1
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Al-kaabi M, Deshpande P, Firth M, Pavlos R, Chopra A, Basiri H, Currenti J, Alves E, Kalams S, Fellay J, Phillips E, Mallal S, John M, Gaudieri S. Epistatic interaction between ERAP2 and HLA modulates HIV-1 adaptation and disease outcome in an Australian population. PLoS Pathog 2024; 20:e1012359. [PMID: 38980912 PMCID: PMC11259285 DOI: 10.1371/journal.ppat.1012359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 07/19/2024] [Accepted: 06/19/2024] [Indexed: 07/11/2024] Open
Abstract
A strong genetic predictor of outcome following untreated HIV-1 infection is the carriage of specific alleles of human leukocyte antigens (HLAs) that present viral epitopes to T cells. Residual variation in outcome measures may be attributed, in part, to viral adaptation to HLA-restricted T cell responses. Variants of the endoplasmic reticulum aminopeptidases (ERAPs) influence the repertoire of T cell epitopes presented by HLA alleles as they trim pathogen-derived peptide precursors to optimal lengths for antigen presentation, along with other functions unrelated to antigen presentation. We investigated whether ERAP variants influence HLA-associated HIV-1 adaptation with demonstrable effects on overall HIV-1 disease outcome. Utilizing host and viral data of 249 West Australian individuals with HIV-1 subtype B infection, we identified a novel association between two linked ERAP2 single nucleotide polymorphisms (SNPs; rs2248374 and rs2549782) with plasma HIV RNA concentration (viral load) (P adjusted = 0.0024 for both SNPs). Greater HLA-associated HIV-1 adaptation in the HIV-1 Gag gene correlated significantly with higher viral load, lower CD4+ T cell count and proportion; P = 0.0103, P = 0.0061, P = 0.0061, respectively). When considered together, there was a significant interaction between the two ERAP2 SNPs and HLA-associated HIV-1 adaptation on viral load (P = 0.0111). In a comprehensive multivariate model, addition of ERAP2 haplotypes and HLA associated adaptation as an interaction term to known HLA and CCR5 determinants and demographic factors, increased the explanatory variance of population viral load from 17.67% to 45.1% in this dataset. These effects were not replicated in publicly available datasets with comparably sized cohorts, suggesting that any true global epistasis may be dependent on specific HLA-ERAP allelic combinations. Our data raises the possibility that ERAP2 variants may shape peptide repertoires presented to HLA class I-restricted T cells to modulate the degree of viral adaptation within individuals, in turn contributing to disease variability at the population level. Analyses of other populations and experimental studies, ideally with locally derived ERAP genotyping and HLA-specific viral adaptations are needed to elucidate this further.
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Affiliation(s)
- Marwah Al-kaabi
- School of Human Sciences, University of Western Australia, Crawley, Australia
| | - Pooja Deshpande
- School of Human Sciences, University of Western Australia, Crawley, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Martin Firth
- School of Physics, Mathematics and Computing, Department of Mathematics and Statistics, University of Western Australia, Crawley, Australia
| | - Rebecca Pavlos
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Hamed Basiri
- School of Human Sciences, University of Western Australia, Crawley, Australia
| | - Jennifer Currenti
- School of Human Sciences, University of Western Australia, Crawley, Australia
| | - Eric Alves
- School of Human Sciences, University of Western Australia, Crawley, Australia
| | - Spyros Kalams
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss HIV Cohort Study, Zurich, Switzerland
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Mina John
- School of Human Sciences, University of Western Australia, Crawley, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Australia
| | - Silvana Gaudieri
- School of Human Sciences, University of Western Australia, Crawley, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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2
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Raja A, Kuiper JJW. Evolutionary immuno-genetics of endoplasmic reticulum aminopeptidase II (ERAP2). Genes Immun 2023; 24:295-302. [PMID: 37925533 PMCID: PMC10721543 DOI: 10.1038/s41435-023-00225-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023]
Abstract
Endoplasmic reticulum aminopeptidase 2 (ERAP2) is a proteolytic enzyme involved in adaptive immunity. The ERAP2 gene is highly polymorphic and encodes haplotypes that confer resistance against lethal infectious diseases, but also increase the risk for autoimmune disorders. Identifying how ERAP2 influences susceptibility to these traits requires an understanding of the selective pressures that shaped and maintained allelic variation throughout human evolution. Our review discusses the genetic regulation of haplotypes and diversity in naturally occurring ERAP2 allotypes in the global population. We outline how these ERAP2 haplotypes evolved during human history and highlight the presence of Neanderthal DNA sequences in ERAP2 of modern humans. Recent evidence suggests that human adaptation during the last ~10,000 years and historic pandemics left a significant mark on the ERAP2 gene that determines susceptibility to infectious and inflammatory diseases today.
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Affiliation(s)
- Aroosha Raja
- Department of Ophthalmology, Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Jonas J W Kuiper
- Department of Ophthalmology, Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands.
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3
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Pagadala M, Sears TJ, Wu VH, Pérez-Guijarro E, Kim H, Castro A, Talwar JV, Gonzalez-Colin C, Cao S, Schmiedel BJ, Goudarzi S, Kirani D, Au J, Zhang T, Landi T, Salem RM, Morris GP, Harismendy O, Patel SP, Alexandrov LB, Mesirov JP, Zanetti M, Day CP, Fan CC, Thompson WK, Merlino G, Gutkind JS, Vijayanand P, Carter H. Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response. Nat Commun 2023; 14:2744. [PMID: 37173324 PMCID: PMC10182072 DOI: 10.1038/s41467-023-38271-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
With the continued promise of immunotherapy for treating cancer, understanding how host genetics contributes to the tumor immune microenvironment (TIME) is essential to tailoring cancer screening and treatment strategies. Here, we study 1084 eQTLs affecting the TIME found through analysis of The Cancer Genome Atlas and literature curation. These TIME eQTLs are enriched in areas of active transcription, and associate with gene expression in specific immune cell subsets, such as macrophages and dendritic cells. Polygenic score models built with TIME eQTLs reproducibly stratify cancer risk, survival and immune checkpoint blockade (ICB) response across independent cohorts. To assess whether an eQTL-informed approach could reveal potential cancer immunotherapy targets, we inhibit CTSS, a gene implicated by cancer risk and ICB response-associated polygenic models; CTSS inhibition results in slowed tumor growth and extended survival in vivo. These results validate the potential of integrating germline variation and TIME characteristics for uncovering potential targets for immunotherapy.
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Affiliation(s)
- Meghana Pagadala
- Biomedical Sciences Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Timothy J Sears
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Victoria H Wu
- Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA, 92093, USA
| | - Eva Pérez-Guijarro
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Hyo Kim
- Undergraduate Bioengineering Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andrea Castro
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - James V Talwar
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Steven Cao
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | | | | | - Divya Kirani
- Undergraduate Biology and Bioinformatics Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jessica Au
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Rany M Salem
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Olivier Harismendy
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Sandip Pravin Patel
- Center for Personalized Cancer Therapy, Division of Hematology and Oncology, UC San Diego Moores Cancer Center, San Diego, CA, 92037, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jill P Mesirov
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- The Laboratory of Immunology and Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Chun Chieh Fan
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK, 74136, USA
- Department of Radiology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wesley K Thompson
- Division of Biostatistics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - J Silvio Gutkind
- Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA, 92093, USA
| | | | - Hannah Carter
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
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4
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Hamilton F, Mentzer AJ, Parks T, Baillie JK, Smith GD, Ghazal P, Timpson NJ. Variation in ERAP2 has opposing effects on severe respiratory infection and autoimmune disease. Am J Hum Genet 2023; 110:691-702. [PMID: 36889308 PMCID: PMC10119032 DOI: 10.1016/j.ajhg.2023.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/06/2023] [Indexed: 03/09/2023] Open
Abstract
ERAP2 is an aminopeptidase involved in immunological antigen presentation. Genotype data in human samples from before and after the Black Death, an epidemic due to Yersinia pestis, have marked changes in allele frequency of the single-nucleotide polymorphism (SNP) rs2549794, with the T allele suggested to be deleterious during this period, while ERAP2 is also implicated in autoimmune diseases. This study explored the association between variation at ERAP2 and (1) infection, (2) autoimmune disease, and (3) parental longevity. Genome-wide association studies (GWASs) of these outcomes were identified in contemporary cohorts (UK Biobank, FinnGen, and GenOMICC). Effect estimates were extracted for rs2549794 and rs2248374, a haplotype tagging SNP. Additionally, cis expression and protein quantitative trait loci (QTLs) for ERAP2 were used in Mendelian randomization (MR) analyses. Consistent with decreased survival in the Black Death, the T allele of rs2549794 showed evidence of association with respiratory infection (odds ratio; OR for pneumonia 1.03; 95% CI 1.01-1.05). Effect estimates were larger for more severe phenotypes (OR for critical care admission with pneumonia 1.08; 95% CI 1.02-1.14). In contrast, opposing effects were identified for Crohn disease (OR 0.86; 95% CI 0.82-0.90). This allele was shown to associate with decreased ERAP2 expression and protein levels, independent of haplotype. MR analyses suggest that ERAP2 expression may be mediating disease associations. Decreased ERAP2 expression is associated with severe respiratory infection with an opposing association with autoimmune diseases. These data support the hypothesis of balancing selection at this locus driven by autoimmune and infectious disease.
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Affiliation(s)
- Fergus Hamilton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Infection Science, North Bristol NHS Trust, Bristol, UK.
| | | | - Tom Parks
- Wellcome Centre For Human Genetics, University of Oxford, Oxford, UK; Department of Infectious Disease, Imperial College London, London, UK
| | - J Kenneth Baillie
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK; Roslin Institute, University of Edinburgh, Edinburgh, UK; Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | | | | | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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5
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Zhou YH, Gallins PJ, Etheridge AS, Jima D, Scholl E, Wright FA, Innocenti F. A resource for integrated genomic analysis of the human liver. Sci Rep 2022; 12:15151. [PMID: 36071064 PMCID: PMC9452507 DOI: 10.1038/s41598-022-18506-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/08/2022] [Indexed: 11/18/2022] Open
Abstract
In this study, we generated whole-transcriptome RNA-Seq from n = 192 genotyped liver samples and used these data with existing data from the GTEx Project (RNA-Seq) and previous liver eQTL (microarray) studies to create an enhanced transcriptomic sequence resource in the human liver. Analyses of genotype-expression associations show pronounced enrichment of associations with genes of drug response. The associations are primarily consistent across the two RNA-Seq datasets, with some modest variation, indicating the importance of obtaining multiple datasets to produce a robust resource. We further used an empirical Bayesian model to compare eQTL patterns in liver and an additional 20 GTEx tissues, finding that MHC genes, and especially class II genes, are enriched for liver-specific eQTL patterns. To illustrate the utility of the resource to augment GWAS analysis with small sample sizes, we developed a novel meta-analysis technique to combine several liver eQTL data sources. We also illustrate its application using a transcriptome-enhanced re-analysis of a study of neutropenia in pancreatic cancer patients. The associations of genotype with liver expression, including splice variation and its genetic associations, are made available in a searchable genome browser.
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Affiliation(s)
- Yi-Hui Zhou
- Department of Biological Sciences, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA.
- Bioinformatics Research Center, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA.
| | - Paul J Gallins
- Bioinformatics Research Center, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA
| | - Amy S Etheridge
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Dereje Jima
- Bioinformatics Research Center, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA
| | - Elizabeth Scholl
- Bioinformatics Research Center, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA
| | - Fred A Wright
- Department of Biological Sciences, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA
- Department of Statistics, North Carolina State University, Raleigh NC State University, Raleigh, NC, 27695, USA
| | - Federico Innocenti
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA.
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6
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Mpakali A, Georgiadis D, Stratikos E, Giastas P. Inhibitor-Dependent Usage of the S1' Specificity Pocket of ER Aminopeptidase 2. ACS Med Chem Lett 2022; 13:218-224. [PMID: 35178178 PMCID: PMC8842112 DOI: 10.1021/acsmedchemlett.1c00582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/10/2022] [Indexed: 01/16/2023] Open
Abstract
Endoplasmic reticulum aminopeptidase 2 (ERAP2) is an intracellular enzyme involved in the processing of antigenic peptides intended for presentation by major histocompatibility complex class I (MHCI) molecules. Because of its role in regulating immune responses, ERAP2 is an emerging pharmacological target. Phosphinic pseudopeptides are potent transition-state analogue inhibitors of ERAP2. Previous structure-activity studies have revealed a complex but ambiguous relationship between the occupation of putative specificity pockets and the inhibitor efficacy. To address these problems, we solved crystal structures of ERAP2 in complex with two phosphinic pseudotripeptide inhibitors. Both compounds are found in the catalytic site in a canonical orientation for transition-state analogues and utilize the S1 and S2' pockets in a similar fashion. Strikingly, their P1' side chains exhibit different orientations and make interactions with distinct shallow pockets near the ERAP2 active site. These structures suggest that S1' pocket usage in ERAP2 may be inhibitor-dependent and constitute useful starting templates for the further optimization of this class of compounds.
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Affiliation(s)
- Anastasia Mpakali
- National
Centre for Scientific Research Demokritos, Agia Paraskevi, Athens 15341, Greece,
| | - Dimitris Georgiadis
- Laboratory
of Organic Chemistry, Chemistry Department, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens 15771, Greece
| | - Efstratios Stratikos
- National
Centre for Scientific Research Demokritos, Agia Paraskevi, Athens 15341, Greece,Laboratory
of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens 15771 Greece
| | - Petros Giastas
- Department
of Neurobiology, Hellenic Pasteur Institute, Athens 11521, Greece,Department
of Biotechnology, School of Applied Biology & Biotechnology, Agricultural University of Athens, Athens 11855, Greece,
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7
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Genetic association of ERAP1 and ERAP2 with eclampsia and preeclampsia in northeastern Brazilian women. Sci Rep 2021; 11:6764. [PMID: 33762660 PMCID: PMC7990956 DOI: 10.1038/s41598-021-86240-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/09/2021] [Indexed: 01/28/2023] Open
Abstract
The clinical spectrum of hypertensive disorders of pregnancy (HDP) is determined by the interplay between environmental and genetic factors, most of which remains unknown. ERAP1, ERAP2 and LNPEP genes code for multifunctional aminopeptidases involved with antigen processing and degradation of small peptides such as angiotensin II (Ang II), vasopressin and oxytocin. We aimed to test for associations between genetic variants in aminopeptidases and HDP. A total of 1282 pregnant women (normotensive controls, n = 693; preeclampsia, n = 342; chronic hypertension with superimposed preeclampsia, n = 61; eclampsia, n = 74; and HELLP syndrome, n = 112) were genotyped for variants in LNPEP (rs27300, rs38034, rs2303138), ERAP1 (rs27044, rs30187) and ERAP2 (rs2549796 rs2927609 rs11135484). We also evaluated the effect of ERAP1 rs30187 on plasma Ang II levels in an additional cohort of 65 pregnant women. The genotype C/C, in ERAP1 rs30187 variant (c.1583 T > C, p.Lys528Arg), was associated with increased risk of eclampsia (OR = 1.85, p = 0.019) whereas ERAP2 haplotype rs2549796(C)–rs2927609(C)–rs11135484(G) was associated with preeclampsia (OR = 1.96, corrected p-value = 0.01). Ang II plasma levels did not differ across rs30187 genotypic groups (p = 0.895). In conclusion, ERAP1 gene is associated with eclampsia whereas ERAP2 is associated with preeclampsia, although the mechanism by which genetic variants in ERAPs influence the risk of preeclampsia and eclampsia remain to be elucidated.
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8
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Hutchinson JP, Temponeras I, Kuiper J, Cortes A, Korczynska J, Kitchen S, Stratikos E. Common allotypes of ER aminopeptidase 1 have substrate-dependent and highly variable enzymatic properties. J Biol Chem 2021; 296:100443. [PMID: 33617882 PMCID: PMC8024916 DOI: 10.1016/j.jbc.2021.100443] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
Polymorphic variation of immune system proteins can drive variability of individual immune responses. Endoplasmic reticulum aminopeptidase 1 (ERAP1) generates antigenic peptides for presentation by major histocompatibility complex class I molecules. Coding SNPs in ERAP1 have been associated with predisposition to inflammatory rheumatic disease and shown to affect functional properties of the enzyme, but the interplay between combinations of these SNPs as they exist in allotypes has not been thoroughly explored. We used phased genotype data to estimate ERAP1 allotype frequency in 2504 individuals across five major human populations, generated highly pure recombinant enzymes corresponding to the ten most common ERAP1 allotypes, and systematically characterized their in vitro enzymatic properties. We find that ERAP1 allotypes possess a wide range of enzymatic activities, up to 60-fold, whose ranking is substrate dependent. Strikingly, allotype 10, previously associated with Behçet’s disease, is consistently a low-activity outlier, suggesting that a significant percentage of individuals carry a subactive ERAP1 gene. Enzymatic analysis revealed that ERAP1 allotypes can differ in both catalytic efficiency and substrate affinity, differences that can change intermediate accumulation in multistep trimming reactions. Alterations in efficacy of an allosteric inhibitor that targets the regulatory site suggest that allotypic variation influences the communication between the regulatory and the active site. Our work defines the wide landscape of ERAP1 activity in human populations and demonstrates how common allotypes can induce substrate-dependent variability in antigen processing, thus contributing, in synergy with major histocompatibility complex haplotypes, to immune response variability and predisposition to chronic inflammatory conditions.
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Affiliation(s)
| | - Ioannis Temponeras
- Protein Chemistry Laboratory, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - Jonas 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
| | - Adrian Cortes
- Human Genetics, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Justyna Korczynska
- Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Semra Kitchen
- Adaptive Immunity Research Unit, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Efstratios Stratikos
- Protein Chemistry Laboratory, National Centre for Scientific Research "Demokritos", Athens, Greece; Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, Greece.
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9
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Zhang S, Liu S, Liu N, Li C, Wang H, Shi L, Zhang X, Bao L, Yao Y, Shi L. Polymorphisms in ERAP1 and ERAP2 Genes Are Associated With Tuberculosis in the Han Chinese. Front Genet 2020; 11:566190. [PMID: 33250919 PMCID: PMC7676896 DOI: 10.3389/fgene.2020.566190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/07/2020] [Indexed: 11/13/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) in the endoplasmic reticulum aminopeptidase (ERAP1 and ERAP2) genes are associated with the pathogenesis of bacterial and viral infections. To search for the variations in the ERAP1 and ERAP2 genes associated with tuberculosis (TB), 449 TB cases and 435 healthy individuals of the Han population in the Yunnan province of China were included in the present study. Eleven SNPs of ERAPs were genotyped using the SNaPshot SNP assay. Allelic, genotypic, and haplotypic association analyses were performed between the TB and control groups. Furthermore, stratification analyses among pulmonary TB (PTB), extrapulmonary TB (EPTB), and healthy controls; and initial treatment TB (ITTB), retreatment TB (RTB), and healthy controls were also performed. The TT genotype of rs26618 in ERAP1 exhibited a protective factor for TB, compared with the role of the CC/CT genotype (P = 0.003; OR = 1.490, 95% CI: 1.140-1.940). In ERAP2, the frequency of the G allele of rs2549782 was higher in the case group than in the control group (0.491 vs. 0.417, P = 0.002, OR = 1.350, 95% CI: 1.118-1.631), and the TT genotype exhibited a protective factor for TB, compared with the role of the GG/GT genotype (P = 0.001; OR = 1.650, 95% CI: 1.230-2.220). The frequency of the C allele of rs1056893 was higher in the case group than in the control group (0.468 vs. 0.394, P = 0.002, OR = 1.350, 95% CI: 1.118-1.631), and the genotype exhibited a difference in the log-additive model (P = 0.002; OR = 1.350, 95% CI: 1.120-1.630). The frequencies of the haplotype rs27037-rs27044-s30187-rs26618-rs26653-rs3734016-GCCCGC in ERAP1 (0.290 vs. 0.240, P-adj = 0.028, OR = 1.320, 95% CI: 1.063-1.638) and the haplotypes rs2549782-rs2248374-rs2287988-rs1056893-GTAGC in ERAP2 (0.446 vs. 0.348, P-adj = 4.80E-05, OR = 1.510, 95% CI: 1.246-1.829) was higher in the TB groups, while the frequencies of the haplotypes rs2549782-rs2248374-rs2287988-rs1056893-TAGAT (0.478 vs. 0.539, P-adj = 0.020, OR = 0.782, 95% CI: 0.649-0.943) were lower in the TB groups. The allelic and genotypic associations were also investigated in the subsequent stratification between the PTB, EPTB and control groups as well as between the ITTB, RTB, and control groups. In conclusion, variations in ERAP1 and ERAP2 genes were identified to be associated with TB in the Han Chinese population.
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Affiliation(s)
| | - Shuyuan Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Nannan Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Chuanyin Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China
| | - Hui Wang
- The Third People's Hospital of Kunming, Kunming, China
| | - Lei Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Xinwen Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China
| | - Ling Bao
- The Third People's Hospital of Kunming, Kunming, China
| | - Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China
| | - Li Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
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10
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Saulle I, Vanetti C, Goglia S, Vicentini C, Tombetti E, Garziano M, Clerici M, Biasin M. A New ERAP2/Iso3 Isoform Expression Is Triggered by Different Microbial Stimuli in Human Cells. Could It Play a Role in the Modulation of SARS-CoV-2 Infection? Cells 2020; 9:E1951. [PMID: 32847031 PMCID: PMC7563522 DOI: 10.3390/cells9091951] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022] Open
Abstract
Following influenza infection, rs2248374-G ERAP2 expressing cells may transcribe an alternative spliced isoform: ERAP2/Iso3. This variant, unlike ERAP2-wt, is unable to trim peptides to be loaded on MHC class I molecules, but it can still dimerize with both ERAP2-wt and ERAP1-wt, thus contributing to profiling an alternative cellular immune-peptidome. In order to verify if the expression of ERAP2/Iso3 may be induced by other pathogens, PBMCs and MDMs isolated from 20 healthy subjects were stimulated with flu, LPS, CMV, HIV-AT-2, SARS-CoV-2 antigens to analyze its mRNA and protein expression. In parallel, Calu3 cell lines and PBMCs were in vitro infected with growing doses of SARS-CoV-2 (0.5, 5, 1000 MOI) and HIV-1BAL (0.1, 1, and 10 ng p24 HIV-1Bal/1 × 106 PBMCs) viruses, respectively. Results showed that: (1) ERAP2/Iso3 mRNA expression can be prompted by many pathogens and it is coupled with the modulation of several determinants (cytokines, interferon-stimulated genes, activation/inhibition markers, antigen-presentation elements) orchestrating the anti-microbial immune response (Quantigene); (2) ERAP2/Iso3 mRNA is translated into a protein (western blot); (3) ERAP2/Iso3 mRNA expression is sensitive to SARS-CoV-2 and HIV-1 concentration. Considering the key role played by ERAPs in antigen processing and presentation, it is conceivable that these enzymes may be potential targets and modulators of the pathogenicity of infectious diseases and further analyses are needed to define the role played by the different isoforms.
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Affiliation(s)
- Irma Saulle
- Department of Biomedical and Clinical Sciences-L. Sacco, University of Milan, 20157 Milan, Italy; (I.S.); (C.V.); (S.G.); (C.V.); (E.T.); (M.G.)
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy;
| | - Claudia Vanetti
- Department of Biomedical and Clinical Sciences-L. Sacco, University of Milan, 20157 Milan, Italy; (I.S.); (C.V.); (S.G.); (C.V.); (E.T.); (M.G.)
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy;
| | - Sara Goglia
- Department of Biomedical and Clinical Sciences-L. Sacco, University of Milan, 20157 Milan, Italy; (I.S.); (C.V.); (S.G.); (C.V.); (E.T.); (M.G.)
| | - Chiara Vicentini
- Department of Biomedical and Clinical Sciences-L. Sacco, University of Milan, 20157 Milan, Italy; (I.S.); (C.V.); (S.G.); (C.V.); (E.T.); (M.G.)
| | - Enrico Tombetti
- Department of Biomedical and Clinical Sciences-L. Sacco, University of Milan, 20157 Milan, Italy; (I.S.); (C.V.); (S.G.); (C.V.); (E.T.); (M.G.)
| | - Micaela Garziano
- Department of Biomedical and Clinical Sciences-L. Sacco, University of Milan, 20157 Milan, Italy; (I.S.); (C.V.); (S.G.); (C.V.); (E.T.); (M.G.)
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy;
- Don C. Gnocchi Foundation ONLUS, IRCCS, 20148 Milan, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences-L. Sacco, University of Milan, 20157 Milan, Italy; (I.S.); (C.V.); (S.G.); (C.V.); (E.T.); (M.G.)
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11
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Li C, Li Y, Yan Z, Dai S, Liu S, Wang X, Wang J, Zhang X, Shi L, Yao Y. Polymorphisms in endoplasmic reticulum aminopeptidase genes are associated with cervical cancer risk in a Chinese Han population. BMC Cancer 2020; 20:341. [PMID: 32321463 PMCID: PMC7178719 DOI: 10.1186/s12885-020-06832-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/06/2020] [Indexed: 12/23/2022] Open
Abstract
Background Antigen-processing machinery molecules play crucial roles in infectious diseases and cancers. Studies have shown that polymorphisms in endoplasmic reticulum aminopeptidase (ERAP) genes can influence the enzymatic activity of ERAP proteins and are associated with the risk of diseases. In the current study, we evaluated the influence of ERAP gene (ERAP1 and ERAP2) polymorphisms on susceptibility to cervical intraepithelial neoplasia (CIN) and cervical cancer. Methods Six single nucleotide polymorphisms (SNPs) in ERAP1 and 5 SNPs in ERAP2 were selected and genotyped in 556 CIN patients, 1072 cervical cancer patients, and 1262 healthy control individuals. Candidate SNPs were genotyped using SNaPshot assay. And the association of these SNPs with CIN and cervical cancer was analysed. Results The results showed that allelic and genotypic frequencies of rs26653 in ERAP1 were significantly different between cervical cancer and control groups (P = 0.001 and 0.004). The allelic frequencies of rs27044 in ERAP1 and rs2287988 in ERAP2 were significantly different between control and cervical cancer groups (P = 0.003 and 0.004). Inheritance model analysis showed that genotypes of rs27044, rs26618, rs26653 and rs2287988 SNPs may be associated with the risk of cervical cancer (P = 0.003, 0.004, 0.001 and 0.002). Additionally, haplotype analysis results showed that the ERAP1 haplotype, rs27044C-rs30187T-rs26618T-rs26653G-rs3734016C, was associated with a lower risk of cervical cancer (P = 0.001). The ERAP2 haplotypes rs2549782G- rs2548538A-rs2248374A-rs2287988G-rs1056893T (P = 0.009 and 0.006) and rs2549782T-rs2548538T-rs2248374G-rs2287988A-rs1056893T (P = 0.003 and 0.009) might be associated with cervical cancer and the development from CIN to cervical cancer. Conclusion Our results indicated that rs27044, rs26618 and rs26653 in ERAP1 and rs2287988 in ERAP2 influenced susceptibility to cervical cancer.
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Affiliation(s)
- Chuanyin Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, China
| | - Yaheng Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, China
| | - Zhiling Yan
- Department of Gynaecologic Oncology, The 3rd Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Shuying Dai
- School of Basic Medical Science, Kunming Medical University, Kunming, 650500, China
| | - Shuyuan Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, China
| | - Xia Wang
- Department of Gynaecologic Oncology, The 3rd Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Jun Wang
- Department of Gynaecologic Oncology, The 3rd Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Xinwen Zhang
- 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.
| | - Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, China.
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12
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Saulle I, Vicentini C, Clerici M, Biasin M. An Overview on ERAP Roles in Infectious Diseases. Cells 2020; 9:E720. [PMID: 32183384 PMCID: PMC7140696 DOI: 10.3390/cells9030720] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/12/2022] Open
Abstract
Endoplasmic reticulum (ER) aminopeptidases ERAP1 and ERAP2 (ERAPs) are crucial enzymes shaping the major histocompatibility complex I (MHC I) immunopeptidome. In the ER, these enzymes cooperate in trimming the N-terminal residues from precursors peptides, so as to generate optimal-length antigens to fit into the MHC class I groove. Alteration or loss of ERAPs function significantly modify the repertoire of antigens presented by MHC I molecules, severely affecting the activation of both NK and CD8+ T cells. It is, therefore, conceivable that variations affecting the presentation of pathogen-derived antigens might result in an inadequate immune response and onset of disease. After the first evidence showing that ERAP1-deficient mice are not able to control Toxoplasma gondii infection, a number of studies have demonstrated that ERAPs are control factors for several infectious organisms. In this review we describe how susceptibility, development, and progression of some infectious diseases may be affected by different ERAPs variants, whose mechanism of action could be exploited for the setting of specific therapeutic approaches.
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Affiliation(s)
- Irma Saulle
- Cattedra di Immunologia, Dipartimento di Scienze Biomediche e Cliniche L. Sacco”, Università degli Studi di Milano, 20157 Milan, Italy; (C.V.); (M.B.)
- Cattedra di Immunologia, Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti Università degli Studi di Milano, 20122 Milan, Italy;
| | - Chiara Vicentini
- Cattedra di Immunologia, Dipartimento di Scienze Biomediche e Cliniche L. Sacco”, Università degli Studi di Milano, 20157 Milan, Italy; (C.V.); (M.B.)
| | - Mario Clerici
- Cattedra di Immunologia, Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti Università degli Studi di Milano, 20122 Milan, Italy;
- IRCCS Fondazione Don Carlo Gnocchi, 20157 Milan, Italy
| | - Mara Biasin
- Cattedra di Immunologia, Dipartimento di Scienze Biomediche e Cliniche L. Sacco”, Università degli Studi di Milano, 20157 Milan, Italy; (C.V.); (M.B.)
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13
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Fenizia C, Saulle I, Clerici M, Biasin M. Genetic and epigenetic regulation of natural resistance to HIV-1 infection: new approaches to unveil the HESN secret. Expert Rev Clin Immunol 2020; 16:429-445. [PMID: 32085689 DOI: 10.1080/1744666x.2020.1732820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Introduction: Since the identification of HIV, several studies reported the unusual case of small groups of subjects showing natural resistance to HIV infection. These subjects are referred to as HIV-1-exposed seronegative (HESN) individuals and include people located in different areas, with diverse ethnic backgrounds and routes of exposure. The mechanism/s responsible for protection from infection in HESN individuals are basically indefinite and most likely are multifactorial.Areas covered: Host factors, including genetic background as well as natural and acquired immunity, have all been associated with this phenomenon. Recently, epigenetic factors have been investigated as possible determinants of reduced susceptibility to HIV infection. With the advent of the OMICS era, the availability of techniques such as GWAS, RNAseq, and exome-sequencing in both bulk cell populations and single cells will likely lead to great strides in the understanding of the HESN mystery.Expert opinion: The employment of increasingly sophisticated techniques is allowing the gathering of enormous amounts of data. The integration of such information will provide important hints that could lead to the identification of viral and host correlates of protection against HIV infection, allowing the development of more effective preventative and therapeutic regimens.
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Affiliation(s)
- Claudio Fenizia
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy
| | - Irma Saulle
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy.,Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy
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14
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Mechanism for antigenic peptide selection by endoplasmic reticulum aminopeptidase 1. Proc Natl Acad Sci U S A 2019; 116:26709-26716. [PMID: 31843903 DOI: 10.1073/pnas.1912070116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that optimizes the peptide cargo of major histocompatibility class I (MHC-I) molecules and regulates adaptive immunity. It has unusual substrate selectivity for length and sequence, resulting in poorly understood effects on the cellular immunopeptidome. To understand substrate selection by ERAP1, we solved 2 crystal structures of the enzyme with bound transition-state pseudopeptide analogs at 1.68 Å and 1.72 Å. Both peptides have their N terminus bound at the active site and extend away along a large internal cavity, interacting with shallow pockets that can influence selectivity. The longer peptide is disordered through the central region of the cavity and has its C terminus bound in an allosteric pocket of domain IV that features a carboxypeptidase-like structural motif. These structures, along with enzymatic and computational analyses, explain how ERAP1 can select peptides based on length while retaining the broad sequence-specificity necessary for its biological function.
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15
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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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16
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D’Alicandro V, Romania P, Melaiu O, Fruci D. Role of genetic variations on MHC class I antigen-processing genes in human cancer and viral-mediated diseases. Mol Immunol 2019; 113:11-15. [DOI: 10.1016/j.molimm.2018.03.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/11/2018] [Accepted: 03/29/2018] [Indexed: 01/09/2023]
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17
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Saulle I, Ibba SV, Torretta E, Vittori C, Fenizia C, Piancone F, Minisci D, Lori EM, Trabattoni D, Gelfi C, Clerici M, Biasin M. Endoplasmic Reticulum Associated Aminopeptidase 2 (ERAP2) Is Released in the Secretome of Activated MDMs and Reduces in vitro HIV-1 Infection. Front Immunol 2019; 10:1648. [PMID: 31379846 PMCID: PMC6646713 DOI: 10.3389/fimmu.2019.01648] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/02/2019] [Indexed: 12/29/2022] Open
Abstract
Background: Haplotype-specific alternative splicing of the endoplasmic reticulum (ER) aminopeptidase type 2 (ERAP2) gene results in either full-length (FL, haplotype A) or alternatively spliced (AS, haplotype B) mRNA. HapA/HapA homozygous (HomoA) subjects show a reduced susceptibility to HIV-1 infection, probably secondary to the modulation of the antigen processing/presenting machinery. ERAP1 was recently shown to be secreted from the plasma membrane in response to activation; we investigated whether ERAP2 can be released as well and if the secreted form of this enzyme retains its antiviral function. Methods: Human monocyte derived macrophages (MDMs) were differentiated from peripheral blood mononuclear cells (PBMCs) isolated from 6 HomoA healthy controls and stimulated with IFNγ and LPS. ERAP2-FL secretion was evaluated by mass spectrometry. PBMCs (14 HomoA and 16 HomoB) and CD8-depleted PBMCs (CD8−PBMCs) (4 HomoA and 4 HomoB) were in vitro HIV-infected in the absence/presence of recombinant human ERAP2-FL (rhERAP2) protein; p24 viral antigen quantification was used to assess viral replication. IFNγ and CD69 mRNA expression, as well as the percentage of perforin-producing CD8+ T Lymphocytes, were analyzed 3 and 7-days post in vitro HIV-1-infection, respectively. The effect of rhERAP2 addition in cell cultures on T cell apoptosis, proliferation, activation, and maturation was evaluated as well on 24 h-stimulated PBMCs. Results: ERAP2 can be secreted from human MDMs in response to IFNγ/LPS stimulation. Notably, the addition of rhERAP2 to PBMC and CD8−PBMC cultures resulted in the reduction of viral replication, though these differences were statistically significant only in PBMCs (p < 0.05 in both HomoA and HomoB). This protective effect was associated with an increase in IFNγ and CD69 mRNA expression and in the percentage of perforin-expressing CD107+CD8+ cells. RhERAP2 addition also resulted in an increase in CD8+ activated lymphocyte (CD25+HLA−DRII+) and Effector Memory/Terminally differentiated CD8+ T cells ratio. Conclusions: This is the first report providing evidence for the release of ERAP2 in the secretome of immunocompetent cells. Data herein also indicate that exogenous ERAP2-FL exerts its protective function against HIV-1 infection, even in HomoB subjects who do not genetically produce it. Presumably, this defensive extracellular feature is only partially dependent on immune system modulation.
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Affiliation(s)
- Irma Saulle
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Salomè Valentina Ibba
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Enrica Torretta
- Department of Biomedical Science for Health, University of Milan, Milan, Italy
| | - Cecilia Vittori
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Claudio Fenizia
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | | | - Davide Minisci
- Department of Infectious Disease, ASST Fatebenefratelli Sacco, Milan, Italy
| | - Elisa Maria Lori
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Daria Trabattoni
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Cecilia Gelfi
- Department of Biomedical Science for Health, University of Milan, Milan, Italy.,I.R.C.C.S Orthopaedic Institute Galeazzi, Milan, Italy
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Don C. Gnocchi Foundation IRCCS, Milan, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
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18
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ERAP1 allotypes shape the epitope repertoire of virus-specific CD8 + T cell responses in acute hepatitis C virus infection. J Hepatol 2019; 70:1072-1081. [PMID: 30769005 PMCID: PMC6527866 DOI: 10.1016/j.jhep.2019.01.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Endoplasmic reticulum aminopeptidase 1 (ERAP1) polymorphisms are linked with human leukocyte antigen (HLA) class I-associated autoinflammatory disorders, including ankylosing spondylitis and Behçet's disease. Disease-associated ERAP1 allotypes exhibit distinct functional properties, but it remains unclear how differential peptide trimming in vivo affects the repertoire of epitopes presented to CD8+ T cells. The aim of this study was to determine the impact of ERAP1 allotypes on the virus-specific CD8+ T cell epitope repertoire in an HLA-B*27:05+ individual with acute hepatitis C virus (HCV) infection. METHODS We performed genetic and functional analyses of ERAP1 allotypes and characterized the HCV-specific CD8+ T cell repertoire at the level of fine epitope specificity and HLA class I restriction, in a patient who had acquired an HCV genotype 1a infection through a needle-stick injury. RESULTS Two hypoactive allotypic variants of ERAP1 were identified in an individual with acute HCV infection. The associated repertoire of virus-derived epitopes recognized by CD8+ T cells was uncommon in a couple of respects. Firstly, reactivity was directed away from classically immunodominant epitopes, preferentially targeting either novel or subdominant epitopes. Secondly, reactivity was biased towards longer epitopes (10-11-mers). Despite the patient exhibiting favorable prognostic indicators, these atypical immune responses failed to clear the virus and the patient developed persistent low-level infection with HCV. CONCLUSIONS ERAP1 allotypes modify the virus-specific CD8+ T cell epitope repertoire in vivo, leading to altered immunodominance patterns that may contribute to the failure of antiviral immunity after infection with HCV. LAY SUMMARY Endoplasmic reticulum aminopeptidase 1 (ERAP1) plays a key role in antigen presentation. Genetic variants of ERAP1 (leading to distinct allotypes) are linked with specific autoinflammatory disorders, such as ankylosing spondylitis and Behçet's disease. We found that ERAP1 allotypes modified the repertoire of virus-specific CD8+ T cell epitopes in a patient with hepatitis C virus, leading to an altered pattern of immunodominance that may have contributed to the failure of antiviral immunity in this patient.
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19
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ERAP1 shapes just part of the immunopeptidome. Hum Immunol 2019; 80:296-301. [DOI: 10.1016/j.humimm.2019.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/04/2019] [Accepted: 03/04/2019] [Indexed: 01/22/2023]
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20
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Kuśnierczyk P, Stratikos E. Endoplasmic reticulum aminopeptidases as a double-faced tool to increase or decrease efficiency of antigen presentation in health and disease. Hum Immunol 2019; 80:277-280. [PMID: 30928619 DOI: 10.1016/j.humimm.2019.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Piotr Kuśnierczyk
- Laboratory of Immunogenetics and Tissue Immunology, The Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.
| | - Efstratios Stratikos
- National Centre for Scientific Research Demokritos, Agia Paraskevi, Athens, Greece
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21
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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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22
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Ye CJ, Chen J, Villani AC, Gate RE, Subramaniam M, Bhangale T, Lee MN, Raj T, Raychowdhury R, Li W, Rogel N, Simmons S, Imboywa SH, Chipendo PI, McCabe C, Lee MH, Frohlich IY, Stranger BE, De Jager PL, Regev A, Behrens T, Hacohen N. Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection. Genome Res 2018; 28:1812-1825. [PMID: 30446528 PMCID: PMC6280757 DOI: 10.1101/gr.240390.118] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/09/2018] [Indexed: 02/02/2023]
Abstract
While genetic variants are known to be associated with overall gene abundance in stimulated immune cells, less is known about their effects on alternative isoform usage. By analyzing RNA-seq profiles of monocyte-derived dendritic cells from 243 individuals, we uncovered thousands of unannotated isoforms synthesized in response to influenza infection and type 1 interferon stimulation. We identified more than a thousand quantitative trait loci (QTLs) associated with alternate isoform usage (isoQTLs), many of which are independent of expression QTLs (eQTLs) for the same gene. Compared with eQTLs, isoQTLs are enriched for splice sites and untranslated regions, but depleted of sequences upstream of annotated transcription start sites. Both eQTLs and isoQTLs explain a significant proportion of the disease heritability attributed to common genetic variants. At the ERAP2 locus, we shed light on the function of the gene and how two frequent, highly differentiated haplotypes with intermediate frequencies could be maintained by balancing selection. At baseline and following type 1 interferon stimulation, the major haplotype is associated with low ERAP2 expression caused by nonsense-mediated decay, while the minor haplotype, known to increase Crohn's disease risk, is associated with high ERAP2 expression. In response to influenza infection, we found two uncharacterized isoforms expressed from the major haplotype, likely the result of multiple perfectly linked variants affecting the transcription and splicing at the locus. Thus, genetic variants at a single locus could modulate independent gene regulatory processes in innate immune responses and, in the case of ERAP2, may confer a historical fitness advantage in response to virus.
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Affiliation(s)
- Chun Jimmie Ye
- Institute for Human Genetics, Institute for Health and Computational Sciences, Department of Biostatistics and Epidemiology, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA
| | - Jenny Chen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts 02114, USA
| | - Rachel E Gate
- Institute for Human Genetics, Institute for Health and Computational Sciences, Department of Biostatistics and Epidemiology, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA.,Biomedical Informatics Program, University of California, San Francisco, California 94143, USA
| | - Meena Subramaniam
- Institute for Human Genetics, Institute for Health and Computational Sciences, Department of Biostatistics and Epidemiology, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA.,Biomedical Informatics Program, University of California, San Francisco, California 94143, USA
| | - Tushar Bhangale
- Genentech Incorporated, South San Francisco, California 94080, USA
| | - Mark N Lee
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts 02114, USA.,Harvard Medical School, Boston, Massachusetts 02116, USA
| | - Towfique Raj
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02116, USA.,Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | | | - Weibo Li
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Noga Rogel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Sean Simmons
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | | | - Cristin McCabe
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Michelle H Lee
- Harvard Medical School, Boston, Massachusetts 02116, USA
| | | | - Barbara E Stranger
- Section of Genetic Medicine, Department of Medicine, Institute for Genomics and Systems Biology, Center for Data Intensive Science, The University of Chicago, Chicago, Illinois 60637, USA
| | - Philip L De Jager
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02116, USA.,Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Tim Behrens
- Genentech Incorporated, South San Francisco, California 94080, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts 02114, USA
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23
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Bitarello BD, de Filippo C, Teixeira JC, Schmidt JM, Kleinert P, Meyer D, Andrés AM. Signatures of Long-Term Balancing Selection in Human Genomes. Genome Biol Evol 2018; 10:939-955. [PMID: 29608730 PMCID: PMC5952967 DOI: 10.1093/gbe/evy054] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2018] [Indexed: 12/15/2022] Open
Abstract
Balancing selection maintains advantageous diversity in populations through various mechanisms. Although extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here, we describe the Non-central Deviation (NCD), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test. NCD can be applied to a single locus or genomic data, and can be implemented considering only polymorphisms (NCD1) or also considering fixed differences with respect to an outgroup (NCD2) species. Incorporating fixed differences improves power, and NCD2 has higher power to detect LTBS in humans under different frequencies of the balanced allele(s) than other available methods. Applied to genome-wide data from African and European human populations, in both cases using chimpanzee as an outgroup, NCD2 shows that, albeit not prevalent, LTBS affects a sizable portion of the genome: ∼0.6% of analyzed genomic windows and 0.8% of analyzed positions. Significant windows (P < 0.0001) contain 1.6% of SNPs in the genome, which disproportionally fall within exons and change protein sequence, but are not enriched in putatively regulatory sites. These windows overlap ∼8% of the protein-coding genes, and these have larger number of transcripts than expected by chance even after controlling for gene length. Our catalog includes known targets of LTBS but a majority of them (90%) are novel. As expected, immune-related genes are among those with the strongest signatures, although most candidates are involved in other biological functions, suggesting that LTBS potentially influences diverse human phenotypes.
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Affiliation(s)
- Bárbara D Bitarello
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - João C Teixeira
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, France
| | - Joshua M Schmidt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philip Kleinert
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
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24
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Paladini F, Fiorillo MT, Vitulano C, Tedeschi V, Piga M, Cauli A, Mathieu A, Sorrentino R. An allelic variant in the intergenic region between ERAP1 and ERAP2 correlates with an inverse expression of the two genes. Sci Rep 2018; 8:10398. [PMID: 29991817 PMCID: PMC6039459 DOI: 10.1038/s41598-018-28799-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/19/2018] [Indexed: 01/12/2023] Open
Abstract
The Endoplasmatic Reticulum Aminopeptidases ERAP1 and ERAP2 are implicated in a variety of immune and non-immune functions. Most studies however have focused on their role in shaping the HLA class I peptidome by trimming peptides to the optimal size. Genome Wide Association Studies highlighted non-synonymous polymorphisms in their coding regions as associated with several immune mediated diseases. The two genes lie contiguous and oppositely oriented on the 5q15 chromosomal region. Very little is known about the transcriptional regulation and the quantitative variations of these enzymes. Here, we correlated the level of transcripts and proteins of the two aminopeptidases in B-lymphoblastoid cell lines from 44 donors harbouring allelic variants in the intergenic region between ERAP1 and ERAP2. We found that the presence of a G instead of an A at SNP rs75862629 in the ERAP2 gene promoter strongly influences the expression of the two ERAPs with a down-modulation of ERAP2 coupled with a significant higher expression of ERAP1. We therefore show here for the first time a coordinated quantitative regulation of the two ERAP genes, which can be relevant for the setting of specific therapeutic approaches.
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Affiliation(s)
- Fabiana Paladini
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University, Rome, Italy.
| | - Maria Teresa Fiorillo
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University, Rome, Italy
| | - Carolina Vitulano
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University, Rome, Italy
| | - Valentina Tedeschi
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University, Rome, Italy
| | - Matteo Piga
- Rheumatology Unit, University Clinic and AOU of Cagliari, Cagliari, Italy
| | - Alberto Cauli
- Rheumatology Unit, University Clinic and AOU of Cagliari, Cagliari, Italy
| | - Alessandro Mathieu
- Rheumatology Unit, University Clinic and AOU of Cagliari, Cagliari, Italy
| | - Rosa Sorrentino
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University, Rome, Italy.
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25
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Mpakali A, Maben Z, Stern LJ, Stratikos E. Molecular pathways for antigenic peptide generation by ER aminopeptidase 1. Mol Immunol 2018; 113:50-57. [PMID: 29678301 DOI: 10.1016/j.molimm.2018.03.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/11/2018] [Accepted: 03/29/2018] [Indexed: 10/17/2022]
Abstract
Endoplasmic Reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that can generate or destroy potential peptide ligands for MHC class I molecules. ERAP1 activity influences the cell-surface immunopeptidome and epitope immunodominance patterns but in complex and poorly understood manners. Two main distinct pathways have been proposed to account for ERAP1's effects on the nature and quantity of MHCI-bound peptides: i) ERAP1 trims peptides in solution, generating the correct length for binding to MHCI or overtrimming peptides so that they are too short to bind, and ii) ERAP1 trims peptides while they are partially bound onto MHCI in manner that leaves the peptide amino terminus accessible. For both pathways, once an appropriate length peptide is generated it could bind conventionally to MHCI, competing with further trimming by ERAP1. The two pathways, although not necessarily mutually exclusive, provide distinct vantage points for understanding of the rules behind the generation of the immunopeptidome. Resolution of the mechanistic details of ERAP1-mediated antigenic peptide generation can have important consequences for pharmacological efforts to regulate the immunopeptidome for therapeutic applications, and for understanding association of ERAP1 alleles with susceptibility to autoimmune disease and cancer. We review current evidence in support of these two pathways and discuss their relative importance and potential complementarity.
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Affiliation(s)
| | - Zachary Maben
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.
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26
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Genetic and immune determinants of immune activation in HIV-exposed seronegative individuals and their role in protection against HIV infection. INFECTION GENETICS AND EVOLUTION 2017; 66:325-334. [PMID: 29258786 DOI: 10.1016/j.meegid.2017.12.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 12/13/2022]
Abstract
Soon thereafter infection is established, hosts strive for an efficient eradication of microorganisms, with as limited tissue damage as possible, and durable immunological protection against re-infection. On the other hand, pathogens have developed countermeasures to escape host surveillance and to warrant diffusion to other hosts. In this molecular arms race the final results relies on multiple variables, including the genetic and immunologic e correlates of protection available for the host. In the field of HIV-infection, natural protection has been repeatedly associated to the presence of an immune activation state, at least in some cohorts of HESN (HIV-exposed seronegative). Indeed, these subjects, who naturally resist HIV-infection despite repeated exposure to the virus, are characterized by an increased expression of activation markers on circulating cells and greater production of immunological effector molecules both in basal condition and upon specific-stimulation. Although these results are not univocally shared, several publications emphasize the existence of a correlation between polymorphisms in genes associated with increased immune activation and the HESN phenotype. In this review, we will describe some of the genetic variants associated with protection against HIV infection. Understanding the basis of HIV resistance in HESN is mandatory to develop new preventative and therapeutic interventions.
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27
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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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28
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Vitulano C, Tedeschi V, Paladini F, Sorrentino R, Fiorillo MT. The interplay between HLA-B27 and ERAP1/ERAP2 aminopeptidases: from anti-viral protection to spondyloarthritis. Clin Exp Immunol 2017; 190:281-290. [PMID: 28759104 DOI: 10.1111/cei.13020] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2017] [Indexed: 01/06/2023] Open
Abstract
The human leukocyte antigen class I gene HLA-B27 is the strongest risk factor for ankylosing spondylitis (AS), a chronic inflammatory arthritic disorder. More recently, the Endoplasmic Reticulum Aminopeptidase (ERAP) 1 and 2 genes have been identified by genome wide association studies (GWAS) as additional susceptibility factors. In the ER, these aminopeptidases trim the peptides to a length suitable to fit into the groove of the major histocompatibility complex (MHC) class I molecules. It is noteworthy that an epistatic interaction between HLA-B27 and ERAP1, but not between HLA-B27 and ERAP2, has been highlighted. However, these observations suggest a paramount centrality for the HLA-B27 peptide repertoire that determines the natural B27 immunological function, i.e. the T cell antigen presentation and, as a by-product, elicits HLA-B27 aberrant behaviours: (i) the misfolding leading to ER stress responses and autophagy and (ii) the surface expression of homodimers acting as ligands for innate immune receptors. In this context, it has been observed that the HLA-B27 carriers, besides being prone to autoimmunity, display a far better surveillance to some viral infections. This review focuses on the ambivalent role of HLA-B27 in autoimmunity and viral protection correlating its functions to the quantitative and qualitative effects of ERAP1 and ERAP2 polymorphisms on their enzymatic activity.
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Affiliation(s)
- C Vitulano
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - V Tedeschi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - F Paladini
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - R Sorrentino
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - M T Fiorillo
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
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29
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Mpakali A, Giastas P, Deprez-Poulain R, Papakyriakou A, Koumantou D, Gealageas R, Tsoukalidou S, Vourloumis D, Mavridis IM, Stratikos E, Saridakis E. Crystal Structures of ERAP2 Complexed with Inhibitors Reveal Pharmacophore Requirements for Optimizing Inhibitor Potency. ACS Med Chem Lett 2017; 8:333-337. [PMID: 28337326 DOI: 10.1021/acsmedchemlett.6b00505] [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: 12/14/2016] [Accepted: 02/21/2017] [Indexed: 11/29/2022] Open
Abstract
Endoplasmic reticulum aminopeptidase 2 assists with the generation of antigenic peptides for presentation onto Major Histocompatibility Class I molecules in humans. Recent evidence has suggested that the activity of ERAP2 may contribute to the generation of autoimmunity, thus making ERAP2 a possible pharmacological target for the regulation of adaptive immune responses. To better understand the structural elements of inhibitors that govern their binding affinity to the ERAP2 active site, we cocrystallized ERAP2 with a medium activity 3,4-diaminobenzoic acid inhibitor and a poorly active hydroxamic acid derivative. Comparison of these two crystal structures with a previously solved structure of ERAP2 in complex with a potent phosphinic pseudopeptide inhibitor suggests that engaging the substrate N-terminus recognition properties of the active site is crucial for inhibitor binding even in the absence of a potent zinc-binding group. Proper utilization of all five major pharmacophores is necessary, however, to optimize inhibitor potency.
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Affiliation(s)
- Anastasia Mpakali
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
| | - Petros Giastas
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
| | - Rebecca Deprez-Poulain
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177−Drugs & Molecules for Living Systems, F-59000 Lille, France
| | | | - Despoina Koumantou
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
| | - Ronan Gealageas
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177−Drugs & Molecules for Living Systems, F-59000 Lille, France
| | - Sofia Tsoukalidou
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
| | - Dionisios Vourloumis
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
| | - Irene M. Mavridis
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
| | - Efstratios Stratikos
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
| | - Emmanuel Saridakis
- National Center for Scientific Research Demokritos, Agia Paraskevi, GR-15310 Athens, Greece
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30
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Cagan A, Theunert C, Laayouni H, Santpere G, Pybus M, Casals F, Prüfer K, Navarro A, Marques-Bonet T, Bertranpetit J, Andrés AM. Natural Selection in the Great Apes. Mol Biol Evol 2016; 33:3268-3283. [PMID: 27795229 PMCID: PMC5100057 DOI: 10.1093/molbev/msw215] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Natural selection is crucial for the adaptation of populations to their environments. Here, we present the first global study of natural selection in the Hominidae (humans and great apes) based on genome-wide information from population samples representing all extant species (including most subspecies). Combining several neutrality tests we create a multi-species map of signatures of natural selection covering all major types of natural selection. We find that the estimated efficiency of both purifying and positive selection varies between species and is significantly correlated with their long-term effective population size. Thus, even the modest differences in population size among the closely related Hominidae lineages have resulted in differences in their ability to remove deleterious alleles and to adapt to changing environments. Most signatures of balancing and positive selection are species-specific, with signatures of balancing selection more often being shared among species. We also identify loci with evidence of positive selection across several lineages. Notably, we detect signatures of positive selection in several genes related to brain function, anatomy, diet and immune processes. Our results contribute to a better understanding of human evolution by putting the evidence of natural selection in humans within its larger evolutionary context. The global map of natural selection in our closest living relatives is available as an interactive browser at http://tinyurl.com/nf8qmzh.
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Affiliation(s)
- Alexander Cagan
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Christoph Theunert
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA
| | - Hafid Laayouni
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Catalonia, Spain
| | - Gabriel Santpere
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
| | - Marc Pybus
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Arcadi Navarro
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Tomas Marques-Bonet
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Jaume Bertranpetit
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Department of Archaeology and Anthropology, Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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31
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Kokkala P, Mpakali A, Mauvais FX, Papakyriakou A, Daskalaki I, Petropoulou I, Kavvalou S, Papathanasopoulou M, Agrotis S, Fonsou TM, van Endert P, Stratikos E, Georgiadis D. Optimization and Structure-Activity Relationships of Phosphinic Pseudotripeptide Inhibitors of Aminopeptidases That Generate Antigenic Peptides. J Med Chem 2016; 59:9107-9123. [PMID: 27606717 DOI: 10.1021/acs.jmedchem.6b01031] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The oxytocinase subfamily of M1 aminopeptidases, consisting of ER aminopeptidase 1 (ERAP1), ER aminopeptidase 2 (ERAP2), and insulin-regulated aminopeptidase (IRAP), plays critical roles in the generation of antigenic peptides and indirectly regulates human adaptive immune responses. We have previously demonstrated that phosphinic pseudotripeptides can constitute potent inhibitors of this group of enzymes. In this study, we used synthetic methodologies able to furnish a series of stereochemically defined phosphinic pseudotripeptides and demonstrate that side chains at P1' and P2' positions are critical determinants in driving potency and selectivity. We identified low nanomolar inhibitors of ERAP2 and IRAP that display selectivity of more than 2 and 3 orders of magnitude, respectively. Cellular analysis demonstrated that one of the compounds that is a selective IRAP inhibitor can reduce IRAP-dependent but not ERAP1-dependent cross-presentation by dendritic cells with nanomolar efficacy. Our results encourage further preclinical development of phosphinic pseudotripeptides as regulators of adaptive immune responses.
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Affiliation(s)
- Paraskevi Kokkala
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens , Panepistimiopolis, Zografou, 15771, Athens, Greece
| | - Anastasia Mpakali
- National Center for Scientific Research "Demokritos" , GR 15310 Agia Paraskevi, Attikis, Greece
| | - Francois-Xavier Mauvais
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Université Paris Descartes, Sorbonne Paris Cité, Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France
| | - Athanasios Papakyriakou
- National Center for Scientific Research "Demokritos" , GR 15310 Agia Paraskevi, Attikis, Greece
| | - Ira Daskalaki
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens , Panepistimiopolis, Zografou, 15771, Athens, Greece
| | - Ioanna Petropoulou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens , Panepistimiopolis, Zografou, 15771, Athens, Greece
| | - Sofia Kavvalou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens , Panepistimiopolis, Zografou, 15771, Athens, Greece
| | - Mirto Papathanasopoulou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens , Panepistimiopolis, Zografou, 15771, Athens, Greece
| | - Stefanos Agrotis
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens , Panepistimiopolis, Zografou, 15771, Athens, Greece
| | - Theodora-Markisia Fonsou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens , Panepistimiopolis, Zografou, 15771, Athens, Greece
| | - Peter van Endert
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Université Paris Descartes, Sorbonne Paris Cité, Centre National de la Recherche Scientifique, Unité 8253, 75015 Paris, France
| | - Efstratios Stratikos
- National Center for Scientific Research "Demokritos" , GR 15310 Agia Paraskevi, Attikis, Greece
| | - Dimitris Georgiadis
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens , Panepistimiopolis, Zografou, 15771, Athens, Greece
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Polymorphisms in ERAP1 and ERAP2 are shared by Caninae and segregate within and between random- and pure-breeds of dogs. Vet Immunol Immunopathol 2016; 179:46-57. [PMID: 27590425 DOI: 10.1016/j.vetimm.2016.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 01/01/2023]
Abstract
Specific polymorphisms in the endoplasmic reticulum amino peptidase genes ERAP1 and ERAP2, when present with certain MHC class receptor types, have been associated with increased risk for specific cancers, infectious diseases and autoimmune disorders in humans. This increased risk has been linked to distinct polymorphisms in both ERAPs and MHC class I receptors that affect the way cell-generated peptides are screened for antigenicity. The incidence of cancer, infectious disease and autoimmune disorders differ greatly among pure breeds of dogs as it does in humans and it is possible that this heightened susceptibility is also due to specific polymorphisms in ERAP1 and ERAP2. In order to determine if such polymorphisms exist, the ERAP1 and ERAP2 genes of 10 dogs of nine diverse breeds were sequenced and SNPs causing synonymous or non-synonymous amino acid changes, deletions or insertions were identified. Eight ERAP1 and 10 ERAP2 SNPs were used to create a Sequenom MassARRAY iPLEX based test panel which defined 24 ERAP1, 36 ERAP2 and 128 ERAP1/2 haplotypes. The prevalence of these haplotypes was then measured among dog, wolf, coyote, jackal and red fox populations. Some haplotypes were species specific, while others were shared across species, especially between dog, wolf, coyote and jackal. The prevalence of these haplotypes was then compared among various canid populations, and in particular between various populations of random- and pure-bred dogs. Human-directed positive selection has led to loss of ERAP diversity and segregation of certain haplotypes among various dog breeds. A phylogenetic tree generated from 45 of the most common ERAP1/2 haplotypes demonstrated three distinct clades, all of which were rooted with haplotypes either shared among species or specific to contemporary dogs, coyote and wolf.
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Lucena G, Reyes-Botella C, García-Martínez O, Ramos-Torrecillas J, De Luna Bertos E, Ruiz C. Effect of NSAIDs on the aminopeptidase activity of cultured human osteoblasts. Mol Cell Endocrinol 2016; 426:146-54. [PMID: 26930569 DOI: 10.1016/j.mce.2016.02.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 12/17/2022]
Abstract
Aminopeptidases (APs) are involved in various physiological and pathological processes. In tumor tissues the expression of APs, cyclooxygenase-2 and its metabolites are increased. The objective was to determine the effect of certain NSAIDs on the AP activity of osteoblasts. Primary cultures of osteoblast were treated with different concentrations of indomethacin, meloxicam, naproxen, nimesulide, and piroxicam. The AP activity was fluorimetrically determined using aminoacyl-β-naphthylamides (aa-βNAs) as substrates: Ala-βNA, Arg-βNA, Gly-βNA, Leu-βNA, Lys-βNA, Met-βNA, and Phe-βNA. The five NSAIDs showed an inhibitory effect of AP activity against the study substrates depending on the dose tested. Meloxicam and piroxicam had the highest inhibitory effect on enzymatic activity, with an IC50 of around 70 μM. Our results suggest that the physiological alteration of osteoblasts in the presence of NSAIDs may be a consequence of AP inhibition, suggesting a potential clinical role for these drugs against cancer in combination with chemotherapeutic agents.
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Affiliation(s)
- G Lucena
- Biobanco, Sistema Sanitario Público de Andalucía, Junta de Andalucía, Granada, Spain
| | - C Reyes-Botella
- Biomedical Group (BIO277), Department of Stomatology, School of Dentistry, University of Granada. Instituto Investigación Biosanitaria, ibs.Granada, Spain
| | - O García-Martínez
- Biomedical Group (BIO277), Department of Nursing, Faculty of Health Sciences. University of Granada. Instituto Investigación Biosanitaria, ibs.Granada, Spain
| | - J Ramos-Torrecillas
- Biomedical Group (BIO277), Department of Nursing, Faculty of Health Sciences. University of Granada. Instituto Investigación Biosanitaria, ibs.Granada, Spain
| | - E De Luna Bertos
- Biomedical Group (BIO277), Department of Nursing, Faculty of Health Sciences. University of Granada. Instituto Investigación Biosanitaria, ibs.Granada, Spain
| | - C Ruiz
- Biomedical Group (BIO277), Department of Nursing, Faculty of Health Sciences. University of Granada. Instituto Investigación Biosanitaria, ibs.Granada, Spain; Institute of Neuroscience, Parque Tecnológico Ciencias de la Salud, Armilla, Granada, University of Granada, Spain.
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Mpakali A, Giastas P, Mathioudakis N, Mavridis IM, Saridakis E, Stratikos E. Structural Basis for Antigenic Peptide Recognition and Processing by Endoplasmic Reticulum (ER) Aminopeptidase 2. J Biol Chem 2015; 290:26021-32. [PMID: 26381406 DOI: 10.1074/jbc.m115.685909] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Indexed: 01/26/2023] Open
Abstract
Endoplasmic reticulum (ER) aminopeptidases process antigenic peptide precursors to generate epitopes for presentation by MHC class I molecules and help shape the antigenic peptide repertoire and cytotoxic T-cell responses. To perform this function, ER aminopeptidases have to recognize and process a vast variety of peptide sequences. To understand how these enzymes recognize substrates, we determined crystal structures of ER aminopeptidase 2 (ERAP2) in complex with a substrate analogue and a peptidic product to 2.5 and 2.7 Å, respectively, and compared them to the apo-form structure determined to 3.0 Å. The peptides were found within the internal cavity of the enzyme with no direct access to the outside solvent. The substrate analogue extends away from the catalytic center toward the distal end of the internal cavity, making interactions with several shallow pockets along the path. A similar configuration was evident for the peptidic product, although decreasing electron density toward its C terminus indicated progressive disorder. Enzymatic analysis confirmed that visualized interactions can either positively or negatively impact in vitro trimming rates. Opportunistic side-chain interactions and lack of deep specificity pockets support a limited-selectivity model for antigenic peptide processing by ERAP2. In contrast to proposed models for the homologous ERAP1, no specific recognition of the peptide C terminus by ERAP2 was evident, consistent with functional differences in length selection and self-activation between these two enzymes. Our results suggest that ERAP2 selects substrates by sequestering them in its internal cavity and allowing opportunistic interactions to determine trimming rates, thus combining substrate permissiveness with sequence bias.
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Affiliation(s)
- Anastasia Mpakali
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Petros Giastas
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Nikolas Mathioudakis
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Irene M Mavridis
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Emmanuel Saridakis
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
| | - Efstratios Stratikos
- From the National Center for Scientific Research Demokritos, Agia Paraskevi, Athens 15310, Greece
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Warren WC, Jasinska AJ, García-Pérez R, Svardal H, Tomlinson C, Rocchi M, Archidiacono N, Capozzi O, Minx P, Montague MJ, Kyung K, Hillier LW, Kremitzki M, Graves T, Chiang C, Hughes J, Tran N, Huang Y, Ramensky V, Choi OW, Jung YJ, Schmitt CA, Juretic N, Wasserscheid J, Turner TR, Wiseman RW, Tuscher JJ, Karl JA, Schmitz JE, Zahn R, O'Connor DH, Redmond E, Nisbett A, Jacquelin B, Müller-Trutwin MC, Brenchley JM, Dione M, Antonio M, Schroth GP, Kaplan JR, Jorgensen MJ, Thomas GWC, Hahn MW, Raney BJ, Aken B, Nag R, Schmitz J, Churakov G, Noll A, Stanyon R, Webb D, Thibaud-Nissen F, Nordborg M, Marques-Bonet T, Dewar K, Weinstock GM, Wilson RK, Freimer NB. The genome of the vervet (Chlorocebus aethiops sabaeus). Genome Res 2015; 25:1921-33. [PMID: 26377836 PMCID: PMC4665013 DOI: 10.1101/gr.192922.115] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/10/2015] [Indexed: 01/20/2023]
Abstract
We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), for which it is the most abundant natural host species, and of a wide range of health-related phenotypes assessed in Caribbean vervets (C. a. sabaeus), whose numbers have expanded dramatically since Europeans introduced small numbers of their ancestors from West Africa during the colonial era. We use the reference to characterize the genomic relationship between vervets and other primates, the intra-generic phylogeny of vervet subspecies, and genome-wide structural variations of a pedigreed C. a. sabaeus population. Through comparative analyses with human and rhesus macaque, we characterize at high resolution the unique chromosomal fission events that differentiate the vervets and their close relatives from most other catarrhine primates, in whom karyotype is highly conserved. We also provide a summary of transposable elements and contrast these with the rhesus macaque and human. Analysis of sequenced genomes representing each of the main vervet subspecies supports previously hypothesized relationships between these populations, which range across most of sub-Saharan Africa, while uncovering high levels of genetic diversity within each. Sequence-based analyses of major histocompatibility complex (MHC) polymorphisms reveal extremely low diversity in Caribbean C. a. sabaeus vervets, compared to vervets from putatively ancestral West African regions. In the C. a. sabaeus research population, we discover the first structural variations that are, in some cases, predicted to have a deleterious effect; future studies will determine the phenotypic impact of these variations.
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Affiliation(s)
- Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA; Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Raquel García-Pérez
- ICREA at Institut de Biologia Evolutiva, (UPF-CSIC) and Centro Nacional de Analisis Genomico (CNAG), PRBB/PCB, 08003 Barcelona, Spain
| | - Hannes Svardal
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Chad Tomlinson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Mariano Rocchi
- Department of Biology, University of Bari, Bari 70126, Italy
| | | | - Oronzo Capozzi
- Department of Biology, University of Bari, Bari 70126, Italy
| | - Patrick Minx
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Michael J Montague
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Kim Kyung
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - LaDeana W Hillier
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Milinn Kremitzki
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Tina Graves
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Colby Chiang
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | | | - Nam Tran
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Yu Huang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Vasily Ramensky
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Oi-Wa Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Yoon J Jung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Christopher A Schmitt
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Nikoleta Juretic
- Department of Human Genetics, McGill University, Montreal QC H3A 1B1, Canada
| | | | - Trudy R Turner
- Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53705, USA; Department of Genetics Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9300 South Africa
| | - Roger W Wiseman
- Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Jennifer J Tuscher
- Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Julie A Karl
- Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Jörn E Schmitz
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
| | - Roland Zahn
- Crucell Holland B.V., 2333 CN Leiden, The Netherlands
| | - David H O'Connor
- Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Eugene Redmond
- St. Kitts Biomedical Research Foundation, St. Kitts, West Indies
| | - Alex Nisbett
- St. Kitts Biomedical Research Foundation, St. Kitts, West Indies
| | - Béatrice Jacquelin
- Institut Pasteur, Unité de Régulation des Infections Rétrovirales, 75015 Paris, France
| | | | - Jason M Brenchley
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland 20892-9821, USA
| | | | | | | | - Jay R Kaplan
- Center for Comparative Medicine Research, Wake Forest School of Medicine, Winston-Salem 27157-1040, USA
| | - Matthew J Jorgensen
- Center for Comparative Medicine Research, Wake Forest School of Medicine, Winston-Salem 27157-1040, USA
| | - Gregg W C Thomas
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Brian J Raney
- University of California Santa Cruz, Santa Cruz, California 95060, USA
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Juergen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany
| | - Gennady Churakov
- Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany; Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Angela Noll
- Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany
| | - Roscoe Stanyon
- Department of Biology, University of Florence, 50122 Florence, Italy
| | - David Webb
- National Center for Biotechnology Information, Bethesda, Maryland 20894, USA
| | | | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Tomas Marques-Bonet
- ICREA at Institut de Biologia Evolutiva, (UPF-CSIC) and Centro Nacional de Analisis Genomico (CNAG), PRBB/PCB, 08003 Barcelona, Spain
| | - Ken Dewar
- Department of Human Genetics, McGill University, Montreal QC H3A 1B1, Canada
| | - George M Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06001, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA
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Kenna TJ, Robinson PC, Haroon N. Endoplasmic reticulum aminopeptidases in the pathogenesis of ankylosing spondylitis. Rheumatology (Oxford) 2015; 54:1549-56. [PMID: 26070942 DOI: 10.1093/rheumatology/kev218] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Indexed: 01/05/2023] Open
Abstract
There has been significant progress in our understanding of the pathogenesis of AS. The advent of genome-wide association studies has increased the known loci associated with AS to more than 40. The endoplasmic reticulum resident aminopeptidases (ERAP) 1 and 2 were identified in this manner and are of particular interest. There appears to be a genetic as well as a functional interaction of ERAP1 and 2 with HLA-B27 based on the known functions of these molecules. Recent studies on the structure, immunological effects and the peptide-trimming properties of ERAP 1 and 2 have helped to provide insight into their pathogenic potential in AS. In this review, we explore the role of ERAP 1 and 2 in the pathogenesis of AS.
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Affiliation(s)
- Tony J Kenna
- The University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Princess Alexandra Hospital, Brisbane
| | - Philip C Robinson
- Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Nigil Haroon
- Division of Rheumatology, University of Toronto and University Health Network, Toronto, Ontario, Canada
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Kuiper J, Rothova A, de Boer J, Radstake T. The immunopathogenesis of birdshot chorioretinopathy; a bird of many feathers. Prog Retin Eye Res 2015; 44:99-110. [DOI: 10.1016/j.preteyeres.2014.11.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/22/2014] [Accepted: 11/18/2014] [Indexed: 01/01/2023]
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Stratikos E, Stamogiannos A, Zervoudi E, Fruci D. A role for naturally occurring alleles of endoplasmic reticulum aminopeptidases in tumor immunity and cancer pre-disposition. Front Oncol 2014; 4:363. [PMID: 25566501 PMCID: PMC4271575 DOI: 10.3389/fonc.2014.00363] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 11/28/2014] [Indexed: 01/29/2023] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 and 2 (ERAP1 and ERAP2) are key components on the pathway that generates antigenic epitopes for presentation to cytotoxic T-lymphocytes (CTLs). Coding single nucleotide polymorphisms (SNPs) in these enzymes have been associated with pre-disposition to several major human diseases including inflammatory diseases with autoimmune etiology, viral infections, and virally induced cancer. The function of these enzymes has been demonstrated to affect CTL and natural killer cell responses toward healthy and malignant cells as well as the production of inflammatory cytokines. Recent studies have demonstrated that SNPs in ERAP1 and ERAP2 can affect their ability to generate or destroy antigenic epitopes and define the immunopeptidome. In this review, we examine the potential role of these enzymes and their polymorphic states on the generation of cytotoxic responses toward malignantly transformed cells. Given the current state-of-the-art, it is possible that polymorphic variation in these enzymes may contribute to the individual’s pre-disposition to cancer through altered generation or destruction of tumor antigens that can facilitate tumor immune evasion.
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Affiliation(s)
| | | | - Efthalia Zervoudi
- National Center for Scientific Research Demokritos , Athens , Greece
| | - Doriana Fruci
- Department of Paediatric Haematology/Oncology, IRCCS, Ospedale Pediatrico Bambino Gesù , Rome , Italy
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40
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Abstract
The endoplasmic reticulum aminopeptidase 1 (ERAP1) performs a major role in antigen processing, trimming N-terminally extended peptides to the final epitope for presentation by major histocompatibility complex class I molecules. Recent genome-wide association studies have identified single nucleotide polymorphisms (SNPs) within ERAP1 as being associated with disease, in particular ankylosing spondylitis (AS). AS is a polygenic chronic inflammatory disease with a strong genetic link to HLA-B27 known for over 40 years. The association of ERAP1 SNPs with AS susceptibility is only observed in HLA-B27-positive individuals, which intersect on the antigen processing pathway. Recent evidence examining the trimming activity of polymorphic ERAP1 highlights its role in generating peptides for loading onto and stabilizing HLA-B27, and the consequent alterations in the interaction of specific NK cell receptors, and the activation of the unfolded protein response as important in the mechanism of disease pathogenesis. Here, we discuss the recent genetic association findings linking ERAP1 SNPs with AS disease susceptibility and the effect of these variants on ERAP1 function, highlighting mechanisms by which AS may arise. The identification of these functional variants of ERAP1 may lead to better stratification of AS patients by providing a diagnostic tool and a potential therapeutic target.
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Affiliation(s)
- Emma Reeves
- Cancer Sciences Unit, Somers Cancer Research Building, Southampton General Hospital, Mailpoint 824, Tremona Road, Southampton, SO16 6YD, UK
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Key FM, Teixeira JC, de Filippo C, Andrés AM. Advantageous diversity maintained by balancing selection in humans. Curr Opin Genet Dev 2014; 29:45-51. [PMID: 25173959 DOI: 10.1016/j.gde.2014.08.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 07/30/2014] [Accepted: 08/02/2014] [Indexed: 11/16/2022]
Abstract
Most human polymorphisms are neutral or slightly deleterious, but some genetic variation is advantageous and maintained in populations by balancing selection. Considered a rarity and overlooked for years, balanced polymorphisms have recently received renewed attention with several lines of evidence showing their relevance in human evolution. From theoretical work on its role in adaptation to empirical studies that identify its targets, recent developments have showed that balancing selection is more prevalent than previously thought. Here we review these developments and discuss their implications in our understanding of the influence of balancing selection in human evolution. We also review existing evidence on the biological functions that benefit most from advantageous diversity, and the functional consequences of these variants. Overall, we argue that balancing selection must be considered an important selective force in human evolution.
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Affiliation(s)
- Felix M Key
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - João C Teixeira
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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42
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Stratikos E. Regulating adaptive immune responses using small molecule modulators of aminopeptidases that process antigenic peptides. Curr Opin Chem Biol 2014; 23:1-7. [PMID: 25173825 DOI: 10.1016/j.cbpa.2014.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/10/2014] [Accepted: 08/12/2014] [Indexed: 01/19/2023]
Abstract
Antigenic peptide processing by intracellular aminopeptidases has emerged recently as an important pathway that regulates adaptive immune responses. Pathogens and cancer can manipulate the activity of key enzymes of this pathway to promote immune evasion. Furthermore, the activity of these enzymes is naturally variable due to polymorphic variation, contributing to predisposition to disease, most notably autoimmunity. Here, we review recent findings that suggest that the pharmacological regulation of the activity of these aminopeptidases constitutes a valid approach for regulating human immune responses. We furthermore review the state of the art in chemical tools for inhibiting these enzymes and how these tools can be useful for the development of innovative therapeutic approaches for a variety of diseases including cancer, viral infections and autoimmunity.
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Affiliation(s)
- Efstratios Stratikos
- National Center for Scientific Research Demokritos, Agia Paraskevi, Athens, Greece.
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Evnouchidou I, Weimershaus M, Saveanu L, van Endert P. ERAP1-ERAP2 dimerization increases peptide-trimming efficiency. THE JOURNAL OF IMMUNOLOGY 2014; 193:901-8. [PMID: 24928998 DOI: 10.4049/jimmunol.1302855] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The endoplasmic reticulum aminopeptidases (ERAP)1 and ERAP2 play a critical role in the production of final epitopes presented by MHC class I molecules. Formation of heterodimers by ERAP1 and ERAP2 has been proposed to facilitate trimming of epitope precursor peptides, but the effects of dimerization on ERAP function remain unknown. In this study, we produced stabilized ERAP1-ERAP2 heterodimers and found that they produced several mature epitopes more efficiently than a mix of the two enzymes unable to dimerize. Physical interaction with ERAP2 changes basic enzymatic parameters of ERAP1 and improves its substrate-binding affinity. Thus, by bringing the two enzymes in proximity and by producing allosteric effects on ERAP1, dimerization of ERAP1/2 creates complexes with superior peptide-trimming efficacy. Such complexes are likely to enhance Ag presentation by cells displaying coordinated expression of the two enzymes.
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Affiliation(s)
- Irini Evnouchidou
- INSERM Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8253, 75015 Paris, France; and Faculté de Medicine, Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Mirjana Weimershaus
- INSERM Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8253, 75015 Paris, France; and Faculté de Medicine, Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Loredana Saveanu
- INSERM Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8253, 75015 Paris, France; and Faculté de Medicine, Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Peter van Endert
- INSERM Unité 1151, 75015 Paris, France; Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8253, 75015 Paris, France; and Faculté de Medicine, Université Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
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Tsui FW, Tsui HW, Akram A, Haroon N, Inman RD. The genetic basis of ankylosing spondylitis: new insights into disease pathogenesis. APPLICATION OF CLINICAL GENETICS 2014; 7:105-15. [PMID: 24971029 PMCID: PMC4070859 DOI: 10.2147/tacg.s37325] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ankylosing spondylitis (AS) is a complex disease involving multiple risk factors, both genetic and environmental. AS patients are predominantly young men, and the disease is characterized by inflammation and ankylosis, mainly at the cartilage–bone interface and enthesis. HLA-B27 has been known to be the major AS-susceptibility gene for more than 40 years. Despite advances made in the past few years, progress in the search for non-human leukocyte antigen susceptibility genes has been hampered by the heterogeneity of the disease. Compared to other complex diseases, such as inflammatory bowel disease (IBD), fewer susceptibility loci have been identified in AS. Furthermore, non-major histocompatibility-complex susceptibility loci discovered, such as ERAP1 and IL23R, are likely contributors to joint inflammation. Identification and confirmation of functional variants remains a significant challenge of investigations involving genome-wide association studies (GWAS). It remains unclear why none of the AS-susceptibility genes identified in GWAS appear to be directly involved in the ankylosing process. Numerous reviews have recently been published on the genetics of AS. Therefore, aside from a brief summary of what AS GWAS has successfully achieved thus far, this review will focus on directions that could address unanswered questions raised by GWAS.
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Affiliation(s)
- Florence Wl Tsui
- Genetics and Development Division, Toronto Western Research Institute, University Health Network ; Department of Immunology
| | - Hing Wo Tsui
- Genetics and Development Division, Toronto Western Research Institute, University Health Network
| | - Ali Akram
- Genetics and Development Division, Toronto Western Research Institute, University Health Network ; Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Nigil Haroon
- Genetics and Development Division, Toronto Western Research Institute, University Health Network ; Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Robert D Inman
- Genetics and Development Division, Toronto Western Research Institute, University Health Network ; Institute of Medical Science, University of Toronto, Toronto, ON, Canada
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45
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An evolutionary analysis of antigen processing and presentation across different timescales reveals pervasive selection. PLoS Genet 2014; 10:e1004189. [PMID: 24675550 PMCID: PMC3967941 DOI: 10.1371/journal.pgen.1004189] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 01/06/2014] [Indexed: 12/28/2022] Open
Abstract
The antigenic repertoire presented by MHC molecules is generated by the antigen processing and presentation (APP) pathway. We analyzed the evolutionary history of 45 genes involved in APP at the inter- and intra-species level. Results showed that 11 genes evolved adaptively in mammals. Several positively selected sites involve positions of fundamental importance to the protein function (e.g. the TAP1 peptide-binding domains, the sugar binding interface of langerin, and the CD1D trafficking signal region). In CYBB, all selected sites cluster in two loops protruding into the endosomal lumen; analysis of missense mutations responsible for chronic granulomatous disease (CGD) showed the action of different selective forces on the very same gene region, as most CGD substitutions involve aminoacid positions that are conserved in all mammals. As for ERAP2, different computational methods indicated that positive selection has driven the recurrent appearance of protein-destabilizing variants during mammalian evolution. Application of a population-genetics phylogenetics approach showed that purifying selection represented a major force acting on some APP components (e.g. immunoproteasome subunits and chaperones) and allowed identification of positive selection events in the human lineage. We also investigated the evolutionary history of APP genes in human populations by developing a new approach that uses several different tests to identify the selection target, and that integrates low-coverage whole-genome sequencing data with Sanger sequencing. This analysis revealed that 9 APP genes underwent local adaptation in human populations. Most positive selection targets are located within noncoding regions with regulatory function in myeloid cells or act as expression quantitative trait loci. Conversely, balancing selection targeted nonsynonymous variants in TAP1 and CD207 (langerin). Finally, we suggest that selected variants in PSMB10 and CD207 contribute to human phenotypes. Thus, we used evolutionary information to generate experimentally-testable hypotheses and to provide a list of sites to prioritize in follow-up analyses. Antigen-presenting cells digest intracellular and extracellular proteins and display the resulting antigenic repertoire on cell surface molecules for recognition by T cells. This process initiates cell-mediated immune responses and is essential to detect infections. The antigenic repertoire is generated by the antigen processing and presentation pathway. Because several pathogens evade immune recognition by hampering this process, genes involved in antigen processing and presentation may represent common natural selection targets. Thus, we analyzed the evolutionary history of these genes during mammalian evolution and in the more recent history of human populations. Evolutionary analyses in mammals indicated that positive selection targeted a very high proportion of genes (24%), and revealed that many selected sites affect positions of fundamental importance to the protein function. In humans, we found different signatures of natural selection acting both on regions that are expected to regulate gene expression levels or timing and on coding variants; two human selected polymorphisms may modulate the susceptibility to Crohn's disease and to HIV-1 infection. Therefore, we provide a comprehensive evolutionary analysis of antigen processing and we show that evolutionary studies can provide useful information concerning the location and nature of functional variants, ultimately helping to clarify phenotypic differences between and within species.
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46
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Rationally designed inhibitor targeting antigen-trimming aminopeptidases enhances antigen presentation and cytotoxic T-cell responses. Proc Natl Acad Sci U S A 2013; 110:19890-5. [PMID: 24248368 DOI: 10.1073/pnas.1309781110] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intracellular aminopeptidases endoplasmic reticulum aminopeptidases 1 and 2 (ERAP1 and ERAP2), and as well as insulin-regulated aminopeptidase (IRAP) process antigenic epitope precursors for loading onto MHC class I molecules and regulate the adaptive immune response. Their activity greatly affects the antigenic peptide repertoire presented to cytotoxic T lymphocytes and as a result can regulate cytotoxic cellular responses contributing to autoimmunity or immune evasion by viruses and cancer cells. Therefore, pharmacological regulation of their activity is a promising avenue for modulating the adaptive immune response with possible applications in controlling autoimmunity, in boosting immune responses to pathogens, and in cancer immunotherapy. In this study we exploited recent structural and biochemical analysis of ERAP1 and ERAP2 to design and develop phosphinic pseudopeptide transition state analogs that can inhibit this family of enzymes with nM affinity. X-ray crystallographic analysis of one such inhibitor in complex with ERAP2 validated our design, revealing a canonical mode of binding in the active site of the enzyme, and highlighted the importance of the S2' pocket for achieving inhibitor potency. Antigen processing and presentation assays in HeLa and murine colon carcinoma (CT26) cells showed that these inhibitors induce increased cell-surface antigen presentation of transfected and endogenous antigens and enhance cytotoxic T-cell responses, indicating that these enzymes primarily destroy epitopes in those systems. This class of inhibitors constitutes a promising tool for controlling the cellular adaptive immune response in humans by modulating the antigen processing and presentation pathway.
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47
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Biasin M, De Luca M, Gnudi F, Clerici M. The genetic basis of resistance to HIV infection and disease progression. Expert Rev Clin Immunol 2013; 9:319-34. [PMID: 23557268 DOI: 10.1586/eci.13.16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Susceptibility to HIV infection and the modulation of disease progression are strictly dependent on inter-individual variability, much of which is secondary to host genetic heterogeneity. The study of host factors that control these phenomena relies not only on candidate gene approaches but also on unbiased genome-wide genetic and functional analyses. Additional new insights stem from the study of mechanisms that control the expression of host and viral genes, such as miRNA. The genetic host factors that have been suggested to be associated either with resistance to HIV-1 infection or with absent/delayed progression to AIDS are nevertheless unable to fully justify the phenomenon of differential susceptibility to HIV. Multidisciplinary approaches are needed to further analyze individuals who deviate from the expected response to HIV exposure/infection. Results of these analyses will facilitate the identification of novel targets that could be exploited in the setting up of innovative therapeutic or vaccine approaches.
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Affiliation(s)
- Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, Via GB Grassi 74, 20157 Milan, Italy.
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48
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Hattori A, Tsujimoto M. Endoplasmic reticulum aminopeptidases: biochemistry, physiology and pathology. J Biochem 2013; 154:219-28. [PMID: 23946506 DOI: 10.1093/jb/mvt066] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The human endoplasmic reticulum aminopeptidase (ERAP) 1 and 2 proteins were initially identified as homologues of human placental leucine aminopeptidase/insulin-regulated aminopeptidase. They are categorized as a unique class of proteases based on their subcellular localization on the luminal side of the endoplasmic reticulum. ERAPs play an important role in the N-terminal processing of the antigenic precursors that are presented on the major histocompatibility complex (MHC) class I molecules. ERAPs are also implicated in the regulation of a wide variety of physiological phenomena and pathogenic conditions. In this review, the current knowledge on ERAPs is summarized.
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Affiliation(s)
- Akira Hattori
- Division of Bioinformatics and Chemical Genomics, Department of System Chemotherapy and Molecular Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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49
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Genetic insights into common pathways and complex relationships among immune-mediated diseases. Nat Rev Genet 2013; 14:661-73. [PMID: 23917628 DOI: 10.1038/nrg3502] [Citation(s) in RCA: 390] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Shared aetiopathogenic factors among immune-mediated diseases have long been suggested by their co-familiality and co-occurrence, and molecular support has been provided by analysis of human leukocyte antigen (HLA) haplotypes and genome-wide association studies. The interrelationships can now be better appreciated following the genotyping of large immune disease sample sets on a shared SNP array: the 'Immunochip'. Here, we systematically analyse loci shared among major immune-mediated diseases. This reveals that several diseases share multiple susceptibility loci, but there are many nuances. The most associated variant at a given locus frequently differs and, even when shared, the same allele often has opposite associations. Interestingly, risk alleles conferring the largest effect sizes are usually disease-specific. These factors help to explain why early evidence of extensive 'sharing' is not always reflected in epidemiological overlap.
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50
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McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S, Carrington M, Cossarizza A, Dalmau J, Deeks SG, Delaneau O, De Luca A, Goedert JJ, Haas D, Herbeck JT, Kathiresan S, Kirk GD, Lambotte O, Luo M, Mallal S, van Manen D, Martinez-Picado J, Meyer L, Miro JM, Mullins JI, Obel N, O'Brien SJ, Pereyra F, Plummer FA, Poli G, Qi Y, Rucart P, Sandhu MS, Shea PR, Schuitemaker H, Theodorou I, Vannberg F, Veldink J, Walker BD, Weintrob A, Winkler CA, Wolinsky S, Telenti A, Goldstein DB, de Bakker PIW, Zagury JF, Fellay J. Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls. PLoS Pathog 2013; 9:e1003515. [PMID: 23935489 PMCID: PMC3723635 DOI: 10.1371/journal.ppat.1003515] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/07/2013] [Indexed: 11/18/2022] Open
Abstract
Multiple genome-wide association studies (GWAS) have been performed in HIV-1 infected individuals, identifying common genetic influences on viral control and disease course. Similarly, common genetic correlates of acquisition of HIV-1 after exposure have been interrogated using GWAS, although in generally small samples. Under the auspices of the International Collaboration for the Genomics of HIV, we have combined the genome-wide single nucleotide polymorphism (SNP) data collected by 25 cohorts, studies, or institutions on HIV-1 infected individuals and compared them to carefully matched population-level data sets (a list of all collaborators appears in Note S1 in Text S1). After imputation using the 1,000 Genomes Project reference panel, we tested approximately 8 million common DNA variants (SNPs and indels) for association with HIV-1 acquisition in 6,334 infected patients and 7,247 population samples of European ancestry. Initial association testing identified the SNP rs4418214, the C allele of which is known to tag the HLA-B*57:01 and B*27:05 alleles, as genome-wide significant (p = 3.6×10−11). However, restricting analysis to individuals with a known date of seroconversion suggested that this association was due to the frailty bias in studies of lethal diseases. Further analyses including testing recessive genetic models, testing for bulk effects of non-genome-wide significant variants, stratifying by sexual or parenteral transmission risk and testing previously reported associations showed no evidence for genetic influence on HIV-1 acquisition (with the exception of CCR5Δ32 homozygosity). Thus, these data suggest that genetic influences on HIV acquisition are either rare or have smaller effects than can be detected by this sample size. Comparing the frequency differences between common DNA variants in disease-affected cases and in unaffected controls has been successful in uncovering the genetic component of multiple diseases. This approach is most effective when large samples of cases and controls are available. Here we combine information from multiple studies of HIV infected patients, including more than 6,300 HIV+ individuals, with data from 7,200 general population samples of European ancestry to test nearly 8 million common DNA variants for an impact on HIV acquisition. With this large sample we did not observe any single common genetic variant that significantly associated with HIV acquisition. We further tested 22 variants previously identified by smaller studies as influencing HIV acquisition. With the exception of a deletion polymorphism in the CCR5 gene (CCR5Δ32) we found no convincing evidence to support these previous associations. Taken together these data suggest that genetic influences on HIV acquisition are either rare or have smaller effects than can be detected by this sample size.
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Affiliation(s)
- Paul J. McLaren
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Cédric Coulonges
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
| | - Stephan Ripke
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Leonard van den Berg
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
| | - Andrea Cossarizza
- Department of Surgery, Medicine, Dentistry and Morphological Sciences University of Modena and Reggio Emilia School of Medicine, Modena, Italy
| | - Judith Dalmau
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Olivier Delaneau
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Andrea De Luca
- University Division of Infectious Diseases, Siena University Hospital, Siena, Italy
- Institute of Clinical infectious Diseases, Università Cattolica del Sacro Cuore, Roma, Italy
| | - James J. Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - David Haas
- Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Joshua T. Herbeck
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gregory D. Kirk
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Olivier Lambotte
- INSERM U1012, Bicêtre, France
- University Paris-Sud, Bicêtre, France
- AP-HP, Department of Internal Medicine and Infectious Diseases, Bicêtre Hospital, Bicêtre, France
| | - Ma Luo
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Simon Mallal
- Institute for Immunology & Infectious Diseases, Murdoch University and Pathwest, Perth, Australia
| | - Daniëlle van Manen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Laurence Meyer
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
- Inserm, CESP U1018, University Paris-Sud, UMRS 1018, Faculté de Médecine Paris-Sud; AP-HP, Hopital Bicêtre, Epidemiology and Public Health Service, Le Kremlin Bicêtre, France
| | - José M. Miro
- Infectious Diseases Service. Hospital Clinic – IDIBAPS, University of Barcelona, Barcelona, Spain
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Niels Obel
- Department of Infectious Diseases, The National University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Stephen J. O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Florencia Pereyra
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
- Division of Infectious Disease, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Francis A. Plummer
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Guido Poli
- Division of Immunology, Transplantation and Infectious Diseases, Vita-Salute San Raffaele University, School of Medicine & San Raffaele Scientific Institute, Milan, Italy
| | - Ying Qi
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Pierre Rucart
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
| | - Manj S. Sandhu
- Genetic Epidemiology Group, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Non-Communicable Disease Research Group, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Patrick R. Shea
- Center for Human Genome Variation, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Ioannis Theodorou
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
- INSERM UMRS 945, Paris, France
| | - Fredrik Vannberg
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Jan Veldink
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Amy Weintrob
- Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Cheryl A. Winkler
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Center for Cancer Research, NCI, SAIC-Frederick, Inc., Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Steven Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Amalio Telenti
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - David B. Goldstein
- Center for Human Genome Variation, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Paul I. W. de Bakker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Genetics Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Epidemiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jean-François Zagury
- Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- ANRS Genomic Group (French Agency for Research on AIDS and Hepatitis), Paris, France
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
- * E-mail:
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