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Zhu F, He S, Ni C, Wu Y, Wu H, Wen L. Study on the structure-activity relationship of rice immunopeptides based on molecular docking. Food Chem X 2024; 21:101158. [PMID: 38322762 PMCID: PMC10843992 DOI: 10.1016/j.fochx.2024.101158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 01/14/2024] [Accepted: 01/21/2024] [Indexed: 02/08/2024] Open
Abstract
Research on food-derived immunoregulatory peptides has attracted increasing attention of scientists worldwide. However, the structure-activity relationship of rice immunopeptides was not clearly. Herein, 114 rice immunopeptides were obtained by simulating the enzymatic hydrolysis of rice proteins and were further analyzed by NetMHCIipan-4.0. Subsequently, the molecular docking was used to simulate the binding of immunoreactive peptides to major histocompatibility complex class II (MHC-II) molecules. Results show that S, R, D, E, and T amino acid could easily form hydrogen bonds with MHC-II molecules, thus enhancing innate and adaptive immunity. Finally, glucose-modified rice immunopeptides were to investigate the binding of the peptides with MHC-II molecules after glycosylation modification; this provided a theoretical basis for the targeted modification of the generated immunopeptides. All in all, the present study provides a theoretical foundation to further utilize rice processing byproducts and other food products to enhance immunity.
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Affiliation(s)
- Fan Zhu
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha 410114, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Shuwen He
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Ce Ni
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Ying Wu
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Hao Wu
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Li Wen
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha 410114, China
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Federico L, Malone B, Tennøe S, Chaban V, Osen JR, Gainullin M, Smorodina E, Kared H, Akbar R, Greiff V, Stratford R, Clancy T, Munthe LA. Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence. Front Immunol 2023; 14:1265044. [PMID: 38045681 PMCID: PMC10691274 DOI: 10.3389/fimmu.2023.1265044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/01/2023] [Indexed: 12/05/2023] Open
Abstract
During the COVID-19 pandemic we utilized an AI-driven T cell epitope prediction tool, the NEC Immune Profiler (NIP) to scrutinize and predict regions of T cell immunogenicity (hotspots) from the entire SARS-CoV-2 viral proteome. These immunogenic regions offer potential for the development of universally protective T cell vaccine candidates. Here, we validated and characterized T cell responses to a set of minimal epitopes from these AI-identified universal hotspots. Utilizing a flow cytometry-based T cell activation-induced marker (AIM) assay, we identified 59 validated screening hits, of which 56% (33 peptides) have not been previously reported. Notably, we found that most of these novel epitopes were derived from the non-spike regions of SARS-CoV-2 (Orf1ab, Orf3a, and E). In addition, ex vivo stimulation with NIP-predicted peptides from the spike protein elicited CD8+ T cell response in PBMC isolated from most vaccinated donors. Our data confirm the predictive accuracy of AI platforms modelling bona fide immunogenicity and provide a novel framework for the evaluation of vaccine-induced T cell responses.
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Affiliation(s)
- Lorenzo Federico
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | - Viktoriia Chaban
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Julie Røkke Osen
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Murat Gainullin
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eva Smorodina
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Oslo University Hospital, Oslo, Norway
| | - Hassen Kared
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Rahmad Akbar
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Oslo University Hospital, Oslo, Norway
| | - Victor Greiff
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Oslo University Hospital, Oslo, Norway
| | | | | | - Ludvig Andre Munthe
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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3
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Goodson H, Kawahara R, Chatterjee S, Goncalves G, Fehring J, Purcell AW, Croft NP, Thaysen-Andersen M. Profound N-glycan remodelling accompanies MHC-II immunopeptide presentation. Front Immunol 2023; 14:1258518. [PMID: 38022636 PMCID: PMC10663315 DOI: 10.3389/fimmu.2023.1258518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Immunopeptidomics, the study of peptide antigens presented on the cell surface by the major histocompatibility complex (MHC), offers insights into how our immune system recognises self/non-self in health and disease. We recently discovered that hyper-processed (remodelled) N-glycans are dominant features decorating viral spike immunopeptides presented via MHC-class II (MHC-II) molecules by dendritic cells pulsed with SARS-CoV-2 spike protein, but it remains unknown if endogenous immunopeptides also undergo N-glycan remodelling. Taking a multi-omics approach, we here interrogate published MHC-II immunopeptidomics datasets of cultured monocyte-like (THP-1) and breast cancer-derived (MDA-MB-231) cell lines for overlooked N-glycosylated peptide antigens, which we compare to their source proteins in the cellular glycoproteome using proteomics and N-glycomics data from matching cell lines. Hyper-processed chitobiose core and paucimannosidic N-glycans alongside under-processed oligomannosidic N-glycans were found to prevalently modify MHC-II-bound immunopeptides isolated from both THP-1 and MDA-MB-231, while complex/hybrid-type N-glycans were (near-)absent in the immunopeptidome as supported further by new N-glycomics data generated from isolated MHC-II-bound peptides derived from MDA-MB-231 cells. Contrastingly, the cellular proteomics and N-glycomics data from both cell lines revealed conventional N-glycosylation rich in complex/hybrid-type N-glycans, which, together with the identification of key lysosomal glycosidases, suggest that MHC-II peptide antigen processing is accompanied by extensive N-glycan trimming. N-glycan remodelling appeared particularly dramatic for cell surface-located glycoproteins while less remodelling was observed for lysosomal-resident glycoproteins. Collectively, our findings indicate that both under- and hyper-processed N-glycans are prevalent features of endogenous MHC-II immunopeptides, an observation that demands further investigation to enable a better molecular-level understanding of immune surveillance.
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Affiliation(s)
- Hayley Goodson
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Rebeca Kawahara
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| | - Sayantani Chatterjee
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- Department of Biochemistry & Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, United States
| | - Gabriel Goncalves
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Joshua Fehring
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Nathan P. Croft
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
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Li CW, Osman R, Menconi F, Hou H, Schechter C, Kozhakhmetova A, Tomer Y. Effective Inhibition of Thyroid Antigen Presentation Using Retro-Inverso Peptides in Experimental Autoimmune Thyroiditis: A Pathway Toward Immune Therapies of Thyroid Autoimmunity. Thyroid 2023; 33:492-500. [PMID: 36762945 PMCID: PMC10325802 DOI: 10.1089/thy.2022.0511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Background: Autoimmune thyroid diseases (AITD) represent the most common autoimmune diseases. However, current therapies focus on relieving the symptoms instead of curing AITD, and new therapies to reverse the autoimmune attack on the thyroid are needed. HLA-DRβ1-Arg74 is the key HLA class II allele that triggers AITD by presenting pathogenic thyroglobulin (Tg) peptides that activate thyroid self-reactive T cells. We hypothesized that blocking the presentation of Tg peptides to T cells within the HLA-DRβ1-Arg74 peptide binding cleft could reverse the autoimmune response to the thyroid in AITD. Methods: The approach we used to block Tg peptide presentation within HLA-DRβ1-Arg74 is to design retro-inverso D-amino acid (RID) peptides that have high affinity to the HLA-DRβ1-Arg74 peptide binding pocket. Results: By using computational approaches and molecular dynamics simulations, we designed two RID peptides, RT-15 and VT-15, that blocked peptide binding to recombinant HLA-DRβ1-Arg74 molecule, as well as T cell activation in vitro. Furthermore, RT-15 and VT-15 blocked in vivo T cell activation by thyroglobulin in humanized NOD-DR3 mice induced with experimental autoimmune thyroiditis. Conclusions: In summary, we discovered two RID peptides that block thyroglobulin peptide binding to HLA-DRβ1-Arg74 and their presentation to T cells in AITD. These findings set the stage for a personalized medicine therapeutic approach for AITD patients who carry the DRβ1-Arg74 allele. This antigen-specific therapeutic strategy can potentially be extended to other autoimmune diseases.
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Affiliation(s)
- Cheuk Wun Li
- The Fleischer Institute for Diabetes and Metabolism, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Roman Osman
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Francesca Menconi
- Department of Clinical and Experimental Medicine, Endocrinology Unit II, University of Pisa and University Hospital of Pisa, Pisa, Italy
| | - Hanxi Hou
- The Fleischer Institute for Diabetes and Metabolism, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Clyde Schechter
- Department of Family and Social Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Aizhan Kozhakhmetova
- The Fleischer Institute for Diabetes and Metabolism, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yaron Tomer
- The Fleischer Institute for Diabetes and Metabolism, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
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Sakai K, Miyadera H, Kubo M, Nakajima F, Matsumoto M. Overlapping ADAMTS13 peptide binding profiles of DRB1∗08:03 and DRB1∗11:01 suggest a common etiology of immune-mediated thrombotic thrombocytopenic purpura. J Thromb Haemost 2023; 21:616-628. [PMID: 36696200 DOI: 10.1016/j.jtha.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/05/2022] [Accepted: 09/23/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND Immune-mediated thrombotic thrombocytopenic purpura (iTTP) is an ultra-rare autoimmune disorder caused by autoantibodies against ADAMTS13. A strong association of DRB1∗11 with iTTP and DRB1∗11-restricted T-cell epitopes in ADAMTS13 have been reported in Europeans, whereas we previously found DRB1∗08:03 as a susceptible allele in Japanese. OBJECTIVES The limited information is available regarding a susceptible allele and its T-cell epitopes in Japanese patients with iTTP. MATERIALS AND METHODS We conducted a reanalysis on iTTP-predisposing alleles using 3 distinct Japanese control groups. Subsequently, a novel human leukocyte antigen (HLA)-peptide expression assay (MHC-density assay) was used to identify the presentation of 24 ADAMTS13-derived peptides, including the regions that were identified previously by MHC-peptidome analysis and/or T-cell assays or predicted by NetMHCIIpan-4.0, to DRB1∗08:03 and DRB1∗11:01. RESULTS We reconfirmed the strong association of DRB1∗08:03 with iTTP, as well as the absence of the secondary risk alleles and protective alleles in Japanese iTTP, which altogether reveal that the HLA association pattern is completely different between the European and Japanese iTTP. MHC-density assay found the 3 ADAMTS13-derived peptides in the spacer domain as a potential strong binder to DRB1∗08:03. Moreover, 6 peptides in the metalloprotease, spacer, sixth thrombospondin-1 repeat, and CUB domains in ADAMTS13 showed increased presentation by both DRB1∗08:03 and DRB1∗11:01. CONCLUSION Altogether, the findings of distinct HLA-DR association with iTTP across populations and the presentation of common peptides by DRB1∗08:03 and DRB1∗11:01 suggest that the same ADAMTS13-derived peptides might be presented and trigger the activation of autoreactive CD4+ T cells, leading to production of anti-ADAMTS13 autoantibodies by autoreactive B cells.
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Affiliation(s)
- Kazuya Sakai
- Department of Blood Transfusion Medicine, Nara Medical University, Kashihara, Japan
| | - Hiroko Miyadera
- Department of Medical Genetics, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Masayuki Kubo
- Department of Blood Transfusion Medicine, Nara Medical University, Kashihara, Japan
| | | | - Masanori Matsumoto
- Department of Blood Transfusion Medicine, Nara Medical University, Kashihara, Japan.
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Li CW, Osman R, Menconi F, Faustino LC, Kim K, Clarke OB, Hou H, Tomer Y. Cepharanthine Blocks Presentation of Thyroid and Islet Peptides in a Novel Humanized Autoimmune Diabetes and Thyroiditis Mouse Model. Front Immunol 2021; 12:796552. [PMID: 34987519 PMCID: PMC8721038 DOI: 10.3389/fimmu.2021.796552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
Autoimmune polyglandular syndrome type 3 variant (APS3v) refers to an autoimmune condition in which both type 1 diabetes (T1D) and autoimmune thyroiditis (AITD) develop in the same individual. HLA-DR3 confers the strongest susceptibility to APS3v. Previously we reported a unique amino acid signature pocket that predisposes to APS3v. We found that this pocket is flexible and can trigger APS3v by presenting both thyroid (Tg.1571, TPO.758) and islet (GAD.492) peptides to induce autoimmune response. We hypothesized that blocking the specific APS3v-HLA-DR3 pocket from presenting thyroid/islet antigens can block the autoimmune response in APS3v. To test this hypothesis we performed a virtual screen of small molecules blocking APS3v-HLA-DR3, and identified 11 small molecules hits that were predicted to block APS3v-HLA-DR3. Using the baculovirus-produced recombinant APS3v-HLA-DR3 protein we tested the 11 small molecules in an in vitro binding assay. We validated 4 small molecule hits, S9, S5, S53 and S15, that could block the APS3v-HLA-DR3 pocket in vitro. We then developed a novel humanized APS3v mouse model induced by co-immunizing a peptide mix of Tg.1571, TPO.758 and GAD.492. The immunized mice developed strong T-cell and antibody responses to the thyroid/islet peptides, as well as mouse thyroglobulin. In addition, the mice showed significantly lower free T4 levels compared to controls. Using the APS3v mouse model, we showed that one of the 4 small molecules, Cepharanthine (S53), blocked T-cell activation by thyroid/islet peptides ex vivo and in vivo. These findings suggested Cepharanthine may have a therapeutic potential in APS3v patients carrying the specific APS3v-HLA-DR3 pocket.
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MESH Headings
- Animals
- Anti-Inflammatory Agents, Non-Steroidal/therapeutic use
- Antigen Presentation
- Autoantigens/immunology
- Benzylisoquinolines/therapeutic use
- Binding Sites/genetics
- Cells, Cultured
- Diabetes Mellitus, Type 1/drug therapy
- Diabetes Mellitus, Type 1/immunology
- Disease Models, Animal
- Genetic Predisposition to Disease
- Glutamate Decarboxylase/immunology
- HLA-DR3 Antigen/genetics
- HLA-DR3 Antigen/metabolism
- Humans
- Immunity, Humoral
- Immunization
- Iodide Peroxidase/immunology
- Iron-Binding Proteins/immunology
- Islets of Langerhans/immunology
- Lymphocyte Activation
- Mice
- Mice, SCID
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Polyendocrinopathies, Autoimmune/drug therapy
- Polyendocrinopathies, Autoimmune/immunology
- T-Lymphocytes/immunology
- Thyroglobulin/genetics
- Thyroglobulin/immunology
- Thyroiditis, Autoimmune/drug therapy
- Thyroiditis, Autoimmune/immunology
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Affiliation(s)
- Cheuk Wun Li
- The Fleischer Institute for Diabetes and Metabolism, Department of Medicine, Albert Einstein College of Medicine, New York, NY, United States
| | - Roman Osman
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Larissa C. Faustino
- The Fleischer Institute for Diabetes and Metabolism, Department of Medicine, Albert Einstein College of Medicine, New York, NY, United States
| | - Kookjoo Kim
- Department of Anesthesiology, Columbia University, New York, NY, United States
- Department of Physiology, Columbia University, New York, NY, United States
| | - Oliver B. Clarke
- Department of Anesthesiology, Columbia University, New York, NY, United States
- Department of Physiology, Columbia University, New York, NY, United States
| | - Hanxi Hou
- The Fleischer Institute for Diabetes and Metabolism, Department of Medicine, Albert Einstein College of Medicine, New York, NY, United States
| | - Yaron Tomer
- The Fleischer Institute for Diabetes and Metabolism, Department of Medicine, Albert Einstein College of Medicine, New York, NY, United States
- *Correspondence: Yaron Tomer,
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Aran A, Peg V, Rabanal RM, Bernadó C, Zamora E, Molina E, Arribas YA, Arribas J, Pérez J, Roura-Mir C, Carrascal M, Cortés J, Martí M. Epstein-Barr Virus+ B Cells in Breast Cancer Immune Response: A Case Report. Front Immunol 2021; 12:761798. [PMID: 34868006 PMCID: PMC8637110 DOI: 10.3389/fimmu.2021.761798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022] Open
Abstract
EBV-specific T cells have been recently described to be involved in fatal encephalitis and myocarditis in cancer patients after immune checkpoint therapies. Here, we report the study of a human triple-negative breast cancer tumor (TNBC) and EBV-transformed B cells obtained from a patient-derived xenograft (PDX) that progressed into a lymphocytic neoplasm named xenograft-associated B-cell lymphoma (XABCL). T-cell receptor (TCR) high-throughput sequencing was performed to monitor the T-cell clonotypes present in the different samples. Forty-three T-cell clonotypes were found infiltrating the XABCL tissue after three passes in mice along 6 months. Eighteen of these (42%) were also found in the TNBC biopsy. TCR infiltrating the XABCL tissue showed a very restricted T-cell repertoire as compared with the biopsy-infiltrating T cells. Consequently, T cells derived from the TNBC biopsy were expanded in the presence of the B-cell line obtained from the XABCL (XABCL-LCL), after which the TCR repertoire obtained was again very restricted, i.e., only certain clonotypes were selected by the B cells. A number of these TCRs had previously been reported as sequences involved in infection, cancer, and/or autoimmunity. We then analyzed the immunopeptidome from the XABCL-LCL, to identify putative B-cell-associated peptides that might have been expanding these T cells. The HLA class I and class II-associated peptides from XABCL-LCL were then compared with published repertoires from LCL of different HLA typing. Proteins from the antigen processing and presentation pathway remained significantly enriched in the XABCL-LCL repertoire. Interestingly, some class II-presented peptides were derived from cancer-related proteins. These results suggest that bystander tumor-infiltrating EBV+ B cells acting as APC may be able to interact with tumor-infiltrating T cells and influence the TCR repertoire in the tumor site.
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Affiliation(s)
- Andrea Aran
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Vicente Peg
- Translational Molecular Pathology, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Rosa Maria Rabanal
- Unitat de Patologia Murina i Comparada, Department of Animal Medicine and Surgery, Veterinary Faculty, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Cristina Bernadó
- Preclinical and Translational Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Esther Zamora
- Breast Cancer Unit, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Elisa Molina
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Yago A Arribas
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Joaquín Arribas
- Preclinical and Translational Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - José Pérez
- International Breast Cancer Center (BCC), Quironsalud Group, Barcelona, Spain
| | - Carme Roura-Mir
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Montserrat Carrascal
- Biological and Environmental Proteomics, Institute of Biomedical Research of Barcelona, Spanish National Research Council, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IIBB-CSIC/IDIBAPS), Barcelona, Spain
| | - Javier Cortés
- Breast Cancer Unit, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Barcelona, Spain.,International Breast Cancer Center (BCC), Quironsalud Group, Barcelona, Spain
| | - Mercè Martí
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
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8
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Ramarathinam SH, Ho BK, Dudek NL, Purcell AW. HLA class II immunopeptidomics reveals that co-inherited HLA-allotypes within an extended haplotype can improve proteome coverage for immunosurveillance. Proteomics 2021; 21:e2000160. [PMID: 34357683 DOI: 10.1002/pmic.202000160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 01/05/2023]
Abstract
Human leucocyte antigen (HLA) class II molecules in humans are encoded by three different loci, HLA-DR, -DQ, and -DP. These molecules share approximately 70% sequence similarity and all present peptide ligands to circulating T cells. While the peptide repertoires of numerous HLA-DR, -DQ, and -DP allotypes have been examined, there have been few reports on the combined repertoire of these co-inherited molecules expressed in a single cell as an extended HLA haplotype. Here we describe the endogenous peptide repertoire of a human B lymphoblastoid cell line (C1R) expressing the class II haplotype HLA-DR12/DQ7/DP4. We have identified 71350 unique naturally processed peptides presented collectively by HLA-DR12, HLA-DQ7, or HLA-DP4. The resulting "haplodome" is complemented by the cellular proteome defined by standard LC-MS/MS approaches. This large dataset has shed light on properties of these class II ligands especially the preference for membrane and extracellular source proteins. Our data also provides insights into the co-evolution of these conserved haplotypes of closely linked and co-inherited HLA molecules; which together increase sequence coverage of cellular proteins for immune surveillance with minimal overlap between each co-inherited HLA-class II allomorph.
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Affiliation(s)
- Sri H Ramarathinam
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Bosco K Ho
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Nadine L Dudek
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
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9
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Höttler A, März L, Lübke M, Rammensee HG, Stevanović S. Broad and Efficient Activation of Memory CD4 + T Cells by Novel HAdV- and HCMV-Derived Peptide Pools. Front Immunol 2021; 12:700438. [PMID: 34322126 PMCID: PMC8312486 DOI: 10.3389/fimmu.2021.700438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/21/2021] [Indexed: 12/03/2022] Open
Abstract
Reactivation of Human Cytomegalovirus (HCMV) and Human Adenovirus (HAdV) in immunocompromised patients following stem cell transplantation (SCT) or solid organ transplantation (SOT) is associated with high morbidity and mortality. The adoptive transfer of virus-specific CD8+ and CD4+ T cells has been shown to re-establish the antiviral T-cell response and improve clinical outcome. The viral load in immunocompromised patients can efficiently be reduced solely by the infusion of virus-specific CD4+ T cells. The identification of CD4+ T-cell epitopes has mainly focused on a limited number of viral proteins that were characterized as immunodominant. Here, we used in silico prediction to determine promiscuous CD4+ T-cell epitopes from the entire proteomes of HCMV and HAdV. Immunogenicity testing with enzyme-linked immuno spot (ELISpot) assays and intracellular cytokine staining (ICS) revealed numerous novel CD4+ T-cell epitopes derived from a broad spectrum of viral antigens. We identified 17 novel HCMV-derived and seven novel HAdV-derived CD4+ T-cell epitopes that were recognized by > 50% of the assessed peripheral blood mononuclear cell (PBMC) samples. The newly identified epitopes were pooled with previously published, retested epitopes to stimulate virus-specific memory T cells in PBMCs from numerous randomly selected blood donors. Our peptide pools induced strong IFNγ secretion in 46 out of 48 (HCMV) and 31 out of 31 (HAdV) PBMC cultures. In conclusion, we applied an efficient method to screen large viral proteomes for promiscuous CD4+ T-cell epitopes to improve the detection and isolation of virus-specific T cells in a clinical setting.
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Affiliation(s)
- Alexander Höttler
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Léo März
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Maren Lübke
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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10
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Hosseini SS, Aghaiypour Kolyani K, Rafiei Tabatabaei R, Goudarzi H, Akhavan Sepahi A, Salemi M. In silico prediction of B and T cell epitopes based on NDV fusion protein for vaccine development against Newcastle disease virus. Vet Res Forum 2021; 12:157-165. [PMID: 34345381 PMCID: PMC8328245 DOI: 10.30466/vrf.2019.98625.2351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/07/2019] [Indexed: 11/24/2022]
Abstract
Newcastle disease (ND) is known as the most common diseases of economic importance worldwide. Vaccination against virulent strains of Newcastle disease virus (NDV) has failed during some outbreaks. Here, we aimed to assess the epitopes of NDV fusion protein as targets for a peptide-based vaccine. To explore the most antigenic epitopes on the F protein, we retrieved virulent strains of genotype VII from National Center for Biotechnology Information (NCBI). Linear and conformational B-cell epitopes were identified. Moreover, T-cell epitopes with high and moderate binding affinities to human major histocompatibility complex (MHC) class I and class II alleles were predicted using bioinformatics tools. Subsequently, the overlapped epitopes of B-cell and MHC class I and MHC class II were determined. To validate our predictions, the best epitopes were docked, to chicken MHC class I (B-F) alleles using the HADDOCK flexible docking server. Seven ‘high ranked epitopes’ were identified. Among them, ‘LYCTRIVTF’ and ‘MRATYLETL’ showed the highest scores. The other five epitopes including LSGEFDATY, LTTPPYMALK, LYLTELTTV, DCIKITQQV and SIAATNEAV obtained very encouraging results as well. SIAATNEAV had been recognized as a neutralizing epitope of F protein using monoclonal antibodies before. Taken together, our results demonstrated that the identified epitopes needed to be tested by in vitro and in vivo experiments.
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Affiliation(s)
| | - Khosrow Aghaiypour Kolyani
- Department of Genomics and Genetic Engineering, Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Robab Rafiei Tabatabaei
- Department of Microbiology, Faculty of Basic Sciences, Islamic Azad University, Tehran North Branch, Tehran, Iran
| | - Hossein Goudarzi
- Central Laboratory Department, Razi Vaccine and Serum Research Institute Agricultural Research, AREEO, Karaj, Iran
| | - Abbas Akhavan Sepahi
- Department of Microbiology, Faculty of Science, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Maryam Salemi
- Department of Genomics and Genetic Engineering, Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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11
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Haabeth OAW, Hennig K, Fauskanger M, Løset GÅ, Bogen B, Tveita A. CD4+ T-cell killing of multiple myeloma cells is mediated by resident bone marrow macrophages. Blood Adv 2020; 4:2595-605. [PMID: 32544236 DOI: 10.1182/bloodadvances.2020001434] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/10/2020] [Indexed: 12/30/2022] Open
Abstract
CD4+ T cells may induce potent antitumor immune responses through interaction with antigen-presenting cells within the tumor microenvironment. Using a murine model of multiple myeloma, we demonstrated that adoptive transfer of idiotype-specific CD4+ T cells may elicit curative responses against established multifocal myeloma in bone marrow. This finding indicates that the myeloma bone marrow niche contains antigen-presenting cells that may be rendered tumoricidal. Given the complexity of the bone marrow microenvironment, the mechanistic basis of such immunotherapeutic responses is not known. Through a functional characterization of antitumor CD4+ T-cell responses within the bone marrow microenvironment, we found that killing of myeloma cells is orchestrated by a population of bone marrow-resident CD11b+F4/80+MHC-IIHigh macrophages that have taken up and present secreted myeloma protein. The present results demonstrate the potential of resident macrophages as powerful mediators of tumor killing within the bone marrow and provide a basis for novel therapeutic strategies against multiple myeloma and other malignancies that affect the bone marrow.
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12
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Demmers LC, Wu W, Heck AJR. HLA Class II Presentation Is Specifically Altered at Elevated Temperatures in the B-Lymphoblastic Cell Line JY. Mol Cell Proteomics 2021; 20:100089. [PMID: 33933681 PMCID: PMC8724904 DOI: 10.1016/j.mcpro.2021.100089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/25/2021] [Accepted: 04/13/2021] [Indexed: 12/22/2022] Open
Abstract
Human leukocyte antigen (HLA) molecules play critical roles in our adaptive immune system by signaling a cell's health status to the immune system, through presentation of small peptides. Understanding HLA biology is important because of its prominent role in autoimmune diseases and cancer immunotherapy. Although both the HLA class I and class II antigen processing and presentation pathways have been studied extensively, the fundamental rules in HLA class II antigen presentation still remain less understood. To clarify the mechanistic and adaptive differences between the HLA systems, we challenged a B lymphoblastic cell line (JY), widely used as model system in studying antigen presentation, with a high temperature treatment to mimic a "fever-like state", representing one of the most common physiological responses to infection. In the absence of real invading pathogenic peptides to present, we could focus on delineating the intrinsic HLA pathway adaptations in response to high temperature in this particular cell line. Following a three-pronged approach, we performed quantitative analyses of the proteome, the HLA class I ligandome, as well as the HLA class II ligandome. The data reveals that elevated temperature may already prepare these cells for an immune-like response through increased HLA class II presentation capacity and specific release of, from the invariant chain originating, CLIP peptides. Interestingly, at high temperature, prominent changes in the composition of the CLIP repertoire were observed, with enrichment of peptides containing C-terminal extensions beyond the CLIP-core region. Collectively, these illustrate intriguing temperature sensitive adaptations in this B cell line.
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Affiliation(s)
- Laura C Demmers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands; Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands; Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands; Netherlands Proteomics Centre, Utrecht, Netherlands.
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13
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Schmidt KG, Nganou-Makamdop K, Tenbusch M, El Kenz B, Maier C, Lapuente D, Überla K, Spriewald B, Bergmann S, Harrer EG, Harrer T. SARS-CoV-2-Seronegative Subjects Target CTL Epitopes in the SARS-CoV-2 Nucleoprotein Cross-Reactive to Common Cold Coronaviruses. Front Immunol 2021; 12:627568. [PMID: 33995351 PMCID: PMC8113865 DOI: 10.3389/fimmu.2021.627568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/15/2021] [Indexed: 12/22/2022] Open
Abstract
The beta-coronavirus SARS-CoV-2 induces severe disease (COVID-19) mainly in elderly persons with risk factors, whereas the majority of patients experience a mild course of infection. As the circulating common cold coronaviruses OC43 and HKU1 share some homologous sequences with SARS-CoV-2, beta-coronavirus cross-reactive T-cell responses could influence the susceptibility to SARS-CoV-2 infection and the course of COVID-19. To investigate the role of beta-coronavirus cross-reactive T-cells, we analyzed the T-cell response against a 15 amino acid long peptide (SCoV-DP15: DLSPRWYFYYLGTGP) from the SARS-CoV-2 nucleoprotein sequence with a high homology to the corresponding sequence (QLLPRWYFYYLGTGP) in OC43 and HKU1. SCoV-DP15-specific T-cells were detected in 4 out of 23 (17.4%) SARS-CoV-2-seronegative healthy donors. As HIV-1 infection is a potential risk factor for COVID-19, we also studied a cohort of HIV-1-infected patients on antiretroviral therapy. 44 out of these 116 HIV-1-infected patients (37.9%) showed a specific recognition of the SCoV-DP15 peptide or of shorter peptides within SCoV-DP15 by CD4+ T-cells and/or by CD8+ T-cells. We could define several new cross-reactive HLA-I-restricted epitopes in the SARS-CoV-2 nucleoprotein such as SPRWYFYYL (HLA-B*07, HLA-B*35), DLSPRWYFYY (HLA-A*02), LSPRWYFYY (HLA-A*29), WYFYYLGTGP and WYFYYLGT. Epitope specific CD8+ T-cell lines recognized corresponding epitopes within OC43 and HKU1 to a similar degree or even at lower peptide concentrations suggesting that they were induced by infection with OC43 or HKU1. Our results confirm that SARS-CoV-2-seronegative subjects can target SARS-CoV-2 not only by beta-coronavirus cross-reactive CD4+ T-cells but also by cross-reactive CD8+ cytotoxic T-cells (CTL). The delineation of cross-reactive T-cell epitopes contributes to an efficient epitope-specific immunomonitoring of SARS-CoV-2-specific T-cells. Further prospective studies are needed to prove a protective role of cross-reactive T-cells and their restricting HLA alleles for control of SARS-CoV-2 infection. The frequent observation of SARS-CoV-2-reactive T-cells in HIV-1-infected subjects could be a reason that treated HIV-1 infection does not seem to be a strong risk factor for the development of severe COVID-19.
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Affiliation(s)
- Katja G. Schmidt
- Infectious Disease and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Krystelle Nganou-Makamdop
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Matthias Tenbusch
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Boutaina El Kenz
- Infectious Disease and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Clara Maier
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Dennis Lapuente
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Klaus Überla
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Bernd Spriewald
- Department of Medicine 5, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Silke Bergmann
- Infectious Disease and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Ellen G. Harrer
- Infectious Disease and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Harrer
- Infectious Disease and Immunodeficiency Section, Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
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14
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Azam A, Mallart S, Illiano S, Duclos O, Prades C, Maillère B. Introduction of Non-natural Amino Acids Into T-Cell Epitopes to Mitigate Peptide-Specific T-Cell Responses. Front Immunol 2021; 12:637963. [PMID: 33777029 PMCID: PMC7991740 DOI: 10.3389/fimmu.2021.637963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/17/2021] [Indexed: 11/18/2022] Open
Abstract
Non-natural modifications are widely introduced into peptides to improve their therapeutic efficacy, but their impact on immunogenicity remains largely unknown. As the CD4 T-cell response is a key factor in triggering immunogenicity, we investigated the effect of introducing D-amino acids (Daa), amino isobutyric acid (Aib), N-methylation, Cα-methylation, reduced amide, and peptoid bonds into an immunoprevalent T-cell epitope on binding to a set of HLA-DR molecules, recognition, and priming of human T cells. Modifications are differentially accepted at multiple positions, but are all tolerated in the flanking regions. Introduction of Aib and Daa in the binding core had the most deleterious effect on binding to HLA-DR molecules and T-cell activation. Their introduction at the positions close to the P1 anchor residue abolished T-cell priming, suggesting they might be sufficient to dampen peptide immunogenicity. Other modifications led to variable effects on binding to HLA-DR molecules and T-cell reactivity, but none exhibited an increased ability to stimulate T cells. Altogether, non-natural modifications appear generally to diminish binding to HLA-DR molecules and hence T-cell stimulation. These data might guide the design of therapeutic peptides to make them less immunogenic.
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Affiliation(s)
- Aurélien Azam
- Sanofi, Biologics Research, Vitry-sur-Seine, France.,Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
| | - Sergio Mallart
- Sanofi R&D, Integrated Drug Discovery, Chilly-Mazarin, France
| | - Stephane Illiano
- Sanofi R&D, Cardiovascular Diseases & Metabolism, Chilly-Mazarin, France
| | - Olivier Duclos
- Sanofi R&D, Integrated Drug Discovery, Chilly-Mazarin, France
| | | | - Bernard Maillère
- Université de Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SIMoS, Gif-sur-Yvette, France
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15
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Roerden M, Märklin M, Salih HR, Bethge WA, Klein R, Rammensee HG, Nelde A, Walz JS. Expression levels of HLA-DR in acute myeloid leukemia: implications for antigenicity and clinical outcome. Leuk Lymphoma 2021; 62:1907-1919. [PMID: 33648413 DOI: 10.1080/10428194.2021.1885659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Low human leukocyte antigen (HLA)-DR expression might compromise CD4+ T-cell-mediated anti-tumor immunity. Its immunological and clinical significance however remain undefined in non-promyelocytic acute myeloid leukemia (AML). Taking advantage of mass spectrometry-based immunopeptidome analysis of primary AML samples (n = 31), we studied the implications of low HLA-DR expression for antigen presentation and analyzed its association with disease characteristics and survival within a cohort of 399 AML patients. Remarkably, overall HLA-DR/DQ immunopeptidome diversity was preserved in AML with low HLA-DR expression (HLA-DRlow AML) and was associated with a shift in HLA-DR/DQ allotype abundances (HLA-DQ to HLA-DR/DQ ligand ratio 0.36 vs 0.19 in HLA-DRlow and HLA-DRhigh patients, respectively). Consistent with unimpaired antigenicity, survival was similar in HLA-DRlow and HLA-DRhigh patients. Demonstrating for the first time that overall HLA-DR/DQ antigen presentation is preserved in HLA-DRlow AML, our findings provide a rationale for the non-inferior outcome observed in HLA-DRlow AML patients.
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Affiliation(s)
- Malte Roerden
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Melanie Märklin
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Wolfgang A Bethge
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, Germany
| | - Annika Nelde
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
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16
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Forlani G, Michaux J, Pak H, Huber F, Marie Joseph EL, Ramia E, Stevenson BJ, Linnebacher M, Accolla RS, Bassani-Sternberg M. CIITA-Transduced Glioblastoma Cells Uncover a Rich Repertoire of Clinically Relevant Tumor-Associated HLA-II Antigens. Mol Cell Proteomics 2021; 20:100032. [PMID: 33592498 PMCID: PMC8724627 DOI: 10.1074/mcp.ra120.002201] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 12/30/2022] Open
Abstract
CD4+ T cell responses are crucial for inducing and maintaining effective anticancer immunity, and the identification of human leukocyte antigen class II (HLA-II) cancer-specific epitopes is key to the development of potent cancer immunotherapies. In many tumor types, and especially in glioblastoma (GBM), HLA-II complexes are hardly ever naturally expressed. Hence, little is known about immunogenic HLA-II epitopes in GBM. With stable expression of the class II major histocompatibility complex transactivator (CIITA) coupled to a detailed and sensitive mass spectrometry-based immunopeptidomics analysis, we here uncovered a remarkable breadth of the HLA-ligandome in HROG02, HROG17, and RA GBM cell lines. The effect of CIITA expression on the induction of the HLA-II presentation machinery was striking in each of the three cell lines, and it was significantly higher compared with interferon gamma (IFNɣ) treatment. In total, we identified 16,123 unique HLA-I peptides and 32,690 unique HLA-II peptides. In order to genuinely define the identified peptides as true HLA ligands, we carefully characterized their association with the different HLA allotypes. In addition, we identified 138 and 279 HLA-I and HLA-II ligands, respectively, most of which are novel in GBM, derived from known GBM-associated tumor antigens that have been used as source proteins for a variety of GBM vaccines. Our data further indicate that CIITA-expressing GBM cells acquired an antigen presenting cell-like phenotype as we found that they directly present external proteins as HLA-II ligands. Not only that CIITA-expressing GBM cells are attractive models for antigen discovery endeavors, but also such engineered cells have great therapeutic potential through massive presentation of a diverse antigenic repertoire.
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Affiliation(s)
- Greta Forlani
- Laboratories of General Pathology and Immunology "Giovanna Tosi", Department of Medicine and Surgery, School of Medicine, University of Insubria, Varese, Italy
| | - Justine Michaux
- Ludwig Cancer Research Center, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - HuiSong Pak
- Ludwig Cancer Research Center, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Florian Huber
- Ludwig Cancer Research Center, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Elodie Lauret Marie Joseph
- Ludwig Cancer Research Center, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Elise Ramia
- Laboratories of General Pathology and Immunology "Giovanna Tosi", Department of Medicine and Surgery, School of Medicine, University of Insubria, Varese, Italy
| | | | - Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, University Medical Center Rostock, Rostock, Germany
| | - Roberto S Accolla
- Laboratories of General Pathology and Immunology "Giovanna Tosi", Department of Medicine and Surgery, School of Medicine, University of Insubria, Varese, Italy
| | - Michal Bassani-Sternberg
- Ludwig Cancer Research Center, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.
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17
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Forlani G, Shallak M, Celesti F, Accolla RS. Unveiling the Hidden Treasury: CIITA-Driven MHC Class II Expression in Tumor Cells to Dig up the Relevant Repertoire of Tumor Antigens for Optimal Stimulation of Tumor Specific CD4+ T Helper Cells. Cancers (Basel) 2020; 12:cancers12113181. [PMID: 33138029 PMCID: PMC7693840 DOI: 10.3390/cancers12113181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 12/11/2022] Open
Abstract
Despite the recent enthusiasm generated by novel immunotherapeutic approaches against cancer based on immune checkpoint inhibitors, it becomes increasingly clear that single immune-based strategies are not sufficient to defeat the various forms and types of tumors. Within this frame, novel vaccination strategies that are based on optimal stimulation of the key cell governing adaptive immunity, the CD4+ T helper cell, will certainly help in constructing more efficient treatments. In this review, we will focus on this aspect, mainly describing our past and recent contributions that, starting with a rather unorthodox approach, have ended up with the proposition of a new idea for making available an unprecedented extended repertoire of tumor antigens, both in quantitative and qualitative terms, to tumor-specific CD4+ T helper cells. Our approach is based on rendering the very same tumor cells antigen presenting cells for their own tumor antigens by gene transfer of CIITA, the major transcriptional coordinator of MHC class II expression discovered in our laboratory. CIITA-driven MHC class II-expressing tumor cells optimally stimulate in vivo tumor specific MHC class II-restricted CD4 T cells generating specific and long lasting protective immunity against the tumor. We will discuss the mechanism underlying protection and elaborate not only on the applicability of this approach for novel vaccination strategies amenable to clinical setting, but also on the consequence of our discoveries on sedimented immunological dogmas that are related to antigen presentation.
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18
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Wang J, Jelcic I, Mühlenbruch L, Haunerdinger V, Toussaint NC, Zhao Y, Cruciani C, Faigle W, Naghavian R, Foege M, Binder TMC, Eiermann T, Opitz L, Fuentes-Font L, Reynolds R, Kwok WW, Nguyen JT, Lee JH, Lutterotti A, Münz C, Rammensee HG, Hauri-Hohl M, Sospedra M, Stevanovic S, Martin R. HLA-DR15 Molecules Jointly Shape an Autoreactive T Cell Repertoire in Multiple Sclerosis. Cell 2020; 183:1264-1281.e20. [PMID: 33091337 PMCID: PMC7707104 DOI: 10.1016/j.cell.2020.09.054] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 08/04/2020] [Accepted: 09/18/2020] [Indexed: 12/16/2022]
Abstract
The HLA-DR15 haplotype is the strongest genetic risk factor for multiple sclerosis (MS), but our understanding of how it contributes to MS is limited. Because autoreactive CD4+ T cells and B cells as antigen-presenting cells are involved in MS pathogenesis, we characterized the immunopeptidomes of the two HLA-DR15 allomorphs DR2a and DR2b of human primary B cells and monocytes, thymus, and MS brain tissue. Self-peptides from HLA-DR molecules, particularly from DR2a and DR2b themselves, are abundant on B cells and thymic antigen-presenting cells. Furthermore, we identified autoreactive CD4+ T cell clones that can cross-react with HLA-DR-derived self-peptides (HLA-DR-SPs), peptides from MS-associated foreign agents (Epstein-Barr virus and Akkermansia muciniphila), and autoantigens presented by DR2a and DR2b. Thus, both HLA-DR15 allomorphs jointly shape an autoreactive T cell repertoire by serving as antigen-presenting structures and epitope sources and by presenting the same foreign peptides and autoantigens to autoreactive CD4+ T cells in MS. HLA-DR15 present abundant HLA-DR-derived self-peptides on B cells Autoreactive T cells in MS recognize HLA-DR-derived self-peptides/DR15 complexes Foreign peptides/DR15 complexes trigger potential autoreactive T cells in MS HLA-DR15 shape an autoreactive T cell repertoire by cross-reactivity/restriction
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Affiliation(s)
- Jian Wang
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Ivan Jelcic
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Lena Mühlenbruch
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Veronika Haunerdinger
- Pediatric Stem Cell Transplantation, University Children's Hospital Zurich, Zurich 8032, Switzerland
| | - Nora C Toussaint
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich 8093, Switzerland; Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, MD 20850, USA
| | - Carolina Cruciani
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Wolfgang Faigle
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Reza Naghavian
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Magdalena Foege
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Thomas M C Binder
- HLA Laboratory of the Stefan Morsch Foundation (SMS), Birkenfeld 55765, Germany
| | - Thomas Eiermann
- Department of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Lennart Opitz
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology and University of Zurich, Zurich 8057, Switzerland
| | - Laura Fuentes-Font
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - Richard Reynolds
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Julie T Nguyen
- One Lambda, Inc., a part of Transplant Diagnostics Thermo Fisher Scientific, 22801 Roscoe Blvd., West Hills, CA 91304, USA
| | - Jar-How Lee
- One Lambda, Inc., a part of Transplant Diagnostics Thermo Fisher Scientific, 22801 Roscoe Blvd., West Hills, CA 91304, USA
| | - Andreas Lutterotti
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Hans-Georg Rammensee
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Mathias Hauri-Hohl
- Pediatric Stem Cell Transplantation, University Children's Hospital Zurich, Zurich 8032, Switzerland
| | - Mireia Sospedra
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Stefan Stevanovic
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Roland Martin
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland.
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19
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Heuberger C, Pott J, Maloy KJ. Why do intestinal epithelial cells express MHC class II? Immunology 2020; 162:357-367. [PMID: 32966619 PMCID: PMC7968399 DOI: 10.1111/imm.13270] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 12/23/2022] Open
Abstract
Intestinal epithelial cells (IECs) constitute the border between the vast antigen load present in the intestinal lumen and the mucosal immune compartment. Their ability to express antigen processing and presentation machinery evokes the question whether IECs function as non-conventional antigen-presenting cells. Major histocompatibility complex (MHC) class II expression by non-haematopoietic cells, such as IECs, is tightly regulated by the class II transactivator (CIITA) and is classically induced by IFN-γ. As MHC class II expression by IECs is upregulated under inflammatory conditions, it has been proposed to activate effector CD4+ T (Teff) cells. However, other studies have reported contradictory results and instead suggested a suppressive role of antigen presentation by IECs, through regulatory T (Treg)-cell activation. Recent studies investigating the role of MHC class II + exosomes released by IECs also reported conflicting findings of either immune enhancing or immunosuppressive activities. Moreover, in addition to modulating inflammatory responses, recent findings suggest that MHC class II expression by intestinal stem cells may elicit crosstalk that promotes epithelial renewal. A more complete understanding of the different consequences of IEC MHC class II antigen presentation will guide future efforts to modulate this pathway to selectively invoke protective immunity while maintaining tolerance to beneficial antigens.
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Affiliation(s)
- Cornelia Heuberger
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Johanna Pott
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Hubrecht Organoid Technology, Utrecht, Netherlands
| | - Kevin Joseph Maloy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
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20
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Wendorff M, Garcia Alvarez HM, Østerbye T, ElAbd H, Rosati E, Degenhardt F, Buus S, Franke A, Nielsen M. Unbiased Characterization of Peptide-HLA Class II Interactions Based on Large-Scale Peptide Microarrays; Assessment of the Impact on HLA Class II Ligand and Epitope Prediction. Front Immunol 2020; 11:1705. [PMID: 32903714 PMCID: PMC7438773 DOI: 10.3389/fimmu.2020.01705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/25/2020] [Indexed: 12/12/2022] Open
Abstract
Human Leukocyte Antigen class II (HLA-II) molecules present peptides to T lymphocytes and play an important role in adaptive immune responses. Characterizing the binding specificity of single HLA-II molecules has profound impacts for understanding cellular immunity, identifying the cause of autoimmune diseases, for immunotherapeutics, and vaccine development. Here, novel high-density peptide microarray technology combined with machine learning techniques were used to address this task at an unprecedented level of high-throughput. Microarrays with over 200,000 defined peptides were assayed with four exemplary HLA-II molecules. Machine learning was applied to mine the signals. The comparison of identified binding motifs, and power for predicting eluted ligands and CD4+ epitope datasets to that obtained using NetMHCIIpan-3.2, confirmed a high quality of the chip readout. These results suggest that the proposed microarray technology offers a novel and unique platform for large-scale unbiased interrogation of peptide binding preferences of HLA-II molecules.
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Affiliation(s)
- Mareike Wendorff
- Genetics & Bioinformatics, Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Thomas Østerbye
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Hesham ElAbd
- Genetics & Bioinformatics, Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Elisa Rosati
- Genetics & Bioinformatics, Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Frauke Degenhardt
- Genetics & Bioinformatics, Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Søren Buus
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Andre Franke
- Genetics & Bioinformatics, Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Morten Nielsen
- IIBIO, UNSAM-CONICET, Buenos Aires, Argentina.,Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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21
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Qi J, Wang TJ, Li HX, Wu D, Du D, Wu JH, Shang LX, Chen L, Wang MN, Wang XF. Association of HLA class II (-DRB1,-DQB1,-DPB1) alleles and haplotypes on susceptibility to aplastic anemia in northern Chinese Han. Hum Immunol 2020; 81:685-691. [PMID: 32693929 DOI: 10.1016/j.humimm.2020.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 06/16/2020] [Accepted: 07/05/2020] [Indexed: 11/17/2022]
Abstract
The Human Leukocyte Antigen (HLA) genes, playing key roles in mediating the immune response, especially HLA class II alleles were suggested to play a role in the activation of autoreactive T-cells in aplastic anemia (AA). Previous studies in different ethnic groups have indicated that some of HLA-A,-B,-DRB1 alleles had a protective or susceptive association with the prevalence, pathogenesis and development of AA. HLA class II genes, especially HLA-DQB1 and -DPB1 alleles or haplotypes at high-resolution level associated with AA have not been fully identified in northern Chinese Han populations. The aim of this study was to identify association of the variations in HLA class II region with AA in northern Chinese Han population. A recent case-control study, including 96 AA patients and 824 healthy controls was performed. The high-resolution HLA genotyping was conducted by PCR-SBT, -SSO and NGS-ION S5TM platform. Based on genotypic data of the three loci, haplotype estimation was carried out. HLA-DRB1*15:01 (Pc = 2.87 × 10-3; OR = 2.11, 95% CI = 1.45-3.07) and HLA-DQB1*06:02 (Pc = 1.86 × 10-2; OR = 2.01, 95% CI = 1.32-3.06) were the risk and predisposition alleles to AA in northern Chinese Han after considering multiple testing. Moreover, the HLA-DRB1*15:01-DQB1*06:02 (Pc = 4.90 × 10-3; OR = 2.09, 95% CI = 1.37-3.19) and HLA-DRB1*14:05-DQB1*05:03 (Pc = 2.65 × 10-2; OR = 2.82, 95%CI = 1.45-5.50) haplotypes had direct strong relevance to AA and were the susceptible haplotypes. HLA-DPB1 alleles and 23 polymorphic amino acid residues spanning exon 2 ~ 4 of DPβ1 molecules have showed no statistically significant associations between AA and controls. The present findings establish a novel link between inherited HLA-DRB1,-DQB1,-DPB1 risk alleles and haplotypes in northern Chinese Han with AA, and open new avenues for development of targeted therapies to prevent or redirect immunopathology in AA.
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Affiliation(s)
- Jun Qi
- HLA Laboratory, Blood Center of Shaanxi Province, Institute of Xi'an Blood Bank, Xi'an, China.
| | - Tian-Ju Wang
- HLA Laboratory, Blood Center of Shaanxi Province, Institute of Xi'an Blood Bank, Xi'an, China
| | - Heng-Xin Li
- HLA Laboratory, Blood Center of Shaanxi Province, Institute of Xi'an Blood Bank, Xi'an, China
| | - Di Wu
- Department of Hematology, the First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an 710061, Shaanxi Province, China
| | - Dan Du
- Department of Tech Service, China Marrow Donor Program, Beijing 100013, China
| | - Jun-Hua Wu
- HLA Laboratory, Blood Center of Shaanxi Province, Institute of Xi'an Blood Bank, Xi'an, China
| | - Li-Xia Shang
- HLA Laboratory, Blood Center of Shaanxi Province, Institute of Xi'an Blood Bank, Xi'an, China
| | - Le Chen
- HLA Laboratory, Blood Center of Shaanxi Province, Institute of Xi'an Blood Bank, Xi'an, China
| | - Man-Ni Wang
- HLA Laboratory, Blood Center of Shaanxi Province, Institute of Xi'an Blood Bank, Xi'an, China
| | - Xiao-Fang Wang
- HLA Laboratory, Blood Center of Shaanxi Province, Institute of Xi'an Blood Bank, Xi'an, China
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22
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Jawa V, Terry F, Gokemeijer J, Mitra-Kaushik S, Roberts BJ, Tourdot S, De Groot AS. T-Cell Dependent Immunogenicity of Protein Therapeutics Pre-clinical Assessment and Mitigation-Updated Consensus and Review 2020. Front Immunol 2020; 11:1301. [PMID: 32695107 PMCID: PMC7338774 DOI: 10.3389/fimmu.2020.01301] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/22/2020] [Indexed: 01/01/2023] Open
Abstract
Immune responses to protein and peptide drugs can alter or reduce their efficacy and may be associated with adverse effects. While anti-drug antibodies (ADA) are a standard clinical measure of protein therapeutic immunogenicity, T cell epitopes in the primary sequences of these drugs are the key drivers or modulators of ADA response, depending on the type of T cell response that is stimulated (e.g., T helper or Regulatory T cells, respectively). In a previous publication on T cell-dependent immunogenicity of biotherapeutics, we addressed mitigation efforts such as identifying and reducing the presence of T cell epitopes or T cell response to protein therapeutics prior to further development of the protein therapeutic for clinical use. Over the past 5 years, greater insight into the role of regulatory T cell epitopes and the conservation of T cell epitopes with self (beyond germline) has improved the preclinical assessment of immunogenic potential. In addition, impurities contained in therapeutic drug formulations such as host cell proteins have also attracted attention and become the focus of novel risk assessment methods. Target effects have come into focus, given the emergence of protein and peptide drugs that target immune receptors in immuno-oncology applications. Lastly, new modalities are entering the clinic, leading to the need to revise certain aspects of the preclinical immunogenicity assessment pathway. In addition to drugs that have multiple antibody-derived domains or non-antibody scaffolds, therapeutic drugs may now be introduced via viral vectors, cell-based constructs, or nucleic acid based therapeutics that may, in addition to delivering drug, also prime the immune system, driving immune response to the delivery vehicle as well as the encoded therapeutic, adding to the complexity of assessing immunogenicity risk. While it is challenging to keep pace with emerging methods for the preclinical assessment of protein therapeutics and new biologic therapeutic modalities, this collective compendium provides a guide to current best practices and new concepts in the field.
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Affiliation(s)
- Vibha Jawa
- Predictive and Clinical Immunogenicity, PPDM, Merck & Co., Kenilworth, NJ, United States
| | | | - Jochem Gokemeijer
- Discovery Biotherapeutics, Bristol-Myers Squibb, Cambridge, MA, United States
| | | | | | - Sophie Tourdot
- BioMedicine Design, Pfizer Inc., Andover, MA, United States
| | - Anne S De Groot
- EpiVax, Inc., Providence, RI, United States.,Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
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23
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Schorer M, Lambert K, Rakebrandt N, Rost F, Kao KC, Yermanos A, Spörri R, Oderbolz J, Raeber ME, Keller CW, Lünemann JD, Rogler G, Boyman O, Oxenius A, Joller N. Rapid expansion of Treg cells protects from collateral colitis following a viral trigger. Nat Commun 2020; 11:1522. [PMID: 32251280 PMCID: PMC7090079 DOI: 10.1038/s41467-020-15309-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 02/28/2020] [Indexed: 12/12/2022] Open
Abstract
Foxp3+ regulatory T (Treg) cells are essential for maintaining peripheral tolerance and preventing autoimmunity. While genetic factors may predispose for autoimmunity, additional environmental triggers, such as viral infections, are usually required to initiate the onset of disease. Here, we show that viral infection with LCMV results in type I IFN-dependent Treg cell loss that is rapidly compensated by the conversion and expansion of Vβ5+ conventional T cells into iTreg cells. Using Vβ5-deficient mice, we show that these Vβ5+ iTreg cells are dispensable for limiting anti-viral immunity. Rather, the delayed replenishment of Treg cells in Vβ5-deficient mice compromises suppression of microbiota-dependent activation of CD8+ T cells, resulting in colitis. Importantly, recovery from clinical symptoms in IBD patients is marked by expansion of the corresponding Vβ2+ Treg population in humans. Collectively, we provide a link between a viral trigger and an impaired Treg cell compartment resulting in the initiation of immune pathology.
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Affiliation(s)
- Michelle Schorer
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Katharina Lambert
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Benaroya Research Institute at Virginia Mason, Seattle, WA, 98101, USA
| | - Nikolas Rakebrandt
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Felix Rost
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Kung-Chi Kao
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Alexander Yermanos
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
- Laboratory for Systems and Synthetic Immunology, D-BSSE, ETH Zurich, 4058, Basel, Switzerland
| | - Roman Spörri
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Josua Oderbolz
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Miro E Raeber
- Department of Immunology, University Hospital Zurich, Häldeliweg 4, 8044, Zurich, Switzerland
| | - Christian W Keller
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Department of Neurology with Institute of Translational Neurology, University Hospital Munster, 48149, Munster, Germany
| | - Jan D Lünemann
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Department of Neurology with Institute of Translational Neurology, University Hospital Munster, 48149, Munster, Germany
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, Häldeliweg 4, 8044, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Pestalozzistrasse 3/5, 8091, Zurich, Switzerland
| | - Annette Oxenius
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Nicole Joller
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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24
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Huszthy PC, Gopalakrishnan RP, Jacobsen JT, Haabeth OAW, Løset GÅ, Braathen R, Schenck K, Tveita AA, Munthe LA, Bogen B. B cell receptor ligation induces display of V-region peptides on MHC class II molecules to T cells. Proc Natl Acad Sci U S A 2019; 116:25850-9. [PMID: 31796587 DOI: 10.1073/pnas.1902836116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
B and T lymphocytes collaborate during immune responses to antigens. B cells use membrane-bound antibody as part of their antigen receptor while T cells use a different receptor that recognizes antigen fragments bound to MHC molecules. We show here that T cells can recognize the variable parts of the B cell receptor when these are presented on MHC molecules. A prerequisite for such receptor cross-talk is that the B cell receptor binds antigen. The cross-talk results in collaboration between B and T cells and production of antibodies directed against the antigen. The findings have implications for basic immune regulation. The results may also help us understand the mechanism behind the development of SLE-like autoimmune diseases and B cell lymphomas. The B cell receptors (BCRs) for antigen express variable (V) regions that are enormously diverse, thus serving as markers on individual B cells. V region-derived idiotypic (Id) peptides can be displayed as pId:MHCII complexes on B cells for recognition by CD4+ T cells. It is not known if naive B cells spontaneously display pId:MHCII in vivo or if BCR ligation is required for expression, thereby enabling collaboration between Id+ B cells and Id-specific T cells. Here, using a mouse model, we show that naive B cells do not express readily detectable levels of pId:MHCII. However, BCR ligation by Ag dramatically increases physical display of pId:MHCII, leading to activation of Id-specific CD4+ T cells, extrafollicular T–B cell collaboration and some germinal center formation, and production of Id+ IgG. Besides having implications for immune regulation, the results may explain how persistent activation of self-reactive B cells induces the development of autoimmune diseases and B cell lymphomas.
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25
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Abstract
The versatile clinical manifestations of the Hashimoto's chronic autoimmune thyroiditis often include psycho-neurological disorders. Although hypothyroidism disturbs significantly the ontogenesis and functions of central nervous system, causing in severe cases of myxedema profound impairment of cognitive abilities and even psychosis, the behavioral, motor and other psychoneurological disorders accompany euthyroid and slightly hypothyroid cases and periods of Hashimoto's disease as well, thus constituting the picture of so called "Hashimoto's encephalopathy". The entity, although discussed and explored for more than 50 years since its initial descriptions, remains an enigma of thyroidology and psychiatry, because its etiology and pathogenesis are obscure. The paper describes the development of current views on the role of thyroid in ontogeny and functions of brain, as well as classical and newest ideas on the etiology and pathogenesis of Hashimot's encephalopathy. The synopsis of the world case reports and research literature on this disorder is added with authors' own results obtained by study of 17 cases of Hashimoto's thyroiditis with schizophrenia-like clinical manifestations. The relation of the disease to adjuvant-like etiological factors is discussed. Three major mechanistic concepts of Hashimoto's encephalopathy are detailed, namely cerebral vasculitis theory, hormone dysregulation theory and concept, explaining the disease via direct action of the autoantibodies against various thyroid (thyroperoxidase, thyroglobulin, and TSH-receptor) and several extrathyroid antigens (alpha-enolase and other enzymes, gangliosides and MOG-protein, onconeuronal antigens) - all of them expressed in the brain. The article demonstrates that all above mentioned concepts intermingle and prone to unification, suggesting the unified scheme of pathogenesis for the Hashimoto's encephalopathy. The clinical manifestations, criteria, forms, course, treatment and prognosis of Hashimoto's encephalopathy and its comorbidity to other diseases - are also discussed in brief. The relation between Hashimoto's encephalopathy and non-vasculitis autoimmune encephalomyelitides of paraneoplastic and non-paraneoplastic origin is emphasized [1 figure, bibliography - 200 references].
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Affiliation(s)
- Leonid P Churilov
- Laboratory of the Mosaic of Autoimmunity, Saint Petersburg State University, Russia.
| | - Polina A Sobolevskaia
- Laboratory of the Mosaic of Autoimmunity, Saint Petersburg State University, Russia.
| | - Yuri I Stroev
- Laboratory of the Mosaic of Autoimmunity, Saint Petersburg State University, Russia.
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26
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Almond N, Berry N, Stebbings R, Preston M, Ham C, Page M, Ferguson D, Rose N, Li B, Mee ET, Hassall M, Stahl-Hennig C, Athanasopoulos T, Papagatsias T, Herath S, Benlahrech A, Dickson G, Meiser A, Patterson S. Vaccination of Macaques with DNA Followed by Adenoviral Vectors Encoding Simian Immunodeficiency Virus (SIV) Gag Alone Delays Infection by Repeated Mucosal Challenge with SIV. J Virol 2019; 93:e00606-19. [PMID: 31413132 DOI: 10.1128/JVI.00606-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/06/2019] [Indexed: 12/16/2022] Open
Abstract
The simian immunodeficiency virus (SIV) macaque model represents the best animal model for testing new human immunodeficiency virus type 1 (HIV-1) vaccines. Previous studies employing replication-defective adenovirus (rAd) vectors that transiently express SIV internal proteins induced T cell responses that controlled virus load but did not protect against virus challenge. However, we show for the first time that SIV gag delivered in a DNA prime followed by a boost with an rAd vector confers resistance to SIV intrarectal challenge. Other partially successful SIV/HIV-1 protective vaccines induce antibody to the envelope and neutralize the virus or mediate antibody-dependent cytotoxicity. Induction of CD8 T cells which do not prevent initial infection but eradicate infected cells before infection becomes established has also shown some success. In contrast, the vaccine described here mediates resistance by a different mechanism from that described above, which may reflect CD4 T cell activity. This could indicate an alternative approach for HIV-1 vaccine development. Vaccines aimed at inducing T cell responses to protect against human immunodeficiency virus (HIV) infection have been under development for more than 15 years. Replication-defective adenovirus (rAd) vaccine vectors are at the forefront of this work and have been tested extensively in the simian immunodeficiency virus (SIV) challenge macaque model. Vaccination with rAd vectors coding for SIV Gag or other nonenvelope proteins induces T cell responses that control virus load but disappointingly is unsuccessful so far in preventing infection, and attention has turned to inducing antibodies to the envelope. However, here we report that Mauritian cynomolgus macaques (MCM), Macaca fascicularis, vaccinated with unmodified SIV gag alone in a DNA prime followed by an rAd boost exhibit increased protection from infection by repeated intrarectal challenge with low-dose SIVmac251. There was no evidence of infection followed by eradication. A significant correlation was observed between cytokine expression by CD4 T cells and delayed infection. Vaccination with gag fused to the ubiquitin gene or fragmented, designed to increase CD8 magnitude and breadth, did not confer resistance to challenge or enhance immunity. On infection, a significant reduction in peak virus load was observed in all vaccinated animals, including those vaccinated with modified gag. These findings suggest that a nonpersistent viral vector vaccine coding for internal virus proteins may be able to protect against HIV type 1 (HIV-1) infection. The mechanisms are probably distinct from those of antibody-mediated virus neutralization or cytotoxic CD8 cell killing of virus-infected cells and may be mediated in part by CD4 T cells. IMPORTANCE The simian immunodeficiency virus (SIV) macaque model represents the best animal model for testing new human immunodeficiency virus type 1 (HIV-1) vaccines. Previous studies employing replication-defective adenovirus (rAd) vectors that transiently express SIV internal proteins induced T cell responses that controlled virus load but did not protect against virus challenge. However, we show for the first time that SIV gag delivered in a DNA prime followed by a boost with an rAd vector confers resistance to SIV intrarectal challenge. Other partially successful SIV/HIV-1 protective vaccines induce antibody to the envelope and neutralize the virus or mediate antibody-dependent cytotoxicity. Induction of CD8 T cells which do not prevent initial infection but eradicate infected cells before infection becomes established has also shown some success. In contrast, the vaccine described here mediates resistance by a different mechanism from that described above, which may reflect CD4 T cell activity. This could indicate an alternative approach for HIV-1 vaccine development.
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Kampstra ASB, van Heemst J, Janssen GM, de Ru AH, van Lummel M, van Veelen PA, Toes REM. Ligandomes obtained from different HLA-class II-molecules are homologous for N- and C-terminal residues outside the peptide-binding cleft. Immunogenetics 2019; 71:519-530. [PMID: 31520135 PMCID: PMC6790208 DOI: 10.1007/s00251-019-01129-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/23/2019] [Indexed: 12/31/2022]
Abstract
Human CD4+ T lymphocytes play an important role in inducing potent immune responses. T cells are activated and stimulated by peptides presented in human leucocyte antigen (HLA)-class II molecules. These HLA-class II molecules typically present peptides of between 12 and 20 amino acids in length. The region that interacts with the HLA molecule, designated as the peptide-binding core, is highly conserved in the residues which anchor the peptide to the molecule. In addition, as these peptides are the product of proteolytic cleavages, certain conserved residues may be expected at the N- and C-termini outside the binding core. To study whether similar conserved residues are present in different cell types, potentially harbouring different proteolytic enzymes, the ligandomes of HLA-DRB1*03:01/HLA-DRB > 1 derived from two different cell types (dendritic cells and EBV-transformed B cells) were identified with mass spectrometry and the binding core and N- and C-terminal residues of a total of 16,568 peptides were analysed using the frequencies of the amino acids in the human proteome. Similar binding motifs were found as well as comparable conservations in the N- and C-terminal residues. Furthermore, the terminal conservations of these ligandomes were compared to the N- and C-terminal conservations of the ligandome acquired from dendritic cells homozygous for HLA-DRB1*04:01. Again, comparable conservations were evident with only minor differences. Taken together, these data show that there are conservations in the terminal residues of peptides, presumably the result of the activity of proteases involved in antigen processing.
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Affiliation(s)
- Arieke S B Kampstra
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Jurgen van Heemst
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - George M Janssen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H de Ru
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Menno van Lummel
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - René E M Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
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28
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Singh A, Ramachandran S, Graham ML, Daneshmandi S, Heller D, Suarez-Pinzon WL, Balamurugan AN, Ansite JD, Wilhelm JJ, Yang A, Zhang Y, Palani NP, Abrahante JE, Burlak C, Miller SD, Luo X, Hering BJ. Long-term tolerance of islet allografts in nonhuman primates induced by apoptotic donor leukocytes. Nat Commun 2019; 10:3495. [PMID: 31375697 PMCID: PMC6677762 DOI: 10.1038/s41467-019-11338-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 07/09/2019] [Indexed: 02/06/2023] Open
Abstract
Immune tolerance to allografts has been pursued for decades as an important goal in transplantation. Administration of apoptotic donor splenocytes effectively induces antigen-specific tolerance to allografts in murine studies. Here we show that two peritransplant infusions of apoptotic donor leukocytes under short-term immunotherapy with antagonistic anti-CD40 antibody 2C10R4, rapamycin, soluble tumor necrosis factor receptor and anti-interleukin 6 receptor antibody induce long-term (≥1 year) tolerance to islet allografts in 5 of 5 nonsensitized, MHC class I-disparate, and one MHC class II DRB allele-matched rhesus macaques. Tolerance in our preclinical model is associated with a regulatory network, involving antigen-specific Tr1 cells exhibiting a distinct transcriptome and indirect specificity for matched MHC class II and mismatched class I peptides. Apoptotic donor leukocyte infusions warrant continued investigation as a cellular, nonchimeric and translatable method for inducing antigen-specific tolerance in transplantation. Injection of donor apoptotic cells induces graft tolerance in mice. Here the authors combine this approach with short immunosuppressive therapy to achieve long-term tolerance to allogeneic islets and restoration of normoglycemia in diabetic nonhuman primates, and delineate cellular and molecular correlates of tolerance induction.
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Affiliation(s)
- Amar Singh
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Sabarinathan Ramachandran
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Melanie L Graham
- Preclinical Research Center, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Saeed Daneshmandi
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - David Heller
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wilma Lucia Suarez-Pinzon
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Appakalai N Balamurugan
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA.,Center for Cellular Transplantation, Cardiovascular Innovation Institute, Department of Surgery, University of Louisville, Louisville, KY, 40202, USA
| | - Jeffrey D Ansite
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Joshua J Wilhelm
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Amy Yang
- Biostatistics Collaboration Center, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Ying Zhang
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Nagendra P Palani
- University of Minnesota Genomics Center, Minneapolis, MN, 55455, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, Minneapolis, MN, 55455, USA
| | - Christopher Burlak
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Stephen D Miller
- Department of Microbiology-Immunology and Interdepartmental Immunology Center, Northwestern University, Chicago, IL, 60611, USA.
| | - Xunrong Luo
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. .,Biostatistics Collaboration Center, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. .,Duke Transplant Center, Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA.
| | - Bernhard J Hering
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA.
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29
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Accolla RS, Ramia E, Tedeschi A, Forlani G. CIITA-Driven MHC Class II Expressing Tumor Cells as Antigen Presenting Cell Performers: Toward the Construction of an Optimal Anti-tumor Vaccine. Front Immunol 2019; 10:1806. [PMID: 31417570 PMCID: PMC6682709 DOI: 10.3389/fimmu.2019.01806] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/17/2019] [Indexed: 12/11/2022] Open
Abstract
Construction of an optimal vaccine against tumors relies on the availability of appropriate tumor-specific antigens capable to stimulate CD4+ T helper cells (TH) and CD8+ cytolytic T cells (CTL). CTL are considered the major effectors of the anti-tumor adaptive immune response as they recognize antigens presented on MHC class I (MHC-I) molecules usually expressed in all cells and thus also in tumors. However, attempts to translate in clinics vaccination protocols based only on tumor-specific MHC-I-bound peptides have resulted in very limited, if any, success. We believe failure was mostly due to inadequate triggering of the TH arm of adaptive immunity, as TH cells are necessary to trigger and maintain the proliferation of all the immune effector cells required to eliminate tumor cells. In this review, we focus on a novel strategy of anti-tumor vaccination established in our laboratory and based on the persistent expression of MHC class II (MHC-II) molecules in tumor cells. MHC-II are the restricting elements of TH recognition. They are usually not expressed in solid tumors. By genetically modifying tumor cells of distinct histological origin with the MHC-II transactivator CIITA, the physiological controller of MHC-II gene expression discovered in our laboratory, stable expression of all MHC class II genes was obtained. This resulted in tumor rejection or strong retardation of tumor growth in vivo in mice, mediated primarily by tumor-specific TH cells as assessed by both depletion and adoptive cell transfer experiments. Importantly these findings led us to apply this methodology to human settings for the purification of MHC-II-bound tumor specific peptides directly from tumor cells, specifically from hepatocarcinomas, and the construction of a multi-peptide (MHC-II and MHC-I specific) immunotherapeutic vaccine. Additionally, our approach unveiled a noticeable exception to the dogma that dendritic cells are the sole professional antigen presenting cells (APC) capable to prime naïve TH cells, because CIITA-dependent MHC-II expressing tumor cells could also perform this function. Thus, our approach has served not only to select the most appropriate tumor specific peptides to activate the key lymphocytes triggering the anti-tumor effector functions but also to increase our knowledge of intimate mechanisms governing basic immunological processes.
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Affiliation(s)
- Roberto S Accolla
- Laboratories of General Pathology and Immunology "Giovanna Tosi", Department of Medicine and Surgery, School of Medicine, University of Insubria, Varese, Italy
| | - Elise Ramia
- Laboratories of General Pathology and Immunology "Giovanna Tosi", Department of Medicine and Surgery, School of Medicine, University of Insubria, Varese, Italy
| | - Alessandra Tedeschi
- Laboratories of General Pathology and Immunology "Giovanna Tosi", Department of Medicine and Surgery, School of Medicine, University of Insubria, Varese, Italy
| | - Greta Forlani
- Laboratories of General Pathology and Immunology "Giovanna Tosi", Department of Medicine and Surgery, School of Medicine, University of Insubria, Varese, Italy
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Becerra-Artiles A, Cruz J, Leszyk JD, Sidney J, Sette A, Shaffer SA, Stern LJ. Naturally processed HLA-DR3-restricted HHV-6B peptides are recognized broadly with polyfunctional and cytotoxic CD4 T-cell responses. Eur J Immunol 2019; 49:1167-1185. [PMID: 31020640 DOI: 10.1002/eji.201948126] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/13/2019] [Accepted: 04/23/2019] [Indexed: 01/06/2023]
Abstract
Human herpes virus 6B (HHV-6B) is a widespread virus that infects most people early in infancy and establishes a chronic life-long infection with periodic reactivation. CD4 T cells have been implicated in control of HHV-6B, but antigenic targets and functional characteristics of the CD4 T-cell response are poorly understood. We identified 25 naturally processed MHC-II peptides, derived from six different HHV-6B proteins, and showed that they were recognized by CD4 T-cell responses in HLA-matched donors. The peptides were identified by mass spectrometry after elution from HLA-DR molecules isolated from HHV-6B-infected T cells. The peptides showed strong binding to matched HLA alleles and elicited recall T-cell responses in vitro. T-cell lines expanded in vitro were used for functional characterization of the response. Responding cells were mainly CD3+ CD4+ , produced IFN-γ, TNF-α, and low levels of IL-2, alone or in combination, highlighting the presence of polyfunctional T cells in the overall response. Many of the responding cells mobilized CD107a, stored granzyme B, and mediated specific killing of peptide-pulsed target cells. These results highlight a potential role for polyfunctional cytotoxic CD4 T cells in the long-term control of HHV-6B infection.
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Affiliation(s)
| | - John Cruz
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA
| | - John D Leszyk
- Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, MA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, San Diego, CA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, San Diego, CA.,Department of Medicine, University of California, San Diego, CA
| | - Scott A Shaffer
- Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, MA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
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31
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Malaker SA, Ferracane MJ. Mass Spectrometric Identification and Molecular Modeling of Glycopeptides Presented by MHC Class I and II Processing Pathways. Methods Mol Biol 2019; 2024:269-285. [PMID: 31364056 DOI: 10.1007/978-1-4939-9597-4_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Aberrant glycosylation is a hallmark of cancer that contributes to the disease's ability to evade the immune system. As the MHC processing pathways communicate cellular health to circulating CD8+ and CD4+ T-cells, MHC-associated glycopeptides are likely a source of neoantigens in cancer. In fact, recent advances in mass spectrometry have allowed for the detection and sequencing of tumor-specific glycopeptides from the MHC class I and class II processing pathways. Here, we describe methods for detecting, sequencing, and modeling these MHC-associated glycopeptides.
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Affiliation(s)
- Stacy A Malaker
- Department of Chemistry, Stanford University, Stanford, CA, USA
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32
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Abstract
MHC molecules on the surface of cells are responsible for the presentation of antigenic peptides to CD8+ and CD4+ T cells. Downstream analysis of these peptides can offer insight into various disease processes with an immune component, as in autoimmune diseases and cancer. A critical step in studying MHC-associated peptides is their isolation from MHC molecules on the surface of cells. In this chapter, we detail anti-MHC antibody conjugation to beads, immunoaffinity purification of the MHC molecules, and peptide elution. This method can be used for analysis of unmodified and/or posttranslationally modified peptides by mass spectrometry.
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Affiliation(s)
- Sarah A Penny
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Stacy A Malaker
- Department of Chemistry, Stanford University, Stanford, CA, USA.
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33
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Graham DB, Luo C, O'Connell DJ, Lefkovith A, Brown EM, Yassour M, Varma M, Abelin JG, Conway KL, Jasso GJ, Matar CG, Carr SA, Xavier RJ. Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes. Nat Med 2018; 24:1762-72. [PMID: 30349087 DOI: 10.1038/s41591-018-0203-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/20/2018] [Indexed: 01/01/2023]
Abstract
Identifying immunodominant T cell epitopes remains a significant challenge in the context of infectious disease, autoimmunity, and immuno-oncology. To address the challenge of antigen discovery, we developed a quantitative proteomic approach that enabled unbiased identification of major histocompatibility complex class II (MHCII)-associated peptide epitopes and biochemical features of antigenicity. On the basis of these data, we trained a deep neural network model for genome-scale predictions of immunodominant MHCII-restricted epitopes. We named this model bacteria originated T cell antigen (BOTA) predictor. In validation studies, BOTA accurately predicted novel CD4 T cell epitopes derived from the model pathogen Listeria monocytogenes and the commensal microorganism Muribaculum intestinale. To conclusively define immunodominant T cell epitopes predicted by BOTA, we developed a high-throughput approach to screen DNA-encoded peptide-MHCII libraries for functional recognition by T cell receptors identified from single-cell RNA sequencing. Collectively, these studies provide a framework for defining the immunodominance landscape across a broad range of immune pathologies.
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34
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Abstract
INTRODUCTION Our immune system discriminates self from non-self by examining the peptide cargo of human leukocyte antigen (HLA) molecules displayed on the cell surface. Successful recognition of HLA-bound non-self peptides can induce T cell responses leading to, for example, the destruction of infected cells. Today, largely due to advances in technology, we have an unprecedented capability to identify the nature of these presented peptides and unravel the true complexity of antigen presentation. Areas covered: In addition to conventional linear peptides, HLA molecules also present post-translationally modified sequences comprising a wealth of chemical and structural modifications, including a novel class of noncontiguous spliced peptides. This review focuses on these emerging themes in antigen presentation and how mass spectrometry in particular has contributed to a new view of the antigenic landscape that is presented to the immune system. Expert Commentary: Advances in the sensitivity of mass spectrometers and use of hybrid fragmentation technologies will provide more information-rich spectra of HLA bound peptides leading to more definitive identification of T cell epitopes. Coupled with improvements in sample preparation and new informatics workflows, studies will access novel classes of peptide antigen and allow interrogation of rare and clinically relevant samples.
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Affiliation(s)
- Sri H Ramarathinam
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Nathan P Croft
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Patricia T Illing
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Pouya Faridi
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Anthony W Purcell
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
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35
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Nowak J, Nestorowicz K, Graczyk-Pol E, Mika-Witkowska R, Rogatko-Koros M, Jaskula E, Koscinska K, Madej S, Tomaszewska A, Nasilowska-Adamska B, Szczepinski A, Halaburda K, Dybko J, Kuliczkowski K, Czerw T, Giebel S, Holowiecki J, Baranska M, Pieczonka A, Wachowiak J, Czyz A, Gil L, Lojko-Dankowska A, Komarnicki M, Bieniaszewska M, Kucharska A, Hellmann A, Gronkowska A, Jedrzejczak WW, Markiewicz M, Koclega A, Kyrcz-Krzemien S, Mielcarek M, Kalwak K, Styczynski J, Wysocki M, Drabko K, Wojcik B, Kowalczyk J, Gozdzik J, Pawliczak D, Gwozdowicz S, Dziopa J, Szlendak U, Witkowska A, Zubala M, Gawron A, Warzocha K, Lange A. HLA-inferred extended haplotype disparity level is more relevant than the level of HLA mismatch alone for the patients survival and GvHD in T cell-replate hematopoietic stem cell transplantation from unrelated donor. Hum Immunol 2018; 79:403-412. [PMID: 29605688 DOI: 10.1016/j.humimm.2018.03.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 03/18/2018] [Accepted: 03/27/2018] [Indexed: 10/17/2022]
Abstract
Serious risks in unrelated hematopoietic stem cell transplantation (HSCT) including graft versus host disease (GvHD) and mortality are associated with HLA disparity between donor and recipient. The increased risks might be dependent on disparity in not-routinely-tested multiple polymorphisms in genetically dense MHC region, being organized in combinations of two extended MHC haplotypes (Ehp). We assessed the clinical role of donor-recipient Ehp disparity levels in N = 889 patients by the population-based detection of HLA allele phase mismatch. We found increased GvHD incidences and mortality rates with increasing Ehp mismatch level even with the same HLA mismatch level. In multivariate analysis HLA mismatch levels were excluded from models and Ehp disparity level remained independent prognostic factor for high grade acute GvHD (p = 0.000037, HR = 10.68, 95%CI 5.50-32.5) and extended chronic GvHD (p < 0.000001, HR = 15.51, CI95% 5.36-44.8). In group with single HLA mismatch, patients with double Ehp disparity had worse 5-year overall survival (45% vs. 56%, p = 0.00065, HR = 4.05, CI95% 1.69-9.71) and non-relapse mortality (40% vs. 31%, p = 0.00037, HR = 5.63, CI95% 2.04-15.5) than patients with single Ehp disparity. We conclude that Ehp-linked factors contribute to the high morbidity and mortality in recipients given HLA-mismatched unrelated transplant and Ehp matching should be considered in clinical HSCT.
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Affiliation(s)
- Jacek Nowak
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland.
| | - Klaudia Nestorowicz
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Elzbieta Graczyk-Pol
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Renata Mika-Witkowska
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Marta Rogatko-Koros
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Emilia Jaskula
- Department of Clinical Immunology, L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland; Lower Silesian Center for Cellular Transplantation with National Bone Marrow Donor Registry, Wrocław, Poland
| | - Katarzyna Koscinska
- Lower Silesian Center for Cellular Transplantation with National Bone Marrow Donor Registry, Wrocław, Poland
| | - Sylwia Madej
- Lower Silesian Center for Cellular Transplantation with National Bone Marrow Donor Registry, Wrocław, Poland
| | - Agnieszka Tomaszewska
- Department of Hematopoietic Stem Cell Transplantation, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Barbara Nasilowska-Adamska
- Department of Hematopoietic Stem Cell Transplantation, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Andrzej Szczepinski
- Department of Hematopoietic Stem Cell Transplantation, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Kazimierz Halaburda
- Department of Hematopoietic Stem Cell Transplantation, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Jaroslaw Dybko
- Department of Hematology, Blood Malignancies and Bone Marrow Transplantation, Wroclaw Medical University, Wroclaw, Poland
| | - Kazimierz Kuliczkowski
- Department of Hematology, Blood Malignancies and Bone Marrow Transplantation, Wroclaw Medical University, Wroclaw, Poland
| | - Tomasz Czerw
- Department of Bone Marrow Transplantation and Oncohematology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch, Gliwice, Poland
| | - Sebastian Giebel
- Department of Bone Marrow Transplantation and Oncohematology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch, Gliwice, Poland
| | - Jerzy Holowiecki
- Department of Bone Marrow Transplantation and Oncohematology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch, Gliwice, Poland
| | - Malgorzata Baranska
- Department of Oncology Hematology and Paediatric Transplantology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Pieczonka
- Department of Oncology Hematology and Paediatric Transplantology, Poznan University of Medical Sciences, Poznan, Poland
| | - Jacek Wachowiak
- Department of Oncology Hematology and Paediatric Transplantology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Czyz
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Lidia Gil
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Lojko-Dankowska
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Mieczyslaw Komarnicki
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Maria Bieniaszewska
- Department of Hematology and Transplantology, Gdansk Medical University Clinical Center, Gdansk, Poland
| | - Agnieszka Kucharska
- Department of Hematology and Transplantology, Gdansk Medical University Clinical Center, Gdansk, Poland
| | - Andrzej Hellmann
- Department of Hematology and Transplantology, Gdansk Medical University Clinical Center, Gdansk, Poland
| | - Anna Gronkowska
- Department of Hematology, Oncology and Internal Medicine, Warsaw Medical University, Warsaw, Poland
| | - Wieslaw W Jedrzejczak
- Department of Hematology, Oncology and Internal Medicine, Warsaw Medical University, Warsaw, Poland
| | - Miroslaw Markiewicz
- Department of Hematology and Bone Marrow Transplantation, Silesian Medical University, Katowice, Poland
| | - Anna Koclega
- Department of Hematology and Bone Marrow Transplantation, Silesian Medical University, Katowice, Poland
| | - Slawomira Kyrcz-Krzemien
- Department of Hematology and Bone Marrow Transplantation, Silesian Medical University, Katowice, Poland
| | - Monika Mielcarek
- Department of Pediatric Hematology Oncology and Bone Marrow Transplantation, Wroclaw Medical University, Wroclaw, Poland
| | - Krzysztof Kalwak
- Department of Pediatric Hematology Oncology and Bone Marrow Transplantation, Wroclaw Medical University, Wroclaw, Poland
| | - Jan Styczynski
- Department of Pediatric Hematology and Oncology, Collegium Medicum Nicolaus Copernicus University Hospital, Bydgoszcz, Poland
| | - Mariusz Wysocki
- Department of Pediatric Hematology and Oncology, Collegium Medicum Nicolaus Copernicus University Hospital, Bydgoszcz, Poland
| | - Katarzyna Drabko
- Department of Paediatric Hematology, Oncology and Transplantology, Medical University, Lublin, Poland
| | - Beata Wojcik
- Department of Paediatric Hematology, Oncology and Transplantology, Medical University, Lublin, Poland
| | - Jerzy Kowalczyk
- Department of Paediatric Hematology, Oncology and Transplantology, Medical University, Lublin, Poland
| | - Jolanta Gozdzik
- Department of Transplantation Children's University Hospital, Polish-American Institute of Pediatrics, Jagiellonian University Medical College, Cracow, Poland
| | - Daria Pawliczak
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Slawomir Gwozdowicz
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Joanna Dziopa
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Urszula Szlendak
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Agnieszka Witkowska
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Marta Zubala
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Agnieszka Gawron
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Krzysztof Warzocha
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Andrzej Lange
- Department of Clinical Immunology, L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland; Lower Silesian Center for Cellular Transplantation with National Bone Marrow Donor Registry, Wrocław, Poland
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Høglund RA, Lossius A, Johansen JN, Homan J, Benth JŠ, Robins H, Bogen B, Bremel RD, Holmøy T. In Silico Prediction Analysis of Idiotope-Driven T-B Cell Collaboration in Multiple Sclerosis. Front Immunol 2017; 8:1255. [PMID: 29038659 PMCID: PMC5630699 DOI: 10.3389/fimmu.2017.01255] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/20/2017] [Indexed: 12/02/2022] Open
Abstract
Memory B cells acting as antigen-presenting cells are believed to be important in multiple sclerosis (MS), but the antigen they present remains unknown. We hypothesized that B cells may activate CD4+ T cells in the central nervous system of MS patients by presenting idiotopes from their own immunoglobulin variable regions on human leukocyte antigen (HLA) class II molecules. Here, we use bioinformatics prediction analysis of B cell immunoglobulin variable regions from 11 MS patients and 6 controls with other inflammatory neurological disorders (OINDs), to assess whether the prerequisites for such idiotope-driven T–B cell collaboration are present. Our findings indicate that idiotopes from the complementarity determining region (CDR) 3 of MS patients on average have high predicted affinities for disease associated HLA-DRB1*15:01 molecules and are predicted to be endosomally processed by cathepsin S and L in positions that allows such HLA binding to occur. Additionally, complementarity determining region 3 sequences from cerebrospinal fluid (CSF) B cells from MS patients contain on average more rare T cell-exposed motifs that could potentially escape tolerance and stimulate CD4+ T cells than CSF B cells from OIND patients. Many of these features were associated with preferential use of the IGHV4 gene family by CSF B cells from MS patients. This is the first study to combine high-throughput sequencing of patient immune repertoires with large-scale prediction analysis and provides key indicators for future in vitro and in vivo analyses.
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Affiliation(s)
- Rune A Høglund
- Department of Neurology, Akershus University Hospital, Lørenskog, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Andreas Lossius
- Department of Neurology, Akershus University Hospital, Lørenskog, Norway.,Faculty of Medicine, Department of Immunology and Transfusion Medicine, University of Oslo and Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Jorunn N Johansen
- Faculty of Medicine, Department of Immunology and Transfusion Medicine, University of Oslo and Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Jane Homan
- EigenBio LLC, Madison, WI, United States
| | - Jūratė Šaltytė Benth
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway
| | - Harlan Robins
- Adaptive Biotechnologies, Seattle, WA, United States
| | - Bjarne Bogen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Faculty of Medicine, Department of Immunology and Transfusion Medicine, University of Oslo and Oslo University Hospital Rikshospitalet, Oslo, Norway.,Centre for Immune Regulation, University of Oslo, Oslo, Norway
| | | | - Trygve Holmøy
- Department of Neurology, Akershus University Hospital, Lørenskog, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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Afridi S, Hoessli DC, Hameed MW. Mechanistic understanding and significance of small peptides interaction with MHC class II molecules for therapeutic applications. Immunol Rev 2017; 272:151-68. [PMID: 27319349 DOI: 10.1111/imr.12435] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Major histocompatibility complex (MHC) class II molecules are expressed by antigen-presenting cells and stimulate CD4(+) T cells, which initiate humoral immune responses. Over the past decade, interest has developed to therapeutically impact the peptides to be exposed to CD4(+) T cells. Structurally diverse small molecules have been discovered that act on the endogenous peptide exchanger HLA-DM by different mechanisms. Exogenously delivered peptides are highly susceptible to proteolytic cleavage in vivo; however, it is only when successfully incorporated into stable MHC II-peptide complexes that these peptides can induce an immune response. Many of the small molecules so far discovered have highlighted the molecular interactions mediating the formation of MHC II-peptide complexes. As potential drugs, these small molecules open new therapeutic approaches to modulate MHC II antigen presentation pathways and influence the quality and specificity of immune responses. This review briefly introduces how CD4(+) T cells recognize antigen when displayed by MHC class II molecules, as well as MHC class II-peptide-loading pathways, structural basis of peptide binding and stabilization of the peptide-MHC complexes. We discuss the concept of MHC-loading enhancers, how they could modulate immune responses and how these molecules have been identified. Finally, we suggest mechanisms whereby MHC-loading enhancers could act upon MHC class II molecules.
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Affiliation(s)
- Saifullah Afridi
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Daniel C Hoessli
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Muhammad Waqar Hameed
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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Abstract
Autophagy describes catabolic pathways that deliver cytoplasmic constituents for lysosomal degradation. Since major histocompatibility complex (MHC) molecules sample protein degradation products and present them to T cells for adaptive immunity, it is maybe not too surprising that autophagy contributes to this protein antigen processing for MHC presentation. However, the recently recognized breath of pathways, by which autophagy contributes to MHC antigen processing, is exciting. Macroautophagy does not only seem to deliver intracellular but facilitates also extracellular antigen processing by lysosomal hydrolysis for MHC class II presentation. Moreover, even MHC class I molecules that usually display proteasomal products are regulated by macroautophagy, probably using a pool of these molecules outside the endoplasmic reticulum, where MHC class I molecules are loaded with peptide during canonical MHC class I antigen processing. This review aims to summarize these recent developments and point out gaps of knowledge, which should be filled by further investigation, in order to harness the different antigen-processing pathways via autophagy for vaccine improvement.
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Affiliation(s)
- Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
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Veerappan Ganesan AP, Eisenlohr LC. The elucidation of non-classical MHC class II antigen processing through the study of viral antigens. Curr Opin Virol 2017; 22:71-6. [PMID: 28081485 DOI: 10.1016/j.coviro.2016.11.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 11/22/2016] [Indexed: 11/22/2022]
Abstract
By convention, CD4+ T cells are activated predominantly by Major Histocompatibility Complex class II-bound peptides derived from extracellular (exogenous) antigens. It has been known for decades that alternative sources of antigen, particularly those synthesized within the antigen-presenting cell, can also supply peptides but the impact on TCD4+ responses, sometimes considerable, has only recently become appreciated. This review focuses on the contributions that studies of viral antigen have made to this shift in perspective, concluding with discussions of relevance to rational vaccine design, autoimmunity and cancer immunotherapy.
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Li CW, Osman R, Menconi F, Concepcion ES, Tomer Y. Flexible peptide recognition by HLA-DR triggers specific autoimmune T-cell responses in autoimmune thyroiditis and diabetes. J Autoimmun 2017; 76:1-9. [PMID: 27670087 PMCID: PMC5752120 DOI: 10.1016/j.jaut.2016.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/15/2016] [Accepted: 09/17/2016] [Indexed: 11/18/2022]
Abstract
Autoimmune polyglandular syndrome 3 variant (APS3v) refers to the co-occurrence of autoimmune thyroiditis (AITD) and type 1 diabetes (T1D) within the same individual. HLA class II confers the strongest susceptibility to APS3v. We previously identified a unique amino acid signature of the HLA-DR pocket (designated APS3v HLA-DR pocket) that predisposes to APS3v. We hypothesized that both thyroid and islet peptides can be presented by the unique APS3v HLA-DR pocket, triggering AITD + T1D together. To test this hypothesis we screened islet and thyroid peptides for their ability to bind to the APS3v HLA-DR pocket. Virtual screen of all possible thyroglobulin (Tg), thyroid-stimulating hormone receptor (TSHR), thyroid peroxidase (TPO), insulin (Ins), and glutamic acid decarboxylase 65 (GAD65) peptides identified 36 peptides that bound to this unique pocket. In vitro binding assays using baculovirus-produced recombinant APS3v HLA-DR identified 11 thyroid/islet peptides (of the 36 predicted binders) that bound with high affinity. By immunizing humanized HLA-DR3 mice carrying the APS3v HLA-DR pocket we identified 4 peptides (Tg.1571, GAD.492, TPO.758, TPO.338) that were presented by antigen presenting cells and elicited T-cell response. We conclude that both thyroid and islet peptides can bind to this flexible APS3v HLA-DR pocket and induce thyroid and islet specific T-cell responses. These findings set the stage to developing specific inhibitors of the APS3v HLA-DR pocket as a precision medicine approach to treating or preventing APS3v in patients that carry this genetic HLA-DR pocket variant.
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Affiliation(s)
- Cheuk Wun Li
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Roman Osman
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Erlinda S Concepcion
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Yaron Tomer
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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Wang Q, Drouin EE, Yao C, Zhang J, Huang Y, Leon DR, Steere AC, Costello CE. Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis. J Proteome Res 2016; 16:122-136. [PMID: 27726376 DOI: 10.1021/acs.jproteome.6b00386] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Human leukocyte antigen-antigen D related (HLA-DR) molecules are highly expressed in synovial tissue (ST), the target of the immune response in chronic inflammatory forms of arthritis. Here, we used LC-MS/MS to identify HLA-DR-presented self-peptides in cells taken directly from clinical samples: ST, synovial fluid mononuclear cells (SFMC), or peripheral blood mononuclear cells (PBMC) from five patients with rheumatoid arthritis (RA) and eight with Lyme arthritis (LA). We identified 1593 non-redundant HLA-DR-presented peptides, derived from 870 source proteins. A total of 67% of the peptides identified in SFMC and 55% of those found in PBMC were found in ST, but analysis of SFMC/PBMC also revealed new antigen-presented peptides. Peptides were synthesized and examined for reactivity with the patients' PBMC. To date, three autoantigens in RA and four novel autoantigens in LA, presented in ST and/or PBMC, were shown to be targets of T- and B-cell responses in these diseases; ongoing analyses may add to this list. Thus, immunoprecipitation and LC-MS/MS can now identify hundreds of HLA-DR-presented self-peptides from individual patients' tissues or fluids with mixed cell populations. Importantly, identification of HLA-DR-presented peptides from SFMC or PBMC allows testing of more patients, including those early in the disease. Direct analysis of clinical samples facilitates identification of novel immunogenic T-cell epitopes.
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Affiliation(s)
- Qi Wang
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Elise E Drouin
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School , Boston, Massachusetts 02114, United States
| | - Chunxiang Yao
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Jiyang Zhang
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States.,National University of Defense Technology , Changsha, 410000 Hunan Province, China
| | - Yu Huang
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Deborah R Leon
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Allen C Steere
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School , Boston, Massachusetts 02114, United States
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
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Scholz E, Mestre-Ferrer A, Daura X, García-Medel N, Carrascal M, James EA, Kwok WW, Canals F, Álvarez I. A Comparative Analysis of the Peptide Repertoires of HLA-DR Molecules Differentially Associated With Rheumatoid Arthritis. Arthritis Rheumatol 2016; 68:2412-21. [PMID: 27158783 DOI: 10.1002/art.39736] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/26/2016] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To evaluate similarity of the peptide repertoires bound to HLA-DR molecules that are differentially associated with rheumatoid arthritis (RA), and to define structural features of the shared peptides. METHODS Peptide pools bound to HLA-DRB1*01:01, HLA-DRB1*04:01, and HLA-DRB1*10:01 (RA associated) and those bound to HLA-DRB1*15:01 (non-RA-associated) were purified and analyzed by liquid chromatography (LC) matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MS) and LC-ion-trap MS. Peptide pools from each allotype were compared in terms of size, protein origin, composition, and affinity (both theoretical and experimental with some peptides). Finally, 1 peptide sequenced from DR1, DR4, and DR10, but not from DR15, was modeled in complex with all 4 HLA-DRB1 molecules and HLA-DRB5*01:01. RESULTS A total of 6,309 masses and 962 unique peptide sequences were compared. DR10 shared 29 peptides with DR1, 9 with DR4, and 1 with DR15; DR1 shared 6 peptides with DR4 and 9 with DR15; and DR4 and DR15 shared 4 peptides. The direct identification of peptide ligands indicated that DR1 and DR10 were the most similar molecules regarding the peptides that they could share. The peptides common to these molecules contained a high proportion of Leu at P4 and basic residues at P8 binding core positions. CONCLUSION The degree of overlap between peptide repertoires associated with different HLA-DR molecules is low. The repertoires associated with DR1 and DR10 have the highest similarity among the molecules analyzed (∼10% overlap). Among the peptides shared between DR1 and DR10, a high proportion contained Leu(4) and basic residues at the P8 position of the binding core.
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Affiliation(s)
- Erika Scholz
- Institut de Biotecnologia i de Biomedicina and Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Anna Mestre-Ferrer
- Institut de Biotecnologia i de Biomedicina and Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Xavier Daura
- Institut de Biotecnologia i de Biomedicina and Universitat Autònoma de Barcelona, Bellaterra, Spain, and Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | | | - Montserrat Carrascal
- CSIC/UAB Proteomics Laboratory, IIBB-CSIC/Institut d'Investigacions Biomèdiques August Pi i Sunyer, Bellaterra, Spain
| | - Eddie A James
- Benaroya Research Institute at Virginia Mason, Seattle, Washington
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, Washington
| | - Francesc Canals
- Vall d'Hebron University Hospital Research Institute Proteomics Laboratory, Barcelona, Spain
| | - Iñaki Álvarez
- Institut de Biotecnologia i de Biomedicina and Universitat Autònoma de Barcelona, Bellaterra, Spain.
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44
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Malaker SA, Ferracane MJ, Depontieu FR, Zarling AL, Shabanowitz J, Bai DL, Topalian SL, Engelhard VH, Hunt DF. Identification and Characterization of Complex Glycosylated Peptides Presented by the MHC Class II Processing Pathway in Melanoma. J Proteome Res 2016; 16:228-237. [PMID: 27550523 DOI: 10.1021/acs.jproteome.6b00496] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The MHC class II (MHCII) processing pathway presents peptides derived from exogenous or membrane-bound proteins to CD4+ T cells. Several studies have shown that glycopeptides are necessary to modulate CD4+ T cell recognition, though glycopeptide structures in these cases are generally unknown. Here, we present a total of 93 glycopeptides from three melanoma cell lines and one matched EBV-transformed line with most found only in the melanoma cell lines. The glycosylation we detected was diverse and comprised 17 different glycoforms. We then used molecular modeling to demonstrate that complex glycopeptides are capable of binding the MHC and may interact with complementarity determining regions. Finally, we present the first evidence of disulfide-bonded peptides presented by MHCII. This is the first large scale study to sequence glyco- and disulfide bonded MHCII peptides from the surface of cancer cells and could represent a novel avenue of tumor activation and/or immunoevasion.
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Affiliation(s)
| | - Michael J Ferracane
- Department of Medicinal Chemistry, University of Florida , Gainesville, Florida 32610, United States
| | - Florence R Depontieu
- Department of Surgery, Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
| | | | | | | | - Suzanne L Topalian
- Department of Surgery, Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
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45
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Mou Z, Li J, Boussoffara T, Kishi H, Hamana H, Ezzati P, Hu C, Yi W, Liu D, Khadem F, Okwor I, Jia P, Shitaoka K, Wang S, Ndao M, Petersen C, Chen J, Rafati S, Louzir H, Muraguchi A, Wilkins JA, Uzonna JE. Identification of broadly conserved cross-species protective Leishmania antigen and its responding CD4+ T cells. Sci Transl Med 2016; 7:310ra167. [PMID: 26491077 DOI: 10.1126/scitranslmed.aac5477] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is currently no clinically effective vaccine against leishmaniasis because of poor understanding of the antigens that elicit dominant T cell immunity. Using proteomics and cellular immunology, we identified a dominant naturally processed peptide (PEPCK335-351) derived from Leishmania glycosomal phosphoenolpyruvate carboxykinase (PEPCK). PEPCK was conserved in all pathogenic Leishmania, expressed in glycosomes of promastigotes and amastigotes, and elicited strong CD4(+) T cell responses in infected mice and humans. I-A(b)-PEPCK335-351 tetramer identified protective Leishmania-specific CD4(+) T cells at a clonal level, which comprised ~20% of all Leishmania-reactive CD4(+) T cells at the peak of infection. PEPCK335-351-specific CD4(+) T cells were oligoclonal in their T cell receptor usage, produced polyfunctional cytokines (interleukin-2, interferon-γ, and tumor necrosis factor), and underwent expansion, effector activities, contraction, and stable maintenance after lesion resolution. Vaccination with PEPCK peptide, DNA expressing full-length PEPCK, or rPEPCK induced strong durable cross-species protection in both resistant and susceptible mice. The effectiveness and durability of protection in vaccinated mice support the development of a broadly cross-species protective vaccine against different forms of leishmaniasis by targeting PEPCK.
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Affiliation(s)
- Zhirong Mou
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada
| | - Jintao Li
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada. Institute of Tropical Medicine, Third Military Medical University, Chongqing 400038, China
| | - Thouraya Boussoffara
- Laboratory of Transmission, Control and Immunobiology of Infections, Pasteur Institute of Tunis, Tunis 1002, Tunisia
| | - Hiroyuki Kishi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Hiroshi Hamana
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Peyman Ezzati
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Health Sciences Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Chuanmin Hu
- Department of Clinical Biochemistry, Laboratory Sciences, Third Military Medical University, Chongqing 400038, China
| | - Weijing Yi
- Department of Clinical Biochemistry, Laboratory Sciences, Third Military Medical University, Chongqing 400038, China
| | - Dong Liu
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada
| | - Forough Khadem
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada
| | - Ifeoma Okwor
- Department of Medical Microbiology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Ping Jia
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada
| | - Kiyomi Shitaoka
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Shufeng Wang
- Department of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Momar Ndao
- National Reference Centre for Parasitology, Department of Medicine, Division of Infectious Diseases, McGill University, Montreal, Quebec H3G 1A4, Canada
| | | | - Jianping Chen
- Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610065, China
| | - Sima Rafati
- Molecular Immunology and Vaccine Research Laboratory, Pasteur Institute of Iran, Tehran 13164, Iran
| | - Hechmi Louzir
- Laboratory of Transmission, Control and Immunobiology of Infections, Pasteur Institute of Tunis, Tunis 1002, Tunisia
| | - Atsushi Muraguchi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - John A Wilkins
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Health Sciences Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Jude E Uzonna
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada. Department of Medical Microbiology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada.
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Mintern JD, Macri C, Chin WJ, Panozza SE, Segura E, Patterson NL, Zeller P, Bourges D, Bedoui S, McMillan PJ, Idris A, Nowell CJ, Brown A, Radford KJ, Johnston AP, Villadangos JA. Differential use of autophagy by primary dendritic cells specialized in cross-presentation. Autophagy 2016; 11:906-17. [PMID: 25950899 DOI: 10.1080/15548627.2015.1045178] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Antigen-presenting cells survey their environment and present captured antigens bound to major histocompatibility complex (MHC) molecules. Formation of MHC-antigen complexes occurs in specialized compartments where multiple protein trafficking routes, still incompletely understood, converge. Autophagy is a route that enables the presentation of cytosolic antigen by MHC class II molecules. Some reports also implicate autophagy in the presentation of extracellular, endocytosed antigen by MHC class I molecules, a pathway termed "cross-presentation." The role of autophagy in cross-presentation is controversial. This may be due to studies using different types of antigen presenting cells for which the use of autophagy is not well defined. Here we report that active use of autophagy is evident only in DC subtypes specialized in cross-presentation. However, the contribution of autophagy to cross-presentation varied depending on the form of antigen: it was negligible in the case of cell-associated antigen or antigen delivered via receptor-mediated endocytosis, but more prominent when the antigen was a soluble protein. These findings highlight the differential use of autophagy and its machinery by primary cells equipped with specific immune function, and prompt careful reassessment of the participation of this endocytic pathway in antigen cross-presentation.
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Key Words
- 3-MA, 3-methyladenine
- Atg7-DC CKO, Atg7 DC conditional knockout
- BafA, bafilomycin A1
- CD, cluster of differentiation
- CTL, cytotoxic T lymphocyte
- DALIS, dendritic cell aggresome-like inducible structures
- DC, dendritic cell
- IFC imaging flow cytometry
- LAP, LC3 associated phagocytosis
- LC3B, microtubule-associated protein 1 light chain 3 β
- MHC I, major histocompatibility complex class I
- MHC II, major histocompatibility complex class II
- OT-I, OVA-specific CD8+ T cell
- OT-II, OVA-specific CD4+ T cell; SIM, structured illumination microscopy.
- OVA, ovalbumin
- antigen presentation
- autophagy
- dendritic cells
- green fluorescent protein, GFP
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Degauque N, Brouard S, Soulillou JP. Cross-Reactivity of TCR Repertoire: Current Concepts, Challenges, and Implication for Allotransplantation. Front Immunol 2016; 7:89. [PMID: 27047489 PMCID: PMC4805583 DOI: 10.3389/fimmu.2016.00089] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/22/2016] [Indexed: 01/18/2023] Open
Abstract
Being able to track donor reactive T cells during the course of organ transplantation is a key to improve the graft survival, to prevent graft dysfunction, and to adapt the immunosuppressive regimen. The attempts of transplant immunologists have been for long hampered by the large size of the alloreactive T cell repertoire. Understanding how self-TCR can interact with allogeneic MHC is a key to critically appraise the different assays available to analyze the TCR Vβ repertoire usage. In this report, we will review conceptually and experimentally the process of cross-reactivity. We will then highlight what can be learned from allotransplantation, a situation of artificial cross-reactivity. Finally, the low- and high-resolution techniques to characterize the TCR Vβ repertoire usage in transplantation will be critically discussed.
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Affiliation(s)
- Nicolas Degauque
- UMR 1064, INSERM, Nantes, France; ITUN, CHU de Nantes, Nantes, France; Faculté de Médecine, Université de Nantes, Nantes, France; LabEx IGO "Immunotherapy Graft Oncology", Nantes, France
| | - Sophie Brouard
- UMR 1064, INSERM, Nantes, France; ITUN, CHU de Nantes, Nantes, France; Faculté de Médecine, Université de Nantes, Nantes, France; LabEx IGO "Immunotherapy Graft Oncology", Nantes, France; CIC Biothérapie, Nantes, France; CRB, CHU Nantes, Nantes, France; LabEx Transplantex, Nantes, France
| | - Jean-Paul Soulillou
- UMR 1064, INSERM, Nantes, France; Faculté de Médecine, Université de Nantes, Nantes, France; LabEx Transplantex, Nantes, France
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Abstract
Autophagy is an important cellular catabolic process conserved from yeast to man. Double-membrane vesicles deliver their cargo to the lysosome for degradation. Hence, autophagy is one of the key mechanisms mammalian cells deploy to rid themselves of intracellular pathogens including viruses. However, autophagy serves many more functions during viral infection. First, it regulates the immune response through selective degradation of immune components, thus preventing possibly harmful overactivation and inflammation. Additionally, it delivers virus-derived antigens to antigen-loading compartments for presentation to T lymphocytes. Second, it might take an active part in the viral life cycle by, eg, facilitating its release from cells. Lastly, in the constant arms race between host and virus, autophagy is often hijacked by viruses and manipulated to their own advantage. In this review, we will highlight key steps during viral infection in which autophagy plays a role. We have selected some exemplary viruses and will describe the molecular mechanisms behind their intricate relationship with the autophagic machinery, a result of host-pathogen coevolution.
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Affiliation(s)
- P Paul
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - C Münz
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland.
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Tafti M, Lammers GJ, Dauvilliers Y, Overeem S, Mayer G, Nowak J, Pfister C, Dubois V, Eliaou JF, Eberhard HP, Liblau R, Wierzbicka A, Geisler P, Bassetti CL, Mathis J, Lecendreux M, Khatami R, Heinzer R, Haba-Rubio J, Feketeova E, Baumann CR, Kutalik Z, Tiercy JM. Narcolepsy-Associated HLA Class I Alleles Implicate Cell-Mediated Cytotoxicity. Sleep 2016; 39:581-7. [PMID: 26518595 DOI: 10.5665/sleep.5532] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/11/2015] [Indexed: 02/01/2023] Open
Abstract
STUDY OBJECTIVES Narcolepsy with cataplexy is tightly associated with the HLA class II allele DQB1*06:02. Evidence indicates a complex contribution of HLA class II genes to narcolepsy susceptibility with a recent independent association with HLA-DPB1. The cause of narcolepsy is supposed be an autoimmune attack against hypocretin-producing neurons. Despite the strong association with HLA class II, there is no evidence for CD4+ T-cell-mediated mechanism in narcolepsy. Since neurons express class I and not class II molecules, the final effector immune cells involved might include class I-restricted CD8+ T-cells. METHODS HLA class I (A, B, and C) and II (DQB1) genotypes were analyzed in 944 European narcolepsy with cataplexy patients and in 4,043 control subjects matched by country of origin. All patients and controls were DQB1*06:02 positive and class I associations were conditioned on DQB1 alleles. RESULTS HLA-A*11:01 (OR = 1.49 [1.18-1.87] P = 7.0*10(-4)), C*04:01 (OR = 1.34 [1.10-1.63] P = 3.23*10(-3)), and B*35:01 (OR = 1.46 [1.13-1.89] P = 3.64*10(-3)) were associated with susceptibility to narcolepsy. Analysis of polymorphic class I amino-acids revealed even stronger associations with key antigen-binding residues HLA-A-Tyr(9) (OR = 1.32 [1.15-1.52] P = 6.95*10(-5)) and HLA-C-Ser(11) (OR = 1.34 [1.15-1.57] P = 2.43*10(-4)). CONCLUSIONS Our findings provide a genetic basis for increased susceptibility to infectious factors or an immune cytotoxic mechanism in narcolepsy, potentially targeting hypocretin neurons.
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Affiliation(s)
- Mehdi Tafti
- Center for Integrative Genomics (CIG) University of Lausanne, Lausanne, Switzerland.,Center for Investigation and Research in Sleep (CIRS), Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Gert J Lammers
- Department of Neurology, Leiden University Medical Centre, Leiden, the Netherlands.,Sleep-Wake Center of the Stichting Epilepsie Instellingen Netherland, Heemstede, the Netherlands
| | - Yves Dauvilliers
- INSERM-1061, Montpellier, France.,National Reference Network for Orphan Diseases (Narcolepsy and Idiopathic Hypersomnia), Department of Neurology, Gui-de-Chauliac Hospital, Montpellier, France
| | | | - Geert Mayer
- Hephata-Clinic for Neurology, Schwalmstadt-Treysa, Germany
| | - Jacek Nowak
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Corinne Pfister
- Center for Integrative Genomics (CIG) University of Lausanne, Lausanne, Switzerland
| | - Valérie Dubois
- HLA Laboratory, Etablissement Français du Sang, Lyon, France
| | - Jean-François Eliaou
- Department of Immunology, CHRU of Montpellier, University of Montpellier, France
| | | | - Roland Liblau
- INSERM-UMR1043, CNRS-U5282, Université de Toulouse, Centre de Physiopathologie Toulouse Purpan (CPTP), Toulouse, France
| | - Aleksandra Wierzbicka
- Institute of Psychiatry and Neurology, Department of Clinical Neurophysiology and Sleep Disorders Center, Warsaw, Poland
| | - Peter Geisler
- Sleep Disorders and Research Center, Department of Psychiatry and Psychotherapy, University Hospital Regensburg, Regensburg, Germany
| | - Claudio L Bassetti
- Department of Neurology, Inselspital, Bern University Hospital and University of Bern, Switzerland
| | - Johannes Mathis
- Department of Neurology, Inselspital, Bern University Hospital and University of Bern, Switzerland
| | - Michel Lecendreux
- Pediatric Sleep Center, National Reference Network for Orphan Diseases (Narcolepsy and Idiopathic Hypersomnia), Department of Child and Adolescent Psychopathology, Robert Debré Hospital, Paris VII University, Paris, France
| | | | - Raphaël Heinzer
- Center for Investigation and Research in Sleep (CIRS), Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - José Haba-Rubio
- Center for Investigation and Research in Sleep (CIRS), Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Eva Feketeova
- Department of Neurology, Faculty of Medicine, Safarikiensis University and Louis Pasteur Faculty Hospital Kosice, Kosice, Slovakia
| | | | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Institute of Social and Preventive Medicine (IUMSP), Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne 1010, Switzerland
| | - Jean-Marie Tiercy
- National Reference Laboratory for Histocompatibility, Transplantation Immunology Unit, Department of Genetics and Laboratory Medicine, University Hospital Geneva, Geneva, Switzerland
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50
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Abstract
MHC class II (MHC-II) molecules are critical in the control of many immune responses. They are also involved in most autoimmune diseases and other pathologies. Here, we describe the biology of MHC-II and MHC-II variations that affect immune responses. We discuss the classic cell biology of MHC-II and various perturbations. Proteolysis is a major process in the biology of MHC-II, and we describe the various components forming and controlling this endosomal proteolytic machinery. This process ultimately determines the MHC-II-presented peptidome, including cryptic peptides, modified peptides, and other peptides that are relevant in autoimmune responses. MHC-II also variable in expression, glycosylation, and turnover. We illustrate that MHC-II is variable not only in amino acids (polymorphic) but also in its biology, with consequences for both health and disease.
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Affiliation(s)
- Emil R Unanue
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110;
| | - Vito Turk
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, SI-1000 Ljubljana, Slovenia;
| | - Jacques Neefjes
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; .,Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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