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Johnson M, Chelysheva I, Öner D, McGinley J, Lin GL, O'Connor D, Robinson H, Drysdale SB, Gammin E, Vernon S, Muller J, Wolfenden H, Westcar S, Anguvaa L, Thwaites RS, Bont L, Wildenbeest J, Martinón-Torres F, Aerssens J, Openshaw PJM, Pollard AJ. A Genome-Wide Association Study of Respiratory Syncytial Virus Infection Severity in Infants. J Infect Dis 2024; 229:S112-S119. [PMID: 38271230 DOI: 10.1093/infdis/jiae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a significant cause of infant morbidity and mortality worldwide. Most children experience at least one 1 RSV infection by the age of two 2 years, but not all develop severe disease. However, the understanding of genetic risk factors for severe RSV is incomplete. Consequently, we conducted a genome-wide association study of RSV severity. METHODS Disease severity was assessed by the ReSVinet scale, in a cohort of 251 infants aged 1 week to 1 year. Genotyping data were collected from multiple European study sites as part of the RESCEU Consortium. Linear regression models were used to assess the impact of genotype on RSV severity and gene expression as measured by microarray. RESULTS While no SNPs reached the genome-wide statistical significance threshold (P < 5 × 10-8), we identified 816 candidate SNPs with a P-value of <1 × 10-4. Functional annotation of candidate SNPs highlighted genes relevant to neutrophil trafficking and cytoskeletal functions, including LSP1 and RAB27A. Moreover, SNPs within the RAB27A locus significantly altered gene expression (false discovery rate, FDR P < .05). CONCLUSIONS These findings may provide insights into genetic mechanisms driving severe RSV infection, offering biologically relevant information for future investigations.
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Affiliation(s)
- Mari Johnson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Irina Chelysheva
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Deniz Öner
- Biomarkers Infectious Diseases, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Joseph McGinley
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Gu-Lung Lin
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Hannah Robinson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Simon B Drysdale
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Emma Gammin
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Sophie Vernon
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Jill Muller
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | | | | | | | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, United Kingdom
| | - Louis Bont
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Netherlands
| | - Joanne Wildenbeest
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Netherlands
| | - Federico Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela
- Genetics, Vaccines and Infections Research Group, Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Jeroen Aerssens
- Biomarkers Infectious Diseases, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, United Kingdom
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
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2
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Motelow JE, Lippa NC, Hostyk J, Feldman E, Nelligan M, Ren Z, Alkelai A, Milner JD, Gharavi AG, Tang Y, Goldstein DB, Kernie SG. Risk Variants in the Exomes of Children With Critical Illness. JAMA Netw Open 2022; 5:e2239122. [PMID: 36306130 PMCID: PMC9617179 DOI: 10.1001/jamanetworkopen.2022.39122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE Diagnostic genetic testing can lead to changes in management in the pediatric intensive care unit. Genetic risk in children with critical illness but nondiagnostic exome sequencing (ES) has not been explored. OBJECTIVE To assess the association between loss-of-function (LOF) variants and pediatric critical illness. DESIGN, SETTING, AND PARTICIPANTS This genetic association study examined ES first screened for causative variants among 267 children at the Morgan Stanley Children's Hospital of NewYork-Presbyterian, of whom 22 were otherwise healthy with viral respiratory failure; 18 deceased children with bronchiolitis from the Office of the Chief Medical Examiner of New York City, of whom 14 were previously healthy; and 9990 controls from the Institute for Genomic Medicine at Columbia University Irving Medical Center. The ES data were generated between January 1, 2015, and December 31, 2020, and analyzed between January 1, 2017, and September 2, 2022. EXPOSURE Critical illness. MAIN OUTCOMES AND MEASURES Odds ratios and P values for genes and gene-sets enriched for rare LOF variants and the loss-of-function observed/expected upper bound fraction (LOEUF) score at which cases have a significant enrichment. RESULTS This study included 285 children with critical illness (median [range] age, 4.1 [0-18.9] years; 148 [52%] male) and 9990 controls. A total of 228 children (80%) did not receive a genetic diagnosis. After quality control (QC), 231 children harbored excess rare LOF variants in genes with a LOEUF score of 0.680 or less (intolerant genes) (P = 1.0 × 10-5). After QC, 176 children without a diagnosis harbored excess ultrarare LOF variants in intolerant genes but only in those without a known disease association (odds ratio, 1.8; 95% CI, 1.3-2.5). After QC, 25 children with viral respiratory failure harbored excess ultrarare LOF variants in intolerant genes but only in those without a known disease association (odds ratio, 2.8; 95% CI, 1.1-6.6). A total of 114 undiagnosed children were enriched for de novo LOF variants in genes without a known disease association (observed, 14; expected, 6.8; enrichment, 2.05). CONCLUSIONS AND RELEVANCE In this genetic association study, excess LOF variants were observed among critically ill children despite nondiagnostic ES. Variants lay in genes without a known disease association, suggesting future investigation may connect phenotypes to causative genes.
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Affiliation(s)
- Joshua E. Motelow
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Natalie C. Lippa
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Joseph Hostyk
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Evin Feldman
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Matthew Nelligan
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Zhong Ren
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York
| | | | - Ali G. Gharavi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, NewYork-Presbyterian, New York, New York
| | - Yingying Tang
- Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, New York, New York
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Steven G. Kernie
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
- NewYork-Presbyterian Hospital, New York, New York
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3
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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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4
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Gómez-Carballa A, Pischedda S, Rivero-Calle I, Montoto-Louzao J, Martinón-Torres F, Salas A. CD14 and related genes in respiratory morbidity after Respiratory Syncytial Virus infection. J Infect Dis 2022; 226:1295-1297. [PMID: 35714332 DOI: 10.1093/infdis/jiac248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
- A Gómez-Carballa
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - S Pischedda
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - I Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - J Montoto-Louzao
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain.,Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - F Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - A Salas
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain.,Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
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5
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Respiratory Syncytial Virus-Associated Neurologic Complications in Children: A Systematic Review and Aggregated Case Series. J Pediatr 2021; 239:39-49.e9. [PMID: 34181989 DOI: 10.1016/j.jpeds.2021.06.045] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/30/2021] [Accepted: 06/21/2021] [Indexed: 12/29/2022]
Abstract
OBJECTIVES To describe the features and frequency of respiratory syncytial virus (RSV)-associated severe acute neurologic disease in children. STUDY DESIGN We performed a systematic review of the literature to identify reports of severe acute neurologic complications associated with acute RSV infection in children aged <15 years (PROSPERO Registration CRD42019125722). Main outcomes included neurologic, clinical, and demographic features of cases and the frequency of disease. We aggregated available case data from the published literature and from the Australian Acute Childhood Encephalitis (ACE) study. RESULTS We identified 87 unique studies from 26 countries describing a spectrum of RSV-associated severe acute neurologic syndromes including proven encephalitis, acute encephalopathy, complex seizures, hyponatremic seizures, and immune-mediated disorders. The frequency of RSV infection in acute childhood encephalitis/encephalopathy was 1.2%-6.5%. We aggregated data from 155 individual cases with RSV-associated severe acute neurologic complications; median age was 11.0 months (IQR 2.0-21.5), most were previously healthy (71/104, 68%). Seizure was the most frequently reported neurologic feature (127/150, 85%). RSV was detected in the central nervous system of 12 cases. Most children recovered (81/122, 66%); however, some reports described partial recovery (33/122, 27%) and death (8/122, 7%). CONCLUSIONS RSV-associated neurologic complications have been widely reported, but there is substantial heterogeneity in the design and quality of existing studies. The findings from our study have implications for the investigation, management, and prevention of RSV-associated neurologic complications. Further, this systematic review can inform the design of future studies aiming to quantify the burden of childhood RSV-associated neurologic disease.
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6
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Benetti E, Giliberti A, Emiliozzi A, Valentino F, Bergantini L, Fallerini C, Anedda F, Amitrano S, Conticini E, Tita R, d’Alessandro M, Fava F, Marcantonio S, Baldassarri M, Bruttini M, Mazzei MA, Montagnani F, Mandalà M, Bargagli E, Furini S, Renieri A, Mari F. Clinical and molecular characterization of COVID-19 hospitalized patients. PLoS One 2020; 15:e0242534. [PMID: 33206719 PMCID: PMC7673557 DOI: 10.1371/journal.pone.0242534] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/05/2020] [Indexed: 01/08/2023] Open
Abstract
Clinical and molecular characterization by Whole Exome Sequencing (WES) is reported in 35 COVID-19 patients attending the University Hospital in Siena, Italy, from April 7 to May 7, 2020. Eighty percent of patients required respiratory assistance, half of them being on mechanical ventilation. Fiftyone percent had hepatic involvement and hyposmia was ascertained in 3 patients. Searching for common genes by collapsing methods against 150 WES of controls of the Italian population failed to give straightforward statistically significant results with the exception of two genes. This result is not unexpected since we are facing the most challenging common disorder triggered by environmental factors with a strong underlying heritability (50%). The lesson learned from Autism-Spectrum-Disorders prompted us to re-analyse the cohort treating each patient as an independent case, following a Mendelian-like model. We identified for each patient an average of 2.5 pathogenic mutations involved in virus infection susceptibility and pinpointing to one or more rare disorder(s). To our knowledge, this is the first report on WES and COVID-19. Our results suggest a combined model for COVID-19 susceptibility with a number of common susceptibility genes which represent the favorite background in which additional host private mutations may determine disease progression.
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Affiliation(s)
- Elisa Benetti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Arianna Emiliozzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Department of Specialized and Internal Medicine, Tropical and Infectious Diseases Unit, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | | | - Laura Bergantini
- Unit of Respiratory Diseases and Lung Transplantation, Department of Internal and Specialist Medicine, University of Siena, Siena, Italy
| | | | - Federico Anedda
- Department of Emergency and Urgency, Medicine, Surgery and Neurosciences, Unit of Intensive Care Medicine, Siena University Hospital, Siena, Italy
| | - Sara Amitrano
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | - Edoardo Conticini
- Rheumatology Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Policlinico Le Scotte, Siena, Italy
| | - Rossella Tita
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | - Miriana d’Alessandro
- Unit of Respiratory Diseases and Lung Transplantation, Department of Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | - Simona Marcantonio
- Department of Emergency and Urgency, Medicine, Surgery and Neurosciences, Unit of Intensive Care Medicine, Siena University Hospital, Siena, Italy
| | | | - Mirella Bruttini
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | - Maria Antonietta Mazzei
- Department of Medical, Surgical and Neuro Sciences and Radiological Sciences, Unit of Diagnostic Imaging, University of Siena, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | - Francesca Montagnani
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Department of Specialized and Internal Medicine, Tropical and Infectious Diseases Unit, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | - Marco Mandalà
- Otolaryngology Unit, University of Siena, Siena, Italy
| | - Elena Bargagli
- Unit of Respiratory Diseases and Lung Transplantation, Department of Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Senese, Italy
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7
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Decoding Susceptibility to Respiratory Viral Infections and Asthma Inception in Children. Int J Mol Sci 2020; 21:ijms21176372. [PMID: 32887352 PMCID: PMC7503410 DOI: 10.3390/ijms21176372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/19/2023] Open
Abstract
Human Respiratory Syncytial Virus and Human Rhinovirus are the most frequent cause of respiratory tract infections in infants and children and are major triggers of acute viral bronchiolitis, wheezing and asthma exacerbations. Here, we will discuss the application of the powerful tools of systems biology to decode the molecular mechanisms that determine risk for infection and subsequent asthma. An important conceptual advance is the understanding that the innate immune system is governed by a Bow-tie architecture, where diverse input signals converge onto a few core pathways (e.g., IRF7), which in turn generate diverse outputs that orchestrate effector and regulatory functions. Molecular profiling studies in children with severe exacerbations of asthma/wheeze have identified two major immunological phenotypes. The IRF7hi phenotype is characterised by robust upregulation of antiviral response networks, and the IRF7lo phenotype is characterised by upregulation of markers of TGFβ signalling and type 2 inflammation. Similar phenotypes have been identified in infants and children with severe viral bronchiolitis. Notably, genome-wide association studies supported by experimental validation have identified key pathways that increase susceptibility to HRV infection (ORMDL3 and CHDR3) and modulate TGFβ signalling (GSDMB, TGFBR1, and SMAD3). Moreover, functional deficiencies in the activation of type I and III interferon responses are already evident at birth in children at risk of developing febrile lower respiratory tract infections and persistent asthma/wheeze, suggesting that the trajectory to asthma begins at birth or in utero. Finally, exposure to microbes and their products reprograms innate immunity and provides protection from the development of allergies and asthma in children, and therefore microbial products are logical candidates for the primary prevention of asthma.
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8
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Nelson PT, Fardo DW, Katsumata Y. The MUC6/AP2A2 Locus and Its Relevance to Alzheimer's Disease: A Review. J Neuropathol Exp Neurol 2020; 79:568-584. [PMID: 32357373 PMCID: PMC7241941 DOI: 10.1093/jnen/nlaa024] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/10/2020] [Indexed: 12/11/2022] Open
Abstract
We recently reported evidence of Alzheimer's disease (AD)-linked genetic variation within the mucin 6 (MUC6) gene on chromosome 11p, nearby the adaptor-related protein complex 2 subunit alpha 2 (AP2A2) gene. This locus has interesting features related to human genomics and clinical research. MUC6 gene variants have been reported to potentially influence viral-including herpesvirus-immunity and the gut microbiome. Within the MUC6 gene is a unique variable number of tandem repeat (VNTR) region. We discovered an association between MUC6 VNTR repeat expansion and AD pathologic severity, particularly tau proteinopathy. Here, we review the relevant literature. The AD-linked VNTR polymorphism may also influence AP2A2 gene expression. AP2A2 encodes a polypeptide component of the adaptor protein complex, AP-2, which is involved in clathrin-coated vesicle function and was previously implicated in AD pathogenesis. To provide background information, we describe some key knowledge gaps in AD genetics research. The "missing/hidden heritability problem" of AD is highlighted. Extensive portions of the human genome, including the MUC6 VNTR, have not been thoroughly evaluated due to limitations of existing high-throughput sequencing technology. We present and discuss additional data, along with cautionary considerations, relevant to the hypothesis that MUC6 repeat expansion influences AD pathogenesis.
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Affiliation(s)
- Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
- Department of Pathology, University of Kentucky, Lexington, Kentucky
| | - David W Fardo
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky
| | - Yuriko Katsumata
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky
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9
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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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10
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A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus. Int J Mol Sci 2020; 21:ijms21051831. [PMID: 32155831 PMCID: PMC7084441 DOI: 10.3390/ijms21051831] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/26/2020] [Accepted: 03/03/2020] [Indexed: 12/30/2022] Open
Abstract
Respiratory syncytial virus (RSV) is one of the major causes of acute lower respiratory tract infection worldwide. The absence of a commercial vaccine and the limited success of current therapeutic strategies against RSV make further research necessary. We used a multi-cohort analysis approach to investigate host transcriptomic biomarkers and shed further light on the molecular mechanism underlying RSV-host interactions. We meta-analyzed seven transcriptome microarray studies from the public Gene Expression Omnibus (GEO) repository containing a total of 922 samples, including RSV, healthy controls, coronaviruses, enteroviruses, influenzas, rhinoviruses, and coinfections, from both adult and pediatric patients. We identified > 1500 genes differentially expressed when comparing the transcriptomes of RSV-infected patients against healthy controls. Functional enrichment analysis showed several pathways significantly altered, including immunologic response mediated by RSV infection, pattern recognition receptors, cell cycle, and olfactory signaling. In addition, we identified a minimal 17-transcript host signature specific for RSV infection by comparing transcriptomic profiles against other respiratory viruses. These multi-genic signatures might help to investigate future drug targets against RSV infection.
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11
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Baschal EE, Larson ED, Bootpetch Roberts TC, Pathak S, Frank G, Handley E, Dinwiddie J, Moloney M, Yoon PJ, Gubbels SP, Scholes MA, Cass SP, Jenkins HA, Frank DN, Yang IV, Schwartz DA, Ramakrishnan VR, Santos-Cortez RLP. Identification of Novel Genes and Biological Pathways That Overlap in Infectious and Nonallergic Diseases of the Upper and Lower Airways Using Network Analyses. Front Genet 2020; 10:1352. [PMID: 32010199 PMCID: PMC6979043 DOI: 10.3389/fgene.2019.01352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022] Open
Abstract
Previous genetic studies on susceptibility to otitis media and airway infections have focused on immune pathways acting within the local mucosal epithelium, and outside of allergic rhinitis and asthma, limited studies exist on the overlaps at the gene, pathway or network level between the upper and lower airways. In this report, we compared [1] pathways identified from network analysis using genes derived from published genome-wide family-based and association studies for otitis media, sinusitis, and lung phenotypes, to [2] pathways identified using differentially expressed genes from RNA-sequence data from lower airway, sinus, and middle ear tissues, in particular cholesteatoma tissue compared to middle ear mucosa. For otitis media, a large number of genes (n = 1,806) were identified as differentially expressed between cholesteatoma and middle ear mucosa, which in turn led to the identification of 68 pathways that are enriched in cholesteatoma. Two differentially expressed genes CR1 and SAA1 overlap in middle ear, sinus, and lower airway samples and are potentially novel genes for otitis media susceptibility. In addition, 56 genes were differentially expressed in both tissues from the middle ear and either sinus or lower airways. Pathways that are common in upper and lower airway diseases, whether from published DNA studies or from our RNA-sequencing analyses, include chromatin organization/remodeling, endocytosis, immune system process, protein folding, and viral process. Taken together, our findings from genetic susceptibility and differential tissue expression studies support the hypothesis that the unified airway theory wherein the upper and lower respiratory tracts act as an integrated unit also applies to infectious and nonallergic airway epithelial disease. Our results may be used as reference for identification of genes or pathways that are relevant to upper and lower airways, whether common across sites, or unique to each disease.
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Affiliation(s)
- Erin E Baschal
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Eric D Larson
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Tori C Bootpetch Roberts
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Shivani Pathak
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Gretchen Frank
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Elyse Handley
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Jordyn Dinwiddie
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Molly Moloney
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Patricia J Yoon
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Samuel P Gubbels
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Melissa A Scholes
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Stephen P Cass
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Herman A Jenkins
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Daniel N Frank
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ivana V Yang
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - David A Schwartz
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Vijay R Ramakrishnan
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Regie Lyn P Santos-Cortez
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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12
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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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13
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Abstract
Pneumonia is a highly prevalent disease with considerable morbidity and mortality. However, diagnosis and therapy still rely on antiquated methods, leading to the vast overuse of antimicrobials, which carries risks for both society and the individual. Furthermore, outcomes in severe pneumonia remain poor. Genomic techniques have the potential to transform the management of pneumonia through deep characterization of pathogens as well as the host response to infection. This characterization will enable the delivery of selective antimicrobials and immunomodulatory therapy that will help to offset the disorder associated with overexuberant immune responses.
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Affiliation(s)
- Samir Gautam
- Pulmonary Critical Care and Sleep Medicine, Center for Pulmonary Infection Research and Treatment, Yale University, 300 Cedar Street, TACS441, New Haven, CT 06520-8057, USA
| | - Lokesh Sharma
- Pulmonary Critical Care and Sleep Medicine, Center for Pulmonary Infection Research and Treatment, Yale University, 300 Cedar Street, TACS441, New Haven, CT 06520-8057, USA
| | - Charles S Dela Cruz
- Pulmonary Critical Care and Sleep Medicine, Center for Pulmonary Infection Research and Treatment, Yale University, 300 Cedar Street, TACS441, New Haven, CT 06520-8057, USA.
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14
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Martinón-Torres F, Bosch X, Rappuoli R, Ladhani S, Redondo E, Vesikari T, García-Sastre A, Rivero-Calle I, Gómez-Rial J, Salas A, Martín C, Finn A, Butler R. TIPICO IX: report of the 9 th interactive infectious disease workshop on infectious diseases and vaccines. Hum Vaccin Immunother 2019; 15:2405-2415. [PMID: 31158041 PMCID: PMC6816368 DOI: 10.1080/21645515.2019.1609823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Ninth Interactive Infectious Disease workshop TIPICO was held on November 22–23, 2018, in Santiago de Compostela, Spain. This 2-day academic experience addressed current and topical issues in the field of infectious diseases and vaccination. Summary findings of the meeting include: cervical cancer elimination will be possible in the future, thanks to the implementation of global vaccination action plans in combination with appropriate screening interventions. The introduction of appropriate immunization programs is key to maintain the success of current effective vaccines such as those against meningococcal disease or rotavirus infection. Additionally, reduced dose schedules might improve the efficiency of some vaccines (i.e., PCV13). New vaccines to improve current preventive alternatives are under development (e.g., against tuberculosis or influenza virus), while others to protect against infectious diseases with no current available vaccines (e.g., enterovirus, parechovirus and flaviviruses) need to be developed. Vaccinomics will be fundamental in this process, while infectomics will allow the application of precision medicine. Further research is also required to understand the impact of heterologous vaccine effects. Finally, vaccination requires education at all levels (individuals, community, healthcare professionals) to ensure its success by helping to overcome major barriers such as vaccine hesitancy and false contraindications.
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Affiliation(s)
- Federico Martinón-Torres
- Translational Paediatrics and Infectious Diseases, Department of Paediatrics, Hospital Clínico Universitario de Santiago de Compostela , Santiago de Compostela , Spain.,Genetics, Vaccines and Infections Research group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Universidad de Santiago de Compostela , Santiago de Compostela , Spain
| | - Xavier Bosch
- Cancer Epidemiology Research Programme (e-oncología), Catalan Institute of Oncology, L'Hospitalet de Llobregat , Barcelona , Spain.,Cancer Prevention and Palliative Care Program, IDIBELL, L'Hospitalet de Llobregat , Barcelona , Spain
| | - Rino Rappuoli
- R&D Centre, GlaxoSmithKline , Siena , Italy.,Department of Medicine, Imperial College London , London , UK
| | - Shamez Ladhani
- Immunisation Department, Public Health England , London , UK
| | - Esther Redondo
- International Vaccination Center of Madrid , Madrid , Spain.,Grupo de Actividades Preventivas y Salud Pública SEMERGEN , Madrid , Spain
| | - Timo Vesikari
- Faculty of Medicine and Life Sciences, Vaccine Research Center, University of Tampere , Tampere , Finland
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York , NY , USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York , NY , USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | - Irene Rivero-Calle
- Translational Paediatrics and Infectious Diseases, Department of Paediatrics, Hospital Clínico Universitario de Santiago de Compostela , Santiago de Compostela , Spain.,Genetics, Vaccines and Infections Research group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Universidad de Santiago de Compostela , Santiago de Compostela , Spain
| | - José Gómez-Rial
- Genetics, Vaccines and Infections Research group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Universidad de Santiago de Compostela , Santiago de Compostela , Spain
| | - Antonio Salas
- Genetics, Vaccines and Infections Research group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Universidad 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, of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS) , Galicia , Spain
| | - Carlos Martín
- Faculty of Medicine, Microbiology Department, University of Zaragoza , Zaragoza , Spain.,CIBER of Respiratory Diseases, Instituto de Salud Carlos III , Madrid , Spain
| | - Adam Finn
- Bristol Children's Vaccine Centre, Schools of Cellular and Molecular Medicine and Population Health Sciences, University of Bristol , Bristol , UK
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15
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Purnell PR, Addicks BL, Zalzal HG, Shapiro S, Wen S, Ramadan HH, Setola V, Siderovski DP. Single Nucleotide Polymorphisms in Chemosensory Pathway Genes GNB3, TAS2R19, and TAS2R38 Are Associated with Chronic Rhinosinusitis. Int Arch Allergy Immunol 2019; 180:72-78. [PMID: 31137020 PMCID: PMC6715503 DOI: 10.1159/000499875] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/22/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Chronic rhinosinusitis (CRS) is a multifaceted disease with a significant genetic component. The importance of taste receptor signaling has recently been highlighted in CRS; single nucleotide polymorphisms (SNPs) of bitter tastant-responsive G-protein-coupled receptors have been linked with CRS and with altered innate immune responses to multiple bacterially derived signals. OBJECTIVE To determine in CRS the frequency of six SNPs in genes with known bitter tastant signaling function. METHODS Genomic DNA was isolated from 74 CRS volunteers in West Virginia, and allele frequency was determined and compared with demographically matched data from the 1,000 Genomes database. RESULTS For two SNPs in a gene recently associated with bitterant signaling regulation, RGS21, there were no associations with CRS (although the frequency of the minor allele of RGS21, rs7528947, was seen to increase with increasing Lund-Mackay CT staging score). Two TAS2R bitter taste receptor gene variants (TAS2R19 rs10772420 and TAS2R38 rs713598), identified in prior CRS genetics studies, were found to have similar associations in this study. CONCLUSION Unique to our study is the establishment of an association between CRS in this patient population and GNB3 SNP rs5443, a variation in an established G protein component downstream of bitterant receptor signal transduction.
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Affiliation(s)
- Phillip R Purnell
- Department of Otolaryngology, Head and Neck Surgery, West Virginia University School of Medicine, Morgantown, West Virginia, USA
| | - Benjamin L Addicks
- Department of Otolaryngology, Head and Neck Surgery, West Virginia University School of Medicine, Morgantown, West Virginia, USA
| | - Habib G Zalzal
- Department of Otolaryngology, Head and Neck Surgery, West Virginia University School of Medicine, Morgantown, West Virginia, USA
| | - Scott Shapiro
- Department of Otolaryngology, Head and Neck Surgery, West Virginia University School of Medicine, Morgantown, West Virginia, USA
| | - Sijin Wen
- Department of Biostatistics, West Virginia University School of Public Health, Morgantown, West Virginia, USA
| | - Hassan H Ramadan
- Department of Otolaryngology, Head and Neck Surgery, West Virginia University School of Medicine, Morgantown, West Virginia, USA
| | - Vincent Setola
- Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown, West Virginia, USA
- Department of Neuroscience, West Virginia University School of Medicine, Morgantown, West Virginia, USA
- Department of Behavioral Medicine and Psychiatry, West Virginia University School of Medicine, Morgantown, West Virginia, USA
| | - David P Siderovski
- Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown, West Virginia, USA,
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16
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A genome-wide association study of tramadol metabolism from post-mortem samples. THE PHARMACOGENOMICS JOURNAL 2019; 20:94-103. [PMID: 30971809 DOI: 10.1038/s41397-019-0088-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 01/08/2019] [Accepted: 03/27/2019] [Indexed: 11/09/2022]
Abstract
Phase I tramadol metabolism requires cytochrome p450 family 2, subfamily D, polypeptide 6 (CYP2D6) to form O-desmethyltramadol (M1). CYP2D6 genetic variants may infer metabolizer phenotype; however, drug ADME (absorption, distribution, metabolism, and excretion) and response depend on protein pathway(s), not CYP2D6 alone. There is a paucity of data regarding the contribution of trans-acting proteins to idiosyncratic phenotypes following drug exposure. A genome-wide association study identified five markers (rs79983226/kgp11274252, rs9384825, rs62435418/kgp10370907, rs72732317/kgp3743668, and rs184199168/exm1592932) associated with the conversion of tramadol to M1 (M1:T). These SNPs reside within five genes previously implicated with adverse reactions. Analysis of accompanying toxicological meta-data revealed a significant positive linear relationship between M1:T and degree of sample polypharmacy. Taken together, these data identify candidate loci for potential clinical inferences of phenotype following exposure to tramadol and highlight sample polypharmacy as a possible diagnostic covariate in post-mortem genetic studies.
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17
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Tahamtan A, Askari FS, Bont L, Salimi V. Disease severity in respiratory syncytial virus infection: Role of host genetic variation. Rev Med Virol 2019; 29:e2026. [DOI: 10.1002/rmv.2026] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/14/2018] [Accepted: 11/18/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Alireza Tahamtan
- Student Research Committee, School of Medicine; Golestan University of Medical Sciences; Gorgan Iran
- Department of Microbiology, School of Medicine; Golestan University of Medical Sciences; Gorgan Iran
| | - Fatemeh Sana Askari
- Student Research Committee, School of Medicine; Golestan University of Medical Sciences; Gorgan Iran
| | - Louis Bont
- Department of Pediatrics, Wilhelmina Children's Hospital; University Medical Centre Utrecht; Utrecht Netherlands
| | - Vahid Salimi
- Department of Virology, School of Public Health; Tehran University of Medical Sciences; Tehran Iran
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18
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Salas A. The natural selection that shapes our genomes. Forensic Sci Int Genet 2018; 39:57-60. [PMID: 30578983 DOI: 10.1016/j.fsigen.2018.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 12/13/2018] [Indexed: 12/14/2022]
Abstract
Most of the variation in the human genome (∼95%) is constrained, directly or indirectly, by purifying selection and GC-biased gene conversion, according to a recent article by Pouyet et al. (2018). The use of 'non-neutral' variation to infer human demographies can lead to undesirable biases; for example, in estimation of the time of the most recent common ancestor. Further examination of 'neutral' variation in entire human genomes from The 1000 Genomes Project reveals that ∼99% of this variation lacks exonic function, but ∼35% of it falls in introns. In addition, estimates of biogeographical ancestry using 'non-neutral' SNPs differ very marginally from inferences obtained from 'neutral' variation. Additional investigations should be carried out before establishing the roadmap for future human population and forensic genetic studies.
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Affiliation(s)
- Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain.
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19
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Priante E, Cavicchiolo ME, Baraldi E. RSV infection and respiratory sequelae. Minerva Pediatr 2018; 70:623-633. [PMID: 30379052 DOI: 10.23736/s0026-4946.18.05327-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION The association between respiratory syncytial virus (RSV) infections and long-term respiratory sequelae has long been recognized. It is estimated that individuals with a history of RSV bronchiolitis have 2- to 12-fold higher risk of developing asthma. Although this risk tends to decrease with age, persistent airway obstruction and hyperresponsiveness are observed even 30 years after RSV infection. EVIDENCE ACQUISITION Our data search strategy was designed to address the following questions: What is the epidemiological evidence available on the association between RSV infection and long-term respiratory morbidity? What are the potential pathogenic pathways linking RSV infection to long-term respiratory morbidity? Are there any host genetic backgrounds that can predispose to both severe RSV lower respiratory tract infection and asthma? Are antiviral therapies and RSV prevention measures effective in reducing respiratory morbidities? EVIDENCE SYNTHESIS This article reviews the recent scientific literature on the epidemiological association and pathogenic links between early RSV infection and long-term respiratory morbidities. CONCLUSIONS Nowadays, asthma is increasingly considered a heterogeneous disease, caused by interactions between several host and environmental factors. Understanding the specific causative role of respiratory viruses, and the pathogenic mechanisms through which bronchiolitis predisposes to asthma, is a challenging, but essential starting point for the development of prevention and treatment strategies potentially capable of preserving lung function.
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Affiliation(s)
- Elena Priante
- Unit of Neonatal Intensive Care, Department of Woman's and Child's Health, University of Padua, Padua, Italy
| | - Maria E Cavicchiolo
- Unit of Neonatal Intensive Care, Department of Woman's and Child's Health, University of Padua, Padua, Italy -
| | - Eugenio Baraldi
- Unit of Neonatal Intensive Care, Department of Woman's and Child's Health, University of Padua, Padua, Italy
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Abstract
Respiratory syncytial virus (RSV) is the most common cause of infant hospitalization and causes a high burden of disease in the elderly, too. This enveloped negative-stranded RNA virus has been recently reclassified in the Pneumoviridae family. Infections of the respiratory cells happens when the two major surface glycoproteins, G and F, take contact with the cell receptor CX3CR1 and mediate entry by fusion, respectively. Viral mRNA transcription, genomic RNA synthesis and nucleocapsid formation occur in large cytoplasmic inclusion bodies to avoid recognition by the host innate immune response. Most progeny virions remain associated to the infected cell surface; fusion of infected with adjacent cells results in the formation of large multinucleated syncytia that eventually undergo apoptosis. Desquamated epithelial cells form the plugs that with mucus and fibrin may cause lower airway obstructions. Pathogenetic mechanism of severe RSV disease likely involve both the extent of viral replication and the host immune response. Regarding the latter, single nucleotide polymorphism analysis and genome-wide association studies showed that genetic susceptibility to severe RSV infection is likely a complex trait, in which many different host genetic variants contribute. Recent studies pointed to the fact that bronchiolitis severity depends more on the specific infecting RSV genotypes than on the amount of viral loads. A population-based surveillance system to better define RSV burden of disease would be of valuable help for implementing future vaccination programs.
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Affiliation(s)
- Alessandra Pierangeli
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University, Rome, Italy -
| | - Carolina Scagnolari
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Guido Antonelli
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University, Rome, Italy
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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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Whole Exome Sequencing Identifies New Host Genomic Susceptibility Factors in Empyema Caused by Streptococcus pneumoniae in Children: A Pilot Study. Genes (Basel) 2018; 9:genes9050240. [PMID: 29751582 PMCID: PMC5977180 DOI: 10.3390/genes9050240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 11/17/2022] Open
Abstract
Pneumonia is the leading cause of death amongst infectious diseases. Streptococcus pneumoniae is responsible for about 25% of pneumonia cases worldwide, and it is a major cause of childhood mortality. We carried out a whole exome sequencing (WES) study in eight patients with complicated cases of pneumococcal pneumonia (empyema). An initial assessment of statistical association of WES variation with pneumonia was carried out using data from the 1000 Genomes Project (1000G) for the Iberian Peninsula (IBS) as reference controls. Pseudo-replication statistical analyses were carried out using different European control groups. Association tests pointed to single nucleotide polymorphism (SNP) rs201967957 (gene MEIS1; chromosome 2; p-valueIBS = 3.71 × 10-13) and rs576099063 (gene TSPAN15; chromosome 10; p-valueIBS = 2.36 × 10-8) as the best candidate variants associated to pneumococcal pneumonia. A burden gene test of pathogenicity signaled four genes, namely, OR9G9, MUC6, MUC3A and APOB, which carry significantly increased pathogenic variation when compared to controls. By analyzing various transcriptomic data repositories, we found strong supportive evidence for the role of MEIS1, TSPAN15 and APOBR (encoding the receptor of the APOB protein) in pneumonia in mouse and human models. Furthermore, the association of the olfactory receptor gene OR9G9 has recently been related to some viral infectious diseases, while the role of mucin genes (MUC6 and MUC3A), encoding mucin glycoproteins, are well-known factors related to chronic obstructive airway disease. WES emerges as a promising technique to disentangle the genetic basis of host genome susceptibility to infectious respiratory diseases.
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