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Kumar V, Pouw RB, Autio MI, Sagmeister MG, Phua ZY, Borghini L, Wright VJ, Hoggart C, Pan B, Tan AKY, Binder A, Brouwer MC, Pinnock E, De Groot R, Hazelzet J, Emonts M, Van Der Flier M, Reiter K, Nöthen MM, Hoffmann P, Schlapbach LJ, Bellos E, Anderson S, Secka F, Martinón-Torres F, Salas A, Fink C, Carrol ED, Pollard AJ, Coin LJ, Zenz W, Wouters D, Ang LT, Hibberd ML, Levin M, Kuijpers TW, Davila S. Variation in CFHR3 determines susceptibility to meningococcal disease by controlling factor H concentrations. Am J Hum Genet 2022; 109:1680-1691. [PMID: 36007525 PMCID: PMC9502058 DOI: 10.1016/j.ajhg.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/31/2022] [Indexed: 11/16/2022] Open
Abstract
Neisseria meningitidis protects itself from complement-mediated killing by binding complement factor H (FH). Previous studies associated susceptibility to meningococcal disease (MD) with variation in CFH, but the causal variants and underlying mechanism remained unknown. Here we attempted to define the association more accurately by sequencing the CFH-CFHR locus and imputing missing genotypes in previously obtained GWAS datasets of MD-affected individuals of European ancestry and matched controls. We identified a CFHR3 SNP that provides protection from MD (rs75703017, p value = 1.1 × 10-16) by decreasing the concentration of FH in the blood (p value = 1.4 × 10-11). We subsequently used dual-luciferase studies and CRISPR gene editing to establish that deletion of rs75703017 increased FH expression in hepatocyte by preventing promotor inhibition. Our data suggest that reduced concentrations of FH in the blood confer protection from MD; with reduced access to FH, N. meningitidis is less able to shield itself from complement-mediated killing.
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Affiliation(s)
- Vikrant Kumar
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore; Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Richard B Pouw
- Division of Pediatric Immunology, Rheumatology, and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, the Netherlands; Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands
| | - Matias I Autio
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore; Cardiovascular Research Institute, Centre for Translational Medicine, National University Health System, Singapore
| | | | - Zai Yang Phua
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Lisa Borghini
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; GenPoB Research Group, Instituto de Investigación Sanitaria de Santiago, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Victoria J Wright
- Section of Paediatric Infectious Disease, Division of Infectious Disease, Department of Medicine, Imperial College London, London, UK
| | - Clive Hoggart
- Section of Paediatric Infectious Disease, Division of Infectious Disease, Department of Medicine, Imperial College London, London, UK
| | - Bangfen Pan
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore; Cardiovascular Research Institute, Centre for Translational Medicine, National University Health System, Singapore
| | - Antson Kiat Yee Tan
- Cancer Stem Cell Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Alexander Binder
- Department of General Paediatrics, Medical University of Graz, Graz, Austria
| | - Mieke C Brouwer
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands
| | | | - Ronald De Groot
- Section of Pediatric Infectious Diseases, Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jan Hazelzet
- Department of Pediatrics, Erasmus Medical Center-Sophia Children's Hospital, University Medical Center, Rotterdam, the Netherlands
| | - Marieke Emonts
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK; National Institute for Health and Care Research Newcastle Biomedical Research Centre Based at Newcastle Upon Tyne Hospitals National Health Service Trust and Newcastle University, Newcastle Upon Tyne, UK; Paediatric Infectious Diseases and Immunology Department, Newcastle Upon Tyne Hospitals Foundation Trust, Great North Children's Hospital, Newcastle Upon Tyne, UK
| | - Michiel Van Der Flier
- Section of Pediatric Infectious Diseases, Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Karl Reiter
- Department of Paediatrics, Division of Paediatric Intensive Care Medicine, Ludwig Maximilian University of Munich and Dr. von Hauner's Children's Hospital, Munich, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | - Luregn J Schlapbach
- Child Health Research Centre, The University of Queensland, Brisbane, Australia; Paediatric Intensive Care Unit, Queensland Children's Hospital, Brisbane, Australia; Department of Intensive Care and Neonatology and Children`s Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Evangelos Bellos
- Section of Paediatric Infectious Disease, Division of Infectious Disease, Department of Medicine, Imperial College London, London, UK
| | | | - Fatou Secka
- Medical Research Council Unit Gambia, Banjul, The Gambia
| | - Federico Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain; Genetics, Vaccines, Infectious Diseases, and Pediatrics Research Group, Instituto de Investigación Sanitaria de Santiago, Universidad de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Antonio Salas
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; GenPoB Research Group, Instituto de Investigación Sanitaria de Santiago, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Colin Fink
- Micropathology, University of Warwick, Coventry, UK
| | - Enitan D Carrol
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Lachlan J Coin
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Werner Zenz
- Department of General Paediatrics, Medical University of Graz, Graz, Austria
| | - Diana Wouters
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands
| | - Lay Teng Ang
- Cancer Stem Cell Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Martin L Hibberd
- Infectious Diseases, Genome Institute of Singapore, Singapore, Singapore; Infectious and Tropical Disease, London School of Hygiene & Tropical Medicine, London, UK
| | - Michael Levin
- Section of Paediatric Infectious Disease, Division of Infectious Disease, Department of Medicine, Imperial College London, London, UK
| | - Taco W Kuijpers
- Division of Pediatric Immunology, Rheumatology, and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, the Netherlands.
| | - Sonia Davila
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore; Duke-National University of Singapore Medical School, Singapore, Singapore; SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore.
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2
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Zhang P, Ganesamoorthy D, Nguyen SH, Au R, Coin LJ, Tey SK. Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy. J Immunother Cancer 2021; 8:jitc-2019-000299. [PMID: 32527930 PMCID: PMC7292043 DOI: 10.1136/jitc-2019-000299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2020] [Indexed: 11/21/2022] Open
Abstract
Background Analysis of vector integration sites in gene-modified cells can provide critical information on clonality and potential biological impact on nearby genes. Current short-read next-generation sequencing methods require specialized instruments and large batch runs. Methods We used nanopore sequencing to analyze the vector integration sites of T cells transduced by the gammaretroviral vector, SFG.iCasp9.2A.ΔCD19. DNA from oligoclonal cell lines and polyclonal clinical samples were restriction enzyme digested with two 6-cutters, NcoI and BspHI; and the flanking genomic DNA amplified by inverse PCR or cassette ligation PCR. Following nested PCR and barcoding, the amplicons were sequenced on the Oxford Nanopore platform. Reads were filtered for quality, trimmed, and aligned. Custom tool was developed to cluster reads and merge overlapping clusters. Results Both inverse PCR and cassette ligation PCR could successfully amplify flanking genomic DNA, with cassette ligation PCR showing less bias. The 4.8 million raw reads were grouped into 12,186 clusters and 6410 clones. The 3′long terminal repeat (LTR)-genome junction could be resolved within a 5-nucleotide span for a majority of clusters and within one nucleotide span for clusters with ≥5 reads. The chromosomal distributions of the insertional sites and their predilection for regions proximate to transcription start sites were consistent with previous reports for gammaretroviral vector integrants as analyzed by short-read next-generation sequencing. Conclusion Our study shows that it is feasible to use nanopore sequencing to map polyclonal vector integration sites. The assay is scalable and requires minimum capital, which together enable cost-effective and timely analysis. Further refinement is required to reduce amplification bias and improve single nucleotide resolution.
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Affiliation(s)
- Ping Zhang
- Department of Immunology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Devika Ganesamoorthy
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Son Hoang Nguyen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Raymond Au
- Department of Immunology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Infectious Disease, Imperial College London, London, London, UK
| | - Siok-Keen Tey
- Department of Immunology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia .,Department of Haematology and Bone Marrow Transplantation, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
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Gliddon HD, Kaforou M, Alikian M, Habgood-Coote D, Zhou C, Oni T, Anderson ST, Brent AJ, Crampin AC, Eley B, Heyderman R, Kern F, Langford PR, Ottenhoff THM, Hibberd ML, French N, Wright VJ, Dockrell HM, Coin LJ, Wilkinson RJ, Levin M. Identification of Reduced Host Transcriptomic Signatures for Tuberculosis Disease and Digital PCR-Based Validation and Quantification. Front Immunol 2021; 12:637164. [PMID: 33763081 PMCID: PMC7982854 DOI: 10.3389/fimmu.2021.637164] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
Recently, host whole blood gene expression signatures have been identified for diagnosis of tuberculosis (TB). Absolute quantification of the concentrations of signature transcripts in blood have not been reported, but would facilitate diagnostic test development. To identify minimal transcript signatures, we applied a transcript selection procedure to microarray data from African adults comprising 536 patients with TB, other diseases (OD) and latent TB (LTBI), divided into training and test sets. Signatures were further investigated using reverse transcriptase (RT)-digital PCR (dPCR). A four-transcript signature (GBP6, TMCC1, PRDM1, and ARG1) measured using RT-dPCR distinguished TB patients from those with OD (area under the curve (AUC) 93.8% (CI95% 82.2-100%). A three-transcript signature (FCGR1A, ZNF296, and C1QB) differentiated TB from LTBI (AUC 97.3%, CI95%: 93.3-100%), regardless of HIV. These signatures have been validated across platforms and across samples offering strong, quantitative support for their use as diagnostic biomarkers for TB.
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Affiliation(s)
- Harriet D Gliddon
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom.,National Public Health Speciality Training Programme, South West, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Mary Alikian
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom.,Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Dominic Habgood-Coote
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Chenxi Zhou
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Tolu Oni
- School of Public Health and Family Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Suzanne T Anderson
- Brighton and Sussex Medical School, Brighton, United Kingdom.,Brighton and Malawi Liverpool Wellcome Trust Unit, Blantyre, Malawi
| | - Andrew J Brent
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Amelia C Crampin
- Malawi Epidemiology and Intervention Research Unit, Chilumba, Malawi.,London School of Hygiene & Tropical Medicine, London, United Kingdom.,Karonga Prevention Study, Chilumba, Malawi
| | - Brian Eley
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children's Hospital, Cape Town, South Africa.,Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Robert Heyderman
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Florian Kern
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom.,Brighton and Sussex University Hospitals National Health Service (NHS) Trust, Brighton, United Kingdom
| | - Paul R Langford
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Neil French
- Tropical and Infectious Disease Unit, Royal Liverpool and Broadgreen University Hospitals National Health Service (NHS) Trust, Liverpool, United Kingdom.,Centre for Global Vaccine Research, Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Victoria J Wright
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Hazel M Dockrell
- Department of Immunology and Infection, and Tuberculosis (TB) Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Robert J Wilkinson
- The Francis Crick Institute, London, United Kingdom.,Department of Medicine, Imperial College London, London, United Kingdom.,Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Michael Levin
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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4
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Lee HJ, Georgiadou A, Walther M, Nwakanma D, Stewart LB, Levin M, Otto TD, Conway DJ, Coin LJ, Cunnington AJ. Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria. Sci Transl Med 2019; 10:10/447/eaar3619. [PMID: 29950443 DOI: 10.1126/scitranslmed.aar3619] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/31/2018] [Accepted: 06/08/2018] [Indexed: 12/13/2022]
Abstract
The pathogenesis of infectious diseases depends on the interaction of host and pathogen. In Plasmodium falciparum malaria, host and parasite processes can be assessed by dual RNA sequencing of blood from infected patients. We performed dual transcriptome analyses on samples from 46 malaria-infected Gambian children to reveal mechanisms driving the systemic pathophysiology of severe malaria. Integrating these transcriptomic data with estimates of parasite load and detailed clinical information allowed consideration of potentially confounding effects due to differing leukocyte proportions in blood, parasite developmental stage, and whole-body pathogen load. We report hundreds of human and parasite genes differentially expressed between severe and uncomplicated malaria, with distinct profiles associated with coma, hyperlactatemia, and thrombocytopenia. High expression of neutrophil granule-related genes was consistently associated with all severe malaria phenotypes. We observed severity-associated variation in the expression of parasite genes, which determine cytoadhesion to vascular endothelium, rigidity of infected erythrocytes, and parasite growth rate. Up to 99% of human differential gene expression in severe malaria was driven by differences in parasite load, whereas parasite gene expression showed little association with parasite load. Coexpression analyses revealed interactions between human and P. falciparum, with prominent co-regulation of translation genes in severe malaria between host and parasite. Multivariate analyses suggested that increased expression of granulopoiesis and interferon-γ-related genes, together with inadequate suppression of type 1 interferon signaling, best explained severity of infection. These findings provide a framework for understanding the contributions of host and parasite to the pathogenesis of severe malaria and identifying new treatments.
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Affiliation(s)
- Hyun Jae Lee
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Michael Walther
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Davis Nwakanma
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Lindsay B Stewart
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Michael Levin
- Section of Paediatrics, Imperial College, London W2 1PG, UK
| | - Thomas D Otto
- Wellcome Trust Sanger Centre, Hinxton, Cambridge CB10 1SA, UK
| | - David J Conway
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
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5
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Borghini L, Png E, Binder A, Wright VJ, Pinnock E, de Groot R, Hazelzet J, Emonts M, Van der Flier M, Schlapbach LJ, Anderson S, Secka F, Salas A, Fink C, Carrol ED, Pollard AJ, Coin LJ, Kuijpers TW, Martinon-Torres F, Zenz W, Levin M, Hibberd ML, Davila S. Identification of regulatory variants associated with genetic susceptibility to meningococcal disease. Sci Rep 2019; 9:6966. [PMID: 31061469 PMCID: PMC6502852 DOI: 10.1038/s41598-019-43292-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/17/2019] [Indexed: 12/30/2022] Open
Abstract
Non-coding genetic variants play an important role in driving susceptibility to complex diseases but their characterization remains challenging. Here, we employed a novel approach to interrogate the genetic risk of such polymorphisms in a more systematic way by targeting specific regulatory regions relevant for the phenotype studied. We applied this method to meningococcal disease susceptibility, using the DNA binding pattern of RELA – a NF-kB subunit, master regulator of the response to infection – under bacterial stimuli in nasopharyngeal epithelial cells. We designed a custom panel to cover these RELA binding sites and used it for targeted sequencing in cases and controls. Variant calling and association analysis were performed followed by validation of candidate polymorphisms by genotyping in three independent cohorts. We identified two new polymorphisms, rs4823231 and rs11913168, showing signs of association with meningococcal disease susceptibility. In addition, using our genomic data as well as publicly available resources, we found evidences for these SNPs to have potential regulatory effects on ATXN10 and LIF genes respectively. The variants and related candidate genes are relevant for infectious diseases and may have important contribution for meningococcal disease pathology. Finally, we described a novel genetic association approach that could be applied to other phenotypes.
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Affiliation(s)
- Lisa Borghini
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore. .,Infectious diseases, Genome Institute of Singapore, Singapore, Singapore.
| | - Eileen Png
- Infectious diseases, Genome Institute of Singapore, Singapore, Singapore
| | - Alexander Binder
- Department of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Victoria J Wright
- Section for Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | - Ellie Pinnock
- Micropathology Ltd, University of Warwick, Warwick, UK
| | - Ronald de Groot
- Department of Pediatrics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jan Hazelzet
- Department of Pediatrics, Erasmus Medical Center-Sophia Children's hospital, University Medical Center, Rotterdam, The Netherlands
| | - Marieke Emonts
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom.,Paediatric Infectious Diseases and Immunology Department, Newcastle upon Tyne Hospitals Foundation Trust, Great North Children's Hospital, Newcastle upon Tyne, United Kingdom
| | - Michiel Van der Flier
- Department of Pediatrics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Luregn J Schlapbach
- Faculty of Medicine, The University of Queensland, Brisbane, Australia.,Paediatric Critical Care Research Group, Mater Research Institute, University of Queensland, Brisbane, Australia.,Paediatric Intensive Care Unit, Lady Cilento Children's Hospital, Brisbane, Australia.,Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Fatou Secka
- Medical Research Council Unit Gambia, Banjul, The Gambia
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Colin Fink
- Micropathology Ltd, University of Warwick, Warwick, UK
| | - Enitan D Carrol
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Lachlan J Coin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Taco W Kuijpers
- Division of Pediatric Hematology, Immunology and Infectious diseases, Emma Children's Hospital Academic Medical Center, Amsterdam, The Netherlands
| | - Federico Martinon-Torres
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - Werner Zenz
- Department of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Michael Levin
- Section for Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | - Martin L Hibberd
- Infectious diseases, Genome Institute of Singapore, Singapore, Singapore.,Infectious and Tropical Disease, London School of Hygiene & Tropical Medicine, London, UK
| | - Sonia Davila
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore. .,SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, Singapore. .,Duke-NUS Medical School, Singapore, Singapore.
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6
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Zhang P, Raju J, Ullah MA, Au R, Varelias A, Gartlan KH, Olver SD, Samson LD, Sturgeon E, Zomerdijk N, Avery J, Gargett T, Brown MP, Coin LJ, Ganesamoorthy D, Hutchins C, Pratt GR, Kennedy GA, Morton AJ, Curley CI, Hill GR, Tey SK. Phase I Trial of Inducible Caspase 9 T Cells in Adult Stem Cell Transplant Demonstrates Massive Clonotypic Proliferative Potential and Long-term Persistence of Transgenic T Cells. Clin Cancer Res 2019; 25:1749-1755. [PMID: 30765390 DOI: 10.1158/1078-0432.ccr-18-3069] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/20/2018] [Accepted: 12/21/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Inducible caspase 9 (iCasp9) is a cellular safety switch that can make T-cell therapy safer. The purpose of this phase I trial was to investigate the use of iCasp9-transduced T-cell addback in adult patients undergoing haploidentical stem cell transplantation for high-risk hematologic malignancies. PATIENTS AND METHODS Patients undergoing myeloablative, CD34-selected haploidentical stem cell transplantation were treated with 0.5-1.0 × 106/kg donor-derived iCasp9-transduced T cells on day +25 or 26 post-transplant, with additional doses allowed for disease relapse, infection, or mixed chimerism. RESULTS Three patients were enrolled. iCasp9-transduced T cells were readily detectable by 4 weeks post-infusion in all patients and remained at high level (114 cells/μL, 11% of T cells) in 1 patient alive at 3.6 years. One patient developed donor-derived Epstein-Barr virus-associated post-transplant lymphoproliferative disease (EBV-PTLD), which was followed by a marked expansion of iCasp9 T cells and cytokine release syndrome (CRS). These iCasp9-transduced T cells infiltrated the affected lymph nodes and secreted IFNγ and IL-10. They peaked at 1,848 cells/μL and were found to be monoclonal by T-cell receptor (TCR) clonotype and oligoclonal by viral integrant analysis, representing a 6-log in vivo expansion of the dominant T-cell clone. These T cells were not autonomous and contracted with the resolution of EBV-PTLD, which did not recur. CONCLUSIONS iCasp9-transduced T cells could persist long-term. They retained very high in vivo clonotypic proliferative capacity and function, and could cause CRS in response to de novo lymphoma development.
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Affiliation(s)
- Ping Zhang
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Jyothy Raju
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Md Ashik Ullah
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Raymond Au
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Antiopi Varelias
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,Faculty of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Kate H Gartlan
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,Faculty of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Stuart D Olver
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Luke D Samson
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Elise Sturgeon
- Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Nienke Zomerdijk
- Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Judy Avery
- Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Tessa Gargett
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, Australia
| | - Michael P Brown
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, Australia
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Devika Ganesamoorthy
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Cheryl Hutchins
- Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Gary R Pratt
- Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Glen A Kennedy
- Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - A James Morton
- Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Cameron I Curley
- Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Geoffrey R Hill
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Siok-Keen Tey
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia. .,Faculty of Medicine, University of Queensland, Herston, Queensland, Australia.,Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
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Lee HJ, Georgiadou A, Otto TD, Levin M, Coin LJ, Conway DJ, Cunnington AJ. Transcriptomic Studies of Malaria: a Paradigm for Investigation of Systemic Host-Pathogen Interactions. Microbiol Mol Biol Rev 2018; 82:e00071-17. [PMID: 29695497 PMCID: PMC5968457 DOI: 10.1128/mmbr.00071-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcriptomics, the analysis of genome-wide RNA expression, is a common approach to investigate host and pathogen processes in infectious diseases. Technical and bioinformatic advances have permitted increasingly thorough analyses of the association of RNA expression with fundamental biology, immunity, pathogenesis, diagnosis, and prognosis. Transcriptomic approaches can now be used to realize a previously unattainable goal, the simultaneous study of RNA expression in host and pathogen, in order to better understand their interactions. This exciting prospect is not without challenges, especially as focus moves from interactions in vitro under tightly controlled conditions to tissue- and systems-level interactions in animal models and natural and experimental infections in humans. Here we review the contribution of transcriptomic studies to the understanding of malaria, a parasitic disease which has exerted a major influence on human evolution and continues to cause a huge global burden of disease. We consider malaria a paradigm for the transcriptomic assessment of systemic host-pathogen interactions in humans, because much of the direct host-pathogen interaction occurs within the blood, a readily sampled compartment of the body. We illustrate lessons learned from transcriptomic studies of malaria and how these lessons may guide studies of host-pathogen interactions in other infectious diseases. We propose that the potential of transcriptomic studies to improve the understanding of malaria as a disease remains partly untapped because of limitations in study design rather than as a consequence of technological constraints. Further advances will require the integration of transcriptomic data with analytical approaches from other scientific disciplines, including epidemiology and mathematical modeling.
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Affiliation(s)
- Hyun Jae Lee
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | | | - Thomas D Otto
- Centre of Immunobiology, University of Glasgow, Glasgow, United Kingdom
| | - Michael Levin
- Section of Paediatrics, Imperial College, London, United Kingdom
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - David J Conway
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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8
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Hemingway C, Berk M, Anderson ST, Wright VJ, Hamilton S, Eleftherohorinou H, Kaforou M, Goldgof GM, Hickman K, Kampmann B, Schoeman J, Eley B, Beatty D, Pienaar S, Nicol MP, Griffiths MJ, Waddell SJ, Newton SM, Coin LJ, Relman DA, Montana G, Levin M. Childhood tuberculosis is associated with decreased abundance of T cell gene transcripts and impaired T cell function. PLoS One 2017; 12:e0185973. [PMID: 29140996 PMCID: PMC5687722 DOI: 10.1371/journal.pone.0185973] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 08/09/2016] [Accepted: 09/24/2017] [Indexed: 11/19/2022] Open
Abstract
The WHO estimates around a million children contract tuberculosis (TB) annually with over 80 000 deaths from dissemination of infection outside of the lungs. The insidious onset and association with skin test anergy suggests failure of the immune system to both recognise and respond to infection. To understand the immune mechanisms, we studied genome-wide whole blood RNA expression in children with TB meningitis (TBM). Findings were validated in a second cohort of children with TBM and pulmonary TB (PTB), and functional T-cell responses studied in a third cohort of children with TBM, other extrapulmonary TB (EPTB) and PTB. The predominant RNA transcriptional response in children with TBM was decreased abundance of multiple genes, with 140/204 (68%) of all differentially regulated genes showing reduced abundance compared to healthy controls. Findings were validated in a second cohort with concordance of the direction of differential expression in both TBM (r2 = 0.78 p = 2x10-16) and PTB patients (r2 = 0.71 p = 2x10-16) when compared to a second group of healthy controls. Although the direction of expression of these significant genes was similar in the PTB patients, the magnitude of differential transcript abundance was less in PTB than in TBM. The majority of genes were involved in activation of leucocytes (p = 2.67E-11) and T-cell receptor signalling (p = 6.56E-07). Less abundant gene expression in immune cells was associated with a functional defect in T-cell proliferation that recovered after full TB treatment (p<0.0003). Multiple genes involved in T-cell activation show decreased abundance in children with acute TB, who also have impaired functional T-cell responses. Our data suggest that childhood TB is associated with an acquired immune defect, potentially resulting in failure to contain the pathogen. Elucidation of the mechanism causing the immune paresis may identify new treatment and prevention strategies.
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Affiliation(s)
- Cheryl Hemingway
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
| | - Maurice Berk
- Department of Mathematics, Faculty of Natural Sciences, Imperial College London, 80 Queen's Gate, London, United Kingdom
| | - Suzanne T. Anderson
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
| | - Victoria J. Wright
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
| | - Shea Hamilton
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
| | - Hariklia Eleftherohorinou
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
| | - Greg M. Goldgof
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
| | - Katy Hickman
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
| | - Beate Kampmann
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
| | - Johan Schoeman
- Tygerberg Hospital, University of Stellenbosch, Cape Town, South Africa
| | - Brian Eley
- Red Cross War Memorial Children’s Hospital, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - David Beatty
- Red Cross War Memorial Children’s Hospital, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Sandra Pienaar
- Red Cross War Memorial Children’s Hospital, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Mark P. Nicol
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Michael J. Griffiths
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Simon J. Waddell
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Sandra M. Newton
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
| | - Lachlan J. Coin
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, United Kingdom
| | - David A. Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California, United States of America
| | - Giovanni Montana
- Department of Mathematics, Faculty of Natural Sciences, Imperial College London, 80 Queen's Gate, London, United Kingdom
- Department of Biomedical Engineering, King's College London, London, United Kingdom
| | - Michael Levin
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
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Anderson ST, Kaforou M, Brent AJ, Wright VJ, Banwell CM, Chagaluka G, Crampin AC, Dockrell HM, French N, Hamilton MS, Hibberd ML, Kern F, Langford PR, Ling L, Mlotha R, Ottenhoff THM, Pienaar S, Pillay V, Scott JAG, Twahir H, Wilkinson RJ, Coin LJ, Heyderman RS, Levin M, Eley B. Diagnosis of childhood tuberculosis and host RNA expression in Africa. N Engl J Med 2014; 370:1712-1723. [PMID: 24785206 PMCID: PMC4069985 DOI: 10.1056/nejmoa1303657] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND Improved diagnostic tests for tuberculosis in children are needed. We hypothesized that transcriptional signatures of host blood could be used to distinguish tuberculosis from other diseases in African children who either were or were not infected with the human immunodeficiency virus (HIV). METHODS The study population comprised prospective cohorts of children who were undergoing evaluation for suspected tuberculosis in South Africa (655 children), Malawi (701 children), and Kenya (1599 children). Patients were assigned to groups according to whether the diagnosis was culture-confirmed tuberculosis, culture-negative tuberculosis, diseases other than tuberculosis, or latent tuberculosis infection. Diagnostic signatures distinguishing tuberculosis from other diseases and from latent tuberculosis infection were identified from genomewide analysis of RNA expression in host blood. RESULTS We identified a 51-transcript signature distinguishing tuberculosis from other diseases in the South African and Malawian children (the discovery cohort). In the Kenyan children (the validation cohort), a risk score based on the signature for tuberculosis and for diseases other than tuberculosis showed a sensitivity of 82.9% (95% confidence interval [CI], 68.6 to 94.3) and a specificity of 83.6% (95% CI, 74.6 to 92.7) for the diagnosis of culture-confirmed tuberculosis. Among patients with cultures negative for Mycobacterium tuberculosis who were treated for tuberculosis (those with highly probable, probable, or possible cases of tuberculosis), the estimated sensitivity was 62.5 to 82.3%, 42.1 to 80.8%, and 35.3 to 79.6%, respectively, for different estimates of actual tuberculosis in the groups. In comparison, the sensitivity of the Xpert MTB/RIF assay for molecular detection of M. tuberculosis DNA in cases of culture-confirmed tuberculosis was 54.3% (95% CI, 37.1 to 68.6), and the sensitivity in highly probable, probable, or possible cases was an estimated 25.0 to 35.7%, 5.3 to 13.3%, and 0%, respectively; the specificity of the assay was 100%. CONCLUSIONS RNA expression signatures provided data that helped distinguish tuberculosis from other diseases in African children with and those without HIV infection. (Funded by the European Union Action for Diseases of Poverty Program and others).
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10
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Kaforou M, Wright VJ, Oni T, French N, Anderson ST, Bangani N, Banwell CM, Brent AJ, Crampin AC, Dockrell HM, Eley B, Heyderman RS, Hibberd ML, Kern F, Langford PR, Ling L, Mendelson M, Ottenhoff TH, Zgambo F, Wilkinson RJ, Coin LJ, Levin M. Detection of tuberculosis in HIV-infected and -uninfected African adults using whole blood RNA expression signatures: a case-control study. PLoS Med 2013; 10:e1001538. [PMID: 24167453 PMCID: PMC3805485 DOI: 10.1371/journal.pmed.1001538] [Citation(s) in RCA: 252] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 09/12/2013] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND A major impediment to tuberculosis control in Africa is the difficulty in diagnosing active tuberculosis (TB), particularly in the context of HIV infection. We hypothesized that a unique host blood RNA transcriptional signature would distinguish TB from other diseases (OD) in HIV-infected and -uninfected patients, and that this could be the basis of a simple diagnostic test. METHODS AND FINDINGS Adult case-control cohorts were established in South Africa and Malawi of HIV-infected or -uninfected individuals consisting of 584 patients with either TB (confirmed by culture of Mycobacterium tuberculosis [M.TB] from sputum or tissue sample in a patient under investigation for TB), OD (i.e., TB was considered in the differential diagnosis but then excluded), or healthy individuals with latent TB infection (LTBI). Individuals were randomized into training (80%) and test (20%) cohorts. Blood transcriptional profiles were assessed and minimal sets of significantly differentially expressed transcripts distinguishing TB from LTBI and OD were identified in the training cohort. A 27 transcript signature distinguished TB from LTBI and a 44 transcript signature distinguished TB from OD. To evaluate our signatures, we used a novel computational method to calculate a disease risk score (DRS) for each patient. The classification based on this score was first evaluated in the test cohort, and then validated in an independent publically available dataset (GSE19491). In our test cohort, the DRS classified TB from LTBI (sensitivity 95%, 95% CI [87-100]; specificity 90%, 95% CI [80-97]) and TB from OD (sensitivity 93%, 95% CI [83-100]; specificity 88%, 95% CI [74-97]). In the independent validation cohort, TB patients were distinguished both from LTBI individuals (sensitivity 95%, 95% CI [85-100]; specificity 94%, 95% CI [84-100]) and OD patients (sensitivity 100%, 95% CI [100-100]; specificity 96%, 95% CI [93-100]). Limitations of our study include the use of only culture confirmed TB patients, and the potential that TB may have been misdiagnosed in a small proportion of OD patients despite the extensive clinical investigation used to assign each patient to their diagnostic group. CONCLUSIONS In our study, blood transcriptional signatures distinguished TB from other conditions prevalent in HIV-infected and -uninfected African adults. Our DRS, based on these signatures, could be developed as a test for TB suitable for use in HIV endemic countries. Further evaluation of the performance of the signatures and DRS in prospective populations of patients with symptoms consistent with TB will be needed to define their clinical value under operational conditions. Please see later in the article for the Editors' Summary.
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Affiliation(s)
- Myrsini Kaforou
- Section of Paediatrics and Wellcome Trust Centre for Clinical Tropical Medicine, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, United Kingdom
| | - Victoria J. Wright
- Section of Paediatrics and Wellcome Trust Centre for Clinical Tropical Medicine, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
| | - Tolu Oni
- Section of Paediatrics and Wellcome Trust Centre for Clinical Tropical Medicine, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
- Clinical Infectious Diseases Research Initiative, Institute of Infectious Diseases & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Neil French
- Karonga Prevention Study, Chilumba, Karonga District, Malawi
- Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Suzanne T. Anderson
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Nonzwakazi Bangani
- Clinical Infectious Diseases Research Initiative, Institute of Infectious Diseases & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Claire M. Banwell
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Andrew J. Brent
- Section of Paediatrics and Wellcome Trust Centre for Clinical Tropical Medicine, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Amelia C. Crampin
- Karonga Prevention Study, Chilumba, Karonga District, Malawi
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Hazel M. Dockrell
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Brian Eley
- Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - Robert S. Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - Florian Kern
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Paul R. Langford
- Section of Paediatrics and Wellcome Trust Centre for Clinical Tropical Medicine, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
| | - Ling Ling
- Infectious Disease, Genome Institute of Singapore, Singapore
| | - Marc Mendelson
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Tom H. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Femia Zgambo
- Karonga Prevention Study, Chilumba, Karonga District, Malawi
| | - Robert J. Wilkinson
- Section of Paediatrics and Wellcome Trust Centre for Clinical Tropical Medicine, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
- Clinical Infectious Diseases Research Initiative, Institute of Infectious Diseases & Molecular Medicine, University of Cape Town, Cape Town, South Africa
- MRC National Institute for Medical Research, London, United Kingdom
| | - Lachlan J. Coin
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, United Kingdom
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Michael Levin
- Section of Paediatrics and Wellcome Trust Centre for Clinical Tropical Medicine, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
- * E-mail:
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11
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Munhoz RP, Teive HA, Eleftherohorinou H, Coin LJ, Lees AJ, Silveira-Moriyama L. Demographic and motor features associated with the occurrence of neuropsychiatric and sleep complications of Parkinson's disease. J Neurol Neurosurg Psychiatry 2013; 84:883-7. [PMID: 23463867 DOI: 10.1136/jnnp-2012-304440] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To determine whether four key neuropsychiatric and sleep related features associated with Parkinson's disease (PD) are associated with the motor handicap and demographic data. BACKGROUND The growing number of recognised non-motor features of PD makes routine screening of all these symptoms impractical. Here, we investigated the hypothesis that standard demographic data and the routine assessment of motor signs is associated with the presence of dementia, psychosis, clinically probable rapid eye movement (REM) sleep behavior disorder (cpRBD) and restless legs syndrome (RLS). METHODS 775 patients with PD underwent standardised assessment of motor features and the presence of dementia, psychosis, cpRBD and RLS. A stepwise feature elimination procedure with fitted logistic regression models was applied to identify which/if any combination of demographic and motor factors is associated with each of the four studied non-motor features. A within-study out-of-sample estimate of the power of the predicted values of the models was calculated using standard evaluation procedures. RESULTS Age and Hoehn&Yahr (H&Y) stage were strongly associated with the presence of dementia (p value<0.001 for both factors in the final selected model) while a combination of age, disease duration, H&Y stage, dopamine agonists and catechol-O-methyltransferase (COMT) inhibitors was associated with the presence of psychosis. Disease duration and H&Y stage were the significant indicators of cpRBD, and the lack of significant motor asymmetry was the only significant feature associated with RLS-type symptoms but the evidence of association was weak. CONCLUSIONS Demographic and motor features routinely collected in patients with PD can estimate the occurrence of neuropsychiatric and sleep-related features of PD.
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Affiliation(s)
- Renato Puppi Munhoz
- Department of Neurology, Hospital de Clínicas, Federal University of Paraná, Curitiba, Brazil
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12
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Ramasamy A, Curjuric I, Coin LJ, Kumar A, McArdle WL, Imboden M, Leynaert B, Kogevinas M, Schmid-Grendelmeier P, Pekkanen J, Wjst M, Bircher AJ, Sovio U, Rochat T, Hartikainen AL, Balding DJ, Jarvelin MR, Probst-Hensch N, Strachan DP, Jarvis DL. A genome-wide meta-analysis of genetic variants associated with allergic rhinitis and grass sensitization and their interaction with birth order. J Allergy Clin Immunol 2011; 128:996-1005. [PMID: 22036096 DOI: 10.1016/j.jaci.2011.08.030] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [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: 02/25/2011] [Revised: 08/22/2011] [Accepted: 08/29/2011] [Indexed: 01/03/2023]
Abstract
BACKGROUND Hay fever or seasonal allergic rhinitis (AR) is a chronic disorder associated with IgE sensitization to grass. The underlying genetic variants have not been studied comprehensively. There is overwhelming evidence that those who have older siblings have less AR, although the mechanism for this remains unclear. OBJECTIVE We sought to identify common genetic variant associations with prevalent AR and grass sensitization using existing genome-wide association study (GWAS) data and to determine whether genetic variants modify the protective effect of older siblings. METHOD Approximately 2.2 million genotyped or imputed single nucleotide polymorphisms were investigated in 4 large European adult cohorts for AR (3,933 self-reported cases vs 8,965 control subjects) and grass sensitization (2,315 cases vs 10,032 control subjects). RESULTS Three loci reached genome-wide significance for either phenotype. The HLA variant rs7775228, which cis-regulates HLA-DRB4, was strongly associated with grass sensitization and weakly with AR (P(grass) = 1.6 × 10(-9); P(AR) = 8.0 × 10(-3)). Variants in a locus near chromosome 11 open reading frame 30 (C11orf30) and leucine-rich repeat containing 32 (LRRC32), which was previously associated with atopic dermatitis and eczema, were also strongly associated with both phenotypes (rs2155219; P(grass) = 9.4 × 10(-9); P(AR) = 3.8 × 10(-8)). The third genome-wide significant variant was rs17513503 (P(grass) = 1.2 × 10(-8); PAR = 7.4 × 10(-7)) which was located near transmembrane protein 232 (TMEM232) and solute carrier family 25, member 46 (SLC25A46). Twelve further loci with suggestive associations were also identified. Using a candidate gene approach, where we considered variants within 164 genes previously thought to be important, we found variants in 3 further genes that may be of interest: thymic stromal lymphopoietin (TSLP), Toll-like receptor 6 (TLR6) and nucleotide-binding oligomerization domain containing 1 (NOD1/CARD4). We found no evidence for variants that modified the effect of birth order on either phenotype. CONCLUSIONS This relatively large meta-analysis of GWASs identified few loci associated with AR and grass sensitization. No birth order interaction was identified in the current analyses.
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Affiliation(s)
- Adaikalavan Ramasamy
- Respiratory Epidemiology and Public Health, Imperial College, London, United Kingdom
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13
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Chambers JC, Zhang W, Sehmi J, Li X, Wass MN, Van der Harst P, Holm H, Sanna S, Kavousi M, Baumeister SE, Coin LJ, Deng G, Gieger C, Heard-Costa NL, Hottenga JJ, Kühnel B, Kumar V, Lagou V, Liang L, Luan J, Vidal PM, Mateo Leach I, O'Reilly PF, Peden JF, Rahmioglu N, Soininen P, Speliotes EK, Yuan X, Thorleifsson G, Alizadeh BZ, Atwood LD, Borecki IB, Brown MJ, Charoen P, Cucca F, Das D, de Geus EJC, Dixon AL, Döring A, Ehret G, Eyjolfsson GI, Farrall M, Forouhi NG, Friedrich N, Goessling W, Gudbjartsson DF, Harris TB, Hartikainen AL, Heath S, Hirschfield GM, Hofman A, Homuth G, Hyppönen E, Janssen HLA, Johnson T, Kangas AJ, Kema IP, Kühn JP, Lai S, Lathrop M, Lerch MM, Li Y, Liang TJ, Lin JP, Loos RJF, Martin NG, Moffatt MF, Montgomery GW, Munroe PB, Musunuru K, Nakamura Y, O'Donnell CJ, Olafsson I, Penninx BW, Pouta A, Prins BP, Prokopenko I, Puls R, Ruokonen A, Savolainen MJ, Schlessinger D, Schouten JNL, Seedorf U, Sen-Chowdhry S, Siminovitch KA, Smit JH, Spector TD, Tan W, Teslovich TM, Tukiainen T, Uitterlinden AG, Van der Klauw MM, Vasan RS, Wallace C, Wallaschofski H, Wichmann HE, Willemsen G, Würtz P, Xu C, Yerges-Armstrong LM, Abecasis GR, Ahmadi KR, Boomsma DI, Caulfield M, Cookson WO, van Duijn CM, Froguel P, Matsuda K, McCarthy MI, Meisinger C, Mooser V, Pietiläinen KH, Schumann G, Snieder H, Sternberg MJE, Stolk RP, Thomas HC, Thorsteinsdottir U, Uda M, Waeber G, Wareham NJ, Waterworth DM, Watkins H, Whitfield JB, Witteman JCM, Wolffenbuttel BHR, Fox CS, Ala-Korpela M, Stefansson K, Vollenweider P, Völzke H, Schadt EE, Scott J, Järvelin MR, Elliott P, Kooner JS. Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. Nat Genet 2011; 43:1131-8. [PMID: 22001757 PMCID: PMC3482372 DOI: 10.1038/ng.970] [Citation(s) in RCA: 410] [Impact Index Per Article: 31.5] [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: 03/08/2011] [Accepted: 09/12/2011] [Indexed: 12/15/2022]
Abstract
Concentrations of liver enzymes in plasma are widely used as indicators of liver disease. We carried out a genome-wide association study in 61,089 individuals, identifying 42 loci associated with concentrations of liver enzymes in plasma, of which 32 are new associations (P = 10(-8) to P = 10(-190)). We used functional genomic approaches including metabonomic profiling and gene expression analyses to identify probable candidate genes at these regions. We identified 69 candidate genes, including genes involved in biliary transport (ATP8B1 and ABCB11), glucose, carbohydrate and lipid metabolism (FADS1, FADS2, GCKR, JMJD1C, HNF1A, MLXIPL, PNPLA3, PPP1R3B, SLC2A2 and TRIB1), glycoprotein biosynthesis and cell surface glycobiology (ABO, ASGR1, FUT2, GPLD1 and ST3GAL4), inflammation and immunity (CD276, CDH6, GCKR, HNF1A, HPR, ITGA1, RORA and STAT4) and glutathione metabolism (GSTT1, GSTT2 and GGT), as well as several genes of uncertain or unknown function (including ABHD12, EFHD1, EFNA1, EPHA2, MICAL3 and ZNF827). Our results provide new insight into genetic mechanisms and pathways influencing markers of liver function.
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Affiliation(s)
- John C Chambers
- Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, UK.
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