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Miller C, Ettridge K, Pettigrew S, Wittert G, Coveney J, Wakefield M, Roder D, Durkin S, Martin J, Kay E, Dono J. Warning labels for sugar-sweetened beverages and fruit juice: evaluation of 27 different labels on health effects, sugar content, energy and exercise equivalency. Public Health 2024; 230:138-148. [PMID: 38547760 DOI: 10.1016/j.puhe.2024.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/19/2023] [Accepted: 01/26/2024] [Indexed: 04/16/2024]
Abstract
OBJECTIVES Front-of-pack warning labels may reduce consumption of sugar-sweetened beverages, potentially mitigating negative health outcomes. Comparisons between different warning label types to inform future research and policy directions are lacking. This study compared 27 warning labels across six message types for their potential to reduce sugar-sweetened beverage consumption. DESIGN AND METHODS A national sample of regular soda (n = 2578) and juice (n = 1048) consumers aged 14-60 years participated in an online survey. Participants evaluated randomly allocated labels; one from each of six warning label sets (health-graphic, sugar-pictogram, sugar-text, exercise equivalents, health-text, energy information) on four measures of perceived effectiveness (PE: overall effectiveness, discourage from drinking, emotional response, persuasive potential). Participants could also provide open comments. A general linear model compared differences in mean scores across label sets for each measure of PE. RESULTS PE ratings differed significantly between label sets. Labels clearly quantifying sugar content (sugar-teaspoons) received consistently high PE ratings, whereas 'high in sugar' labels did not. Health-graphic labels were rated highly across all PE measures except persuasive potential. Exercise labels only rated highly on persuasive potential. Health-text results were mixed, and energy labels were consistently low. CONCLUSIONS Simple, factual labels were easily interpreted and perceived as most effective. Labels quantifying sugar content were consistently high performers and should be advanced into policy to help decrease overconsumption of sugar-sweetened beverages.
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Affiliation(s)
- C Miller
- School of Public Health, The University of Adelaide, Adelaide, Australia; Health Policy Centre, South Australian Health and Medical Research Institute, Adelaide, Australia.
| | - K Ettridge
- Health Policy Centre, South Australian Health and Medical Research Institute, Adelaide, Australia; School of Psychology, The University of Adelaide, Adelaide, Australia
| | - S Pettigrew
- The George Institute for Global Health, University of New South Wales, Sydney, Australia
| | - G Wittert
- Freemasons Centre for Male Health and Wellbeing, South Australian Health and Medical Research Institute and Faculty of Health Sciences, University of Adelaide, Adelaide, Australia
| | - J Coveney
- College of Nursing and Health Sciences, Flinders University, Adelaide, Australia
| | - M Wakefield
- Centre for Behavioural Research in Cancer, Cancer Council Victoria, Melbourne, Australia; School of Psychological Sciences, The University of Melbourne, Melbourne, Australia
| | - D Roder
- Cancer Epidemiology and Population Health, University of South Australia, Australia
| | - S Durkin
- Centre for Behavioural Research in Cancer, Cancer Council Victoria, Melbourne, Australia; School of Psychological Sciences, The University of Melbourne, Melbourne, Australia
| | - J Martin
- Food for Health Alliance, Cancer Council Victoria, Melbourne, Australia
| | - E Kay
- Health Policy Centre, South Australian Health and Medical Research Institute, Adelaide, Australia; College of Education Psychology and Social Work, Flinders University, Adelaide, Australia
| | - J Dono
- Health Policy Centre, South Australian Health and Medical Research Institute, Adelaide, Australia; School of Psychology, The University of Adelaide, Adelaide, Australia
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Jenkins DR, Auckland C, Chadwick C, Dodgson AR, Enoch DA, Goldenberg SD, Hussain A, Martin J, Spooner E, Whalley T. A practical approach to screening for carbapenemase-producing Enterobacterales- views of a group of multidisciplinary experts from English hospitals. BMC Infect Dis 2024; 24:444. [PMID: 38671365 DOI: 10.1186/s12879-024-09307-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
INTRODUCTION Carbapenemase-producing Enterobacterales (CPE) are an important public health threat, with costly operational and economic consequences for NHS Integrated Care Systems and NHS Trusts. UK Health Security Agency guidelines recommend that Trusts use locally developed risk assessments to accurately identify high-risk individuals for screening, and implement the most appropriate method of testing, but this presents many challenges. METHODS A convenience sample of cross-specialty experts from across England met to discuss the barriers and practical solutions to implementing UK Health Security Agency framework into operational and clinical workflows. The group derived responses to six key questions that are frequently asked about screening for CPE. KEY FINDINGS Four patient groups were identified for CPE screening: high-risk unplanned admissions, high-risk elective admissions, patients in high-risk units, and known positive contacts. Rapid molecular testing is a preferred screening method for some of these settings, offering faster turnaround times and more accurate results than culture-based testing. It is important to stimulate action now, as several lessons can be learnt from screening during the COVID-19 pandemic, as well as from CPE outbreaks. CONCLUSION Further decisive and instructive information is needed to establish CPE screening protocols based on local epidemiology and risk factors. Local management should continually evaluate local epidemiology, analysing data and undertaking frequent prevalence studies to understand risks, and prepare resources- such as upscaled screening- to prevent increasing prevalence, clusters or outbreaks. Rapid molecular-based methods will be a crucial part of these considerations, as they can reduce unnecessary isolation and opportunity costs.
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Affiliation(s)
- D R Jenkins
- University Hospitals of Leicester NHS Trust, Leicester, UK.
| | - C Auckland
- Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - C Chadwick
- Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - A R Dodgson
- Manchester University NHS FT, Manchester, UK
| | - D A Enoch
- Cambridge University NHS Foundation Trust, Cambridge, UK
| | - S D Goldenberg
- Centre for Clinical Infection and Diagnostics Research, Guy's and Saint Thomas' Hospitals NHS Trust, London, UK
| | - A Hussain
- University Hospitals Birmingham NHS Foundation Trust, West Midlands, UK
| | - J Martin
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - E Spooner
- Royal Wolverhampton NHS Trust, Wolverhampton, UK
| | - T Whalley
- Lancashire & South Cumbria ICB, Preston, UK
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Baudouin R, Hans S, Lisan Q, Morin B, Adimi Y, Martin J, Lechien JR, Tartour E, Badoual C. Prognostic Significance of the Microenvironment in Human Papillomavirus Oropharyngeal Carcinoma: A Systematic Review. Laryngoscope 2024; 134:1507-1516. [PMID: 37642393 DOI: 10.1002/lary.31010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/01/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
OBJECTIVE The immune microenvironment of HPV-associated (HPV+) oropharyngeal squamous cell carcinomas (OPSCCs) (HPV+OPSCCs) differs from that of HPV-independent oropharyngeal cancers (HPV-independent OPSCCs). The literature on the subject is very abundant, demanding an organized synthesis of this wealth of information to evaluate the hypothesis associating the favorable prognosis of HPV+OPSCC patients with a different immune microenvironment. A systematic review of the literature was conducted regarding the microenvironment of HPV+OPSCCs. DATA SOURCE MEDLINE/PubMed, Embase, and Cochrane Library databases. REVIEW METHODS A literature search was performed following PRISMA guidelines (Moher D. PLoS Med. 2009). The PEO (Population, Exposure, and Outcome) framework is detailed as follows: P: patients with oropharyngeal squamous cell carcinomas, E: human papillomavirus (HPV), and O: histological and immunological composition of the tumoral microenvironment (TME). No meta-analysis was performed. RESULTS From 1,202 studies that were screened, 58 studies were included (n = 6,474 patients; n = 3,581 (55%) HPV+OPSCCs and n = 2,861(45%) HPV-independent OPSCCs). The presence of tumor-infiltrating lymphocytes (TIL), CD3+ in 1,733 patients, CD4+ in 520 patients, and CD8+ (cytotoxic T lymphocytes (CTL)) in 3,104 patients, and high levels of PD-L1 expression in 1,222 patients is strongly correlated with an improved clinical outcome in HPV+OPSCCs. CONCLUSION This systematic review provides the most comprehensive information on the immune microenvironment of HPV+OPSCCs to date. Tumor-infiltrating lymphocytes and PD-L1 expression are associated with a favorable prognosis. B, CD8+ and resident memory cells densities are higher in HPV+OPSCCs. The importance of myeloid lineages is still a matter of debate and research. LEVEL OF EVIDENCE NA Laryngoscope, 134:1507-1516, 2024.
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Affiliation(s)
- R Baudouin
- Department of Otolaryngology-Head & Neck Surgery, Foch Hospital, Suresnes, France
- School of Medicine, UFR Simone Veil, Université Versailles Saint-Quentin-en-Yvelines (Paris Saclay University), Montigny-le-Bretonneux, France
| | - S Hans
- Department of Otolaryngology-Head & Neck Surgery, Foch Hospital, Suresnes, France
- School of Medicine, UFR Simone Veil, Université Versailles Saint-Quentin-en-Yvelines (Paris Saclay University), Montigny-le-Bretonneux, France
| | - Q Lisan
- Department of Otolaryngology-Head & Neck Surgery, Foch Hospital, Suresnes, France
- School of Medicine, UFR Simone Veil, Université Versailles Saint-Quentin-en-Yvelines (Paris Saclay University), Montigny-le-Bretonneux, France
| | - B Morin
- Department of Pathology, Hôpital Européen Georges Pompidou, Université Paris Cité, INSERM, PARCC, Paris, France
- Department of Biological Immunology, Hôpital Européen Georges Pompidou, Université Paris Cité, INSERM, PARCC, Paris, France
| | - Y Adimi
- Department of Pathology, Hôpital Européen Georges Pompidou, Université Paris Cité, INSERM, PARCC, Paris, France
- Department of Biological Immunology, Hôpital Européen Georges Pompidou, Université Paris Cité, INSERM, PARCC, Paris, France
| | - J Martin
- Department of Pathology, Hôpital Européen Georges Pompidou, Université Paris Cité, INSERM, PARCC, Paris, France
- Department of Biological Immunology, Hôpital Européen Georges Pompidou, Université Paris Cité, INSERM, PARCC, Paris, France
| | - J R Lechien
- Department of Otolaryngology-Head & Neck Surgery, Foch Hospital, Suresnes, France
- School of Medicine, UFR Simone Veil, Université Versailles Saint-Quentin-en-Yvelines (Paris Saclay University), Montigny-le-Bretonneux, France
| | - E Tartour
- Department of Biological Immunology, Hôpital Européen Georges Pompidou, Université Paris Cité, INSERM, PARCC, Paris, France
| | - C Badoual
- Department of Pathology, Hôpital Européen Georges Pompidou, Université Paris Cité, INSERM, PARCC, Paris, France
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Farkas K, Kevill JL, Adwan L, Garcia-Delgado A, Dzay R, Grimsley JMS, Lambert-Slosarska K, Wade MJ, Williams RC, Martin J, Drakesmith M, Song J, McClure V, Jones DL. Near-source passive sampling for monitoring viral outbreaks within a university residential setting. Epidemiol Infect 2024; 152:e31. [PMID: 38329110 PMCID: PMC10894896 DOI: 10.1017/s0950268824000190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024] Open
Abstract
Wastewater-based epidemiology (WBE) has proven to be a powerful tool for the population-level monitoring of pathogens, particularly severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For assessment, several wastewater sampling regimes and methods of viral concentration have been investigated, mainly targeting SARS-CoV-2. However, the use of passive samplers in near-source environments for a range of viruses in wastewater is still under-investigated. To address this, near-source passive samples were taken at four locations targeting student hall of residence. These were chosen as an exemplar due to their high population density and perceived risk of disease transmission. Viruses investigated were SARS-CoV-2 and its variants of concern (VOCs), influenza viruses, and enteroviruses. Sampling was conducted either in the morning, where passive samplers were in place overnight (17 h) and during the day, with exposure of 7 h. We demonstrated the usefulness of near-source passive sampling for the detection of VOCs using quantitative polymerase chain reaction (qPCR) and next-generation sequencing (NGS). Furthermore, several outbreaks of influenza A and sporadic outbreaks of enteroviruses (some associated with enterovirus D68 and coxsackieviruses) were identified among the resident student population, providing evidence of the usefulness of near-source, in-sewer sampling for monitoring the health of high population density communities.
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Affiliation(s)
- Kata Farkas
- School of Environmental and Natural Sciences, Bangor University, Bangor, UK
| | - Jessica L. Kevill
- School of Environmental and Natural Sciences, Bangor University, Bangor, UK
| | - Latifah Adwan
- School of Environmental and Natural Sciences, Bangor University, Bangor, UK
| | | | - Rande Dzay
- School of Environmental and Natural Sciences, Bangor University, Bangor, UK
| | - Jasmine M. S. Grimsley
- Data Analytics & Surveillance Group, UK Health Security Agency, London, UK
- The London Data Company, London, UK
| | | | - Matthew J. Wade
- Data Analytics & Surveillance Group, UK Health Security Agency, London, UK
- School of Engineering, Newcastle University, Newcastle-upon-Tyne, UK
| | - Rachel C. Williams
- School of Environmental and Natural Sciences, Bangor University, Bangor, UK
| | - Javier Martin
- Division of Vaccines, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Mark Drakesmith
- Communicable Disease Surveillance Centre, Public Health Wales, Cardiff, UK
| | - Jiao Song
- Communicable Disease Surveillance Centre, Public Health Wales, Cardiff, UK
| | - Victoria McClure
- Communicable Disease Surveillance Centre, Public Health Wales, Cardiff, UK
| | - Davey L. Jones
- School of Environmental and Natural Sciences, Bangor University, Bangor, UK
- Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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5
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Ademuyiwa AO, Bhangu A, Chakrabortee S, Glasbey J, Kamarajah SK, Ledda V, Li E, Morton D, Nepogodiev D, Picciochi M, Simoes JFF, Lapitan MC, Cheetham M, Forkman E, El-Boghdadly E, Ghosh D, Harrison EM, Hutchinson P, Lawani I, Aguilera ML, Martin J, Meara JG, Ntirenganya F, Medina ARDL, Tabiri S. Strategies to strengthen elective surgery systems during the SARS-CoV-2 pandemic: systematic review and framework development. Br J Surg 2024; 111:znad405. [PMID: 38300731 PMCID: PMC10833142 DOI: 10.1093/bjs/znad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/12/2023] [Accepted: 10/27/2023] [Indexed: 02/03/2024]
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6
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Barmada A, Handfield LF, Godoy-Tena G, de la Calle-Fabregat C, Ciudad L, Arutyunyan A, Andrés-León E, Hoo R, Porter T, Oszlanczi A, Richardson L, Calero-Nieto FJ, Wilson NK, Marchese D, Sancho-Serra C, Carrillo J, Presas-Rodríguez S, Ramo-Tello C, Ruiz-Sanmartin A, Ferrer R, Ruiz-Rodriguez JC, Martínez-Gallo M, Munera-Campos M, Carrascosa JM, Göttgens B, Heyn H, Prigmore E, Casafont-Solé I, Solanich X, Sánchez-Cerrillo I, González-Álvaro I, Raimondo MG, Ramming A, Martin J, Martínez-Cáceres E, Ballestar E, Vento-Tormo R, Rodríguez-Ubreva J. Single-cell multi-omics analysis of COVID-19 patients with pre-existing autoimmune diseases shows aberrant immune responses to infection. Eur J Immunol 2024; 54:e2350633. [PMID: 37799110 DOI: 10.1002/eji.202350633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023]
Abstract
In COVID-19, hyperinflammatory and dysregulated immune responses contribute to severity. Patients with pre-existing autoimmune conditions can therefore be at increased risk of severe COVID-19 and/or associated sequelae, yet SARS-CoV-2 infection in this group has been little studied. Here, we performed single-cell analysis of peripheral blood mononuclear cells from patients with three major autoimmune diseases (rheumatoid arthritis, psoriasis, or multiple sclerosis) during SARS-CoV-2 infection. We observed compositional differences between the autoimmune disease groups coupled with altered patterns of gene expression, transcription factor activity, and cell-cell communication that substantially shape the immune response under SARS-CoV-2 infection. While enrichment of HLA-DRlow CD14+ monocytes was observed in all three autoimmune disease groups, type-I interferon signaling as well as inflammatory T cell and monocyte responses varied widely between the three groups of patients. Our results reveal disturbed immune responses to SARS-CoV-2 in patients with pre-existing autoimmunity, highlighting important considerations for disease treatment and follow-up.
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Affiliation(s)
- Anis Barmada
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Gerard Godoy-Tena
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | | | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Anna Arutyunyan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Eduardo Andrés-León
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Regina Hoo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Tarryn Porter
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Agnes Oszlanczi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Laura Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Fernando J Calero-Nieto
- Department of Haematology and Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Nicola K Wilson
- Department of Haematology and Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Carmen Sancho-Serra
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Silvia Presas-Rodríguez
- MS Unit, Department of Neurology, Germans Trias i Pujol University Hospital, Barcelona, Spain
| | - Cristina Ramo-Tello
- MS Unit, Department of Neurology, Germans Trias i Pujol University Hospital, Barcelona, Spain
| | - Adolfo Ruiz-Sanmartin
- Department of Intensive Care, Hospital Universitari Vall d'Hebron, Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Ricard Ferrer
- Department of Intensive Care, Hospital Universitari Vall d'Hebron, Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Juan Carlos Ruiz-Rodriguez
- Department of Intensive Care, Hospital Universitari Vall d'Hebron, Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mónica Martínez-Gallo
- Division of Immunology, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mónica Munera-Campos
- Dermatology Service, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
| | - Jose Manuel Carrascosa
- Dermatology Service, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
| | - Berthold Göttgens
- Department of Haematology and Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Ivette Casafont-Solé
- Department of Rheumatology, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
- Department of Infectious Diseases, Germans Trias i Pujol University Hospital, Barcelona, Spain
| | - Xavier Solanich
- Department of Internal Medicine, Hospital Universitari de Bellvitge, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | | | | | - Maria Gabriella Raimondo
- Department of Internal Medicine 3, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Andreas Ramming
- Department of Internal Medicine 3, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Eva Martínez-Cáceres
- Division of Immunology, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma, Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
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Casares-Marfil D, Martínez-Bueno M, Borghi MO, Pons-Estel G, Reales G, Zuo Y, Espinosa G, Radstake T, van den Hoogen LL, Wallace C, Guthridge J, James JA, Cervera R, Meroni PL, Martin J, Knight JS, Alarcón-Riquelme ME, Sawalha AH. A genome-wide association study suggests new susceptibility loci for primary antiphospholipid syndrome. medRxiv 2023:2023.12.05.23299396. [PMID: 38405993 PMCID: PMC10889036 DOI: 10.1101/2023.12.05.23299396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Objectives Primary antiphospholipid syndrome (PAPS) is a rare autoimmune disease characterized by the presence of antiphospholipid antibodies and the occurrence of thrombotic events and pregnancy complications. Our study aimed to identify novel genetic susceptibility loci associated with PAPS. Methods We performed a genome-wide association study comprising 5,485 individuals (482 affected individuals) of European ancestry. Significant and suggestive independent variants from a meta-analysis of approximately 7 million variants were evaluated for functional and biological process enrichment. The genetic risk variability for PAPS in different populations was also assessed. Hierarchical clustering, Mahalanobis distance, and Dirichlet Process Mixtures with uncertainty clustering methods were used to assess genetic similarities between PAPS and other immune-mediated diseases. Results We revealed genetic associations with PAPS in a regulatory locus within the HLA class II region near HLA-DRA and in STAT4 with a genome-wide level of significance. 34 additional suggestive genetic susceptibility loci for PAPS were also identified. The disease risk allele in the HLA class II locus is associated with overexpression of HLA-DRB6 , HLA-DRB9 , HLA-DPB2 , HLA-DQA2 and HLA-DQB2 , and is independent of the association between PAPS and HLA-DRB1*1302 . Functional analyses highlighted immune and nervous system related pathways in PAPS-associated loci. The comparison with other immune-mediated diseases revealed a close genetic relatedness to neuromyelitis optica, systemic sclerosis, and Sjögren's syndrome, suggesting colocalized causal variations close to STAT4 , TNPO3 , and BLK . Conclusions This study represents a comprehensive large-scale genetic analysis for PAPS and provides new insights into the genetic basis and pathophysiology of this rare disease.
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Chatzigeorgiou C, Barrett JH, Martin J, Morgan AW, Mackie SL. Estimating overdiagnosis in giant cell arteritis diagnostic pathways using genetic data: genetic association study. Rheumatology (Oxford) 2023:kead643. [PMID: 38048604 DOI: 10.1093/rheumatology/kead643] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/12/2023] [Accepted: 10/02/2023] [Indexed: 12/06/2023] Open
Abstract
OBJECTIVES Giant cell arteritis (GCA) may be confirmed by temporal artery biopsy (TAB) but false negatives can occur. GCA may be overdiagnosed in TAB-negative cases, or if neither TAB nor imaging is done. We used Human Leucocyte Antigen (HLA) genetic association of TAB-positive GCA as an "unbiased umpire" test to estimate historic overdiagnosis of GCA. METHODS Patients diagnosed with GCA between 1990-2014 were genotyped. During this era, vascular imaging alone was rarely used to diagnose GCA. HLA region variants were jointly imputed from genome-wide genotypic data of cases and controls. Per-allele frequencies across all HLA variants with p< 1.0x1 0 -5 were compared with population control data to estimate overdiagnosis rates in cases without a positive TAB. RESULTS Genetic data from 663 GCA patients were compared with data from 2619 population controls. TAB-negative GCA (n = 147) and GCA without TAB result (n = 160) had variant frequencies intermediate between TAB-positive GCA (n = 356) and population controls. For example, the allele frequency of HLA-DRB1*04 was 32% for TAB-positive GCA, 29% for GCA without TAB result, 27% for TAB-negative GCA and 20% in population controls. Making several strong assumptions, we estimated that around two-thirds of TAB-negative cases and one-third of cases without TAB result may have been overdiagnosed. From these data, TAB sensitivity is estimated as 88%. CONCLUSIONS Conservatively assuming 95% specificity, TAB has a negative likelihood ratio of around 0.12. Our method for utilising standard genotyping data as an "unbiased umpire" might be used as a way of comparing the accuracy of different diagnostic pathways.
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Affiliation(s)
| | | | - Javier Martin
- Institute of Parasitology and Biomedicine Lopez-Neyra, CSIC, Granada, 18016, Spain
| | - Ann W Morgan
- School of Medicine, University of Leeds, Leeds, UK
- NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- NIHR Leeds Medicines and In Vitro Diagnostics Co-operative, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Sarah L Mackie
- School of Medicine, University of Leeds, Leeds, UK
- NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
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Volle R, Luo L, Razafindratsimandresy R, Sadeuh-Mba SA, Gouandjika-Valisache I, Horwood P, Duong V, Buchy P, Joffret ML, Huang Z, Duizer E, Martin J, Chakrabarti LA, Dussart P, Jouvenet N, Delpeyroux F, Bessaud M. Neutralization of African enterovirus A71 genogroups by antibodies to canonical genogroups. J Gen Virol 2023; 104. [PMID: 37909282 DOI: 10.1099/jgv.0.001911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Enterovirus 71 (EV-A71) is a major public health problem, causing a range of illnesses from hand-foot-and-mouth disease to severe neurological manifestations. EV-A71 strains have been phylogenetically classified into eight genogroups (A to H), based on their capsid-coding genomic region. Genogroups B and C have caused large outbreaks worldwide and represent the two canonical circulating EV-A71 subtypes. Little is known about the antigenic diversity of new genogroups as compared to the canonical ones. Here, we compared the antigenic features of EV-A71 strains that belong to the canonical B and C genogroups and to genogroups E and F, which circulate in Africa. Analysis of the peptide sequences of EV-A71 strains belonging to different genogroups revealed a high level of conservation of the capsid residues involved in known linear and conformational neutralization antigenic sites. Using a published crystal structure of the EV-A71 capsid as a model, we found that most of the residues that are seemingly specific to some genogroups were mapped outside known antigenic sites or external loops. These observations suggest a cross-neutralization activity of anti-genogroup B or C antibodies against strains of genogroups E and F. Neutralization assays were performed with diverse rabbit and mouse anti-EV-A71 sera, anti-EV-A71 human standards and a monoclonal neutralizing antibody. All the batches of antibodies that were tested successfully neutralized all available isolates, indicating an overall broad cross-neutralization between the canonical genogroups B and C and genogroups E and F. A panel constituted of more than 80 individual human serum samples from Cambodia with neutralizing antibodies against EV-A71 subgenogroup C4 showed quite similar cross-neutralization activities between isolates of genogroups C4, E and F. Our results thus indicate that the genetic drift underlying the separation of EV-A71 strains into genogroups A, B, C, E and F does not correlate with the emergence of antigenically distinct variants.
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Affiliation(s)
- Romain Volle
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
- Present address: Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Lingjie Luo
- Present address: Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, PR China
- Institut Pasteur, Control of Chronic Viral Infections (CIVIC) Group, Virus and Immunity Unit, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | | | - Serge Alain Sadeuh-Mba
- Present address: Maryland Department of Agriculture, Salisbury Animal Health Laboratory, Salisbury, USA
- Centre Pasteur of Cameroon, Yaounde, Cameroon
| | | | - Paul Horwood
- Present address: James Cook University, Townsville, Australia
- Institut Pasteur of Cambodia, Phnom Penh, Cambodia
| | - Veasna Duong
- Institut Pasteur of Cambodia, Phnom Penh, Cambodia
| | | | - Marie-Line Joffret
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
| | - Zhong Huang
- Present address: Fudan University, Shanghai, PR China
- Institut Pasteur of Shanghai - Chinese Academy of Sciences, Shanghai, PR China
| | - Erwin Duizer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Javier Martin
- National Institute for Biological Standards and Control (NIBSC), Potters Bar, UK
| | - Lisa A Chakrabarti
- Institut Pasteur, Control of Chronic Viral Infections (CIVIC) Group, Virus and Immunity Unit, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | | | - Nolwenn Jouvenet
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
| | - Francis Delpeyroux
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
| | - Maël Bessaud
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
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10
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Kamau E, Bessaud M, Majumdar M, Martin J, Simmonds P, Harvala H. Estimating prevalence of Enterovirus D111 in human and non-human primate populations using cross-sectional serology. J Gen Virol 2023; 104:001915. [PMID: 37910158 PMCID: PMC10768692 DOI: 10.1099/jgv.0.001915] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023] Open
Abstract
Enteroviruses primarily affect young children with a varying severity of disease. Recent outbreaks of severe respiratory and neurological disease due to EV-D68 and EV-A71, as well as atypical hand-foot-and-mouth-disease due to CVA6, have brought to light the potency of enteroviruses to emerge as severe human pathogens. Enterovirus D111 (EV-D111) is an enteric pathogen initially detected in Central Africa in human and wildlife samples and was recently detected in environmental samples. The natural history and epidemiology of EV-D111 are poorly studied. Here, the presence of serum neutralizing antibodies to EV-D111 was estimated in human and wildlife samples from five countries. We report high prevalence of neutralizing antibodies measured against EV-D111 in human populations (range, 55-83 %), a proxy for previous infection, which indicates active virus circulation in absence of detection in clinical cases and a high number of undiagnosed infections. Notably, seroprevalence in samples from the UK varied by age and was higher in children and older adults (1-5 and >60 years old), but lower in ages 11-60. EV-D111 seroprevalence in apes and Old World monkeys was 50 % (33-66 %), which also suggests prior exposure and supports existing knowledge of enterovirus circulation in wild and captive apes and Old World monkeys. Generally, reported cases of infection likely underestimate the prevalence of infection particularly when the knowledge of community transmission is limited. Continued serologic surveillance and detection of EV-D111 in clinical and environmental samples will allow for a more robust assessment of EV-D111 epidemiology.
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Affiliation(s)
- Everlyn Kamau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mael Bessaud
- Institut Pasteur-Unité de Biologie des Virus Entériques, Paris, France
- WHO Collaborating Centre for Enteroviruses and Viral Vaccines, Paris, France
| | - Manasi Majumdar
- Science Research and Innovation, Medicines and Healthcare Products Regulatory Agency, South Mimms, UK
| | - Javier Martin
- Science Research and Innovation, Medicines and Healthcare Products Regulatory Agency, South Mimms, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Heli Harvala
- Microbiology Services, NHS Blood Transfusion, London, UK
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Rodriguez-Martin I, Villanueva-Martin G, Guillen-Del-Castillo A, Ortego-Centeno N, Callejas JL, Simeón-Aznar CP, Martin J, Acosta-Herrera M. Contribution of Telomere Length to Systemic Sclerosis Onset: A Mendelian Randomization Study. Int J Mol Sci 2023; 24:15589. [PMID: 37958573 PMCID: PMC10648506 DOI: 10.3390/ijms242115589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Although previous studies have suggested a relationship between telomere shortening and systemic sclerosis (SSc), the association between these two traits remains poorly understood. The objective of this study was to assess the causal relationship between telomere length in leukocytes (LTL) and SSc using the two-sample Mendelian randomization approach, with the genome-wide association study data for both LTL and SSc. The results of inverse-variance weighted regression (OR = 0.716 [95% CI 0.528-0.970], p = 0.031) and the Mendelian randomization pleiotropy residual sum and outlier method (OR = 0.716 [95% CI 0.563-0.911], p = 0.035) indicate an association between telomere length and SSc. Specifically, longer genetically predicted LTL is associated with a reduced risk of SSc. Sensitivity tests highlight the significant roles of the variants rs10936599 and rs2736100 annotated to the TERC and TERT genes, respectively. Our findings suggest an influence of telomere length in leukocytes on the development of SSc.
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Affiliation(s)
| | | | | | - Norberto Ortego-Centeno
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, 18012 Granada, Spain
- Department of Medicine, University of Granada, 18016 Granada, Spain
| | - José L. Callejas
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, 18012 Granada, Spain
| | - Carmen P. Simeón-Aznar
- Department of Internal Medicine, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
| | - Javier Martin
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, 18016 Granada, Spain
| | - Marialbert Acosta-Herrera
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, 18016 Granada, Spain
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, 18012 Granada, Spain
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12
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Bubba L, Benschop KSM, Blomqvist S, Duizer E, Martin J, Shaw AG, Bailly JL, Rasmussen LD, Baicus A, Fischer TK, Harvala H. Wastewater Surveillance in Europe for Non-Polio Enteroviruses and Beyond. Microorganisms 2023; 11:2496. [PMID: 37894154 PMCID: PMC10608818 DOI: 10.3390/microorganisms11102496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Wastewater surveillance (WWS) was developed in the early 1960s for the detection of poliovirus (PV) circulation in the population. It has been used to monitor several pathogens, including non-polio enteroviruses (NPEVs), which are increasingly recognised as causes of morbidity in children. However, when applying WWS to a new pathogen, it is important to consider the purpose of such a study as well as the suitability of the chosen methodology. With this purpose, the European Non-Polio Enterovirus Network (ENPEN) organised an expert webinar to discuss its history, methods, and applications; its evolution from a culture-based method to molecular detection; and future implementation of next generation sequencing (NGS). The first simulation experiments with PV calculated that a 400 mL sewage sample is sufficient for the detection of viral particles if 1:10,000 people excrete poliovirus in a population of 700,000 people. If the method is applied correctly, several NPEV types are detected. Despite culture-based methods remaining the gold standard for WWS, direct methods followed by molecular-based and sequence-based assays have been developed, not only for enterovirus but for several pathogens. Along with case-based sentinel and/or syndromic surveillance, WWS for NPEV and other pathogens represents an inexpensive, flexible, anonymised, reliable, population-based tool for monitoring outbreaks and the (re)emergence of these virus types/strains within the general population.
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Affiliation(s)
- Laura Bubba
- European Non-Polio Enterovirus Network (E.N.P.E.N.), 1207 Geneva, Switzerland
| | - Kimberley S. M. Benschop
- National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands; (K.S.M.B.); (E.D.)
| | - Soile Blomqvist
- Finnish Institute for Health and Welfare, P.O. Box 95, 70701 Kuopio, Finland;
| | - Erwin Duizer
- National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands; (K.S.M.B.); (E.D.)
| | - Javier Martin
- Division of Vaccines, Medicines and Healthcare Products Regulatory Agency, Potters Bar EN6 3QG, UK;
| | - Alexander G. Shaw
- MRC Centre for Global Infectious Disease Analysis, London SW7 2AZ, UK;
- Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London SW7 2BX, UK
| | - Jean-Luc Bailly
- Laboratoire Micro-Organismes Genome Environnement (LMGE), Université Clermont Auvergne CNRS, 63001 Clermont-Ferrand, France;
| | - Lasse D. Rasmussen
- Virus Surveillance and Research Section Department of Virus and Microbiological Special Diagnostics Statens Serum Institut, DK-2300 Copenhagen, Denmark;
| | - Anda Baicus
- Enteric Viral Infections Laboratory, Cantacuzino National Institute for Medical-Military Research and Development, 020123 Bucharest, Romania;
| | - Thea K. Fischer
- Department of Clinical Research, University Hospital of Nordsjaelland, 3400 Hilleroed, Denmark
- Department of Public Health, University of Copenhagen, 1172 Copenhagen, Denmark
| | - Heli Harvala
- Microbiology Services National Health Service (NHS) Blood and Transplant, London NW9 5BG, UK;
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
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13
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Harz D, Catalán Gamonal B, Matute García S, Jeremias F, Martin J, Fresno MC. Prevalence and severity of molar-incisor hypomineralization, is there an association with socioeconomic status? A cross-sectional study in Chilean schoolchildren. Eur Arch Paediatr Dent 2023; 24:577-584. [PMID: 37432610 DOI: 10.1007/s40368-023-00820-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 06/24/2023] [Indexed: 07/12/2023]
Abstract
PURPOSE Data about molar-incisor hypomineralization (MIH) prevalence and its severity remains limited for some Latin American countries. Furthermore, its association with socioeconomic status (SES) is still unclear. Thus, this study aims to determine the prevalence and severity of MIH in Santiago, Chile and explore its association with SES. METHODS A cross-sectional study with schoolchildren between 6 and 12 years was conducted. Children were evaluated using the European Academy of Paediatric Dentistry to diagnose MIH, and the Mathu-Muju and Wright criteria to determine its severity. RESULTS A total of 1,270 children were included. The MIH prevalence was 12.8% without association with gender (p = 0.609). Prevalence was higher among schoolchildren ages 8 and 9 (p = 0.002), and in lower SES (p = 0.007). MIH mild cases were the most prevalent (63%), and severity was not related to gender (p = 0.656), age (p = 0.060), or SES (p = 0.174). CONCLUSIONS The prevalence of MIH in the province of Santiago, Chile is 12.8% and was found to have a higher incidence in 8-9-year-old students and among those categorized by low SES. Furthermore, MIH prevalence was associated with low SES. IMPLICATIONS Public health policies to address MIH in Chile should start with schoolchildren aged 8 to 9, and with low SES.
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Affiliation(s)
- D Harz
- Dental School, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | | | - F Jeremias
- Graduate Program in Dental Science Araraquara School of Dentistry, UNESP Univ Estadual Paulista São Paulo, Araraquara, São Paulo, Brazil
| | - J Martin
- Department of Restorative Dentistry, Faculty of Dentistry, University of Chile, Olivos 943, Independencia, Santiago, Chile
| | - M C Fresno
- Faculty of Dentistry, University of Chile, Santiago, Chile.
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14
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Davlantes E, Jorba J, Henderson E, Bullard K, Deka MA, Kfutwah A, Martin J, Bessaud M, Shulman LM, Hawes K, Diop OM, Bandyopadhyay AS, Zipursky S, Burns CC. Notes from the Field: Circulating Vaccine-Derived Poliovirus Type 2 Emergences Linked to Novel Oral Poliovirus Vaccine Type 2 Use - Six African Countries, 2021-2023. MMWR Morb Mortal Wkly Rep 2023; 72:1041-1042. [PMID: 37733626 PMCID: PMC10519714 DOI: 10.15585/mmwr.mm7238a4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
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15
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Shaw AG, Mampuela TK, Lofiko EL, Pratt C, Troman C, Bujaki E, O'Toole Á, Akello JO, Aziza AA, Lusamaki EK, Makangara JC, Akonga M, Lay Y, Nsunda B, White B, Jorgensen D, Pukuta E, Riziki Y, Rankin KE, Rambaut A, Ahuka-Mundeke S, Muyembe JJ, Martin J, Grassly NC, Mbala-Kingebeni P. Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study. Nat Microbiol 2023; 8:1634-1640. [PMID: 37591995 PMCID: PMC10465353 DOI: 10.1038/s41564-023-01453-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
Timely detection of outbreaks is needed for poliovirus eradication, but gold standard detection in the Democratic Republic of the Congo takes 30 days (median). Direct molecular detection and nanopore sequencing (DDNS) of poliovirus in stool samples is a promising fast method. Here we report prospective testing of stool samples from suspected polio cases, and their contacts, in the Democratic Republic of the Congo between 10 August 2021 and 4 February 2022. DDNS detected polioviruses in 62/2,339 (2.7%) of samples, while gold standard combination of cell culture, quantitative PCR and Sanger sequencing detected polioviruses in 51/2,339 (2.2%) of the same samples. DDNS provided case confirmation in 7 days (median) in routine surveillance conditions. DDNS enabled confirmation of three serotype 2 circulating vaccine-derived poliovirus outbreaks 23 days (mean) earlier (range 6-30 days) than the gold standard method. The mean sequence similarity between sequences obtained by the two methods was 99.98%. Our data confirm the feasibility of implementing DDNS in a national poliovirus laboratory.
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Affiliation(s)
- Alexander G Shaw
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
| | - Tresor Kabeya Mampuela
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | - Catherine Pratt
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Catherine Troman
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Erika Bujaki
- Department of Vaccines, National Institute for Biological Standards and Control (NIBSC), Medicines and Healthcare products Regulatory Agency, Potters Bar, UK
| | - Áine O'Toole
- Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK
| | - Joyce Odeke Akello
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Adrienne Amuri Aziza
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Eddy Kinganda Lusamaki
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
- TransVIHMI (Recherches Translationnelles sur le VIH et les Maladies Infectieuses endémiques et émergentes), University of Montpellier (UM), French National Research Institute for Sustainable Development (IRD), INSERM, Montpellier, France
| | - Jean Claude Makangara
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Marceline Akonga
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Yvonne Lay
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Bibiche Nsunda
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Bailey White
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - David Jorgensen
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Elizabeth Pukuta
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Yogolelo Riziki
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK
| | - Steve Ahuka-Mundeke
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Jean-Jacques Muyembe
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Javier Martin
- Department of Vaccines, National Institute for Biological Standards and Control (NIBSC), Medicines and Healthcare products Regulatory Agency, Potters Bar, UK
| | - Nicholas C Grassly
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Placide Mbala-Kingebeni
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
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16
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Villanueva-Martin G, Acosta-Herrera M, Carmona EG, Kerick M, Ortego-Centeno N, Callejas-Rubio JL, Mages N, Klages S, Börno S, Timmermann B, Bossini-Castillo L, Martin J. Non-classical circulating monocytes expressing high levels of microsomal prostaglandin E2 synthase-1 tag an aberrant IFN-response in systemic sclerosis. J Autoimmun 2023; 140:103097. [PMID: 37633117 DOI: 10.1016/j.jaut.2023.103097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/28/2023]
Abstract
Systemic sclerosis (SSc) is a complex disease that affects the connective tissue, causing fibrosis. SSc patients show altered immune cell composition and activation in the peripheral blood (PB). PB monocytes (Mos) are recruited into tissues where they differentiate into macrophages, which are directly involved in fibrosis. To understand the role of CD14+ PB Mos in SSc, a single-cell transcriptome analysis (scRNA-seq) was conducted on 8 SSc patients and 8 controls. Using unsupervised clustering methods, CD14+ cells were assigned to 11 clusters, which added granularity to the known monocyte subsets: classical (cMos), intermediate (iMos) and non-classical Mos (ncMos) or type 2 dendritic cells. NcMos were significantly overrepresented in SSc patients and showed an active IFN-signature and increased expression levels of PTGES, in addition to monocyte motility and adhesion markers. We identified a SSc-related cluster of IRF7+ STAT1+ iMos with an aberrant IFN-response. Finally, a depletion of M2 polarised cMos in SSc was observed. Our results highlighted the potential of PB Mos as biomarkers for SSc and provided new possibilities for putative drug targets for modulating the innate immune response in SSc.
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Affiliation(s)
- Gonzalo Villanueva-Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Marialbert Acosta-Herrera
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain; Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Elio G Carmona
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain; Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Martin Kerick
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Norberto Ortego-Centeno
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain; Department of Medicine, University of Granada, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Jose Luis Callejas-Rubio
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Norbert Mages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Sven Klages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Stefan Börno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Lara Bossini-Castillo
- Department of Genetics and Biotechnology Institute, Biomedical Research Centre (CIBM), University of Granada, 18100, Granada, Spain; Advanced Therapies and Biomedical Technologies (TEC-14), Biosanitary Research Institute Ibs. GRANADA, 18016, Granada, Spain.
| | - Javier Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
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17
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Singanayagam A, Klapsa D, Burton-Fanning S, Hand J, Wilton T, Stephens L, Mate R, Shillitoe B, Celma C, Slatter M, Flood T, Gopal R, Martin J, Zambon M. Asymptomatic immunodeficiency-associated vaccine-derived poliovirus infections in two UK children. Nat Commun 2023; 14:3413. [PMID: 37296153 PMCID: PMC10251316 DOI: 10.1038/s41467-023-39094-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
Increasing detections of vaccine-derived poliovirus (VDPV) globally, including in countries previously declared polio free, is a public health emergency of international concern. Individuals with primary immunodeficiency (PID) can excrete polioviruses for prolonged periods, which could act as a source of cryptic transmission of viruses with potential to cause neurological disease. Here, we report on the detection of immunodeficiency-associated VDPVs (iVDPV) from two asymptomatic male PID children in the UK in 2019. The first child cleared poliovirus with increased doses of intravenous immunoglobulin, the second child following haematopoetic stem cell transplantation. We perform genetic and phenotypic characterisation of the infecting strains, demonstrating intra-host evolution and a neurovirulent phenotype in transgenic mice. Our findings highlight a pressing need to strengthen polio surveillance. Systematic collection of stool from asymptomatic PID patients who are at high risk for poliovirus excretion could improve the ability to detect and contain iVDPVs.
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Affiliation(s)
- Anika Singanayagam
- Polio Reference Service, UK Health Security Agency, Colindale, London, UK.
- Department of Infectious Disease, Imperial College London, London, UK.
| | - Dimitra Klapsa
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, London, UK
| | - Shirelle Burton-Fanning
- Microbiology and Virology Services, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Julian Hand
- Polio Reference Service, UK Health Security Agency, Colindale, London, UK
| | - Thomas Wilton
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, London, UK
| | - Laura Stephens
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, London, UK
| | - Ryan Mate
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, London, UK
| | - Benjamin Shillitoe
- Paediatric Stem Cell Transplant Unit, Great North Children's Hospital, Newcastle upon Tyne, UK
- Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Cristina Celma
- Polio Reference Service, UK Health Security Agency, Colindale, London, UK
| | - Mary Slatter
- Paediatric Stem Cell Transplant Unit, Great North Children's Hospital, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Terry Flood
- Paediatric Stem Cell Transplant Unit, Great North Children's Hospital, Newcastle upon Tyne, UK
| | - Robin Gopal
- Polio Reference Service, UK Health Security Agency, Colindale, London, UK
| | - Javier Martin
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, London, UK
| | - Maria Zambon
- Polio Reference Service, UK Health Security Agency, Colindale, London, UK.
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González‐Serna D, Shi C, Kerick M, Hankinson J, Ding J, McGovern A, Tutino M, Villanueva‐Martin G, Ortego‐Centeno N, Callejas JL, Martin J, Orozco G. Identification of Mechanisms by Which Genetic Susceptibility Loci Influence Systemic Sclerosis Risk Using Functional Genomics in Primary T Cells and Monocytes. Arthritis Rheumatol 2023; 75:1007-1020. [PMID: 36281738 PMCID: PMC10953390 DOI: 10.1002/art.42396] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 02/04/2022] [Revised: 09/08/2022] [Accepted: 10/18/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Systemic sclerosis (SSc) is a complex autoimmune disease with a strong genetic component. However, most of the genes associated with the disease are still unknown because associated variants affect mostly noncoding intergenic elements of the genome. We used functional genomics to translate the genetic findings into a better understanding of the disease. METHODS Promoter capture Hi-C and RNA-sequencing experiments were performed in CD4+ T cells and CD14+ monocytes from 10 SSc patients and 5 healthy controls to link SSc-associated variants with their target genes, followed by differential expression and differential interaction analyses between cell types. RESULTS We linked SSc-associated loci to 39 new potential target genes and confirmed 7 previously known SSc-associated genes. We highlight novel causal genes, such as CXCR5, as the most probable candidate gene for the DDX6 locus. Some previously known SSc-associated genes, such as IRF8, STAT4, and CD247, showed cell type-specific interactions. We also identified 15 potential drug targets already in use in other similar immune-mediated diseases that could be repurposed for SSc treatment. Furthermore, we observed that interactions were directly correlated with the expression of important genes implicated in cell type-specific pathways and found evidence that chromatin conformation is associated with genotype. CONCLUSION Our study revealed potential causal genes for SSc-associated loci, some of them acting in a cell type-specific manner, suggesting novel biologic mechanisms that might mediate SSc pathogenesis.
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Affiliation(s)
- David González‐Serna
- Institute of Parasitology and Biomedicine López‐Neyra, Consejo Superior de Investigaciones Científicas (IPBLN‐CSIC)GranadaSpain
| | - Chenfu Shi
- Division of Musculoskeletal and Dermatological Sciences, Centre for Genetics and Genomics Versus Arthritis, School of Biological Sciences, Faculty of Biology, Medicine and HealthThe University of ManchesterManchesterUK
| | - Martin Kerick
- Institute of Parasitology and Biomedicine López‐Neyra, Consejo Superior de Investigaciones Científicas (IPBLN‐CSIC)GranadaSpain
| | - Jenny Hankinson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and HealthThe University of ManchesterManchesterUK
| | - James Ding
- Division of Musculoskeletal and Dermatological Sciences, Centre for Genetics and Genomics Versus Arthritis, School of Biological Sciences, Faculty of Biology, Medicine and HealthThe University of ManchesterManchesterUK
| | - Amanda McGovern
- Division of Musculoskeletal and Dermatological Sciences, Centre for Genetics and Genomics Versus Arthritis, School of Biological Sciences, Faculty of Biology, Medicine and HealthThe University of ManchesterManchesterUK
| | - Mauro Tutino
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and HealthThe University of ManchesterManchesterUK
| | - Gonzalo Villanueva‐Martin
- Institute of Parasitology and Biomedicine López‐Neyra, Consejo Superior de Investigaciones Científicas (IPBLN‐CSIC)GranadaSpain
| | - Norberto Ortego‐Centeno
- Department of Internal Medicine, Hospital Universitario San CecilioInstitute for Biosanitary Research of Granada (ibs.GRANADA)GranadaSpain
| | - José Luis Callejas
- Department of Internal Medicine, Hospital Universitario San CecilioInstitute for Biosanitary Research of Granada (ibs.GRANADA)GranadaSpain
| | - Javier Martin
- Institute of Parasitology and Biomedicine López‐Neyra, Consejo Superior de Investigaciones Científicas (IPBLN‐CSIC)GranadaSpain
| | - Gisela Orozco
- Division of Musculoskeletal and Dermatological Sciences, Centre for Genetics and Genomics Versus Arthritis, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, and NIHR Manchester Biomedical Research CentreManchester University NHS Foundation Trust, Manchester Academic Health Science CentreManchesterUK
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19
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Ortiz-Fernández L, Carmona EG, Kerick M, Lyons P, Carmona FD, López Mejías R, Khor CC, Grayson PC, Tombetti E, Jiang L, Direskeneli H, Saruhan-Direskeneli G, Callejas-Rubio JL, Vaglio A, Salvarani C, Hernández-Rodríguez J, Cid MC, Morgan AW, Merkel PA, Burgner D, Smith KG, Gonzalez-Gay MA, Sawalha AH, Martin J, Marquez A. Identification of new risk loci shared across systemic vasculitides points towards potential target genes for drug repurposing. Ann Rheum Dis 2023; 82:837-847. [PMID: 36797040 PMCID: PMC10314028 DOI: 10.1136/ard-2022-223697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/04/2023] [Indexed: 02/18/2023]
Abstract
OBJECTIVES The number of susceptibility loci currently associated with vasculitis is lower than in other immune-mediated diseases due in part to small cohort sizes, a consequence of the low prevalence of vasculitides. This study aimed to identify new genetic risk loci for the main systemic vasculitides through a comprehensive analysis of their genetic overlap. METHODS Genome-wide data from 8467 patients with any of the main forms of vasculitis and 29 795 healthy controls were meta-analysed using ASSET. Pleiotropic variants were functionally annotated and linked to their target genes. Prioritised genes were queried in DrugBank to identify potentially repositionable drugs for the treatment of vasculitis. RESULTS Sixteen variants were independently associated with two or more vasculitides, 15 of them representing new shared risk loci. Two of these pleiotropic signals, located close to CTLA4 and CPLX1, emerged as novel genetic risk loci in vasculitis. Most of these polymorphisms appeared to affect vasculitis by regulating gene expression. In this regard, for some of these common signals, potential causal genes were prioritised based on functional annotation, including CTLA4, RNF145, IL12B, IL5, IRF1, IFNGR1, PTK2B, TRIM35, EGR2 and ETS2, each of which has key roles in inflammation. In addition, drug repositioning analysis showed that several drugs, including abatacept and ustekinumab, could be potentially repurposed in the management of the analysed vasculitides. CONCLUSIONS We identified new shared risk loci with functional impact in vasculitis and pinpointed potential causal genes, some of which could represent promising targets for the treatment of vasculitis.
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Affiliation(s)
| | - Elio G Carmona
- Institute of Parasitology and Biomedicine "López- Neyra", CSIC, Granada, Spain
- Unidad de Enfermedades Autoinmunes Sistémicas, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria de Granada ibs.GRANADA, Granada, Spain
| | - Martin Kerick
- Institute of Parasitology and Biomedicine "López- Neyra", CSIC, Granada, Spain
| | - Paul Lyons
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Francisco David Carmona
- Departamento de Genética e Instituto de Biotecnología, Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Raquel López Mejías
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Spain
| | - Chiea Chuen Khor
- Duke-NUS Medical School, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Peter C Grayson
- Systemic Autoimmunity Branch, NIAMS, National Institutes of Health, Bethesda, Maryland, USA
| | - Enrico Tombetti
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Hospital, Milan, Italy
- Department of Biomedical and Clinical Sciences L. Sacco, Milan University, Milan, Italy
| | - Lindi Jiang
- Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
- Evidence-Based Medicine Center, Fudan University, Shanghai, China
| | - Haner Direskeneli
- Department of Internal Medicine, Division of Rheumatology, Marmara University, Faculty of Medicine, Istanbul, Turkey
| | | | - José-Luis Callejas-Rubio
- Systemic Autoimmune Diseases Unit, San Cecilio University Hospital, Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Augusto Vaglio
- Department of Biomedical Experimental and Clinical Sciences "Mario Serio", University of Florence, Florence, Italy
- Nephrology and Dialysis Unit, Meyer Children's Hospital, Florence, Italy
| | - Carlo Salvarani
- Rheumatology Unit, Azienda USL-IRCCS di Reggio Emilia and Azienda Ospedaliero - Universitaria di Modena, Università di Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Jose Hernández-Rodríguez
- Department of Autoimmune Diseases, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Maria Cinta Cid
- Department of Autoimmune Diseases, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ann W Morgan
- School of Medicine and Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- NIHR Leeds Biomedical Research Centre and NIHR Leeds Medtech and In vitro Diagnostics Co-Operative, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Peter A Merkel
- Division of Rheumatology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Epidemiology, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David Burgner
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Department of General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Kenneth Gc Smith
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Miguel Angel Gonzalez-Gay
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, University of Cantabria, Santander, Spain
| | - Amr H Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Javier Martin
- Institute of Parasitology and Biomedicine "López- Neyra", CSIC, Granada, Spain
| | - Ana Marquez
- Institute of Parasitology and Biomedicine "López- Neyra", CSIC, Granada, Spain
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20
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Cosio BG, Shafiek H, Iglesias A, Mosteiro M, Gonzalez-Piñeiro A, Rodríguez M, García-Cosío M, Busto E, Martin J, Mejías L, Benito A, López Vilaro L, Gómez C. Validation of a Pathological Score for the Assessment of Bronchial Biopsies in Severe Uncontrolled Asthma: Beyond Blood Eosinophils. Arch Bronconeumol 2023:S0300-2896(23)00172-2. [PMID: 37414638 DOI: 10.1016/j.arbres.2023.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Blood eosinophil count (BEC) is currently used as a surrogate marker of T2 inflammation in severe asthma but its relationship with tissue T2-related changes is elusive. Bronchial biopsy could add reliable information but lacks standardization. OBJECTIVES To validate a systematic assessment of the bronchial biopsy for the evaluation of severe uncontrolled asthma (SUA) by standardizing a pathological score. METHODS A systematic assessment of submucosal inflammation, tissue eosinophilic count/field (TEC), goblet cells hyperplasia, epithelial changes, basement membrane thickening, prominent airway smooth muscle and submucosal mucous glands was initially agreed and validated in representative bronchial biopsies of 12 patients with SUA by 8 independent pathologists. In a second phase, 62 patients with SUA who were divided according to BEC≥300cells/mm3 or less underwent bronchoscopy with bronchial biopsies and the correlations between the pathological findings and the clinical characteristics were investigated. RESULTS The score yielded good agreement among pathologists regarding submucosal eosinophilia, TEC, goblet cells hyperplasia and mucosal glands (ICC=0.85, 0.81, 0.85 and 0.87 respectively). There was a statistically significant correlation between BEC and TEC (r=0.393, p=0.005) that disappeared after correction by oral corticosteroids (OCS) use (r=0.170, p=0.307). However, there was statistically significant correlation between FeNO and TEC (r=0.481, p=0.006) that was maintained after correction to OCS use (r=0.419, p=0.021). 82.4% of low-BEC had submucosal eosinophilia, 50% of them moderate to severe. CONCLUSION A standardized assessment of endobronchial biopsy is feasible and could be useful for a better phenotyping of SUA especially in those receiving OCS.
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Affiliation(s)
- Borja G Cosio
- Respiratory Medicine Department, Hospital Son Espases-IdISBa-CIBERES, Palma De Mallorca, Spain.
| | - Hanaa Shafiek
- Chest Diseases Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Amanda Iglesias
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid. Instituto de Investigación Sanitaria Illes Balears (IdISBa), Hospital Universitario Son Espases, Palma De Mallorca, Spain
| | - Mar Mosteiro
- Respiratory Medicine Department, Hospital Alvaro Cunqueiro, Vigo, Spain
| | | | - Marta Rodríguez
- Pathology Department, Hospital Universitario de Salamanca, Spain
| | | | - Eladio Busto
- Pathology Department, Hospital Lucus Augusti, Lugo, Spain
| | - Javier Martin
- Pathology Department, Hospital Puerta de Hierro, Madrid, Spain
| | - Luis Mejías
- Pathology Department, Hospital Rey Juan Carlos, Madrid, Spain
| | - Amparo Benito
- Pathology Department, Hospital Ramon y Cajal, Madrid, Spain
| | | | - Cristina Gómez
- Pathology Department, Hospital Universitario Son Espases-IdISBa, Palma De Mallorca, Spain
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21
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Kingston NJ, Snowden JS, Martyna A, Shegdar M, Grehan K, Tedcastle A, Pegg E, Fox H, Macadam AJ, Martin J, Hogle JM, Rowlands DJ, Stonehouse NJ. Production of antigenically stable enterovirus A71 virus-like particles in Pichia pastoris as a vaccine candidate. J Gen Virol 2023; 104:001867. [PMID: 37390009 PMCID: PMC10773253 DOI: 10.1099/jgv.0.001867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/12/2023] [Indexed: 07/02/2023] Open
Abstract
Enterovirus A71 (EVA71) causes widespread disease in young children with occasional fatal consequences. In common with other picornaviruses, both empty capsids (ECs) and infectious virions are produced during the viral lifecycle. While initially antigenically indistinguishable from virions, ECs readily convert to an expanded conformation at moderate temperatures. In the closely related poliovirus, these conformational changes result in loss of antigenic sites required to elicit protective immune responses. Whether this is true for EVA71 remains to be determined and is the subject of this investigation.We previously reported the selection of a thermally resistant EVA71 genogroup B2 population using successive rounds of heating and passage. The mutations found in the structural protein-coding region of the selected population conferred increased thermal stability to both virions and naturally produced ECs. Here, we introduced these mutations into a recombinant expression system to produce stabilized virus-like particles (VLPs) in Pichia pastoris.The stabilized VLPs retain the native virion-like antigenic conformation as determined by reactivity with a specific antibody. Structural studies suggest multiple potential mechanisms of antigenic stabilization, however, unlike poliovirus, both native and expanded EVA71 particles elicited antibodies able to directly neutralize virus in vitro. Therefore, anti-EVA71 neutralizing antibodies are elicited by sites which are not canonically associated with the native conformation, but whether antigenic sites specific to the native conformation provide additional protective responses in vivo remains unclear. VLPs are likely to provide cheaper and safer alternatives for vaccine production and these data show that VLP vaccines are comparable with inactivated virus vaccines at inducing neutralising antibodies.
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Affiliation(s)
- Natalie J. Kingston
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Joseph S. Snowden
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Agnieszka Martyna
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, UK
| | - Mona Shegdar
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Keith Grehan
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Alison Tedcastle
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, UK
| | - Elaine Pegg
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, UK
| | - Helen Fox
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, UK
| | - Andrew J. Macadam
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, UK
| | - Javier Martin
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, UK
| | - James M. Hogle
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - David J. Rowlands
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Nicola J. Stonehouse
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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22
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Cullington HE, Jiang D, Broomfield SJ, Chung M, Craddock LC, Driver S, Edwards D, Gallacher JM, Jones LL, Koleva T, Martin J, Meakin H, Nash R, Rocca C, Schramm DR, Willmott NS, Vanat ZH. Cochlear implant services for children, young people and adults. Quality standard. Cochlear Implants Int 2023:1-13. [PMID: 37114384 DOI: 10.1080/14670100.2023.2197344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Affiliation(s)
- H E Cullington
- University of Southampton Auditory Implant Service, SO17 1BJ, UK
| | - D Jiang
- Hearing Implant Centre, Guy's and St. Thomas NHS Foundation Trust, London, UK
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - S J Broomfield
- West of England Hearing Implant Programme, University Hospitals Bristol and Weston NHS Foundation Trust, UK
| | - M Chung
- Auditory Implant Department, Royal National ENT & Eastman Dental Hospitals, University College London Hospitals NHS Foundation Trust, UK
| | - L C Craddock
- Midlands Hearing Implant Programme (Adult service), University Hospitals Birmingham NHS Foundation Trust, UK
| | - S Driver
- Hearing Implant Centre, Guy's and St. Thomas NHS Foundation Trust, London, UK
| | - D Edwards
- Emmeline Centre for Hearing Implants, Cambridge University Hospitals NHS Trust, UK
| | - J M Gallacher
- Scottish Cochlear Implant Program, Crosshouse Hospital, Kilmarnock, UK
| | - L Ll Jones
- North Wales Auditory Implant Service, Betsi Cadwaladr University Health Board, Bodelwyddan, UK
| | - T Koleva
- Emmeline Centre for Hearing Implants, Cambridge University Hospitals NHS Trust, UK
| | - J Martin
- Cochlear Implant Programme, Great Ormond Street Hospital For Children NHS Foundation Trust, London, UK
| | - H Meakin
- Emmeline Centre for Hearing Implants, Cambridge University Hospitals NHS Trust, UK
| | - R Nash
- Cochlear Implant Programme, Great Ormond Street Hospital For Children NHS Foundation Trust, London, UK
| | - C Rocca
- Hearing Implant Centre, Guy's and St. Thomas NHS Foundation Trust, London, UK
| | - D R Schramm
- University of Ottawa Auditory Implant Centre, Ottawa, Canada
| | - N S Willmott
- Auditory Implant Centre, Belfast Health and Social Care Trust, UK
| | - Z H Vanat
- Emmeline Centre for Hearing Implants, Cambridge University Hospitals NHS Trust, UK
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23
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Hulo S, Jacques J, Sihrener F, Wasielewski E, Jourdan L, Poslednik G, Poulet C, Turlotte A, Gey T, Douadi Y, Thiberville L, Dewolf M, Lecerf JM, Estevié I, Ricard V, Martin J, Romain AC, Locoge N, Matran R, Scherpereel A. 160P Non-invasive analysis of VOCs in exhaled air can distinguish healthy controls from lung cancer patients and may improve the effectiveness of lung cancer screening. J Thorac Oncol 2023. [DOI: 10.1016/s1556-0864(23)00414-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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24
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Akello JO, Bujaki E, Shaw AG, Khurshid A, Arshad Y, Troman C, Majumdar M, O'Toole Á, Rambaut A, Alam MM, Martin J, Grassly NC. Comparison of Eleven RNA Extraction Methods for Poliovirus Direct Molecular Detection in Stool Samples. Microbiol Spectr 2023; 11:e0425222. [PMID: 36939356 PMCID: PMC10100708 DOI: 10.1128/spectrum.04252-22] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/27/2023] [Indexed: 03/21/2023] Open
Abstract
Direct detection by PCR of poliovirus RNA in stool samples provides a rapid diagnostic and surveillance tool that can replace virus isolation by cell culture in global polio surveillance. The sensitivity of direct detection methods is likely to depend on the choice of RNA extraction method and sample volume. We report a comparative analysis of 11 nucleic acid extraction methods (7 manual and 4 semiautomated) for poliovirus molecular detection using stool samples (n = 59) that had been previously identified as poliovirus positive by cell culture. To assess the effect of RNA recovery methods, extracted RNA using each of the 11 methods was tested with a poliovirus-specific reverse transcription-quantitative PCR (RT-qPCR), a pan-poliovirus RT-PCR (near-whole-genome amplification), a pan-enterovirus RT-PCR (entire capsid region), and a nested VP1 PCR that is the basis of a direct detection method based on nanopore sequencing. We also assessed extracted RNA integrity and quantity. The overall effect of extraction method on poliovirus PCR amplification assays tested in this study was found to be statistically significant (P < 0.001), thus indicating that the choice of RNA extraction method is an important component that needs to be carefully considered for any diagnostic based on nucleic acid amplification. Performance of the methods was generally consistent across the different assays used. Of the 11 extraction methods tested, the MagMAX viral RNA isolation kit used manually or automatically was found to be the preferable method for poliovirus molecular direct detection considering performance, cost, and processing time. IMPORTANCE Poliovirus, the causative agent of poliomyelitis, is a target of global eradication led by the World Health Organization since 1988. Direct molecular detection and genomic sequencing without virus propagation in cell culture is arguably a critical tool in the final stages of polio eradication. Efficient recovery of good-quality viral RNA from stool samples is a prerequisite for direct detection by nucleic acid amplification. We tested 11 nucleic acid extraction methods to identify those facilitating sensitive, fast, simple, and cost-effective extraction, with flexibility for manual and automated protocols considered. Several different PCR assays were used to compare the recovered viral RNA to test suitability for poliovirus direct molecular detection. Our findings highlight the importance of choosing a suitable RNA extraction protocol and provide useful information to diagnostic laboratories and researchers facing the choice of RNA extraction method for direct molecular virus detection from stool.
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Affiliation(s)
- Joyce Odeke Akello
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Erika Bujaki
- Division of Vaccines, National Institute for Biological Standards and Control (NIBSC), MHRA, Potters Bar, United Kingdom
| | - Alexander G. Shaw
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Adnan Khurshid
- Department of Virology, National Institute for Health, Islamabad, Pakistan
| | - Yasir Arshad
- Department of Virology, National Institute for Health, Islamabad, Pakistan
| | - Catherine Troman
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Manasi Majumdar
- Division of Vaccines, National Institute for Biological Standards and Control (NIBSC), MHRA, Potters Bar, United Kingdom
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | | | - Javier Martin
- Division of Vaccines, National Institute for Biological Standards and Control (NIBSC), MHRA, Potters Bar, United Kingdom
| | - Nicholas C. Grassly
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
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Barral E, Martin J. Abstract No. 70 Safety and Clinical Outcomes of Aspiration Thrombectomy in Patients with Massive PE: A Single-Center Retrospective Review. J Vasc Interv Radiol 2023. [DOI: 10.1016/j.jvir.2022.12.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
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Ajrawat H, Buchholz J, Triana B, Pabon-Ramos W, Martin J, Kim C, Cline B, Ronald J. Abstract No. 583 Financial Analysis of Intravascular Ultrasound-Guided Transvenous Biopsy in an Outpatient Medicare Population. J Vasc Interv Radiol 2023. [DOI: 10.1016/j.jvir.2022.12.441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
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Gallo C, Cline B, Befera N, Ronald J, Martin J, Sag A, Pabon-Ramos W, Suhocki P, Smith T, Kim C. Abstract No. 97 Safety and Patency of Dedicated Venous Stents for Treatment of Thoracic Central Vein Stenosis Compared with Non-Venous Stents. J Vasc Interv Radiol 2023. [DOI: 10.1016/j.jvir.2022.12.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
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Barral E, Martin J. Abstract No. 501 Safety and Clinical Outcomes of Aspiration Thrombectomy in Patients with Intermediate-High Risk PE: A Single-Center Retrospective Review. J Vasc Interv Radiol 2023. [DOI: 10.1016/j.jvir.2022.12.359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
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Buchholz J, Ajrawat H, Cline B, Martin J, Kim C, Ronald J. Abstract No. 223 Intravascular Ultrasound-Guided Transvenous Biopsy of Retroperitoneal Lymph Nodes: Efficacy and Safety Compared with Percutaneous CT-Guided Biopsy. J Vasc Interv Radiol 2023. [DOI: 10.1016/j.jvir.2022.12.284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
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Grassly NC, Andrews N, Cooper G, Stephens L, Waight P, Jones CE, Heath PT, Calvert A, Southern J, Martin J, Miller E. Effect of maternal immunisation with multivalent vaccines containing inactivated poliovirus vaccine (IPV) on infant IPV immune response: A phase 4, multi-centre randomised trial. Vaccine 2023; 41:1299-1302. [PMID: 36690561 DOI: 10.1016/j.vaccine.2023.01.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023]
Abstract
Multivalent diphtheria, tetanus, acellular pertussis and inactivated poliovirus vaccine (DTaP/IPV) has been offered to pregnant women in the United Kingdom since 2012. To assess the impact of maternal DTaP/IPV immunisation on the infant immune response to IPV, we measured poliovirus-specific neutralising antibodies at 2, 5 and 13 months of age in a randomised, phase 4 study of Repevax or Boostrix/IPV in pregnancy and in a non-randomised group born to women not given DTaP/IPV in pregnancy. Infants whose mothers received DTaP/IPV were less likely to seroconvert after three IPV doses than those whose mothers did not receive DTaP/IPV. At 13 months of age, 63/110 (57.2 %), 46/108 (42.6 %) and 40/108 (37.0 %) were seropositive to types 1 to 3, compared with 20/22 (90.9 %), 20/22 (90.9 %) and 14/20 (70.0 %) (p-values 0.003, <0.001 and 0.012). UK infants whose mothers are given DTaP/IPV in pregnancy may be insufficiently protected against poliomyelitis until their pre-school booster.
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Affiliation(s)
- Nicholas C Grassly
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, UK.
| | - Nick Andrews
- Statistics and Modelling Economics Department, United Kingdom Health Security Agency (UKHSA), UK
| | - Gillian Cooper
- National Institute of Biological Standards and Control (NIBSC), Medicines and Healthcare products Regulatory Agency, UK
| | - Laura Stephens
- National Institute of Biological Standards and Control (NIBSC), Medicines and Healthcare products Regulatory Agency, UK
| | - Pauline Waight
- Immunisation and Countermeasures, National Infection Service, UKHSA, London, UK
| | - Christine E Jones
- Centre for Neonatal and Paediatric Infection & Vaccine Institute, St George's, University of London, London, UK; Faculty of Medicine and Institute for Life Sciences, University of Southampton and National Institute for Health and Care Research (NIHR) Southampton Clinical Research Facility and NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Paul T Heath
- Centre for Neonatal and Paediatric Infection & Vaccine Institute, St George's, University of London, London, UK; St George's University Hospitals NHS Foundation Trust, London, UK
| | - Anna Calvert
- Centre for Neonatal and Paediatric Infection & Vaccine Institute, St George's, University of London, London, UK; St George's University Hospitals NHS Foundation Trust, London, UK
| | - Jo Southern
- Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer Inc, Collegeville, PA, USA
| | - Javier Martin
- National Institute of Biological Standards and Control (NIBSC), Medicines and Healthcare products Regulatory Agency, UK
| | - Elizabeth Miller
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology & Population Health, London School of Hygiene & Tropical Medicine, Keppel St, London WC1E 7HT, UK
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Kingston NJ, Snowden JS, Martyna A, Shegdar M, Grehan K, Tedcastle A, Pegg E, Fox H, Macadam AJ, Martin J, Hogle JM, Rowlands DJ, Stonehouse NJ. Production of antigenically stable enterovirus A71 virus-like particles in Pichia pastoris as a vaccine candidate. bioRxiv 2023:2023.01.30.526315. [PMID: 36778240 PMCID: PMC9915507 DOI: 10.1101/2023.01.30.526315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Enterovirus A71 (EVA71) causes widespread disease in young children with occasional fatal consequences. In common with other picornaviruses, both empty capsids (ECs) and infectious virions are produced during the viral lifecycle. While initially antigenically indistinguishable from virions, ECs readily convert to an expanded conformation at moderate temperatures. In the closely related poliovirus, these conformational changes result in loss of antigenic sites required to elicit protective immune responses. Whether this is true for EVA71 remains to be determined and is the subject of this investigation. We previously reported the selection of a thermally resistant EVA71 genogroup B2 population using successive rounds of heating and passage. The mutations found in the structural protein-coding region of the selected population conferred increased thermal stability to both virions and naturally produced ECs. Here, we introduced these mutations into a recombinant expression system to produce stabilised virus-like particles (VLPs) in Pichia pastoris . The stabilised VLPs retain the native virion-like antigenic conformation as determined by reactivity with a specific antibody. Structural studies suggest multiple potential mechanisms of antigenic stabilisation, however, unlike poliovirus, both native and expanded EVA71 particles elicited antibodies able to directly neutralise virus in vitro . Therefore, the anti-EVA71 neutralising antibodies are elicited by sites which are not canonically associated with the native conformation, but whether antigenic sites specific to the native conformation provide additional protective responses in vivo remains unclear. VLPs are likely to provide cheaper and safer alternatives for vaccine production and these data show that VLP vaccines are comparable with inactivated virus vaccines at inducing neutralising antibodies.
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Affiliation(s)
- Natalie J Kingston
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Joseph S Snowden
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Agnieszka Martyna
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom
| | - Mona Shegdar
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Keith Grehan
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Alison Tedcastle
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom
| | - Elaine Pegg
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom
| | - Helen Fox
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom
| | - Andrew J Macadam
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom
| | - Javier Martin
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom
| | - James M Hogle
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - David J Rowlands
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Nicola J Stonehouse
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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Kasivisvanathan V, Murphy D, Link E, Lawrentschuk N, O’Brien J, Buteau J, Roberts M, Francis R, Tang C, Vela I, Thomas P, Rutherford N, Martin J, Frydenberg M, Shakher R, Wong LM, Taubman K, Lee S, Hsiao E, Nottage M, Kirkwood I, Iravani A, Williams S, Hofman M. Baseline PSMA PET-CT is prognostic for treatment failure in men with intermediate-to-high risk prostate cancer: 54 months follow-up of the proPSMA randomised trial. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)01275-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Rice W, Martin J, Hodgkin M, Carter J, Barrasa A, Sweeting K, Johnson R, Best E, Nahl J, Denton M, Hughes GJ. A protracted outbreak of difficult-to-treat resistant Pseudomonas aeruginosa in a haematology unit: a matched case-control study demonstrating increased risk with use of fluoroquinolone. J Hosp Infect 2023; 132:52-61. [PMID: 36563938 DOI: 10.1016/j.jhin.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/11/2022] [Accepted: 11/20/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Between September 2016 and November 2020, 17 cases of difficult-to-treat resistant Pseudomonas aeruginosa (DTR-PA) were reported in haematology patients at a tertiary referral hospital in the North of England. AIM A retrospective case-control study was conducted to investigate the association between DTR-PA infection and clinical interventions, patient movement, antimicrobial use and comorbidities. METHODS Cases were patients colonized or infected with the outbreak strain of DTR-PA who had been admitted to hospital prior to their positive specimen. Exposures were extracted from medical records, and cases were compared with controls using conditional logistic regression. Environmental and microbiological investigations were also conducted. FINDINGS Seventeen cases and 51 controls were included. The final model included age [>65 years, adjusted OR (aOR) 6.85, P=0.232], sex (aOR 0.60, P=0.688), admission under the transplant team (aOR 14.27, P=0.43) and use of ciprofloxacin (aOR 102.13, P=0.030). Investigations did not indicate case-to-case transmission or a point source, although a common environmental source was highly likely. CONCLUSION This study found that the use of fluoroquinolones is an independent risk factor for DTR-PA in haematology patients. Antimicrobial stewardship and review of fluoroquinolone prophylaxis should be considered as part of PA outbreak investigations in addition to standard infection control interventions.
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Affiliation(s)
- W Rice
- Field Epidemiology Training Programme, United Kingdom Heath Security Agency, London, UK; Field Service, United Kingdom Health Security Agency, Leeds, UK
| | - J Martin
- Leeds Teaching Hospitals NHS Trust, Leeds, UK.
| | - M Hodgkin
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - J Carter
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - A Barrasa
- Field Epidemiology Training Programme, United Kingdom Heath Security Agency, London, UK
| | - K Sweeting
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - R Johnson
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - E Best
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - J Nahl
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - M Denton
- Field Service, United Kingdom Health Security Agency, Leeds, UK; Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - G J Hughes
- Field Service, United Kingdom Health Security Agency, Leeds, UK.
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Badoual C, Adimi Y, Martin J, Morin B, Baudouin R. Les cancers des voies aérodigestives supérieures induits par une infection par Papillomavirus humain : spécificités épidémiologiques, diagnostiques, pronostiques et thérapeutiques. Bulletin de l'Académie Nationale de Médecine 2023. [DOI: 10.1016/j.banm.2022.10.019] [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: 01/26/2023]
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35
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Bermingham WH, Canning B, Wilton T, Kidd M, Klapsa D, Majumdar M, Sooriyakumar K, Martin J, Huissoon AP. Case report: Clearance of longstanding, immune-deficiency-associated, vaccine-derived polio virus infection following remdesivir therapy for chronic SARS-CoV-2 infection. Front Immunol 2023; 14:1135834. [PMID: 36936936 PMCID: PMC10022663 DOI: 10.3389/fimmu.2023.1135834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 02/07/2023] [Indexed: 03/06/2023] Open
Abstract
The global polio eradication campaign has had remarkable success in reducing wild-type poliovirus infection, largely built upon the live attenuated Sabin oral poliovirus vaccine. Whilst rare, vaccine poliovirus strains may cause infection and subsequently revert to a neurovirulent type, termed vaccine-derived poliovirus (VDPV). Persistent, vaccine derived infection may occur in an immunocompromised host (iVDPV), where it is a recognised complication following receipt of the Sabin vaccine. This has significant implications for the global polio eradication campaign and there is currently no agreed global strategy to manage such patients.Here we describe a case of a 50-year-old man with common variable immune deficiency, persistently infected with a neurovirulent vaccine-derived type 2 poliovirus following vaccination in childhood. iVDPV infection had proven resistant to multiple prior attempts at treatment with human breast milk, ribavirin and oral administration of a normal human pooled immunoglobulin product. His iVDPV infection subsequently resolved after 12 days treatment with remdesivir, an adenosine analogue prodrug that is an inhibitor of viral RNA-dependent RNA polymerase, administered as treatment for a prolonged, moderate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. iVDPV from the patient, isolated prior to treatment, was subsequently demonstrated to be sensitive to remdesivir in vitro. Based on the observations made in this case, and the mechanistic rationale for use with iVDPV, there is strong justification for further clinical studies of remdesivir treatment as a potentially curative intervention in patients with iVDPV infection.
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Affiliation(s)
- William Hywel Bermingham
- Department of Immunology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- *Correspondence: William Hywel Bermingham,
| | - Benjamin Canning
- Department of Virology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Thomas Wilton
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Agency, Potters Bar, United Kingdom
| | - Michael Kidd
- Public Health Laboratory, UK Health Security Agency, Birmingham, United Kingdom
| | - Dimitra Klapsa
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Agency, Potters Bar, United Kingdom
| | - Manasi Majumdar
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Agency, Potters Bar, United Kingdom
| | - Kavitha Sooriyakumar
- Department of Immunology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Javier Martin
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Agency, Potters Bar, United Kingdom
| | - Aarnoud P. Huissoon
- Department of Immunology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
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Ward DD, Martin J, Gordon EH. Is There a Sex-Frailty Paradox in Dementia? J Nutr Health Aging 2023; 27:1281-1283. [PMID: 38151880 DOI: 10.1007/s12603-023-2040-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 12/29/2023]
Affiliation(s)
- D D Ward
- David D. Ward, Centre for Health Services Research, The University of Queensland, Level 2, Building 33, Princess Alexandra Hospital, 199 Ipswich Road, Woolloongabba, QLD 4121, Australia.
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Podtschaske AH, Martin J, Ulm B, Jungwirth B, Kagerbauer SM. Sex-specific issues of central and peripheral arginine-vasopressin concentrations in neurocritical care patients. BMC Neurosci 2022; 23:69. [PMID: 36434506 PMCID: PMC9700878 DOI: 10.1186/s12868-022-00757-1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/17/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Arginine-Vasopressin (AVP) is a nonapeptide that exerts multiple functions within the central nervous system and in the blood circulation that might contribute to outcome in critically ill patients. Sex differences have been found for mental and physical effects of AVP. For example, stress response and response due to hemorrhage differ between males and females, at least in animal studies. Data on humans -especially on AVP within the central nervous system (CNS)-are scarce, as cerebrospinal fluid (CSF) which is said to represent central AVP activity, has to be collected by means of invasive procedures. Here we present data on 30 neurocritical care patients where we simultaneously collected blood, CSF and saliva to analyze concentrations in the central and peripheral compartments. PATIENTS AND METHODS 30 neurocritical care patients were included (13 male, 13 postmenopausal female, 4 premenopausal female) with a median age of 60 years. CSF, plasma and saliva were obtained simultaneously once in each patient and analyzed for AVP concentrations. Correlations between the central compartment represented by CSF, and the peripheral compartment represented by plasma and saliva, were identified. Relations between AVP concentrations and serum sodium and hematocrit were also determined. RESULTS In the whole patient collective, only very weak to weak correlations could be detected between AVP plasma/CSF, plasma/saliva and CSF/saliva as well as between AVP concentrations in each of the compartments and serum sodium/hematocrit. Regarding the subgroup of postmenopausal females, a significant moderate correlation could be detected for AVP in plasma and CSF and AVP CSF and serum sodium. CONCLUSION Absolute concentrations of AVP in central and peripheral compartments did not show sex differences. However, correlations between AVP plasma and CSF and AVP CSF and serum sodium in postmenopausal females indicate differences in AVP secretion and AVP response to triggers that deserve further examination.
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Affiliation(s)
- A. H. Podtschaske
- grid.6936.a0000000123222966Department of Anaesthesiology and Intensive Care Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - J. Martin
- grid.6936.a0000000123222966Department of Anaesthesiology and Intensive Care Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - B. Ulm
- grid.6936.a0000000123222966Department of Anaesthesiology and Intensive Care Medicine, School of Medicine, Technical University of Munich, Munich, Germany ,grid.6582.90000 0004 1936 9748Department of Anaesthesiology and Intensive Care Medicine, School of Medicine, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - B. Jungwirth
- grid.6582.90000 0004 1936 9748Department of Anaesthesiology and Intensive Care Medicine, School of Medicine, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - S. M. Kagerbauer
- grid.6936.a0000000123222966Department of Anaesthesiology and Intensive Care Medicine, School of Medicine, Technical University of Munich, Munich, Germany ,grid.6582.90000 0004 1936 9748Department of Anaesthesiology and Intensive Care Medicine, School of Medicine, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
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Martin J, Elster C. Aleatoric Uncertainty for Errors-in-Variables Models in Deep Regression. Neural Process Lett 2022. [DOI: 10.1007/s11063-022-11066-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractA Bayesian treatment of deep learning allows for the computation of uncertainties associated with the predictions of deep neural networks. We show how the concept of Errors-in-Variables can be used in Bayesian deep regression to also account for the uncertainty associated with the input of the employed neural network. The presented approach thereby exploits a relevant, but generally overlooked, source of uncertainty and yields a decomposition of the predictive uncertainty into an aleatoric and epistemic part that is more complete and, in many cases, more consistent from a statistical perspective. We discuss the approach along various simulated and real examples and observe that using an Errors-in-Variables model leads to an increase in the uncertainty while preserving the prediction performance of models without Errors-in-Variables. For examples with known regression function we observe that this ground truth is substantially better covered by the Errors-in-Variables model, indicating that the presented approach leads to a more reliable uncertainty estimation.
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Ishigaki K, Sakaue S, Terao C, Luo Y, Sonehara K, Yamaguchi K, Amariuta T, Too CL, Laufer VA, Scott IC, Viatte S, Takahashi M, Ohmura K, Murasawa A, Hashimoto M, Ito H, Hammoudeh M, Emadi SA, Masri BK, Halabi H, Badsha H, Uthman IW, Wu X, Lin L, Li T, Plant D, Barton A, Orozco G, Verstappen SMM, Bowes J, MacGregor AJ, Honda S, Koido M, Tomizuka K, Kamatani Y, Tanaka H, Tanaka E, Suzuki A, Maeda Y, Yamamoto K, Miyawaki S, Xie G, Zhang J, Amos CI, Keystone E, Wolbink G, van der Horst-Bruinsma I, Cui J, Liao KP, Carroll RJ, Lee HS, Bang SY, Siminovitch KA, de Vries N, Alfredsson L, Rantapää-Dahlqvist S, Karlson EW, Bae SC, Kimberly RP, Edberg JC, Mariette X, Huizinga T, Dieudé P, Schneider M, Kerick M, Denny JC, Matsuda K, Matsuo K, Mimori T, Matsuda F, Fujio K, Tanaka Y, Kumanogoh A, Traylor M, Lewis CM, Eyre S, Xu H, Saxena R, Arayssi T, Kochi Y, Ikari K, Harigai M, Gregersen PK, Yamamoto K, Louis Bridges S, Padyukov L, Martin J, Klareskog L, Okada Y, Raychaudhuri S. Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis. Nat Genet 2022; 54:1640-1651. [PMID: 36333501 PMCID: PMC10165422 DOI: 10.1038/s41588-022-01213-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [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: 12/01/2021] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
Rheumatoid arthritis (RA) is a highly heritable complex disease with unknown etiology. Multi-ancestry genetic research of RA promises to improve power to detect genetic signals, fine-mapping resolution and performances of polygenic risk scores (PRS). Here, we present a large-scale genome-wide association study (GWAS) of RA, which includes 276,020 samples from five ancestral groups. We conducted a multi-ancestry meta-analysis and identified 124 loci (P < 5 × 10-8), of which 34 are novel. Candidate genes at the novel loci suggest essential roles of the immune system (for example, TNIP2 and TNFRSF11A) and joint tissues (for example, WISP1) in RA etiology. Multi-ancestry fine-mapping identified putatively causal variants with biological insights (for example, LEF1). Moreover, PRS based on multi-ancestry GWAS outperformed PRS based on single-ancestry GWAS and had comparable performance between populations of European and East Asian ancestries. Our study provides several insights into the etiology of RA and improves the genetic predictability of RA.
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Affiliation(s)
- Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Kensuke Yamaguchi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tiffany Amariuta
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Chun Lai Too
- Immunogenetics Unit, Allergy and Immunology Research Center, Institute for Medical Research, National Institutes of Health Complex, Ministry of Health, Kuala Lumpur, Malaysia
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Vincent A Laufer
- Department of Clinical Immunology and Rheumatology, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Ian C Scott
- Haywood Academic Rheumatology Centre, Haywood Hospital, Midlands Partnership NHS Foundation Trust, Burslem, UK
- Primary Care Centre Versus Arthritis, School of Medicine, Keele University, Keele, UK
| | - Sebastien Viatte
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Meiko Takahashi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akira Murasawa
- Department of Rheumatology, Niigata Rheumatic Center, Niigata, Japan
| | - Motomu Hashimoto
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Clinical Immunology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Hiromu Ito
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Orthopaedic Surgery, Kurashiki Central Hospital, Kurashiki, Japan
| | - Mohammed Hammoudeh
- Rheumatology Division, Department of Internal Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Samar Al Emadi
- Rheumatology Division, Department of Internal Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Basel K Masri
- Department of Internal Medicine, Jordan Hospital, Amman, Jordan
| | - Hussein Halabi
- Section of Rheumatology, Department of Internal Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Humeira Badsha
- Dr. Humeira Badsha Medical Center, Emirates Hospital, Dubai, United Arab Emirates
| | - Imad W Uthman
- Department of Rheumatology, American University of Beirut, Beirut, Lebanon
| | - Xin Wu
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Li Lin
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Ting Li
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Darren Plant
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Anne Barton
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Suzanne M M Verstappen
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
- Centre for Epidemiology Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | | | - Suguru Honda
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Rheumatology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Masaru Koido
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kohei Tomizuka
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health Japan, Kitakyushu, Japan
| | - Eiichi Tanaka
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Rheumatology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Satoru Miyawaki
- Department of Neurosurgery, Faculty of Medicine, the University of Tokyo, Tokyo, Japan
| | - Gang Xie
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Jinyi Zhang
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Gertjan Wolbink
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center (ARC), Reade, Amsterdam, the Netherlands
| | - Irene van der Horst-Bruinsma
- Department of Rheumatology & Clinical Immunology/ARC, Amsterdam Institute for Infection and Immunity, Amsterdam UMC location Vrije Universiteit, Amsterdam, the Netherlands
| | - Jing Cui
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Katherine P Liao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
| | - Robert J Carroll
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Katherine A Siminovitch
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
- Departments of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Niek de Vries
- Department of Rheumatology & Clinical Immunology/ARC, Amsterdam Institute for Infection and Immunity, Amsterdam UMC location AMC/University of Amsterdam, Amsterdam, the Netherlands
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Elizabeth W Karlson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Robert P Kimberly
- Center for Clinical and Translational Science, Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeffrey C Edberg
- Center for Clinical and Translational Science, Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Xavier Mariette
- Department of Rheumatology, Université Paris-Saclay, Assistance Pubique - Hôpitaux de Paris, Hôpital Bicêtre, INSERM UMR1184, Le Kremlin Bicêtre, France
| | - Tom Huizinga
- Leiden University Medical Center, Leiden, the Netherlands
| | - Philippe Dieudé
- University of Paris Cité, Inserm, PHERE, F-75018, Paris, France
- Department of Rheumatology, Hôpital Bichat, APHP, Paris, France
| | - Matthias Schneider
- Department of Rheumatology & Hiller Research Unit Rheumatology, UKD, Heinrich-Heine University, Düsseldorf, Germany
| | - Martin Kerick
- Institute of Parasitology and Biomedicine Lopez-Neyra, CSIC, Granada, Spain
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
- All of Us Research Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Department of Preventive Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tsuneyo Mimori
- Department of Rheumatology and Clinical immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health Japan, Kitakyushu, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Matthew Traylor
- Department of Medical & Molecular Genetics, King's College London, London, UK
- Department of Genetics, Novo Nordisk Research Centre Oxford, Oxford, UK
- Clinical Pharmacology, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Cathryn M Lewis
- Department of Medical & Molecular Genetics, King's College London, London, UK
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Stephen Eyre
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
- School of Clinical Medicine Tsinghua University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China
| | - Richa Saxena
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Thurayya Arayssi
- Department of Internal Medicine, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsunori Ikari
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Orthopedic Surgery, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
- Division of Multidisciplinary Management of Rheumatic Diseases, Tokyo Women's Medical University, Tokyo, Japan
| | - Masayoshi Harigai
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Division of Rheumatology, Department of Internal Medicine, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - S Louis Bridges
- Department of Medicine, Hospital for Special Surgery, New York, NY, USA
- Division of Rheumatology, Weill Cornell Medicine, New York, NY, USA
| | - Leonid Padyukov
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Javier Martin
- Institute of Parasitology and Biomedicine Lopez-Neyra, CSIC, Granada, Spain
| | - Lars Klareskog
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
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40
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Sandler H, Shore N, Dearnaley D, Freedland S, Smith M, Rosales R, Brookman-May S, Dicker A, McKenzie M, Bossi A, Widmark A, Wiegel T, Martin J, Miladinovic B, Lefresne F, Ciprotti M, McCarthy S, Mundle S, Tombal B, Feng F. Challenges and Solutions during the COVID Pandemic for Patient Retention and Physician Engagement in the Phase 3 ATLAS Study of Apalutamide Added to Androgen Deprivation Therapy (ADT) in High-Risk Localized or Locally Advanced Prostate Cancer (HRLPC). Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.1217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Martin J, Perraton L, Gupta A, Garofolini A, Malliaras P. The use of physical function capacity measures in the management of lower limb tendinopathy: A scoping review of expert recommendations. J Sci Med Sport 2022. [DOI: 10.1016/j.jsams.2022.09.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Klapsa D, Wilton T, Zealand A, Bujaki E, Saxentoff E, Troman C, Shaw AG, Tedcastle A, Majumdar M, Mate R, Akello JO, Huseynov S, Zeb A, Zambon M, Bell A, Hagan J, Wade MJ, Ramsay M, Grassly NC, Saliba V, Martin J. Sustained detection of type 2 poliovirus in London sewage between February and July, 2022, by enhanced environmental surveillance. Lancet 2022; 400:1531-1538. [PMID: 36243024 PMCID: PMC9627700 DOI: 10.1016/s0140-6736(22)01804-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND The international spread of poliovirus exposes all countries to the risk of outbreaks and is designated a Public Health Emergency of International Concern by WHO. This risk can be exacerbated in countries using inactivated polio vaccine, which offers excellent protection against paralysis but is less effective than oral vaccine against poliovirus shedding, potentially allowing circulation without detection of paralytic cases for long periods of time. Our study investigated the molecular properties of type 2 poliovirus isolates found in sewage with an aim to detect virus transmission in the community. METHODS We performed environmental surveillance in London, UK, testing sewage samples using WHO recommended methods that include concentration, virus isolation in cell culture, and molecular characterisation. We additionally implemented direct molecular detection and determined whole-genome sequences of every isolate using novel nanopore protocols. FINDINGS 118 genetically linked poliovirus isolates related to the serotype 2 Sabin vaccine strain were detected in 21 of 52 sequential sewage samples collected in London between Feb 8 and July 4, 2022. Expansion of environmental surveillance sites in London helped localise transmission to several boroughs in north and east London. All isolates have lost two key attenuating mutations, are recombinants with a species C enterovirus, and an increasing proportion (20 of 118) meet the criterion for a vaccine-derived poliovirus, having six to ten nucleotide changes in the gene coding for VP1 capsid protein. INTERPRETATION Environmental surveillance allowed early detection of poliovirus importation and circulation in London, permitting a rapid public health response, including enhanced surveillance and an inactivated polio vaccine campaign among children aged 1-9 years. Whole-genome sequences generated through nanopore sequencing established linkage of isolates and confirmed transmission of a unique recombinant poliovirus lineage that has now been detected in Israel and the USA. FUNDING Medicines and Healthcare products Regulatory Agency, UK Health Security Agency, Bill & Melinda Gates Foundation, and National Institute for Health Research Medical Research Council.
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Affiliation(s)
- Dimitra Klapsa
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, UK
| | - Thomas Wilton
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, UK
| | - Andrew Zealand
- Environmental Monitoring for Health Protection, Data, Analytics and Surveillance Group, UK Health Security Agency, Nobel House, London, UK
| | - Erika Bujaki
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, UK
| | - Eugene Saxentoff
- World Health Organization Regional Office for Europe, Regional Polio Laboratory Network, Copenhagen, Denmark
| | - Catherine Troman
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Alexander G Shaw
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Alison Tedcastle
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, UK
| | - Manasi Majumdar
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, UK
| | - Ryan Mate
- Division of Analytical and Biological Science, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, UK
| | - Joyce O Akello
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Shahin Huseynov
- World Health Organization Regional Office for Europe, Regional Polio Laboratory Network, Copenhagen, Denmark
| | - Ali Zeb
- Environmental Monitoring for Health Protection, Data, Analytics and Surveillance Group, UK Health Security Agency, Nobel House, London, UK
| | - Maria Zambon
- National Polio Laboratory, Reference Services Division, UK Health Security Agency, London, UK
| | - Anita Bell
- North East and North Central London Health Protection Team, UK Health Security Agency, London, UK
| | - José Hagan
- World Health Organization Regional Office for Europe, Regional Polio Laboratory Network, Copenhagen, Denmark
| | - Matthew J Wade
- Environmental Monitoring for Health Protection, Data, Analytics and Surveillance Group, UK Health Security Agency, Nobel House, London, UK
| | - Mary Ramsay
- Immunisation and Vaccine Preventable Disease Division, UK Health Security Agency, London, UK
| | - Nicholas C Grassly
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Vanessa Saliba
- Immunisation and Vaccine Preventable Disease Division, UK Health Security Agency, London, UK
| | - Javier Martin
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, UK.
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Gonzalez A, Anchor T, Hevia A, Posadas A, Wade J, Ansag R, Benko K, Bottoni B, Kazakova V, Alvarez M, Wong J, Martin J, Knauf R, Jantke K, Wu A. The evolution of the fAIble system to automatically compose and narrate stories for children. J EXP THEOR ARTIF IN 2022. [DOI: 10.1080/0952813x.2022.2104382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Affiliation(s)
- A.J. Gonzalez
- Intelligent Systems Laboratory, Computer Science Department, University of Central Florida, Orlando, FL, USA
| | - T. Anchor
- Intelligent Systems Laboratory, Computer Science Department, University of Central Florida, Orlando, FL, USA
| | - A. Hevia
- Intelligent Systems Laboratory, Computer Science Department, University of Central Florida, Orlando, FL, USA
| | - A. Posadas
- Intelligent Systems Laboratory, Computer Science Department, University of Central Florida, Orlando, FL, USA
| | - J. Wade
- Intelligent Systems Laboratory, Computer Science Department, University of Central Florida, Orlando, FL, USA
| | - R.A. Ansag
- Intelligent Systems Laboratory, Computer Science Department, University of Central Florida, Orlando, FL, USA
| | - K. Benko
- Intelligent Systems Laboratory, Computer Science Department, University of Central Florida, Orlando, FL, USA
| | - B. Bottoni
- Intelligent Systems Laboratory, Computer Science Department, University of Central Florida, Orlando, FL, USA
| | - V. Kazakova
- Computer Science Dept, Knox College, Galesburg, IL, USA
| | - M.J. Alvarez
- Intelligent Systems Laboratory, Computer Science Department, University of Central Florida, Orlando, FL, USA
| | - J.M Wong
- Intelligent Systems Laboratory, Computer Science Department, University of Central Florida, Orlando, FL, USA
| | - J. Martin
- Intelligent Systems Laboratory, Computer Science Department, University of Central Florida, Orlando, FL, USA
| | - R. Knauf
- Computer Science Faculty, Technical University Ilmenau, Ilmenau, Germany
| | | | - A.S. Wu
- Intelligent Systems Laboratory, Computer Science Department, University of Central Florida, Orlando, FL, USA
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44
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Kerick M, Acosta-Herrera M, Simeón-Aznar CP, Callejas JL, Assassi S, Proudman SM, Nikpour M, Hunzelmann N, Moroncini G, de Vries-Bouwstra JK, Orozco G, Barton A, Herrick AL, Terao C, Allanore Y, Fonseca C, Alarcón-Riquelme ME, Radstake TRDJ, Beretta L, Denton CP, Mayes MD, Martin J. Complement component C4 structural variation and quantitative traits contribute to sex-biased vulnerability in systemic sclerosis. NPJ Genom Med 2022; 7:57. [PMID: 36198672 PMCID: PMC9534873 DOI: 10.1038/s41525-022-00327-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Copy number (CN) polymorphisms of complement C4 play distinct roles in many conditions, including immune-mediated diseases. We investigated the association of C4 CN with systemic sclerosis (SSc) risk. Imputed total C4, C4A, C4B, and HERV-K CN were analyzed in 26,633 individuals and validated in an independent cohort. Our results showed that higher C4 CN confers protection to SSc, and deviations from CN parity of C4A and C4B augmented risk. The protection contributed per copy of C4A and C4B differed by sex. Stronger protection was afforded by C4A in men and by C4B in women. C4 CN correlated well with its gene expression and serum protein levels, and less C4 was detected for both in SSc patients. Conditioned analysis suggests that C4 genetics strongly contributes to the SSc association within the major histocompatibility complex locus and highlights classical alleles and amino acid variants of HLA-DRB1 and HLA-DPB1 as C4-independent signals.
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Affiliation(s)
- Martin Kerick
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
| | - Marialbert Acosta-Herrera
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain.
| | | | | | - Shervin Assassi
- Department of Rheumatology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Susanna M Proudman
- Rheumatology Unit, Royal Adelaide Hospital and University of Adelaide, Adelaide, SA, Australia
| | - Mandana Nikpour
- The University of Melbourne at St. Vincent's Hospital, Melbourne, VIC, Australia
| | | | - Gianluca Moroncini
- Department of Clinical and Molecular Science, Università Politecnica delle Marche e Ospedali Riuniti, Ancona, Italy
| | | | - Gisela Orozco
- Center for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Center, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Anne Barton
- Center for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Center, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Ariane L Herrick
- Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Northern care Alliance NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yannick Allanore
- Department of Rheumatology A, Hospital Cochin, Paris, Île-de-France, France
| | - Carmen Fonseca
- Center for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Marta Eugenia Alarcón-Riquelme
- Center for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
| | - Timothy R D J Radstake
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lorenzo Beretta
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Christopher P Denton
- Center for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Maureen D Mayes
- Department of Rheumatology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Javier Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
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Jo YG, Ortiz-Fernández L, Coit P, Yilmaz V, Yentür SP, Alibaz-Oner F, Aksu K, Erken E, Düzgün N, Keser G, Cefle A, Yazici A, Ergen A, Alpsoy E, Salvarani C, Kısacık B, Kötter I, Henes J, Çınar M, Schaefer A, Nohutcu RM, Takeuchi F, Harihara S, Kaburaki T, Messedi M, Song YW, Kaşifoğlu T, Martin J, González Escribano MF, Saruhan-Direskeneli G, Direskeneli H, Sawalha AH. Sex-specific analysis in Behçet's disease reveals higher genetic risk in male patients. J Autoimmun 2022; 132:102882. [PMID: 35987173 PMCID: PMC10614427 DOI: 10.1016/j.jaut.2022.102882] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Behçet's disease tends to be more severe in men than women. This study was undertaken to investigate sex-specific genetic effects in Behçet's disease. METHODS A total of 1762 male and 1216 female patients with Behçet's disease from six diverse populations were studied, with the majority of patients of Turkish origin. Genotyping was performed using an Infinium ImmunoArray-24 BeadChip, or extracted from available genotyping data. Following imputation and extensive quality control measures, genome-wide association analysis was performed comparing male to female patients in the Turkish cohort, followed by a meta-analysis of significant results in all six populations. In addition, a weighted genetic risk score for Behçet's disease was calculated and compared between male and female patients. RESULTS Genetic association analysis comparing male to female patients with Behçet's disease from Turkey revealed an association with male sex in HLA-B/MICA within the HLA region with a GWAS level of significance (rs2848712, OR = 1.46, P = 1.22 × 10-8). Meta-analysis of the effect in rs2848712 across six populations confirmed these results. Genetic risk score for Behçet's disease was significantly higher in male compared to female patients from Turkey. Higher genetic risk for Behçet's disease was observed in male patients in HLA-B/MICA (rs116799036, OR = 1.45, P = 1.95 × 10-8), HLA-C (rs12525170, OR = 1.46, P = 5.66 × 10-7), and KLRC4 (rs2617170, OR = 1.20, P = 0.019). In contrast, IFNGR1 (rs4896243, OR = 0.86, P = 0.011) was shown to confer higher genetic risk in female patients. CONCLUSIONS Male patients with Behçet's disease are characterized by higher genetic risk compared to female patients. This genetic difference, primarily derived from our Turkish cohort, is largely explained by risk within the HLA region. These data suggest that genetic factors might contribute to differences in disease presentation between men and women with Behçet's disease.
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Affiliation(s)
- Yun Gun Jo
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lourdes Ortiz-Fernández
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Patrick Coit
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vuslat Yilmaz
- Department of Physiology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Sibel P Yentür
- Department of Physiology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Fatma Alibaz-Oner
- Division of Rheumatology, Department of Internal Medicine, Marmara University, School of Medicine, Istanbul, Turkey
| | - Kenan Aksu
- Division of Rheumatology, Department of Internal Medicine, Ege University, School of Medicine, Izmir, Turkey
| | - Eren Erken
- Division of Rheumatology, Department of Internal Medicine, Çukurova University, School of Medicine, Adana, Turkey
| | - Nursen Düzgün
- Division of Rheumatology, Department of Internal Medicine, Ankara University, School of Medicine, Ankara, Turkey
| | - Gokhan Keser
- Division of Rheumatology, Department of Internal Medicine, Ege University, School of Medicine, Izmir, Turkey
| | - Ayse Cefle
- Division of Rheumatology, Department of Internal Medicine, Kocaeli University, School of Medicine, Kocaeli, Turkey
| | - Ayten Yazici
- Division of Rheumatology, Department of Internal Medicine, Kocaeli University, School of Medicine, Kocaeli, Turkey
| | - Andac Ergen
- Ophthalmology Clinic, Okmeydanı Research and Education Hospital, Istanbul, Turkey
| | - Erkan Alpsoy
- Department of Dermatology and Venereology, Akdeniz University, School of Medicine, Antalya, Turkey
| | - Carlo Salvarani
- Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia and Università di Modena e Reggio Emilia, Modena, Italy
| | - Bünyamin Kısacık
- Division of Rheumatology, Department of Internal Medicine, Gaziantep University, Faculty of Medicine, Gaziantep, Turkey
| | - Ina Kötter
- Division of Rheumatology and Systemic Inflammatory Diseases, University Hospital Eppendorf, Hamburg, and Clinic for Rheumatology and Immunology, Bad Bramstedt, Germany
| | - Jörg Henes
- Center for Interdisciplinary Rheumatology, Immunology and Autoinflammatory Diseases (INDIRA) and Internal Medicine II (hematology, Oncology, Rheumatology and Immunology), University Hospital Tuebingen, Tuebingen, Germany
| | - Muhammet Çınar
- Division of Rheumatology, Department of Internal Medicine, University of Health Sciences Turkey, Gulhane Faculty of Medicine, Ankara, Turkey
| | - Arne Schaefer
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité-University Medicine Berlin, Berlin, Germany
| | - Rahime M Nohutcu
- Department of Periodontology, Faculty of Dentistry, Hacettepe University Sihhiye, Ankara, Turkey
| | - Fujio Takeuchi
- School of Pharmaceutical Science, University of Shizuoka, Shizuoka, Japan
| | - Shinji Harihara
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Toshikatsu Kaburaki
- Department of Ophthalmology, Jichi Medical University Saitama Medical Center, Japan
| | - Meriam Messedi
- Research Laboratory of Molecular Bases of Human Diseases, 12ES17, Faculty of Medicine of Sfax, University of Sfax, 3029 Sfax, Sfax, Tunisia
| | - Yeong-Wook Song
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, And College of Medicine, Medical Research Center, Seoul National University, Seoul, South Korea
| | - Timuçin Kaşifoğlu
- Division of Rheumatology, Department of Internal Medicine, Osmangazi University, School of Medicine, Eskisehir, Turkey
| | - Javier Martin
- Instituto de Parasitología y Biomedicina 'López-Neyra', IPBLN-CSIC, PTS Granada, Granada, Spain
| | | | | | - Haner Direskeneli
- Division of Rheumatology, Department of Internal Medicine, Marmara University, School of Medicine, Istanbul, Turkey
| | - Amr H Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA; Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA.
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Chetty K, Cheng I, Kaliakatsos M, Gonzalez-Granado LI, Klapsa D, Martin J, Bamford A, Breuer J, Booth C. Case report: Novel treatment regimen for enterovirus encephalitis in SCID. Front Immunol 2022; 13:930031. [PMID: 36177038 PMCID: PMC9513597 DOI: 10.3389/fimmu.2022.930031] [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] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Most non-polio enterovirus infections in immunocompetent individuals are acute and self-limiting in nature; however, infection can be severe, chronic and have devastating outcomes in immunocompromised hosts. Therapeutic strategies have predominantly involved supportive care, with the lack of approved antiviral treatments proving challenging for management. We report a case of an 8-month-old child who presented with severe enterovirus encephalitis following gene therapy for X-linked severe combined immunodeficiency (X-SCID) and who demonstrated clinical and microbiological improvement after a novel regimen of favipiravir, fluoxetine, and high-dose intravenous immunoglobulin (IVIg). The patient presented 6 weeks post–gene therapy with rapid neurological deterioration in the context of incomplete immune reconstitution, with microbiological and radiological evidence confirming enterovirus encephalitis. His neurologic examination stabilised 8 weeks after treatment, and he subsequently demonstrated excellent immune recovery. This is the first case report of combined therapy with favipiravir, fluoxetine, and high-dose IVIg in the context of severe enterovirus encephalitis in an immunocompromised host. This case highlights the importance of considering enterovirus encephalitis in immunocompromised patients presenting with both acute and chronic neurological signs, as well as developmental regression. The demonstrated treatment success and the associated low risk of toxicity warrant further investigation of this therapeutic regimen.
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Affiliation(s)
- Kritika Chetty
- Department of Immunology, Great Ormond Street Hospital, London, United Kingdom
- Molecular and Cellular Immunology Section, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Iek Cheng
- Pharmacy department, Great Ormond Street Hospital for Children National Health Service (NHS) Foundation Trust, London, United Kingdom
- UCL Faulty of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Marios Kaliakatsos
- Department of Neurology, Great Ormond Street Hospital, London, United Kingdom
| | - Luis Ignacio Gonzalez-Granado
- Servicio de Pediatria, Hospital Universitario 12 de octubre, Madrid, Spain
- Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Dimitra Klapsa
- Vaccines Division, The Medicines and Healthcare products Regulatory Agency, Potters Bar, United Kingdom
| | - Javier Martin
- Vaccines Division, The Medicines and Healthcare products Regulatory Agency, Potters Bar, United Kingdom
| | - Alasdair Bamford
- Department of Infectious Diseases, Great Ormond Street Hospital for Children, London, United Kingdom
- Infection, Immunity and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, Faculty of Population Health Sciences, University College London, London, United Kingdom
| | - Judith Breuer
- Department of Infectious Diseases, Great Ormond Street Hospital for Children, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Claire Booth
- Department of Immunology, Great Ormond Street Hospital, London, United Kingdom
- Molecular and Cellular Immunology Section, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- *Correspondence: Claire Booth,
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Otten LS, Heine RT, Chiong J, Martin J, van den Heuvel M, Piet B, Burger D. EP08.02-090 Sotorasib Drug-Drug Interactions: Essential Guidance Requested by Physicians Worldwide. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Giraud E, Chiong J, Martin J, Burger D, Erp N, Smolders E. 1595P QTc-prolonging drug-drug interactions related to CDK4/6 inhibitors. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Evans RA, Leavy OC, Richardson M, Elneima O, McAuley HJC, Shikotra A, Singapuri A, Sereno M, Saunders RM, Harris VC, Houchen-Wolloff L, Aul R, Beirne P, Bolton CE, Brown JS, Choudhury G, Diar-Bakerly N, Easom N, Echevarria C, Fuld J, Hart N, Hurst J, Jones MG, Parekh D, Pfeffer P, Rahman NM, Rowland-Jones SL, Shah AM, Wootton DG, Chalder T, Davies MJ, De Soyza A, Geddes JR, Greenhalf W, Greening NJ, Heaney LG, Heller S, Howard LS, Jacob J, Jenkins RG, Lord JM, Man WDC, McCann GP, Neubauer S, Openshaw PJM, Porter JC, Rowland MJ, Scott JT, Semple MG, Singh SJ, Thomas DC, Toshner M, Lewis KE, Thwaites RS, Briggs A, Docherty AB, Kerr S, Lone NI, Quint J, Sheikh A, Thorpe M, Zheng B, Chalmers JD, Ho LP, Horsley A, Marks M, Poinasamy K, Raman B, Harrison EM, Wain LV, Brightling CE, Abel K, Adamali H, Adeloye D, Adeyemi O, Adrego R, Aguilar Jimenez LA, Ahmad S, Ahmad Haider N, Ahmed R, Ahwireng N, Ainsworth M, Al-Sheklly B, Alamoudi A, Ali M, Aljaroof M, All AM, Allan L, Allen RJ, Allerton L, Allsop L, Almeida P, Altmann D, Alvarez Corral M, Amoils S, Anderson D, Antoniades C, Arbane G, Arias A, Armour C, Armstrong L, Armstrong N, Arnold D, Arnold H, Ashish A, Ashworth A, Ashworth M, Aslani S, Assefa-Kebede H, Atkin C, Atkin P, Aung H, Austin L, Avram C, Ayoub A, Babores M, Baggott R, Bagshaw J, Baguley D, Bailey L, Baillie JK, Bain S, Bakali M, Bakau M, Baldry E, Baldwin D, Ballard C, Banerjee A, Bang B, Barker RE, Barman L, Barratt S, Barrett F, Basire D, Basu N, Bates M, Bates A, Batterham R, Baxendale H, Bayes H, Beadsworth M, Beckett P, Beggs M, Begum M, Bell D, Bell R, Bennett K, Beranova E, Bermperi A, Berridge A, Berry C, Betts S, Bevan E, Bhui K, Bingham M, Birchall K, Bishop L, Bisnauthsing K, Blaikely J, Bloss A, Bolger A, Bonnington J, Botkai A, Bourne C, Bourne M, Bramham K, Brear L, Breen G, Breeze J, Bright E, Brill S, Brindle K, Broad L, Broadley A, Brookes C, Broome M, Brown A, Brown A, Brown J, Brown J, Brown M, Brown M, Brown V, Brugha T, Brunskill N, Buch M, Buckley P, Bularga A, Bullmore E, Burden L, Burdett T, Burn D, Burns G, Burns A, Busby J, Butcher R, Butt A, Byrne S, Cairns P, Calder PC, Calvelo E, Carborn H, Card B, Carr C, Carr L, Carson G, Carter P, Casey A, Cassar M, Cavanagh J, Chablani M, Chambers RC, Chan F, Channon KM, Chapman K, Charalambou A, Chaudhuri N, Checkley A, Chen J, Cheng Y, Chetham L, Childs C, Chilvers ER, Chinoy H, Chiribiri A, Chong-James K, Choudhury N, Chowienczyk P, Christie C, Chrystal M, Clark D, Clark C, Clarke J, Clohisey S, Coakley G, Coburn Z, Coetzee S, Cole J, Coleman C, Conneh F, Connell D, Connolly B, Connor L, Cook A, Cooper B, Cooper J, Cooper S, Copeland D, Cosier T, Coulding M, Coupland C, Cox E, Craig T, Crisp P, Cristiano D, Crooks MG, Cross A, Cruz I, Cullinan P, Cuthbertson D, Daines L, Dalton M, Daly P, Daniels A, Dark P, Dasgin J, David A, David C, Davies E, Davies F, Davies G, Davies GA, Davies K, Dawson J, Daynes E, Deakin B, Deans A, Deas C, Deery J, Defres S, Dell A, Dempsey K, Denneny E, Dennis J, Dewar A, Dharmagunawardena R, Dickens C, Dipper A, Diver S, Diwanji SN, Dixon M, Djukanovic R, Dobson H, Dobson SL, Donaldson A, Dong T, Dormand N, Dougherty A, Dowling R, Drain S, Draxlbauer K, Drury K, Dulawan P, Dunleavy A, Dunn S, Earley J, Edwards S, Edwardson C, El-Taweel H, Elliott A, Elliott K, Ellis Y, Elmer A, Evans D, Evans H, Evans J, Evans R, Evans RI, Evans T, Evenden C, Evison L, Fabbri L, Fairbairn S, Fairman A, Fallon K, Faluyi D, Favager C, Fayzan T, Featherstone J, Felton T, Finch J, Finney S, Finnigan J, Finnigan L, Fisher H, Fletcher S, Flockton R, Flynn M, Foot H, Foote D, Ford A, Forton D, Fraile E, Francis C, Francis R, Francis S, Frankel A, Fraser E, Free R, French N, Fu X, Furniss J, Garner L, Gautam N, George J, George P, Gibbons M, Gill M, Gilmour L, Gleeson F, Glossop J, Glover S, Goodman N, Goodwin C, Gooptu B, Gordon H, Gorsuch T, Greatorex M, Greenhaff PL, Greenhalgh A, Greenwood J, Gregory H, Gregory R, Grieve D, Griffin D, Griffiths L, Guerdette AM, Guillen Guio B, Gummadi M, Gupta A, Gurram S, Guthrie E, Guy Z, H Henson H, Hadley K, Haggar A, Hainey K, Hairsine B, Haldar P, Hall I, Hall L, Halling-Brown M, Hamil R, Hancock A, Hancock K, Hanley NA, Haq S, Hardwick HE, Hardy E, Hardy T, Hargadon B, Harrington K, Harris E, Harrison P, Harvey A, Harvey M, Harvie M, Haslam L, Havinden-Williams M, Hawkes J, Hawkings N, Haworth J, Hayday A, Haynes M, Hazeldine J, Hazelton T, Heeley C, Heeney JL, Heightman M, Henderson M, Hesselden L, Hewitt M, Highett V, Hillman T, Hiwot T, Hoare A, Hoare M, Hockridge J, Hogarth P, Holbourn A, Holden S, Holdsworth L, Holgate D, Holland M, Holloway L, Holmes K, Holmes M, Holroyd-Hind B, Holt L, Hormis A, Hosseini A, Hotopf M, Howard K, Howell A, Hufton E, Hughes AD, Hughes J, Hughes R, Humphries A, Huneke N, Hurditch E, Husain M, Hussell T, Hutchinson J, Ibrahim W, Ilyas F, Ingham J, Ingram L, Ionita D, Isaacs K, Ismail K, Jackson T, James WY, Jarman C, Jarrold I, Jarvis H, Jastrub R, Jayaraman B, Jezzard P, Jiwa K, Johnson C, Johnson S, Johnston D, Jolley CJ, Jones D, Jones G, Jones H, Jones H, Jones I, Jones L, Jones S, Jose S, Kabir T, Kaltsakas G, Kamwa V, Kanellakis N, Kaprowska S, Kausar Z, Keenan N, Kelly S, Kemp G, Kerslake H, Key AL, Khan F, Khunti K, Kilroy S, King B, King C, Kingham L, Kirk J, Kitterick P, Klenerman P, Knibbs L, Knight S, Knighton A, Kon O, Kon S, Kon SS, Koprowska S, Korszun A, Koychev I, Kurasz C, Kurupati P, Laing C, Lamlum H, Landers G, Langenberg C, Lasserson D, Lavelle-Langham L, Lawrie A, Lawson C, Lawson C, Layton A, Lea A, Lee D, Lee JH, Lee E, Leitch K, Lenagh R, Lewis D, Lewis J, Lewis V, Lewis-Burke N, Li X, Light T, Lightstone L, Lilaonitkul W, Lim L, Linford S, Lingford-Hughes A, Lipman M, Liyanage K, Lloyd A, Logan S, Lomas D, Loosley R, Lota H, Lovegrove W, Lucey A, Lukaschuk E, Lye A, Lynch C, MacDonald S, MacGowan G, Macharia I, Mackie J, Macliver L, Madathil S, Madzamba G, Magee N, Magtoto MM, Mairs N, Majeed N, Major E, Malein F, Malim M, Mallison G, Mandal S, Mangion K, Manisty C, Manley R, March K, Marciniak S, Marino P, Mariveles M, Marouzet E, Marsh S, Marshall B, Marshall M, Martin J, Martineau A, Martinez LM, Maskell N, Matila D, Matimba-Mupaya W, Matthews L, Mbuyisa A, McAdoo S, Weir McCall J, McAllister-Williams H, McArdle A, McArdle P, McAulay D, McCormick J, McCormick W, McCourt P, McGarvey L, McGee C, Mcgee K, McGinness J, McGlynn K, McGovern A, McGuinness H, McInnes IB, McIntosh J, McIvor E, McIvor K, McLeavey L, McMahon A, McMahon MJ, McMorrow L, Mcnally T, McNarry M, McNeill J, McQueen A, McShane H, Mears C, Megson C, Megson S, Mehta P, Meiring J, Melling L, Mencias M, Menzies D, Merida Morillas M, Michael A, Milligan L, Miller C, Mills C, Mills NL, Milner L, Misra S, Mitchell J, Mohamed A, Mohamed N, Mohammed S, Molyneaux PL, Monteiro W, Moriera S, Morley A, Morrison L, Morriss R, Morrow A, Moss AJ, Moss P, Motohashi K, Msimanga N, Mukaetova-Ladinska E, Munawar U, Murira J, Nanda U, Nassa H, Nasseri M, Neal A, Needham R, Neill P, Newell H, Newman T, Newton-Cox A, Nicholson T, Nicoll D, Nolan CM, Noonan MJ, Norman C, Novotny P, Nunag J, Nwafor L, Nwanguma U, Nyaboko J, O'Donnell K, O'Brien C, O'Brien L, O'Regan D, Odell N, Ogg G, Olaosebikan O, Oliver C, Omar Z, Orriss-Dib L, Osborne L, Osbourne R, Ostermann M, Overton C, Owen J, Oxton J, Pack J, Pacpaco E, Paddick S, Painter S, Pakzad A, Palmer S, Papineni P, Paques K, Paradowski K, Pareek M, Parfrey H, Pariante C, Parker S, Parkes M, Parmar J, Patale S, Patel B, Patel M, Patel S, Pattenadk D, Pavlides M, Payne S, Pearce L, Pearl JE, Peckham D, Pendlebury J, Peng Y, Pennington C, Peralta I, Perkins E, Peterkin Z, Peto T, Petousi N, Petrie J, Phipps J, Pimm J, Piper Hanley K, Pius R, Plant H, Plein S, Plekhanova T, Plowright M, Polgar O, Poll L, Porter J, Portukhay S, Powell N, Prabhu A, Pratt J, Price A, Price C, Price C, Price D, Price L, Price L, Prickett A, Propescu J, Pugmire S, Quaid S, Quigley J, Qureshi H, Qureshi IN, Radhakrishnan K, Ralser M, Ramos A, Ramos H, Rangeley J, Rangelov B, Ratcliffe L, Ravencroft P, Reddington A, Reddy R, Redfearn H, Redwood D, Reed A, Rees M, Rees T, Regan K, Reynolds W, Ribeiro C, Richards A, Richardson E, Rivera-Ortega P, Roberts K, Robertson E, Robinson E, Robinson L, Roche L, Roddis C, Rodger J, Ross A, Ross G, Rossdale J, Rostron A, Rowe A, Rowland A, Rowland J, Roy K, Roy M, Rudan I, Russell R, Russell E, Saalmink G, Sabit R, Sage EK, Samakomva T, Samani N, Sampson C, Samuel K, Samuel R, Sanderson A, Sapey E, Saralaya D, Sargant J, Sarginson C, Sass T, Sattar N, Saunders K, Saunders P, Saunders LC, Savill H, Saxon W, Sayer A, Schronce J, Schwaeble W, Scott K, Selby N, Sewell TA, Shah K, Shah P, Shankar-Hari M, Sharma M, Sharpe C, Sharpe M, Shashaa S, Shaw A, Shaw K, Shaw V, Shelton S, Shenton L, Shevket K, Short J, Siddique S, Siddiqui S, Sidebottom J, Sigfrid L, Simons G, Simpson J, Simpson N, Singh C, Singh S, Sissons D, Skeemer J, Slack K, Smith A, Smith D, Smith S, Smith J, Smith L, Soares M, Solano TS, Solly R, Solstice AR, Soulsby T, Southern D, Sowter D, Spears M, Spencer LG, Speranza F, Stadon L, Stanel S, Steele N, Steiner M, Stensel D, Stephens G, Stephenson L, Stern M, Stewart I, Stimpson R, Stockdale S, Stockley J, Stoker W, Stone R, Storrar W, Storrie A, Storton K, Stringer E, Strong-Sheldrake S, Stroud N, Subbe C, Sudlow CL, Suleiman Z, Summers C, Summersgill C, Sutherland D, Sykes DL, Sykes R, Talbot N, Tan AL, Tarusan L, Tavoukjian V, Taylor A, Taylor C, Taylor J, Te A, Tedd H, Tee CJ, Teixeira J, Tench H, Terry S, Thackray-Nocera S, Thaivalappil F, Thamu B, Thickett D, Thomas C, Thomas S, Thomas AK, Thomas-Woods T, Thompson T, Thompson AAR, Thornton T, Tilley J, Tinker N, Tiongson GF, Tobin M, Tomlinson J, Tong C, Touyz R, Tripp KA, Tunnicliffe E, Turnbull A, Turner E, Turner S, Turner V, Turner K, Turney S, Turtle L, Turton H, Ugoji J, Ugwuoke R, Upthegrove R, Valabhji J, Ventura M, Vere J, Vickers C, Vinson B, Wade E, Wade P, Wainwright T, Wajero LO, Walder S, Walker S, Walker S, Wall E, Wallis T, Walmsley S, Walsh JA, Walsh S, Warburton L, Ward TJC, Warwick K, Wassall H, Waterson S, Watson E, Watson L, Watson J, Welch C, Welch H, Welsh B, Wessely S, West S, Weston H, Wheeler H, White S, Whitehead V, Whitney J, Whittaker S, Whittam B, Whitworth V, Wight A, Wild J, Wilkins M, Wilkinson D, Williams N, Williams N, Williams J, Williams-Howard SA, Willicombe M, Willis G, Willoughby J, Wilson A, Wilson D, Wilson I, Window N, Witham M, Wolf-Roberts R, Wood C, Woodhead F, Woods J, Wormleighton J, Worsley J, Wraith D, Wrey Brown C, Wright C, Wright L, Wright S, Wyles J, Wynter I, Xu M, Yasmin N, Yasmin S, Yates T, Yip KP, Young B, Young S, Young A, Yousuf AJ, Zawia A, Zeidan L, Zhao B, Zongo O. Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study. Lancet Respir Med 2022; 10:761-775. [PMID: 35472304 PMCID: PMC9034855 DOI: 10.1016/s2213-2600(22)00127-8] [Citation(s) in RCA: 144] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/23/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND No effective pharmacological or non-pharmacological interventions exist for patients with long COVID. We aimed to describe recovery 1 year after hospital discharge for COVID-19, identify factors associated with patient-perceived recovery, and identify potential therapeutic targets by describing the underlying inflammatory profiles of the previously described recovery clusters at 5 months after hospital discharge. METHODS The Post-hospitalisation COVID-19 study (PHOSP-COVID) is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID-19 across the UK. Recovery was assessed using patient-reported outcome measures, physical performance, and organ function at 5 months and 1 year after hospital discharge, and stratified by both patient-perceived recovery and recovery cluster. Hierarchical logistic regression modelling was performed for patient-perceived recovery at 1 year. Cluster analysis was done using the clustering large applications k-medoids approach using clinical outcomes at 5 months. Inflammatory protein profiling was analysed from plasma at the 5-month visit. This study is registered on the ISRCTN Registry, ISRCTN10980107, and recruitment is ongoing. FINDINGS 2320 participants discharged from hospital between March 7, 2020, and April 18, 2021, were assessed at 5 months after discharge and 807 (32·7%) participants completed both the 5-month and 1-year visits. 279 (35·6%) of these 807 patients were women and 505 (64·4%) were men, with a mean age of 58·7 (SD 12·5) years, and 224 (27·8%) had received invasive mechanical ventilation (WHO class 7-9). The proportion of patients reporting full recovery was unchanged between 5 months (501 [25·5%] of 1965) and 1 year (232 [28·9%] of 804). Factors associated with being less likely to report full recovery at 1 year were female sex (odds ratio 0·68 [95% CI 0·46-0·99]), obesity (0·50 [0·34-0·74]) and invasive mechanical ventilation (0·42 [0·23-0·76]). Cluster analysis (n=1636) corroborated the previously reported four clusters: very severe, severe, moderate with cognitive impairment, and mild, relating to the severity of physical health, mental health, and cognitive impairment at 5 months. We found increased inflammatory mediators of tissue damage and repair in both the very severe and the moderate with cognitive impairment clusters compared with the mild cluster, including IL-6 concentration, which was increased in both comparisons (n=626 participants). We found a substantial deficit in median EQ-5D-5L utility index from before COVID-19 (retrospective assessment; 0·88 [IQR 0·74-1·00]), at 5 months (0·74 [0·64-0·88]) to 1 year (0·75 [0·62-0·88]), with minimal improvements across all outcome measures at 1 year after discharge in the whole cohort and within each of the four clusters. INTERPRETATION The sequelae of a hospital admission with COVID-19 were substantial 1 year after discharge across a range of health domains, with the minority in our cohort feeling fully recovered. Patient-perceived health-related quality of life was reduced at 1 year compared with before hospital admission. Systematic inflammation and obesity are potential treatable traits that warrant further investigation in clinical trials. FUNDING UK Research and Innovation and National Institute for Health Research.
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Amanova N, Martin J, Elster C. Explainability for deep learning in mammography image quality assessment. Mach Learn : Sci Technol 2022. [DOI: 10.1088/2632-2153/ac7a03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
The application of deep learning has recently been proposed for the assessment of image quality in mammography. It was demonstrated in a proof-of-principle study that the proposed approach can be more efficient than currently applied automated conventional methods. However, in contrast to conventional methods, the deep learning approach has a black-box nature and, before it can be recommended for the routine use, it must be understood more thoroughly. For this purpose, we propose and apply a new explainability method: the oriented, modified integrated gradients (OMIG) method. The design of this method is inspired by the integrated gradientsmethod but adapted considerably to the use case at hand. To further enhance this method, an upsampling technique is developed that produces high-resolution explainability maps for the downsampled data used by the deep learning approach. Comparison with established explainability methods demonstrates that the proposed approach yields substantially more expressive and informative results for our specific use case. Application of the proposed explainability approach generally confirms the validity of the considered deep learning-based mammography image quality assessment (IQA) method. Specifically, it is demonstrated that the predicted image quality is based on a meaningful mapping that makes successful use of certain geometric structures of the images. In addition, the novel explainability method helps us to identify the parts of the employed phantom that have the largest impact on the predicted image quality, and to shed some light on cases in which the trained neural networks fail to work as expected. While tailored to assess a specific approach from deep learning for mammography IQA, the proposed explainability method could also become relevant in other, similar deep learning applications based on high-dimensional images.
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