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Sy A, McCabe L, Hudson E, Ansari AM, Pedergnana V, Lin SK, Santana S, Fiorino M, Ala A, Stone B, Smith M, Nelson M, Barclay ST, McPherson S, Ryder SD, Collier J, Barnes E, Walker AS, Pett SL, Cooke G. Utility of a buccal swab point-of-care test for the IFNL4 genotype in the era of direct acting antivirals for hepatitis C virus. PLoS One 2023; 18:e0280551. [PMID: 36689413 PMCID: PMC9870125 DOI: 10.1371/journal.pone.0280551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/03/2023] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The CC genotype of the IFNL4 gene is known to be associated with increased Hepatitis C (HCV) cure rates with interferon-based therapy and may contribute to cure with direct acting antivirals. The Genedrive® IFNL4 is a CE marked Point of Care (PoC) molecular diagnostic test, designed for in vitro diagnostic use to provide rapid, real-time detection of IFNL4 genotype status for SNP rs12979860. METHODS 120 Participants were consented to a substudy comparing IFNL4 genotyping results from a buccal swab analysed on the Genedrive® platform with results generated using the Affymetix UK Biobank array considered to be the gold standard. RESULTS Buccal swabs were taken from 120 participants for PoC IFNL4 testing and a whole blood sample for genetic sequencing. Whole blood genotyping vs. buccal swab PoC testing identified 40 (33%), 65 (54%), and 15 (13%) had CC, CT and TT IFNL4 genotype respectively. The Buccal swab PoC identified 38 (32%) CC, 64 (53%) CT and 18 (15%) TT IFNL4 genotype respectively. The sensitivity and specificity of the buccal swab test to detect CC vs non-CC was 90% (95% CI 76-97%) and 98% (95% CI 91-100%) respectively. CONCLUSIONS The buccal swab test was better at correctly identifying non-CC genotypes than CC genotypes. The high specificity of the Genedrive® assay prevents CT/TT genotypes being mistaken for CC, and could avoid patients being identified as potentially 'good responders' to interferon-based therapy.
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Affiliation(s)
- Aminata Sy
- MRC Clinical Trials Unit, University College London, London, United Kingdom
| | - Leanne McCabe
- MRC Clinical Trials Unit, University College London, London, United Kingdom
| | - Emma Hudson
- Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Azim M. Ansari
- Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | | | - Shang-Kuan Lin
- Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - S. Santana
- Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Marzia Fiorino
- Mortimer Market Centre, Central and NorthWest London NHS Foundation Trust, London, United Kingdom
- Institute for Global Health, University College London, London, United Kingdom
| | - Aftab Ala
- Clinical and Experimental Medicine, University of Surrey, Guilford, United Kingdom
| | - Ben Stone
- Infectious Diseases, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
| | - M. Smith
- Hepatology, Brighton and Sussex Medical School, Brighton, United Kingdom
| | - Mark Nelson
- HIV Medicine, Chelsea & Westminster NHS Trust, London, United Kingdom
| | | | - Stuart McPherson
- Hepatology, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, United Kingdom
| | - Stephen D. Ryder
- Hepatology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Jane Collier
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, United Kingdom
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, United Kingdom
| | - Ann Sarah Walker
- MRC Clinical Trials Unit, University College London, London, United Kingdom
| | - Sarah L. Pett
- MRC Clinical Trials Unit, University College London, London, United Kingdom
- Mortimer Market Centre, Central and NorthWest London NHS Foundation Trust, London, United Kingdom
- Institute for Global Health, University College London, London, United Kingdom
| | - Graham Cooke
- Department of Infectious Disease, Imperial College London, London, United Kingdom
- NIHR Biomedical Research Centre, Imperial College NHS Trust, London, United Kingdom
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2
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Innes H, Nischalke HD, Guha IN, Weiss KH, Irving W, Gotthardt D, Barnes E, Fischer J, Ansari MA, Rosendahl J, Lin S, Marot A, Pedergnana V, Casper M, Benselin J, Lammert F, McLauchlan J, Lutz PL, Hamill V, Mueller S, Morling JR, Semmler G, Eyer F, von Felden J, Link A, Vogel A, Marquardt JU, Sulk S, Trebicka J, Valenti L, Datz C, Reiberger T, Schafmayer C, Berg T, Deltenre P, Hampe J, Stickel F, Buch S. The rs429358 Locus in Apolipoprotein E Is Associated With Hepatocellular Carcinoma in Patients With Cirrhosis. Hepatol Commun 2022; 6:1213-1226. [PMID: 34958182 PMCID: PMC9035556 DOI: 10.1002/hep4.1886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/02/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022] Open
Abstract
The host genetic background for hepatocellular carcinoma (HCC) is incompletely understood. We aimed to determine if four germline genetic polymorphisms, rs429358 in apolipoprotein E (APOE), rs2642438 in mitochondrial amidoxime reducing component 1 (MARC1), rs2792751 in glycerol-3-phosphate acyltransferase (GPAM), and rs187429064 in transmembrane 6 superfamily member 2 (TM6SF2), previously associated with progressive alcohol-related and nonalcoholic fatty liver disease, are also associated with HCC. Four HCC case-control data sets were constructed, including two mixed etiology data sets (UK Biobank and FinnGen); one hepatitis C virus (HCV) cohort (STOP-HCV), and one alcohol-related HCC cohort (Dresden HCC). The frequency of each variant was compared between HCC cases and cirrhosis controls (i.e., patients with cirrhosis without HCC). Population controls were also considered. Odds ratios (ORs) associations were calculated using logistic regression, adjusting for age, sex, and principal components of genetic ancestry. Fixed-effect meta-analysis was used to determine the pooled effect size across all data sets. Across four case-control data sets, 2,070 HCC cases, 4,121 cirrhosis controls, and 525,779 population controls were included. The rs429358:C allele (APOE) was significantly less frequent in HCC cases versus cirrhosis controls (OR, 0.71; 95% confidence interval [CI], 0.61-0.84; P = 2.9 × 10-5 ). Rs187429064:G (TM6SF2) was significantly more common in HCC cases versus cirrhosis controls and exhibited the strongest effect size (OR, 2.03; 95% CI, 1.45-2.86; P = 3.1 × 10-6 ). In contrast, rs2792751:T (GPAM) was not associated with HCC (OR, 1.01; 95% CI, 0.90-1.13; P = 0.89), whereas rs2642438:A (MARC1) narrowly missed statistical significance (OR, 0.91; 95% CI, 0.84-1.00; P = 0.043). Conclusion: This study associates carriage of rs429358:C (APOE) with a reduced risk of HCC in patients with cirrhosis. Conversely, carriage of rs187429064:G in TM6SF2 is associated with an increased risk of HCC in patients with cirrhosis.
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Affiliation(s)
- Hamish Innes
- School of Health and Life SciencesGlasgow Caledonian UniversityGlasgowUnited Kingdom
- Population and Lifespan SciencesSchool of MedicineUniversity of NottinghamNottinghamUnited Kingdom
- Public Health ScotlandGlasgowUnited Kingdom
| | | | - Indra Neil Guha
- National Institute for Health Research (NIHR), Nottingham Biomedical Research CentreNottingham University Hospitals National Health Service Trust and the University of NottinghamNottinghamUnited Kingdom
| | - Karl Heinz Weiss
- Department of Gastroenterology and HepatologyUniversity Hospital HeidelbergHeidelbergGermany
| | - Will Irving
- National Institute for Health Research (NIHR), Nottingham Biomedical Research CentreNottingham University Hospitals National Health Service Trust and the University of NottinghamNottinghamUnited Kingdom
| | - Daniel Gotthardt
- Department of Internal Medicine IVMedical University of HeidelbergHeidelbergGermany
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen ResearchNuffield Department of Medicine and the Oxford NIHR Biomedical Research CentreOxford UniversityOxfordUnited Kingdom
| | - Janett Fischer
- Division of HepatologyDepartment of Medicine IILaboratory for Clinical and Experimental HepatologyLeipzig University Medical CenterLeipzigGermany
| | - M. Azim Ansari
- Peter Medawar Building for Pathogen ResearchNuffield Department of Medicine and the Oxford NIHR Biomedical Research CentreOxford UniversityOxfordUnited Kingdom
| | - Jonas Rosendahl
- Medical Department 1University Hospital HalleMartin‐Luther Universität Halle‐WittenbergHalleGermany
| | - Shang‐Kuan Lin
- Peter Medawar Building for Pathogen ResearchNuffield Department of Medicine and the Oxford NIHR Biomedical Research CentreOxford UniversityOxfordUnited Kingdom
| | - Astrid Marot
- Division of Gastroenterology and HepatologyCentre Hospitalier Universitaire VaudoisUniversité de LausanneLausanneSwitzerland
- Department of Gastroenterology and HepatologyCentre Hospitalier UniversitaireUCLouvain NamurUniversité Catholique de LouvainYvoirBelgium
| | | | - Markus Casper
- Department of Medicine IISaarland University Medical CenterSaarland UniversityHomburgGermany
| | - Jennifer Benselin
- National Institute for Health Research (NIHR), Nottingham Biomedical Research CentreNottingham University Hospitals National Health Service Trust and the University of NottinghamNottinghamUnited Kingdom
| | - Frank Lammert
- Department of Medicine IISaarland University Medical CenterSaarland UniversityHomburgGermany
| | - John McLauchlan
- Medical Research Council‐University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - Philip L. Lutz
- Department of Internal Medicine IUniversity HospitalUniversity of BonnBonnGermany
| | - Victoria Hamill
- School of Health and Life SciencesGlasgow Caledonian UniversityGlasgowUnited Kingdom
- Public Health ScotlandGlasgowUnited Kingdom
| | - Sebastian Mueller
- Center for Alcohol ResearchUniversity of HeidelbergHeidelbergGermany
- Medical DepartmentSalem Medical CenterHeidelbergGermany
| | - Joanne R. Morling
- Population and Lifespan SciencesSchool of MedicineUniversity of NottinghamNottinghamUnited Kingdom
- National Institute for Health Research (NIHR), Nottingham Biomedical Research CentreNottingham University Hospitals National Health Service Trust and the University of NottinghamNottinghamUnited Kingdom
| | - Georg Semmler
- Department of Internal Medicine IIIDivision of Gastroenterology and HepatologyMedical University of ViennaViennaAustria
- Department of Internal Medicine, General Hospital Oberndorf, Teaching Hospital of the Paracelsus Medical University SalzburgOberndorfAustria
| | - Florian Eyer
- Department of Clinical ToxicologyKlinikum Rechts der IsarTechnical University of MunichMunichGermany
| | - Johann von Felden
- Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Alexander Link
- Department of Gastroenterology, Hepatology, and Infectious DiseasesOtto‐von‐Guericke University HospitalMagdeburgGermany
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology, and EndocrinologyHannover Medical SchoolHannoverGermany
| | - Jens U. Marquardt
- Department of Medicine IUniversity Hospital Schleswig Holstein–Campus LübeckLübeckGermany
| | - Stefan Sulk
- Medical Department 1University Hospital DresdenTechnische Universität DresdenDresdenGermany
| | - Jonel Trebicka
- Department of Internal Medicine IGoethe UniversityFrankfurtGermany
- European Foundation for Study of Chronic Liver FailureBarcelonaSpain
| | - Luca Valenti
- Precision Medicine–Department of Transfusion Medicine and HematologyFondazione IRCCS Ca’ Granda Ospedale Maggiore PoliclinicoMilanItaly
- Department of Pathophysiology and TransplantationUniversità degli Studi di MilanoMilanItaly
| | - Christian Datz
- Department of Internal Medicine, General Hospital Oberndorf, Teaching Hospital of the Paracelsus Medical University SalzburgOberndorfAustria
| | - Thomas Reiberger
- Department of Internal Medicine IIIDivision of Gastroenterology and HepatologyMedical University of ViennaViennaAustria
| | - Clemens Schafmayer
- Department of General, Visceral, Vascular, and Transplant SurgeryRostock University Medical CenterRostockGermany
| | - Thomas Berg
- Division of HepatologyDepartment of Medicine IILaboratory for Clinical and Experimental HepatologyLeipzig University Medical CenterLeipzigGermany
| | - Pierre Deltenre
- Division of Gastroenterology and HepatologyCentre Hospitalier Universitaire VaudoisUniversité de LausanneLausanneSwitzerland
- Department of GastroenterologyHepatopancreatology, and Digestive OncologyUniversity Clinics of Brussels Hospital ErasmeBrusselsBelgium
- Department of Gastroenterology and HepatologyClinique St LucBougeBelgium
| | - Jochen Hampe
- Medical Department 1University Hospital DresdenTechnische Universität DresdenDresdenGermany
- Center for Regenerative Therapies DresdenTechnische Universität DresdenDresdenGermany
| | - Felix Stickel
- Department of Gastroenterology and HepatologyUniversity Hospital of ZurichZurichSwitzerland
| | - Stephan Buch
- Medical Department 1University Hospital DresdenTechnische Universität DresdenDresdenGermany
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3
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Innes H, Walker AJ, Benselin J, Grove JI, Pedergnana V, Azim Ansari M, Lin SK, McLauchlan J, Hutchinson SJ, Barnes E, Irving WL, Guha IN. Comprehensive Comparative Analysis of Standard Validated, Genetic, and Novel Biomarkers to Enhance Prognostic Risk-Stratification in Patients With Hepatitis C Virus Cirrhosis. Clin Transl Gastroenterol 2022; 13:e00462. [PMID: 35142723 PMCID: PMC8963831 DOI: 10.14309/ctg.0000000000000462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Risk-stratifying patients with hepatitis C virus (HCV) cirrhosis according to medium-term prognosis will inform clinical decision-making. It is unclear which biomarkers/models are optimal for this purpose. We quantified the discriminative ability of 14 diverse biomarkers for prognosis prediction over a 4-year time. METHODS We recruited 1196 patients with HCV cirrhosis from the United Kingdom for a prospective study. Genetic risk score, collagen (e.g., PROC3), comorbidity (e.g., CirCom), and validated biomarkers from routine data were measured at enrollment. Participants were linked to UK hospital admission, cancer, and mortality registries. Primary endpoints were (i) liver-related outcomes for patients with compensated cirrhosis and (ii) all-cause mortality for decompensated cirrhosis. The discriminative ability of all biomarkers was quantified individually and also by the fraction of new prognostic information provided. RESULTS At enrollment, 289 (24%) and 907 (76%) had decompensated and compensated cirrhosis, respectively. Participants were followed for 3-4 years on average, with >70% of the follow-up time occurring post-HCV cure. Seventy-five deaths in the decompensated subgroup and 98 liver-related outcomes in the compensated subgroup were reported. The discriminative ability of the albumin-bilirubin-fibrosis-4 index (C-index: 0.71-0.72) was superior to collagen biomarkers (C-index = 0.58-0.67), genetic risk scores (C-index = 0.50-0.57), and comorbidity markers (0.53-0.60). Validated biomarkers showed the greatest prognostic improvement when combined with a comorbidity or a collagen biomarker (generally >30% of new prognostic information added). DISCUSSION Inexpensive biomarkers such as the albumin-bilirubin-fibrosis-4 index predict medium-term cirrhosis prognosis moderately well and outperform collagen, genetic, and comorbidity biomarkers. Improvement of performance was greatest when a validated test was combined with comorbidity or collagen biomarker.
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Affiliation(s)
- Hamish Innes
- School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, UK
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
- Public Health Scotland, Glasgow, UK
| | - Alex J. Walker
- The DataLab, Centre for Evidence-Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK
| | - Jennifer Benselin
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Jane I. Grove
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Vincent Pedergnana
- Laboratoire MIVEGEC (UMR CNRS 5290, UR IRD 224, UM), Montpellier, France
| | - M. Azim Ansari
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the Oxford NIHR Biomedical Research Centre, Oxford University, UK
| | - Shang-Kuan Lin
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the Oxford NIHR Biomedical Research Centre, Oxford University, UK
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Sharon J. Hutchinson
- School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, UK
- Public Health Scotland, Glasgow, UK
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the Oxford NIHR Biomedical Research Centre, Oxford University, UK
| | - William L. Irving
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Indra Neil Guha
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
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4
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Smith DA, Fernandez-Antunez C, Magri A, Bowden R, Chaturvedi N, Fellay J, McLauchlan J, Foster GR, Irving WL, Simmonds P, Pedergnana V, Ramirez S, Bukh J, Barnes E, Ansari MA. Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure. Nat Commun 2021; 12:6105. [PMID: 34671027 PMCID: PMC8528821 DOI: 10.1038/s41467-021-25649-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/11/2021] [Indexed: 12/12/2022] Open
Abstract
Persistent hepatitis C virus (HCV) infection is a major cause of chronic liver disease, worldwide. With the development of direct-acting antivirals, treatment of chronically infected patients has become highly effective, although a subset of patients responds less well to therapy. Sofosbuvir is a common component of current de novo or salvage combination therapies, that targets the HCV NS5B polymerase. We use pre-treatment whole-genome sequences of HCV from 507 patients infected with HCV subtype 3a and treated with sofosbuvir containing regimens to detect viral polymorphisms associated with response to treatment. We find three common polymorphisms in non-targeted HCV NS2 and NS3 proteins are associated with reduced treatment response. These polymorphisms are enriched in post-treatment HCV sequences of patients unresponsive to treatment. They are also associated with lower reductions in viral load in the first week of therapy. Using in vitro short-term dose-response assays, these polymorphisms do not cause any reduction in sofosbuvir potency, suggesting an indirect mechanism of action in decreasing sofosbuvir efficacy. The identification of polymorphisms in NS2 and NS3 proteins associated with poor treatment outcomes emphasises the value of systematic genome-wide analyses of viruses in uncovering clinically relevant polymorphisms that impact treatment.
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Affiliation(s)
- David A Smith
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrea Magri
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Nimisha Chaturvedi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, University Hospital and University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Graham R Foster
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - William L Irving
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Peter Simmonds
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | | | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | - M Azim Ansari
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
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5
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Lin SK, De Maio N, Pedergnana V, Wu CH, Thézé J, Wilson DJ, Barnes E, Ansari MA. Using host genetics to infer the global spread and evolutionary history of HCV subtype 3a. Virus Evol 2021; 7:veab065. [PMID: 34532064 PMCID: PMC8438900 DOI: 10.1093/ve/veab065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/16/2021] [Accepted: 07/08/2021] [Indexed: 11/17/2022] Open
Abstract
Studies have shown that hepatitis C virus subtype 3a (HCV-3a) is likely to have been circulating in South Asia before its global spread. However, the time and route of this dissemination remain unclear. For the first time, we generated host and virus genome-wide data for more than 500 patients infected with HCV-3a from the UK, North America, Australia, and New Zealand. We used the host genomic data to infer the ancestry of the patients and used this information to investigate the epidemic history of HCV-3a. We observed that viruses from hosts of South Asian ancestry clustered together near the root of the tree, irrespective of the sampling country, and that they were more diverse than viruses from other host ancestries. We hypothesized that South Asian hosts are more likely to have been infected in South Asia and used the inferred host ancestries to distinguish between the location where the infection was acquired and where the sample was taken. Next, we inferred that three independent transmission events resulted in the spread of the virus from South Asia to the UK, North America, and Oceania. This initial spread happened during or soon after the end of World War II. This was subsequently followed by many independent transmissions between the UK, North America, and Oceania. Using both host and virus genomic information can be highly informative in studying the virus epidemic history, especially in the context of chronic infections where migration histories need to be accounted for.
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Affiliation(s)
| | | | - Vincent Pedergnana
- MIVEGEC, Université de Montpellier, CNRS, 911 avenue Agropolis, Montpellier 34000, France
| | - Chieh-Hsi Wu
- Building 54, Mathematical Sciences University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Julien Thézé
- Department of Zoology, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3PS, UK,Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Centre INRAE Clermont-Auvergne-Rhône-Alpes, Saint-Genès-Champanelle 63122, France
| | | | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3SY, UK
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6
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Ansari MA, Marchi E, Ramamurthy N, Aschenbrenner D, Morgan S, Hackstein CP, Lin SK, Bowden R, Sharma E, Pedergnana V, Venkateswaran S, Kugathasan S, Mo A, Gibson G, Cooke GS, McLauchlan J, Baillie JK, Teichmann S, Mentzer A, Knight J, Todd JA, Hinks T, Barnes EJ, Uhlig HH, Klenerman P. In vivo negative regulation of SARS-CoV-2 receptor, ACE2, by interferons and its genetic control. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.16559.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Angiotensin I converting enzyme 2 (ACE2) is a receptor for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and differences in its expression may affect susceptibility to infection. Methods: We performed a genome-wide expression quantitative trait loci (eQTL) analysis using hepatitis C virus-infected liver tissue from 190 individuals. Results: We discovered that polymorphism in a type III interferon gene (IFNL4), which eliminates IFN-λ4 production, is associated with a two-fold increase in ACE2 RNA expression. Conversely, among genes negatively correlated with ACE2 expression, IFN-signalling pathways were highly enriched and ACE2 was downregulated after IFN-α treatment. Negative correlation was also found in the gastrointestinal tract where inflammation driven IFN-stimulated genes were negatively correlated with ACE2 expression and in lung tissue from a murine model of SARS-CoV-1 infection suggesting conserved regulation of ACE2 across tissue and species. Conclusions: We conclude that ACE2 is likely a negatively-regulated interferon-stimulated gene (ISG) and carriage of IFNL4 gene alleles which modulates ISGs expression in viral infection may play a role in SARS-CoV-2 pathogenesis with implications for therapeutic interventions.
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7
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Valencia BM, Cvejic E, Vollmer-Conna U, Hickie IB, Wakefield D, Li H, Pedergnana V, Rodrigo C, Lloyd AR. The severity of the pathogen-induced acute sickness response is affected by polymorphisms in genes of the NLRP3 inflammasome pathway. Brain Behav Immun 2021; 93:186-193. [PMID: 33434563 PMCID: PMC7794598 DOI: 10.1016/j.bbi.2021.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/18/2020] [Accepted: 01/06/2021] [Indexed: 12/27/2022] Open
Abstract
The acute sickness response (ASR) is a stereotyped set of symptoms including fatigue, pain, and disturbed mood, which are present in most acute infections. The immunological mechanisms of the ASR are conserved, with variations in severity determined partly by the pathogen, but also by polymorphisms in host genes. The ASR was characterised in three different serologically-confirmed acute infections in Caucasians (n = 484) across four symptom domains or endophenotypes (termed 'Fatigue', 'Musculoskeletal pain', 'Mood disturbance', and 'Acute sickness'). Correlations were sought with functional single nucleotide polymorphisms in the NLRP3 inflammasone pathway and severity of the endophenotypes. Individuals with severe Fatigue, Musculoskeletal pain, or Mood endophenotypes were more likely to have prior episodes of significant fatigue (11.4 vs. 3.8%, p = 0.07), pain (14.3 vs. 1.2%, p = 0.001), or Mood disturbance (13 vs 1%, p=0.001), suggesting trait characteristics. The high functioning allele of the rs35829419 SNP in NLRP3 was more common in those with severe Fatigue (OR = 13.3, 95% CI: 1.7-104), particularly in a dominant inheritance pattern (OR = 13.4, 95% CI: 1.8-586.3). In a multivariable analysis assuming dominant inheritance, both rs35829419 and the rs4848306 SNP in Interleukin(IL)-1β, were independently associated with severe Fatigue (OR = 29.6, 95% CI: 2.6-330.9 and OR = 13, 95% CI: 2.7-61.8, respectively). The severity of fatigue in acute infection is influenced by genetic polymorphisms in NLRP3 and IL-1β.
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Affiliation(s)
- Braulio M. Valencia
- Kirby Institute, The University of New South Wales, Sydney (UNSW Sydney), Wallace Wurth Building, High St, Kensington, NSW 2052, Australia
| | - Erin Cvejic
- The University of Sydney, School of Public Health, Faculty of Medicine and Health, Edward Ford Building (A27), Fisher Rd, NSW 2006, Australia,Department of Human Behaviour, School of Psychiatry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Ute Vollmer-Conna
- Department of Human Behaviour, School of Psychiatry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Ian B. Hickie
- Brain and Mind Centre, The University of Sydney, 94 Mallett St, Camperdown, NSW 2050, Australia
| | - Denis Wakefield
- School of Medical Sciences, UNSW Sydney, Wallace Wurth Building, High St, Kensington, NSW 2052, Australia
| | - Hui Li
- Kirby Institute, The University of New South Wales, Sydney (UNSW Sydney), Wallace Wurth Building, High St, Kensington, NSW 2052, Australia
| | - Vincent Pedergnana
- Laboratoire MIVEGEC, Institut de recherche pour le développement, 39 Avenue Charles Flahault, 34090 Montpellier, France
| | - Chaturaka Rodrigo
- Kirby Institute, The University of New South Wales, Sydney (UNSW Sydney), Wallace Wurth Building, High St, Kensington, NSW 2052, Australia,School of Medical Sciences, UNSW Sydney, Wallace Wurth Building, High St, Kensington, NSW 2052, Australia
| | - Andrew R. Lloyd
- Kirby Institute, The University of New South Wales, Sydney (UNSW Sydney), Wallace Wurth Building, High St, Kensington, NSW 2052, Australia,Corresponding author at: Viral Immunology Systems Program, Kirby Institute, UNSW Sydney, 2052, Australia
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8
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Innes H, Buch S, Hutchinson S, Guha IN, Morling JR, Barnes E, Irving W, Forrest E, Pedergnana V, Goldberg D, Aspinall E, Barclay S, Hayes PC, Dillon J, Nischalke HD, Lutz P, Spengler U, Fischer J, Berg T, Brosch M, Eyer F, Datz C, Mueller S, Peccerella T, Deltenre P, Marot A, Soyka M, McQuillin A, Morgan MY, Hampe J, Stickel F. Genome-Wide Association Study for Alcohol-Related Cirrhosis Identifies Risk Loci in MARC1 and HNRNPUL1. Gastroenterology 2020; 159:1276-1289.e7. [PMID: 32561361 DOI: 10.1053/j.gastro.2020.06.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/10/2020] [Accepted: 06/05/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Little is known about genetic factors that affect development of alcohol-related cirrhosis. We performed a genome-wide association study (GWAS) of samples from the United Kingdom Biobank (UKB) to identify polymorphisms associated with risk of alcohol-related liver disease. METHODS We performed a GWAS of 35,839 participants in the UKB with high intake of alcohol against markers of hepatic fibrosis (FIB-4, APRI, and Forns index scores) and hepatocellular injury (levels of aminotransferases). Loci identified in the discovery analysis were tested for their association with alcohol-related cirrhosis in 3 separate European cohorts (phase 1 validation cohort; n=2545). Variants associated with alcohol-related cirrhosis in the validation at a false discovery rate of less than 20% were then directly genotyped in 2 additional European validation cohorts (phase 2 validation, n=2068). RESULTS In the GWAS of the discovery cohort, we identified 50 independent risk loci with genome-wide significance (P < 5 × 10-8). Nine of these loci were significantly associated with alcohol-related cirrhosis in the phase 1 validation cohort; 6 of these 9 loci were significantly associated with alcohol-related cirrhosis in phase 2 validation cohort, at a false discovery rate below 5%. The loci included variants in the mitochondrial amidoxime reducing component 1 gene (MARC1) and the heterogeneous nuclear ribonucleoprotein U like 1 gene (HNRNPUL1). After we adjusted for age, sex, body mass index, and type-2 diabetes in the phase 2 validation cohort, the minor A allele of MARC1:rs2642438 was associated with reduced risk of alcohol-related cirrhosis (adjusted odds ratio, 0.76; P=.0027); conversely, the minor C allele of HNRNPUL1:rs15052 was associated with an increased risk of alcohol-related cirrhosis (adjusted odds ratio, 1.30; P=.020). CONCLUSIONS In a GWAS of samples from the UKB, we identified and validated (in 5 European cohorts) single-nucleotide polymorphisms that affect risk of alcohol-related cirrhosis in opposite directions: the minor A allele in MARC1:rs2642438 decreases risk, whereas the minor C allele in HNRNPUL1:rs15052 increases risk.
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Affiliation(s)
- Hamish Innes
- School of Health and Life Sciences, Glasgow Caledonian University, Glasgow United Kingdom; Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom; Health Protection Scotland, Glasgow, United Kingdom.
| | - Stephan Buch
- Medical Department 1, University Hospital Dresden, Technische Universität Dresden, Germany
| | - Sharon Hutchinson
- School of Health and Life Sciences, Glasgow Caledonian University, Glasgow United Kingdom; Health Protection Scotland, Glasgow, United Kingdom
| | - Indra Neil Guha
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust and the University of Nottingham, Nottingham, United Kingdom
| | - Joanne R Morling
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom; National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust and the University of Nottingham, Nottingham, United Kingdom
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, and the Oxford National Institute for Health Research Biomedical Research Centre, Oxford University, United Kingdom
| | - Will Irving
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust and the University of Nottingham, Nottingham, United Kingdom
| | - Ewan Forrest
- Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Vincent Pedergnana
- Laboratoire Maladies Infectieuses et Vecteurs Écologie, Génétique, Évolution et Contrôl (UMR CNRS 5290, UR IRD 224, UM), Montpellier, France
| | - David Goldberg
- School of Health and Life Sciences, Glasgow Caledonian University, Glasgow United Kingdom; Health Protection Scotland, Glasgow, United Kingdom
| | - Esther Aspinall
- School of Health and Life Sciences, Glasgow Caledonian University, Glasgow United Kingdom; Health Protection Scotland, Glasgow, United Kingdom
| | | | - Peter C Hayes
- Royal Infirmary Edinburgh, Edinburgh, United Kingdom
| | - John Dillon
- School of Medicine, University of Dundee, Dundee, United Kingdom
| | | | - Philipp Lutz
- Department of Internal Medicine I, University of Bonn, Bonn, Germany
| | - Ulrich Spengler
- Department of Internal Medicine I, University of Bonn, Bonn, Germany
| | - Janett Fischer
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Thomas Berg
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Mario Brosch
- Medical Department 1, University Hospital Dresden, Technische Universität Dresden, Germany
| | - Florian Eyer
- Department of Clinical Toxicology, Klinikum Rechts der Isar, Technical University of Munich, Germany
| | - Christian Datz
- Department of Internal Medicine, Hospital Oberndorf, Teaching Hospital of the Paracelsus Private Medical University of Salzburg, Oberndorf, Austria
| | - Sebastian Mueller
- Department of Internal Medicine and Center for Alcohol Research, Salem Medical Center University Hospital Heidelberg, Heidelberg, Germany
| | - Teresa Peccerella
- Department of Internal Medicine and Center for Alcohol Research, Salem Medical Center University Hospital Heidelberg, Heidelberg, Germany
| | - Pierre Deltenre
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Switzerland
| | - Astrid Marot
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Switzerland
| | - Michael Soyka
- Psychiatric hospital, University of Munich, Munich, Germany, and Department of Psychiatry, Meiringen Hospital, Meiringen, Switzerland
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, United Kingdom
| | - Marsha Y Morgan
- Division of Medicine, University College London Institute for Liver & Digestive Health, Royal Free Campus, University College London, London, United Kingdom
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, Technische Universität Dresden, Germany
| | - Felix Stickel
- Department of Gastroenterology and Hepatology, University Hospital of Zurich, Zurich, Switzerland
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9
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Abstract
Over the last decade, genome-wide association studies led to major advances in identifying human genetic variants associated with infectious disease susceptibility. On the pathogen side, comparable methods are now applied to identify disease-modulating pathogen variants. As host and pathogen variants jointly determine disease outcomes, the most recent development has been to explore simultaneously host and pathogen genomes, through so-called genome-to-genome studies. In this review, we provide some background on the development of genome-to-genome analysis and we detail the first wave of studies in this emerging field, which focused on patients chronically infected with HIV and hepatitis C virus. We also discuss the need for novel statistical methods to better tackle the issues of population stratification and multiple testing. Finally, we speculate on future research areas where genome-to-genome analysis may prove to be particularly effective.
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Affiliation(s)
- Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. .,Precision Medicine Unit, University Hospital and University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Vincent Pedergnana
- French National Center for Scientific Research (CNRS), Laboratory MIVEGEC (CNRS, IRD, UM), Montpellier, France
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10
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Ansari MA, Aranday-Cortes E, Ip CL, da Silva Filipe A, Lau SH, Bamford C, Bonsall D, Trebes A, Piazza P, Sreenu V, Cowton VM, Hudson E, Bowden R, Patel AH, Foster GR, Irving WL, Agarwal K, Thomson EC, Simmonds P, Klenerman P, Holmes C, Barnes E, Spencer CC, McLauchlan J, Pedergnana V. Interferon lambda 4 impacts the genetic diversity of hepatitis C virus. eLife 2019; 8:42463. [PMID: 31478835 PMCID: PMC6721795 DOI: 10.7554/elife.42463] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 08/08/2019] [Indexed: 12/15/2022] Open
Abstract
Hepatitis C virus (HCV) is a highly variable pathogen that frequently establishes chronic infection. This genetic variability is affected by the adaptive immune response but the contribution of other host factors is unclear. Here, we examined the role played by interferon lambda-4 (IFN-λ4) on HCV diversity; IFN-λ4 plays a crucial role in spontaneous clearance or establishment of chronicity following acute infection. We performed viral genome-wide association studies using human and viral data from 485 patients of white ancestry infected with HCV genotype 3a. We demonstrate that combinations of host genetic variants, which determine IFN-λ4 protein production and activity, influence amino acid variation across the viral polyprotein - not restricted to specific viral proteins or HLA restricted epitopes - and modulate viral load. We also observed an association with viral di-nucleotide proportions. These results support a direct role for IFN-λ4 in exerting selective pressure across the viral genome, possibly by a novel mechanism.
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Affiliation(s)
- M Azim Ansari
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Elihu Aranday-Cortes
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Camilla Lc Ip
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Siu Hin Lau
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Connor Bamford
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - David Bonsall
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Amy Trebes
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Paolo Piazza
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Vattipally Sreenu
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Vanessa M Cowton
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | | | - Emma Hudson
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Rory Bowden
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Graham R Foster
- Blizard Institute, Queen Mary University, London, United Kingdom
| | - William L Irving
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Kosh Agarwal
- Institute of Liver Studies, King's College Hospital, London, United Kingdom
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Peter Simmonds
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Chris Holmes
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Eleanor Barnes
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Chris Ca Spencer
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Vincent Pedergnana
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom.,Laboratoire MIVEGEC (UMR CNRS 5290, IRD, UM), Montpellier, France
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11
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Pedergnana V, Irving WL, Barnes E, McLauchlan J, Spencer CCA. Impact of IFNL4 Genetic Variants on Sustained Virologic Response and Viremia in Hepatitis C Virus Genotype 3 Patients. J Interferon Cytokine Res 2019; 39:642-649. [PMID: 31260374 PMCID: PMC6767867 DOI: 10.1089/jir.2019.0013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) genotype 3 is very prevalent in Europe and Asia and is associated with worst outcomes than other genotypes. Genetic factors have been associated with HCV infection; however, no extensive genome-wide study has been performed among HCV genotype 3 patients. In this study, using a large cohort of 1,759 patients infected with HCV genotype 3, we explore the role of genetic variants on the response to interferon (IFN) and direct-acting antiviral (DAA) regimens and viremia in a combined candidate gene and genome-wide analysis. We show that genetic variants within the IFN lambda 4 (IFNL4) locus are the major factors associated with the studied traits, accordingly with observations in other HCV genotypes and with comparable effect sizes. In particular, the functional dinucleotide polymorphism rs368234815 was associated with IFN-based sustained virologic response (SVR) [odds ratio (OR) = 1.5, P = 2.3 × 10−7], viremia (beta = −0.23, P = 8.8 × 10−10), and also DAA-based SVR (OR = 1.7; P = 4.2 × 10−4). Our results provide evidence for a role of genetic variants on HCV viremia and SVR, notably DAA-based, in patients infected with HCV genotype 3.
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Affiliation(s)
- Vincent Pedergnana
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom.,Laboratoire MIVEGEC (UMR CNRS 5290, UR IRD 224, UM), Montpellier, France
| | - William L Irving
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Eleanor Barnes
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - John McLauchlan
- Centre for Virus Research, MRC-University of Glasgow, Glasgow, United Kingdom
| | - Chris C A Spencer
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
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12
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Xu M, Yao Y, Chen H, Zhang S, Cao SM, Zhang Z, Luo B, Liu Z, Li Z, Xiang T, He G, Feng QS, Chen LZ, Guo X, Jia WH, Chen MY, Zhang X, Xie SH, Peng R, Chang ET, Pedergnana V, Feng L, Bei JX, Xu RH, Zeng MS, Ye W, Adami HO, Lin X, Zhai W, Zeng YX, Liu J. Genome sequencing analysis identifies Epstein-Barr virus subtypes associated with high risk of nasopharyngeal carcinoma. Nat Genet 2019; 51:1131-1136. [PMID: 31209392 PMCID: PMC6610787 DOI: 10.1038/s41588-019-0436-5] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 05/07/2019] [Indexed: 12/13/2022]
Abstract
Epstein-Barr virus (EBV) infection is ubiquitous worldwide and is
associated with multiple cancers, including nasopharyngeal carcinoma (NPC). The
importance of EBV viral genomic variation in NPC development and its striking
epidemic in southern China has been poorly explored. Through large-scale genome
sequencing of 270 EBV isolates and two-stage association study of EBV isolates
from China, we identified two non-synonymous EBV variants within
BALF2 strongly associated with the risk of NPC (odds ratio
(OR) = 8.69, P=9.69×10−25 for SNP
162476_C; OR = 6.14, P=2.40×10−32 for
SNP 163364_T). The cumulative effects of these variants contributed to 83% of
the overall risk of NPC in southern China. Phylogenetic analysis of the risk
variants revealed a unique origin in Asia, followed by clonal expansion in
NPC-endemic regions. Our results provide novel insights into NPC endemic in
southern China and also enable the identification of high-risk individuals for
NPC prevention. Whole-genome sequencing and association analysis of 270 Epstein-Barr
virus (EBV) isolates from China identify two non-synonymous EBV variants within
BALF2 strongly associated with the risk of nasopharyngeal carcinoma.
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Affiliation(s)
- Miao Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Youyuan Yao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Comprehensive Medical Oncology, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, Hangzhou, China
| | - Hui Chen
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Shanshan Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Su-Mei Cao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhe Zhang
- Department of Otolaryngology/Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Bing Luo
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Zhiwei Liu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Zilin Li
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Tong Xiang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Guiping He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qi-Sheng Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Li-Zhen Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiang Guo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ming-Yuan Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiao Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shang-Hang Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Roujun Peng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ellen T Chang
- Center for Health Sciences, Exponent, Menlo Park, CA, USA.,Stanford Cancer Institute, Stanford, CA, USA
| | - Vincent Pedergnana
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lin Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jin-Xin Bei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rui-Hua Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Weiwei Zhai
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Jianjun Liu
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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13
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Ramamurthy N, Marchi E, Ansari MA, Pedergnana V, Mclean A, Hudson E, Bowden R, Spencer CC, Barnes E, Klenerman P. Impact of Interferon Lambda 4 Genotype on Interferon-Stimulated Gene Expression During Direct-Acting Antiviral Therapy for Hepatitis C. Hepatology 2018; 68. [PMID: 29534310 PMCID: PMC6207923 DOI: 10.1002/hep.29877] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
New directly acting antivirals (DAAs) provide very high cure rates in most patients infected by hepatitis C virus (HCV). However, some patient groups have been relatively harder to treat, including those with cirrhosis or infected with HCV genotype 3. In the recent BOSON trial, genotype 3, patients with cirrhosis receiving a 16-week course of sofosbuvir and ribavirin had a sustained virological response (SVR) rate of around 50%. In patients with cirrhosis, interferon lambda 4 (IFNL4) CC genotype was significantly associated with SVR. This genotype was also associated with a lower interferon-stimulated gene (ISG) signature in peripheral blood and in liver at baseline. Unexpectedly, patients with the CC genotype showed a dynamic increase in ISG expression between weeks 4 and 16 of DAA therapy, whereas the reverse was true for non-CC patients. Conclusion: These data provide an important dynamic link between host genotype and phenotype in HCV therapy also potentially relevant to naturally acquired infection. (Hepatology 2018; 00:000-000).
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Affiliation(s)
- Narayan Ramamurthy
- Peter Medawar Building for Pathogen Research and Translational Gastroeneterology Unit, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Emanuele Marchi
- Peter Medawar Building for Pathogen Research and Translational Gastroeneterology Unit, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - M. Azim Ansari
- Peter Medawar Building for Pathogen Research and Translational Gastroeneterology Unit, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom,Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom,Oxford Martin SchoolUniversity of OxfordOxfordUnited Kingdom
| | - Vincent Pedergnana
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Angela Mclean
- Department of ZoologyUniversity of OxfordOxfordUnited Kingdom
| | - Emma Hudson
- Peter Medawar Building for Pathogen Research and Translational Gastroeneterology Unit, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | | | - Rory Bowden
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Chris C.A. Spencer
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research and Translational Gastroeneterology Unit, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and Translational Gastroeneterology Unit, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
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14
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Lucas M, Deshpande P, James I, Rauch A, Pfafferott K, Gaylard E, Merani S, Plauzolles A, Lucas A, McDonnell W, Kalams S, Pilkinton M, Chastain C, Barnett L, Prosser A, Mallal S, Fitzmaurice K, Drummer H, Ansari MA, Pedergnana V, Barnes E, John M, Kelleher D, Klenerman P, Gaudieri S. Evidence of CD4 + T cell-mediated immune pressure on the Hepatitis C virus genome. Sci Rep 2018; 8:7224. [PMID: 29740042 PMCID: PMC5940905 DOI: 10.1038/s41598-018-25559-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/19/2018] [Indexed: 12/20/2022] Open
Abstract
Hepatitis C virus (HCV)-specific T cell responses are critical for immune control of infection. Viral adaptation to these responses, via mutations within regions of the virus targeted by CD8+ T cells, is associated with viral persistence. However, identifying viral adaptation to HCV-specific CD4+ T cell responses has been difficult although key to understanding anti-HCV immunity. In this context, HCV sequence and host genotype from a single source HCV genotype 1B cohort (n = 63) were analyzed to identify viral changes associated with specific human leucocyte antigen (HLA) class II alleles, as these variable host molecules determine the set of viral peptides presented to CD4+ T cells. Eight sites across the HCV genome were associated with HLA class II alleles implicated in infection outcome in this cohort (p ≤ 0.01; Fisher’s exact test). We extended this analysis to chronic HCV infection (n = 351) for the common genotypes 1A and 3A. Variation at 38 sites across the HCV genome were associated with specific HLA class II alleles with no overlap between genotypes, suggestive of genotype-specific T cell targets, which has important implications for vaccine design. Here we show evidence of HCV adaptation to HLA class II-restricted CD4+ T cell pressure across the HCV genome in chronic HCV infection without a priori knowledge of CD4+ T cell epitopes.
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Affiliation(s)
- Michaela Lucas
- School of Medicine and Pharmacology, Harry Perkins Institute and School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia, Australia.,Department of Immunology, Sir Charles Gairdner Hospital and Pathwest, Crawley, Western Australia, Australia.,Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Pooja Deshpande
- School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Ian James
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Andri Rauch
- Division of Infectious Diseases, University Hospital Bern and University of Bern, Bern, Switzerland
| | - Katja Pfafferott
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia.,Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Elouise Gaylard
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Shahzma Merani
- School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia.,Department of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | - Anne Plauzolles
- School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Andrew Lucas
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia.,Harry Perkins Institute, University of Western Australia, Crawley, Western Australia, Australia
| | - Wyatt McDonnell
- Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Spyros Kalams
- Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mark Pilkinton
- Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Cody Chastain
- Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Louise Barnett
- Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Amy Prosser
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia.,Harry Perkins Institute, University of Western Australia, Crawley, Western Australia, Australia
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia.,Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Karen Fitzmaurice
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Heidi Drummer
- Department of Immunology and Department of Microbiology, Monash University, Victoria, Australia.,Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - M Azim Ansari
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | | | - Ellie Barnes
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Mina John
- Department of Immunology, Sir Charles Gairdner Hospital and Pathwest, Crawley, Western Australia, Australia.,Department of Clinical Immunology, Royal Perth Hospital and Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Dermot Kelleher
- Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Silvana Gaudieri
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia. .,School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia. .,Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
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15
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Walker AJ, Peacock CJ, Pedergnana V, Irving WL. Host genetic factors associated with hepatocellular carcinoma in patients with hepatitis C virus infection: A systematic review. J Viral Hepat 2018; 25:442-456. [PMID: 29397014 PMCID: PMC6321980 DOI: 10.1111/jvh.12871] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/02/2018] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV)-infected patients are at risk of developing hepatocellular carcinoma (HCC). Individuals at heightened risk could be targeted by intensive follow-up surveillance. We have conducted a systematic review of the literature to identify host genetic predisposition to HCC in HCV-infected patients. A comprehensive search of Medline and Embase databases was performed, and the strength of evidence of associations for each gene on development of HCC was evaluated. We identified 166 relevant studies, relating to 137 different genes, or combinations thereof. Seventeen genes were classified as having "good" evidence of an association, a significant association was observed for 37 genes but this finding had not yet been replicated, 56 genes had mixed or limited evidence of an association, and 27 genes showed no association. IFNL3/4, TNF-α and PNPLA3 genes had the most evidence of an association. There was, however, considerable heterogeneity in study design and data quality. In conclusion, we identified a number of genes with evidence of association with HCC, but also a need for more standardized approaches to address this clinically critical question. It is important to consider the underlying mechanism of these relationships and which are confounded by the presence of other HCC risk factors and response to therapy. We also identified many genes where the evidence of association is contradictory or requires replication, as well as a number where associations have been studied but no evidence found. These findings should help to direct future studies on host genetic predisposition to HCC in HCV-infected patients.
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Affiliation(s)
- A. J. Walker
- National Institute for Health research (NIHR) Nottingham Biomedical Research CentreNottingham University Hospitals NHS TrustUniversity of NottinghamNottinghamUK,Centre for Evidence Based MedicineDepartment of Primary Care Health SciencesUniversity of OxfordOxfordUK
| | - C. J. Peacock
- National Institute for Health research (NIHR) Nottingham Biomedical Research CentreNottingham University Hospitals NHS TrustUniversity of NottinghamNottinghamUK
| | - V. Pedergnana
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | | | - W. L. Irving
- National Institute for Health research (NIHR) Nottingham Biomedical Research CentreNottingham University Hospitals NHS TrustUniversity of NottinghamNottinghamUK
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16
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Meyts I, Bosch B, Bolze A, Boisson B, Itan Y, Belkadi A, Pedergnana V, Moens L, Picard C, Cobat A, Bossuyt X, Abel L, Casanova JL. Exome and genome sequencing for inborn errors of immunity. J Allergy Clin Immunol 2017; 138:957-969. [PMID: 27720020 DOI: 10.1016/j.jaci.2016.08.003] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 01/03/2023]
Abstract
The advent of next-generation sequencing (NGS) in 2010 has transformed medicine, particularly the growing field of inborn errors of immunity. NGS has facilitated the discovery of novel disease-causing genes and the genetic diagnosis of patients with monogenic inborn errors of immunity. Whole-exome sequencing (WES) is presently the most cost-effective approach for research and diagnostics, although whole-genome sequencing offers several advantages. The scientific or diagnostic challenge consists in selecting 1 or 2 candidate variants among thousands of NGS calls. Variant- and gene-level computational methods, as well as immunologic hypotheses, can help narrow down this genome-wide search. The key to success is a well-informed genetic hypothesis on 3 key aspects: mode of inheritance, clinical penetrance, and genetic heterogeneity of the condition. This determines the search strategy and selection criteria for candidate alleles. Subsequent functional validation of the disease-causing effect of the candidate variant is critical. Even the most up-to-date dry lab cannot clinch this validation without a seasoned wet lab. The multifariousness of variations entails an experimental rigor even greater than traditional Sanger sequencing-based approaches in order not to assign a condition to an irrelevant variant. Finding the needle in the haystack takes patience, prudence, and discernment.
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Affiliation(s)
- Isabelle Meyts
- Department of Immunology and Microbiology, Childhood Immunology, Department of Pediatrics, University Hospitals Leuven and KU Leuven, Leuven, Belgium.
| | - Barbara Bosch
- Department of Pediatrics, University Hospitals Leuven and KU Leuven, Leuven, Belgium; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Alexandre Bolze
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Helix, San Carlos, Calif
| | - Bertrand Boisson
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Yuval Itan
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Aziz Belkadi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Leen Moens
- Laboratory Medicine, Experimental Laboratory Immunology, Department of Laboratory Medicine, University Hospitals Leuven and KU Leuven, Leuven, Belgium
| | - Capucine Picard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Paris Descartes University-Sorbonne Paris Cité, Paris, France; Study Center for Immunodeficiency, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Xavier Bossuyt
- Laboratory Medicine, Experimental Laboratory Immunology, Department of Laboratory Medicine, University Hospitals Leuven and KU Leuven, Leuven, Belgium
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Howard Hughes Medical Institute, New York, NY; Pediatric Hematology and Immunology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France
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17
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Ansari MA, Pedergnana V, L C Ip C, Magri A, Von Delft A, Bonsall D, Chaturvedi N, Bartha I, Smith D, Nicholson G, McVean G, Trebes A, Piazza P, Fellay J, Cooke G, Foster GR, Hudson E, McLauchlan J, Simmonds P, Bowden R, Klenerman P, Barnes E, Spencer CCA. Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus. Nat Genet 2017; 49:666-673. [PMID: 28394351 PMCID: PMC5873514 DOI: 10.1038/ng.3835] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 03/10/2017] [Indexed: 12/11/2022]
Abstract
Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. We use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals chronically infected with HCV, predominately genotype 3. We show that both HLA alleles and interferon lambda innate immune system genes drive viral genome polymorphism, and that IFNL4 genotypes determine HCV viral load through a mechanism that is dependent on a specific polymorphism in the HCV polyprotein. We highlight the interplay between innate immune responses and the viral genome in HCV control.
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Affiliation(s)
- M Azim Ansari
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Oxford Martin School, University of Oxford, Oxford, UK.,Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Vincent Pedergnana
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Camilla L C Ip
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Andrea Magri
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Annette Von Delft
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - David Bonsall
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Nimisha Chaturvedi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Istvan Bartha
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - David Smith
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | | | - Gilean McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Amy Trebes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Graham Cooke
- Wright-Fleming Institute, Imperial College London, London, UK
| | | | | | - Emma Hudson
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Peter Simmonds
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Chris C A Spencer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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18
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Pedergnana V, Martel-Jantin C, Nicol JTJ, Leblond V, Tortevoye P, Coursaget P, Touzé A, Abel L, Gessain A. Trichodysplasia Spinulosa Polyomavirus Infection Occurs during Early Childhood with Intrafamilial Transmission, Especially from Mother to Child. J Invest Dermatol 2017; 137:1181-1183. [PMID: 28108298 DOI: 10.1016/j.jid.2016.12.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/14/2016] [Accepted: 12/23/2016] [Indexed: 11/16/2022]
Affiliation(s)
- Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Claire Martel-Jantin
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, Paris, France; CNRS, UMR3569, Paris, France; Université Paris Diderot, Cellule Pasteur, Paris, France
| | - Jérôme T J Nicol
- Université F Rabelais, Faculté des Sciences Pharmaceutiques, Tours, France; INRA UMR 1282, Infectiologie et Santé Publique, Tours, France
| | - Valérie Leblond
- Université F Rabelais, Faculté des Sciences Pharmaceutiques, Tours, France; INRA UMR 1282, Infectiologie et Santé Publique, Tours, France
| | - Patricia Tortevoye
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, Paris, France; CNRS, UMR3569, Paris, France
| | - Pierre Coursaget
- Université F Rabelais, Faculté des Sciences Pharmaceutiques, Tours, France
| | - Antoine Touzé
- Université F Rabelais, Faculté des Sciences Pharmaceutiques, Tours, France; INRA UMR 1282, Infectiologie et Santé Publique, Tours, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Antoine Gessain
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, Paris, France; CNRS, UMR3569, Paris, France.
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19
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Pedergnana V, Smith D, Klenerman P, Barnes E, Spencer CCA, Ansari MA. Interferon lambda 4 variant rs12979860 is not associated with RAV NS5A Y93H in hepatitis C virus genotype 3a. Hepatology 2016; 64:1377-8. [PMID: 26945900 PMCID: PMC5042047 DOI: 10.1002/hep.28533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 02/10/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Vincent Pedergnana
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - David Smith
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | | | - Paul Klenerman
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Eleanor Barnes
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Chris C. A. Spencer
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - M. Azim Ansari
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom,Oxford Martin SchoolUniversity of OxfordOxfordUnited Kingdom
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20
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Pedergnana V, Abdel-Hamid M, Guergnon J, Theodorou I, Fontanet A, Abel L, Cobat A. Refined association of melanoma differentiation-associated gene 5 variants with spontaneous hepatitis C virus clearance in Egypt. Hepatology 2016; 63:1059-61. [PMID: 26105514 DOI: 10.1002/hep.27951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Affiliation(s)
- Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch Institut National de la Santé et de la Recherche Médicale U1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,Wellcome Trust Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mohamed Abdel-Hamid
- Viral Hepatitis Research Laboratory, National Hepatology and Tropical Medicine Research Institute, Cairo, Egypt.,Department of Microbiology, Minia Faculty of Medicine, Minia, Egypt
| | - Julien Guergnon
- Laboratory of Immunity and Infection, Institut National de la Santé et de la Recherche Médicale UMR-S 945, UPMC University Paris 6, Groupe Hospitalier Pitié-Salpêtrière AP-HP, Paris, France
| | - Ioannis Theodorou
- Laboratory of Immunity and Infection, Institut National de la Santé et de la Recherche Médicale UMR-S 945, UPMC University Paris 6, Groupe Hospitalier Pitié-Salpêtrière AP-HP, Paris, France
| | - Arnaud Fontanet
- Institut Pasteur, Unité d'Epidémiologie des Maladies Emergentes, Paris, France.,Conservatoire National des Arts et Métiers, Chaire Santé et Développement, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch Institut National de la Santé et de la Recherche Médicale U1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch Institut National de la Santé et de la Recherche Médicale U1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
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21
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About F, Oudot-Mellakh T, Niay J, Rabiéga P, Pedergnana V, Duffy D, Sultanik P, Cagnot C, Carrat F, Marcellin P, Zoulim F, Larrey D, Hézode C, Fontaine H, Bronowicki JP, Pol S, Albert ML, Theodorou I, Cobat A, Abel L. Impact of IL28B, APOH and ITPA Polymorphisms on Efficacy and Safety of TVR- or BOC-Based Triple Therapy in Treatment-Experienced HCV-1 Patients with Compensated Cirrhosis from the ANRS CO20-CUPIC Study. PLoS One 2015; 10:e0145105. [PMID: 26670100 PMCID: PMC4682920 DOI: 10.1371/journal.pone.0145105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/29/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Human genetic factors influence the outcome of pegylated interferon and ribavirin hepatitis C therapy. We explored the role of IL28B, APOH and ITPA SNPs on the outcomes of triple therapy including telaprevir or boceprevir in patients with compensated cirrhosis chronically infected with HCV-1. PATIENTS AND METHODS A total of 256 HCV-1 Caucasian treatment-experienced patients with compensated cirrhosis from the ANRS CO20-CUPIC cohort were genotyped for a total of 10 candidate SNPs in IL28B (rs12979860 and rs368234815), APOH (rs8178822, rs12944940, rs10048158, rs52797880, rs1801689 and rs1801690) and ITPA (rs1127354 and rs7270101). We tested the association of IL28B and APOH SNPs with sustained virological response and of ITPA SNPs with anemia related phenotypes by means of logistic regression assuming an additive genetic model. RESULTS None of the six APOH SNPs were associated with sustained virological response. The favorable alleles of the IL28B SNPs rs12979860 and rs368234815 were associated with sustained virological response (rs12979860: OR = 2.35[1.50-3.70], P = 2x10(-4)). Refined analysis showed that the effect of IL28B SNPs on sustained virological response was restricted to prior PegIFN/RBV relapse (OR = 3.80[1.82-8.92], P = 8x10(-4)). We also confirmed the association between ITPA low activity alleles and protection against early hemoglobin decline in triple therapy (P = 2x10(-5)). CONCLUSION Our results suggest that the screening of rs12979860 may remain interesting for decision making in prior relapse HCV-1 Caucasian patients with compensated cirrhosis eligible for a telaprevir- or boceprevir-based therapy.
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Affiliation(s)
- Frédégonde About
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | - Tiphaine Oudot-Mellakh
- Laboratory of Immunity and Infection, Centre d’Immunologie et des Maladies Infectieuses de Paris (CIMI), INSERM U1135, Groupe Hospitalier Pitié Salpétrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Plateforme Génomique Inserm-ANRS, Groupe Hospitalier Pitié Salpétrière, AP-HP, UPMC Université Paris 6, Paris, France
| | - Jonathan Niay
- Laboratory of Immunity and Infection, Centre d’Immunologie et des Maladies Infectieuses de Paris (CIMI), INSERM U1135, Groupe Hospitalier Pitié Salpétrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Plateforme Génomique Inserm-ANRS, Groupe Hospitalier Pitié Salpétrière, AP-HP, UPMC Université Paris 6, Paris, France
| | - Pascaline Rabiéga
- Sorbonne Universités, UPMC Université Paris 06, INSERM, Institut Pierre Louis d’épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
| | - Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Darragh Duffy
- Centre for Human Immunology, Department of Immunology, Institut Pasteur, Paris, France
- The Laboratory of Dendritic Cell Biology, Department of Immunology, Institut Pasteur, INSERM U818, Paris, France
| | - Philippe Sultanik
- Département d'Hépatologie, Hôpital Cochin, AP-HP, Université Paris Descartes, Paris, France
- INSERM UMS20, Institut Pasteur, Paris, France
| | - Carole Cagnot
- Unit for Basic and Clinical research on Viral Hepatitis, Inserm-ANRS (France REcherche Nord & sud Sida-HIV Hépatites-FRENSH), Paris, France
| | - Fabrice Carrat
- Sorbonne Universités, UPMC Université Paris 06, INSERM, Institut Pierre Louis d’épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
- Service de Santé Publique, Hôpital Saint Antoine, AP-HP, Paris, France
| | | | - Fabien Zoulim
- Centre de recherche en cancérologie de Lyon (CRCL), INSERM UMR I 1052/CNRS 5286, Lyon cedex 03, France
- Université Claude-Bernard Lyon 1, Villeurbanne, France
- Hospices civils de Lyon, Hôpital de la Croix-Rousse, service d'hépatologie et de gastroentérologie, Lyon, France
| | | | - Christophe Hézode
- Department of Hepatology and Gastroenterology, Hôpital Henri Mondor, AP-HP, Université Paris-Est Créteil (UPEC), Créteil, France
- Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, UPEC, Créteil, France
| | - Hélène Fontaine
- Département d'Hépatologie, Hôpital Cochin, AP-HP, Université Paris Descartes, Paris, France
- INSERM UMS20, Institut Pasteur, Paris, France
| | - Jean-Pierre Bronowicki
- Department of Hepatogastroenterology, INSERM U954, CHU de Nancy, Université de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Stanislas Pol
- Département d'Hépatologie, Hôpital Cochin, AP-HP, Université Paris Descartes, Paris, France
- INSERM UMS20, Institut Pasteur, Paris, France
| | - Matthew L. Albert
- Centre for Human Immunology, Department of Immunology, Institut Pasteur, Paris, France
- The Laboratory of Dendritic Cell Biology, Department of Immunology, Institut Pasteur, INSERM U818, Paris, France
- INSERM UMS20, Institut Pasteur, Paris, France
| | - Ioannis Theodorou
- Laboratory of Immunity and Infection, Centre d’Immunologie et des Maladies Infectieuses de Paris (CIMI), INSERM U1135, Groupe Hospitalier Pitié Salpétrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Plateforme Génomique Inserm-ANRS, Groupe Hospitalier Pitié Salpétrière, AP-HP, UPMC Université Paris 6, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, United States of America
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Dobbs K, Domínguez Conde C, Zhang SY, Parolini S, Audry M, Chou J, Haapaniemi E, Keles S, Bilic I, Okada S, Massaad MJ, Rounioja S, Alwahadneh AM, Serwas NK, Capuder K, Ciftci E, Felgentreff K, Ohsumi TK, Pedergnana V, Boisson B, Haskoloğlu S, Ensari A, Schuster M, Moretta A, Itan Y, Patrizi O, Rozenberg F, Lebon P, Saarela J, Knip M, Petrovski S, Goldstein DB, Parrott RE, Savas B, Schambach A, Tabellini G, Bock C, Chatila T, Comeau AM, Geha RS, Abel L, Buckley RH, Ikincioğullari A, Al-Herz W, Helminen M, Doğu F, Casanova JL, Boztuğ K, Notarangelo LD. Inherited DOCK2 Deficiency in Patients with Early-Onset Invasive Infections. N Engl J Med 2015; 372:2409-22. [PMID: 26083206 PMCID: PMC4480434 DOI: 10.1056/nejmoa1413462] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background Combined immunodeficiencies are marked by inborn errors of T-cell immunity in which the T cells that are present are quantitatively or functionally deficient. Impaired humoral immunity is also common. Patients have severe infections, autoimmunity, or both. The specific molecular, cellular, and clinical features of many types of combined immunodeficiencies remain unknown. Methods We performed genetic and cellular immunologic studies involving five unrelated children with early-onset invasive bacterial and viral infections, lymphopenia, and defective T-cell, B-cell, and natural killer (NK)-cell responses. Two patients died early in childhood; after allogeneic hematopoietic stem-cell transplantation, the other three had normalization of T-cell function and clinical improvement. Results We identified biallelic mutations in the dedicator of cytokinesis 2 gene (DOCK2) in these five patients. RAC1 activation was impaired in the T cells. Chemokine-induced migration and actin polymerization were defective in the T cells, B cells, and NK cells. NK-cell degranulation was also affected. Interferon-α and interferon-λ production by peripheral-blood mononuclear cells was diminished after viral infection. Moreover, in DOCK2-deficient fibroblasts, viral replication was increased and virus-induced cell death was enhanced; these conditions were normalized by treatment with interferon alfa-2b or after expression of wild-type DOCK2. Conclusions Autosomal recessive DOCK2 deficiency is a new mendelian disorder with pleiotropic defects of hematopoietic and nonhematopoietic immunity. Children with clinical features of combined immunodeficiencies, especially with early-onset, invasive infections, may have this condition. (Supported by the National Institutes of Health and others.).
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23
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Ciancanelli MJ, Huang SXL, Luthra P, Garner H, Itan Y, Volpi S, Lafaille FG, Trouillet C, Schmolke M, Albrecht RA, Israelsson E, Lim HK, Casadio M, Hermesh T, Lorenzo L, Leung LW, Pedergnana V, Boisson B, Okada S, Picard C, Ringuier B, Troussier F, Chaussabel D, Abel L, Pellier I, Notarangelo LD, García-Sastre A, Basler CF, Geissmann F, Zhang SY, Snoeck HW, Casanova JL. Infectious disease. Life-threatening influenza and impaired interferon amplification in human IRF7 deficiency. Science 2015; 348:448-53. [PMID: 25814066 DOI: 10.1126/science.aaa1578] [Citation(s) in RCA: 331] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 03/12/2015] [Indexed: 12/24/2022]
Abstract
Severe influenza disease strikes otherwise healthy children and remains unexplained. We report compound heterozygous null mutations in IRF7, which encodes the transcription factor interferon regulatory factor 7, in an otherwise healthy child who suffered life-threatening influenza during primary infection. In response to influenza virus, the patient's leukocytes and plasmacytoid dendritic cells produced very little type I and III interferons (IFNs). Moreover, the patient's dermal fibroblasts and induced pluripotent stem cell (iPSC)-derived pulmonary epithelial cells produced reduced amounts of type I IFN and displayed increased influenza virus replication. These findings suggest that IRF7-dependent amplification of type I and III IFNs is required for protection against primary infection by influenza virus in humans. They also show that severe influenza may result from single-gene inborn errors of immunity.
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Affiliation(s)
- Michael J Ciancanelli
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Sarah X L Huang
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY, USA. Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Priya Luthra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hannah Garner
- Centre for Molecular and Cellular Biology of Inflammation (CMCBI), King's College London, London SE1 1UL, UK
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Stefano Volpi
- Division of Immunology and Manton Center for Orphan Disease Research, Children's Hospital, Harvard Medical School, Boston, MA, USA. Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132 Genoa, Italy
| | - Fabien G Lafaille
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Céline Trouillet
- Centre for Molecular and Cellular Biology of Inflammation (CMCBI), King's College London, London SE1 1UL, UK
| | - Mirco Schmolke
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elisabeth Israelsson
- Department of Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Hye Kyung Lim
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Melina Casadio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Tamar Hermesh
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France. University Paris Descartes, Imagine Institute, Paris, France
| | - Lawrence W Leung
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France. University Paris Descartes, Imagine Institute, Paris, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Satoshi Okada
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA. Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Capucine Picard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA. Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France. University Paris Descartes, Imagine Institute, Paris, France. Study Centre for Primary Immunodeficiencies, AP-HP, Necker Hospital, Paris, France
| | | | | | - Damien Chaussabel
- Department of Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA. Department of Systems Biology, Sidra Medical and Research Center, Doha, Qatar
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA. Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France. University Paris Descartes, Imagine Institute, Paris, France
| | - Isabelle Pellier
- Pediatric Immunology, Hematology and Oncology Unit, University Hospital Centre of Angers, Angers, France. INSERM U892, CNRS U6299, Angers, France
| | - Luigi D Notarangelo
- Division of Immunology and Manton Center for Orphan Disease Research, Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Frédéric Geissmann
- Centre for Molecular and Cellular Biology of Inflammation (CMCBI), King's College London, London SE1 1UL, UK
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA. Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France. University Paris Descartes, Imagine Institute, Paris, France
| | - Hans-Willem Snoeck
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY, USA. Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA. Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France. University Paris Descartes, Imagine Institute, Paris, France. Pediatric Immuno-Hematology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France. Howard Hughes Medical Institute, New York, NY, USA.
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24
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Lanternier F, Mahdaviani SA, Barbati E, Chaussade H, Koumar Y, Levy R, Denis B, Brunel AS, Martin S, Loop M, Peeters J, de Selys A, Vanclaire J, Vermylen C, Nassogne MC, Chatzis O, Liu L, Migaud M, Pedergnana V, Desoubeaux G, Jouvion G, Chretien F, Darazam IA, Schäffer AA, Netea MG, De Bruycker JJ, Bernard L, Reynes J, Amazrine N, Abel L, Van der Linden D, Harrison T, Picard C, Lortholary O, Mansouri D, Casanova JL, Puel A. Inherited CARD9 deficiency in otherwise healthy children and adults with Candida species-induced meningoencephalitis, colitis, or both. J Allergy Clin Immunol 2015; 135:1558-68.e2. [PMID: 25702837 DOI: 10.1016/j.jaci.2014.12.1930] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 12/02/2014] [Accepted: 12/10/2014] [Indexed: 02/06/2023]
Abstract
BACKGROUND Invasive infections of the central nervous system (CNS) or digestive tract caused by commensal fungi of the genus Candida are rare and life-threatening. The known risk factors include acquired and inherited immunodeficiencies, with patients often displaying a history of multiple infections. Cases of meningoencephalitis, colitis, or both caused by Candida species remain unexplained. OBJECTIVE We studied 5 previously healthy children and adults with unexplained invasive disease of the CNS, digestive tract, or both caused by Candida species. The patients were aged 39, 7, 17, 37, and 26 years at the time of infection and were unrelated, but each was born to consanguineous parents of Turkish (2 patients), Iranian, Moroccan, or Pakistani origin. Meningoencephalitis was reported in 3 patients, meningoencephalitis associated with colitis was reported in a fourth patient, and the fifth patient had colitis only. METHODS Inherited caspase recruitment domain family, member 9 (CARD9) deficiency was recently reported in otherwise healthy patients with other forms of severe disease caused by Candida, Trichophyton, Phialophora, and Exophiala species, including meningoencephalitis but not colitis caused by Candida and Exophiala species. Therefore we sequenced CARD9 in the 5 patients. RESULTS All patients were found to be homozygous for rare and deleterious mutant CARD9 alleles: R70W and Q289* for the 3 patients with Candida albicans-induced meningoencephalitis, R35Q for the patient with meningoencephalitis and colitis caused by Candida glabrata, and Q295* for the patient with Candida albicans-induced colitis. Regardless of their levels of mutant CARD9 protein, the patients' monocyte-derived dendritic cells responded poorly to CARD9-dependent fungal agonists (curdlan, heat-killed C albicans, Saccharomyces cerevisiae, and Exophiala dermatitidis). CONCLUSION Invasive infections of the CNS or digestive tract caused by Candida species in previously healthy children and even adults might be caused by inherited CARD9 deficiency.
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Affiliation(s)
- Fanny Lanternier
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Necker Pasteur Infectious Diseases Center, Necker Hospital, Assistance Publique des Hôpitaux de Paris (AP-HP), Imagine Institute, Paris, France
| | - Seyed Alireza Mahdaviani
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elisa Barbati
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | | | | | - Romain Levy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Blandine Denis
- Paris Descartes University, Imagine Institute, Paris, France; Necker Pasteur Infectious Diseases Center, Necker Hospital, Assistance Publique des Hôpitaux de Paris (AP-HP), Imagine Institute, Paris, France
| | | | - Sophie Martin
- Pediatric Infectious Diseases Unit, Saint-Luc University Hospital, UCL, Brussels, Belgium
| | - Michèle Loop
- Pediatric-Neonatology Unit, Saint-Jean Hospital, Brussels, Belgium
| | - Julie Peeters
- Pediatric Infectious Diseases Unit, Saint-Luc University Hospital, UCL, Brussels, Belgium
| | - Ariel de Selys
- Pediatric-Neonatology Unit, Saint-Jean Hospital, Brussels, Belgium
| | - Jean Vanclaire
- Pediatric-Neonatology Unit, Saint-Jean Hospital, Brussels, Belgium
| | - Christiane Vermylen
- Pediatric Hematology-Oncology Unit, Saint-Luc University Hospital, UCL, Brussels, Belgium
| | | | - Olga Chatzis
- Pediatric Infectious Diseases Unit, Saint-Luc University Hospital, UCL, Brussels, Belgium
| | - Luyan Liu
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Guillaume Desoubeaux
- Parasitology-Mycology-Tropical Medicine Unit, Bretonneau Hospital, Center for the Study of Respiratory Diseases, INSERM U1100/Equipe 3 School of Medicine, Tours, France
| | - Gregory Jouvion
- Human Histopathology and Animal Models, Infection and Epidemiology Department, Pasteur Institute, Paris, France
| | - Fabrice Chretien
- Human Histopathology and Animal Models, Infection and Epidemiology Department, Pasteur Institute, Paris, France; Neuropathology Laboratory, Sainte-Anne Hospital, Paris, France
| | - Ilad Alavi Darazam
- Department of Clinical Immunology and Allergy, National Research Institute of Tuberculosis and Lung Diseases, Masih Daneshvari Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Md
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jean J De Bruycker
- Immunology and Rheumatology Unit, Saint-Justine Hospital University Center, Montreal, Quebec, Canada
| | - Louis Bernard
- Infectious Diseases Unit, Bretonneau Hospital, Tours, France
| | | | | | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Dimitri Van der Linden
- Pediatric Infectious Diseases Unit, Saint-Luc University Hospital, UCL, Brussels, Belgium
| | - Tom Harrison
- Infection and Immunity Research Institute, Saint George's University of London, London, United Kingdom
| | - Capucine Picard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Department of Neurosurgery, Tangier, Morocco; Study Center for Immunodeficiency, Necker Hospital, AP-HP, Paris, France; Pediatric Hematology-Immunology Unit, Necker Hospital, AP-HP, Paris, France
| | - Olivier Lortholary
- Paris Descartes University, Imagine Institute, Paris, France; Necker Pasteur Infectious Diseases Center, Necker Hospital, Assistance Publique des Hôpitaux de Paris (AP-HP), Imagine Institute, Paris, France; National Reference Center for Invasive Mycoses and Antifungals, Molecular Mycology Unit, Pasteur Institute, Paris, France
| | - Davood Mansouri
- Department of Clinical Immunology and Allergy, National Research Institute of Tuberculosis and Lung Diseases, Masih Daneshvari Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Pediatric Hematology-Immunology Unit, Necker Hospital, AP-HP, Paris, France; Howard Hughes Medical Institute, New York, NY
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France.
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Martínez-Barricarte R, Megged O, Stepensky P, Casimir P, Moncada-Velez M, Averbuch D, Assous MV, Abuzaitoun O, Kong XF, Pedergnana V, Deswarte C, Migaud M, Rose-John S, Itan Y, Boisson B, Belkadi A, Conti F, Abel L, Vogt G, Boisson-Dupuis S, Casanova JL, Bustamante J. Mycobacterium simiae infection in two unrelated patients with different forms of inherited IFN-γR2 deficiency. J Clin Immunol 2014; 34:904-9. [PMID: 25135595 DOI: 10.1007/s10875-014-0085-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/30/2014] [Indexed: 01/04/2023]
Abstract
Interferon-γ receptor 2 (IFN-γR2) deficiency is a rare primary immunodeficiency characterized by predisposition to infections with weakly virulent mycobacteria, such as environmental mycobacteria and BCG vaccines. We describe here two children with IFN-γR2 deficiency, from unrelated, consanguineous kindreds of Arab and Israeli descent. The first patient was a boy who died at the age of 4.5 years, from recurrent, disseminated disease caused by Mycobacterium simiae. His IFN-γR2 defect was autosomal recessive and complete. The second patient was a girl with multiple disseminated mycobacterial infections, including infection with M. simiae. She died at the age of 5 years, a short time after the transplantation of umbilical cord blood cells from an unrelated donor. Her IFN-γR2 defect was autosomal recessive and partial. Autosomal recessive IFN-γR2 deficiency is life-threatening, even in its partial form, and genetic diagnosis and familial counseling are therefore particularly important for this condition. These two cases are the first of IFN-γR2 deficiency associated with M. simiae infection to be described.
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Affiliation(s)
- Rubén Martínez-Barricarte
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
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26
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Lanternier F, Barbati E, Meinzer U, Liu L, Pedergnana V, Migaud M, Héritier S, Chomton M, Frémond ML, Gonzales E, Galeotti C, Romana S, Jacquemin E, Angoulvant A, Bidault V, Canioni D, Lachenaud J, Mansouri D, Mahdaviani SA, Adimi P, Mansouri N, Jamshidi M, Bougnoux ME, Abel L, Lortholary O, Blanche S, Casanova JL, Picard C, Puel A. Inherited CARD9 deficiency in 2 unrelated patients with invasive Exophiala infection. J Infect Dis 2014; 211:1241-50. [PMID: 25057046 DOI: 10.1093/infdis/jiu412] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Exophiala species are mostly responsible for skin infections. Invasive Exophiala dermatitidis disease is a rare and frequently fatal infection, with 42 cases reported. About half of these cases had no known risk factors. Similarly, invasive Exophiala spinifera disease is extremely rare, with only 3 cases reported, all in patients with no known immunodeficiency. Autosomal recessive CARD9 deficiency has recently been reported in otherwise healthy patients with severe fungal diseases caused by Candida species, dermatophytes, or Phialophora verrucosa. METHODS We investigated an 8-year-old girl from a nonconsanguineous Angolan kindred, who was born in France and developed disseminated E. dermatitidis disease and a 26 year-old woman from an Iranian consaguineous kindred, who was living in Iran and developed disseminated E. spinifera disease. Both patients were otherwise healthy. RESULTS We sequenced CARD9 and found both patients to be homozygous for loss-of-function mutations (R18W and E323del). The first patient had segmental uniparental disomy of chromosome 9, carrying 2 copies of the maternal CARD9 mutated allele. CONCLUSIONS These are the first 2 patients with inherited CARD9 deficiency and invasive Exophiala disease to be described. CARD9 deficiency should thus be considered in patients with unexplained invasive Exophiala species disease, even in the absence of other infections.
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Affiliation(s)
- Fanny Lanternier
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163 Paris Descartes University-Sorbonne Paris Cité, Imagine Institute Department of Infectious Diseases, Necker-Enfants malades Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Centre d'Infectiologie Necker Pasteur
| | - Elisa Barbati
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163 Paris Descartes University-Sorbonne Paris Cité, Imagine Institute
| | - Ulrich Meinzer
- Department of General Pediatrics and Internal Medicine, Robert Debré Hospital, AP-HP University Paris 7 Denis Diderot, Paris Sorbonne Cité
| | - Luyan Liu
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163 Paris Descartes University-Sorbonne Paris Cité, Imagine Institute
| | - Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163 Paris Descartes University-Sorbonne Paris Cité, Imagine Institute
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163 Paris Descartes University-Sorbonne Paris Cité, Imagine Institute
| | - Sébastien Héritier
- Paris Descartes University-Sorbonne Paris Cité, Imagine Institute Pediatric Hematology-Immunology Unit
| | - Maryline Chomton
- Paris Descartes University-Sorbonne Paris Cité, Imagine Institute Pediatric Hematology-Immunology Unit
| | - Marie-Louise Frémond
- Paris Descartes University-Sorbonne Paris Cité, Imagine Institute Pediatric Hematology-Immunology Unit
| | - Emmanuel Gonzales
- Pediatric Hepatology Unit, DHU Hépatinov, INSERM U757, Paris-Sud 11 University, Bicêtre Hospital, AP-HP
| | - Caroline Galeotti
- Pediatric Rheumatology Unit, Bicêtre Hospital, AP-HP, Paris Sud University, CeReMAI
| | | | - Emmanuel Jacquemin
- Pediatric Hepatology Unit, DHU Hépatinov, INSERM U757, Paris-Sud 11 University, Bicêtre Hospital, AP-HP
| | | | - Valeska Bidault
- Pediatric Surgery Unit, Bicêtre Hospital, AP-HP, Kremlin Bicêtre
| | | | - Julie Lachenaud
- Department of Pediatrics, Pontoise Hospital, Cergy Pontoise, France, EU
| | - Davood Mansouri
- Department of Clinical Immunology and Allergy, National Research Institute of Tuberculosis and Lung Diseases, Masih Daneshvari Hospital
| | - Seyed Alireza Mahdaviani
- Pediatric Respiratory Disease Research Centre, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences
| | - Parvaneh Adimi
- Department of Medical Mycology and Parasitology, Islamic Azad University Tehran Medical Branch
| | - Nahal Mansouri
- Department of Clinical Immunology and Allergy, National Research Institute of Tuberculosis and Lung Diseases, Masih Daneshvari Hospital
| | - Mahin Jamshidi
- Department of Infectious Disease, Iran University of Medical Sciences, Tehran, Iran
| | - Marie-Elisabeth Bougnoux
- Paris Descartes University-Sorbonne Paris Cité, Imagine Institute Microbiology Laboratory Fungal Biology and Pathogenicity, INRA USC 2019, Institut Pasteur
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163 Paris Descartes University-Sorbonne Paris Cité, Imagine Institute St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York
| | - Olivier Lortholary
- Paris Descartes University-Sorbonne Paris Cité, Imagine Institute Department of Infectious Diseases, Necker-Enfants malades Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Centre d'Infectiologie Necker Pasteur Molecular Mycology Unit, National Reference Center for Invasive Mycoses and Antifungals, Institut Pasteur, Paris
| | - Stéphane Blanche
- Paris Descartes University-Sorbonne Paris Cité, Imagine Institute Pediatric Hematology-Immunology Unit
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163 Paris Descartes University-Sorbonne Paris Cité, Imagine Institute Pediatric Hematology-Immunology Unit St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York
| | - Capucine Picard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163 Paris Descartes University-Sorbonne Paris Cité, Imagine Institute Pediatric Hematology-Immunology Unit Study Center for Primary Immunodeficiencies, Necker-Enfants malades Hospital, AP-HP
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163 Paris Descartes University-Sorbonne Paris Cité, Imagine Institute
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Pedergnana V, Syx L, Cobat A, Guergnon J, Brice P, Fermé C, Carde P, Hermine O, Pendeven CL, Amiel C, Taoufik Y, Alcaïs A, Theodorou I, Besson C, Abel L. Combined linkage and association studies show that HLA class II variants control levels of antibodies against Epstein-Barr virus antigens. PLoS One 2014; 9:e102501. [PMID: 25025336 PMCID: PMC4099326 DOI: 10.1371/journal.pone.0102501] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/18/2014] [Indexed: 11/18/2022] Open
Abstract
Over 95% of the adult population worldwide is infected with Epstein-Barr virus (EBV). EBV infection is associated with the development of several cancers, including Hodgkin lymphoma (HL). Elevated levels of anti-EBV antibodies have been associated with increased risk of HL. There is growing evidence that genetic factors control the levels of antibodies against EBV antigens. Here, we conducted linkage and association studies to search for genetic factors influencing either anti-viral capsid antigen (VCA) or anti-Epstein Barr nuclear antigen-1 (EBNA-1) IgG levels in a unique cohort of 424 individuals of European origin from 119 French families recruited through a Hodgkin lymphoma (HL) patient. No major locus controlling anti-VCA antibody levels was identified. However, we found that the HLA region influenced anti-EBNA-1 IgG titers. Refined association studies in this region identified a cluster of HLA class II variants associated with anti-EBNA-1 IgG titers (e.g. p = 5×10–5 for rs9268403). The major allele of rs9268403 conferring a predisposition to high anti-EBNA-1 antibody levels was also associated with an increased risk of HL (p = 0.02). In summary, this study shows that HLA class II variants influenced anti-EBNA-1 IgG titers in a European population. It further shows the role of the same variants in the risk of HL.
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Affiliation(s)
- Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, Paris, France
- University Paris Descartes, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Laurène Syx
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, Paris, France
- University Paris Descartes, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, Paris, France
- University Paris Descartes, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Julien Guergnon
- Laboratory of Immunity and Infection, Institut National de la Santé et de la Recherche Médicale UMR-S 945, Université Pierre et Marie Curie Université Paris 6, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Pauline Brice
- Service d’Onco-Hématologie, Hôpital Saint-Louis, Paris, France
| | - Christophe Fermé
- Department of Medicine, Hôpital Gustave Roussy, Villejuif, France
| | - Patrice Carde
- Department of Medicine, Hôpital Gustave Roussy, Villejuif, France
| | - Olivier Hermine
- Service d’Hématologie adultes, Hôpital Necker, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Catherine Le- Pendeven
- Laboratoire de Virologie, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Corinne Amiel
- Laboratoire de Virologie, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Yassine Taoufik
- Assistance Publique-Hôpitaux de Paris, CHU Bicetre, Service d’Hématologie et Immunologie Biologiques, Le Kremlin-Bicetre, France, and Université Paris Sud, Faculte de Médecine, Le Kremlin-Bicetre, France, and Institut National de la Santé et de la Recherche Médicale U1012, Le Kremlin-Bicetre, France
| | - Alexandre Alcaïs
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, Paris, France
- University Paris Descartes, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Ioannis Theodorou
- Laboratory of Immunity and Infection, Institut National de la Santé et de la Recherche Médicale UMR-S 945, Université Pierre et Marie Curie Université Paris 6, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Caroline Besson
- Assistance Publique-Hôpitaux de Paris, CHU Bicetre, Service d’Hématologie et Immunologie Biologiques, Le Kremlin-Bicetre, France, and Université Paris Sud, Faculte de Médecine, Le Kremlin-Bicetre, France, and Institut National de la Santé et de la Recherche Médicale U1012, Le Kremlin-Bicetre, France
- * E-mail: (CB); (LA)
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, Paris, France
- University Paris Descartes, Sorbonne Paris Cité, Imagine Institute, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
- * E-mail: (CB); (LA)
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Pedergnana V, Syx L, Cobat A, Guergnon J, Brice P, Ferme C, Carde P, Hermine O, Le Pendeven C, Amiel C, Theodorou I, Abel L, Besson C. Combined Linkage and Association Studies of Antibodies against EBV Antigens Confirm the Role of HLA Class II Variants in the Control of Anti-EBNA1 IgG Levels and in the Risk of Hodgkin's Lymphoma. Klin Padiatr 2014. [DOI: 10.1055/s-0034-1371107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Boisson B, Wang C, Pedergnana V, Wu L, Cypowyj S, Rybojad M, Belkadi A, Picard C, Abel L, Fieschi C, Puel A, Li X, Casanova JL. An ACT1 mutation selectively abolishes interleukin-17 responses in humans with chronic mucocutaneous candidiasis. Immunity 2013; 39:676-86. [PMID: 24120361 PMCID: PMC3873857 DOI: 10.1016/j.immuni.2013.09.002] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 07/22/2013] [Indexed: 11/21/2022]
Abstract
Patients with inborn errors of interleukin-17F (IL-17F) or IL-17RA display chronic mucocutaneous candidiasis (CMC). We report a biallelic missense mutation (T536I) in the adaptor molecule ACT1 in two siblings with CMC. The mutation, located in the SEFIR domain, abolished the homotypic interaction of ACT1 with IL-17 receptors, with no effect on homodimerization. The patients' fibroblasts failed to respond to IL-17A and IL-17F, and their T cells to IL-17E. By contrast, healthy individuals homozygous for the common variant D10N, located in the ACT1 tumor necrosis factor receptor-associated factor-interacting domain and previously associated with psoriasis, had impaired, but not abolished, responses to IL-17 cytokines. SEFIR-independent interactions of ACT1 with other proteins, such as CD40, heat shock protein 70 (HSP70) and HSP90, were not affected by the T536I mutation. Overall, human IL-17A and IL-17F depend on ACT1 to mediate protective mucocutaneous immunity. Moreover, other ACT1-dependent IL-17 cytokines seem to be largely redundant in host defense.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Adult
- Amino Acid Sequence
- CD40 Antigens/genetics
- CD40 Antigens/immunology
- Candidiasis, Chronic Mucocutaneous/genetics
- Candidiasis, Chronic Mucocutaneous/immunology
- Candidiasis, Chronic Mucocutaneous/pathology
- Female
- Fibroblasts/immunology
- Fibroblasts/pathology
- Heat-Shock Proteins/genetics
- Heat-Shock Proteins/immunology
- Homozygote
- Humans
- Immunity, Innate
- Immunity, Mucosal
- Interleukin-17/genetics
- Interleukin-17/immunology
- Male
- Molecular Sequence Data
- Mutation, Missense
- Pedigree
- Protein Multimerization
- Protein Structure, Tertiary
- Receptors, Interleukin-17/genetics
- Receptors, Interleukin-17/immunology
- Siblings
- T-Lymphocytes/immunology
- T-Lymphocytes/pathology
- Tumor Necrosis Factor Receptor-Associated Peptides and Proteins/genetics
- Tumor Necrosis Factor Receptor-Associated Peptides and Proteins/immunology
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Affiliation(s)
- Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch; The Rockefeller University; New York, NY, 10065; USA
| | - Chenhui Wang
- Department of Immunology; Lerner Research Institute, Cleveland Clinic; Cleveland, OH 44195; USA
| | - Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch; INSERM U980, Necker Medical School; Paris, 75015 France, EU
| | - Ling Wu
- Department of Immunology; Lerner Research Institute, Cleveland Clinic; Cleveland, OH 44195; USA
| | - Sophie Cypowyj
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch; The Rockefeller University; New York, NY, 10065; USA
| | - Michel Rybojad
- Dermatology Unit; Saint-Louis Hospital; Paris, 75010; France, EU
| | - Aziz Belkadi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch; INSERM U980, Necker Medical School; Paris, 75015 France, EU
- Paris Descartes University, Sorbonne Paris Cité; Imagine Institute; Paris 75015; France, EU
| | - Capucine Picard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch; INSERM U980, Necker Medical School; Paris, 75015 France, EU
- Study Center for Primary Immunodeficiencies, AP-HP; Necker Enfants Malades Hospital; Paris, 75015; France, EU
- Pediatric Hematology-Immunology Unit; Necker Hospital; Paris, 75015; France, EU
- Paris Descartes University, Sorbonne Paris Cité; Imagine Institute; Paris 75015; France, EU
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch; INSERM U980, Necker Medical School; Paris, 75015 France, EU
- Pediatric Hematology-Immunology Unit; Necker Hospital; Paris, 75015; France, EU
- Paris Descartes University, Sorbonne Paris Cité; Imagine Institute; Paris 75015; France, EU
| | - Claire Fieschi
- Adult Immunopathology Unit; Saint-Louis Hospital; Paris, 75010; France, EU
- Paris Diderot University, Paris 7, Paris, 75013; France, EU
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch; INSERM U980, Necker Medical School; Paris, 75015 France, EU
- Paris Descartes University, Sorbonne Paris Cité; Imagine Institute; Paris 75015; France, EU
| | - Xiaoxia Li
- Department of Immunology; Lerner Research Institute, Cleveland Clinic; Cleveland, OH 44195; USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch; The Rockefeller University; New York, NY, 10065; USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch; INSERM U980, Necker Medical School; Paris, 75015 France, EU
- Pediatric Hematology-Immunology Unit; Necker Hospital; Paris, 75015; France, EU
- Paris Descartes University, Sorbonne Paris Cité; Imagine Institute; Paris 75015; France, EU
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Byun M, Ma CS, Akçay A, Pedergnana V, Palendira U, Myoung J, Avery DT, Liu Y, Abhyankar A, Lorenzo L, Schmidt M, Lim HK, Cassar O, Migaud M, Rozenberg F, Canpolat N, Aydogan G, Fleckenstein B, Bustamante J, Picard C, Gessain A, Jouanguy E, Cesarman E, Olivier M, Gros P, Abel L, Croft M, Tangye SG, Casanova JL. Inherited human OX40 deficiency underlying classic Kaposi sarcoma of childhood. ACTA ACUST UNITED AC 2013; 210:1743-59. [PMID: 23897980 PMCID: PMC3754857 DOI: 10.1084/jem.20130592] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Human OX40 is necessary for robust CD4+ T cell memory and confers selective protective immunity against HHV-8 infection in endothelial cells. Kaposi sarcoma (KS), a human herpes virus 8 (HHV-8; also called KSHV)–induced endothelial tumor, develops only in a small fraction of individuals infected with HHV-8. We hypothesized that inborn errors of immunity to HHV-8 might underlie the exceedingly rare development of classic KS in childhood. We report here autosomal recessive OX40 deficiency in an otherwise healthy adult with childhood-onset classic KS. OX40 is a co-stimulatory receptor expressed on activated T cells. Its ligand, OX40L, is expressed on various cell types, including endothelial cells. We found OX40L was abundantly expressed in KS lesions. The mutant OX40 protein was poorly expressed on the cell surface and failed to bind OX40L, resulting in complete functional OX40 deficiency. The patient had a low proportion of effector memory CD4+ T cells in the peripheral blood, consistent with impaired CD4+ T cell responses to recall antigens in vitro. The proportion of effector memory CD8+ T cells was less diminished. The proportion of circulating memory B cells was low, but the antibody response in vivo was intact, including the response to a vaccine boost. Together, these findings suggest that human OX40 is necessary for robust CD4+ T cell memory and confers apparently selective protective immunity against HHV-8 infection in endothelial cells.
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Affiliation(s)
- Minji Byun
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA.
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31
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Martel-Jantin C, Pedergnana V, Nicol JTJ, Leblond V, Trégouët DA, Tortevoye P, Plancoulaine S, Coursaget P, Touzé A, Abel L, Gessain A. Merkel cell polyomavirus infection occurs during early childhood and is transmitted between siblings. J Clin Virol 2013; 58:288-91. [PMID: 23829968 DOI: 10.1016/j.jcv.2013.06.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 05/24/2013] [Accepted: 06/04/2013] [Indexed: 10/26/2022]
Abstract
Merkel cell polyomavirus (MCPyV) is thought to be the etiological agent of Merkel cell carcinoma, but little is known about its distribution and modes of transmission. We conducted seroepidemiological surveys in more than 1000 individuals, from two populations from Cameroon. Overall MCPyV seroprevalence was high in both populations (>75% in adults). Data from the first population, comprising mainly children, indicated that MCPyV infections mostly occurred during early childhood, after the disappearance of specific maternal antibodies. Results from the second family-based population provided evidence for familial aggregation of MCPyV infection status. We observed significant sib-sib correlation (odds ratio=3.42 [95% CI 1.27-9.19], p=0.014), particularly for siblings close together in age, and a trend for mother-child correlation (OR=2.71 [0.86-8.44], p=0.08). Overall, our results suggest that MCPyV infection is acquired through close contact, possibly involving saliva and/or the skin, especially between young siblings and between mothers and their children.
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Affiliation(s)
- Claire Martel-Jantin
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, F-75015 Paris, France
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Crequer A, Picard C, Pedergnana V, Lim A, Zhang SY, Abel L, Majewski S, Casanova JL, Jablonska S, Orth G, Jouanguy E. EVER2 deficiency is associated with mild T-cell abnormalities. J Clin Immunol 2012; 33:14-21. [PMID: 22903682 DOI: 10.1007/s10875-012-9749-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 07/18/2012] [Indexed: 10/28/2022]
Abstract
Epidermodysplasia verruciformis (EV) is a rare genodermatosis characterized by persistent flat warts or pityriasis versicolor-like lesions caused by betapapillomaviruses (EV-HPVs). Autosomal recessive EVER1 and EVER2 deficiencies account for EV in most patients. The mechanisms by which mutations in these partners of the Zinc transporter ZnT1 impair host defense against EV-HPVs are still poorly understood. Keratinocytes of EVER-deficient patients display an alteration of zinc homeostasis and an enhanced proliferative activity. Since EVER proteins are highly expressed in T lymphocytes, we aimed to assess the impact of EVER2 deficiency on T-cell development and function. We studied circulating lymphocyte populations in three adult EV patients sharing the same EVER2 mutation (T150fsX3). We found a normal count of CD4(+) and CD8(+) T cells and a normal proliferative capacity in response to anti-CD3 stimulation. However, we observed a significant increase of memory CD4(+) and effector memory CD8(+) T cells, a bias of the TCR Vαβ and Vγδ repertoires and an increase of skin-homing CD4(+) T-cell subsets. Our findings suggest that EVER2-deficient patients display mild T-cell abnormalities. It remains unclear whether these abnormalities result from EVER deficiency, chronic EV-HPV infection, or both.
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Affiliation(s)
- Amandine Crequer
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
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Crequer A, Troeger A, Patin E, Ma CS, Picard C, Pedergnana V, Fieschi C, Lim A, Abhyankar A, Gineau L, Mueller-Fleckenstein I, Schmidt M, Taieb A, Krueger J, Abel L, Tangye SG, Orth G, Williams DA, Casanova JL, Jouanguy E. Human RHOH deficiency causes T cell defects and susceptibility to EV-HPV infections. J Clin Invest 2012; 122:3239-47. [PMID: 22850876 DOI: 10.1172/jci62949] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 06/20/2012] [Indexed: 01/05/2023] Open
Abstract
Epidermodysplasia verruciformis (EV) is a rare genetic disorder characterized by increased susceptibility to specific human papillomaviruses, the betapapillomaviruses. These EV-HPVs cause warts and increase the risk of skin carcinomas in otherwise healthy individuals. Inactivating mutations in epidermodysplasia verruciformis 1 (EVER1) or EVER2 have been identified in most, but not all, patients with autosomal recessive EV. We found that 2 young adult siblings presenting with T cell deficiency and various infectious diseases, including persistent EV-HPV infections, were homozygous for a mutation creating a stop codon in the ras homolog gene family member H (RHOH) gene. RHOH encodes an atypical Rho GTPase expressed predominantly in hematopoietic cells. Patients' circulating T cells contained predominantly effector memory T cells, which displayed impaired TCR signaling. Additionally, very few circulating T cells expressed the β7 integrin subunit, which homes T cells to specific tissues. Similarly, Rhoh-null mice exhibited a severe overall T cell defect and abnormally small numbers of circulating β7-positive cells. Expression of the WT, but not of the mutated RHOH, allele in Rhoh-/- hematopoietic stem cells corrected the T cell lymphopenia in mice after bone marrow transplantation. We conclude that RHOH deficiency leads to T cell defects and persistent EV-HPV infections, suggesting that T cells play a role in the pathogenesis of chronic EV-HPV infections.
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Affiliation(s)
- Amandine Crequer
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
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Pedergnana V, Abdel-Hamid M, Guergnon J, Mohsen A, Le Fouler L, Theodorou I, Mohamed MK, Fontanet A, Plancoulaine S, Abel L. Analysis of IL28B variants in an Egyptian population defines the 20 kilobases minimal region involved in spontaneous clearance of hepatitis C virus. PLoS One 2012; 7:e38578. [PMID: 22719902 PMCID: PMC3375300 DOI: 10.1371/journal.pone.0038578] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 05/07/2012] [Indexed: 12/31/2022] Open
Abstract
Spontaneous clearance of hepatitis C virus (HCV) occurs in ~30% of acute infections. Host genetics play a major role in HCV clearance, with a strong effect of single nucleotide polymorphisms (SNPs) of the IL28B gene already found in different populations, mostly infected with viral genotypes 1 and 3. Egypt has the highest prevalence of HCV infection in the world, which is mostly due to viral genotype 4. We investigated the role of several IL28B SNPs in HCV spontaneous clearance in an Egyptian population. We selected nine SNPs within the IL28B genomic region covering the linkage disequilibrium (LD) block known to be associated with HCV clearance in European populations. These SNPs were genotyped in 261 HCV-infected Egyptian subjects (130 with spontaneous clearance and 131 with chronic infection). The most associated SNPs were rs12979860 (P = 1.6 × 10(-7)) and the non-synonymous IL28B SNP, rs8103142 (P = 1.6 × 10(-7)). Interestingly, three SNPs at the two bounds of the region were monomorphic, reducing the size of the LD block in which the causal variants are potentially located to ∼20 kilobases. HCV clearance in Egypt was associated with a region of IL28B smaller than that identified in European populations, and involved the non-synonymous IL28B SNP, rs8103142.
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Affiliation(s)
- Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U980, Paris, France
- University Paris Descartes, Paris, France
| | - Mohamed Abdel-Hamid
- Viral Hepatitis Research Laboratory, National Hepatology and Tropical Medicine Research Institute, Cairo, Egypt
- Department of Microbiology, Minia Faculty of Medicine, Minia, Egypt
| | - Julien Guergnon
- Laboratory of Immunity and Infection, Institut National de la Santé et de la Recherche Médicale UMR-S 945, University Pierre et Marie Curie Paris 6, Groupe Hospitalier Pitié-Salpêtrière AP-HP, Paris, France
| | - Amira Mohsen
- Department of Community, Environmental and Occupational Medicine, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Lénaïg Le Fouler
- Institut Pasteur, Unité d’Epidémiologie des Maladies Emergentes, Paris, France
| | - Ioannis Theodorou
- Laboratory of Immunity and Infection, Institut National de la Santé et de la Recherche Médicale UMR-S 945, University Pierre et Marie Curie Paris 6, Groupe Hospitalier Pitié-Salpêtrière AP-HP, Paris, France
| | - Mostafa Kamal Mohamed
- Department of Community, Environmental and Occupational Medicine, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Arnaud Fontanet
- Institut Pasteur, Unité d’Epidémiologie des Maladies Emergentes, Paris, France
- Conservatoire National des Arts et Métiers, Chaire Santé et Développement, Paris, France
| | - Sabine Plancoulaine
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U980, Paris, France
- University Paris Descartes, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U980, Paris, France
- University Paris Descartes, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
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35
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Pedergnana V, Gessain A, Tortevoye P, Byun M, Bacq-Daian D, Boland A, Casanova JL, Abel L, Plancoulaine S. A major locus on chromosome 3p22 conferring predisposition to human herpesvirus 8 infection. Eur J Hum Genet 2012; 20:690-5. [PMID: 22258534 DOI: 10.1038/ejhg.2011.260] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Infection with human herpesvirus 8 (HHV-8), the etiological agent of Kaposi's sarcoma, has been shown to display strong familial aggregation, in countries in which HHV-8 infection is endemic. We investigated 40 large families (608 subjects aged one to 88 years) living in an isolated area of Cameroon in which HHV-8 is highly endemic. We performed a two-step genetic analysis for HHV-8 infection status (HHV-8+/HHV-8- determined by immunofluorescence) consisting of an initial segregation analysis followed by a model-based genome-wide linkage analysis. Overall HHV-8 seroprevalence was 60%, increasing with age. Segregation analysis provided strong evidence for a recessive major gene conferring predisposition to HHV-8 infection. This gene is predicted to have a major effect during childhood, with almost all homozygous predisposed subjects (∼7% of the population) becoming infected by the age of 10. Linkage analysis was carried out on the 15 most informative families, corresponding to 205 genotyped subjects. A single region on chromosome 3p22 was significantly linked to HHV-8 infection (LOD score=3.83, P=2.0 × 10(-5)). This study provides the first evidence that HHV-8 infection in children in endemic areas has a strong genetic basis involving at least one recessive major locus on chromosome 3p22.
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Affiliation(s)
- Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U980, Paris, France
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Leroy S, Moshous D, Cassar O, Reguerre Y, Byun M, Pedergnana V, Canioni D, Gessain A, Oksenhendler E, Fieschi C, Mahlaoui N, Rivière JP, Herbigneaux RM, Muszlak M, Arnaud JP, Fischer A, Picard C, Blanche S, Plancoulaine S, Casanova JL. Multicentric Castleman disease in an HHV8-infected child born to consanguineous parents with systematic review. Pediatrics 2012; 129:e199-203. [PMID: 22157133 PMCID: PMC3273364 DOI: 10.1542/peds.2010-2739] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Childhood multicentric Castleman disease (MCD) is a rare and unexplained lymphoproliferative disorder. We report a human herpesvirus-8 (HHV-8)-infected child, born to consanguineous Comorian parents, who displayed isolated MCD in the absence of any known immunodeficiency. We also systematically review the clinical features of the 32 children previously reported with isolated and unexplained MCD. The characteristics of this patient and the geographic areas of origin of most previous cases suggest that pediatric MCD is associated with HHV-8 infection. Moreover, as previously suggested for Kaposi sarcoma, MCD in childhood may result from inborn errors of immunity to HHV-8 infection.
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Affiliation(s)
- Sandrine Leroy
- Department of Pediatric Immunology and Hematology, Necker Hospital, AP-HP, Paris, France.
| | - Despina Moshous
- aDepartment of Pediatric Immunology and Hematology, Necker Hospital, AP-HP, Paris, France;,bParis-Descartes University, Necker Medical School, Paris, France
| | - Olivier Cassar
- Institut Pasteur, Unité d’Epidémiologie et Physiologie des Virus Oncogènes, Département de Virologie, Paris, France;,Centre National de la Recherche, URA3015, Paris, France
| | - Yves Reguerre
- Pediatric Onco-Hematology Unit, St Denis La Réunion, France, EU
| | - Minji Byun
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York
| | - Vincent Pedergnana
- Unit of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U980, Paris, France
| | - Danielle Canioni
- bParis-Descartes University, Necker Medical School, Paris, France;,Department of Pathology, Necker Hospital, Paris-Descartes University, Paris, France
| | - Antoine Gessain
- Institut Pasteur, Unité d’Epidémiologie et Physiologie des Virus Oncogènes, Département de Virologie, Paris, France;,Centre National de la Recherche, URA3015, Paris, France
| | - Eric Oksenhendler
- Department of Clinical Immunology, Saint-Louis Hospital, and René Diderot University, Paris, France
| | - Claire Fieschi
- Department of Clinical Immunology, Saint-Louis Hospital, and René Diderot University, Paris, France
| | - Nizar Mahlaoui
- aDepartment of Pediatric Immunology and Hematology, Necker Hospital, AP-HP, Paris, France;,bParis-Descartes University, Necker Medical School, Paris, France
| | - Jean-Pierre Rivière
- Department of Pathology, Centre Hospitalier Regional Félix Guyon, La Réunion, France
| | | | - Matthias Muszlak
- Departement of Pediatrics, Mayotte Hospital, Mamoudzou, Mayotte, France
| | | | - Alain Fischer
- aDepartment of Pediatric Immunology and Hematology, Necker Hospital, AP-HP, Paris, France;,bParis-Descartes University, Necker Medical School, Paris, France;,Institut National de la Santé et de la Recherche Médicale U768, Necker Branch, Paris, France; and
| | - Capucine Picard
- bParis-Descartes University, Necker Medical School, Paris, France;,Institut National de la Santé et de la Recherche Médicale U768, Necker Branch, Paris, France; and,Study Center for Primary Immunodeficiencies Necker Hospital, AP-HP, Paris, France
| | - Stéphane Blanche
- aDepartment of Pediatric Immunology and Hematology, Necker Hospital, AP-HP, Paris, France;,bParis-Descartes University, Necker Medical School, Paris, France
| | - Sabine Plancoulaine
- bParis-Descartes University, Necker Medical School, Paris, France;,Unit of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U980, Paris, France
| | - Jean-Laurent Casanova
- aDepartment of Pediatric Immunology and Hematology, Necker Hospital, AP-HP, Paris, France;,bParis-Descartes University, Necker Medical School, Paris, France;,St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York;,Unit of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U980, Paris, France
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