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Jackson HR, Zandstra J, Menikou S, Hamilton MS, McArdle AJ, Fischer R, Thorne AM, Huang H, Tanck MW, Jansen MH, De T, Agyeman PKA, Von Both U, Carrol ED, Emonts M, Eleftheriou I, Van der Flier M, Fink C, Gloerich J, De Groot R, Moll HA, Pokorn M, Pollard AJ, Schlapbach LJ, Tsolia MN, Usuf E, Wright VJ, Yeung S, Zavadska D, Zenz W, Coin LJM, Casals-Pascual C, Cunnington AJ, Martinon-Torres F, Herberg JA, de Jonge MI, Levin M, Kuijpers TW, Kaforou M. A multi-platform approach to identify a blood-based host protein signature for distinguishing between bacterial and viral infections in febrile children (PERFORM): a multi-cohort machine learning study. Lancet Digit Health 2023; 5:e774-e785. [PMID: 37890901 DOI: 10.1016/s2589-7500(23)00149-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 06/08/2023] [Accepted: 07/26/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Differentiating between self-resolving viral infections and bacterial infections in children who are febrile is a common challenge, causing difficulties in identifying which individuals require antibiotics. Studying the host response to infection can provide useful insights and can lead to the identification of biomarkers of infection with diagnostic potential. This study aimed to identify host protein biomarkers for future development into an accurate, rapid point-of-care test that can distinguish between bacterial and viral infections, by recruiting children presenting to health-care settings with fever or a history of fever in the previous 72 h. METHODS In this multi-cohort machine learning study, patient data were taken from EUCLIDS, the Swiss Pediatric Sepsis study, the GENDRES study, and the PERFORM study, which were all based in Europe. We generated three high-dimensional proteomic datasets (SomaScan and two via liquid chromatography tandem mass spectrometry, referred to as MS-A and MS-B) using targeted and untargeted platforms (SomaScan and liquid chromatography mass spectrometry). Protein biomarkers were then shortlisted using differential abundance analysis, feature selection using forward selection-partial least squares (FS-PLS; 100 iterations), along with a literature search. Identified proteins were tested with Luminex and ELISA and iterative FS-PLS was done again (25 iterations) on the Luminex results alone, and the Luminex and ELISA results together. A sparse protein signature for distinguishing between bacterial and viral infections was identified from the selected proteins. The performance of this signature was finally tested using Luminex assays and by calculating disease risk scores. FINDINGS 376 children provided serum or plasma samples for use in the discovery of protein biomarkers. 79 serum samples were collected for the generation of the SomaScan dataset, 147 plasma samples for the MS-A dataset, and 150 plasma samples for the MS-B dataset. Differential abundance analysis, and the first round of feature selection using FS-PLS identified 35 protein biomarker candidates, of which 13 had commercial ELISA or Luminex tests available. 16 proteins with ELISA or Luminex tests available were identified by literature review. Further evaluation via Luminex and ELISA and the second round of feature selection using FS-PLS revealed a six-protein signature: three of the included proteins are elevated in bacterial infections (SELE, NGAL, and IFN-γ), and three are elevated in viral infections (IL18, NCAM1, and LG3BP). Performance testing of the signature using Luminex assays revealed area under the receiver operating characteristic curve values between 89·4% and 93·6%. INTERPRETATION This study has led to the identification of a protein signature that could be ultimately developed into a blood-based point-of-care diagnostic test for rapidly diagnosing bacterial and viral infections in febrile children. Such a test has the potential to greatly improve care of children who are febrile, ensuring that the correct individuals receive antibiotics. FUNDING European Union's Horizon 2020 research and innovation programme, the European Union's Seventh Framework Programme (EUCLIDS), Imperial Biomedical Research Centre of the National Institute for Health Research, the Wellcome Trust and Medical Research Foundation, Instituto de Salud Carlos III, Consorcio Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Grupos de Refeencia Competitiva, Swiss State Secretariat for Education, Research and Innovation.
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Affiliation(s)
- Heather R Jackson
- Section of Paediatric Infectious Disease, Faculty of Medicine, and Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Judith Zandstra
- Sanquin Research and Landsteiner Laboratory, Department of Immunopathology, Sanquin Blood Supply, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands; Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
| | - Stephanie Menikou
- Section of Paediatric Infectious Disease, Faculty of Medicine, and Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Melissa Shea Hamilton
- Section of Paediatric Infectious Disease, Faculty of Medicine, and Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Andrew J McArdle
- Section of Paediatric Infectious Disease, Faculty of Medicine, and Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Roman Fischer
- Discovery Proteomics Facility, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adam M Thorne
- Department of Surgery, Section of Hepatobiliary Surgery and Liver Transplantation, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Honglei Huang
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Michael W Tanck
- Department of Epidemiology and Data Science, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
| | - Machiel H Jansen
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
| | - Tisham De
- Section of Paediatric Infectious Disease, Faculty of Medicine, and Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Philipp K A Agyeman
- Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ulrich Von Both
- Infectious Diseases, Department of Pediatrics, Dr von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Enitan D Carrol
- Department of Clinical Infection Microbiology and Immunology, University of Liverpool Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Marieke Emonts
- Paediatric Infectious Diseases and Immunology Department, Newcastle upon Tyne Hospitals Foundation Trust, Great North Children's Hospital, Newcastle upon Tyne, UK
| | - Irini Eleftheriou
- Second Department of Paediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, Panagiotis & Aglaia, Kyriakou Children's Hospital, Athens, Greece
| | - Michiel Van der Flier
- Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands; Pediatric Infectious Diseases and Immunology Amalia Children's Hospital, Department of Laboratory Medicine, Radboud Institute of Molecular Life Sciences, Radboud UMC, Nijmegen, Netherlands; Laboratory of Infectious Diseases, Department of Laboratory Medicine, Radboud Institute of Molecular Life Sciences, Radboud UMC, Nijmegen, Netherlands
| | - Colin Fink
- Micropathology, University of Warwick, Warwick, UK
| | - Jolein Gloerich
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute of Molecular Life Sciences, Radboud UMC, Nijmegen, Netherlands
| | - Ronald De Groot
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute of Molecular Life Sciences, Radboud UMC, Nijmegen, Netherlands
| | | | - Marko Pokorn
- Division of Paediatrics, University Medical Centre Ljubljana and Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andrew J Pollard
- Oxford Vaccine Group Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Luregn J Schlapbach
- Department of Intensive Care and Neonatology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland; Child Health Research Centre, The University of Queensland, Brisbane, NSW, Australia
| | - Maria N Tsolia
- Second Department of Paediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, Panagiotis & Aglaia, Kyriakou Children's Hospital, Athens, Greece
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Fajara, Gambia
| | - Victoria J Wright
- Section of Paediatric Infectious Disease, Faculty of Medicine, and Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Shunmay Yeung
- Clinical Research Department, Faculty of Infectious and Tropical Disease, London School of Hygiene & Tropical Medicine, London, UK
| | - Dace Zavadska
- Children's Clinical University Hospital, Rīga Stradins University, Rïga, Latvia
| | - Werner Zenz
- University Clinic of Paediatrics and Adolescent Medicine, Department of General Paediatrics, Medical University Graz, Graz, Austria
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Climent Casals-Pascual
- Department of Clinical Microbiology, CDB, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease, Faculty of Medicine, and Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Federico Martinon-Torres
- Translational Pediatrics and Infectious Diseases Section, Pediatrics Department, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Genetics, Vaccines, Infectious Diseases, and Pediatrics research group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Consorcio Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Jethro A Herberg
- Section of Paediatric Infectious Disease, Faculty of Medicine, and Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Marien I de Jonge
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute of Molecular Life Sciences, Radboud UMC, Nijmegen, Netherlands; Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud Institute of Molecular Life Sciences, Radboud UMC, Nijmegen, Netherlands
| | - Michael Levin
- Section of Paediatric Infectious Disease, Faculty of Medicine, and Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Taco W Kuijpers
- Sanquin Research and Landsteiner Laboratory, Department of Immunopathology, Sanquin Blood Supply, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands; Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease, Faculty of Medicine, and Centre for Paediatrics and Child Health, Imperial College London, London, UK.
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van der Velden FJS, de Vries G, Martin A, Lim E, von Both U, Kolberg L, Carrol ED, Khanijau A, Herberg JA, De T, Galassini R, Kuijpers TW, Martinón-Torres F, Rivero-Calle I, Vermont CL, Hagedoorn NN, Pokorn M, Pollard AJ, Schlapbach LJ, Tsolia M, Elefhteriou I, Yeung S, Zavadska D, Fink C, Voice M, Zenz W, Kohlmaier B, Agyeman PKA, Usuf E, Secka F, de Groot R, Levin M, van der Flier M, Emonts M, Cunnington A, De T, Herberg J, Kaforou M, Wright V, Baumard L, Bellos E, D’Souza G, Galassini R, Habgood-Coote D, Hamilton S, Hoggart C, Hourmat S, Jackson H, Maconochie I, Menikou S, Lin N, Nichols S, Nijman R, Powell O, Pena Paz I, Shah P, Shen CF, Vito O, Wilson C, Abdulla A, Ali L, Darnell S, Jorgensen R, Mustafa S, Persand S, Stevens MM, Kim N, Kim E, Fidler K, Dudley J, Richmond V, Tavliavini E, Shen CF, Liu CC, Wang SM, Martinón-Torres F, Salas A, González FÁ, Farto CB, Barral-Arca R, Castro MB, Bello X, García MB, Carnota S, Cebey-López M, Curras-Tuala MJ, Suárez CD, Vicente LG, Gómez-Carballa A, Rial JG, Iglesias PL, Martinón-Torres F, Martinón-Torres N, Sánchez JMM, Pérez BM, Pardo-Seco J, Rodríguez LP, Pischedda S, Vázquez SR, Calle IR, Rodríguez-Tenreiro C, Redondo-Collazo L, Ora MS, Salas A, Fernández SS, Trasorras CS, Iglesias MV, Zavadska D, Balode A, Bārzdiņa A, Deksne D, Gardovska D, Grāvele D, Grope I, Meiere A, Nokalna I, Pavāre J, Pučuka Z, Selecka K, Rudzāte A, Svile D, Urbāne UN, Usuf E, Bojang K, Zaman SMA, Secka F, Anderson S, Sarr AR, Saidykhan M, Darboe S, Ceesay S, D’alessandro U, Moll HA, Vermont CL, Borensztajn DM, Hagedoorn NN, Tan C, Zachariasse J, Dik W, Agyeman PKA, Berger C, Giannoni E, Stocker M, Posfay-Barbe KM, Heininger U, Bernhard-Stirnemann S, Niederer-Loher A, Kahlert CR, Natalucci G, Relly C, Riedel T, Aebi C, Schlapbach LJ, Carrol ED, Cocklin E, Jennings R, Johnston J, Khanijau A, Leigh S, Lewis-Burke N, Newall K, Romaine S, Tsolia M, Eleftheriou I, Tambouratzi M, Marmarinos A, Xagorari M, Syggelou K, Fink C, Voice M, Calvo-Bado L, Zenz W, Kohlmaier B, Schweintzger NA, Sagmeister MG, Kohlfürst DS, Zurl C, Binder A, Hösele S, Leitner M, Pölz L, Rajic G, Bauchinger S, Baumgart H, Benesch M, Ceolotto A, Eber E, Gallistl S, Gores G, Haidl H, Hauer A, Hude C, Keldorfer M, Krenn L, Pilch H, Pfleger A, Pfurtscheller K, Nordberg G, Niedrist T, Rödl S, Skrabl-Baumgartner A, Sperl M, Stampfer L, Strenger V, Till H, Trobisch A, Löffler S, Yeung S, Dewez JE, Hibberd M, Bath D, Miners A, Nijman R, Fitchett E, de Groot R, van der Flier M, de Jonge MI, van Aerde K, Alkema W, van den Broek B, Gloerich J, van Gool AJ, Henriet S, Huijnen M, Philipsen R, Willems E, Gerrits G, van Leur M, Heidema J, de Haan L, Miedema C, Neeleman C, Obihara C, Tramper-Stranders G, Pollard AJ, Kandasamy R, Paulus S, Carter MJ, O’Connor D, Bibi S, Kelly DF, Gurung M, Thorson S, Ansari I, Murdoch DR, Shrestha S, Oliver Z, Emonts M, Lim E, Valentine L, Allen K, Bell K, Chan A, Crulley S, Devine K, Fabian D, King S, McAlinden P, McDonald S, McDonnell A, Pickering A, Thomson E, Wood A, Wallia D, Woodsford P, Baxter F, Bell A, Rhodes M, Agbeko R, Mackerness C, Baas B, Kloosterhuis L, Oosthoek W, Arif T, Bennet J, Collings K, van der Giessen I, Martin A, Rashid A, Rowlands E, de Vries G, van der Velden F, Soon J, Valentine L, Martin M, Mistry R, von Both U, Kolberg L, Zwerenz M, Buschbeck J, Bidlingmaier C, Binder V, Danhauser K, Haas N, Griese M, Feuchtinger T, Keil J, Kappler M, Lurz E, Muench G, Reiter K, Schoen C, Mallet F, Brengel-Pesce K, Pachot A, Mommert M, Pokorn M, Kolnik M, Vincek K, Srovin TP, Bahovec N, Prunk P, Osterman V, Avramoska T, Kuijpers T, Jongerius I, van den Berg JM, Schonenberg D, Barendregt AM, Pajkrt D, van der Kuip M, van Furth AM, Sprenkeler E, Zandstra J, van Mierlo G, Geissler J. Correction to: Febrile illness in high-risk children: a prospective, international observational study. Eur J Pediatr 2023; 182:555-556. [PMID: 36689005 PMCID: PMC9899168 DOI: 10.1007/s00431-022-04788-y] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Fabian J. S. van der Velden
- grid.459561.a0000 0004 4904 7256Paediatric Immunology, Infectious Diseases & Allergy, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK ,grid.1006.70000 0001 0462 7212Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gabriella de Vries
- grid.459561.a0000 0004 4904 7256Paediatric Immunology, Infectious Diseases & Allergy, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK ,grid.416135.40000 0004 0649 0805Department of General Paediatrics, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Alexander Martin
- grid.459561.a0000 0004 4904 7256Paediatric Immunology, Infectious Diseases & Allergy, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK ,grid.1006.70000 0001 0462 7212Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Emma Lim
- grid.459561.a0000 0004 4904 7256Paediatric Immunology, Infectious Diseases & Allergy, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK ,grid.1006.70000 0001 0462 7212Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Ulrich von Both
- grid.5252.00000 0004 1936 973XDivision Paediatric Infectious Diseases, Dr. Von Hauner Children’s Hospital, University Hospital LMU Munich, Munich, Germany
| | - Laura Kolberg
- grid.5252.00000 0004 1936 973XDivision Paediatric Infectious Diseases, Dr. Von Hauner Children’s Hospital, University Hospital LMU Munich, Munich, Germany
| | - Enitan D. Carrol
- grid.10025.360000 0004 1936 8470Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK ,grid.417858.70000 0004 0421 1374Alder Hey Children’s NHS Foundation Trust, Liverpool, UK
| | - Aakash Khanijau
- grid.10025.360000 0004 1936 8470Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK ,grid.417858.70000 0004 0421 1374Alder Hey Children’s NHS Foundation Trust, Liverpool, UK
| | - Jethro A. Herberg
- grid.7445.20000 0001 2113 8111Section of Paediatric Infectious Disease, Wright-Fleming Institute, Imperial College London, London, UK
| | - Tisham De
- grid.7445.20000 0001 2113 8111Section of Paediatric Infectious Disease, Wright-Fleming Institute, Imperial College London, London, UK
| | - Rachel Galassini
- grid.7445.20000 0001 2113 8111Section of Paediatric Infectious Disease, Wright-Fleming Institute, Imperial College London, London, UK
| | - Taco W. Kuijpers
- grid.7177.60000000084992262Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Amsterdam University Medical Center, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Federico Martinón-Torres
- grid.411048.80000 0000 8816 6945Pediatrics Department, Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain ,grid.11794.3a0000000109410645Grupo de Genetica, Vacunas, Infecciones y Pediatria, Instituto de Investigacion Sanitaria de Santiago, Universidad de Santiago, Santiago de Compostela, Spain ,grid.512891.6Consorcio Centro de Investigacion Biomedicaen Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Irene Rivero-Calle
- grid.411048.80000 0000 8816 6945Pediatrics Department, Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Clementien L. Vermont
- grid.416135.40000 0004 0649 0805Department of Pediatrics, Division of Pediatric Infectious Diseases & Immunology, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Nienke N. Hagedoorn
- grid.416135.40000 0004 0649 0805Department of General Paediatrics, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Marko Pokorn
- grid.29524.380000 0004 0571 7705University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Andrew J. Pollard
- grid.4991.50000 0004 1936 8948Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Luregn J. Schlapbach
- grid.412341.10000 0001 0726 4330Neonatal and Pediatric Intensive Care Unit, Children’s Research Center, University Children’s Hospital Zürich, University of Zürich, Zurich, Switzerland
| | - Maria Tsolia
- grid.5216.00000 0001 2155 08002nd Department of Pediatrics, National and Kapodistrian University of Athens, Children’s Hospital ‘P, and A. Kyriakou’, Athens, Greece
| | - Irini Elefhteriou
- grid.5216.00000 0001 2155 08002nd Department of Pediatrics, National and Kapodistrian University of Athens, Children’s Hospital ‘P, and A. Kyriakou’, Athens, Greece
| | - Shunmay Yeung
- grid.8991.90000 0004 0425 469XClinical Research Department, Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, UK
| | - Dace Zavadska
- grid.17330.360000 0001 2173 9398Department of Pediatrics, Rīgas Stradina Universitāte, Children’s Clinical University Hospital, Riga, Latvia
| | - Colin Fink
- grid.7372.10000 0000 8809 1613Micropathology Ltd, University of Warwick, Warwick, UK
| | - Marie Voice
- grid.7372.10000 0000 8809 1613Micropathology Ltd, University of Warwick, Warwick, UK
| | - Werner Zenz
- grid.11598.340000 0000 8988 2476Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Benno Kohlmaier
- grid.11598.340000 0000 8988 2476Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Philipp K. A. Agyeman
- grid.5734.50000 0001 0726 5157Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Effua Usuf
- grid.415063.50000 0004 0606 294XMedical Research Council Unit, Serrekunda, The Gambia
| | - Fatou Secka
- grid.415063.50000 0004 0606 294XMedical Research Council Unit, Serrekunda, The Gambia
| | - Ronald de Groot
- grid.461578.9Pediatric Infectious Diseases and Immunology, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael Levin
- grid.7445.20000 0001 2113 8111Section of Paediatric Infectious Disease, Wright-Fleming Institute, Imperial College London, London, UK
| | - Michiel van der Flier
- grid.461578.9Pediatric Infectious Diseases and Immunology, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.7692.a0000000090126352Pediatric Infectious Diseases and Immunology, Wilhelmina Children’s Hospital University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marieke Emonts
- Paediatric Immunology, Infectious Diseases & Allergy, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK. .,Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK. .,NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Trust and Newcastle University, Newcastle upon Tyne, UK.
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Abstract
Proteomics is the study of a large number of proteins in biological systems. We aim to introduce the complex field to paediatricians and present some recent examples of applications to paediatric problems. Various approaches have been used to study proteomes. The current mainstay is tandem mass spectrometry of enzymatically digested proteins ('bottom-up proteomics'), and we describe the experimental and computational approach further. Proteomics can offer advantages over transcriptomics by giving direct information about proteins rather than RNA; however, typically data are obtained at lower depth and the confident identification of mass spectra can be challenging. Proteomics frequently complements transcriptomics and other -omics. Used effectively, proteomics offers promise to help answer important clinical and biological questions.
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Affiliation(s)
| | - Stephanie Menikou
- Department of Infectious Disease, Imperial College London, London, UK
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Abstract
Kawasaki disease (KD) is an inflammatory disease in children associated with vasculitis affecting predominantly the coronary arteries and is now the most common cause of acquired heart disease in children in developed countries. The etiology of KD is unknown but epidemiological studies implicate an infectious agent or toxin, which causes disease in genetically predisposed individuals. The presence of immune complexes (ICs) in the serum of children with KD was established in numerous studies during the 1970s and 80s. More recent genetic studies have identified variation in Fcγ receptors and genes controlling immunoglobulin production associated with KD. In this review we link the genetic findings and IC studies and suggest a key role for their interaction in pathophysiology of the disease.
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Affiliation(s)
- Stephanie Menikou
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
| | - Paul R Langford
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
| | - Michael Levin
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
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Menikou S, McArdle A, Kaforou M, Shimizu C, Wright VJ, Herberg JA, Kanegaye JT, Tremoulet A, Burns JC, Levin M. Characterisation of immune complexes in Kawasaki Disease and other infectious diseases by protein sequencing. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.182.61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Abstract
Background
Kawasaki Disease is a paediatric inflammatory disease associated with self-limiting vasculitis. It has a world-wide distribution with an ethnic bias towards East Asian populations and is the most common cause of acquired heart disease in children in developed countries. The immunopathogenesis of KD remains poorly understood. The presence of antibody-antigens (pathogen) known as immune complexes in the blood of children with KD was established in numerous studies leading to the hypothesis that immune complexes contribute to the damages of the coronary artery.
Methodology
Using proteomic technologies we characterised the composition of immune complexes in KD and compare the immune complexes in KD with those in children with other febrile illnesses, TB and healthy children. Immune complexes were precipitated from the blood of 80 children with KD, 80 children with other febrile conditions, 30 with TB and 30 healthy children. We used Lumos Orbitrap mass spectrometry to identify the recovered proteins. Using the bioinformatics program PEAKS, we performed database searches and compared the protein abundances between the different comparator groups.
Conclusions
Immune complexes isolated from children with KD are different from those recovered from other febrile illnesses in terms of the nature of proteins within the complex. The pattern of proteins in the immune complexes containing immunoglobulins, complement proteins as well as other serum proteins, provides insight into the nature of the unique inflammatory response in KD versus the other inflammatory diseases.
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Wright VJ, Herberg JA, Kaforou M, Shimizu C, Eleftherohorinou H, Shailes H, Barendregt AM, Menikou S, Gormley S, Berk M, Hoang LT, Tremoulet AH, Kanegaye JT, Coin LJM, Glodé MP, Hibberd M, Kuijpers TW, Hoggart CJ, Burns JC, Levin M. Diagnosis of Kawasaki Disease Using a Minimal Whole-Blood Gene Expression Signature. JAMA Pediatr 2018; 172:e182293. [PMID: 30083721 PMCID: PMC6233768 DOI: 10.1001/jamapediatrics.2018.2293] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
IMPORTANCE To date, there is no diagnostic test for Kawasaki disease (KD). Diagnosis is based on clinical features shared with other febrile conditions, frequently resulting in delayed or missed treatment and an increased risk of coronary artery aneurysms. OBJECTIVE To identify a whole-blood gene expression signature that distinguishes children with KD in the first week of illness from other febrile conditions. DESIGN, SETTING, AND PARTICIPANTS The case-control study comprised a discovery group that included a training and test set and a validation group of children with KD or comparator febrile illness. The setting was pediatric centers in the United Kingdom, Spain, the Netherlands, and the United States. The training and test discovery group comprised 404 children with infectious and inflammatory conditions (78 KD, 84 other inflammatory diseases, and 242 bacterial or viral infections) and 55 healthy controls. The independent validation group comprised 102 patients with KD, including 72 in the first 7 days of illness, and 130 febrile controls. The study dates were March 1, 2009, to November 14, 2013, and data analysis took place from January 1, 2015, to December 31, 2017. MAIN OUTCOMES AND MEASURES Whole-blood gene expression was evaluated using microarrays, and minimal transcript sets distinguishing KD were identified using a novel variable selection method (parallel regularized regression model search). The ability of transcript signatures (implemented as disease risk scores) to discriminate KD cases from controls was assessed by area under the curve (AUC), sensitivity, and specificity at the optimal cut point according to the Youden index. RESULTS Among 404 patients in the discovery set, there were 78 with KD (median age, 27 months; 55.1% male) and 326 febrile controls (median age, 37 months; 56.4% male). Among 202 patients in the validation set, there were 72 with KD (median age, 34 months; 62.5% male) and 130 febrile controls (median age, 17 months; 56.9% male). A 13-transcript signature identified in the discovery training set distinguished KD from other infectious and inflammatory conditions in the discovery test set, with AUC of 96.2% (95% CI, 92.5%-99.9%), sensitivity of 81.7% (95% CI, 60.0%-94.8%), and specificity of 92.1% (95% CI, 84.0%-97.0%). In the validation set, the signature distinguished KD from febrile controls, with AUC of 94.6% (95% CI, 91.3%-98.0%), sensitivity of 85.9% (95% CI, 76.8%-92.6%), and specificity of 89.1% (95% CI, 83.0%-93.7%). The signature was applied to clinically defined categories of definite, highly probable, and possible KD, resulting in AUCs of 98.1% (95% CI, 94.5%-100%), 96.3% (95% CI, 93.3%-99.4%), and 70.0% (95% CI, 53.4%-86.6%), respectively, mirroring certainty of clinical diagnosis. CONCLUSIONS AND RELEVANCE In this study, a 13-transcript blood gene expression signature distinguished KD from other febrile conditions. Diagnostic accuracy increased with certainty of clinical diagnosis. A test incorporating the 13-transcript disease risk score may enable earlier diagnosis and treatment of KD and reduce inappropriate treatment in those with other diagnoses.
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Affiliation(s)
| | - Jethro A. Herberg
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Chisato Shimizu
- Department of Pediatrics, University of California San Diego, La Jolla,Rady Children’s Hospital–San Diego, San Diego, California
| | | | - Hannah Shailes
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Anouk M. Barendregt
- Department of Pediatric Hematology, Immunology & Infectious Diseases, Emma Children’s Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Stephanie Menikou
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Stuart Gormley
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Maurice Berk
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | | | - Adriana H. Tremoulet
- Department of Pediatrics, University of California San Diego, La Jolla,Rady Children’s Hospital–San Diego, San Diego, California
| | - John T. Kanegaye
- Department of Pediatrics, University of California San Diego, La Jolla,Rady Children’s Hospital–San Diego, San Diego, California
| | - Lachlan J. M. Coin
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, United Kingdom,Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Mary P. Glodé
- Section of Infectious Diseases, Department of Pediatrics, University of Colorado Denver School of Medicine Anschutz Medical Campus, Aurora,Children’s Hospital Colorado, Aurora
| | - Martin Hibberd
- Infectious Diseases, Genome Institute of Singapore, Singapore
| | - Taco W. Kuijpers
- Department of Pediatric Hematology, Immunology & Infectious Diseases, Emma Children’s Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands,Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Clive J. Hoggart
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Jane C. Burns
- Department of Pediatrics, University of California San Diego, La Jolla,Rady Children’s Hospital–San Diego, San Diego, California
| | - Michael Levin
- Section of Paediatrics, Imperial College London, London, United Kingdom
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Menikou S, Patel MP, Rose KL, Botto M, Warner JO, Pickering MC, Boyle RJ. Relationship between complotype and reported severity of systemic allergic reactions to peanut. J Allergy Clin Immunol 2012; 129:1398-1401.e3. [PMID: 22325069 DOI: 10.1016/j.jaci.2011.10.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 10/26/2011] [Accepted: 10/31/2011] [Indexed: 11/19/2022]
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