (T1D). Recently, we demonstrated that the phenotype of impaired negative costimulation, due to reduced levels of V-set domain-containing T cell activation inhibitor 1 (VTCN1) protein on APCs, is shared between diabetes-susceptible NOD mice and human T1D patients. In this study, we show that a similar process takes place in the target organ, as both α and β cells within pancreatic islets gradually lose their VTCN1 protein during autoimmune diabetes development despite upregulation of the VTCN1 gene. Diminishment of functional islet cells' VTCN1 is caused by the active proteolysis by metalloproteinase N-arginine dibasic convertase 1 (NRD1) and leads to the significant induction of proliferation and cytokine production by diabetogenic T cells. Inhibition of NRD1 activity, alternatively, stabilizes VTCN1 and dulls the anti-islet T cell responses. Therefore, we suggest a general endogenous mechanism of defective VTCN1 negative costimulation, which affects both lymphoid and peripheral target tissues during T1D progression and results in aggressive anti-islet T cell responses. This mechanism is tied to upregulation of NRD1 expression and likely acts in two synergistic proteolytic modes: cell-intrinsic intracellular and cell-extrinsic systemic. Our results highlight an importance of VTCN1 stabilization on cell surfaces for the restoration of altered balance of immune control during T1D.
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Affiliation(s)
- Ilian A Radichev
- The Sanford Project, Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104; and
| | - Lilia V Maneva-Radicheva
- The Sanford Project, Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104; and
| | - Christina Amatya
- The Sanford Project, Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104; and
| | - Maryam Salehi
- The Sanford Project, Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104; and
| | - Camille Parker
- The Sanford Project, Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104; and
| | - Jacob Ellefson
- The Sanford Project, Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104; and
| | - Paul Burn
- The Sanford Project, Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104; and
| | - Alexei Y Savinov
- The Sanford Project, Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104; and Department of Pediatrics, University of South Dakota School of Medicine, Sioux Falls, SD 57105
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28
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Proteolytic enzymes involved in MHC class I antigen processing: A guerrilla army that partners with the proteasome. Mol Immunol 2015; 68:72-6. [DOI: 10.1016/j.molimm.2015.04.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 04/06/2015] [Accepted: 04/13/2015] [Indexed: 10/23/2022]
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29
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Lopez J, Bittame A, Massera C, Vasseur V, Effantin G, Valat A, Buaillon C, Allart S, Fox BA, Rommereim LM, Bzik DJ, Schoehn G, Weissenhorn W, Dubremetz JF, Gagnon J, Mercier C, Cesbron-Delauw MF, Blanchard N. Intravacuolar Membranes Regulate CD8 T Cell Recognition of Membrane-Bound Toxoplasma gondii Protective Antigen. Cell Rep 2015; 13:2273-86. [PMID: 26628378 DOI: 10.1016/j.celrep.2015.11.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 08/11/2015] [Accepted: 10/30/2015] [Indexed: 11/20/2022] Open
Abstract
Apicomplexa parasites such as Toxoplasma gondii target effectors to and across the boundary of their parasitophorous vacuole (PV), resulting in host cell subversion and potential presentation by MHC class I molecules for CD8 T cell recognition. The host-parasite interface comprises the PV limiting membrane and a highly curved, membranous intravacuolar network (IVN) of uncertain function. Here, using a cell-free minimal system, we dissect how membrane tubules are shaped by the parasite effectors GRA2 and GRA6. We show that membrane association regulates access of the GRA6 protective antigen to the MHC I pathway in infected cells. Although insertion of GRA6 in the PV membrane is key for immunogenicity, association of GRA6 with the IVN limits presentation and curtails GRA6-specific CD8 responses in mice. Thus, membrane deformations of the PV regulate access of antigens to the MHC class I pathway, and the IVN may play a role in immune modulation.
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Affiliation(s)
- Jodie Lopez
- INSERM, U1043, Toulouse 31300, France; CNRS, UMR 5282, Toulouse 31300, France; Centre de Physiopathologie de Toulouse Purpan (CPTP), Université de Toulouse, UPS, Toulouse 31300, France
| | - Amina Bittame
- CNRS, UMR 5163, Grenoble 38000, France; Laboratoire Adaptation et Pathogénie des Microorganismes (LAPM), Université Grenoble Alpes, Grenoble 38000, France
| | - Céline Massera
- CNRS, UMR 5163, Grenoble 38000, France; Laboratoire Adaptation et Pathogénie des Microorganismes (LAPM), Université Grenoble Alpes, Grenoble 38000, France
| | - Virginie Vasseur
- INSERM, U1043, Toulouse 31300, France; CNRS, UMR 5282, Toulouse 31300, France; Centre de Physiopathologie de Toulouse Purpan (CPTP), Université de Toulouse, UPS, Toulouse 31300, France
| | - Grégory Effantin
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, Grenoble 38044, France; CNRS, IBS, Grenoble 38044, France; CEA, IBS, Grenoble 38044, France; CNRS, Unit for Virus Host-Cell Interactions (UVHCI), Grenoble 38042, France
| | - Anne Valat
- CNRS, UMR 5163, Grenoble 38000, France; Laboratoire Adaptation et Pathogénie des Microorganismes (LAPM), Université Grenoble Alpes, Grenoble 38000, France
| | - Célia Buaillon
- INSERM, U1043, Toulouse 31300, France; CNRS, UMR 5282, Toulouse 31300, France; Centre de Physiopathologie de Toulouse Purpan (CPTP), Université de Toulouse, UPS, Toulouse 31300, France
| | - Sophie Allart
- INSERM, U1043, Toulouse 31300, France; CNRS, UMR 5282, Toulouse 31300, France; Centre de Physiopathologie de Toulouse Purpan (CPTP), Université de Toulouse, UPS, Toulouse 31300, France
| | - Barbara A Fox
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Leah M Rommereim
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - David J Bzik
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Guy Schoehn
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, Grenoble 38044, France; CNRS, IBS, Grenoble 38044, France; CEA, IBS, Grenoble 38044, France; CNRS, Unit for Virus Host-Cell Interactions (UVHCI), Grenoble 38042, France
| | - Winfried Weissenhorn
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, Grenoble 38044, France; CNRS, IBS, Grenoble 38044, France; CEA, IBS, Grenoble 38044, France; CNRS, Unit for Virus Host-Cell Interactions (UVHCI), Grenoble 38042, France
| | | | - Jean Gagnon
- CNRS, UMR 5163, Grenoble 38000, France; Laboratoire Adaptation et Pathogénie des Microorganismes (LAPM), Université Grenoble Alpes, Grenoble 38000, France
| | - Corinne Mercier
- CNRS, UMR 5163, Grenoble 38000, France; Laboratoire Adaptation et Pathogénie des Microorganismes (LAPM), Université Grenoble Alpes, Grenoble 38000, France
| | - Marie-France Cesbron-Delauw
- CNRS, UMR 5163, Grenoble 38000, France; Laboratoire Adaptation et Pathogénie des Microorganismes (LAPM), Université Grenoble Alpes, Grenoble 38000, France
| | - Nicolas Blanchard
- INSERM, U1043, Toulouse 31300, France; CNRS, UMR 5282, Toulouse 31300, France; Centre de Physiopathologie de Toulouse Purpan (CPTP), Université de Toulouse, UPS, Toulouse 31300, France.
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Critical roles of nardilysin in the maintenance of body temperature homoeostasis. Nat Commun 2015; 5:3224. [PMID: 24492630 PMCID: PMC3926010 DOI: 10.1038/ncomms4224] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 01/09/2014] [Indexed: 01/15/2023] Open
Abstract
Body temperature homoeostasis in mammals is governed centrally through the regulation of shivering and non-shivering thermogenesis and cutaneous vasomotion. Non-shivering thermogenesis in brown adipose tissue (BAT) is mediated by sympathetic activation, followed by PGC-1α induction, which drives UCP1. Here we identify nardilysin (Nrd1 and NRDc) as a critical regulator of body temperature homoeostasis. Nrd1−/− mice show increased energy expenditure owing to enhanced BAT thermogenesis and hyperactivity. Despite these findings, Nrd1−/− mice show hypothermia and cold intolerance that are attributed to the lowered set point of body temperature, poor insulation and impaired cold-induced thermogenesis. Induction of β3-adrenergic receptor, PGC-1α and UCP1 in response to cold is severely impaired in the absence of NRDc. At the molecular level, NRDc and PGC-1α interact and co-localize at the UCP1 enhancer, where NRDc represses PGC-1α activity. These findings reveal a novel nuclear function of NRDc and provide important insights into the mechanism of thermoregulation. The precise regulation of mammalian body temperature is important for survival. Here the authors show that the peptidase nardilysin represses the transcription factor PGC-1α, and identify nardilysin as a regulator of basal body temperature, cold-induced thermogenesis and body insulation.
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31
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Human Tumor Antigens and Cancer Immunotherapy. BIOMED RESEARCH INTERNATIONAL 2015; 2015:948501. [PMID: 26161423 PMCID: PMC4487697 DOI: 10.1155/2015/948501] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/03/2015] [Indexed: 01/21/2023]
Abstract
With the recent developments of adoptive T cell therapies and the use of new monoclonal antibodies against the immune checkpoints, immunotherapy is at a turning point. Key players for the success of these therapies are the cytolytic T lymphocytes, which are a subset of T cells able to recognize and kill tumor cells. Here, I review the nature of the antigenic peptides recognized by these T cells and the processes involved in their presentation. I discuss the importance of understanding how each antigenic peptide is processed in the context of immunotherapy and vaccine delivery.
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Oliveira CC, van Hall T. Alternative Antigen Processing for MHC Class I: Multiple Roads Lead to Rome. Front Immunol 2015; 6:298. [PMID: 26097483 PMCID: PMC4457021 DOI: 10.3389/fimmu.2015.00298] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/22/2015] [Indexed: 12/31/2022] Open
Abstract
The well described conventional antigen-processing pathway is accountable for most peptides that end up in MHC class I molecules at the cell surface. These peptides experienced liberation by the proteasome and transport by the peptide transporter TAP. However, there are multiple roads that lead to Rome, illustrated by the increasing number of alternative processing pathways that have been reported during last years. Interestingly, TAP-deficient individuals do not succumb to viral infections, suggesting that CD8 T cell immunity is sufficiently supported by alternative TAP-independent processing pathways. To date, a diversity of viral and endogenous TAP-independent peptides have been identified in the grooves of different MHC class I alleles. Some of these peptides are not displayed by normal TAP-positive cells and we therefore called them TEIPP, for “T-cell epitopes associated with impaired peptide processing.” TEIPPs are hidden self-antigens, are derived from normal housekeeping proteins, and are processed via unconventional processing pathways. Per definition, TEIPPs are presented via TAP-independent pathways, but recent data suggest that part of this repertoire still depend on proteasome and metalloprotease activity. An exception is the C-terminal peptide of the endoplasmic reticulum (ER)-membrane-spanning ceramide synthase Trh4 that is surprisingly liberated by the signal peptide peptidase (SPP), the proteolytic enzyme involved in cleaving leader sequences. The intramembrane cleaving SPP is thereby an important contributor of TAP-independent peptides. Its family members, like the Alzheimer’s related presenilins, might contribute as well, according to our preliminary data. Finally, alternative peptide routing is an emerging field and includes processes like the unfolded protein response, the ER-associated degradation, and autophagy-associated vesicular pathways. These data convince us that there is a world to be discovered in the field of unconventional antigen processing.
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Affiliation(s)
- Cláudia C Oliveira
- Department of Clinical Oncology, Leiden University Medical Center , Leiden , Netherlands
| | - Thorbald van Hall
- Department of Clinical Oncology, Leiden University Medical Center , Leiden , Netherlands
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Role of peptide processing predictions in T cell epitope identification: contribution of different prediction programs. Immunogenetics 2014; 67:85-93. [PMID: 25475908 PMCID: PMC4297296 DOI: 10.1007/s00251-014-0815-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/10/2014] [Indexed: 10/27/2022]
Abstract
Proteolysis is the general term to describe the process of protein degradation into peptides. Proteasomes are the main actors in cellular proteolysis, and their activity can be measured in in vitro digestion experiments. However, in vivo proteolysis can be different than what is measured in these experiments if other proteases participate or if proteasomal activity is different in vivo. The in vivo proteolysis can be measured only indirectly, by the analysis of peptides presented on MHC-I molecules. MHC-I presented peptides are protected from further degradation, thus enabling an indirect view on the underlying in vivo proteolysis. The ligands presented on different MHC-I molecules enable different views on this process; in combination, they might give a complete picture. Based on in vitro proteasome-only digestions and MHC-I ligand data, different proteolysis predictors have been developed. With new in vitro digestion and MHC-I ligand data sets, we benchmarked how well these predictors capture in vitro proteasome-only activity and in vivo whole-cell proteolysis, respectively. Even though the in vitro proteasome digestion patterns were best captured by methods trained on such data (ProteaSMM and NetChop 20S), the in vivo whole-cell proteolysis was best predicted by a method trained on MHC-I ligand data (NetChop Cterm). Follow-up analysis showed that the likely source of this difference is the activity from proteases other than the proteasome, such as TPPII. This non-proteasomal in vivo activity is captured by NetChop Cterm and should be taken into account in MHC-I ligand predictions.
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Proteasome subtypes and regulators in the processing of antigenic peptides presented by class I molecules of the major histocompatibility complex. Biomolecules 2014; 4:994-1025. [PMID: 25412285 PMCID: PMC4279167 DOI: 10.3390/biom4040994] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/02/2014] [Accepted: 10/29/2014] [Indexed: 02/07/2023] Open
Abstract
The proteasome is responsible for the breakdown of cellular proteins. Proteins targeted for degradation are allowed inside the proteasome particle, where they are cleaved into small peptides and released in the cytosol to be degraded into amino acids. In vertebrates, some of these peptides escape degradation in the cytosol, are loaded onto class I molecules of the major histocompatibility complex (MHC) and displayed at the cell surface for scrutiny by the immune system. The proteasome therefore plays a key role for the immune system: it provides a continued sampling of intracellular proteins, so that CD8-positive T-lymphocytes can kill cells expressing viral or tumoral proteins. Consequently, the repertoire of peptides displayed by MHC class I molecules at the cell surface depends on proteasome activity, which may vary according to the presence of proteasome subtypes and regulators. Besides standard proteasomes, cells may contain immunoproteasomes, intermediate proteasomes and thymoproteasomes. Cells may also contain regulators of proteasome activity, such as the 19S, PA28 and PA200 regulators. Here, we review the effects of these proteasome subtypes and regulators on the production of antigenic peptides. We also discuss an unexpected function of the proteasome discovered through the study of antigenic peptides: its ability to splice peptides.
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35
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Gamrekelashvili J, Greten TF, Korangy F. Immunogenicity of necrotic cell death. Cell Mol Life Sci 2014; 72:273-83. [PMID: 25274062 DOI: 10.1007/s00018-014-1741-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/03/2014] [Accepted: 09/22/2014] [Indexed: 12/20/2022]
Abstract
The mode of tumor cell death has significant effects on anti-tumor immunity. Although, previously it was thought that cell death is an inert effect, different investigators have clearly shown that dying tumors can attract, activate and mature professional antigen presenting cells and dendritic cells. In addition, others and we have shown that the type of tumor cell death not only controls the presence or absence of specific tumor antigens, but also can result in immunological responses ranging from immunosuppression to anti-tumor immunity. More importantly, it is possible to enhance anti-tumor immunity both in vitro and in vivo by targeting specific molecular mechanisms such as oligopeptidases and the proteasome. These studies not only extend our knowledge on basic immunological questions and the induction of anti-tumor immunity, but also have implications for all types of cancer treatments, in which rapid tumor cell death is induced. This review is a comprehensive summary of cell death and particularly necrosis and the pivotal role it plays in anti-tumor immunity.
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Radichev IA, Maneva-Radicheva LV, Amatya C, Parker C, Ellefson J, Wasserfall C, Atkinson M, Burn P, Savinov AY. Nardilysin-dependent proteolysis of cell-associated VTCN1 (B7-H4) marks type 1 diabetes development. Diabetes 2014; 63:3470-82. [PMID: 24848066 PMCID: PMC4171653 DOI: 10.2337/db14-0213] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
T-cell responses directed against insulin-secreting pancreatic β-cells are the key events highlighting type 1 diabetes (T1D). Therefore, a defective control of T-cell activation is thought to underlie T1D development. Recent studies implicated a B7-like negative costimulatory protein, V-set domain-containing T-cell activation inhibitor-1 (VTCN1), as a molecule capable of inhibiting T-cell activation and, potentially, an important constituent in experimental models of T1D. Here, we unravel a general deficiency within the VTCN1 pathway that is shared between diabetes-prone mice and a subset of T1D patients. Gradual loss of membrane-tethered VTCN1 from antigen-presenting cells combined with an increased release of soluble VTCN1 (sVTCN1) occurs in parallel to natural T1D development, potentiating hyperproliferation of diabetogenic T cells. Mechanistically, we demonstrate that the loss of membrane-tethered VTCN1 is linked to proteolytic cleavage mediated by the metalloproteinase nardilysin. The cleaved sVTCN1 fragment was detected at high levels in the peripheral blood of 53% T1D patients compared with only 9% of the healthy subjects. Elevated blood sVTCN1 levels appeared early in the disease progression and correlated with the aggressive pace of disease, highlighting the potential use of sVTCN1 as a new T1D biomarker, and identifying nardilysin as a potential therapeutic target.
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Affiliation(s)
- Ilian A Radichev
- Sanford Project/Children's Health Research Center at Sanford Research, Sioux Falls, SD Department of Pediatrics, University of South Dakota School of Medicine, Sioux Falls, SD
| | - Lilia V Maneva-Radicheva
- Sanford Project/Children's Health Research Center at Sanford Research, Sioux Falls, SD Department of Pediatrics, University of South Dakota School of Medicine, Sioux Falls, SD
| | - Christina Amatya
- Sanford Project/Children's Health Research Center at Sanford Research, Sioux Falls, SD Department of Pediatrics, University of South Dakota School of Medicine, Sioux Falls, SD
| | - Camille Parker
- Sanford Project/Children's Health Research Center at Sanford Research, Sioux Falls, SD Department of Pediatrics, University of South Dakota School of Medicine, Sioux Falls, SD
| | - Jacob Ellefson
- Sanford Project/Children's Health Research Center at Sanford Research, Sioux Falls, SD Department of Pediatrics, University of South Dakota School of Medicine, Sioux Falls, SD
| | - Clive Wasserfall
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL
| | - Mark Atkinson
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL
| | - Paul Burn
- Sanford Project/Children's Health Research Center at Sanford Research, Sioux Falls, SD Department of Pediatrics, University of South Dakota School of Medicine, Sioux Falls, SD
| | - Alexei Y Savinov
- Sanford Project/Children's Health Research Center at Sanford Research, Sioux Falls, SD Department of Pediatrics, University of South Dakota School of Medicine, Sioux Falls, SD
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Dinter J, Gourdain P, Lai NY, Duong E, Bracho-Sanchez E, Rucevic M, Liebesny PH, Xu Y, Shimada M, Ghebremichael M, Kavanagh DG, Le Gall S. Different antigen-processing activities in dendritic cells, macrophages, and monocytes lead to uneven production of HIV epitopes and affect CTL recognition. THE JOURNAL OF IMMUNOLOGY 2014; 193:4322-4334. [PMID: 25230751 DOI: 10.4049/jimmunol.1400491] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Dendritic cells (DCs), macrophages (MPs), and monocytes are permissive to HIV. Whether they similarly process and present HIV epitopes to HIV-specific CD8 T cells is unknown despite the critical role of peptide processing and presentation for recognition and clearance of infected cells. Cytosolic peptidases degrade endogenous proteins originating from self or pathogens, exogenous Ags preprocessed in endolysosomes, thus shaping the peptidome available for endoplasmic reticulum translocation, trimming, and MHC-I presentation. In this study, we compared the capacity of DCs, MPs, and monocyte cytosolic extracts to produce epitope precursors and epitopes. We showed differences in the proteolytic activities and expression levels of cytosolic proteases between monocyte-derived DCs and MPs and upon maturation with LPS, R848, and CL097, with mature MPs having the highest activities. Using cytosol as a source of proteases to degrade epitope-containing HIV peptides, we showed by mass spectrometry that the degradation patterns of long peptides and the kinetics and amount of antigenic peptides produced differed among DCs, MPs, and monocytes. Additionally, variable intracellular stability of HIV peptides prior to loading onto MHC may accentuate the differences in epitope availability for presentation by MHC-I between these subsets. Differences in peptide degradation led to 2- to 25-fold differences in the CTL responses elicited by the degradation peptides generated in DCs, MPs, and monocytes. Differences in Ag-processing activities between these subsets might lead to variations in the timing and efficiency of recognition of HIV-infected cells by CTLs and contribute to the unequal capacity of HIV-specific CTLs to control viral load.
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Affiliation(s)
- Jens Dinter
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Pauline Gourdain
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Nicole Y Lai
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Ellen Duong
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Edith Bracho-Sanchez
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Marijana Rucevic
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Paul H Liebesny
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Yang Xu
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Mariko Shimada
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Musie Ghebremichael
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Daniel G Kavanagh
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Sylvie Le Gall
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
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38
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Qi L, Li SH, Si LB, Lu M, Tian H. Expression of THOP1 and its relationship to prognosis in non-small cell lung cancer. PLoS One 2014; 9:e106665. [PMID: 25180910 PMCID: PMC4152321 DOI: 10.1371/journal.pone.0106665] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 07/30/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The study was designed to detect the expression level of thimet oligopeptidase (THOP1) protein in non-small cell lung cancer (NSCLC) and investigate its correlation with clinicopathologic features and prognosis. METHODS Immunohistochemical staining was used to determine the expression of THOP1 protein in 120 NSCLC specimens and 53 distant normal lung tissues. Quantitative real-time PCR and western blotting were employed to measure the expression of THOP1 in 16 pairs of primary NSCLC and corresponding normal tissues. RESULTS Analysis of immunohistochemical staining suggested low THOP1 expression was found in 71 (59.2%) of the 120 NSCLC specimens and significantly correlated with positive lymph node metastasis (P = 0.048). However, low THOP1 expression was found in 22 (41.5%) of the 53 normal lung tissues. Chi-square test suggested that the expression of THOP1 was significantly higher in the normal lung tissues than that in the NSCLC specimens (P = 0.032). Real-Time PCR and western blotting showed that NSCLC specimens had decreased THOP1 mRNA and protein expression compared to corresponding normal tissues. Univariate analysis demonstrated that low THOP1 expression significantly predicted decreased 5-year disease-free survival (P = 0.038) and overall survival (P = 0.017). In addition, positive lymph node metastasis (P = 0.025) and advanced TNM stage (P = 0.009) significantly predicted decreased 5-year overall survival. However, multivariate Cox regression analysis showed that only low THOP1 expression retained its significance as an independent prognostic factor for unfavorable 5-year disease-free survival (P = 0.046) and overall survival (P = 0.021). CONCLUSIONS THOP1 may have clinical potentials to be employed as a promising biomarker to identify individuals with better prognosis and a novel antitumor agent for therapy of patients with NSCLC.
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Affiliation(s)
- Lei Qi
- Department of Thoracic Surgery, Qi Lu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Shu-hai Li
- Department of Thoracic Surgery, Qi Lu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Li-bo Si
- Department of Thoracic Surgery, Qi Lu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Ming Lu
- Department of Thoracic Surgery, Qi Lu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Hui Tian
- Department of Thoracic Surgery, Qi Lu Hospital, Shandong University, Jinan, Shandong Province, China
- * E-mail:
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Stratikos E. Regulating adaptive immune responses using small molecule modulators of aminopeptidases that process antigenic peptides. Curr Opin Chem Biol 2014; 23:1-7. [PMID: 25173825 DOI: 10.1016/j.cbpa.2014.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/10/2014] [Accepted: 08/12/2014] [Indexed: 01/19/2023]
Abstract
Antigenic peptide processing by intracellular aminopeptidases has emerged recently as an important pathway that regulates adaptive immune responses. Pathogens and cancer can manipulate the activity of key enzymes of this pathway to promote immune evasion. Furthermore, the activity of these enzymes is naturally variable due to polymorphic variation, contributing to predisposition to disease, most notably autoimmunity. Here, we review recent findings that suggest that the pharmacological regulation of the activity of these aminopeptidases constitutes a valid approach for regulating human immune responses. We furthermore review the state of the art in chemical tools for inhibiting these enzymes and how these tools can be useful for the development of innovative therapeutic approaches for a variety of diseases including cancer, viral infections and autoimmunity.
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Affiliation(s)
- Efstratios Stratikos
- National Center for Scientific Research Demokritos, Agia Paraskevi, Athens, Greece.
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40
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Mechanisms of HIV protein degradation into epitopes: implications for vaccine design. Viruses 2014; 6:3271-92. [PMID: 25196483 PMCID: PMC4147695 DOI: 10.3390/v6083271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/06/2014] [Accepted: 08/11/2014] [Indexed: 12/02/2022] Open
Abstract
The degradation of HIV-derived proteins into epitopes displayed by MHC-I or MHC-II are the first events leading to the priming of HIV-specific immune responses and to the recognition of infected cells. Despite a wealth of information about peptidases involved in protein degradation, our knowledge of epitope presentation during HIV infection remains limited. Here we review current data on HIV protein degradation linking epitope production and immunodominance, viral evolution and impaired epitope presentation. We propose that an in-depth understanding of HIV antigen processing and presentation in relevant primary cells could be exploited to identify signatures leading to efficient or inefficient epitope presentation in HIV proteomes, and to improve the design of immunogens eliciting immune responses efficiently recognizing all infected cells.
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Oliveira CC, Sluijter M, Querido B, Ossendorp F, van der Burg SH, van Hall T. Dominant contribution of the proteasome and metalloproteinases to TAP-independent MHC-I peptide repertoire. Mol Immunol 2014; 62:129-36. [PMID: 24983205 DOI: 10.1016/j.molimm.2014.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 06/03/2014] [Accepted: 06/08/2014] [Indexed: 10/25/2022]
Abstract
Tumors frequently display defects in the MHC-I antigen processing machinery, such as deficiency of the peptide transporter TAP. Interestingly, the residual peptide repertoire contains neo-antigens which are not presented by processing-proficient cells. We termed these immunogenic peptides TEIPP ('T-cell epitopes associated with impaired peptide processing') and were interested to unravel their TAP-independent processing pathways. With an array of chemical inhibitors we assessed the participation of numerous proteases to TAP-independent peptides and found that the previously described catalytic enzymes signal peptidase and furin contributed in a cell-type and MHC-I allele-specific way. In addition, a dominant role for the proteasome and metallopeptidases was observed. These findings raised the question how these proteasome products get access to MHC-I molecules. A novel TEIPP peptide-epitope that represented this intracellular route revealed that the lysosomal peptide transporter ABCB9 ('TAP-like') was dispensable for its presentation. Interestingly, prevention of endolysosomal vesicle acidification by bafilomycin enhanced the surface display of this TEIPP peptide, suggesting that this proteasome-dependent pathway intersects endolysosomes and that these antigens are merely destroyed there. In conclusion, the proteasome has a surprisingly dominant role in shaping the TAP-independent MHC-I peptide repertoire and some of these antigens might be targeted to the endocytic vesicular pathway.
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Affiliation(s)
- Cláudia C Oliveira
- Department of Clinical Oncology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; Graduate Program in Areas of Basic and Applied Biology, Porto, Portugal
| | - Marjolein Sluijter
- Department of Clinical Oncology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Bianca Querido
- Department of Clinical Oncology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Ferry Ossendorp
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Sjoerd H van der Burg
- Department of Clinical Oncology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Thorbald van Hall
- Department of Clinical Oncology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.
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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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43
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Tenzer S, Crawford H, Pymm P, Gifford R, Sreenu VB, Weimershaus M, de Oliveira T, Burgevin A, Gerstoft J, Akkad N, Lunn D, Fugger L, Bell J, Schild H, van Endert P, Iversen AKN. HIV-1 adaptation to antigen processing results in population-level immune evasion and affects subtype diversification. Cell Rep 2014; 7:448-463. [PMID: 24726370 PMCID: PMC4005910 DOI: 10.1016/j.celrep.2014.03.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 12/04/2013] [Accepted: 03/11/2014] [Indexed: 02/01/2023] Open
Abstract
The recent HIV-1 vaccine failures highlight the need to better understand virus-host interactions. One key question is why CD8(+) T cell responses to two HIV-Gag regions are uniquely associated with delayed disease progression only in patients expressing a few rare HLA class I variants when these regions encode epitopes presented by ~30 more common HLA variants. By combining epitope processing and computational analyses of the two HIV subtypes responsible for ~60% of worldwide infections, we identified a hitherto unrecognized adaptation to the antigen-processing machinery through substitutions at subtype-specific motifs. Multiple HLA variants presenting epitopes situated next to a given subtype-specific motif drive selection at this subtype-specific position, and epitope abundances correlate inversely with the HLA frequency distribution in affected populations. This adaptation reflects the sum of intrapatient adaptations, is predictable, facilitates viral subtype diversification, and increases global HIV diversity. Because low epitope abundance is associated with infrequent and weak T cell responses, this most likely results in both population-level immune evasion and inadequate responses in most people vaccinated with natural HIV-1 sequence constructs. Our results suggest that artificial sequence modifications at subtype-specific positions in vitro could refocus and reverse the poor immunogenicity of HIV proteins.
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Affiliation(s)
- Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University of Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany
| | - Hayley Crawford
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK; Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK
| | - Phillip Pymm
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK; Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK
| | - Robert Gifford
- Aaron Diamond AIDS Research Center, 455 First Avenue, New York, NY 10016, USA
| | - Vattipally B Sreenu
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK
| | - Mirjana Weimershaus
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Centre National de la Recherche Scientifique, UMR8253, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 rue de Sèvres, 75015 Paris, France
| | - Tulio de Oliveira
- Africa Centre for Health and Population Studies, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, KwaZulu-Natal 3935, South Africa; Research Department of Infection, University College London, Cruciform Building, 90 Gower Street, London WC1E 6BT, UK
| | - Anne Burgevin
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Centre National de la Recherche Scientifique, UMR8253, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 rue de Sèvres, 75015 Paris, France
| | - Jan Gerstoft
- Department of Infectious Diseases, Rigshospitalet, The National University Hospital, Blegdamsvej 9, 2100 Kbh Ø Copenhagen, Denmark
| | - Nadja Akkad
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University of Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany
| | - Daniel Lunn
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Lars Fugger
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK; Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK
| | - John Bell
- Office of the Regius Professor of Medicine, The Richard Doll Building, University of Oxford, Old Road Campus, Roosevelt Drive 1, Oxford OX3 7LF, UK
| | - Hansjörg Schild
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University of Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany
| | - Peter van Endert
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Centre National de la Recherche Scientifique, UMR8253, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 rue de Sèvres, 75015 Paris, France
| | - Astrid K N Iversen
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK; Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK.
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44
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Lindenstrøm T, Aagaard C, Christensen D, Agger EM, Andersen P. High-frequency vaccine-induced CD8⁺ T cells specific for an epitope naturally processed during infection with Mycobacterium tuberculosis do not confer protection. Eur J Immunol 2014; 44:1699-709. [PMID: 24677089 DOI: 10.1002/eji.201344358] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 02/03/2014] [Accepted: 02/11/2014] [Indexed: 12/26/2022]
Abstract
Relatively few MHC class I epitopes have been identified from Mycobacterium tuberculosis, but during the late stage of infection, CD8(+) T-cell responses to these epitopes are often primed at an extraordinary high frequency. Although clearly available for recognition during infection, their role in resistance to mycobacterial infections still remain unclear. As an alternative to DNA and viral vaccination platforms, we have exploited a novel CD8(+) T-cell-inducing adjuvant, cationic adjuvant formulation 05 (dimethyldioctadecylammonium/trehalose dibehenate/poly (inositic:cytidylic) acid), to prime high-frequency CD8 responses to the immunodominant H2-K(b) -restricted IMYNYPAM epitope contained in the vaccine Ag tuberculosis (TB)10.4/Rv0288/ESX-H (where ESX is mycobacterial type VII secretion system). We report that the amino acid C-terminal to this minimal epitope plays a decisive role in proteasomal cleavage and epitope priming. The primary structure of TB10.4 is suboptimal for proteasomal processing of the epitope and amino acid substitutions in the flanking region markedly increased epitope-specific CD8(+) T-cell responses. One of the optimized sequences was contained in the closely related TB10.3/Rv3019c/ESX-R Ag and when recombinantly expressed and administered in the cationic adjuvant formulation 05 adjuvant, this Ag promoted very high CD8(+) T-cell responses. This abundant T-cell response was functionally active but provided no protection against challenge, suggesting that CD8(+) T cells play a limited role in protection against M. tuberculosis in the mouse model.
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Affiliation(s)
- Thomas Lindenstrøm
- Department of Infectious Disease Immunology, Statens Serum Institut, Denmark
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An evolutionary analysis of antigen processing and presentation across different timescales reveals pervasive selection. PLoS Genet 2014; 10:e1004189. [PMID: 24675550 PMCID: PMC3967941 DOI: 10.1371/journal.pgen.1004189] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 01/06/2014] [Indexed: 12/28/2022] Open
Abstract
The antigenic repertoire presented by MHC molecules is generated by the antigen processing and presentation (APP) pathway. We analyzed the evolutionary history of 45 genes involved in APP at the inter- and intra-species level. Results showed that 11 genes evolved adaptively in mammals. Several positively selected sites involve positions of fundamental importance to the protein function (e.g. the TAP1 peptide-binding domains, the sugar binding interface of langerin, and the CD1D trafficking signal region). In CYBB, all selected sites cluster in two loops protruding into the endosomal lumen; analysis of missense mutations responsible for chronic granulomatous disease (CGD) showed the action of different selective forces on the very same gene region, as most CGD substitutions involve aminoacid positions that are conserved in all mammals. As for ERAP2, different computational methods indicated that positive selection has driven the recurrent appearance of protein-destabilizing variants during mammalian evolution. Application of a population-genetics phylogenetics approach showed that purifying selection represented a major force acting on some APP components (e.g. immunoproteasome subunits and chaperones) and allowed identification of positive selection events in the human lineage. We also investigated the evolutionary history of APP genes in human populations by developing a new approach that uses several different tests to identify the selection target, and that integrates low-coverage whole-genome sequencing data with Sanger sequencing. This analysis revealed that 9 APP genes underwent local adaptation in human populations. Most positive selection targets are located within noncoding regions with regulatory function in myeloid cells or act as expression quantitative trait loci. Conversely, balancing selection targeted nonsynonymous variants in TAP1 and CD207 (langerin). Finally, we suggest that selected variants in PSMB10 and CD207 contribute to human phenotypes. Thus, we used evolutionary information to generate experimentally-testable hypotheses and to provide a list of sites to prioritize in follow-up analyses. Antigen-presenting cells digest intracellular and extracellular proteins and display the resulting antigenic repertoire on cell surface molecules for recognition by T cells. This process initiates cell-mediated immune responses and is essential to detect infections. The antigenic repertoire is generated by the antigen processing and presentation pathway. Because several pathogens evade immune recognition by hampering this process, genes involved in antigen processing and presentation may represent common natural selection targets. Thus, we analyzed the evolutionary history of these genes during mammalian evolution and in the more recent history of human populations. Evolutionary analyses in mammals indicated that positive selection targeted a very high proportion of genes (24%), and revealed that many selected sites affect positions of fundamental importance to the protein function. In humans, we found different signatures of natural selection acting both on regions that are expected to regulate gene expression levels or timing and on coding variants; two human selected polymorphisms may modulate the susceptibility to Crohn's disease and to HIV-1 infection. Therefore, we provide a comprehensive evolutionary analysis of antigen processing and we show that evolutionary studies can provide useful information concerning the location and nature of functional variants, ultimately helping to clarify phenotypic differences between and within species.
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Ménager J, Ebstein F, Oger R, Hulin P, Nedellec S, Duverger E, Lehmann A, Kloetzel PM, Jotereau F, Guilloux Y. Cross-presentation of synthetic long peptides by human dendritic cells: a process dependent on ERAD component p97/VCP but Not sec61 and/or Derlin-1. PLoS One 2014; 9:e89897. [PMID: 24587108 PMCID: PMC3937416 DOI: 10.1371/journal.pone.0089897] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/25/2014] [Indexed: 12/22/2022] Open
Abstract
Antitumor vaccination using synthetic long peptides (SLP) is an additional therapeutic strategy currently under development. It aims to activate tumor-specific CD8+ CTL by professional APCs such as DCs. DCs can activate T lymphocytes by MHC class I presentation of exogenous antigens - a process referred to as “cross-presentation”. Until recently, the intracellular mechanisms involved in cross-presentation of soluble antigens have been unclear. Here, we characterize the cross-presentation pathway of SLP Melan-A16–40 containing the HLA-A2-restricted epitope26–35 (A27L) in human DCs. Using confocal microscopy and specific inhibitors, we show that SLP16–40 is rapidly taken up by DC and follows a classical TAP- and proteasome-dependent cross-presentation pathway. Our data support a role for the ER-associated degradation machinery (ERAD)-related protein p97/VCP in the transport of SLP16–40 from early endosomes to the cytoplasm but formally exclude both sec61 and Derlin-1 as possible retro-translocation channels for cross-presentation. In addition, we show that generation of the Melan-A26–35 peptide from the SLP16–40 was absolutely not influenced by the proteasome subunit composition in DC. Altogether, our findings propose a model for cross-presentation of SLP which tends to enlarge the repertoire of potential candidates for retro-translocation of exogenous antigens to the cytosol.
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Affiliation(s)
- Jérémie Ménager
- INSERM U892, Nantes, France
- Université de Nantes, Nantes, France
- CNRS, UMR 6299, Nantes, France
| | - Frédéric Ebstein
- Institut of Biochemistry, Charité University Hospital, Humboldt University, Berlin, Germany
| | - Romain Oger
- INSERM U892, Nantes, France
- Université de Nantes, Nantes, France
- CNRS, UMR 6299, Nantes, France
| | - Philippe Hulin
- INSERM U892, Nantes, France
- CNRS, UMR 6299, Nantes, France
| | | | - Eric Duverger
- Glycobiochimie, ICOA, Université d’Orléans, Orléans, France
| | - Andrea Lehmann
- Institut of Biochemistry, Charité University Hospital, Humboldt University, Berlin, Germany
| | - Peter-Michael Kloetzel
- Institut of Biochemistry, Charité University Hospital, Humboldt University, Berlin, Germany
| | - Francine Jotereau
- INSERM U892, Nantes, France
- Université de Nantes, Nantes, France
- CNRS, UMR 6299, Nantes, France
| | - Yannick Guilloux
- INSERM U892, Nantes, France
- Université de Nantes, Nantes, France
- CNRS, UMR 6299, Nantes, France
- * E-mail:
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47
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Gamrekelashvili J, Kapanadze T, Han M, Wissing J, Ma C, Jaensch L, Manns MP, Armstrong T, Jaffee E, White AO, Citrin DE, Korangy F, Greten TF. Peptidases released by necrotic cells control CD8+ T cell cross-priming. J Clin Invest 2014; 123:4755-68. [PMID: 24216478 DOI: 10.1172/jci65698] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 08/08/2013] [Indexed: 12/22/2022] Open
Abstract
Cross-priming of CD8+ T cells and generation of effector immune responses is pivotal for tumor immunity as well as for successful anticancer vaccination and therapy. Dead and dying cells produce signals that can influence Ag processing and presentation; however, there is conflicting evidence regarding the immunogenicity of necrotic cell death. We used a mouse model of sterile necrosis, in which mice were injected with sterile primary necrotic cells, to investigate a role of these cells in priming of CD8+ T cells. We discovered a molecular mechanism operating in Ag donor cells that regulates cross-priming of CD8+ T cells during primary sterile necrosis and thereby controls adaptive immune responses. We found that the cellular peptidases dipeptidyl peptidase 3 (DPP-3) and thimet oligopeptidase 1 (TOP-1), both of which are present in nonimmunogenic necrotic cells, eliminated proteasomal degradation products and blocked Ag cross-presentation. While sterile necrotic tumor cells failed to induce CD8+ T cell responses, their nonimmunogenicity could be reversed in vitro and in vivo by inactivation of DPP-3 and TOP-1. These results indicate that control of cross-priming and thereby immunogenicity of primary sterile necrosis relies on proteasome-dependent oligopeptide generation and functional status of peptidases in Ag donor cells.
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48
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Culina S, Mauvais FX, Hsu HT, Burgevin A, Guénette S, Moser A, van Endert P. No major role for insulin-degrading enzyme in antigen presentation by MHC molecules. PLoS One 2014; 9:e88365. [PMID: 24516642 PMCID: PMC3917890 DOI: 10.1371/journal.pone.0088365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 01/06/2014] [Indexed: 12/27/2022] Open
Abstract
Antigen presentation by MHC class I molecules requires degradation of epitope source proteins in the cytosol. Although the preeminent role of the proteasome is clearly established, evidence suggesting a significant role for proteasome-independent generation of class I ligands has been reported repeatedly. However, an enzyme responsible for such a role has not been identified. Recently insulin-degrading enzyme (IDE) was shown to produce an antigenic peptide derived from the tumor antigen MAGE-A3 in an entirely proteasome-independent manner, raising the question of the global impact of IDE in MHC class I antigen processing. Here we report that IDE knockdown in human cell lines, or knockout in two different mouse strains, has no effect on cell surface expression of various MHC class I molecules, including allomorphs such as HLA-A3 and HLA-B27 suggested to be loaded in an at least a partly proteasome-independent manner. Moreover, reduced or absent IDE expression does not affect presentation of five epitopes including epitopes derived from beta amyloid and proinsulin, two preferred IDE substrates. Thus, IDE does not play a major role in MHC class I antigen processing, confirming the dominant and almost exclusive role of the proteasome in cytosolic production of MHC class I ligands.
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Affiliation(s)
- Slobodan Culina
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine Paris Descartes, Paris, France
| | - François-Xavier Mauvais
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine Paris Descartes, Paris, France
| | - Hsiang-Ting Hsu
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine Paris Descartes, Paris, France
| | - Anne Burgevin
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine Paris Descartes, Paris, France
| | - Suzanne Guénette
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Charlestown, Massachusetts, United States of America
| | - Anna Moser
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine Paris Descartes, Paris, France
| | - Peter van Endert
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine Paris Descartes, Paris, France
- * E-mail:
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49
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Coulie PG, Van den Eynde BJ, van der Bruggen P, Boon T. Tumour antigens recognized by T lymphocytes: at the core of cancer immunotherapy. Nat Rev Cancer 2014; 14:135-46. [PMID: 24457417 DOI: 10.1038/nrc3670] [Citation(s) in RCA: 795] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this Timeline, we describe the characteristics of tumour antigens that are recognized by spontaneous T cell responses in cancer patients and the paths that led to their identification. We explain on what genetic basis most, but not all, of these antigens are tumour specific: that is, present on tumour cells but not on normal cells. We also discuss how strategies that target these tumour-specific antigens can lead either to tumour-specific or to crossreactive T cell responses, which is an issue that has important safety implications in immunotherapy. These safety issues are even more of a concern for strategies targeting antigens that are not known to induce spontaneous T cell responses in patients.
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Affiliation(s)
- Pierre G Coulie
- 1] de Duve Institute and the Université catholique de Louvain, B-1200 Brussels, Belgium. [2] WELBIO (Walloon Excellence in Lifesciences and Biotechnology), B-1200 Brussels, Belgium
| | - Benoît J Van den Eynde
- 1] de Duve Institute and the Université catholique de Louvain, B-1200 Brussels, Belgium. [2] Ludwig Institute for Cancer Research, B-1200 Brussels, Belgium. [3] WELBIO (Walloon Excellence in Lifesciences and Biotechnology), B-1200 Brussels, Belgium
| | - Pierre van der Bruggen
- 1] de Duve Institute and the Université catholique de Louvain, B-1200 Brussels, Belgium. [2] Ludwig Institute for Cancer Research, B-1200 Brussels, Belgium. [3] WELBIO (Walloon Excellence in Lifesciences and Biotechnology), B-1200 Brussels, Belgium
| | - Thierry Boon
- 1] de Duve Institute and the Université catholique de Louvain, B-1200 Brussels, Belgium. [2] Ludwig Institute for Cancer Research, B-1200 Brussels, Belgium
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50
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van Kasteren SI, Overkleeft H, Ovaa H, Neefjes J. Chemical biology of antigen presentation by MHC molecules. Curr Opin Immunol 2013; 26:21-31. [PMID: 24556397 DOI: 10.1016/j.coi.2013.10.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 10/03/2013] [Indexed: 11/25/2022]
Abstract
MHC class I and MHC class II molecules present peptides to the immune system to drive proper T cell responses. Pharmacological modulation of T-cell responses can offer treatment options for a range of immune-related diseases. Pharmacological downregulation of MHC molecules may find application in treatment of auto-immunity and transplantation rejection while pharmacological activation of antigen presentation would support immune responses to infection and cancer. Since the cell biology of MHC class I and MHC class II antigen presentation is understood in great detail, many potential targets for manipulation have been defined over the years. Here, we discuss how antigen presentation by MHC molecules can be modulated by pharmacological agents and how chemistry can further support the study of antigen presentation in general. The chemical biology of antigen presentation by MHC molecules shows surprising options for immune modulation and the development of future therapies.
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Affiliation(s)
- Sander I van Kasteren
- The Netherlands Cancer Institute, Division of Cell Biology, Plesmanlaan 121, Amsterdam, Netherlands; Leiden Institute of Chemistry (LIC), Division of Bio-Organic Chemistry, Einsteinweg 55, Leiden, Netherlands
| | - Hermen Overkleeft
- The Netherlands Cancer Institute, Division of Cell Biology, Plesmanlaan 121, Amsterdam, Netherlands; Leiden Institute of Chemistry (LIC), Division of Bio-Organic Chemistry, Einsteinweg 55, Leiden, Netherlands
| | - Huib Ovaa
- The Netherlands Cancer Institute, Division of Cell Biology, Plesmanlaan 121, Amsterdam, Netherlands; Leiden Institute of Chemistry (LIC), Division of Bio-Organic Chemistry, Einsteinweg 55, Leiden, Netherlands
| | - Jacques Neefjes
- The Netherlands Cancer Institute, Division of Cell Biology, Plesmanlaan 121, Amsterdam, Netherlands; Leiden Institute of Chemistry (LIC), Division of Bio-Organic Chemistry, Einsteinweg 55, Leiden, Netherlands.
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