1
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Ratnasiri K, Zheng H, Toh J, Yao Z, Duran V, Donato M, Roederer M, Kamath M, Todd JPM, Gagne M, Foulds KE, Francica JR, Corbett KS, Douek DC, Seder RA, Einav S, Blish CA, Khatri P. Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans. Cell Rep 2024; 43:113706. [PMID: 38294906 PMCID: PMC10915397 DOI: 10.1016/j.celrep.2024.113706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/02/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Viral pandemics and epidemics pose a significant global threat. While macaque models of viral disease are routinely used, it remains unclear how conserved antiviral responses are between macaques and humans. Therefore, we conducted a cross-species analysis of transcriptomic data from over 6,088 blood samples from macaques and humans infected with one of 31 viruses. Our findings demonstrate that irrespective of primate or viral species, there are conserved antiviral responses that are consistent across infection phase (acute, chronic, or latent) and viral genome type (DNA or RNA viruses). Leveraging longitudinal data from experimental challenges, we identify virus-specific response kinetics such as host responses to Coronaviridae and Orthomyxoviridae infections peaking 1-3 days earlier than responses to Filoviridae and Arenaviridae viral infections. Our results underscore macaque studies as a powerful tool for understanding viral pathogenesis and immune responses that translate to humans, with implications for viral therapeutic development and pandemic preparedness.
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Affiliation(s)
- Kalani Ratnasiri
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jiaying Toh
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhiyuan Yao
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Veronica Duran
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Michele Donato
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megha Kamath
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John-Paul M Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph R Francica
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shirit Einav
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Catherine A Blish
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.
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2
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Torraca V, White RJ, Sealy IM, Mazon-Moya M, Duggan G, Willis AR, Busch-Nentwich EM, Mostowy S. Transcriptional profiling of zebrafish identifies host factors controlling susceptibility to Shigella flexneri. Dis Model Mech 2024; 17:dmm050431. [PMID: 38131137 PMCID: PMC10846535 DOI: 10.1242/dmm.050431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
Shigella flexneri is a human-adapted pathovar of Escherichia coli that can invade the intestinal epithelium, causing inflammation and bacillary dysentery. Although an important human pathogen, the host response to S. flexneri has not been fully described. Zebrafish larvae represent a valuable model for studying human infections in vivo. Here, we use a Shigella-zebrafish infection model to generate mRNA expression profiles of host response to Shigella infection at the whole-animal level. Immune response-related processes dominate the signature of early Shigella infection (6 h post-infection). Consistent with its clearance from the host, the signature of late Shigella infection (24 h post-infection) is significantly changed, and only a small set of immune-related genes remain differentially expressed, including acod1 and gpr84. Using mutant lines generated by ENU, CRISPR mutagenesis and F0 crispants, we show that acod1- and gpr84-deficient larvae are more susceptible to Shigella infection. Together, these results highlight the power of zebrafish to model infection by bacterial pathogens and reveal the mRNA expression of the early (acutely infected) and late (clearing) host response to Shigella infection.
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Affiliation(s)
- Vincenzo Torraca
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
- School of Life Sciences, University of Westminster, London W1W 6UW, UK
| | - Richard J. White
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London E1 4NS, UK
| | - Ian M. Sealy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London E1 4NS, UK
| | - Maria Mazon-Moya
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Gina Duggan
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Alexandra R. Willis
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Elisabeth M. Busch-Nentwich
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London E1 4NS, UK
| | - Serge Mostowy
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
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3
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Pividori M, Lu S, Li B, Su C, Johnson ME, Wei WQ, Feng Q, Namjou B, Kiryluk K, Kullo IJ, Luo Y, Sullivan BD, Voight BF, Skarke C, Ritchie MD, Grant SFA, Greene CS. Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms. Nat Commun 2023; 14:5562. [PMID: 37689782 PMCID: PMC10492839 DOI: 10.1038/s41467-023-41057-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 08/18/2023] [Indexed: 09/11/2023] Open
Abstract
Genes act in concert with each other in specific contexts to perform their functions. Determining how these genes influence complex traits requires a mechanistic understanding of expression regulation across different conditions. It has been shown that this insight is critical for developing new therapies. Transcriptome-wide association studies have helped uncover the role of individual genes in disease-relevant mechanisms. However, modern models of the architecture of complex traits predict that gene-gene interactions play a crucial role in disease origin and progression. Here we introduce PhenoPLIER, a computational approach that maps gene-trait associations and pharmacological perturbation data into a common latent representation for a joint analysis. This representation is based on modules of genes with similar expression patterns across the same conditions. We observe that diseases are significantly associated with gene modules expressed in relevant cell types, and our approach is accurate in predicting known drug-disease pairs and inferring mechanisms of action. Furthermore, using a CRISPR screen to analyze lipid regulation, we find that functionally important players lack associations but are prioritized in trait-associated modules by PhenoPLIER. By incorporating groups of co-expressed genes, PhenoPLIER can contextualize genetic associations and reveal potential targets missed by single-gene strategies.
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Affiliation(s)
- Milton Pividori
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Sumei Lu
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Binglan Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Chun Su
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Matthew E Johnson
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Wei-Qi Wei
- Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Qiping Feng
- Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Bahram Namjou
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, 10032, USA
| | | | - Yuan Luo
- Northwestern University, Chicago, IL, 60611, USA
| | - Blair D Sullivan
- Kahlert School of Computing, University of Utah, Salt Lake City, UT, 84112, USA
| | - Benjamin F Voight
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Carsten Skarke
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Struan F A Grant
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Casey S Greene
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
- Center for Health AI, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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4
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Habgood-Coote D, Wilson C, Shimizu C, Barendregt AM, Philipsen R, Galassini R, Calle IR, Workman L, Agyeman PKA, Ferwerda G, Anderson ST, van den Berg JM, Emonts M, Carrol ED, Fink CG, de Groot R, Hibberd ML, Kanegaye J, Nicol MP, Paulus S, Pollard AJ, Salas A, Secka F, Schlapbach LJ, Tremoulet AH, Walther M, Zenz W, Van der Flier M, Zar HJ, Kuijpers T, Burns JC, Martinón-Torres F, Wright VJ, Coin LJM, Cunnington AJ, Herberg JA, Levin M, Kaforou M. Diagnosis of childhood febrile illness using a multi-class blood RNA molecular signature. MED 2023; 4:635-654.e5. [PMID: 37597512 DOI: 10.1016/j.medj.2023.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 08/21/2023]
Abstract
BACKGROUND Appropriate treatment and management of children presenting with fever depend on accurate and timely diagnosis, but current diagnostic tests lack sensitivity and specificity and are frequently too slow to inform initial treatment. As an alternative to pathogen detection, host gene expression signatures in blood have shown promise in discriminating several infectious and inflammatory diseases in a dichotomous manner. However, differential diagnosis requires simultaneous consideration of multiple diseases. Here, we show that diverse infectious and inflammatory diseases can be discriminated by the expression levels of a single panel of genes in blood. METHODS A multi-class supervised machine-learning approach, incorporating clinical consequence of misdiagnosis as a "cost" weighting, was applied to a whole-blood transcriptomic microarray dataset, incorporating 12 publicly available datasets, including 1,212 children with 18 infectious or inflammatory diseases. The transcriptional panel identified was further validated in a new RNA sequencing dataset comprising 411 febrile children. FINDINGS We identified 161 transcripts that classified patients into 18 disease categories, reflecting individual causative pathogen and specific disease, as well as reliable prediction of broad classes comprising bacterial infection, viral infection, malaria, tuberculosis, or inflammatory disease. The transcriptional panel was validated in an independent cohort and benchmarked against existing dichotomous RNA signatures. CONCLUSIONS Our data suggest that classification of febrile illness can be achieved with a single blood sample and opens the way for a new approach for clinical diagnosis. FUNDING European Union's Seventh Framework no. 279185; Horizon2020 no. 668303 PERFORM; Wellcome Trust (206508/Z/17/Z); Medical Research Foundation (MRF-160-0008-ELP-KAFO-C0801); NIHR Imperial BRC.
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Affiliation(s)
- Dominic Habgood-Coote
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Clare Wilson
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Chisato Shimizu
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Anouk M Barendregt
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Ria Philipsen
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Rachel Galassini
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Irene Rivero Calle
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Lesley Workman
- Department of Paediatrics & Child Health, Red Cross Childrens Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Philipp K A Agyeman
- Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Gerben Ferwerda
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Suzanne T Anderson
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - J Merlijn van den Berg
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Marieke Emonts
- Great North Children's Hospital, Department of Paediatric Immunology, Infectious Diseases & Allergy and NIHR Newcastle Biomedical Research Centre, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK; Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Enitan D Carrol
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool Institute of Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Colin G Fink
- Micropathology Ltd Research and Diagnosis, Coventry, UK; University of Warwick, Coventry, UK
| | - Ronald de Groot
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Martin L Hibberd
- Department of Infection Biology, Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, UK
| | - John Kanegaye
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Mark P Nicol
- Marshall Centre, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Stéphane Paulus
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool Institute of Infection, Veterinary and Ecological Sciences, Liverpool, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Antonio Salas
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Fatou Secka
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - Luregn J Schlapbach
- Pediatric and Neonatal Intensive Care Unit, and Children`s Research Center, University Children's Hospital Zurich, Zurich, Switzerland; Child Health Research Centre, The University of Queensland, and Paediatric Intensive Care Unit, Queensland Children's Hospital, Brisbane, QLD, Australia
| | - Adriana H Tremoulet
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Walther
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - Werner Zenz
- University Clinic of Paediatrics and Adolescent Medicine, Department of General Paediatrics, Medical University of Graz, Graz, Austria
| | - Michiel Van der Flier
- Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands; Paediatric Infectious Diseases and Immunology Amalia Children's Hospital, Radboudumc, Nijmegen, the Netherlands
| | - Heather J Zar
- Department of Paediatrics & Child Health, Red Cross Childrens Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Taco Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands; Department of Blood Cell Research, Sanquin Blood Supply, Division Research and Landsteiner Laboratory of Amsterdam UMC (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Jane C Burns
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Federico Martinón-Torres
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Victoria J Wright
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Jethro A Herberg
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Michael Levin
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK.
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5
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Miyagi Y. Identification of Pediatric Bacterial Gastroenteritis From Blood Counts and Interviews Based on Machine Learning. Cureus 2023; 15:e43644. [PMID: 37600437 PMCID: PMC10434729 DOI: 10.7759/cureus.43644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2023] [Indexed: 08/22/2023] Open
Abstract
INTRODUCTION Differentiating between bacterial and viral gastroenteritis is crucial in pediatric enteritis practice. Our objective was to use machine learning (ML) to identify acute gastroenteritis (AG) caused by bacteria based on blood cell counts and interview findings. METHODS ML was performed using a decision tree classifier based on data from previously published papers. We included 164 children between one and 108 months diagnosed with gastroenteritis, with 112 having bacterial AG and 52 having viral AG as subjects and controls. Feature selection was performed using least absolute shrinkage and selection operator (LASSO), and the classifier's performance was evaluated by five-fold cross-validation. Additionally, we presented a tree diagram of the decision tree classifier as a flowchart for practical applications. RESULTS The area under curve (AUC) was 0.80, indicating a moderate model. Three important features in this model were platelet-lymphocyte ratio, eosinophil count, and leukocyte count. CONCLUSIONS In conclusion, this study demonstrates that bacterial AG can be estimated from blood cell counts with moderate accuracy. These findings may be valuable in narrowing down bacterial AG in children with gastrointestinal symptoms.
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Affiliation(s)
- Yoshifumi Miyagi
- Department of Pediatrics, Haibara General Hospital, Shizuoka, JPN
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6
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Wolf S, Melo D, Garske KM, Pallares LF, Lea AJ, Ayroles JF. Characterizing the landscape of gene expression variance in humans. PLoS Genet 2023; 19:e1010833. [PMID: 37410774 DOI: 10.1371/journal.pgen.1010833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023] Open
Abstract
Gene expression variance has been linked to organismal function and fitness but remains a commonly neglected aspect of molecular research. As a result, we lack a comprehensive understanding of the patterns of transcriptional variance across genes, and how this variance is linked to context-specific gene regulation and gene function. Here, we use 57 large publicly available RNA-seq data sets to investigate the landscape of gene expression variance. These studies cover a wide range of tissues and allowed us to assess if there are consistently more or less variable genes across tissues and data sets and what mechanisms drive these patterns. We show that gene expression variance is broadly similar across tissues and studies, indicating that the pattern of transcriptional variance is consistent. We use this similarity to create both global and within-tissue rankings of variation, which we use to show that function, sequence variation, and gene regulatory signatures contribute to gene expression variance. Low-variance genes are associated with fundamental cell processes and have lower levels of genetic polymorphisms, have higher gene-gene connectivity, and tend to be associated with chromatin states associated with transcription. In contrast, high-variance genes are enriched for genes involved in immune response, environmentally responsive genes, immediate early genes, and are associated with higher levels of polymorphisms. These results show that the pattern of transcriptional variance is not noise. Instead, it is a consistent gene trait that seems to be functionally constrained in human populations. Furthermore, this commonly neglected aspect of molecular phenotypic variation harbors important information to understand complex traits and disease.
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Affiliation(s)
- Scott Wolf
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Diogo Melo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Kristina M Garske
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Luisa F Pallares
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Amanda J Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Child and Brain Development, Canadian Institute for Advanced Research, Toronto, Canada
| | - Julien F Ayroles
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
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7
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Pennisi I, Moniri A, Miscourides N, Miglietta L, Moser N, Habgood-Coote D, Herberg JA, Levin M, Kaforou M, Rodriguez-Manzano J, Georgiou P. Discrimination of bacterial and viral infection using host-RNA signatures integrated in a lab-on-chip platform. Biosens Bioelectron 2022; 216:114633. [PMID: 36081245 DOI: 10.1016/j.bios.2022.114633] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 07/13/2022] [Accepted: 08/09/2022] [Indexed: 11/02/2022]
Abstract
The unmet clinical need for accurate point-of-care (POC) diagnostic tests able to discriminate bacterial from viral infection demands a solution that can be used both within healthcare settings and in the field, and that can also stem the tide of antimicrobial resistance. Our approach to solve this problem combine the use of host gene signatures with our Lab-on-a-Chip (LoC) technology enabling low-cost POC expression analysis to detect Infectious Disease. Transcriptomics have been extensively investigated as a potential tool to be implemented in the diagnosis of infectious disease. On the other hand, LoC technologies using ion-sensitive field-effect transistor (ISFET), in conjunction with isothermal chemistries, are offering a promising alternative to conventional amplification instruments, owing to their portable and affordable nature. Currently, the data analysis of ISFET arrays are restricted to established methods by averaging the output of every sensor to give a single time-series. This simple approach makes unrealistic assumptions, leading to insufficient performance for applications that require accurate quantification such as Host-Transcriptomics. In order to reliably quantify transcripts on our LoC platform enabling the classification of infectious disease on-chip, we propose a novel data-driven algorithm for extracting time-to-positive values from ISFET arrays. The algorithm proposed correctly outputs a time-to-positive for all the reactions, with a high correlation to RT-qLAMP (0.85, R2 = 0.98, p < 0.01), resulting in a classification accuracy of 100% (CI, 95-100%). This work aims to bridge the gap between translating assays from microarray analysis to ISFET arrays providing benefits on tackling infectious disease and diagnostic testing in hard-to-reach areas of the world.
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Affiliation(s)
- Ivana Pennisi
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK; Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Ahmad Moniri
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK
| | - Nicholas Miscourides
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK
| | - Luca Miglietta
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK; Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Nicolas Moser
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK
| | - Dominic Habgood-Coote
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Jethro A Herberg
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Michael Levin
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Myrsini Kaforou
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | | | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK
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8
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Gómez-Carballa A, Rivero-Calle I, Pardo-Seco J, Gómez-Rial J, Rivero-Velasco C, Rodríguez-Núñez N, Barbeito-Castiñeiras G, Pérez-Freixo H, Cebey-López M, Barral-Arca R, Rodriguez-Tenreiro C, Dacosta-Urbieta A, Bello X, Pischedda S, Currás-Tuala MJ, Viz-Lasheras S, Martinón-Torres F, Salas A. A multi-tissue study of immune gene expression profiling highlights the key role of the nasal epithelium in COVID-19 severity. ENVIRONMENTAL RESEARCH 2022; 210:112890. [PMID: 35202626 PMCID: PMC8861187 DOI: 10.1016/j.envres.2022.112890] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/11/2022] [Accepted: 02/02/2022] [Indexed: 05/08/2023]
Abstract
Coronavirus Disease-19 (COVID-19) symptoms range from mild to severe illness; the cause for this differential response to infection remains unknown. Unravelling the immune mechanisms acting at different levels of the colonization process might be key to understand these differences. We carried out a multi-tissue (nasal, buccal and blood; n = 156) gene expression analysis of immune-related genes from patients affected by different COVID-19 severities, and healthy controls through the nCounter technology. Mild and asymptomatic cases showed a powerful innate antiviral response in nasal epithelium, characterized by activation of interferon (IFN) pathway and downstream cascades, successfully controlling the infection at local level. In contrast, weak macrophage/monocyte driven innate antiviral response and lack of IFN signalling activity were present in severe cases. Consequently, oral mucosa from severe patients showed signals of viral activity, cell arresting and viral dissemination to the lower respiratory tract, which ultimately could explain the exacerbated innate immune response and impaired adaptative immune responses observed at systemic level. Results from saliva transcriptome suggest that the buccal cavity might play a key role in SARS-CoV-2 infection and dissemination in patients with worse prognosis. Co-expression network analysis adds further support to these findings, by detecting modules specifically correlated with severity involved in the abovementioned biological routes; this analysis also provides new candidate genes that might be tested as biomarkers in future studies. We also found tissue specific severity-related signatures mainly represented by genes involved in the innate immune system and cytokine/chemokine signalling. Local immune response could be key to determine the course of the systemic response and thus COVID-19 severity. Our findings provide a framework to investigate severity host gene biomarkers and pathways that might be relevant to diagnosis, prognosis, and therapy.
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Affiliation(s)
- Alberto Gómez-Carballa
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jacobo Pardo-Seco
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - José Gómez-Rial
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Laboratorio de Inmunología. Servicio de Análisis Clínicos. Hospital Clínico Universitario (SERGAS), Galicia, Spain
| | - Carmen Rivero-Velasco
- Intensive Medicine Department, Hospital Clìnico Universitario de Santiago de Compostela, Galicia, Spain
| | - Nuria Rodríguez-Núñez
- Pneumology Department, Hospital Clìnico Universitario de Santiago de Compostela, Galicia, Spain
| | - Gema Barbeito-Castiñeiras
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Hugo Pérez-Freixo
- Preventive Medicine Department, Hospital Clínico Universitario de Santiago de Compostela, Spain
| | - Miriam Cebey-López
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Ruth Barral-Arca
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Carmen Rodriguez-Tenreiro
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana Dacosta-Urbieta
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Xabier Bello
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Sara Pischedda
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - María José Currás-Tuala
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Sandra Viz-Lasheras
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Salas
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain.
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9
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Casu A, Grippo PJ, Wasserfall C, Sun Z, Linsley PS, Hamerman JA, Fife BT, Lacy-Hulbert A, Toledo FGS, Hart PA, Papachristou GI, Bellin MD, Yadav D, Laughlin MR, Goodarzi MO, Speake C. Evaluating the Immunopathogenesis of Diabetes After Acute Pancreatitis in the Diabetes RElated to Acute Pancreatitis and Its Mechanisms Study: From the Type 1 Diabetes in Acute Pancreatitis Consortium. Pancreas 2022; 51:580-585. [PMID: 36206462 PMCID: PMC9555855 DOI: 10.1097/mpa.0000000000002076] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
ABSTRACT The association between acute pancreatitis (AP) and diabetes mellitus (DM) has long been established, with the initial descriptions of AP patients presenting with DM after a bout of AP published in the 1940s and 50s. However, the potential mechanisms involved, particularly those components related to the immune system, have not been well defined. The Diabetes RElated to Acute pancreatitis and its Mechanisms (DREAM) study is a multicenter clinical study designed to understand the frequency and phenotype of DM developing after AP. This article describes one objective of the DREAM study: to determine the immunologic mechanisms of DM after AP, including the contribution of β-cell autoimmunity. This component of the study will assess the presence of islet autoimmunity, as well as the magnitude and kinetics of the innate and adaptive immune response at enrollment and during longitudinal follow-up after 1 or more episodes of AP. Finally, DREAM will evaluate the relationship between immune features, DM development, and pancreatitis etiology and severity.
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Affiliation(s)
- Anna Casu
- From the Translational Research Institute, AdventHealth Orlando, Orlando, FL
| | - Paul J Grippo
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois-Chicago, Chicago, IL
| | - Clive Wasserfall
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL
| | - Zhaoli Sun
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Peter S Linsley
- Center for Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA
| | - Jessica A Hamerman
- Center for Fundamental Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA
| | - Brian T Fife
- Department of Medicine, Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Adam Lacy-Hulbert
- Center for Fundamental Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA
| | - Frederico G S Toledo
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Phil A Hart
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Georgios I Papachristou
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
| | | | - Dhiraj Yadav
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Maren R Laughlin
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Cate Speake
- Diabetes Clinical Research Program, Center for Interventional Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA
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10
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Buonsenso D, Sodero G, Valentini P. Transcript host-RNA signatures to discriminate bacterial and viral infections in febrile children. Pediatr Res 2022; 91:454-463. [PMID: 34912024 DOI: 10.1038/s41390-021-01890-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 11/08/2021] [Accepted: 11/30/2021] [Indexed: 12/29/2022]
Abstract
Traditional laboratory markers, such as white blood cell count, C-reactive protein, and procalcitonin, failed to discriminate viral and bacterial infections in children. The lack of an accurate diagnostic test has a negative impact on child's care, limiting the ability of early diagnosis and appropriate management of children. This, on the one hand, may lead to delayed recognition of sepsis and severe bacterial infections, which still represent the leading causes of child morbidity and mortality. On the other hand, this may lead to overuse of empiric antibiotic therapies, particularly for specific subgroups of patients, such as infants younger than 90 days of life or neutropenic patients. This approach has an adverse effect on costs, antibiotic resistance, and pediatric microbiota. Transcript host-RNA signatures are a new tool used to differentiate viral from bacterial infections by analyzing the transcriptional biosignatures of RNA in host leukocytes. In this systematic review, we evaluate the efficacy and the possible application of this new diagnostic method in febrile children, along with challenges in its implementation. Our review support the growing evidence that the application of these new tools can improve the characterization of the spectrum of bacterial and viral infections and optimize the use of antibiotics in children. IMPACT: Transcript host RNA signatures may allow to better characterize the spectrum of viral, bacterial, and inflammatory illnesses in febrile children and can be used with traditional diagnostic methods to determine if and when to start antibiotic therapy. This is the first review on the use of transcript RNA signatures in febrile children to distinguish viral from bacterial infections. Our review identified a wide variability of target populations and gold standards used to define sepsis and SBIs, limiting the generalization of our findings.
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Affiliation(s)
- Danilo Buonsenso
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy. .,Global Health Research Institute, Istituto di Igiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy. .,Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168, Rome, Italy. .,Danilo Buonsenso, Largo A. Gemelli 8, 00168, Rome, Italy.
| | - Giorgio Sodero
- Istituto di Pediatria, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Piero Valentini
- Global Health Research Institute, Istituto di Igiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy.,Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168, Rome, Italy.,Istituto di Pediatria, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
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11
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Keddy KH, Saha S, Okeke IN, Kalule JB, Qamar FN, Kariuki S. Combating Childhood Infections in LMICs: evaluating the contribution of Big Data Big data, biomarkers and proteomics: informing childhood diarrhoeal disease management in Low- and Middle-Income Countries. EBioMedicine 2021; 73:103668. [PMID: 34742129 PMCID: PMC8579132 DOI: 10.1016/j.ebiom.2021.103668] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 09/26/2021] [Accepted: 10/20/2021] [Indexed: 01/20/2023] Open
Abstract
Despite efforts to reduce the global burden of childhood diarrhoea, 50% of all cases globally occur in children under five years in Low–Income and Middle- Income Countries (LMICs) and knowledge gaps remain regarding the aetiological diagnosis, introduction of diarrhoeal vaccines, and the role of environmental enteric dysfunction and severe acute malnutrition. Biomarkers may assist in understanding disease processes, from diagnostics, to management of childhood diarrhoea and the sequelae to vaccine development. Proteomics has the potential to assist in the identification of new biomarkers to understand the processes in the development of childhood diarrhoea and to aid in developing new vaccines. Centralised repositories that enable mining of large data sets to better characterise risk factors, the proteome of both the patient and the different diarrhoeal pathogens, and the environment, could inform patient management and vaccine development, providing a systems biological approach to address the burden of childhood diarrhoea in LMICs.
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Affiliation(s)
- Karen H Keddy
- Tuberculosis Platform, South African Medical Research Council, 1 Soutpansberg Rd, Pretoria, 0001, South Africa.
| | - Senjuti Saha
- Child Health Research Foundation, 23/2 Khilji Road, Mohammadpur, Dhaka 1207, Bangladesh
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - John Bosco Kalule
- Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Uganda
| | - Farah Naz Qamar
- Department of Pediatrics and Child Health. Aga Khan University, Stadoum road Karachi, Pakistan 74800
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Off Mbagathi Road, Nairobi, Kenya
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12
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Ebrahimpoor M, Goeman JJ. Inflated false discovery rate due to volcano plots: problem and solutions. Brief Bioinform 2021; 22:bbab053. [PMID: 33758907 PMCID: PMC8425469 DOI: 10.1093/bib/bbab053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 02/01/2021] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION Volcano plots are used to select the most interesting discoveries when too many discoveries remain after application of Benjamini-Hochberg's procedure (BH). The volcano plot suggests a double filtering procedure that selects features with both small adjusted $P$-value and large estimated effect size. Despite its popularity, this type of selection overlooks the fact that BH does not guarantee error control over filtered subsets of discoveries. Therefore the selected subset of features may include an inflated number of false discoveries. RESULTS In this paper, we illustrate the substantially inflated type I error rate of volcano plot selection with simulation experiments and RNA-seq data. In particular, we show that the feature with the largest estimated effect is a very likely false positive result. Next, we investigate two alternative approaches for multiple testing with double filtering that do not inflate the false discovery rate. Our procedure is implemented in an interactive web application and is publicly available.
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Affiliation(s)
- Mitra Ebrahimpoor
- Medical statistics, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Jelle J Goeman
- Medical statistics, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
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13
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Pennisi I, Rodriguez-Manzano J, Moniri A, Kaforou M, Herberg JA, Levin M, Georgiou P. Translation of a Host Blood RNA Signature Distinguishing Bacterial From Viral Infection Into a Platform Suitable for Development as a Point-of-Care Test. JAMA Pediatr 2021; 175:417-419. [PMID: 33393977 PMCID: PMC7783591 DOI: 10.1001/jamapediatrics.2020.5227] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/23/2020] [Indexed: 01/24/2023]
Affiliation(s)
- Ivana Pennisi
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jesus Rodriguez-Manzano
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Ahmad Moniri
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, United Kingdom
| | - Myrsini Kaforou
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jethro A. Herberg
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Michael Levin
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, United Kingdom
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14
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Gómez-Carballa A, Barral-Arca R, Cebey-López M, Bello X, Pardo-Seco J, Martinón-Torres F, Salas A. Identification of a Minimal 3-Transcript Signature to Differentiate Viral from Bacterial Infection from Best Genome-Wide Host RNA Biomarkers: A Multi-Cohort Analysis. Int J Mol Sci 2021; 22:ijms22063148. [PMID: 33808774 PMCID: PMC8003556 DOI: 10.3390/ijms22063148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/24/2022] Open
Abstract
The fight against the spread of antibiotic resistance is one of the most important challenges facing health systems worldwide. Given the limitations of current diagnostic methods, the development of fast and accurate tests for the diagnosis of viral and bacterial infections would improve patient management and treatment, as well as contribute to reducing antibiotic misuse in clinical settings. In this scenario, analysis of host transcriptomics constitutes a promising target to develop new diagnostic tests based on the host-specific response to infections. We carried out a multi-cohort meta-analysis of blood transcriptomic data available in public databases, including 11 different studies and 1209 samples from virus- (n = 695) and bacteria- (n = 514) infected patients. We applied a Parallel Regularized Regression Model Search (PReMS) on a set of previously reported genes that distinguished viral from bacterial infection to find a minimum gene expression bio-signature. This strategy allowed us to detect three genes, namely BAFT, ISG15 and DNMT1, that clearly differentiate groups of infection with high accuracy (training set: area under the curve (AUC) 0.86 (sensitivity: 0.81; specificity: 0.87); testing set: AUC 0.87 (sensitivity: 0.82; specificity: 0.86)). BAFT and ISG15 are involved in processes related to immune response, while DNMT1 is related to the preservation of methylation patterns, and its expression is modulated by pathogen infections. We successfully tested this three-transcript signature in the 11 independent studies, demonstrating its high performance under different scenarios. The main advantage of this three-gene signature is the low number of genes needed to differentiate both groups of patient categories.
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Affiliation(s)
- Alberto Gómez-Carballa
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Ruth Barral-Arca
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Miriam Cebey-López
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Xabier Bello
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Jacobo Pardo-Seco
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706 Galicia, Spain
| | - Antonio Salas
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706 Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15706 Galicia, Spain
- Correspondence:
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Gómez-Carballa A, Barral-Arca R, Cebey-López M, Currás-Tuala MJ, Pischedda S, Gómez-Rial J, Habgood-Coote D, Herberg JA, Kaforou M, Martinón-Torres F, Salas A. Host Transcriptomic Response Following Administration of Rotavirus Vaccine in Infants' Mimics Wild Type Infection. Front Immunol 2021; 11:580219. [PMID: 33552046 PMCID: PMC7859632 DOI: 10.3389/fimmu.2020.580219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Background Rotavirus (RV) is an enteric pathogen that has devastating impact on childhood morbidity and mortality worldwide. The immunologic mechanism underlying the protection achieved after RV vaccination is not yet fully understood. Methods We compared the transcriptome of children affected by community-acquired RV infection and children immunized with a live attenuated RV vaccine (RotaTeq®). Results RV vaccination mimics the wild type infection causing similar changes in children's transcriptome, including transcripts associated with cell cycle, diarrhea, nausea, vomiting, intussusception, and abnormal morphology of midgut. A machine learning approach allowed to detect a combination of nine-transcripts that differentiates vaccinated from convalescent-naturally infected children (AUC: 90%; 95%CI: 70-100) and distinguishes between acute-infected and healthy control children (in both cases, AUC: 100%; 95%CI: 100-100). We identified a miRNA hsa-mir-149 that seems to play a role in the host defense against viral pathogens and may have an antiviral role. Discussion Our findings might shed further light in the understanding of RV infection, its functional link to intussusception causes, as well as guide development of antiviral treatments and safer and more effective vaccines. The nine-transcript signature may constitute a marker of vaccine protection and helps to differentiate vaccinated from naturally infected or susceptible children.
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Affiliation(s)
- Alberto Gómez-Carballa
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Spain
| | - Ruth Barral-Arca
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Spain
| | - Miriam Cebey-López
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Spain
| | - Maria José Currás-Tuala
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Spain
| | - Sara Pischedda
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Spain
| | - José Gómez-Rial
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Spain
| | - Dominic Habgood-Coote
- Section of Pediatric Infectious Diseases, Imperial College London, London, United Kingdom
| | - Jethro A Herberg
- Section of Pediatric Infectious Diseases, Imperial College London, London, United Kingdom
| | - Myrsini Kaforou
- Section of Pediatric Infectious Diseases, Imperial College London, London, United Kingdom
| | - Federico Martinón-Torres
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Salas
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigacinó Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Spain
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Buggiotti L, Cheng Z, Wathes DC. Mining the Unmapped Reads in Bovine RNA-Seq Data Reveals the Prevalence of Bovine Herpes Virus-6 in European Dairy Cows and the Associated Changes in Their Phenotype and Leucocyte Transcriptome. Viruses 2020; 12:v12121451. [PMID: 33339352 PMCID: PMC7768445 DOI: 10.3390/v12121451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/27/2022] Open
Abstract
Microbial RNA is detectable in host samples by aligning unmapped reads from RNA sequencing against taxon reference sequences, generating a score proportional to the microbial load. An RNA-Seq data analysis showed that 83.5% of leukocyte samples from six dairy herds in different EU countries contained bovine herpes virus-6 (BoHV-6). Phenotypic data on milk production, metabolic function, and disease collected during their first 50 days in milk (DIM) were compared between cows with low (1–200 and n = 114) or high (201–1175 and n = 24) BoHV-6 scores. There were no differences in milk production parameters, but high score cows had numerically fewer incidences of clinical mastitis (4.2% vs. 12.2%) and uterine disease (54.5% vs. 62.7%). Their metabolic status was worse, based on measurements of IGF-1 and various metabolites in blood and milk. A comparison of the global leukocyte transcriptome between high and low BoHV-6 score cows at around 14 DIM yielded 485 differentially expressed genes (DEGs). The top pathway from Gene Ontology (GO) enrichment analysis was the immune system process. Down-regulated genes in the high BoHV-6 cows included those encoding proteins involved in viral detection (DDX6 and DDX58), interferon response, and E3 ubiquitin ligase activity. This suggested that BoHV-6 may largely evade viral detection and that it does not cause clinical disease in dairy cows.
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Barral-Arca R, Gómez-Carballa A, Cebey-López M, Currás-Tuala MJ, Pischedda S, Viz-Lasheras S, Bello X, Martinón-Torres F, Salas A. RNA-Seq Data-Mining Allows the Discovery of Two Long Non-Coding RNA Biomarkers of Viral Infection in Humans. Int J Mol Sci 2020; 21:ijms21082748. [PMID: 32326627 PMCID: PMC7215422 DOI: 10.3390/ijms21082748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/03/2020] [Accepted: 04/11/2020] [Indexed: 12/15/2022] Open
Abstract
There is a growing interest in unraveling gene expression mechanisms leading to viral host invasion and infection progression. Current findings reveal that long non-coding RNAs (lncRNAs) are implicated in the regulation of the immune system by influencing gene expression through a wide range of mechanisms. By mining whole-transcriptome shotgun sequencing (RNA-seq) data using machine learning approaches, we detected two lncRNAs (ENSG00000254680 and ENSG00000273149) that are downregulated in a wide range of viral infections and different cell types, including blood monocluclear cells, umbilical vein endothelial cells, and dermal fibroblasts. The efficiency of these two lncRNAs was positively validated in different viral phenotypic scenarios. These two lncRNAs showed a strong downregulation in virus-infected patients when compared to healthy control transcriptomes, indicating that these biomarkers are promising targets for infection diagnosis. To the best of our knowledge, this is the very first study using host lncRNAs biomarkers for the diagnosis of human viral infections.
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Affiliation(s)
- Ruth Barral-Arca
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; (R.B.-A.); (A.G.-C.); (M.C.-L.); (M.J.C.-T.); (S.P.); (S.V.-L.); (X.B.)
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706 Galicia, Spain;
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; (R.B.-A.); (A.G.-C.); (M.C.-L.); (M.J.C.-T.); (S.P.); (S.V.-L.); (X.B.)
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706 Galicia, Spain;
| | - Miriam Cebey-López
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; (R.B.-A.); (A.G.-C.); (M.C.-L.); (M.J.C.-T.); (S.P.); (S.V.-L.); (X.B.)
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706 Galicia, Spain;
| | - María José Currás-Tuala
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; (R.B.-A.); (A.G.-C.); (M.C.-L.); (M.J.C.-T.); (S.P.); (S.V.-L.); (X.B.)
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706 Galicia, Spain;
| | - Sara Pischedda
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; (R.B.-A.); (A.G.-C.); (M.C.-L.); (M.J.C.-T.); (S.P.); (S.V.-L.); (X.B.)
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706 Galicia, Spain;
| | - Sandra Viz-Lasheras
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; (R.B.-A.); (A.G.-C.); (M.C.-L.); (M.J.C.-T.); (S.P.); (S.V.-L.); (X.B.)
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706 Galicia, Spain;
| | - Xabier Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; (R.B.-A.); (A.G.-C.); (M.C.-L.); (M.J.C.-T.); (S.P.); (S.V.-L.); (X.B.)
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706 Galicia, Spain;
| | - Federico Martinón-Torres
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706 Galicia, Spain;
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706 Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; (R.B.-A.); (A.G.-C.); (M.C.-L.); (M.J.C.-T.); (S.P.); (S.V.-L.); (X.B.)
- GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), 15706 Galicia, Spain;
- Correspondence:
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Barral-Arca R, Pardo-Seco J, Bello X, Martinón-Torres F, Salas A. Ancestry patterns inferred from massive RNA-seq data. RNA (NEW YORK, N.Y.) 2019; 25:857-868. [PMID: 31010885 PMCID: PMC6573782 DOI: 10.1261/rna.070052.118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/16/2019] [Indexed: 05/24/2023]
Abstract
There is a growing body of evidence suggesting that patterns of gene expression vary within and between human populations. However, the impact of this variation in human diseases has been poorly explored, in part owing to the lack of a standardized protocol to estimate biogeographical ancestry from gene expression studies. Here we examine several studies that provide new solid evidence indicating that the ancestral background of individuals impacts gene expression patterns. Next, we test a procedure to infer genetic ancestry from RNA-seq data in 25 data sets where information on ethnicity was reported. Genome data of reference continental populations retrieved from The 1000 Genomes Project were used for comparisons. Remarkably, only eight out of 25 data sets passed FastQC default filters. We demonstrate that, for these eight population sets, the ancestral background of donors could be inferred very efficiently, even in data sets including samples with complex patterns of admixture (e.g., American-admixed populations). For most of the gene expression data sets of suboptimal quality, ancestral inference yielded odd patterns. The present study thus brings a cautionary note for gene expression studies highlighting the importance to control for the potential confounding effect of ancestral genetic background.
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Affiliation(s)
- Ruth Barral-Arca
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Xabi Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Federico Martinón-Torres
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
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A 2-transcript host cell signature distinguishes viral from bacterial diarrhea and it is influenced by the severity of symptoms. Sci Rep 2018; 8:8043. [PMID: 29795312 PMCID: PMC5966427 DOI: 10.1038/s41598-018-26239-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/08/2018] [Indexed: 02/03/2023] Open
Abstract
Recently, a biomarker signature consisting of 2-transcript host RNAs was proposed for discriminating bacterial from viral infections in febrile children. We evaluated the performance of this signature in a different disease scenario, namely a cohort of Mexican children (n = 174) suffering from acute diarrhea of different infectious etiologies. We first examined the admixed background of the patients, indicating that most of them have a predominantly Native American genetic ancestry with a variable amount of European background (ranging from 0% to 57%). The results confirm that the RNA test can discriminate between viral and bacterial causes of infection (t-test; P-value = 6.94×10−11; AUC = 80%; sensitivity: 68% [95% CI: 55%–79%]; specificity: 84% [95% CI: 78%–90%]), but the strength of the signal differs substantially depending on the causal pathogen, with the stronger signal being that of Shigella (P-value = 3.14 × 10−12; AUC = 89; sensitivity: 70% [95% CI: 57%–83%]; specificity: 100% [95% CI: 100%–100%]). The accuracy of this test improves significantly when excluding mild cases (P-value = 2.13 × 10−6; AUC = 85%; sensitivity: 79% [95% CI: 58%–95%]; specificity: 78% [95% CI: 65%–88%]). The results broaden the scope of previous studies by incorporating different pathogens, variable levels of disease severity, and different ancestral background of patients, and add confirmatory support to the clinical utility of these 2-transcript biomarkers.
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