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Țiburcă L, Zaha DC, Jurca MC, Severin E, Jurca A, Jurca AD. The Role of Aminopeptidase ERAP1 in Human Pathology-A Review. Curr Issues Mol Biol 2024; 46:1651-1667. [PMID: 38534723 DOI: 10.3390/cimb46030107] [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: 01/23/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/28/2024] Open
Abstract
Aminopeptidases are a group of enzymatic proteins crucial for protein digestion, catalyzing the cleavage of amino acids at the N-terminus of peptides. Among them are ERAP1 (coding for endoplasmic reticulum aminopeptidase 1), ERAP2 (coding for endoplasmic reticulum aminopeptidase 2), and LNPEP (coding for leucyl and cystinyl aminopeptidase). These genes encoding these enzymes are contiguous and located on the same chromosome (5q21); they share structural homology and functions and are associated with immune-mediated diseases. These aminopeptidases play a key role in immune pathology by cleaving peptides to optimal sizes for binding to the major histocompatibility complex (MHC) and contribute to cellular homeostasis. By their ability to remove the extracellular region of interleukin 2 and 6 receptors (IL2, IL6) and the tumor necrosis factor receptor (TNF), ERAP1 and ERAP2 are involved in regulating the innate immune response and, finally, in blood pressure control and angiogenesis. The combination of specific genetic variations in these genes has been linked to various conditions, including autoimmune and autoinflammatory diseases and cancer, as well as hematological and dermatological disorders. This literature review aims to primarily explore the impact of ERAP1 polymorphisms on its enzymatic activity and function. Through a systematic examination of the available literature, this review seeks to provide valuable insights into the role of ERAP1 in the pathogenesis of various diseases and its potential implications for targeted therapeutic interventions. Through an exploration of the complex interplay between ERAP1 and various disease states, this review contributes to the synthesis of current biomedical research findings and their implications for personalized medicine.
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Affiliation(s)
- Laura Țiburcă
- Faculty of Medicine and Pharmacy, University of Oradea, Universității Street 1, 410087 Oradea, Romania
| | - Dana Carmen Zaha
- Faculty of Medicine and Pharmacy, University of Oradea, Universității Street 1, 410087 Oradea, Romania
| | - Maria Claudia Jurca
- Faculty of Medicine and Pharmacy, University of Oradea, Universității Street 1, 410087 Oradea, Romania
- Regional Center of Medical Genetics Bihor, County Emergency Clinical Hospital, Bihor, 65-67, Gheorghe Doja Street, 410169 Oradea, Romania
| | - Emilia Severin
- Department of Genetics, Carol Davila University of Medicine and Pharmacy, Dionisie Lupu 37 Street, 020021 Bucharest, Romania
| | - Aurora Jurca
- Faculty of Medicine and Pharmacy, University of Oradea, Universității Street 1, 410087 Oradea, Romania
| | - Alexandru Daniel Jurca
- Faculty of Medicine and Pharmacy, University of Oradea, Universității Street 1, 410087 Oradea, Romania
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2
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Stern LJ, Clement C, Galluzzi L, Santambrogio L. Non-mutational neoantigens in disease. Nat Immunol 2024; 25:29-40. [PMID: 38168954 PMCID: PMC11075006 DOI: 10.1038/s41590-023-01664-1] [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: 08/04/2023] [Accepted: 09/29/2023] [Indexed: 01/05/2024]
Abstract
The ability of mammals to mount adaptive immune responses culminating with the establishment of immunological memory is predicated on the ability of the mature T cell repertoire to recognize antigenic peptides presented by syngeneic MHC class I and II molecules. Although it is widely believed that mature T cells are highly skewed towards the recognition of antigenic peptides originating from genetically diverse (for example, foreign or mutated) protein-coding regions, preclinical and clinical data rather demonstrate that novel antigenic determinants efficiently recognized by mature T cells can emerge from a variety of non-mutational mechanisms. In this Review, we describe various mechanisms that underlie the formation of bona fide non-mutational neoantigens, such as epitope mimicry, upregulation of cryptic epitopes, usage of non-canonical initiation codons, alternative RNA splicing, and defective ribosomal RNA processing, as well as both enzymatic and non-enzymatic post-translational protein modifications. Moreover, we discuss the implications of the immune recognition of non-mutational neoantigens for human disease.
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Affiliation(s)
- Lawrence J Stern
- Department of Pathology, UMass Chan Medical School, Worcester, MA, USA
- Immunology and Microbiology Program, UMass Chan Medical School, Worcester, MA, USA
| | - Cristina Clement
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, New York, NY, USA.
- Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA.
| | - Laura Santambrogio
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, New York, NY, USA.
- Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA.
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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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4
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Venema WJ, Hiddingh S, Janssen GMC, Ossewaarde-van Norel J, van Loon ND, de Boer JH, van Veelen PA, Kuiper JJW. Retina-arrestin specific CD8+ T cells are not implicated in HLA-A29-positive birdshot chorioretinitis. Clin Immunol 2023; 247:109219. [PMID: 36581221 DOI: 10.1016/j.clim.2022.109219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND HLA-A29-positive birdshot chorioretinitis (BCR) is an inflammatory eye disorder that is generally assumed to be caused by an autoimmune response to HLA-A29-presented peptides from retinal arrestin (SAG), yet the epitopes recognized by CD8+ T cells from patients remain to be identified. OBJECTIVES The identification of natural ligands of SAG presented by HLA-A29. To quantify CD8+ T cells reactive to antigenic SAG peptides presented by HLA-A29 in patients and controls. METHODS We performed mass-spectrometry based immunopeptidomics of HLA-A29 of antigen-presenting cell lines from patients engineered to express SAG. MHC-I Dextramer technology was utilised to determine expansion of antigen-specific CD8+ T cells reactive to SAG peptides in complex with HLA-A29 in a cohort of BCR patients, HLA-A29-positive controls, and HLA-A29-negative controls. RESULTS We report on the naturally presented antigenic SAG peptides identified by sequencing the HLA-A29 immunopeptidome of antigen-presenting cells of patients. We show that the N-terminally extended SAG peptide precursors can be trimmed in vitro by the antigen-processing aminopeptidases ERAP1 and ERAP2. Unexpectedly, no enhanced antigen engagement by CD8+ T cells upon stimulation with SAG peptides was observed in patients or HLA-A29-positive controls. Multiplexed HLA-A29-peptide dextramer profiling of a case-control cohort revealed that CD8+ T cells specific for these SAG peptides were neither detectable in peripheral blood nor in eye biopsies of patients. CONCLUSIONS Collectively, these findings demonstrate that SAG is not a CD8+ T cell autoantigen and sharply contrast the paradigm in the pathogenesis of BCR. Therefore, the mechanism by which HLA-A29 is associated with BCR does not involve SAG.
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Affiliation(s)
- W J Venema
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - S Hiddingh
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - G M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - J Ossewaarde-van Norel
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - N Dam van Loon
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - J H de Boer
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - P A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - J J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands.
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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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Kessler BM. Nilabh Shastri - Towards understanding classical and non-classical MHC-I antigen processing and presentation. Cell Immunol 2022; 382:104638. [PMID: 36371991 DOI: 10.1016/j.cellimm.2022.104638] [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: 08/20/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
Major histocompatibility complex (MHC-I) peptide antigen processing and presentation has experienced a revived interest in the context of immuno oncology, immune surveillance escape by pathogen mutations and technical advances that accelerate vaccine design. This sheds new light on the discoveries made by Nilabh Shastri and colleagues that includes the characterisation of cryptic MHC-I peptide antigen epitopes derived from untranslated regions and the N-terminal trimming of peptide antigen precursors by the aminopeptidase ERAAP (ERAP1/2 / ARTS1/LRAP) in the endoplasmic reticulum (ER) prior to the complete assembly of MHC-I complexes and their subsequent exposure to the cell surface. These scientific findings have important implications for developing novel therapeutic approaches in immunotherapy and modern vaccine design.
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Affiliation(s)
- Benedikt M Kessler
- Chinese Academy of Medical Science Oxford Institute, Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK.
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Arya R, Maben Z, Rane D, Ali A, Stern LJ. Phenylsulfamoyl Benzoic Acid Inhibitor of ERAP2 with a Novel Mode of Inhibition. ACS Chem Biol 2022; 17:1756-1768. [PMID: 35767698 DOI: 10.1021/acschembio.2c00093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ERAP1 and ERAP2 are endoplasmic reticulum zinc-binding aminopeptidases that play crucial roles in processing peptides for loading onto class I major histocompatibility complex proteins. These enzymes are therapeutic targets in cancer and autoimmune disorders. The discovery of inhibitors specific to ERAP1 or ERAP2 has been challenging due to the similarity in their active site residues and domain architectures. Here, we identify 4-methoxy-3-{[2-piperidin-1-yl-4-(trifluoromethyl) phenyl] sulfamoyl} benzoic acid (compound 61) as a novel inhibitor of ERAP2 and determine the crystal structure of ERAP2 bound to compound 61. Compound 61 binds near the catalytic center of ERAP2, at a distinct site from previously known peptidomimetic inhibitors, and inhibits by an uncompetitive mechanism. Surprisingly, for ERAP1, compound 61 was found to activate model substrate hydrolysis, similarly to the previously characterized 5-trifluoromethyl regioisomer of compound 61, known as compound 3. We characterized the specificity determinants of ERAP1 and ERAP2 that control the binding of compounds 3 and 61. At the active site of ERAP1, Lys380 in the S1' pocket is a key determinant for the binding of both compounds 3 and 61. At the allosteric site, ERAP1 binds either compound, leading to the activation of model substrate hydrolysis. Although ERAP2 substrate hydrolysis is not activated by either compound, the mutation of His904 to alanine reveals a cryptic allosteric site that allows for the activation by compound 3. Thus, we have identified selectivity determinants in the active and allosteric sites of ERAP2 that govern the binding of two similar compounds, which potentially could be exploited to develop more potent and specific inhibitors.
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Affiliation(s)
- Richa Arya
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, United States
| | - Zachary Maben
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, United States
| | - Digamber Rane
- Kansas University Specialized Chemistry Center, Lawrence, Kansas 66047, United States
| | - Akbar Ali
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, United States
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, United States.,Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, United States
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Huang XF, Brown MA. Progress in the genetics of uveitis. Genes Immun 2022; 23:57-65. [PMID: 35379982 PMCID: PMC9042703 DOI: 10.1038/s41435-022-00168-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
Abstract
Uveitis is the most common form of intraocular inflammatory disease and is a significant cause of visual impairment worldwide. Aetiologically, uveitis can also be classified into infectious uveitis and non-infectious uveitis. The common non-infectious forms of uveitis include acute anterior uveitis (AAU), Behçet’s disease (BD), Vogt-Koyanagi-Harada (VKH) disease, birdshot chorioretinopathy (BSCR), sarcoid uveitis. In addition, a few monogenic autoinflammatory disorders can also cause uveitis, such as Blau Syndrome and haploinsufficiency of A20 (HA20). Although the exact pathogenesis of non-infectious uveitis is still unclear, it is well-recognised that it involves both genetic and environmental risk factors. A hallmark of uveitis is its strong associations with human leucocyte antigens (HLA). For examples, AAU, BD and BSCR are strongly associated with HLA-B27, HLA-B51, and HLA-A29, respectively. In uveitis studies, multiple GWAS have successfully been conducted and led to identification of novel susceptibility loci, for example, IL23R has been identified in BD, VKH and AAU. In this review, we summarize the latest progress on the genetic associations of both HLA and non-HLA genes with major forms of uveitis, including AAU, BD, VKH, BSCR, sarcoid uveitis, Blau Syndrome and HA20, and potential future research directions.
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Affiliation(s)
- Xiu-Feng Huang
- The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.,Queensland University of Technology, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Translational Research Institute, Woolloongabba, Qld, Australia
| | - Matthew A Brown
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, England. .,Genomics England, London, UK.
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Temponeras I, Stamatakis G, Samiotaki M, Georgiadis D, Pratsinis H, Panayotou G, Stratikos E. ERAP2 Inhibition Induces Cell-Surface Presentation by MOLT-4 Leukemia Cancer Cells of Many Novel and Potentially Antigenic Peptides. Int J Mol Sci 2022; 23:ijms23031913. [PMID: 35163832 PMCID: PMC8836666 DOI: 10.3390/ijms23031913] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/05/2022] [Accepted: 02/06/2022] [Indexed: 02/01/2023] Open
Abstract
Recent studies have linked the activity of ER aminopeptidase 2 (ERAP2) to increased efficacy of immune-checkpoint inhibitor cancer immunotherapy, suggesting that pharmacological inhibition of ERAP2 could have important therapeutic implications. To explore the effects of ERAP2 inhibition on the immunopeptidome of cancer cells, we treated MOLT-4 T lymphoblast leukemia cells with a recently developed selective ERAP2 inhibitor, isolated Major Histocompatibility class I molecules (MHCI), and sequenced bound peptides by liquid chromatography tandem mass spectrometry. Inhibitor treatment induced significant shifts on the immunopeptidome so that more than 20% of detected peptides were either novel or significantly upregulated. Most of the inhibitor-induced peptides were 9mers and had sequence motifs and predicted affinity consistent with being optimal ligands for at least one of the MHCI alleles carried by MOLT-4 cells. Such inhibitor-induced peptides could serve as triggers for novel cytotoxic responses against cancer cells and synergize with the therapeutic effect of immune-checkpoint inhibitors.
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Affiliation(s)
- Ioannis Temponeras
- National Centre for Scientific Research “Demokritos”, 15341 Agia Paraskevi, Greece; (I.T.); (H.P.)
- Department of Pharmacy, University of Patras, 26504 Patra, Greece
| | - George Stamatakis
- Biomedical Sciences Research Center “Alexander Fleming”, Institute for Bioinnovation, 16672 Vari, Greece; (G.S.); (M.S.); (G.P.)
| | - Martina Samiotaki
- Biomedical Sciences Research Center “Alexander Fleming”, Institute for Bioinnovation, 16672 Vari, Greece; (G.S.); (M.S.); (G.P.)
| | - Dimitris Georgiadis
- Department of Chemistry, National and Kapodistrian University of Athens, 15784 Zografou, Greece;
| | - Harris Pratsinis
- National Centre for Scientific Research “Demokritos”, 15341 Agia Paraskevi, Greece; (I.T.); (H.P.)
| | - George Panayotou
- Biomedical Sciences Research Center “Alexander Fleming”, Institute for Bioinnovation, 16672 Vari, Greece; (G.S.); (M.S.); (G.P.)
| | - Efstratios Stratikos
- National Centre for Scientific Research “Demokritos”, 15341 Agia Paraskevi, Greece; (I.T.); (H.P.)
- Department of Chemistry, National and Kapodistrian University of Athens, 15784 Zografou, Greece;
- Correspondence: or
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Kubiniok P, Marcu A, Bichmann L, Kuchenbecker L, Schuster H, Hamelin DJ, Duquette JD, Kovalchik KA, Wessling L, Kohlbacher O, Rammensee HG, Neidert MC, Sirois I, Caron E. Understanding the constitutive presentation of MHC class I immunopeptidomes in primary tissues. iScience 2022; 25:103768. [PMID: 35141507 PMCID: PMC8810409 DOI: 10.1016/j.isci.2022.103768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/15/2021] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
Understanding the molecular principles that govern the composition of the MHC-I immunopeptidome across different primary tissues is fundamentally important to predict how T cells respond in different contexts in vivo. Here, we performed a global analysis of the MHC-I immunopeptidome from 29 to 19 primary human and mouse tissues, respectively. First, we observed that different HLA-A, HLA-B, and HLA-C allotypes do not contribute evenly to the global composition of the MHC-I immunopeptidome across multiple human tissues. Second, we found that tissue-specific and housekeeping MHC-I peptides share very distinct properties. Third, we discovered that proteins that are evolutionarily hyperconserved represent the primary source of the MHC-I immunopeptidome at the organism-wide scale. Fourth, we uncovered new components of the antigen processing and presentation network, including the carboxypeptidases CPE, CNDP1/2, and CPVL. Together, this study opens up new avenues toward a system-wide understanding of antigen presentation in vivo across mammalian species. Tissue-specific and housekeeping MHC class I peptides share distinct properties HLA-A, HLA-B, and HLA-C allotypes contribute very unevenly to the pool of class I peptides MHC-I immunopeptidomes are represented by evolutionarily conserved proteins An extended antigen processing and presentation pathway is uncovered
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Affiliation(s)
- Peter Kubiniok
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Ana Marcu
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- Cluster of Excellence iFIT (EXC 2180), “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
| | - Leon Bichmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72074 Tübingen, Baden-Württemberg, Germany
| | - Leon Kuchenbecker
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72074 Tübingen, Baden-Württemberg, Germany
| | - Heiko Schuster
- Immatics Biotechnologies GmbH, 72076 Tübingen, Baden-Württemberg, Germany
| | - David J. Hamelin
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | | | | | - Laura Wessling
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72074 Tübingen, Baden-Württemberg, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, 72076 Tübingen, Baden-Württemberg, Germany
- Cluster of Excellence Machine Learning in the Sciences (EXC 2064), University of Tübingen, 72074 Tübingen, Baden-Württemberg, Germany
- Translational Bioinformatics, University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- Cluster of Excellence iFIT (EXC 2180), “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), 72076 Tübingen, Baden-Württemberg, Germany
| | - Marian C. Neidert
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zürich, 8057&8091 Zürich, Switzerland
| | - Isabelle Sirois
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
- Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, QC H3T 1J4, Canada
- Corresponding author
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Gelfman S, Monnet D, Ligocki AJ, Tabary T, Moscati A, Bai X, Freudenberg J, Cooper B, Kosmicki JA, Wolf S, Ferreira MAR, Overton J, Weyne J, Stahl EA, Baras A, Romano C, Cohen JHM, Coppola G, Brézin A. ERAP1, ERAP2, and Two Copies of HLA-Aw19 Alleles Increase the Risk for Birdshot Chorioretinopathy in HLA-A29 Carriers. Invest Ophthalmol Vis Sci 2021; 62:3. [PMID: 34727153 PMCID: PMC8572510 DOI: 10.1167/iovs.62.14.3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Purpose Birdshot chorioretinopathy (BSCR) is strongly associated with HLA-A29. This study was designed to elucidate the genetic modifiers of BSCR in HLA-A29 carriers. Methods We sequenced the largest BSCR cohort to date, including 286 cases and 108 HLA-A29–positive controls to determine genome-wide common and rare variant associations. We further typed the HLA alleles of cases and 45,386 HLA-A29 controls of European ancestry to identify HLA alleles that associate with BSCR risk. Results Carrying a second allele that belongs to the HLA-Aw19 broad antigen family (including HLA-A29, -A30, -A31, and -A33) increases the risk for BSCR (odds ratio [OR] = 4.44; P = 2.2e-03). This result was validated by comparing allele frequencies to large HLA-A29-controlled cohorts (n = 45,386; OR > 2.5; P < 1.3e-06). We also confirm that ERAP1 and ERAP2 haplotypes modulate disease risk. A meta-analysis with an independent dataset confirmed that ERAP1 and ERAP2 haplotypes modulate the risk for disease at a genome-wide significant level: ERAP1-rs27432 (OR = 2.46; 95% confidence interval [CI], 1.85–3.26; P = 4.07e-10), an expression quantitative trait locus (eQTL) decreasing ERAP1 expression; and ERAP2-rs10044354 (OR = 1.95; 95% CI, 1.55–2.44; P = 6.2e-09), an eQTL increasing ERAP2 expression. Furthermore, ERAP2-rs2248374 that disrupts ERAP2 expression is protective (OR = 0.56; 95% CI, 0.45–0.70; P = 2.39e-07). BSCR risk is additively increased when combining ERAP1/ERAP2 risk genotypes with two copies of HLA-Aw19 alleles (OR = 13.53; 95% CI, 3.79–54.77; P = 1.17e-05). Conclusions The genetic factors increasing BSCR risk demonstrate a pattern of increased processing, as well as increased presentation of ERAP2-specific peptides. This suggests a mechanism in which exceeding a peptide presentation threshold activates the immune response in choroids of A29 carriers.
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Affiliation(s)
- Sahar Gelfman
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Dominique Monnet
- Université de Paris, Hôpital Cochin, service d'ophtalmologie, Paris, France
| | - Ann J Ligocki
- Regeneron Pharmaceuticals, Tarrytown, New York, United States
| | | | - Arden Moscati
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Xiaodong Bai
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Jan Freudenberg
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Blerta Cooper
- Regeneron Pharmaceuticals, Tarrytown, New York, United States
| | - Jack A Kosmicki
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Sarah Wolf
- Regeneron Genetics Center, Tarrytown, New York, United States
| | | | - John Overton
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Jonathan Weyne
- Regeneron Pharmaceuticals, Tarrytown, New York, United States
| | - Eli A Stahl
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Carmelo Romano
- Regeneron Pharmaceuticals, Tarrytown, New York, United States
| | | | | | - Antoine Brézin
- Université de Paris, Hôpital Cochin, service d'ophtalmologie, Paris, France
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12
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Venema WJ, Hiddingh S, de Boer JH, Claas FHJ, Mulder A, den Hollander AI, Stratikos E, Sarkizova S, van der Veken LT, Janssen GMC, van Veelen PA, Kuiper JJW. ERAP2 Increases the Abundance of a Peptide Submotif Highly Selective for the Birdshot Uveitis-Associated HLA-A29. Front Immunol 2021; 12:634441. [PMID: 33717175 PMCID: PMC7950316 DOI: 10.3389/fimmu.2021.634441] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/12/2021] [Indexed: 11/13/2022] Open
Abstract
Birdshot Uveitis (BU) is a blinding inflammatory eye condition that only affects HLA-A29-positive individuals. Genetic association studies linked ERAP2 with BU, an aminopeptidase which trims peptides before their presentation by HLA class I at the cell surface, which suggests that ERAP2-dependent peptide presentation by HLA-A29 drives the pathogenesis of BU. However, it remains poorly understood whether the effects of ERAP2 on the HLA-A29 peptidome are distinct from its effect on other HLA allotypes. To address this, we focused on the effects of ERAP2 on the immunopeptidome in patient-derived antigen presenting cells. Using complementary HLA-A29-based and pan-class I immunopurifications, isotope-labeled naturally processed and presented HLA-bound peptides were sequenced by mass spectrometry. We show that the effects of ERAP2 on the N-terminus of ligands of HLA-A29 are shared across endogenous HLA allotypes, but discover and replicate that one peptide motif generated in the presence of ERAP2 is specifically bound by HLA-A29. This motif can be found in the amino acid sequence of putative autoantigens. We further show evidence for internal sequence specificity for ERAP2 imprinted in the immunopeptidome. These results reveal that ERAP2 can generate an HLA-A29-specific antigen repertoire, which supports that antigen presentation is a key disease pathway in BU.
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Affiliation(s)
- Wouter J Venema
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Sanne Hiddingh
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Joke H de Boer
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Frans H J Claas
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Arend Mulder
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Efstratios Stratikos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Greece
| | - Siranush Sarkizova
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Lars T van der Veken
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
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13
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Tedeschi V, Paldino G, Paladini F, Mattorre B, Tuosto L, Sorrentino R, Fiorillo MT. The Impact of the 'Mis-Peptidome' on HLA Class I-Mediated Diseases: Contribution of ERAP1 and ERAP2 and Effects on the Immune Response. Int J Mol Sci 2020; 21:ijms21249608. [PMID: 33348540 PMCID: PMC7765998 DOI: 10.3390/ijms21249608] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/09/2020] [Accepted: 12/14/2020] [Indexed: 01/08/2023] Open
Abstract
The strong association with the Major Histocompatibility Complex (MHC) class I genes represents a shared trait for a group of autoimmune/autoinflammatory disorders having in common immunopathogenetic basis as well as clinical features. Accordingly, the main risk factors for Ankylosing Spondylitis (AS), prototype of the Spondyloarthropathies (SpA), the Behçet's disease (BD), the Psoriasis (Ps) and the Birdshot Chorioretinopathy (BSCR) are HLA-B*27, HLA-B*51, HLA-C*06:02 and HLA-A*29:02, respectively. Despite the strength of the association, the HLA pathogenetic role in these diseases is far from being thoroughly understood. Furthermore, Genome-Wide Association Studies (GWAS) have highlighted other important susceptibility factors such as Endoplasmic Reticulum Aminopeptidase (ERAP) 1 and, less frequently, ERAP2 that refine the peptidome presented by HLA class I molecules to CD8+ T cells. Mass spectrometry analysis provided considerable knowledge of HLA-B*27, HLA-B*51, HLA-C*06:02 and HLA-A*29:02 immunopeptidome. However, the combined effect of several ERAP1 and ERAP2 allelic variants could generate an altered pool of peptides accounting for the "mis-immunopeptidome" that ranges from suboptimal to pathogenetic/harmful peptides able to induce non-canonical or autoreactive CD8+ T responses, activation of NK cells and/or garbling the classical functions of the HLA class I molecules. This review will focus on this class of epitopes as possible elicitors of atypical/harmful immune responses which can contribute to the pathogenesis of chronic inflammatory diseases.
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Affiliation(s)
- Valentina Tedeschi
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University, 00185 Rome, Italy; (G.P.); (F.P.); (B.M.); (L.T.); (R.S.); (M.T.F.)
- Correspondence:
| | - Giorgia Paldino
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University, 00185 Rome, Italy; (G.P.); (F.P.); (B.M.); (L.T.); (R.S.); (M.T.F.)
| | - Fabiana Paladini
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University, 00185 Rome, Italy; (G.P.); (F.P.); (B.M.); (L.T.); (R.S.); (M.T.F.)
| | - Benedetta Mattorre
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University, 00185 Rome, Italy; (G.P.); (F.P.); (B.M.); (L.T.); (R.S.); (M.T.F.)
| | - Loretta Tuosto
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University, 00185 Rome, Italy; (G.P.); (F.P.); (B.M.); (L.T.); (R.S.); (M.T.F.)
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University, 00185 Rome, Italy
| | - Rosa Sorrentino
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University, 00185 Rome, Italy; (G.P.); (F.P.); (B.M.); (L.T.); (R.S.); (M.T.F.)
| | - Maria Teresa Fiorillo
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University, 00185 Rome, Italy; (G.P.); (F.P.); (B.M.); (L.T.); (R.S.); (M.T.F.)
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14
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Kuiper JJW, Venema WJ. HLA-A29 and Birdshot Uveitis: Further Down the Rabbit Hole. Front Immunol 2020; 11:599558. [PMID: 33262772 PMCID: PMC7687429 DOI: 10.3389/fimmu.2020.599558] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/16/2020] [Indexed: 12/26/2022] Open
Abstract
HLA class I alleles constitute established risk factors for non-infectious uveitis and preemptive genotyping of HLA class I alleles is standard practice in the diagnostic work-up. The HLA-A29 serotype is indispensable to Birdshot Uveitis (BU) and renders this enigmatic eye condition a unique model to better understand how the antigen processing and presentation machinery contributes to non-infectious uveitis or chronic inflammatory conditions in general. This review will discuss salient points regarding the protein structure of HLA-A29 and how key amino acid positions impact the peptide binding preference and interaction with T cells. We discuss to what extent the risk genes ERAP1 and ERAP2 uniquely affect HLA-A29 and how the discovery of a HLA-A29-specific submotif may impact autoantigen discovery. We further provide a compelling argument to solve the long-standing question why BU only affects HLA-A29-positive individuals from Western-European ancestry by exploiting data from the 1000 Genomes Project. We combine novel insights from structural and immunopeptidomic studies and discuss the functional implications of genetic associations across the HLA class I antigen presentation pathway to refine the etiological basis of Birdshot Uveitis.
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Affiliation(s)
- Jonas J. W. Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Wouter J. Venema
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
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15
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Paladini F, Fiorillo MT, Tedeschi V, Mattorre B, Sorrentino R. The Multifaceted Nature of Aminopeptidases ERAP1, ERAP2, and LNPEP: From Evolution to Disease. Front Immunol 2020; 11:1576. [PMID: 32793222 PMCID: PMC7390905 DOI: 10.3389/fimmu.2020.01576] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/15/2020] [Indexed: 12/11/2022] Open
Abstract
In the human genome, the aminopeptidases ERAP1, ERAP2 and LNPEP lie contiguously on chromosome 5. They share sequence homology, functions and associations with immune-mediated diseases. By analyzing their multifaceted activities as well as their expression in the zoological scale, we suggest here that the progenitor of the three aminopeptidases might be LNPEP from which the other two aminopeptidases could have derived by gene duplications. We also propose that their functions are partially redundant. More precisely, the evolutionary story of the three aminopeptidases might have been dictated by their role in regulating the renin–angiotensin system, which requires their controlled and coordinated expression. This hypothesis is supported by the many species that lack one or the other gene as well as by the lack of ERAP2 in rodents and a null expression in 25% of humans. Finally, we speculate that their role in antigen presentation has been acquired later on during evolution. They have therefore been diversified between those residing in the ER, ERAP1 and ERAP2, whose role is to refine the MHC-I peptidomes, and LNPEP, mostly present in the endosomal vesicles where it can contribute to antigen cross-presentation or move to the cell membrane as receptor for angiotensin IV. Their association with autoinflammatory/autoimmune diseases can therefore be two-fold: as “contributors” to the shaping of the immune-peptidomes as well as to the regulation of the vascular response.
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Affiliation(s)
- Fabiana Paladini
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Maria Teresa Fiorillo
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Valentina Tedeschi
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Benedetta Mattorre
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Rosa Sorrentino
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
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16
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Mutis T, Xagara A, Spaapen RM. The Connection Between Minor H Antigens and Neoantigens and the Missing Link in Their Prediction. Front Immunol 2020; 11:1162. [PMID: 32670277 PMCID: PMC7326952 DOI: 10.3389/fimmu.2020.01162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/12/2020] [Indexed: 12/26/2022] Open
Abstract
For hundreds of thousands of years, the human genome has extensively evolved, resulting in genetic variations in almost every gene. Immunological reflections of these genetic variations become clearly visible after an allogeneic stem cell transplantation (allo-SCT) as minor Histocompatibility (H) antigens. Minor H antigens are peptides cleaved from genetically encoded variable protein regions after which they are presented at the cell surface by HLA molecules. After allo-SCT with minor H antigen mismatches between donor and recipient, donor T cells recognize the minor H antigens of the recipient as foreign, evoking strong alloreactive immune responses. Studies in the late eighties have discovered that a subset of minor H antigens are encoded by hematopoietic system-specific genes. After allo-SCT, this subset is strictly expressed on the hematopoietic malignant cells and was therefore the first well-defined highly immunogenic group of tumor-specific antigens. In the last decade, neoantigens derived from genetic mutations in tumors have been identified as another group of immunogenic tumor-specific antigens. Therefore, hematopoietic minor H antigens and neoantigens are therapeutic equivalents. This review will connect our current knowledge about the immune biology and identification of minor H antigens and neoantigens leading to novel conclusions on their prediction.
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Affiliation(s)
- Tuna Mutis
- Department of Hematology, Amsterdam UMC, VU Medical Center, Amsterdam, Netherlands
| | - Anastasia Xagara
- Department of Immunopathology, Sanquin Research, Amsterdam, Netherlands.,Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Robbert M Spaapen
- Department of Immunopathology, Sanquin Research, Amsterdam, Netherlands.,Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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17
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Lorente E, Fontela MG, Barnea E, Martín-Galiano AJ, Mir C, Galocha B, Admon A, Lauzurica P, López D. Modulation of Natural HLA-B*27:05 Ligandome by Ankylosing Spondylitis-associated Endoplasmic Reticulum Aminopeptidase 2 (ERAP2). Mol Cell Proteomics 2020; 19:994-1004. [PMID: 32265295 PMCID: PMC7261815 DOI: 10.1074/mcp.ra120.002014] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
The HLA-B*27:05 allele and the endoplasmic reticulum-resident aminopeptidases are strongly associated with AS, a chronic inflammatory spondyloarthropathy. This study examined the effect of ERAP2 in the generation of the natural HLA-B*27:05 ligandome in live cells. Complexes of HLA-B*27:05-bound peptide pools were isolated from human ERAP2-edited cell clones, and the peptides were identified using high-throughput mass spectrometry analyses. The relative abundance of a thousand ligands was established by quantitative tandem mass spectrometry and bioinformatics analysis. The residue frequencies at different peptide position, identified in the presence or absence of ERAP2, determined structural features of ligands and their interactions with specific pockets of the antigen-binding site of the HLA-B*27:05 molecule. Sequence alignment of ligands identified with species of bacteria associated with HLA-B*27-dependent reactive arthritis was performed. In the absence of ERAP2, peptides with N-terminal basic residues and minority canonical P2 residues are enriched in the natural ligandome. Further, alterations of residue frequencies and hydrophobicity profile at P3, P7, and PΩ positions were detected. In addition, several ERAP2-dependent cellular peptides were highly similar to protein sequences of arthritogenic bacteria, including one human HLA-B*27:05 ligand fully conserved in a protein from Campylobacter jejuni These findings highlight the pathogenic role of this aminopeptidase in the triggering of AS autoimmune disease.
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Affiliation(s)
- Elena Lorente
- Unidad de Presentación y Regulación Inmunes, 28220 Majadahonda (Madrid), Spain
| | - Miguel G Fontela
- Unidad de Presentación y Regulación Inmunes, 28220 Majadahonda (Madrid), Spain
| | - Eilon Barnea
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | | | - Carmen Mir
- Unidad de Presentación y Regulación Inmunes, 28220 Majadahonda (Madrid), Spain
| | - Begoña Galocha
- Unidad de Presentación y Regulación Inmunes, 28220 Majadahonda (Madrid), Spain
| | - Arie Admon
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Pilar Lauzurica
- Unidad de Presentación y Regulación Inmunes, 28220 Majadahonda (Madrid), Spain
| | - Daniel López
- Unidad de Presentación y Regulación Inmunes, 28220 Majadahonda (Madrid), Spain.
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18
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Mavridis G, Arya R, Domnick A, Zoidakis J, Makridakis M, Vlahou A, Mpakali A, Lelis A, Georgiadis D, Tampé R, Papakyriakou A, Stern LJ, Stratikos E. A systematic re-examination of processing of MHCI-bound antigenic peptide precursors by endoplasmic reticulum aminopeptidase 1. J Biol Chem 2020; 295:7193-7210. [PMID: 32184355 PMCID: PMC7247305 DOI: 10.1074/jbc.ra120.012976] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/09/2020] [Indexed: 11/06/2022] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) trims antigenic peptide precursors to generate mature antigenic peptides for presentation by major histocompatibility complex class I (MHCI) molecules and regulates adaptive immune responses. ERAP1 has been proposed to trim peptide precursors both in solution and in preformed MHCI-peptide complexes, but which mode is more relevant to its biological function remains controversial. Here, we compared ERAP1-mediated trimming of antigenic peptide precursors in solution or when bound to three MHCI alleles, HLA-B*58, HLA-B*08, and HLA-A*02. For all MHCI-peptide combinations, peptide binding onto MHCI protected against ERAP1-mediated trimming. In only a single MHCI-peptide combination, trimming of an HLA-B*08-bound 12-mer progressed at a considerable rate, albeit still slower than in solution. Results from thermodynamic, kinetic, and computational analyses suggested that this 12-mer is highly labile and that apparent on-MHC trimming rates are always slower than that of MHCI-peptide dissociation. Both ERAP2 and leucine aminopeptidase, an enzyme unrelated to antigen processing, could trim this labile peptide from preformed MHCI complexes as efficiently as ERAP1. A pseudopeptide analogue with high affinity for both HLA-B*08 and the ERAP1 active site could not promote the formation of a ternary ERAP1/MHCI/peptide complex. Similarly, no interactions between ERAP1 and purified peptide-loading complex were detected in the absence or presence of a pseudopeptide trap. We conclude that MHCI binding protects peptides from ERAP1 degradation and that trimming in solution along with the dynamic nature of peptide binding to MHCI are sufficient to explain ERAP1 processing of antigenic peptide precursors.
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Affiliation(s)
- George Mavridis
- National Centre for Scientific Research Demokritos, Agia Paraskevi 15341, Greece
| | - Richa Arya
- University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Alexander Domnick
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt/Main, Germany
| | - Jerome Zoidakis
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens 11527, Greece
| | - Manousos Makridakis
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens 11527, Greece
| | - Antonia Vlahou
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens 11527, Greece
| | - Anastasia Mpakali
- National Centre for Scientific Research Demokritos, Agia Paraskevi 15341, Greece
| | - Angelos Lelis
- Laboratory of Organic Chemistry, Chemistry Department, University of Athens, Athens 15772, Greece
| | - Dimitris Georgiadis
- Laboratory of Organic Chemistry, Chemistry Department, University of Athens, Athens 15772, Greece
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt/Main, Germany
| | | | - Lawrence J Stern
- University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Efstratios Stratikos
- National Centre for Scientific Research Demokritos, Agia Paraskevi 15341, Greece.
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19
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Pavlos R, Deshpande P, Chopra A, Leary S, Strautins K, Nolan D, Thorborn D, Shaefer M, Rauch A, Dunn D, Montaner J, Rachlis A, Almeida CA, Choo L, James I, Redwood AJ, Li Y, Gaudieri S, Mallal SA, Phillips EJ. New genetic predictors for abacavir tolerance in HLA-B*57:01 positive individuals. Hum Immunol 2020; 81:300-304. [PMID: 32173028 DOI: 10.1016/j.humimm.2020.02.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/17/2020] [Accepted: 02/21/2020] [Indexed: 01/11/2023]
Abstract
Abacavir hypersensitivity syndrome (ABC HSS) is strongly associated with carriage of human leukocyte antigen (HLA)-B*57:01, which has a 100% negative predictive value for the development of ABC HSS. However, 45% of individuals who carry HLA-B*57:01 can tolerate ABC. We investigated immune and non-immune related genes in ABC HSS (n = 95) and ABC tolerant (n = 43) HLA-B*57:01 + patients to determine other factors required for the development of ABC HSS. Assignment of phenotype showed that ABC HSS subjects were significantly less likely than tolerants to carry only ERAP1 hypoactive trimming allotypes (p = 0.02). An altered self-peptide repertoire model by which abacavir activates T cells is in keeping with observation that endoplasmic reticulum aminopeptidase 1 (ERAP1) allotypes that favour efficient peptide trimming are more common in ABC HSS patients compared to patients who tolerate ABC. Independently, non-specific immune activation via soluble cluster of differentiation antigen 14 (sCD14) may also influence susceptibility to ABC HSS.
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Affiliation(s)
- Rebecca Pavlos
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia; Telethon Kids Institute, Western Australia, Australia
| | - Pooja Deshpande
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia; School of Human Sciences, University of Western Australia, Western Australia, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Kaija Strautins
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - David Nolan
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia; Department of Clinical Immunology, Royal Perth Hospital, Western Australia, Australia
| | | | - Mark Shaefer
- ViiV Healthcare at Research Triangle Park, NC, USA
| | | | - David Dunn
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Julio Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver British Columbia, Canada
| | - Anita Rachlis
- Sunnybrook Health Sciences Centre, Toronto, Canada; University of Toronto,Toronto, Canada
| | - Coral-Ann Almeida
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia; Department of Haematology, Fiona Stanley Hospital, Western Australia, Australia
| | - Linda Choo
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Ian James
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Alec J Redwood
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia; Institute for Respiratory Health, University of Western Australia, Western Australia, Australia
| | - Yueran Li
- School of Human Sciences, University of Western Australia, Western Australia, Australia
| | - Silvana Gaudieri
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia; School of Human Sciences, University of Western Australia, Western Australia, Australia; Vanderbilt University Medical Centre, Nashville, USA
| | - Simon A Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia; Vanderbilt University Medical Centre, Nashville, USA
| | - Elizabeth J Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia; Vanderbilt University Medical Centre, Nashville, USA.
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Babaie F, Hosseinzadeh R, Ebrazeh M, Seyfizadeh N, Aslani S, Salimi S, Hemmatzadeh M, Azizi G, Jadidi-Niaragh F, Mohammadi H. The roles of ERAP1 and ERAP2 in autoimmunity and cancer immunity: New insights and perspective. Mol Immunol 2020; 121:7-19. [PMID: 32135401 DOI: 10.1016/j.molimm.2020.02.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 02/06/2023]
Abstract
Autoimmunity and cancer affect millions worldwide and both, in principal, result from dysregulated immune responses. There are many well-known molecules involved in immunological process playing as a double-edged sword, by which associating autoimmune diseases and cancer. In this regard, Endoplasmic reticulum aminopeptidases (ERAP) 1, which belongs to the M1 family of aminopeptidases, plays a central role as a "molecular ruler", proteolyzing of N-terminal of the antigenic peptides before their loading onto HLA-I molecules for antigen presentation in the Endoplasmic Reticulum (ER). Several genome-wide association studies (GWAS) highlighted the significance of ERAP1 and ERAP2 in autoimmune diseases, including Ankylosing spondylitis, Psoriasis, Bechet's disease, and Birdshot chorioretinopathy, as well as in cancers. The expression of ERAP1/2 is mostly altered in different cancers compared to normal cells, but how this affects anti-cancer immune responses and cancer growth has been little explored. Recent studies on the immunological outcomes and the catalytic functions of ERAP1 and ERAP2 have provided a better understanding of their potential pathogenetic role in autoimmunity and cancer. In this review, we summarize the role of ERAP1 and ERAP2 in the autoimmune diseases and cancer immunity based on the recent advances in GWAS studies.
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Affiliation(s)
- Farhad Babaie
- Department of Immunology and Genetic, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran; Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Ramin Hosseinzadeh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Ebrazeh
- Department of Biology, Bonab Branch, Islamic Azad University, Bonab, Iran
| | - Narges Seyfizadeh
- Department of Medical Oncology, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Saeed Aslani
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Soraya Salimi
- Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Maryam Hemmatzadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran; Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Gholamreza Azizi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Farhad Jadidi-Niaragh
- Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Mohammadi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran; Department of Immunology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.
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21
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Georgiadis D, Mpakali A, Koumantou D, Stratikos E. Inhibitors of ER Aminopeptidase 1 and 2: From Design to Clinical Application. Curr Med Chem 2019; 26:2715-2729. [PMID: 29446724 DOI: 10.2174/0929867325666180214111849] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/04/2018] [Accepted: 01/31/2018] [Indexed: 12/19/2022]
Abstract
Endoplasmic Reticulum aminopeptidase 1 and 2 are two homologous enzymes that help generate peptide ligands for presentation by Major Histocompatibility Class I molecules. Their enzymatic activity influences the antigenic peptide repertoire and indirectly controls adaptive immune responses. Accumulating evidence suggests that these two enzymes are tractable targets for the regulation of immune responses with possible applications ranging from cancer immunotherapy to treating inflammatory autoimmune diseases. Here, we review the state-of-the-art in the development of inhibitors of ERAP1 and ERAP2 as well as their potential and limitations for clinical applications.
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Affiliation(s)
- Dimitris Georgiadis
- Department of Chemistry, National and Kapodistrian University of Athens, Zografou, 15771, Athens, Greece
| | - Anastasia Mpakali
- National Center for Scientific Research Demokritos, Agia Paraskevi, 15341, Greece
| | - Despoina Koumantou
- National Center for Scientific Research Demokritos, Agia Paraskevi, 15341, Greece
| | - Efstratios Stratikos
- National Center for Scientific Research Demokritos, Agia Paraskevi, 15341, Greece
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22
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Hanson AL, Morton CJ, Parker MW, Bessette D, Kenna TJ. The genetics, structure and function of the M1 aminopeptidase oxytocinase subfamily and their therapeutic potential in immune-mediated disease. Hum Immunol 2019; 80:281-289. [DOI: 10.1016/j.humimm.2018.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/16/2018] [Accepted: 11/05/2018] [Indexed: 12/31/2022]
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23
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Yao Y, Liu N, Zhou Z, Shi L. Influence of ERAP1 and ERAP2 gene polymorphisms on disease susceptibility in different populations. Hum Immunol 2019; 80:325-334. [PMID: 30797823 DOI: 10.1016/j.humimm.2019.02.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/14/2019] [Accepted: 02/21/2019] [Indexed: 02/07/2023]
Abstract
The endoplasmic reticulum aminopeptidases (ERAPs), ERAP1 and ERAP2, makes a role in shaping the HLA class I peptidome by trimming peptides to the optimal size in MHC-class I-mediated antigen presentation and educating the immune system to differentiate between self-derived and foreign antigens. Association studies have shown that genetic variations in ERAP1 and ERAP2 genes increase susceptibility to autoimmune diseases, infectious diseases, and cancers. Both ERAP1 and ERAP2 genes exhibit diverse polymorphisms in different populations, which may influence their susceptibly to the aforementioned diseases. In this article, we review the distribution of ERAP1 and ERAP2 gene polymorphisms in various populations; discuss the risk or protective influence of these gene polymorphisms in autoimmune diseases, infectious diseases, and cancers; and highlight how ERAP genetic variations can influence disease associations.
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Affiliation(s)
- Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China
| | - Nannan Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China
| | - Ziyun Zhou
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China
| | - Li Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China.
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24
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Kuiper JJW, van Setten J, Devall M, Cretu-Stancu M, Hiddingh S, Ophoff RA, Missotten TOAR, van Velthoven M, Den Hollander AI, Hoyng CB, James E, Reeves E, Cordero-Coma M, Fonollosa A, Adán A, Martín J, Koeleman BPC, de Boer JH, Pulit SL, Márquez A, Radstake TRDJ. Functionally distinct ERAP1 and ERAP2 are a hallmark of HLA-A29-(Birdshot) Uveitis. Hum Mol Genet 2018; 27:4333-4343. [PMID: 30215709 PMCID: PMC6276832 DOI: 10.1093/hmg/ddy319] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022] Open
Abstract
Birdshot Uveitis (Birdshot) is a rare eye condition that affects HLA-A29-positive individuals and could be considered a prototypic member of the recently proposed 'MHC-I (major histocompatibility complex class I)-opathy' family. Genetic studies have pinpointed the endoplasmic reticulum aminopeptidase (ERAP1) and (ERAP2) genes as shared associations across MHC-I-opathies, which suggests ERAP dysfunction may be a root cause for MHC-I-opathies. We mapped the ERAP1 and ERAP2 haplotypes in 84 Dutch cases and 890 controls. We identified association at variant rs10044354, which mediated a marked increase in ERAP2 expression. We also identified and cloned an independently associated ERAP1 haplotype (tagged by rs2287987) present in more than half of the cases; this ERAP1 haplotype is also the primary risk and protective haplotype for other MHC-I-opathies. We show that the risk ERAP1 haplotype conferred significantly altered expression of ERAP1 isoforms in transcriptomic data (n = 360), resulting in lowered protein expression and distinct enzymatic activity. Both the association for rs10044354 (meta-analysis: odds ratio (OR) [95% CI]=2.07[1.58-2.71], P = 1.24 × 10(-7)) and rs2287987 (OR[95% CI]: =2.01[1.51-2.67], P = 1.41 × 10(-6)) replicated and showed consistent direction of effect in an independent Spanish cohort of 46 cases and 2103 controls. In both cohorts, the combined rs2287987-rs10044354 haplotype associated with Birdshot more strongly than either variant alone [meta-analysis: P=3.9 × 10(-9)]. Finally, we observed that ERAP2 protein expression is dependent on the ERAP1 background across three European populations (n = 3353). In conclusion, a functionally distinct combination of ERAP1 and ERAP2 are a hallmark of Birdshot and provide rationale for strategies designed to correct ERAP function for treatment of Birdshot and MHC-I-opathies more broadly.
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Affiliation(s)
- Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
- Laboratory of Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Jessica van Setten
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Matthew Devall
- Laboratory of Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Mircea Cretu-Stancu
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Sanne Hiddingh
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
- Laboratory of Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Roel A Ophoff
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Netherlands
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | | | | | - Anneke I Den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, Netherlands
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Edward James
- Centre for Cancer Immunology, Faculty of Medicine, University Hospital Southampton, Southampton, UK
| | - Emma Reeves
- Centre for Cancer Immunology, Faculty of Medicine, University Hospital Southampton, Southampton, UK
| | - Miguel Cordero-Coma
- Ophthalmology Department, Hospital de León, IBIOMED, Universidad de León, León, Spain
| | - Alejandro Fonollosa
- Ophthalmology Department, BioCruces Health Research Institute, Hospital Universitario Cruces, Barakaldo, Spain
| | - Alfredo Adán
- Ophthalmology Department, Hospital Clinic, Barcelona, Spain
| | - Javier Martín
- Instituto de Parasitología y Biomedicina ‘López-Neyra’, CSIC, PTS Granada, Granada Spain
| | - Bobby P C Koeleman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Joke H de Boer
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Sara L Pulit
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Centre for Health Information and Discovery, Big Data Institute, Oxford University, Oxford, UK
| | - Ana Márquez
- Systemic Autoimmune Disease Unit, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria de Granada, Granada Spain
| | - Timothy R D J Radstake
- Laboratory of Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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25
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de Castro JAL, Stratikos E. Intracellular antigen processing by ERAP2: Molecular mechanism and roles in health and disease. Hum Immunol 2018; 80:310-317. [PMID: 30414458 DOI: 10.1016/j.humimm.2018.11.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/19/2018] [Accepted: 11/05/2018] [Indexed: 02/05/2023]
Abstract
Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) is an intracellular enzyme localized in the ER that has been shown to play roles in the generation of peptides that serve as ligands for MHC class I (MHC-1) molecules. Although ERAP2 has been primarily described as an accessory and complementary enzyme to the homologous ERAP1, several lines of evidence during the last few years suggest that it can play distinct and important roles in processing antigenic peptides and influencing cellular cytotoxic immune responses. Such emerging evidence has been shaping ERAP2 as a potentially tractable target for regulating select autoimmune and anti-cancer responses for therapeutic purposes. Here, we review the state-of-the-art knowledge on the role of ERAP2 in antigen processing, its structure and molecular mechanism, influence on shaping MHC-I-bound immunopeptidomes and its involvement in disease pathogenesis.
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Affiliation(s)
- José A López de Castro
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma), Madrid, Spain.
| | - Efstratios Stratikos
- National Centre for Scientific Research Demokritos, Agia Paraskevi, Athens, Greece.
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26
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López de Castro JA. How ERAP1 and ERAP2 Shape the Peptidomes of Disease-Associated MHC-I Proteins. Front Immunol 2018; 9:2463. [PMID: 30425713 PMCID: PMC6219399 DOI: 10.3389/fimmu.2018.02463] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/04/2018] [Indexed: 12/28/2022] Open
Abstract
Four inflammatory diseases are strongly associated with Major Histocompatibility Complex class I (MHC-I) molecules: birdshot chorioretinopathy (HLA-A*29:02), ankylosing spondylitis (HLA-B*27), Behçet's disease (HLA-B*51), and psoriasis (HLA-C*06:02). The endoplasmic reticulum aminopeptidases (ERAP) 1 and 2 are also risk factors for these diseases. Since both enzymes are involved in the final processing steps of MHC-I ligands it is reasonable to assume that MHC-I-bound peptides play a significant pathogenetic role. This review will mainly focus on recent studies concerning the effects of ERAP1 and ERAP2 polymorphism and expression on shaping the peptidome of disease-associated MHC-I molecules in live cells. These studies will be discussed in the context of the distinct mechanisms and substrate preferences of both enzymes, their different patterns of genetic association with various diseases, the role of polymorphisms determining changes in enzymatic activity or expression levels, and the distinct peptidomes of disease-associated MHC-I allotypes. ERAP1 and ERAP2 polymorphism and expression induce significant changes in multiple MHC-I-bound peptidomes. These changes are MHC allotype-specific and, without excluding a degree of functional inter-dependence between both enzymes, reflect largely separate roles in their processing of MHC-I ligands. The studies reviewed here provide a molecular basis for the distinct patterns of genetic association of ERAP1 and ERAP2 with disease and for the pathogenetic role of peptides. The allotype-dependent alterations induced on distinct peptidomes may explain that the joint association of both enzymes and unrelated MHC-I alleles influence different pathological outcomes.
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27
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Brown MA, Wordsworth BP. Genetics in ankylosing spondylitis - Current state of the art and translation into clinical outcomes. Best Pract Res Clin Rheumatol 2018; 31:763-776. [PMID: 30509439 DOI: 10.1016/j.berh.2018.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/10/2018] [Accepted: 08/22/2018] [Indexed: 12/20/2022]
Abstract
Ankylosing spondylitis (AS) is the prototypic form of axial spondyloarthritis (axSpA). It is highly heritable, with studies conducted in twins and in unrelated cases and controls showing that the heritability for AS is much higher than those for inflammatory bowel disease or rheumatoid arthritis. To date, 116 loci have been identified, contributing to 28% of the genetic variation in the disease. These loci provide important clues into pathogenic pathways in the disease that have led to therapeutic advances such as the repositioning of IL-17 inhibitors in the disease. Much more research is currently required to determine the functional mechanisms by which the genetic associations operate, from which it is likely that novel therapeutic approaches will be developed.
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Affiliation(s)
- Matthew A Brown
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Brisbane, Australia.
| | - B Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
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28
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The role of polymorphic ERAP1 in autoinflammatory disease. Biosci Rep 2018; 38:BSR20171503. [PMID: 30054427 PMCID: PMC6131210 DOI: 10.1042/bsr20171503] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/19/2018] [Accepted: 07/23/2018] [Indexed: 01/29/2023] Open
Abstract
Autoimmune and autoinflammatory conditions represent a group of disorders characterized by self-directed tissue damage due to aberrant changes in innate and adaptive immune responses. These disorders possess widely varying clinical phenotypes and etiology; however, they share a number of similarities in genetic associations and environmental influences. Whilst the pathogenic mechanisms of disease remain poorly understood, genome wide association studies (GWAS) have implicated a number of genetic loci that are shared between several autoimmune and autoinflammatory conditions. Association of particular HLA alleles with disease susceptibility represents one of the strongest genetic associations. Furthermore, recent GWAS findings reveal strong associations with single nucleotide polymorphisms in the endoplasmic reticulum aminopeptidase 1 (ERAP1) gene and susceptibility to a number of these HLA-associated conditions. ERAP1 plays a major role in regulating the repertoire of peptides presented on HLA class I alleles at the cell surface, with the presence of single nucleotide polymorphisms in ERAP1 having a significant impact on peptide processing function and the repertoire of peptides presented. The impact of this dysfunctional peptide generation on CD8+ T-cell responses has been proposed as a mechanism of pathogenesis diseases where HLA and ERAP1 are associated. More recently, studies have highlighted a role for ERAP1 in innate immune-mediated pathways involved in inflammatory responses. Here, we discuss the role of polymorphic ERAP1 in various immune cell functions, and in the context of autoimmune and autoinflammatory disease pathogenesis.
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29
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Sanz-Bravo A, Martín-Esteban A, Kuiper JJW, García-Peydró M, Barnea E, Admon A, López de Castro JA. Allele-specific Alterations in the Peptidome Underlie the Joint Association of HLA-A*29:02 and Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) with Birdshot Chorioretinopathy. Mol Cell Proteomics 2018; 17:1564-1577. [PMID: 29769354 DOI: 10.1074/mcp.ra118.000778] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Indexed: 11/06/2022] Open
Abstract
Virtually all patients of the rare inflammatory eye disease birdshot chorioretinopathy (BSCR) carry the HLA-A*29:02 allele. BSCR is also associated with endoplasmic reticulum aminopeptidase 2 (ERAP2), an enzyme involved in processing HLA class I ligands, thus implicating the A*29:02 peptidome in this disease. To investigate the relationship between both risk factors we employed label-free quantitative mass spectrometry to characterize the effects of ERAP2 on the A*29:02-bound peptidome. An ERAP2-negative cell line was transduced with lentiviral constructs containing GFP-ERAP2 or GFP alone, and the A*29:02 peptidomes from both transduced cells were compared. A similar analysis was performed with two additional A*29:02-positive, ERAP1-concordant, cell lines expressing or not ERAP2. In both comparisons the presence of ERAP2 affected the following features of the A*29:02 peptidome: 1) Length, with increased amounts of peptides >9-mers, and 2) N-terminal residues, with less ERAP2-susceptible and more hydrophobic ones. The paradoxical effects on peptide length suggest that unproductive binding to ERAP2 might protect some peptides from ERAP1 over-trimming. The influence on N-terminal residues can be explained by a direct effect of ERAP2 on trimming, without ruling out and improved processing in concert with ERAP1. The alterations in the A*29:02 peptidome suggest that the association of ERAP2 with BSCR is through its effects on peptide processing. These differ from those on the ankylosing spondylitis-associated HLA-B*27. Thus, ERAP2 alters the peptidome of distinct HLA molecules as a function of their specific binding preferences, influencing different pathological outcomes in an allele-dependent way.
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Affiliation(s)
- Alejandro Sanz-Bravo
- From the ‡Centro de Biología Molecular Severo Ochoa (CSIC-UAM), 28049 Madrid, Spain
| | | | - Jonas J W Kuiper
- §Department of Ophthalmology, University Medical Center Utrecht, The Netherlands
| | - Marina García-Peydró
- From the ‡Centro de Biología Molecular Severo Ochoa (CSIC-UAM), 28049 Madrid, Spain
| | - Eilon Barnea
- ¶Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Arie Admon
- ¶Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
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30
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Padula MC, Leccese P, Padula AA, D'Angelo S, Martelli G. ERAP1 molecular characterization: Identification of a de novo allelic variant. HLA 2018; 92:44-45. [PMID: 29577660 DOI: 10.1111/tan.13262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/07/2018] [Accepted: 03/22/2018] [Indexed: 11/27/2022]
Abstract
The novel ERAP1 allelic variant is a missense polymorphism leading to the Arg53Pro substitution.
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Affiliation(s)
- M C Padula
- Rheumatology Institute of Lucania (IReL) and Rheumatology Department of Lucania, San Carlo Hospital of Potenza and Madonna delle Grazie Hospital of Matera, Potenza, Italy
- Department of Science, University of Basilicata, Potenza, Italy
| | - P Leccese
- Rheumatology Institute of Lucania (IReL) and Rheumatology Department of Lucania, San Carlo Hospital of Potenza and Madonna delle Grazie Hospital of Matera, Potenza, Italy
| | - A A Padula
- Rheumatology Institute of Lucania (IReL) and Rheumatology Department of Lucania, San Carlo Hospital of Potenza and Madonna delle Grazie Hospital of Matera, Potenza, Italy
| | - S D'Angelo
- Rheumatology Institute of Lucania (IReL) and Rheumatology Department of Lucania, San Carlo Hospital of Potenza and Madonna delle Grazie Hospital of Matera, Potenza, Italy
- Basilicata Ricerca Biomedica (BRB) Foundation, Potenza, Italy
| | - G Martelli
- Department of Science, University of Basilicata, Potenza, Italy
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31
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Liu S, Cao D, Shen Y, Li Y, Li Y, Shi L, Yu J, Li C, Zhang X, Sun M, Yao Y. The ERAP gene is associated with HCV chronic infection in a Chinese Han population. Hum Immunol 2017; 78:731-738. [PMID: 29037997 DOI: 10.1016/j.humimm.2017.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/15/2017] [Accepted: 10/11/2017] [Indexed: 02/01/2023]
Abstract
Endoplasmic reticulum aminopeptidases (ERAPs), ERAP1 and ERAP2, are critical components in the antigen-presentation system and are specialized to produce optimal-sized peptides for HLA I binding. ERAP gene polymorphisms have been correlated with HLA-associated diseases. To investigate the association between ERAP gene polymorphisms and HCV chronic infection, a TaqMan assay was used to genotype 4 SNPs (rs27044, rs30187, rs26618 and rs26653) in ERAP1 and 2 SNPs (rs2248374 and rs2549782) in ERAP2 genes in 376 Chinese Han HCV chronic infections and 324 healthy Chinese Han controls. The allelic distribution of rs26618 in the ERAP1 gene and rs2248374 in ERAP2 gene were both significantly different in case and control groups. The C-allele of rs26618 had an increased HCV chronicity risk compared with the T-allele (P=.025, OR=1.318, 95%CI: 1.035-1.677), and the same effect was found in A-allele of rs2248374 compared with G-allele (P=0.046, OR=1.244, 95%CI: 1.004-1.540). There were notable differences in the genotype distribution in analysis using the dominant genetic model in rs26618 (CC+CT vs. TT; P=0.007, OR=1.473, 95%CI: 1.091-1.989) and recessive genetic model in rs2248374 (AA vs. AG+GG; P=0.003, OR=1.548, 95%CI: 1.026-2.335). In addition, rs26618 and rs2248374-genotype combination played noteable effects on the clinical parameters. These results indicated that the ERAP gene may play a critical role in HCV chronicity in this Chinese Han population.
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Affiliation(s)
- Shuyuan Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China
| | - Danfeng Cao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China
| | - Yunsong Shen
- The First People's Hospital in Yunnan Province & The Affiliated Hospital of Kunming Science and Technology University, Kunming 650032, China
| | - Yalin Li
- The First People's Hospital in Yunnan Province & The Affiliated Hospital of Kunming Science and Technology University, Kunming 650032, China
| | - Ying Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China
| | - Li Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China
| | - Jiankun Yu
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China
| | - Chuanyin Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China
| | - Xinwen Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China
| | - Mingbo Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China.
| | - Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China.
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Solving the pathogenesis of ankylosing spondylitis. Clin Immunol 2017; 186:46-50. [PMID: 28736277 DOI: 10.1016/j.clim.2017.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 12/12/2022]
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Martín-Esteban A, Guasp P, Barnea E, Admon A, López de Castro JA. Functional Interaction of the Ankylosing Spondylitis-Associated Endoplasmic Reticulum Aminopeptidase 2 With the HLA-B*27 Peptidome in Human Cells. Arthritis Rheumatol 2017; 68:2466-75. [PMID: 27110896 DOI: 10.1002/art.39734] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/21/2016] [Indexed: 01/09/2023]
Abstract
OBJECTIVE To determine the influence of endoplasmic reticulum aminopeptidase 2 (ERAP-2) expression on the HLA-B*27 peptidome in live cells. METHODS Using immunoaffinity chromatography and acid extraction, HLA-B*27:05-bound peptides were isolated from 2 ERAP-2-negative lymphoblastoid cell lines and 1 ERAP-2-positive lymphoblastoid cell line expressing functionally indistinguishable ERAP-1 variants. More than 2,000-4,000 B*27:05 ligands were identified from each cell line, and their relative abundance was established by quantitative tandem mass spectrometry and MaxQuant-based peptide analyses. Pairwise comparisons were used to determine the structural features of peptides whose relative abundance was dependent on the presence of ERAP-2. Synthetic peptide digestions were performed with recombinant ERAP-1 and ERAP-2. Peptide affinity was estimated with standard algorithms. RESULTS The B*27:05 peptidome from ERAP-2-positive cells showed 3-4% fewer peptides with N-terminal basic residues than did the peptidome from ERAP-2-negative cells. Among the shared peptides, those most abundant in the presence of ERAP-2 included more nonamers, fewer decamers, and fewer N-terminal basic residues than the peptides predominant in ERAP-2-negative cells. These ERAP-2-dependent changes did not alter the global affinity of the B*27:05 peptidome. CONCLUSION ERAP-2 significantly influences the B*27:05-bound peptidome by destroying some ligands and decreasing the abundance of many more ligands with N-terminal basic residues, while increasing the abundance of nonamers. The former effects are best explained by direct ERAP-2 trimming. The effects on peptide length might be attributed to ERAP-2-induced activation of ERAP-1 trimming. These data support the notion of a peptide-mediated mechanism as the basis for the association of ERAP-2 with ankylosing spondylitis. Analogous effects on other major histocompatibility complex class I peptidomes might explain the involvement of ERAP-2 in HLA-B27-negative spondyloarthritis.
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Affiliation(s)
- Adrian Martín-Esteban
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma), Madrid, Spain
| | - Pablo Guasp
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma), Madrid, Spain
| | - Eilon Barnea
- Technion-Israel Institute of Technology, Haifa, Israel
| | - Arie Admon
- Technion-Israel Institute of Technology, Haifa, Israel
| | - José A López de Castro
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma), Madrid, Spain.
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Steinbach A, Winter J, Reuschenbach M, Blatnik R, Klevenz A, Bertrand M, Hoppe S, von Knebel Doeberitz M, Grabowska AK, Riemer AB. ERAP1 overexpression in HPV-induced malignancies: A possible novel immune evasion mechanism. Oncoimmunology 2017; 6:e1336594. [PMID: 28811980 DOI: 10.1080/2162402x.2017.1336594] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 01/17/2023] Open
Abstract
Immune evasion of tumors poses a major challenge for immunotherapy. For human papillomavirus (HPV)-induced malignancies, multiple immune evasion mechanisms have been described, including altered expression of antigen processing machinery (APM) components. These changes can directly influence epitope presentation and thus T-cell responses against tumor cells. To date, the APM had not been studied systematically in a large array of HPV+ tumor samples. Therefore in this study, systematic expression analysis of the APM was performed on the mRNA and protein level in a comprehensive collection of HPV16+ cell lines. Subsequently, HPV+ cervical tissue samples were examined by immunohistochemistry. ERAP1 (endoplasmic reticulum aminopeptidase 1) was the only APM component consistently altered - namely overexpressed - in HPV16+ tumor cell lines. ERAP1 was also found to be overexpressed in cervical intraepithelial neoplasia and cervical cancer samples; expression levels were increasing with disease stage. On the functional level, the influence of ERAP1 expression levels on HPV16 E7-derived epitope presentation was investigated by mass spectrometry and in cytotoxicity assays with HPV16-specific T-cell lines. ERAP1 overexpression did not cause a complete destruction of any of the HPV epitopes analyzed, however, an influence of ERAP1 overexpression on the presentation levels of certain HPV epitopes could be demonstrated by HPV16-specific CD8+ T-cells. These showed enhanced killing toward HPV16+ CaSki cells whose ERAP1 expression had been attenuated to normal levels. ERAP1 overexpression may thus represent a novel immune evasion mechanism in HPV-induced malignancies, in cases when presentation of clinically relevant epitopes is reduced by overactivity of this peptidase.
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Affiliation(s)
- Alina Steinbach
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Jan Winter
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Miriam Reuschenbach
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Renata Blatnik
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Alexandra Klevenz
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Miriam Bertrand
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephanie Hoppe
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | | | - Agnieszka K Grabowska
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika B Riemer
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
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Argikar UA, Dumouchel JL, Dunne CE, Bushee AJ. Ocular non-P450 oxidative, reductive, hydrolytic, and conjugative drug metabolizing enzymes. Drug Metab Rev 2017; 49:372-394. [PMID: 28438049 DOI: 10.1080/03602532.2017.1322609] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Metabolism in the eye for any species, laboratory animals or human, is gaining rapid interest as pharmaceutical scientists aim to treat a wide range of so-called incurable ocular diseases. Over a period of decades, reports of metabolic activity toward various drugs and biochemical markers have emerged in select ocular tissues of animals and humans. Ocular cytochrome P450 (P450) enzymes and transporters have been recently reviewed. However, there is a dearth of collated information on non-P450 drug metabolizing enzymes in eyes of various preclinical species and humans in health and disease. In an effort to complement ocular P450s and transporters, which have been well reviewed in the literature, this review is aimed at presenting collective information on non-P450 oxidative, hydrolytic, and conjugative ocular drug metabolizing enzymes. Herein, we also present a list of xenobiotics or drugs that have been reported to be metabolized in the eye.
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Affiliation(s)
- Upendra A Argikar
- a Analytical Sciences and Imaging , Novartis Institutes for Biomedical Research, Inc , Cambridge , MA , USA
| | - Jennifer L Dumouchel
- a Analytical Sciences and Imaging , Novartis Institutes for Biomedical Research, Inc , Cambridge , MA , USA
| | - Christine E Dunne
- b Department of Chemistry , Colorado State University , Fort Collins , CO , USA
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Abstract
Purpose Birdshot Uveitis (BU) is an archetypical chronic inflammatory eye disease, with poor visual prognosis, that provides an excellent model for studying chronic inflammation. BU typically affects patients in the fifth decade of life. This suggests that it may represent an age-related chronic inflammatory disease, which has been linked to increased erosion of telomere length of leukocytes. Methods To study this in detail, we exploited a sensitive standardized quantitative real-time polymerase chain reaction to determine the peripheral blood leukocyte telomere length (LTL) in 91 genotyped Dutch BU patients and 150 unaffected Dutch controls. Results Although LTL erosion rates were very similar between BU patients and healthy controls, we observed that BU patients displayed longer LTL, with a median of log (LTL) = 4.87 (= 74131 base pair) compared to 4.31 (= 20417 base pair) in unaffected controls (P<0.0001). The cause underpinning the difference in LTL could not be explained by clinical parameters, immune cell-subtype distribution, nor genetic predisposition based upon the computed weighted genetic risk score of genotyped validated variants in TERC, TERT, NAF1, OBFC1 and RTEL1. Conclusions These findings suggest that BU is accompanied by significantly longer LTL.
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Abstract
Over the past 5 years, advances in high-throughput techniques and studies involving large cohorts of patients have led to considerable advances in the identification of novel genetic associations and immune pathways involved in ankylosing spondylitis (AS). These discoveries include genes encoding cytokine receptors, transcription factors, signalling molecules and transport proteins. Although progress has been made in understanding the functions and potential pathogenic roles of some of these molecules, much work remains to be done to comprehend their complex interactions and therapeutic potential in AS. In this Review, we outline the current knowledge of AS pathogenesis, including genetic risk associations, HLA-B27-mediated pathology, perturbations in antigen-presentation pathways and the contribution of the type 3 immune response.
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38
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Abstract
The monocyte-lymphocyte ratio (MLR) is a useful biomarker for disease development, but little is known about the extent to which genetic and environmental factors influence MLR variation. Here, we study the genetic architecture of MLR and determine the influence of demographic and lifestyle factors on MLR in data from a Dutch non-patient twin-family population. Data were obtained in 9,501 individuals from the Netherlands Twin Register. We used regression analyses to determine the effects of age, sex, smoking, and body mass index (BMI) on MLR and its subcomponents. Data on twins, siblings and parents (N = 7,513) were analyzed by genetic structural equation modeling to establish heritability and genome wide single nucleotide polymorphism (SNP) data from a genotyped subsample (N = 5,892) and used to estimate heritability explained by SNPs. SNP and phenotype data were also analyzed in a genome-wide association study to identify the genes involved in MLR. Linkage disequilibrium (LD) score regression and expression quantitative trait loci (eQTL) analyses were performed to further explore the genetic findings. Results showed that age, sex, and age × sex interaction effects were present for MLR and its subcomponents. Variation in MLR was not related to BMI, but smoking was positively associated with MLR. Heritability was estimated at 40% for MLR, 58% for monocyte, and 58% for lymphocyte count. The Genome-wide association study (GWAS) identified a locus on ITGA4 that was associated with MLR and only marginally significantly associated with monocyte count. For monocyte count, additional genetic variants were identified on ITPR3, LPAP1, and IRF8. For lymphocyte count, GWAS provided no significant findings. Taking all measured SNPs together, their effects accounted for 13% of the heritability of MLR, while all known and identified genetic loci explained 1.3% of variation in MLR. eQTL analyses showed that these genetic variants were unlikely to be eQTLs. In conclusion, variation in MLR level in the general population is heritable and influenced by age, sex, and smoking. We identified gene variants in the ITGA4 gene associated with variation in MLR. The significant SNP-heritability indicates that more genetic variants are likely to be involved.
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Barnea E, Melamed Kadosh D, Haimovich Y, Satumtira N, Dorris ML, Nguyen MT, Hammer RE, Tran TM, Colbert RA, Taurog JD, Admon A. The Human Leukocyte Antigen (HLA)-B27 Peptidome in Vivo, in Spondyloarthritis-susceptible HLA-B27 Transgenic Rats and the Effect of Erap1 Deletion. Mol Cell Proteomics 2017; 16:642-662. [PMID: 28188227 DOI: 10.1074/mcp.m116.066241] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/05/2017] [Indexed: 01/20/2023] Open
Abstract
HLA-B27 is a class I major histocompatibility (MHC-I) allele that confers susceptibility to the rheumatic disease ankylosing spondylitis (AS) by an unknown mechanism. ERAP1 is an aminopeptidase that trims peptides in the endoplasmic reticulum for binding to MHC-I molecules. ERAP1 shows genetic epistasis with HLA-B27 in conferring susceptibility to AS. Male HLA-B27 transgenic rats develop arthritis and serve as an animal model of AS, whereas female B27 transgenic rats remain healthy. We used large scale quantitative mass spectrometry to identify over 15,000 unique HLA-B27 peptide ligands, isolated after immunoaffinity purification of the B27 molecules from the spleens of HLA-B27 transgenic rats. Heterozygous deletion of Erap1, which reduced the Erap1 level to less than half, had no qualitative or quantitative effects on the B27 peptidome. Homozygous deletion of Erap1 affected approximately one-third of the B27 peptidome but left most of the B27 peptidome unchanged, suggesting the possibility that some of the HLA-B27 immunopeptidome is not processed in the presence of Erap1. Deletion of Erap1 was permissive for the AS-like phenotype, increased mean peptide length and increased the frequency of C-terminal hydrophobic residues and of N-terminal Ala, Ser, or Lys. The presence of Erap1 increased the frequency of C-terminal Lys and Arg, of Glu and Asp at intermediate residues, and of N-terminal Gly. Several peptides of potential interest in AS pathogenesis, previously identified in human cell lines, were isolated. However, rats susceptible to arthritis had B27 peptidomes similar to those of non-susceptible rats, and no peptides were found to be uniquely associated with arthritis. Whether specific B27-bound peptides are required for AS pathogenesis remains to be determined. Data are available via ProteomeXchange with identifier PXD005502.
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Affiliation(s)
- Eilon Barnea
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Dganit Melamed Kadosh
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Yael Haimovich
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Nimman Satumtira
- §Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8884
| | - Martha L Dorris
- §Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8884
| | - Mylinh T Nguyen
- ¶Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8816
| | - Robert E Hammer
- ¶Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8816
| | - Tri M Tran
- ‖NIAMS, National Institutes of Health, Bethesda, Maryland 20892-1560
| | - Robert A Colbert
- ‖NIAMS, National Institutes of Health, Bethesda, Maryland 20892-1560
| | - Joel D Taurog
- §Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8884;
| | - Arie Admon
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel;
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Separate effects of the ankylosing spondylitis associated ERAP1 and ERAP2 aminopeptidases determine the influence of their combined phenotype on the HLA-B*27 peptidome. J Autoimmun 2017; 79:28-38. [PMID: 28063628 DOI: 10.1016/j.jaut.2016.12.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 12/28/2016] [Accepted: 12/29/2016] [Indexed: 01/01/2023]
Abstract
Ankylosing spondylitis (AS) is an inflammatory disease strongly associated with the Major Histocompatibility Complex class I (MHC-I) allotype HLA-B*27. The endoplasmic reticulum aminopeptidases (ERAP)1 and 2, which trim peptides to their optimal length for MHC-I binding, are also susceptibility factors for this disease. Both highly active ERAP1 variants and ERAP2 expression favor AS, whereas loss-of-function ERAP1 and loss-of-expression ERAP2 variants are protective. Yet, only ERAP1 is in epistasis with HLA-B*27. We addressed two issues concerning the functional interaction of ERAP1 and ERAP2 with the HLA-B*27 peptidome in human cells: 1) distinguishing the effects of ERAP1 from those of ERAP2, and 2) determining the influence of ERAP2 in distinct ERAP1 contexts. Quantitative comparisons of the HLA-B*27:05 peptidomes from cells with various ERAP1/ERAP2 phenotypes were carried out. When cells expressing ERAP2 and either high or low activity ERAP1 variants were compared, increased amounts of nonamers, relative to longer ligands, and decreased amounts of peptides with Ala1, were observed in the more active ERAP1 context. When cells expressing ERAP2 in a low activity ERAP1 context or lacking ERAP2 but expressing a highly active ERAP1 variant were compared, the same effects on peptide length and Ala1, but also significantly lower amounts of peptides with N-terminal basic residues and lower affinity of the peptidome, were observed in the ERAP2-positive context. Thus, ERAP1 and ERAP2 have significant and distinct effects on the HLA-B*27 peptidome, suggesting that both enzymes largely act as separate entities in vivo. This may explain their different patterns of association with AS.
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Molecular and pathogenic effects of endoplasmic reticulum aminopeptidases ERAP1 and ERAP2 in MHC-I-associated inflammatory disorders: Towards a unifying view. Mol Immunol 2016; 77:193-204. [DOI: 10.1016/j.molimm.2016.08.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/04/2016] [Accepted: 08/04/2016] [Indexed: 12/22/2022]
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Nagarajan NA, de Verteuil DA, Sriranganadane D, Yahyaoui W, Thibault P, Perreault C, Shastri N. ERAAP Shapes the Peptidome Associated with Classical and Nonclassical MHC Class I Molecules. THE JOURNAL OF IMMUNOLOGY 2016; 197:1035-43. [PMID: 27371725 DOI: 10.4049/jimmunol.1500654] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 04/19/2016] [Indexed: 11/19/2022]
Abstract
The peptide repertoire presented by classical as well as nonclassical MHC class I (MHC I) molecules is altered in the absence of the endoplasmic reticulum aminopeptidase associated with Ag processing (ERAAP). To characterize the extent of these changes, peptides from cells lacking ERAAP were eluted from the cell surface and analyzed by high-throughput mass spectrometry. We found that most peptides found in wild-type (WT) cells were retained in the absence of ERAAP. In contrast, a subset of "ERAAP-edited" peptides was lost in WT cells, and ERAAP-deficient cells presented a unique "unedited" repertoire. A substantial fraction of MHC-associated peptides from ERAAP-deficient cells contained N-terminal extensions and had a different molecular composition than did those from WT cells. We found that the number and immunogenicity of peptides associated with nonclassical MHC I was increased in the absence of ERAAP. Conversely, only peptides presented by classical MHC I were immunogenic in ERAAP-sufficient cells. Finally, MHC I peptides were also derived from different intracellular sources in ERAAP-deficient cells.
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Affiliation(s)
- Niranjana A Nagarajan
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720; and
| | - Danielle A de Verteuil
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Dev Sriranganadane
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Wafaa Yahyaoui
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720; and
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Guasp P, Alvarez-Navarro C, Gomez-Molina P, Martín-Esteban A, Marcilla M, Barnea E, Admon A, López de Castro JA. The Peptidome of Behçet's Disease-Associated HLA-B*51:01 Includes Two Subpeptidomes Differentially Shaped by Endoplasmic Reticulum Aminopeptidase 1. Arthritis Rheumatol 2016; 68:505-15. [PMID: 26360328 DOI: 10.1002/art.39430] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/03/2015] [Indexed: 01/09/2023]
Abstract
OBJECTIVE To characterize the peptidome of the Behçet's disease-associated HLA-B*51:01 allotype as well as the differential features of major peptide subsets and their distinct endoplasmic reticulum aminopeptidase 1 (ERAP-1)-mediated processing. METHODS The endogenous B*51:01-bound peptidome was characterized from 721.221 transfectant cells, after affinity chromatography and acid extraction, by tandem mass spectrometry. Recombinant ERAP-1 variants were used to digest synthetic B*51:01 ligands. HLA and transporter associated with antigen processing (TAP) binding affinities of peptide ligands were calculated with well-established algorithms. ERAP-1 and ERAP-2 from 721.221 cells were characterized by genomic sequencing and Western blotting. RESULTS The B*51:01 peptidome consisted of 29.5% octamers, 61.7% nonamers, 4.8% decamers, and 4.0% longer peptides. The major peptide motif consisted of Pro and Ala at position 2, aliphatic/aromatic position 3 residues, and Val and Ile at the C-terminal position. The ligands with Pro or Ala at position 2 constituted 2 distinct subpeptidomes. Peptides with Pro at position 2 showed higher affinity for B*51:01 and lower affinity for TAP than those with Ala at position 2. Most important, both peptide subsets differed drastically in the susceptibility of their position 1 residues to ERAP-1, revealing a distinct influence of this enzyme on both subpeptidomes, which may alter their balance, affecting the global affinity of B*51:01-peptide complexes. CONCLUSION ERAP-1 has a significant influence on the B*51:01 peptidome and its affinity. This influence is based on very distinct effects on the 2 subpeptidomes, whereby only peptides in the subpeptidome with Ala at position 2 are extensively destroyed, except when their position 1 residues are ERAP-1 resistant. This pattern provides a mechanism for the epistatic association of ERAP-1 and B*51:01 in Behçet's disease.
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Affiliation(s)
- Pablo Guasp
- CSIC, Centro de Biología Molecular Severo Ochoa, Madrid, Spain
| | | | | | | | | | - Eilon Barnea
- Technion-Israel Institute of Technology, Haifa, Israel
| | - Arie Admon
- Technion-Israel Institute of Technology, Haifa, Israel
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Lucchese G. Understanding Neuropsychiatric Diseases, Analyzing the Peptide Sharing between Infectious Agents and the Language-Associated NMDA 2A Protein. Front Psychiatry 2016; 7:60. [PMID: 27148089 PMCID: PMC4827103 DOI: 10.3389/fpsyt.2016.00060] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/29/2016] [Indexed: 11/13/2022] Open
Abstract
Language disorders and infections may occur together and often concur, to a different extent and via different modalities, in characterizing brain pathologies, such as schizophrenia, autism, epilepsies, bipolar disorders, frontotemporal neurodegeneration, and encephalitis, inter alia. The biological mechanism(s) that might channel language dysfunctions and infections into etiological pathways connected to neuropathologic sequelae are unclear. Searching for molecular link(s) between language disorders and infections, the present study explores the language-associated NMDA 2A subunit for peptide sharing with pathogens that have been described in concomitance with neuropsychiatric diseases. It was found that a vast peptide commonality links the human glutamate ionotropic receptor NMDA 2A subunit to infectious agents. Such a link expands to and interfaces with neuropsychiatric disorders in light of the specific allocation of NMDA 2A gene expression in brain areas related to language functions. The data hint at a possible pathologic scenario based on anti-pathogen immune responses cross-reacting with NMDA 2A in the brain.
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Affiliation(s)
- Guglielmo Lucchese
- Brain and Language Laboratory, Freie Universität Berlin , Berlin , Germany
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45
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Joyce S. Immunoproteasomes edit tumors, which then escapes immune recognition. Eur J Immunol 2015; 45:3241-5. [PMID: 26527367 PMCID: PMC4695966 DOI: 10.1002/eji.201546100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 10/27/2015] [Accepted: 10/30/2015] [Indexed: 01/23/2023]
Abstract
In 1985, John Monaco--the discoverer of LMP-2 and -7, the inducible components of the immunoproteasome--asked his advanced immunology class as to why the MHC region contained not only structural genes, but several others as well, whose functions were then unknown. As we drew a blank, he quipped: perchance because many of the MHC genes are induced by IFN-γ! The ensuing three decades have witnessed the unveiling of the profound fundamental and clinical implications of that classroom tête-à-tête. Amongst its multitudinous effects, IFN-γ induces genes enhancing antigen processing and presentation to T cells; such as those encoding cellular proteases and activators of proteases. In this issue, Keller et al. [Eur. J. Immunol. 2015. 45: 3257-3268] demonstrate that the limited success of MART-1/Melan-A-targeted immunotherapy in melanoma patients could be due to inefficient MART-1(26-35) presentation, owing to the proteolytic activities of IFN-γ-inducible β2i/MECL-1, proteasome activator 28 (PA28), and endoplasmic reticulum-associated aminopeptidase-associated with antigen processing (ERAP). Specifically, whilst β2i and PA28 impede MART-1(26-35) liberation from its precursor protein, ERAP-1 degrades this epitope. Hence, critical to effective cancer immunotherapy is deep knowledge of T-cell-targeted tumor antigens and how cellular proteases generate protective epitope(s) from them, or destroy them.
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Affiliation(s)
- Sebastian Joyce
- Veterans Administration Tennessee Valley Healthcare System and the Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
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46
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Abstract
The spondyloarthropathies comprise ankylosing spondylitis (AS), reactive arthritis, psoriatic arthritis (PsA) and arthritis associated with inflammatory bowel disease. In this Perspectives article, we describe how Behçet disease and several clinically distinct spondyloarthropathies-all associated with MHC class I (MHC-I) alleles such as HLA-B(*)51, HLA-C(*)0602 and HLA-B(*)27 and epistatic ERAP-1 interactions-have a shared immunopathogenetic basis. As a unifying concept, we propose that barrier dysfunction in environmentally exposed organs such as the skin, and aberrant innate immune reactions at sites of mechanical stress, can often trigger secondary adaptive immune CD8(+) T-cell responses with prominent neutrophilic inflammation that culminate in exacerbation and recurrence of these diseases. Of note, these 'MHC-I-opathies' show a differential immunopathology, probably reflecting antigenic differences within target tissues: HLA-B(*)51 is linked to ocular and mucocutaneous disease but not gut involvement, and HLA-C(*)0602 is linked to type I psoriasis but not scalp or nail disease.
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Emma R, Edward J. The Role of Endoplasmic Reticulum Aminopeptidase 1 Biology in Immune Evasion by Tumours. ACTA ACUST UNITED AC 2015. [DOI: 10.17352/jvi.000007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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