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Fougiaxis V, He B, Khan T, Vatinel R, Koutroumpa NM, Afantitis A, Lesire L, Sierocki P, Deprez B, Deprez-Poulain R. ERAP Inhibitors in Autoimmunity and Immuno-Oncology: Medicinal Chemistry Insights. J Med Chem 2024; 67:11597-11621. [PMID: 39011823 DOI: 10.1021/acs.jmedchem.4c00840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Endoplasmic reticulum aminopeptidases ERAP1 and 2 are intracellular aminopeptidases that trim antigenic precursors and generate antigens presented by major histocompatibility complex class I (MHC-I) molecules. They thus modulate the antigenic repertoire and drive the adaptive immune response. ERAPs are considered as emerging targets for precision immuno-oncology or for the treatment of autoimmune diseases, in particular MHC-I-opathies. This perspective covers the structural and biological characterization of ERAP, their relevance to these diseases and the ongoing research on small-molecule inhibitors. We describe the chemical and pharmacological space explored by medicinal chemists to exploit the potential of these targets given their localization, biological functions, and family depth. Specific emphasis is put on the binding mode, potency, selectivity, and physchem properties of inhibitors featuring diverse scaffolds. The discussion provides valuable insights for the future development of ERAP inhibitors and analysis of persisting challenges for the translation for clinical applications.
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Affiliation(s)
- Vasileios Fougiaxis
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ben He
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
| | - Tuhina Khan
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
| | - Rodolphe Vatinel
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
| | | | | | - Laetitia Lesire
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
| | - Pierre Sierocki
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
| | - Benoit Deprez
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
| | - Rebecca Deprez-Poulain
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
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Brunnberg J, Barends M, Frühschulz S, Winter C, Battin C, de Wet B, Cole DK, Steinberger P, Tampé R. Dual role of the peptide-loading complex as proofreader and limiter of MHC-I presentation. Proc Natl Acad Sci U S A 2024; 121:e2321600121. [PMID: 38771881 PMCID: PMC11145271 DOI: 10.1073/pnas.2321600121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/17/2024] [Indexed: 05/23/2024] Open
Abstract
Antigen presentation via major histocompatibility complex class I (MHC-I) molecules is essential for surveillance by the adaptive immune system. Central to this process is the peptide-loading complex (PLC), which translocates peptides from the cytosol to the endoplasmic reticulum and catalyzes peptide loading and proofreading of peptide-MHC-I (pMHC-I) complexes. Despite its importance, the impact of individual PLC components on the presented pMHC-I complexes is still insufficiently understood. Here, we used stoichiometrically defined antibody-nanobody complexes and engineered soluble T cell receptors (sTCRs) to quantify different MHC-I allomorphs and defined pMHC-I complexes, respectively. Thereby, we uncovered distinct effects of individual PLC components on the pMHC-I surface pool. Knockouts of components of the PLC editing modules, namely tapasin, ERp57, or calreticulin, changed the MHC-I surface composition to a reduced proportion of HLA-A*02:01 presentation compensated by a higher ratio of HLA-B*40:01 molecules. Intriguingly, these knockouts not only increased the presentation of suboptimally loaded HLA-A*02:01 complexes but also elevated the presentation of high-affinity peptides overexpressed in the cytosol. Our findings suggest that the components of the PLC editing module serve a dual role, acting not only as peptide proofreaders but also as limiters for abundant peptides. This dual function ensures the presentation of a broad spectrum of antigenic peptides.
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Affiliation(s)
- Jamina Brunnberg
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Martina Barends
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Stefan Frühschulz
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Christian Winter
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Claire Battin
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna1090, Austria
| | - Ben de Wet
- Immunocore Ltd., AbingdonOX14 4RY, United Kingdom
| | | | - Peter Steinberger
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna1090, Austria
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
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3
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Bordbar A, Manches O, Nowatzky J. Biology of HLA class I associated inflammatory diseases. Best Pract Res Clin Rheumatol 2024; 38:101977. [PMID: 39085016 DOI: 10.1016/j.berh.2024.101977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
Human leukocyte antigen (HLA) class I association is a well-established feature of common and uncommon inflammatory diseases, but it is unknown whether it impacts the pathogenesis of these disorders. The "arthritogenic peptide" hypothesis proposed initially for HLA-B27-associated ankylosing spondylitis (AS) seems the most intuitive to serve as a model for other HLA class I-associated diseases, but evidence supporting it has been scarce. Recent technological advances and the discovery of epistatic relationships between disease-associated HLA class I and endoplasmic reticulum aminopeptidase (ERAP) coding variants have led to the generation of new data and conceptual approaches to the problem requiring its re-examination. Continued success in these endeavors holds promise to resolve a Gordian Knot in human immunobiology. It may ultimately benefit patients by enabling the development of new therapies and precision tools for assessing disease risk and predicting treatment responses.
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Affiliation(s)
- Ali Bordbar
- New York University Grossman School of Medicine, Department of Medicine, New York, NY, USA
| | - Olivier Manches
- New York University Grossman School of Medicine, Department of Medicine, New York, NY, USA
| | - Johannes Nowatzky
- New York University Grossman School of Medicine, Department of Medicine, New York, NY, USA; New York University Grossman School of Medicine, Department of Pathology, USA; New York University Grossman School of Medicine, Department of Medicine Division of Rheumatology, NYU Langone Ocular Rheumatology Program, New York, NY, USA; New York University Grossman School of Medicine, Department of Medicine, Division of Rheumatology, NYU Langone Center for Behçet's Disease, New York, NY, USA.
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4
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Gomez-Zepeda D, Arnold-Schild D, Beyrle J, Declercq A, Gabriels R, Kumm E, Preikschat A, Łącki MK, Hirschler A, Rijal JB, Carapito C, Martens L, Distler U, Schild H, Tenzer S. Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS 2Rescore with MS 2PIP timsTOF fragmentation prediction model. Nat Commun 2024; 15:2288. [PMID: 38480730 PMCID: PMC10937930 DOI: 10.1038/s41467-024-46380-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 02/26/2024] [Indexed: 03/17/2024] Open
Abstract
Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, and patient individuality. Here, we develop a highly sensitive method for identifying HLAIps using liquid chromatography-ion mobility-tandem mass spectrometry (LC-IMS-MS/MS). In addition, we train a timsTOF-specific peak intensity MS2PIP model for tryptic and non-tryptic peptides and implement it in MS2Rescore (v3) together with the CCS predictor from ionmob. The optimized method, Thunder-DDA-PASEF, semi-selectively fragments singly and multiply charged HLAIps based on their IMS and m/z. Moreover, the method employs the high sensitivity mode and extended IMS resolution with fewer MS/MS frames (300 ms TIMS ramp, 3 MS/MS frames), doubling the coverage of immunopeptidomics analyses, compared to the proteomics-tailored DDA-PASEF (100 ms TIMS ramp, 10 MS/MS frames). Additionally, rescoring boosts the HLAIps identification by 41.7% to 33%, resulting in 5738 HLAIps from as little as one million JY cell equivalents, and 14,516 HLAIps from 20 million. This enables in-depth profiling of HLAIps from diverse human cell lines and human plasma. Finally, profiling JY and Raji cells transfected to express the SARS-CoV-2 spike protein results in 16 spike HLAIps, thirteen of which have been reported to elicit immune responses in human patients.
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Affiliation(s)
- David Gomez-Zepeda
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany.
- Helmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, Division 191, Heidelberg, Germany.
| | - Danielle Arnold-Schild
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Julian Beyrle
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
- Helmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Division 191, Heidelberg, Germany
| | - Arthur Declercq
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Elena Kumm
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Annica Preikschat
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Mateusz Krzysztof Łącki
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Aurélie Hirschler
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS, ProFI - FR2048, Strasbourg, France
| | - Jeewan Babu Rijal
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS, ProFI - FR2048, Strasbourg, France
| | - Christine Carapito
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS, ProFI - FR2048, Strasbourg, France
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Ute Distler
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Hansjörg Schild
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany.
- Helmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, Division 191, Heidelberg, Germany.
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University, Mainz, Germany.
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5
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Luo X, Qiu Y, Fitzsimonds ZR, Wang Q, Chen Q, Lei YL. Immune escape of head and neck cancer mediated by the impaired MHC-I antigen presentation pathway. Oncogene 2024; 43:388-394. [PMID: 38177410 DOI: 10.1038/s41388-023-02912-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
Tumor immune evasion is a hallmark of Head and Neck Cancers. The advent of immune checkpoint inhibitors (ICIs) in the first-line setting has transformed the management of these tumors. Unfortunately, the response rate of Head and Neck Squamous Cell Carcinomas (HNSCC) to ICIs is below 15%, regardless of the human papillomavirus (HPV) status, which might be partially related with impaired antigen presentation machinery (APM). Mechanistically, HNSCC cells are usually defective in the expression of MHC-I associated APM, while this transcriptional pathway is critical for the activation of tumor-killing effector T-cells. To specifically illuminate the phenomenon and seek for therapeutic strategies, this review summarizes the most recently identified role of genetic and functional dysregulation of the MHC-I pathway, specifically through changes at the genetic, epigenetic, post-transcriptional, and post-translational levels, which substantially contributes to HNSCC immune escape and ICI resistance. Several treatment modalities can be potentially exploited to restore APM signaling in tumors, which improves anti-tumor immunity through the activation of interferons, vaccines or rimantadine against HPV and the inhibition of EGFR, SHP-2, PI3K and MEK. Additionally, the combinatorial use of radiotherapy or cytotoxic agents with ICIs can synergize to potentiate APM signaling. Future directions would include further dissection of MHC-I related APM signaling in HNSCC and whether reversing this inhibition in combination with ICIs would elicit a more robust immune response leading to improved response rates in HNSCC. Therapeutic approaches to restore the MHC-I antigen presentation machinery in Head and Neck Cancer. (Red color texts represent the according strategies and the outcomes).
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Affiliation(s)
- Xiaobo Luo
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yan Qiu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zackary R Fitzsimonds
- Department of Periodontics and Oral Medicine, Department of Otolaryngology-Head and Neck Surgery, Rogel Cancer Center, the University of Michigan, Ann Arbor, MI, 48109, USA
| | - Qiuhao Wang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Yu Leo Lei
- Department of Periodontics and Oral Medicine, Department of Otolaryngology-Head and Neck Surgery, Rogel Cancer Center, the University of Michigan, Ann Arbor, MI, 48109, USA.
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Sears T, Pagadala M, Castro A, Lee KH, Kong J, Tanaka K, Lippman S, Zanetti M, Carter H. Integrated germline and somatic features reveal divergent immune pathways driving ICB response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575430. [PMID: 38293085 PMCID: PMC10827124 DOI: 10.1101/2024.01.12.575430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Immune Checkpoint Blockade (ICB) has revolutionized cancer treatment, however mechanisms determining patient response remain poorly understood. Here we used machine learning to predict ICB response from germline and somatic biomarkers and interpreted the learned model to uncover putative mechanisms driving superior outcomes. Patients with higher T follicular helper infiltrates were robust to defects in the class-I Major Histocompatibility Complex (MHC-I). Further investigation uncovered different ICB responses in MHC-I versus MHC-II neoantigen reliant tumors across patients. Despite similar response rates, MHC-II reliant responses were associated with significantly longer durable clinical benefit (Discovery: Median OS=63.6 vs. 34.5 months P=0.0074; Validation: Median OS=37.5 vs. 33.1 months, P=0.040). Characteristics of the tumor immune microenvironment reflected MHC neoantigen reliance, and analysis of immune checkpoints revealed LAG3 as a potential target in MHC-II but not MHC-I reliant responses. This study highlights the value of interpretable machine learning models in elucidating the biological basis of therapy responses.
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Affiliation(s)
- Timothy Sears
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA USA
| | - Meghana Pagadala
- Biomedical Sciences Program, University of California San Diego, La Jolla, CA,, USA
| | - Andrea Castro
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Ko-Han Lee
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA USA
| | - JungHo Kong
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego, La Jolla, CA USA
| | - Kairi Tanaka
- School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Scott Lippman
- Moores Cancer Center, University of California San Diego, La Jolla, CA USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA USA
- The Laboratory of Immunology, Moores Cancer Center and Department of Medicine, University of California San Diego, La Jolla, CA USA
| | - Hannah Carter
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA USA
- The Laboratory of Immunology, Moores Cancer Center and Department of Medicine, University of California San Diego, La Jolla, CA USA
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7
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Khan MA. HLA-B*27 and Ankylosing Spondylitis: 50 Years of Insights and Discoveries. Curr Rheumatol Rep 2023; 25:327-340. [PMID: 37950822 DOI: 10.1007/s11926-023-01118-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2023]
Abstract
PURPOSE OF REVIEW To commemorate the 50th anniversary of the groundbreaking discovery of a remarkably strong association between HLA-B*27 and ankylosing spondylitis (AS). RECENT FINDINGS In addition to HLA-B*27, more than 116 other recognized genetic risk variants have been identified, while epigenetic factors largely remain unexplored in this context. Among patients with AS who carry the HLA-B*27 gene, clonally expanded CD8 + T cells can be found in their bloodstream and within inflamed tissues. Moreover, the α and β chain motifs of these T-cell receptors demonstrate a distinct affinity for certain self- and microbial-derived peptides, leading to an autoimmune response that ultimately results in the onset of the disease. These distinctive peptide-binding and presentation characteristics are a hallmark of the disease-associated HLA-B*27:05 subtype but are absent in HLA-B*27:09, a subtype not associated with the disease, differing by only a single amino acid. This discovery represents a significant advancement in unraveling the 50-year-old puzzle of how HLA-B*27 contributes to the development of AS. These findings will significantly accelerate the process of identifying peptides, both self- and microbial-derived, that instigate autoimmunity. This, in return, will pave the way for the development of more accurate and effective targeted treatments. Moreover, the discovery of improved biomarkers, in conjunction with the emerging technology of electric field molecular fingerprinting, has the potential to greatly bolster early diagnosis capabilities. A very recently published groundbreak paper underscores the remarkable effectiveness of targeting and eliminating disease-causing T cells in a HLA-B*27 patients with AS. This pivotal advancement not only signifies a paradigm shift but also bolsters the potential for preventing the disease in individuals carrying high-risk genetic variants.
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Affiliation(s)
- Muhammad A Khan
- Case Western Reserve School of Medicine, Cleveland, OH, USA.
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Blander JM, Yee Mon KJ, Jha A, Roycroft D. The show and tell of cross-presentation. Adv Immunol 2023; 159:33-114. [PMID: 37996207 DOI: 10.1016/bs.ai.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Cross-presentation is the culmination of complex subcellular processes that allow the processing of exogenous proteins and the presentation of resultant peptides on major histocompatibility class I (MHC-I) molecules to CD8 T cells. Dendritic cells (DCs) are a cell type that uniquely specializes in cross-presentation, mainly in the context of viral or non-viral infection and cancer. DCs have an extensive network of endovesicular pathways that orchestrate the biogenesis of an ideal cross-presentation compartment where processed antigen, MHC-I molecules, and the MHC-I peptide loading machinery all meet. As a central conveyor of information to CD8 T cells, cross-presentation allows cross-priming of T cells which carry out robust adaptive immune responses for tumor and viral clearance. Cross-presentation can be canonical or noncanonical depending on the functional status of the transporter associated with antigen processing (TAP), which in turn influences the vesicular route of MHC-I delivery to internalized antigen and the cross-presented repertoire of peptides. Because TAP is a central node in MHC-I presentation, it is targeted by immune evasive viruses and cancers. Thus, understanding the differences between canonical and noncanonical cross-presentation may inform new therapeutic avenues against cancer and infectious disease. Defects in cross-presentation on a cellular and genetic level lead to immune-related disease progression, recurrent infection, and cancer progression. In this chapter, we review the process of cross-presentation beginning with the DC subsets that conduct cross-presentation, the signals that regulate cross-presentation, the vesicular trafficking pathways that orchestrate cross-presentation, the modes of cross-presentation, and ending with disease contexts where cross-presentation plays a role.
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Affiliation(s)
- J Magarian Blander
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, United States; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, United States; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Cornell University, New York, NY, United States; Immunology and Microbial Pathogenesis Programs, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, United States.
| | - Kristel Joy Yee Mon
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, United States; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Atimukta Jha
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, United States; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Dylan Roycroft
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, United States; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States
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9
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Kim SH, Lee SH. Updates on ankylosing spondylitis: pathogenesis and therapeutic agents. JOURNAL OF RHEUMATIC DISEASES 2023; 30:220-233. [PMID: 37736590 PMCID: PMC10509639 DOI: 10.4078/jrd.2023.0041] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 09/23/2023]
Abstract
Ankylosing spondylitis (AS) is an autoinflammatory disease that manifests with the unique feature of enthesitis. Gut microbiota, HLA-B*27, and biomechanical stress mutually influence and interact resulting in setting off a flame of inflammation. In the HLA-B*27 positive group, dysbiosis in the gut environment disrupts the barrier to exogenous bacteria or viruses. Additionally, biomechanical stress induces inflammation through enthesial resident or gut-origin immune cells. On this basis, innate and adaptive immunity can propagate inflammation and lead to chronic disease. Finally, bone homeostasis is regulated by cytokines, by which the inflamed region is substituted into new bone. Agents that block cytokines are constantly being developed to provide diverse therapeutic options for preventing the progression of inflammation. In addition, some antibodies have been shown to distinguish disease selectively, which support the involvement of autoimmune immunity in AS. In this review, we critically analyze the complexity and uniqueness of the pathogenesis with updates on the findings of immunity and provide new information about biologics and biomarkers.
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Affiliation(s)
- Se Hee Kim
- Division of Rheumatology, Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Sang-Hoon Lee
- Division of Rheumatology, Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul, Korea
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van de Sande MGH, Elewaut D. Pathophysiology and immunolgical basis of axial spondyloarthritis. Best Pract Res Clin Rheumatol 2023; 37:101897. [PMID: 38030467 DOI: 10.1016/j.berh.2023.101897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023]
Abstract
Over the recent years the wider availability and application of state-of-the-art immunological technologies greatly advanced the insight into the mechanisms that play an important role in axial spondyloarthritis (axSpA) pathophysiology. This increased understanding has facilitated the development of novel treatments that target disease relevant pathways, hereby improving outcome for axSpA patients. In axSpA pathophysiology genetic and environmental factors as well as immune activation by mechanical or bacterial stress resulting in a chronic inflammatory response have a central role. The TNF and IL-23/IL-17 immune pathways play a pivotal role in these disease mechanisms. This review provides an outline of the immunological basis of axSpA with a focus on key genetic risk factors and their link to activation of the pathological immune response, as well as on the role of the gut and entheses in the initiation of inflammation with subsequent new bone formation in axSpA.
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Affiliation(s)
- Marleen G H van de Sande
- Department of Rheumatology & Clinical Immunology and Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands; Amsterdam Rheumatology & Immunology Center (ARC), Academic Medical Center, Amsterdam, the Netherlands.
| | - Dirk Elewaut
- Unit Molecular Immunology and Inflammation, VIB Centre for Inflammation Research, Ghent University and Department of Rheumatology, Ghent University Hospital, C. Heymanslaan 10, Ghent, 9000, Belgium.
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11
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Schmalen A, Kammerl IE, Meiners S, Noessner E, Deeg CA, Hauck SM. A Lysine Residue at the C-Terminus of MHC Class I Ligands Correlates with Low C-Terminal Proteasomal Cleavage Probability. Biomolecules 2023; 13:1300. [PMID: 37759700 PMCID: PMC10527444 DOI: 10.3390/biom13091300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/10/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The majority of peptides presented by MHC class I result from proteasomal protein turnover. The specialized immunoproteasome, which is induced during inflammation, plays a major role in antigenic peptide generation. However, other cellular proteases can, either alone or together with the proteasome, contribute peptides to MHC class I loading non-canonically. We used an immunopeptidomics workflow combined with prediction software for proteasomal cleavage probabilities to analyze how inflammatory conditions affect the proteasomal processing of immune epitopes presented by A549 cells. The treatment of A549 cells with IFNγ enhanced the proteasomal cleavage probability of MHC class I ligands for both the constitutive proteasome and the immunoproteasome. Furthermore, IFNγ alters the contribution of the different HLA allotypes to the immunopeptidome. When we calculated the HLA allotype-specific proteasomal cleavage probabilities for MHC class I ligands, the peptides presented by HLA-A*30:01 showed characteristics hinting at a reduced C-terminal proteasomal cleavage probability independently of the type of proteasome. This was confirmed by HLA-A*30:01 ligands from the immune epitope database, which also showed this effect. Furthermore, two additional HLA allotypes, namely, HLA-A*03:01 and HLA-A*11:01, presented peptides with a markedly reduced C-terminal proteasomal cleavage probability. The peptides eluted from all three HLA allotypes shared a peptide binding motif with a C-terminal lysine residue, suggesting that this lysine residue impairs proteasome-dependent HLA ligand production and might, in turn, favor peptide generation by other cellular proteases.
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Affiliation(s)
- Adrian Schmalen
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, Martinsried, 82152 Planegg, Germany
- Core Facility—Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), 80939 Munich, Germany
| | - Ilona E. Kammerl
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians-University, Helmholtz Center Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Silke Meiners
- Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), 23845 Borstel, Germany
- Institute of Experimental Medicine, Christian-Albrechts University Kiel, 24118 Kiel, Germany
| | - Elfriede Noessner
- Immunoanalytics Research Group—Tissue Control of Immunocytes, Helmholtz Center Munich, 81377 Munich, Germany
| | - Cornelia A. Deeg
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, Martinsried, 82152 Planegg, Germany
| | - Stefanie M. Hauck
- Core Facility—Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), 80939 Munich, Germany
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12
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Temponeras I, Samiotaki M, Koumantou D, Nikopaschou M, Kuiper JJW, Panayotou G, Stratikos E. Distinct modulation of cellular immunopeptidome by the allosteric regulatory site of ER aminopeptidase 1. Eur J Immunol 2023; 53:e2350449. [PMID: 37134263 DOI: 10.1002/eji.202350449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/22/2023] [Accepted: 05/02/2023] [Indexed: 05/05/2023]
Abstract
ER aminopeptidase 1 (ERAP1) is an ER-resident aminopeptidase that excises N-terminal residues of peptides that then bind onto Major Histocompatibility Complex I molecules (MHC-I) and indirectly modulates adaptive immune responses. ERAP1 contains an allosteric regulatory site that accommodates the C-terminus of at least some peptide substrates, raising questions about its exact influence on antigen presentation and the potential of allosteric inhibition for cancer immunotherapy. We used an inhibitor that targets this regulatory site to study its effect on the immunopeptidome of a human cancer cell line. The immunopeptidomes of allosterically inhibited and ERAP1 KO cells contain high-affinity peptides with sequence motifs consistent with the cellular HLA class I haplotypes but are strikingly different in peptide composition. Compared to KO cells, allosteric inhibition did not affect the length distribution of peptides and skewed the peptide repertoire both in terms of sequence motifs and HLA allele utilization, indicating significant mechanistic differences between the two ways of disrupting ERAP1 function. These findings suggest that the regulatory site of ERAP1 plays distinct roles in antigenic peptide selection, which should be taken into consideration when designing therapeutic interventions targeting the cancer immunopeptidome.
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Affiliation(s)
- Ioannis Temponeras
- National Centre for Scientific Research Demokritos, Agia Paraskevi, Greece
- Department of Pharmacy, University of Patras, Patra, Greece
| | - Martina Samiotaki
- Biomedical Sciences Research Center "Alexander Fleming,", Institute for Bioinnovation, Vari, Greece
| | - Despoina Koumantou
- National Centre for Scientific Research Demokritos, Agia Paraskevi, Greece
| | - Martha Nikopaschou
- National Centre for Scientific Research Demokritos, Agia Paraskevi, Greece
- Department of Chemistry, National and Kapodistrian University of Athens, Zografou, Greece
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - George Panayotou
- Biomedical Sciences Research Center "Alexander Fleming,", Institute for Bioinnovation, Vari, Greece
| | - Efstratios Stratikos
- National Centre for Scientific Research Demokritos, Agia Paraskevi, Greece
- Department of Chemistry, National and Kapodistrian University of Athens, Zografou, Greece
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13
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Talwar JV, Laub D, Pagadala MS, Castro A, Lewis M, Luebeck GE, Gorman BR, Pan C, Dong FN, Markianos K, Teerlink CC, Lynch J, Hauger R, Pyarajan S, Tsao PS, Morris GP, Salem RM, Thompson WK, Curtius K, Zanetti M, Carter H. Autoimmune alleles at the major histocompatibility locus modify melanoma susceptibility. Am J Hum Genet 2023; 110:1138-1161. [PMID: 37339630 PMCID: PMC10357503 DOI: 10.1016/j.ajhg.2023.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/22/2023] Open
Abstract
Autoimmunity and cancer represent two different aspects of immune dysfunction. Autoimmunity is characterized by breakdowns in immune self-tolerance, while impaired immune surveillance can allow for tumorigenesis. The class I major histocompatibility complex (MHC-I), which displays derivatives of the cellular peptidome for immune surveillance by CD8+ T cells, serves as a common genetic link between these conditions. As melanoma-specific CD8+ T cells have been shown to target melanocyte-specific peptide antigens more often than melanoma-specific antigens, we investigated whether vitiligo- and psoriasis-predisposing MHC-I alleles conferred a melanoma-protective effect. In individuals with cutaneous melanoma from both The Cancer Genome Atlas (n = 451) and an independent validation set (n = 586), MHC-I autoimmune-allele carrier status was significantly associated with a later age of melanoma diagnosis. Furthermore, MHC-I autoimmune-allele carriers were significantly associated with decreased risk of developing melanoma in the Million Veteran Program (OR = 0.962, p = 0.024). Existing melanoma polygenic risk scores (PRSs) did not predict autoimmune-allele carrier status, suggesting these alleles provide orthogonal risk-relevant information. Mechanisms of autoimmune protection were neither associated with improved melanoma-driver mutation association nor improved gene-level conserved antigen presentation relative to common alleles. However, autoimmune alleles showed higher affinity relative to common alleles for particular windows of melanocyte-conserved antigens and loss of heterozygosity of autoimmune alleles caused the greatest reduction in presentation for several conserved antigens across individuals with loss of HLA alleles. Overall, this study presents evidence that MHC-I autoimmune-risk alleles modulate melanoma risk unaccounted for by current PRSs.
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Affiliation(s)
- James V Talwar
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - David Laub
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Meghana S Pagadala
- Biomedical Science Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrea Castro
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - McKenna Lewis
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Georg E Luebeck
- Public Health Sciences Division, Herbold Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Bryan R Gorman
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Booz Allen Hamilton, Inc., McLean, VA 22102, USA
| | - Cuiping Pan
- Palo Alto Epidemiology Research and Information Center for Genomics, VA Palo Alto, CA, USA
| | - Frederick N Dong
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Booz Allen Hamilton, Inc., McLean, VA 22102, USA
| | - Kyriacos Markianos
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02115, USA
| | - Craig C Teerlink
- Department of Veterans Affairs Informatics and Computing Infrastructure (VINCI), VA Salt Lake City Healthcare System, Salt Lake City, UT, USA; Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Julie Lynch
- Department of Veterans Affairs Informatics and Computing Infrastructure (VINCI), VA Salt Lake City Healthcare System, Salt Lake City, UT, USA; Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Richard Hauger
- VA San Diego Healthcare System, La Jolla, CA, USA; Center for Behavioral Genetics of Aging, University of California San Diego, La Jolla, CA, USA; Center of Excellence for Stress and Mental Health (CESAMH), VA San Diego Healthcare System, San Diego, CA, USA
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Department of Medicine, Brigham Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Philip S Tsao
- Palo Alto Epidemiology Research and Information Center for Genomics, VA Palo Alto, CA, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Rany M Salem
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA 92093, USA
| | - Wesley K Thompson
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK 74136, USA
| | - Kit Curtius
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; The Laboratory of Immunology, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, Division of Hematology and Oncology, University of California San Diego, La Jolla, CA 92093, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA.
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14
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Cozzi G, Scagnellato L, Lorenzin M, Savarino E, Zingone F, Ometto F, Favero M, Doria A, Vavricka SR, Ramonda R. Spondyloarthritis with inflammatory bowel disease: the latest on biologic and targeted therapies. Nat Rev Rheumatol 2023:10.1038/s41584-023-00984-8. [PMID: 37386288 DOI: 10.1038/s41584-023-00984-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2023] [Indexed: 07/01/2023]
Abstract
Spondyloarthritis (SpA) encompasses a heterogeneous group of chronic inflammatory diseases that can affect both axial and peripheral joints, tendons and entheses. Among the extra-articular manifestations, inflammatory bowel disease (IBD) is associated with considerable morbidity and effects on quality of life. In everyday clinical practice, treatment of these conditions requires a close collaboration between gastroenterologists and rheumatologists to enable early detection of joint and intestinal manifestations during follow-up and to choose the most effective therapeutic regimen, implementing precision medicine for each patient's subtype of SpA and IBD. The biggest issue in this field is the dearth of drugs that are approved for both diseases, as only TNF inhibitors are currently approved for the treatment of full-spectrum SpA-IBD. Janus tyrosine kinase inhibitors are among the most promising drugs for the treatment of peripheral and axial SpA, as well as for intestinal manifestations. Other therapies such as inhibitors of IL-23 and IL-17, phosphodiesterase 4 inhibitor, α4β7 integrin blockers and faecal microbiota transplantation seem to only be able to control some disease domains, or require further studies. Given the growing interest in the development of novel drugs to treat both conditions, it is important to understand the current state of the art and the unmet needs in the management of SpA-IBD.
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Affiliation(s)
- Giacomo Cozzi
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Laura Scagnellato
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Mariagrazia Lorenzin
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Edoardo Savarino
- Gastroenterology Unit, Department of Surgery, Oncology and Gastroenterology, University Hospital of Padova, Padova, Italy
| | - Fabiana Zingone
- Gastroenterology Unit, Department of Surgery, Oncology and Gastroenterology, University Hospital of Padova, Padova, Italy
| | - Francesca Ometto
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Marta Favero
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Andrea Doria
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Stephan R Vavricka
- Department of Gastroenterology and Hepatology, University Hospital Zürich and Center for Gastroenterology and Hepatology, Zürich, Switzerland
| | - Roberta Ramonda
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy.
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15
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Admon A. The biogenesis of the immunopeptidome. Semin Immunol 2023; 67:101766. [PMID: 37141766 DOI: 10.1016/j.smim.2023.101766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.
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Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Israel.
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16
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Cruz FM, Chan A, Rock KL. Pathways of MHC I cross-presentation of exogenous antigens. Semin Immunol 2023; 66:101729. [PMID: 36804685 PMCID: PMC10023513 DOI: 10.1016/j.smim.2023.101729] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/18/2023]
Abstract
Phagocytes, particularly dendritic cells (DCs), generate peptide-major histocompatibility complex (MHC) I complexes from antigens they have collected from cells in tissues and report this information to CD8 T cells in a process called cross-presentation. This process allows CD8 T cells to detect, respond and eliminate abnormal cells, such as cancers or cells infected with viruses or intracellular microbes. In some settings, cross-presentation can help tolerize CD8 T cells to self-antigens. One of the principal ways that DCs acquire tissue antigens is by ingesting this material through phagocytosis. The resulting phagosomes are key hubs in the cross-presentation (XPT) process and in fact experimentally conferring the ability to phagocytize antigens can be sufficient to allow non-professional antigen presenting cells (APCs) to cross-present. Once in phagosomes, exogenous antigens can be cross-presented (XPTed) through three distinct pathways. There is a vacuolar pathway in which peptides are generated and then bind to MHC I molecules within the confines of the vacuole. Ingested exogenous antigens can also be exported from phagosomes to the cytosol upon vesicular rupture and/or possibly transport. Once in the cytosol, the antigen is degraded by the proteasome and the resulting oligopeptides can be transported to MHC I molecule in the endoplasmic reticulum (ER) (a phagosome-to-cytosol (P2C) pathway) or in phagosomes (a phagosome-to-cytosol-to-phagosome (P2C2P) pathway). Here we review how phagosomes acquire the necessary molecular components that support these three mechanisms and the contribution of these pathways. We describe what is known as well as the gaps in our understanding of these processes.
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Affiliation(s)
- Freidrich M Cruz
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Amanda Chan
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kenneth L Rock
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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17
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Alanine-based spacers promote an efficient antigen processing and presentation in neoantigen polypeptide vaccines. Cancer Immunol Immunother 2023:10.1007/s00262-023-03409-3. [PMID: 36820900 DOI: 10.1007/s00262-023-03409-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/12/2023] [Indexed: 02/24/2023]
Abstract
Neoantigens are tumor-specific antigens that are mostly particular for each patient. Since the immune system is able to mount a specific immune response against these neoantigens, they are a promising tool for the development of therapeutic personalized cancer vaccines. Neoantigens must be presented to T cells by antigen presenting cells (APC) in the context of MHC-I or MHC-II molecules. Therefore, the strategy of vaccine delivery may have a major impact on the magnitude and quality of T cell responses. Neoantigen-based vaccines are frequently administered as a pool of individual synthetic peptides that induce mainly CD4+ T cell responses. MHC-I-mediated presentation and the elicitation of CD8+ T cell responses may be improved using DNA or RNA sequences that code for a unique long polypeptide that concatenates the different neoantigens spaced by linker sequences. When administered this way, the selection of the spacer between neoantigens is of special interest, as it might influence the processing and presentation of the right peptides by APCs. Here, we evaluate the impact of such linker regions on the MHC-I-dependent antigen presentation using an in vitro assay that assesses the MHC-I presentation of SIINFEKL, a H-2 Kb-restricted OVA peptide. Our results show that spacers used to generate epitope concatenates have a large impact on the efficiency of neoantigen processing and presentation by MHC-I molecules; in contrast, the peptide position and the flanking regions have a minimal impact. Moreover, linkers based on alanine residues promote a more efficient peptide presentation than the commonly used GGGS linker.
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18
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Prinz JC. Immunogenic self-peptides - the great unknowns in autoimmunity: Identifying T-cell epitopes driving the autoimmune response in autoimmune diseases. Front Immunol 2023; 13:1097871. [PMID: 36700227 PMCID: PMC9868241 DOI: 10.3389/fimmu.2022.1097871] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
HLA-associated autoimmune diseases likely arise from T-cell-mediated autoimmune responses against certain self-peptides from the broad HLA-presented immunopeptidomes. The limited knowledge of the autoimmune target peptides has so far compromised the basic understanding of autoimmune pathogenesis. This is due to the complexity of antigen processing and presentation as well as the polyspecificity of T-cell receptors (TCRs), which pose high methodological challenges on the discovery of immunogenic self-peptides. HLA-class I molecules present peptides to CD8+ T cells primarily derived from cytoplasmic proteins. Therefore, HLA-class I-restricted autoimmune responses should be directed against target cells expressing the corresponding parental protein. In HLA-class II-associated diseases, the origin of immunogenic peptides is not pre-specified, because peptides presented by HLA-class II molecules to CD4+ T cells may originate from both extracellular and cellular self-proteins. The different origins of HLA-class I and class II presented peptides determine the respective strategy for the discovery of immunogenic self-peptides in approaches based on the TCRs isolated from clonally expanded pathogenic T cells. Both involve identifying the respective restricting HLA allele as well as determining the recognition motif of the TCR under investigation by peptide library screening, which is required to search for homologous immunogenic self-peptides. In HLA-class I-associated autoimmune diseases, identification of the target cells allows for defining the restricting HLA allotype from the 6 different HLA-class I alleles of the individual HLA haplotype. It furthermore limits the search for immunogenic self-peptides to the transcriptome or immunopeptidome of the target cells, although neoepitopes generated by peptide splicing or translational errors may complicate identification. In HLA class II-associated autoimmune diseases, the lack of a defined target cell and differential antigen processing in different antigen-presenting cells complicate identification of the HLA restriction of autoreactive TCRs from CD4+ T cells. To avoid that all corresponding HLA-class II allotypes have to be included in the peptide discovery, autoantigens defined by autoantibodies can guide the search for immunogenic self-peptides presented by the respective HLA-class II risk allele. The objective of this article is to highlight important aspects to be considered in the discovery of immunogenic self-peptides in autoimmune diseases.
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19
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Giannos P, Prokopidis K, Isanejad M, Wright HL. Markers of immune dysregulation in response to the ageing gut: insights from aged murine gut microbiota transplants. BMC Gastroenterol 2022; 22:533. [PMID: 36544093 PMCID: PMC9773626 DOI: 10.1186/s12876-022-02613-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Perturbations in the composition and diversity of the gut microbiota are accompanied by a decline in immune homeostasis during ageing, characterized by chronic low-grade inflammation and enhanced innate immunity. Genetic insights into the interaction between age-related alterations in the gut microbiota and immune function remain largely unexplored. METHODS We investigated publicly available transcriptomic gut profiles of young germ-free mouse hosts transplanted with old donor gut microbiota to identify immune-associated differentially expressed genes (DEGs). Literature screening of the Gene Expression Omnibus and PubMed identified one murine (Mus musculus) gene expression dataset (GSE130026) that included small intestine tissues from young (5-6 weeks old) germ-free mice hosts that were compared following 8 weeks after transplantation with either old (~ 24-month old; n = 5) or young (5-6 weeks old; n = 4) mouse donor gut microbiota. RESULTS A total of 112 differentially expressed genes (DEGs) were identified and used to construct a gut network of encoded proteins, in which DEGs were functionally annotated as being involved in an immune process based on gene ontology. The association between the expression of immune-process DEGs and abundance of immune infiltrates from gene signatures in normal colorectal tissues was estimated from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) project. The analysis revealed a 25-gene signature of immune-associated DEGs and their expression profile was positively correlated with naïve T-cell, effector memory T-cell, central memory T-cell, resident memory T-cell, exhausted T-cell, resting Treg T-cell, effector Treg T-cell and Th1-like colorectal gene signatures. Conclusions These genes may have a potential role as candidate markers of immune dysregulation during gut microbiota ageing. Moreover, these DEGs may provide insights into the altered immune response to microbiota in the ageing gut, including reduced antigen presentation and alterations in cytokine and chemokine production.
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Affiliation(s)
- Panagiotis Giannos
- Society of Meta-Research and Biomedical Innovation, London, UK.,Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Konstantinos Prokopidis
- Society of Meta-Research and Biomedical Innovation, London, UK.,Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Masoud Isanejad
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Helen L Wright
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
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20
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Salaffi F, Siragusano C, Alciati A, Cassone G, D’Angelo S, Guiducci S, Favalli EG, Conti F, Gremese E, Iannone F, Caporali R, Sebastiani M, Ferraccioli GF, Lapadula G, Atzeni F. Axial Spondyloarthritis: Reshape the Future-From the "2022 GISEA International Symposium". J Clin Med 2022; 11:jcm11247537. [PMID: 36556152 PMCID: PMC9780899 DOI: 10.3390/jcm11247537] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/02/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The term "axial spondyloarthritis" (axSpA) refers to a group of chronic rheumatic diseases that predominantly involve the axial skeleton and consist of ankylosing spondylitis, reactive arthritis, arthritis/spondylitis associated with psoriasis (PsA) and arthritis/spondylitis associated with inflammatory bowel diseases (IBD). Moreover, pain is an important and common symptom of axSpA. It may progress to chronic pain, a more complicated bio-psychosocial phenomena, leading to a significant worsening of quality of life. The development of the axSpA inflammatory process is grounded in the complex interaction between genetic (such as HLA B27), epigenetic, and environmental factors associated with a dysregulated immune response. Considering the pivotal contribution of IL-23 and IL-17 in axSpA inflammation, the inhibition of these cytokines has been evaluated as a potential therapeutic strategy. With this context, here we discuss the main pathogenetic mechanisms, therapeutic approaches and the role of pain in axSpA from the 2022 International GISEA/OEG Symposium.
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Affiliation(s)
- Fausto Salaffi
- Rheumatology Clinic, Ospedale Carlo Urbani, Università Politecnica delle Marche, 60035 Jesi, Italy
| | - Cesare Siragusano
- Rheumatology Unit, Department of Experimental and Internal Medicine, University of Messina, 98125 Messina, Italy
| | - Alessandra Alciati
- Department of Clinical Neurosciences, Hermanas Hospitalarias, Villa San Benedetto Menni Hospital, Como, and Humanitas Clinical and Research Centre, Rozzano, 20089 Milan, Italy
| | - Giulia Cassone
- Rheumatology Unit, Azienda Ospedaliera Policlinico di Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Salvatore D’Angelo
- Rheumatology Institute of Lucania and Rheumatology Department of Lucania, San Carlo Hospital of Potenza, 85100 Potenza, Italy
| | - Serena Guiducci
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Ennio Giulio Favalli
- Division of Clinical Rheumatology, ASST Gaetano Pini-CTO Institute, 20122 Milan, Italy
- Department of Clinical Sciences and Community Health, Research Center for Adult and Pediatric Rheumatic Diseases, University of Milan, 20122 Milan, Italy
| | - Fabrizio Conti
- Lupus Clinic, Dipartimento di Scienze Cliniche Internistiche, Anestesiologiche e Cardiovascolari, Sapienza University of Rome, 00161 Rome, Italy
| | - Elisa Gremese
- Rheumatology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Florenzo Iannone
- Rheumatology Unit, Department of Emergency Surgery and Organ Transplantations, University of Bari, 70121 Bari, Italy
| | - Roberto Caporali
- Division of Clinical Rheumatology, ASST Gaetano Pini-CTO Institute, 20122 Milan, Italy
- Department of Clinical Sciences and Community Health, Research Center for Adult and Pediatric Rheumatic Diseases, University of Milan, 20122 Milan, Italy
| | - Marco Sebastiani
- Rheumatology Unit, Azienda Ospedaliera Policlinico di Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Correspondence:
| | | | - Giovanni Lapadula
- Rheumatology Unit, Department of Emergency Surgery and Organ Transplantations, University of Bari, 70121 Bari, Italy
| | - Fabiola Atzeni
- Rheumatology Unit, Department of Experimental and Internal Medicine, University of Messina, 98125 Messina, Italy
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21
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Martín-Esteban A, Rodriguez JC, Peske D, Lopez de Castro JA, Shastri N, Sadegh-Nasseri S. The ER Aminopeptidases, ERAP1 and ERAP2, synergize to self-modulate their respective activities. Front Immunol 2022; 13:1066483. [PMID: 36569828 PMCID: PMC9774488 DOI: 10.3389/fimmu.2022.1066483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction Critical steps in Major Histocompatibility Complex Class I (MHC-I) antigen presentation occur in the endoplasmic reticulum (ER). In general, peptides that enter the ER are longer than the optimal length for MHC-I binding. The final trimming of MHC-I epitopes is performed by two related aminopeptidases, ERAP1 and ERAP2 in humans that possess unique and complementary substrate trimming specificities. While ERAP1 efficiently trims peptides longer than 9 residues, ERAP2 preferentially trims peptides shorter than 9 residues. Materials and Methods Using a combination of biochemical and proteomic studies followed by biological verification. Results We demonstrate that the optimal ligands for either enzyme act as inhibitors of the other enzyme. Specifically, the presence of octamers reduced the trimming of long peptides by ERAP1, while peptides longer than nonomers inhibit ERAP2 activity. Discussion We propose a mechanism for how ERAP1 and ERAP2 synergize to modulate their respective activities and shape the MHC-I peptidome by generating optimal peptides for presentation.
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Affiliation(s)
- Adrian Martín-Esteban
- Department of Pathology, Immunopathology Division, Johns Hopkins University, Baltimore, MD, United States,Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain,*Correspondence: Scheherazade Sadegh-Nasseri, ; Adrian Martín-Esteban,
| | - Jesus Contreras Rodriguez
- Department of Pathology, Immunopathology Division, Johns Hopkins University, Baltimore, MD, United States
| | - David Peske
- Department of Pathology, Immunopathology Division, Johns Hopkins University, Baltimore, MD, United States
| | | | - Nilabh Shastri
- Department of Pathology, Immunopathology Division, Johns Hopkins University, Baltimore, MD, United States
| | - Scheherazade Sadegh-Nasseri
- Department of Pathology, Immunopathology Division, Johns Hopkins University, Baltimore, MD, United States,*Correspondence: Scheherazade Sadegh-Nasseri, ; Adrian Martín-Esteban,
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22
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Yang X, Garner LI, Zvyagin IV, Paley MA, Komech EA, Jude KM, Zhao X, Fernandes RA, Hassman LM, Paley GL, Savvides CS, Brackenridge S, Quastel MN, Chudakov DM, Bowness P, Yokoyama WM, McMichael AJ, Gillespie GM, Garcia KC. Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides. Nature 2022; 612:771-777. [PMID: 36477533 PMCID: PMC10511244 DOI: 10.1038/s41586-022-05501-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
Human leucocyte antigen B*27 (HLA-B*27) is strongly associated with inflammatory diseases of the spine and pelvis (for example, ankylosing spondylitis (AS)) and the eye (that is, acute anterior uveitis (AAU))1. How HLA-B*27 facilitates disease remains unknown, but one possible mechanism could involve presentation of pathogenic peptides to CD8+ T cells. Here we isolated orphan T cell receptors (TCRs) expressing a disease-associated public β-chain variable region-complementary-determining region 3β (BV9-CDR3β) motif2-4 from blood and synovial fluid T cells from individuals with AS and from the eye in individuals with AAU. These TCRs showed consistent α-chain variable region (AV21) chain pairing and were clonally expanded in the joint and eye. We used HLA-B*27:05 yeast display peptide libraries to identify shared self-peptides and microbial peptides that activated the AS- and AAU-derived TCRs. Structural analysis revealed that TCR cross-reactivity for peptide-MHC was rooted in a shared binding motif present in both self-antigens and microbial antigens that engages the BV9-CDR3β TCRs. These findings support the hypothesis that microbial antigens and self-antigens could play a pathogenic role in HLA-B*27-associated disease.
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Affiliation(s)
- Xinbo Yang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lee I Garner
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ivan V Zvyagin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Michael A Paley
- Rheumatology Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Ekaterina A Komech
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiang Zhao
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ricardo A Fernandes
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lynn M Hassman
- Department of Ophthalmology, Washington University School of Medicine, St Louis, MO, USA
| | - Grace L Paley
- Department of Ophthalmology, Washington University School of Medicine, St Louis, MO, USA
| | - Christina S Savvides
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Simon Brackenridge
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Max N Quastel
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dmitriy M Chudakov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Paul Bowness
- Nuffield Department of Orthopaedics Rheumatology and Muscuoskeletal Science (NDORMS), Botnar Research Center, University of Oxford, Oxford, UK
| | - Wayne M Yokoyama
- Rheumatology Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
| | - Andrew J McMichael
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Geraldine M Gillespie
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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23
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Schott BH, Wang L, Zhu X, Harding AT, Ko ER, Bourgeois JS, Washington EJ, Burke TW, Anderson J, Bergstrom E, Gardener Z, Paterson S, Brennan RG, Chiu C, McClain MT, Woods CW, Gregory SG, Heaton NS, Ko DC. Single-cell genome-wide association reveals that a nonsynonymous variant in ERAP1 confers increased susceptibility to influenza virus. CELL GENOMICS 2022; 2:100207. [PMID: 36465279 PMCID: PMC9718543 DOI: 10.1016/j.xgen.2022.100207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/26/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
During pandemics, individuals exhibit differences in risk and clinical outcomes. Here, we developed single-cell high-throughput human in vitro susceptibility testing (scHi-HOST), a method for rapidly identifying genetic variants that confer resistance and susceptibility. We applied this method to influenza A virus (IAV), the cause of four pandemics since the start of the 20th century. scHi-HOST leverages single-cell RNA sequencing (scRNA-seq) to simultaneously assign genetic identity to cells in mixed infections of cell lines of European, African, and Asian origin, reveal associated genetic variants for viral burden, and identify expression quantitative trait loci. Integration of scHi-HOST with human challenge and experimental validation demonstrated that a missense variant in endoplasmic reticulum aminopeptidase 1 (ERAP1; rs27895) increased IAV burden in cells and human volunteers. rs27895 exhibits population differentiation, likely contributing to greater permissivity of cells from African populations to IAV. scHi-HOST is a broadly applicable method and resource for decoding infectious-disease genetics.
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Affiliation(s)
- Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- These authors contributed equally
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- These authors contributed equally
| | - Xinyu Zhu
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Alfred T Harding
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Emily R Ko
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Hospital Medicine, Division of General Internal Medicine, Department of Medicine, Duke Regional Hospital, Durham, NC 27705, USA
| | - Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Erica J Washington
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Jack Anderson
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Emma Bergstrom
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Zoe Gardener
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Suzanna Paterson
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Richard G Brennan
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Christopher Chiu
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Micah T McClain
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
- Lead contact
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24
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Xiong Y, Cai M, Xu Y, Dong P, Chen H, He W, Zhang J. Joint together: The etiology and pathogenesis of ankylosing spondylitis. Front Immunol 2022; 13:996103. [PMID: 36325352 PMCID: PMC9619093 DOI: 10.3389/fimmu.2022.996103] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/28/2022] [Indexed: 08/16/2023] Open
Abstract
Spondyloarthritis (SpA) refers to a group of diseases with inflammation in joints and spines. In this family, ankylosing spondylitis (AS) is a rare but classic form that mainly involves the spine and sacroiliac joint, leading to the loss of flexibility and fusion of the spine. Compared to other diseases in SpA, AS has a very distinct hereditary disposition and pattern of involvement, and several hypotheses about its etiopathogenesis have been proposed. In spite of significant advances made in Th17 dynamics and AS treatment, the underlying mechanism remains concealed. To this end, we covered several topics, including the nature of the immune response, the microenvironment in the articulation that is behind the disease's progression, and the split between the hypotheses and the evidence on how the intestine affects arthritis. In this review, we describe the current findings of AS and SpA, with the aim of providing an integrated view of the initiation of inflammation and the development of the disease.
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Affiliation(s)
- Yuehan Xiong
- Department of Immunology, Chinese Academy of Medical Sciences (CAMS) Key Laboratory of T Cell and Cancer Immunotherapy, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Menghua Cai
- Department of Immunology, Chinese Academy of Medical Sciences (CAMS) Key Laboratory of T Cell and Cancer Immunotherapy, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yi Xu
- Department of Immunology, Chinese Academy of Medical Sciences (CAMS) Key Laboratory of T Cell and Cancer Immunotherapy, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Peng Dong
- Changzhou Xitaihu Institute for Frontier Technology of Cell Therapy, Changzhou, China
| | - Hui Chen
- Department of Immunology, Chinese Academy of Medical Sciences (CAMS) Key Laboratory of T Cell and Cancer Immunotherapy, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Changzhou Xitaihu Institute for Frontier Technology of Cell Therapy, Changzhou, China
| | - Wei He
- Department of Immunology, Chinese Academy of Medical Sciences (CAMS) Key Laboratory of T Cell and Cancer Immunotherapy, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Changzhou Xitaihu Institute for Frontier Technology of Cell Therapy, Changzhou, China
| | - Jianmin Zhang
- Department of Immunology, Chinese Academy of Medical Sciences (CAMS) Key Laboratory of T Cell and Cancer Immunotherapy, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Changzhou Xitaihu Institute for Frontier Technology of Cell Therapy, Changzhou, China
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25
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Mattorre B, Tedeschi V, Paldino G, Fiorillo MT, Paladini F, Sorrentino R. The emerging multifunctional roles of ERAP1, ERAP2 and IRAP between antigen processing and renin-angiotensin system modulation. Front Immunol 2022; 13:1002375. [PMID: 36203608 PMCID: PMC9531115 DOI: 10.3389/fimmu.2022.1002375] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
The Endoplasmic Reticulum Aminopeptidase 1 and 2 (ERAP1 and ERAP2) and Insulin Regulated Aminopeptidase (IRAP) are three M1 zinc metalloproteases whose role in antigen processing is the refining of peptidome either in the Endoplasmic reticulum (ERAP1 and ERAP2), or in the endosomes (IRAP). However, other novel and distinct functions are emerging. Here, we focus specifically on ERAP2. This gene has a peculiar evolutionary history, being absent in rodents and undergoing in humans to a balanced selection of two haplotypes, one of which not expressing the full length ERAP2. These observations suggest that its role in antigen presentation is not essential. An additional, less investigated role is in the regulation of the Renin Angiotensin System (RAS). ERAP1 and ERAP2 cleave Angiotensin II (Ang II) into Ang III and IV, which counteract the action of Ang II whereas IRAP is itself the receptor for Ang IV. We have recently reported that macrophages, independently from the haplotype, express and release a N-terminus ERAP2 “short” form which directly binds IRAP and the two molecules are co-expressed in the endosomes and on the cell membrane. This new evidence suggests that the maintenance of the ERAP2 gene in humans could be due to its activity in the regulation of the RAS system, possibly as an Ang IV agonist. Its role in the immune-mediated diseases as well as in disorders more specifically related to an imbalance of the RAS system, including hypertension, pre-eclampsia but also viral infections such as COVID-19, is discussed here.
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26
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Cavers A, Kugler MC, Ozguler Y, Al-Obeidi AF, Hatemi G, Ueberheide BM, Ucar D, Manches O, Nowatzky J. Behçet's disease risk-variant HLA-B51/ERAP1-Hap10 alters human CD8 T cell immunity. Ann Rheum Dis 2022; 81:1603-1611. [PMID: 35922122 DOI: 10.1136/ard-2022-222277] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/27/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVES The endoplasmic reticulum aminopeptidase (ERAP1) haplotype Hap10 encodes for a variant allotype of the endoplasmic reticulum (ER)-resident peptide-trimming aminopeptidase ERAP1 with low enzymatic activity. This haplotype recessively confers the highest risk for Behçet's diseases (BD) currently known, but only in carriers of HLA-B*51, the classical risk factor for the disease. The mechanistic implications and biological consequences of this epistatic relationship are unknown. Here, we aimed to determine its biological relevance and functional impact. METHODS We genotyped and immune phenotyped a cohort of 26 untreated Turkish BD subjects and 22 healthy donors, generated CRISPR-Cas9 ERAP1 KOs from HLA-B*51 + LCL, analysed the HLA class I-bound peptidome for peptide length differences and assessed immunogenicity of genome-edited cells in CD8 T cell co-culture systems. RESULTS Allele frequencies of ERAP1-Hap10 were similar to previous studies. There were frequency shifts between antigen-experienced and naïve CD8 T cell populations of carriers and non-carriers of ERAP1-Hap10 in an HLA-B*51 background. ERAP1 KO cells showed peptidomes with longer peptides above 9mer and significant differences in their ability to stimulate alloreactive CD8 T cells compared with wild-type control cells. CONCLUSIONS We demonstrate that hypoactive ERAP1 changes immunogenicity to CD8 T cells, mediated by an HLA class I peptidome with undertrimmed peptides. Naïve/effector CD8 T cell shifts in affected carriers provide evidence of the biological relevance of ERAP1-Hap10/HLA-B*51 at the cellular level and point to an HLA-B51-restricted process. Our findings suggest that variant ERAP1-Hap10 partakes in BD pathogenesis by generating HLA-B51-restricted peptides, causing a change in immunodominance of the ensuing CD8 T cell response.
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Affiliation(s)
- Ann Cavers
- Department of Medicine, Division of Rheumatology, NYU Langone Behçet's Disease Program, NYU Langone Ocular Rheumatology Program, New York University Grossman School of Medicine, New York, NY, USA
| | - Matthias Christian Kugler
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Yesim Ozguler
- Department of Medicine, Division of Rheumatology, NYU Langone Behçet's Disease Program, NYU Langone Ocular Rheumatology Program, New York University Grossman School of Medicine, New York, NY, USA.,Department of Internal Medicine, Division of Rheumatology, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey.,Behçet's Disease Research Center, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Arshed Fahad Al-Obeidi
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Gulen Hatemi
- Department of Internal Medicine, Division of Rheumatology, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey.,Behçet's Disease Research Center, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Beatrix M Ueberheide
- Department of Biochemistry and Molecular Pharmacology, Department of Neurology, Perlmutter Cancer Center, Proteomics Laboratory at the Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, USA
| | - Didar Ucar
- Behçet's Disease Research Center, Istanbul University-Cerrahpasa, Istanbul, Turkey.,Department of Ophthalmology, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Olivier Manches
- Immunobiology and Immunotherapy in Chronic Diseases, Institute for Advanced Biosciences, Inserm U 1209, Université Grenoble-Alpes, Grenoble, France.,Recherche et Développement, Etablissement Français du Sang Auvergne-Rhône-Alpes, La Tronche, France
| | - Johannes Nowatzky
- Department of Medicine, Division of Rheumatology, NYU Langone Behçet's Disease Program, NYU Langone Ocular Rheumatology Program, New York University Grossman School of Medicine, New York, NY, USA .,Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
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27
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Atzeni F, Siragusano C, Masala IF, Antonio C, Valentina P, D'Angelo S. IL-23 in axial spondyloarthritis and psoriatic arthritis: a good fit for biological treatment? Expert Opin Biol Ther 2022; 22:843-853. [PMID: 35722768 DOI: 10.1080/14712598.2022.2090834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Interleukin 23 (IL-23) is a pro-inflammatory cytokine that plays a protective role against bacterial and fungal infections. However, the dysregulation of the IL-23/IL-17 axis provides a solid substrate for the development of various inflammatory diseases, such as psoriatic arthritis (PsA) and ankylosing spondylitis (AS). AREAS COVERED In different clinical trials, several drugs against IL-23 have shown efficacy and safety towards PsA, with excellent results on skin and joint scores. However, the same drugs did not show the same efficacy in AS, suggesting that IL-23 may not be a relevant driver of the pathobiology and clinical symptoms of active axial spondyloarthritis (axSpA). EXPERT OPINION These drugs have shown an excellent efficacy and a good safety profile towards PsA, while in AS the efficacy of the IL-23 blockade is lacking for reasons not yet known. Several hypotheses have been reported, but further studies will be needed for a greater understanding. This suggests the involvement of pathways or mechanisms for the development of SpA that remain unknown. In order to allow a wide use of IL-23 inhibitors, further clinical trials and long-term prospective studies are necessary.
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Affiliation(s)
- Fabiola Atzeni
- Rheumatology Unit, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Cesare Siragusano
- Rheumatology Unit, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | | | - Carriero Antonio
- Rheumatology Institute of Lucania (IReL): Rheumatology Department of Lucania, San Carlo Hospital of Potenza and Madonna delle Grazie Hospital of Matera, Potenza, Italy.,PhD Scholarship in Translational and Clinical Medicine, Department of Medicine and Health Sciences, University of Molise, Campobasso, Italy
| | - Picerno Valentina
- Rheumatology Institute of Lucania (IReL): Rheumatology Department of Lucania, San Carlo Hospital of Potenza and Madonna delle Grazie Hospital of Matera, Potenza, Italy
| | - Salvatore D'Angelo
- Rheumatology Institute of Lucania (IReL): Rheumatology Department of Lucania, San Carlo Hospital of Potenza and Madonna delle Grazie Hospital of Matera, Potenza, Italy
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28
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Darmon A, Zhang P, Marill J, Mohamed Anesary N, Da silva J, Paris S. Radiotherapy-activated NBTXR3 nanoparticles modulate cancer cell immunogenicity and TCR repertoire. Cancer Cell Int 2022; 22:208. [PMID: 35659676 PMCID: PMC9164428 DOI: 10.1186/s12935-022-02615-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/09/2022] [Indexed: 12/23/2022] Open
Abstract
Abstract
Background
Radiotherapy is a powerful and widely used technique for the treatment of solid tumors. Beyond its ability to destroy tumor cells, it has been demonstrated that radiotherapy can stimulate the anti-tumor immune response. Unfortunately, this effect is mainly restricted to the irradiated lesion, as tumor control outside the treated field (called the ‘abscopal effect’) is rarely obtained. In addition, many pro-tumoral factors prevent this anti-tumor immune response from being sustained and efficient. We previously reported that radiotherapy-activated NBTXR3 produced a significant CD8-dependent abscopal effect in immunocompetent mice bearing CT26.WT tumors, while radiotherapy failed to generate such a response.
Methods
To identify the mechanisms that may explain this response, we evaluated the capacity of radiotherapy-activated NBTXR3 to modulate the immunogenicity of tumor cells by analysis of immunogenic cell death biomarkers and immunopeptidome sequencing. In vivo, we analyzed treated tumors for CD4+, CD8 + and CD68 + cell infiltrates by immunohistochemistry and digital pathology and sequenced the T cell receptor (TCR) repertoire in both treated and untreated distant tumors.
Results
We showed that NBTXR3 activated by radiotherapy both increased immunogenic cell death biomarkers and modulated the immunopeptidome profile of CT26.WT cells. Immunohistochemistry analysis of treated tumors revealed a significant increase in CD4+, CD8 + and CD68 + cell infiltrates for NBTXR3 activated by radiotherapy group, compared to radiotherapy. We also measured significant modifications in TCR repertoire diversity in the radiotherapy-activated NBTXR3 group, both in treated and distant untreated tumors, compared to radiotherapy alone.
Conclusions
These results indicate that radiotherapy-activated NBTXR3 can act as an effective immunomodulator, modifying tumor cell immunogenicity and impacting the lymphocyte population.
Graphical Abstract
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Liu H, Hu B, Huang J, Wang Q, Wang F, Pan F, Chen L. Endoplasmic Reticulum Aminopeptidase 1 Is Involved in Anti-viral Immune Response of Hepatitis B Virus by Trimming Hepatitis B Core Antigen to Generate 9-Mers Peptides. Front Microbiol 2022; 13:829241. [PMID: 35602060 PMCID: PMC9115554 DOI: 10.3389/fmicb.2022.829241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 03/17/2022] [Indexed: 02/05/2023] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) is a processing enzyme of antigenic peptides presented to major histocompatibility complex (MHC) class I molecules. ERAP1-dependent trimming of epitope repertoire determines an efficacy of adoptive CD8+ T-cell responses in several viral diseases; however, its role in hepatitis B virus (HBV) infection remains unknown. Here, we show that the serum level of ERAP1 in patients with chronic hepatitis B (CHB) (n = 128) was significantly higher than that of healthy controls (n = 44) (8.78 ± 1.82 vs. 3.52 ± 1.61, p < 0.001). Furthermore, peripheral ERAP1 level is moderately correlated with HBV DNA level in patients with CHB (r = 0.731, p < 0.001). HBV-transfected HepG2.2.15 cells had substantially increased ERAP1 expression and secretion than the germline HepG2 cells (p < 0.001). The co-culture of ERAP1-specific inhibitor ERAP1-IN-1 pretreated HepG2.2.15 cells or ERAP1 knockdown HepG2.2.15 cells with CD8+ T cells led to 14-24% inhibition of the proliferation of CD8+ T cells. Finally, liquid chromatography tandem mass spectrometry (LC-MS/MS) test demonstrated that ERAP1-IN-1 blocks completely the production of a 9-mers peptide (30-38, LLDTASALY) derived from Hepatitis B core antigen (HBcAg). The predictive analysis by NetMHCpan-4.1 server showed that human leukocyte antigen (HLA)-C*04:01 is a strong binder for the 9-mers peptide in HepG2.2.15 cells. Taken together, our results demonstrated that ERAP1 trims HBcAg to produce 9-mers LLDTASALY peptides for binding onto HLA-C*04:01 in HepG2.2.15 cells, facilitating the potential activation of CD8+ T cells.
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Affiliation(s)
- Huanhuan Liu
- Department of Laboratory Medicine, Second Hospital of Anhui Medical University, Hefei, China
| | - Bingqi Hu
- Department of Laboratory Medicine, Second Hospital of Anhui Medical University, Hefei, China
| | - Junfeng Huang
- Department of Laboratory Medicine, Second Hospital of Anhui Medical University, Hefei, China
| | - Qin Wang
- Department of Laboratory Medicine, Second Hospital of Anhui Medical University, Hefei, China
| | - Feier Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Faming Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Liwen Chen
- Department of Laboratory Medicine, Second Hospital of Anhui Medical University, Hefei, China
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Pishesha N, Harmand TJ, Ploegh HL. A guide to antigen processing and presentation. Nat Rev Immunol 2022; 22:751-764. [PMID: 35418563 DOI: 10.1038/s41577-022-00707-2] [Citation(s) in RCA: 224] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2022] [Indexed: 12/13/2022]
Abstract
Antigen processing and presentation are the cornerstones of adaptive immunity. B cells cannot generate high-affinity antibodies without T cell help. CD4+ T cells, which provide such help, use antigen-specific receptors that recognize major histocompatibility complex (MHC) molecules in complex with peptide cargo. Similarly, eradication of virus-infected cells often depends on cytotoxic CD8+ T cells, which rely on the recognition of peptide-MHC complexes for their action. The two major classes of glycoproteins entrusted with antigen presentation are the MHC class I and class II molecules, which present antigenic peptides to CD8+ T cells and CD4+ T cells, respectively. This Review describes the essentials of antigen processing and presentation. These pathways are divided into six discrete steps that allow a comparison of the various means by which antigens destined for presentation are acquired and how the source proteins for these antigens are tagged for degradation, destroyed and ultimately displayed as peptides in complex with MHC molecules for T cell recognition.
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Affiliation(s)
- Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Society of Fellows, Harvard University, Cambridge, MA, USA.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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31
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Blake MK, O'Connell P, Pepelyayeva Y, Godbehere S, Aldhamen YA, Amalfitano A. ERAP1 is a critical regulator of inflammasome-mediated proinflammatory and ER stress responses. BMC Immunol 2022; 23:9. [PMID: 35246034 PMCID: PMC8895631 DOI: 10.1186/s12865-022-00481-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/08/2022] [Indexed: 11/26/2022] Open
Abstract
Background In addition to its role in antigen presentation, recent reports establish a new role for endoplasmic reticulum aminopeptidase 1 (ERAP1) in innate immunity; however, the mechanisms underlying these functions are not fully defined. We previously confirmed that loss of ERAP1 functions resulted in exaggerated innate immune responses in a murine in vivo model. Here, we investigated the role of ERAP1 in suppressing inflammasome pathways and their dependence on ER stress responses. Results Using bone marrow-derived macrophages (BMDMs), we found that loss of ERAP1 in macrophages resulted in exaggerated production of IL-1β and IL-18 and augmented caspase-1 activity, relative to wild type macrophages. Moreover, an in vivo colitis model utilizing dextran sodium sulfate (DSS) confirmed increased levels of proinflammatory cytokines and chemokines in the colon of DSS treated ERAP1−/− mice as compared to identically stimulated WT mice. Interestingly, stimulated ERAP1−/− BMDMs and CD4+ T cells simultaneously demonstrated exaggerated ER stress, assessed by increased expression of ER stress-associated genes, a state that could be reverted to WT levels with use of the ER stress inhibitor Tauroursodeoxycholic acid (TUDCA). Conclusions Together, these results not only suggest that ERAP1 is important for regulating inflammasome dependent innate immune response pathways in vivo, but also propose a mechanism that underlies these changes, that may be associated with increased ER stress due to lack of normal ERAP1 functions. Supplementary Information The online version contains supplementary material available at 10.1186/s12865-022-00481-9.
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Affiliation(s)
- Maja K Blake
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Patrick O'Connell
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Yuliya Pepelyayeva
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Sarah Godbehere
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Yasser A Aldhamen
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Andrea Amalfitano
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA. .,Department of Pediatrics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA.
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Pymm P, Tenzer S, Wee E, Weimershaus M, Burgevin A, Kollnberger S, Gerstoft J, Josephs TM, Ladell K, McLaren JE, Appay V, Price DA, Fugger L, Bell JI, Schild H, van Endert P, Harkiolaki M, Iversen AKN. Epitope length variants balance protective immune responses and viral escape in HIV-1 infection. Cell Rep 2022; 38:110449. [PMID: 35235807 PMCID: PMC9631117 DOI: 10.1016/j.celrep.2022.110449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 10/31/2021] [Accepted: 02/07/2022] [Indexed: 11/21/2022] Open
Abstract
Cytotoxic T lymphocyte (CTL) and natural killer (NK) cell responses to a single optimal 10-mer epitope (KK10) in the human immunodeficiency virus type-1 (HIV-1) protein p24Gag are associated with enhanced immune control in patients expressing human leukocyte antigen (HLA)-B∗27:05. We find that proteasomal activity generates multiple length variants of KK10 (4-14 amino acids), which bind TAP and HLA-B∗27:05. However, only epitope forms ≥8 amino acids evoke peptide length-specific and cross-reactive CTL responses. Structural analyses reveal that all epitope forms bind HLA-B∗27:05 via a conserved N-terminal motif, and competition experiments show that the truncated epitope forms outcompete immunogenic epitope forms for binding to HLA-B∗27:05. Common viral escape mutations abolish (L136M) or impair (R132K) production of KK10 and longer epitope forms. Peptide length influences how well the inhibitory NK cell receptor KIR3DL1 binds HLA-B∗27:05 peptide complexes and how intraepitope mutations affect this interaction. These results identify a viral escape mechanism from CTL and NK responses based on differential antigen processing and peptide competition.
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Affiliation(s)
- Phillip Pymm
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK; Walter and Eliza Hall Institute of Medical Research, University of Melbourne, 1G Royalparade, Parkville, VIC 3052, Australia
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University of Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany
| | - Edmund Wee
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Mirjana Weimershaus
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France
| | - Anne Burgevin
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France
| | - Simon Kollnberger
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, CF14 4XN Cardiff, UK
| | - Jan Gerstoft
- Department of Infectious Diseases, Rigshospitalet, The National University Hospital, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Tracy M Josephs
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, CF14 4XN Cardiff, UK
| | - James E McLaren
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, CF14 4XN Cardiff, UK
| | - Victor Appay
- Institut National de la Santé et de la Recherche Médicale, Unité 1135, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Université, Boulevard de l'Hopital, 75013 Paris, France; International Research Center of Medical Sciences, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto City 860-0811, Japan
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, CF14 4XN Cardiff, UK; Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Tenovus Building, CF14 4XN Cardiff, UK
| | - Lars Fugger
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK; Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, OX3 9DS Oxford, UK
| | - John I Bell
- Office of the Regius Professor of Medicine, The Richard Doll Building, University of Oxford, Old Road Campus, OX3 7LF Oxford, UK
| | - Hansjörg Schild
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University of Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany
| | - Peter van Endert
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France
| | - Maria Harkiolaki
- Structural Biology Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Old Road Campus, OX3 7LF Oxford, UK; Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, OX11 0DE Didcot, UK
| | - Astrid K N Iversen
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK.
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Craig DJ, Bailey MM, Noe OB, Williams KK, Stanbery L, Hamouda DM, Nemunaitis JJ. Subclonal landscape of cancer drives resistance to immune therapy. Cancer Treat Res Commun 2022; 30:100507. [PMID: 35007928 DOI: 10.1016/j.ctarc.2021.100507] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 02/06/2023]
Abstract
Tumor mutation burden (TMB) is often used as a biomarker for immunogenicity and prerequisite for immune checkpoint inhibitor (ICI) therapy. However, it is becoming increasingly evident that not all tumors with high TMB respond to ICIs as expected. It has been shown that the ability of T-cells to infiltrate the tumor microenvironment and elicit a specific immune response is dependent not only on the TMB, but also on intra-tumor heterogeneity and the fraction of low-frequency subclonal mutations that make up the tumor. High intra-tumor heterogeneity leads to inefficient recognition of tumor neoantigens by T-cells due to their diluted frequency and spatial heterogeneity. Clinical studies have shown that tumors with a high degree of intra-tumor heterogeneity respond poorly to ICI therapy, and previous cytotoxic treatment may increase the intra-tumor heterogeneity and render second-line ICI therapy less effective. This paper reviews the role of ICI therapy when following chemotherapy or radiation to determine if they may be better suited as first-line therapy in patients with high TMB, low intra-tumor heterogeneity, and high PD-1, PD-L1, or CTLA-4 expression.
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Affiliation(s)
- Daniel J Craig
- University of Toledo Medical Center, Toledo, OH, 43614, USA
| | | | - Olivia B Noe
- University of Toledo Medical Center, Toledo, OH, 43614, USA
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Arakawa A, Reeves E, Vollmer S, Arakawa Y, He M, Galinski A, Stöhr J, Dornmair K, James E, Prinz JC. ERAP1 Controls the Autoimmune Response against Melanocytes in Psoriasis by Generating the Melanocyte Autoantigen and Regulating Its Amount for HLA-C*06:02 Presentation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:2235-2244. [PMID: 34580106 PMCID: PMC7611875 DOI: 10.4049/jimmunol.2100686] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/17/2021] [Indexed: 01/05/2023]
Abstract
Autoimmune diseases develop when autoantigens activate previously quiescent self-reactive lymphocytes. Gene-gene interaction between certain HLA class I risk alleles and variants of the endoplasmic reticulum aminopeptidase ERAP1 controls the risk for common immune-mediated diseases, including psoriasis, ankylosing spondylitis, and Behçet disease. The functional mechanisms underlying this statistical association are unknown. In psoriasis, HLA-C*06:02 mediates an autoimmune response against melanocytes by autoantigen presentation. Using various genetically modified cell lines together with an autoreactive psoriatic TCR in a TCR activation assay, we demonstrate in this study that in psoriasis, ERAP1 generates the causative melanocyte autoantigen through trimming N-terminal elongated peptide precursors to the appropriate length for presentation by HLA-C*06:02. An ERAP1 risk haplotype for psoriasis produced the autoantigen much more efficiently and increased HLA-C expression and stimulation of the psoriatic TCR by melanocytes significantly more than a protective haplotype. Compared with the overall HLA class I molecules, cell surface expression of HLA-C decreased significantly more upon ERAP1 knockout. The combined upregulation of ERAP1 and HLA-C on melanocytes in psoriasis lesions emphasizes the pathogenic relevance of their interaction in patients. We conclude that in psoriasis pathogenesis, the increased generation of an ERAP1-dependent autoantigen by an ERAP1 risk haplotype enhances the likelihood that autoantigen presentation by HLA-C*06:02 will exceed the threshold for activation of potentially autoreactive T cells, thereby triggering CD8+ T cell-mediated autoimmune disease. These data identify ERAP1 function as a central checkpoint and promising therapeutic target in psoriasis and possibly other HLA class I-associated diseases with a similar genetic predisposition.
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Affiliation(s)
- Akiko Arakawa
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany;
| | - Emma Reeves
- Centre for Cancer Immunology, University Hospital Southampton, Southampton, United Kingdom; and
| | - Sigrid Vollmer
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Yukiyasu Arakawa
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Mengwen He
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Adrian Galinski
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Julia Stöhr
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Klaus Dornmair
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Edward James
- Centre for Cancer Immunology, University Hospital Southampton, Southampton, United Kingdom; and
| | - Jörg C Prinz
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany;
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35
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Watts E, Potts GK, Ready DB, George Thompson AM, Lee J, Escobar EE, Patterson MJ, Brodbelt JS. Characterization of HLA-A*02:01 MHC Immunopeptide Antigens Enhanced by Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2021; 93:13134-13142. [PMID: 34553926 DOI: 10.1021/acs.analchem.1c01002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identifying major histocompatibility complex (MHC) class I immunopeptide antigens represents a key step in the development of immune-based targeted therapeutics and vaccines. However, the complete characterization of these antigens by tandem mass spectrometry remains challenging due to their short sequence length, high degree of hydrophobicity, and/or lack of sufficiently basic amino acids. This study seeks to address the potential for 193 nm ultraviolet photodissociation (UVPD) to improve the analysis of MHC class I immunopeptides by offering enhanced characterization of these sequences in lower charge states and differentiation of prominent isomeric leucine and isoleucine residues in the HLA-A*02:01 motif. Although electron transfer dissociation-higher energy collisional dissociation (EThcD) offered some success in the differentiation of leucine and isoleucine, 193 nm UVPD was able to confirm the identity of nearly 60% of leucine and isoleucine residues in a synthetic peptide mixture. Furthermore, 193 nm UVPD led to significantly more peptide identifications and higher scoring metrics than EThcD for peptides obtained from immunoprecipitation of MHC class I immunopeptides from in vitro cell culture. Additionally, 193 nm UVPD represents a promising complementary technique to higher-energy collisional dissociation (HCD), in which 424 of the 2593 peptides identified by 193 nm UVPD were not identified by HCD in HLA-A*02:01-specific immunoprecipitation and 804 of the 3300 peptides identified by 193 nm UVPD were not identified by HCD for pan HLA-A, -B, and -C immunoprecipitation. These results highlight that 193 nm UVPD offers an option for the characterization of immunopeptides, including differentiation of leucine and isoleucine residues.
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Affiliation(s)
- Eleanor Watts
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
| | - Gregory K Potts
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | - Damien B Ready
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | | | - Janice Lee
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | - Edwin E Escobar
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
| | | | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
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Maben Z, Arya R, Georgiadis D, Stratikos E, Stern LJ. Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism. Nat Commun 2021; 12:5302. [PMID: 34489420 PMCID: PMC8421391 DOI: 10.1038/s41467-021-25564-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 08/10/2021] [Indexed: 11/27/2022] Open
Abstract
The endoplasmic-reticulum aminopeptidase ERAP1 processes antigenic peptides for loading on MHC-I proteins and recognition by CD8 T cells as they survey the body for infection and malignancy. Crystal structures have revealed ERAP1 in either open or closed conformations, but whether these occur in solution and are involved in catalysis is not clear. Here, we assess ERAP1 conformational states in solution in the presence of substrates, allosteric activators, and inhibitors by small-angle X-ray scattering. We also characterize changes in protein conformation by X-ray crystallography, and we localize alternate C-terminal binding sites by chemical crosslinking. Structural and enzymatic data suggest that the structural reconfigurations of ERAP1 active site are physically linked to domain closure and are promoted by binding of long peptide substrates. These results clarify steps required for ERAP1 catalysis, demonstrate the importance of conformational dynamics within the catalytic cycle, and provide a mechanism for the observed allosteric regulation and Lys/Arg528 polymorphism disease association.
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Affiliation(s)
- Zachary Maben
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Richa Arya
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dimitris Georgiadis
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Efstratios Stratikos
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.
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Joyce S, Ternette N. Know thy immune self and non-self: Proteomics informs on the expanse of self and non-self, and how and where they arise. Proteomics 2021; 21:e2000143. [PMID: 34310018 PMCID: PMC8865197 DOI: 10.1002/pmic.202000143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022]
Abstract
T cells play an important role in the adaptive immune response to a variety of infections and cancers. Initiation of a T cell mediated immune response requires antigen recognition in a process termed MHC (major histocompatibility complex) restri ction. A T cell antigen is a composite structure made up of a peptide fragment bound within the antigen‐binding groove of an MHC‐encoded class I or class II molecule. Insight into the precise composition and biology of self and non‐self immunopeptidomes is essential to harness T cell mediated immunity to prevent, treat, or cure infectious diseases and cancers. T cell antigen discovery is an arduous task! The pioneering work in the early 1990s has made large‐scale T cell antigen discovery possible. Thus, advancements in mass spectrometry coupled with proteomics and genomics technologies make possible T cell antigen discovery with ease, accuracy, and sensitivity. Yet we have only begun to understand the breadth and the depth of self and non‐self immunopeptidomes because the molecular biology of the cell continues to surprise us with new secrets directly related to the source, and the processing and presentation of MHC ligands. Focused on MHC class I molecules, this review, therefore, provides a brief historic account of T cell antigen discovery and, against a backdrop of key advances in molecular cell biologic processes, elaborates on how proteogenomics approaches have revolutionised the field.
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Affiliation(s)
- Sebastian Joyce
- Department of Veterans Affairs, Tennessee Valley Healthcare System and the Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nicola Ternette
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Deddouche-Grass S, Andouche C, Bärenz F, Halter C, Hohwald A, Lebrun L, Membré N, Morales R, Muzet N, Poirot M, Reynaud M, Roujean V, Weber F, Zimmermann A, Heng R, Basse N. Discovery and Optimization of a Series of Benzofuran Selective ERAP1 Inhibitors: Biochemical and In Silico Studies. ACS Med Chem Lett 2021; 12:1137-1142. [PMID: 34267884 DOI: 10.1021/acsmedchemlett.1c00235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/03/2021] [Indexed: 01/22/2023] Open
Abstract
ERAP1 is a key aminopeptidase involved in peptide trimming before major histocompatibility complex (MHC) presentation. A single nucleotide polymorphism (SNP) in the ERAP1 gene can lead to impaired trimming activity and affect ERAP1 function. ERAP1 genetic variations have been linked to an increased susceptibility to cancer and autoimmune disease. Here, we report the discovery of novel ERAP1 inhibitors using a high throughput screening approach. Due to ERAP1 broad substrate specificity, the hit finding strategy included testing inhibitors with a range of biochemical assays. Based on the hit potency, selectivity, and in vitro absorption, distribution, metabolism, excretion, and toxicity, the benzofuran series was selected. Fifteen derivatives were designed and synthesized, the compound potency was improved to the nanomolar range, and the structure-activity relationship supported by modeling studies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Rama Heng
- Evotec, 31036 Toulouse cedex, France
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Aflalo A, Boyle LH. Polymorphisms in MHC class I molecules influence their interactions with components of the antigen processing and presentation pathway. Int J Immunogenet 2021; 48:317-325. [PMID: 34176210 DOI: 10.1111/iji.12546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
MHC class I (MHC-I) molecules undergo an intricate folding process in order to pick up antigenic peptide to present to the immune system. In recent years, the discovery of a new peptide editor for MHC-I has added an extra level of complexity in our understanding of how peptide presentation is regulated. On top of this, the incredible diversity in MHC-I molecules leads to significant variation in the interaction between MHC-I and components of the antigen processing and presentation pathway. Here, we review our current understanding regarding how polymorphisms in human leukocyte antigen class I molecules influence their interactions with key components of the antigen processing and presentation pathway. A deeper understanding of this may offer new insights regarding how apparently subtle variation in MHC-I can have a significant impact on susceptibility to disease.
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Affiliation(s)
- Aure Aflalo
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Cambridge, UK
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40
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Light control of the peptide-loading complex synchronizes antigen translocation and MHC I trafficking. Commun Biol 2021; 4:430. [PMID: 33785857 PMCID: PMC8010092 DOI: 10.1038/s42003-021-01890-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/17/2021] [Indexed: 12/16/2022] Open
Abstract
Antigen presentation via major histocompatibility complex class I (MHC I) molecules is essential to mount an adaptive immune response against pathogens and cancerous cells. To this end, the transporter associated with antigen processing (TAP) delivers snippets of the cellular proteome, resulting from proteasomal degradation, into the ER lumen. After peptide loading and editing by the peptide-loading complex (PLC), stable peptide-MHC I complexes are released for cell surface presentation. Since the process of MHC I trafficking is poorly defined, we established an approach to control antigen presentation by introduction of a photo-caged amino acid in the catalytic ATP-binding site of TAP. By optical control, we initiate TAP-dependent antigen translocation, thus providing new insights into TAP function within the PLC and MHC I trafficking in living cells. Moreover, this versatile approach has the potential to be applied in the study of other cellular pathways controlled by P-loop ATP/GTPases. Brunnberg et al. establish a protocol that enables them to optically control translocation of the transporter associated with antigen processing (TAP), which plays a role in delivering proteasomal degradation products into the ER lumen. Their versatile approach provides insights into TAP function in the context of peptide-loading complex and stable peptide-MHC I complex trafficking in living cells, but has the potential to be applied to the investigation of other pathways.
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41
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Dhatchinamoorthy K, Colbert JD, Rock KL. Cancer Immune Evasion Through Loss of MHC Class I Antigen Presentation. Front Immunol 2021; 12:636568. [PMID: 33767702 PMCID: PMC7986854 DOI: 10.3389/fimmu.2021.636568] [Citation(s) in RCA: 396] [Impact Index Per Article: 132.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/05/2021] [Indexed: 02/03/2023] Open
Abstract
Major histocompatibility class I (MHC I) molecules bind peptides derived from a cell's expressed genes and then transport and display this antigenic information on the cell surface. This allows CD8 T cells to identify pathological cells that are synthesizing abnormal proteins, such as cancers that are expressing mutated proteins. In order for many cancers to arise and progress, they need to evolve mechanisms to avoid elimination by CD8 T cells. MHC I molecules are not essential for cell survival and therefore one mechanism by which cancers can evade immune control is by losing MHC I antigen presentation machinery (APM). Not only will this impair the ability of natural immune responses to control cancers, but also frustrate immunotherapies that work by re-invigorating anti-tumor CD8 T cells, such as checkpoint blockade. Here we review the evidence that loss of MHC I antigen presentation is a frequent occurrence in many cancers. We discuss new insights into some common underlying mechanisms through which some cancers inactivate the MHC I pathway and consider some possible strategies to overcome this limitation in ways that could restore immune control of tumors and improve immunotherapy.
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42
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Yang S, Tang D, Zhao YC, Liu H, Luo S, Stinchcombe TE, Glass C, Su L, Shen S, Christiani DC, Wang Q, Wei Q. Potentially functional variants of ERAP1, PSMF1 and NCF2 in the MHC-I-related pathway predict non-small cell lung cancer survival. Cancer Immunol Immunother 2021; 70:2819-2833. [PMID: 33651148 DOI: 10.1007/s00262-021-02877-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/01/2021] [Indexed: 01/21/2023]
Abstract
BACKGROUND Cellular immunity against tumor cells is highly dependent on antigen presentation by major histocompatibility complex class I (MHC-I) molecules. However, few published studies have investigated associations between functional variants of MHC-I-related genes and clinical outcomes of lung cancer patients. METHODS We performed a two-phase Cox proportional hazards regression analysis by using two previously published genome-wide association studies to evaluate associations between genetic variants in the MHC-I-related gene set and the survival of non-small cell lung cancer (NSCLC) patients, followed by expression quantitative trait loci analysis. RESULTS Of the 7811 single-nucleotide polymorphisms (SNPs) in 89 genes of 1185 NSCLC patients in the discovery dataset of the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial, 24 SNPs remained statistically significant after validation in additional 984 NSCLC patients from the Harvard Lung Cancer Susceptibility Study. In a multivariate stepwise Cox model, three independent functional SNPs (ERAP1 rs469783 T > C, PSMF1 rs13040574 C > A and NCF2 rs36071574 G > A) remained significant with an adjusted hazards ratio (HR) of 0.83 [95% confidence interval (CI) = 0.77-0.89, P = 8.0 × 10-7], 0.86 (0.80-0.93, P = 9.4 × 10-5) and 1.31 (1.11-1.54, P = 0.001) for overall survival (OS), respectively. Further combined genotypes revealed a poor survival in a dose-response manner in association with the number of unfavorable genotypes (Ptrend < 0.0001 and 0.0002 for OS and disease-specific survival, respectively). Also, ERAP1 rs469783C and PSMF1 rs13040574A alleles were associated with higher mRNA expression levels of their genes. CONCLUSION These potentially functional SNPs of the MHC-I-related genes may be biomarkers for NSCLC survival, possibly through modulating the expression of corresponding genes.
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Affiliation(s)
- Sen Yang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Dongfang Tang
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Yu Chen Zhao
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Hongliang Liu
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Thomas E Stinchcombe
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Carolyn Glass
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Pathology, Duke ©University School of Medicine, Durham, NC, 27710, USA
| | - Li Su
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
| | - Sipeng Shen
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
| | - David C Christiani
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Qiming Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.
| | - Qingyi Wei
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA.
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
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43
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Lee MY, Robbins Y, Sievers C, Friedman J, Abdul Sater H, Clavijo PE, Judd N, Tsong E, Silvin C, Soon-Shiong P, Padget MR, Schlom J, Hodge J, Hinrichs C, Allen C. Chimeric antigen receptor engineered NK cellular immunotherapy overcomes the selection of T-cell escape variant cancer cells. J Immunother Cancer 2021; 9:e002128. [PMID: 33741731 PMCID: PMC7986659 DOI: 10.1136/jitc-2020-002128] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND As heterogeneous tumors develop in the face of intact immunity, tumor cells harboring genomic or expression defects that favor evasion from T-cell detection or elimination are selected. For patients with such tumors, T cell-based immunotherapy alone infrequently results in durable tumor control. METHODS Here, we developed experimental models to study mechanisms of T-cell escape and demonstrated that resistance to T-cell killing can be overcome by the addition of natural killer (NK) cells engineered to express a chimeric antigen receptor (CAR) targeting programmed death ligand-1 (PD-L1). RESULTS In engineered models of tumor heterogeneity, PD-L1 CAR-engineered NK cells (PD-L1 t-haNKs) prevented the clonal selection of T cell-resistant tumor cells observed with T-cell treatment alone in multiple models. Treatment of heterogenous cancer cell populations with T cells resulted in interferon gamma (IFN-γ) release and subsequent upregulation of PD-L1 on tumor cells that escaped T-cell killing through defects in antigen processing and presentation, priming escape cell populations for PD-L1 dependent killing by PD-L1 t-haNKs in vitro and in vivo. CONCLUSIONS These results describe the underlying mechanisms governing synergistic antitumor activity between T cell-based immunotherapy that results in IFN-γ production, upregulation of PD-L1 on T-cell escape cells, and the use of PD-L1 CAR-engineered NK cells to target and eliminate resistant tumor cell populations.
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MESH Headings
- Animals
- B7-H1 Antigen/genetics
- B7-H1 Antigen/metabolism
- CRISPR-Cas Systems
- Cell Line, Tumor
- Databases, Genetic
- Gene Editing
- HLA Antigens/metabolism
- Head and Neck Neoplasms/genetics
- Head and Neck Neoplasms/immunology
- Head and Neck Neoplasms/metabolism
- Head and Neck Neoplasms/therapy
- Humans
- Immunotherapy, Adoptive
- Interferon-gamma/metabolism
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Killer Cells, Natural/transplantation
- Lymphocyte Activation
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Mice, Inbred NOD
- Mice, SCID
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/immunology
- Squamous Cell Carcinoma of Head and Neck/genetics
- Squamous Cell Carcinoma of Head and Neck/immunology
- Squamous Cell Carcinoma of Head and Neck/metabolism
- Squamous Cell Carcinoma of Head and Neck/therapy
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- T-Lymphocytes/transplantation
- Tumor Burden
- Tumor Escape
- Tumor Microenvironment
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Maxwell Y Lee
- NIDCD, National Institutes of Health, Bethesda, Maryland, USA
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yvette Robbins
- NIDCD, National Institutes of Health, Bethesda, Maryland, USA
| | - Cem Sievers
- NIDCD, National Institutes of Health, Bethesda, Maryland, USA
| | - Jay Friedman
- NIDCD, National Institutes of Health, Bethesda, Maryland, USA
| | - Houssein Abdul Sater
- Genitourinary Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul E Clavijo
- NIDCD, National Institutes of Health, Bethesda, Maryland, USA
| | - Nancy Judd
- Mid-Atlantic Permanente Medical Group, Rockville, Maryland, USA
| | - Edward Tsong
- Mid-Atlantic Permanente Medical Group, Rockville, Maryland, USA
| | - Chris Silvin
- NIDCD, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Michelle R Padget
- Laboratory of Tumor Immunology and Biology, National Cancer Institute, Bethesda, Maryland, USA
| | - Jeffrey Schlom
- Laboratory of Tumor Immunology and Biology, National Cancer Institute, Bethesda, Maryland, USA
| | - James Hodge
- Laboratory of Tumor Immunology and Biology, National Cancer Institute, Bethesda, Maryland, USA
| | - Christian Hinrichs
- Genitourinary Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Clint Allen
- NIDCD, National Institutes of Health, Bethesda, Maryland, USA
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de Waard AA, Verkerk T, Jongsma MLM, Hoefakker K, Sethumadhavan S, Gerke C, Bliss S, Kong X, Janssen GMC, de Ru AH, Claas FHJ, Mulder A, Tampé R, van Veelen PA, Halenius A, Spaapen RM. PAKC: A novel panel of HLA class I antigen presentation machinery knockout cells from the same genetic origin. Eur J Immunol 2021; 51:734-737. [PMID: 33275281 PMCID: PMC7986913 DOI: 10.1002/eji.202048599] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 09/30/2020] [Accepted: 11/27/2020] [Indexed: 01/08/2023]
Abstract
A single model system for integrative studies on multiple facets of antigen presentation is lacking. PAKC is a novel panel of ten cell lines knocked out for individual components of the HLA class I antigen presentation pathway. PAKC will accelerate HLA-I research in the fields of oncology, infectiology, and autoimmunity.
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Affiliation(s)
- Antonius A. de Waard
- Department of ImmunopathologySanquin ResearchAmsterdamThe Netherlands
- Landsteiner Laboratory, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Tamara Verkerk
- Department of ImmunopathologySanquin ResearchAmsterdamThe Netherlands
- Landsteiner Laboratory, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Marlieke L. M. Jongsma
- Department of ImmunopathologySanquin ResearchAmsterdamThe Netherlands
- Landsteiner Laboratory, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode Institute and Department of Cell and Chemical BiologyLUMCLeidenThe Netherlands
| | - Kelly Hoefakker
- Department of ImmunopathologySanquin ResearchAmsterdamThe Netherlands
- Landsteiner Laboratory, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | | | - Carolin Gerke
- Institute of VirologyMedical Center University of FreiburgFreiburgGermany
- Faculty of MedicineUniversity of FreiburgFreiburgGermany
- Spemann Graduate School of Biology and MedicineUniversity of FreiburgFreiburgGermany
- Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Sophie Bliss
- Department of ImmunopathologySanquin ResearchAmsterdamThe Netherlands
- Landsteiner Laboratory, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Xiangrui Kong
- Department of ImmunopathologySanquin ResearchAmsterdamThe Netherlands
- Landsteiner Laboratory, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | | | - Arnoud H. de Ru
- Center for Proteomics and MetabolomicsLUMCLeidenThe Netherlands
| | | | - Arend Mulder
- Department of ImmunologyLUMCLeidenThe Netherlands
| | - Robert Tampé
- Institute of Biochemistry, BiocenterGoethe University FrankfurtFrankfurtGermany
| | | | - Anne Halenius
- Institute of VirologyMedical Center University of FreiburgFreiburgGermany
- Faculty of MedicineUniversity of FreiburgFreiburgGermany
| | - Robbert M. Spaapen
- Department of ImmunopathologySanquin ResearchAmsterdamThe Netherlands
- Landsteiner Laboratory, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
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45
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Schinocca C, Rizzo C, Fasano S, Grasso G, La Barbera L, Ciccia F, Guggino G. Role of the IL-23/IL-17 Pathway in Rheumatic Diseases: An Overview. Front Immunol 2021; 12:637829. [PMID: 33692806 PMCID: PMC7937623 DOI: 10.3389/fimmu.2021.637829] [Citation(s) in RCA: 149] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/25/2021] [Indexed: 12/14/2022] Open
Abstract
Interleukin-23 (IL-23) is a pro-inflammatory cytokine composed of two subunits, IL-23A (p19) and IL-12/23B (p40), the latter shared with Interleukin-12 (IL-12). IL-23 is mainly produced by macrophages and dendritic cells, in response to exogenous or endogenous signals, and drives the differentiation and activation of T helper 17 (Th17) cells with subsequent production of IL-17A, IL-17F, IL-6, IL-22, and tumor necrosis factor α (TNF-α). Although IL-23 plays a pivotal role in the protective immune response to bacterial and fungal infections, its dysregulation has been shown to exacerbate chronic immune-mediated inflammation. Well-established experimental data support the concept that IL-23/IL-17 axis activation contributes to the development of several inflammatory diseases, such as PsA, Psoriasis, Psoriatic Arthritis; AS, Ankylosing Spondylitis; IBD, Inflammatory Bowel Disease; RA, Rheumatoid Arthritis; SS, Sjogren Syndrome; MS, Multiple Sclerosis. As a result, emerging clinical studies have focused on the blockade of this pathogenic axis as a promising therapeutic target in several autoimmune disorders; nevertheless, a greater understanding of its contribution still requires further investigation. This review aims to elucidate the most recent studies and literature data on the pathogenetic role of IL-23 and Th17 cells in inflammatory rheumatic diseases.
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Affiliation(s)
- Claudia Schinocca
- Rheumatology Section, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University Hospital “P. Giaccone”, Palermo, Italy
| | - Chiara Rizzo
- Rheumatology Section, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University Hospital “P. Giaccone”, Palermo, Italy
| | - Serena Fasano
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Giulia Grasso
- Rheumatology Section, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University Hospital “P. Giaccone”, Palermo, Italy
| | - Lidia La Barbera
- Rheumatology Section, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University Hospital “P. Giaccone”, Palermo, Italy
| | - Francesco Ciccia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Giuliana Guggino
- Rheumatology Section, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University Hospital “P. Giaccone”, Palermo, Italy
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Fruci D, Locatelli F, Cifaldi L. ERAAP modulation: A possible novel strategy for cancer immunotherapy? Oncoimmunology 2021; 1:81-82. [PMID: 22720218 DOI: 10.4161/onci.1.1.17828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recent findings demonstrate that loss of ERAAP, an endoplasmic reticulum aminopeptidase involved in antigen processing, plays a key role in stimulating anti-tumor innate and adaptive immune responses. We show that MHC class I molecules produced in the absence of ERAAP retain their capability of presenting antigens to CD8+ T cells, but not of inhibiting NK cells.
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Affiliation(s)
- Doriana Fruci
- Oncohaematology Department; IRCCS, Ospedale Pediatrico "Bambino Gesù"; Rome, Italy
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47
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Nakamura A, Boroojeni SF, Haroon N. Aberrant antigen processing and presentation: Key pathogenic factors leading to immune activation in Ankylosing spondylitis. Semin Immunopathol 2021; 43:245-253. [PMID: 33532928 DOI: 10.1007/s00281-020-00833-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Abstract
The strong association of HLA-B*27 with ankylosing spondylitis (AS) was first reported nearly 50 years ago. However, the mechanistic link between HLA-B*27 and AS has remained an enigma. While 85-90% of AS patients possess HLA-B*27, majority of HLA-B*27 healthy individuals do not develop AS. This suggests that additional genes and genetic regions interplay with HLA-B*27 to cause AS. Previous genome-wide association studies (GWAS) identified key genes that are distinctively expressed in AS, including the Endoplasmic Reticulum Aminopeptidase (ERAP) 1 and ERAP2. As these gene-encoding molecules are primarily implicated in the process of peptide processing and presentation, potential pathological interaction of these molecules with HLA-B*27 may operate to cause AS by activating downstream immune responses. The aberrant peptide processing also gives rise to the accumulation of unstable protein complex in endoplasmic reticulum (ER), which drives endoplasmic reticulum-associated protein degradation (ERAD) and unfolded protein response (UPR) and activates autophagy. In this review, we describe the current hypotheses of AS pathogenesis, focusing on antigen processing and presentation operated by HLA-B*27 and associated molecules that may contribute to the disease initiation and progression of AS.
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Affiliation(s)
- Akihiro Nakamura
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada.,Spondylitis Program, University Health Network, Toronto, Ontario, Canada.,Division of Genetics and Development, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada.,Division of Rheumatology, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada.,Institute of Medical Science, Department of Medicine, University of Toronto, 399 Bathurst Street, Toronto, Ontario, M5T 2S8, Canada
| | - Shaghayegh Foroozan Boroojeni
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada.,Spondylitis Program, University Health Network, Toronto, Ontario, Canada.,Division of Genetics and Development, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada.,Institute of Medical Science, Department of Medicine, University of Toronto, 399 Bathurst Street, Toronto, Ontario, M5T 2S8, Canada
| | - Nigil Haroon
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada. .,Spondylitis Program, University Health Network, Toronto, Ontario, Canada. .,Division of Genetics and Development, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada. .,Division of Rheumatology, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada. .,Institute of Medical Science, Department of Medicine, University of Toronto, 399 Bathurst Street, Toronto, Ontario, M5T 2S8, Canada.
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48
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Jiang P, Veenstra RN, Seitz A, Nolte IM, Hepkema BG, Visser L, van den Berg A, Diepstra A. Interaction between ERAP Alleles and HLA Class I Types Support a Role of Antigen Presentation in Hodgkin Lymphoma Development. Cancers (Basel) 2021; 13:cancers13030414. [PMID: 33499248 PMCID: PMC7865538 DOI: 10.3390/cancers13030414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Hodgkin lymphoma (HL) is a common lymphoma in young adults derived from B cells. Emerging evidence suggests that antigen presentation by the malignant B cells is critically involved in HL pathogenesis. In fact, genetic variants of the antigen presenting Human Leukocyte Antigens (HLA) are strongly associated with HL susceptibility. Interestingly, the endoplasmic reticulum aminopeptidase (ERAP)1 and ERAP2 genes, that code for enzymes that process antigens, also appear to be associated. In this study, we show that genetic variants of ERAP genes strongly affect expression levels of ERAP1 and ERAP2. In addition, we find that certain ERAP variants interact with specific HLA class I types in HL patients. This suggests that mechanisms that determine the repertoire of antigens that are presented to the immune system, affect the chance of developing HL. Our findings therefore support a prominent role of antigen presentation in HL susceptibility. Abstract Genetic variants in the HLA region are the strongest risk factors for developing Hodgkin lymphoma (HL), suggesting an important role for antigen presentation. This is supported by another HL-associated genomic region which contains the loci of two enzymes that process endogenous proteins to peptides to be presented by HLA class I, i.e., endoplasmic reticulum aminopeptidase 1 (ERAP1) and ERAP2. We hypothesized that ERAP and HLA class I type interact in HL susceptibility, as shown previously for several autoimmune diseases. We detected ERAP1 and ERAP2 expression in tumor cells and cells in the microenvironment in primary HL tissue samples. Seven ERAP SNPs and ERAP1 haplotypes showed strong associations with RNA and protein levels of ERAP1 and ERAP2 in LCLs and HL cell lines. Analysis of HLA class I types, ERAP SNPs and ERAP haplotypes by direct genotyping or imputation from genome-wide association data in 390 HL patients revealed significant interactions between HLA-A11, rs27038 and the rs27038 associated ERAP haplotype, as well as between HLA-Cw2 and rs26618. In conclusion, our results show that ERAP and HLA class I interact in genetic susceptibility to HL, providing further evidence that antigen presentation is an important process in HL susceptibility and pathogenesis.
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Affiliation(s)
- Peijia Jiang
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands; (P.J.); (R.N.V.); (A.S.); (L.V.); (A.v.d.B.)
- Department of Laboratory Medicine, Shenyang Huanggu National Defense Hospital, Shenyang 110032, China
| | - Rianne N. Veenstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands; (P.J.); (R.N.V.); (A.S.); (L.V.); (A.v.d.B.)
| | - Annika Seitz
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands; (P.J.); (R.N.V.); (A.S.); (L.V.); (A.v.d.B.)
| | - Ilja M. Nolte
- Department of Epidemiology, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands;
| | - Bouke G. Hepkema
- Department of Laboratory Medicine, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands;
| | - Lydia Visser
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands; (P.J.); (R.N.V.); (A.S.); (L.V.); (A.v.d.B.)
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands; (P.J.); (R.N.V.); (A.S.); (L.V.); (A.v.d.B.)
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands; (P.J.); (R.N.V.); (A.S.); (L.V.); (A.v.d.B.)
- Correspondence:
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Sharip A, Kunz J. Understanding the Pathogenesis of Spondyloarthritis. Biomolecules 2020; 10:biom10101461. [PMID: 33092023 PMCID: PMC7588965 DOI: 10.3390/biom10101461] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
Spondyloarthritis comprises a group of inflammatory diseases of the joints and spine, with various clinical manifestations. The group includes ankylosing spondylitis, reactive arthritis, psoriatic arthritis, arthritis associated with inflammatory bowel disease, and undifferentiated spondyloarthritis. The exact etiology and pathogenesis of spondyloarthritis are still unknown, but five hypotheses explaining the pathogenesis exist. These hypotheses suggest that spondyloarthritis is caused by arthritogenic peptides, an unfolded protein response, HLA-B*27 homodimer formation, malfunctioning endoplasmic reticulum aminopeptidases, and, last but not least, gut inflammation and dysbiosis. Here we discuss the five hypotheses and the evidence supporting each. In all of these hypotheses, HLA-B*27 plays a central role. It is likely that a combination of these hypotheses, with HLA-B*27 taking center stage, will eventually explain the development of spondyloarthritis in predisposed individuals.
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MESH Headings
- Arthritis, Psoriatic/genetics
- Arthritis, Psoriatic/immunology
- Arthritis, Psoriatic/metabolism
- Arthritis, Psoriatic/pathology
- Arthritis, Reactive/genetics
- Arthritis, Reactive/immunology
- Arthritis, Reactive/metabolism
- Arthritis, Reactive/pathology
- HLA-B27 Antigen/genetics
- HLA-B27 Antigen/immunology
- Humans
- Inflammation/genetics
- Inflammation/immunology
- Inflammation/metabolism
- Inflammation/pathology
- Inflammatory Bowel Diseases/genetics
- Inflammatory Bowel Diseases/immunology
- Inflammatory Bowel Diseases/metabolism
- Inflammatory Bowel Diseases/pathology
- Joints/immunology
- Joints/pathology
- Spine/immunology
- Spine/pathology
- Spondylarthritis/genetics
- Spondylarthritis/immunology
- Spondylarthritis/metabolism
- Spondylarthritis/pathology
- Spondylitis, Ankylosing/genetics
- Spondylitis, Ankylosing/immunology
- Spondylitis, Ankylosing/metabolism
- Spondylitis, Ankylosing/pathology
- Unfolded Protein Response/genetics
- Unfolded Protein Response/immunology
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Perazzio SF, Allenspach EJ, Eklund KK, Varjosalo M, Shinohara MM, Torgerson TR, Seppänen MRJ. Behçet disease (BD) and BD-like clinical phenotypes: NF-κB pathway in mucosal ulcerating diseases. Scand J Immunol 2020; 92:e12973. [PMID: 32889730 DOI: 10.1111/sji.12973] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/08/2020] [Accepted: 08/30/2020] [Indexed: 02/06/2023]
Abstract
Behçet's disease (BD) is a heterogeneous multi-organ disorder in search of a unified pathophysiological theory and classification. The disease frequently has overlapping features resembling other disease clusters, such as vasculitides, spondyloarthritides and thrombophilias with similar genetic risk variants, namely HLA-B*51, ERAP1, IL-10, IL-23R. Many of the BD manifestations, such as unprovoked recurrent episodes of inflammation and increased expression of IL-1, IL-6 and TNFα, overlap with those of the hereditary monogenic autoinflammatory syndromes, positioning BD at the crossroads between autoimmune and autoinflammatory syndromes. BD-like disease associates with various inborn errors of immunity, including familial Mediterranean fever, conditions related to dysregulated NF-κB activation (eg TNFAIP3, NFKB1, OTULIN, RELA, IKBKG) and either constitutional trisomy 8 or acquired trisomy 8 in myelodysplastic syndromes. We review here the recent advances in the immunopathology of BD, BD-like diseases and the NF-κB pathway suggesting new elements in the elusive BD etiopathogenesis.
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Affiliation(s)
- Sandro F Perazzio
- Seattle Children's Research Institute, University of Washington and Center for Immunity and Immunotherapies, Seattle, WA, USA.,Division of Rheumatology, Federal University of Sao Paulo, Sao Paulo, Brazil
| | - Eric J Allenspach
- Seattle Children's Research Institute, University of Washington and Center for Immunity and Immunotherapies, Seattle, WA, USA
| | - Kari K Eklund
- Division of Rheumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,ORTON Orthopaedic Hospital of the Orton Foundation, Helsinki, Finland
| | - Markku Varjosalo
- Division of Rheumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,ORTON Orthopaedic Hospital of the Orton Foundation, Helsinki, Finland.,Molecular Systems Biology Research Group and Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Michi M Shinohara
- Divisions of Dermatology and Dermatopathology, University of Washington, Seattle, WA, USA
| | | | - Mikko R J Seppänen
- Rare Disease and Pediatric Research Centers, Hospital for Children and Adolescents and Adult Immunodeficiency Unit, Inflammation Center, University of Helsinki and HUS Helsinki University Hospital, Helsinki, Finland
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