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Abstract
Influenza viruses infect millions of people around the globe annually, usually causing self-limited upper respiratory tract infections. However, a small but non-negligible proportion of patients suffer from life-threatening pulmonary disease. Those affected include otherwise healthy individuals, and children with primary infections in particular. Much effort has been devoted to virological studies of influenza and vaccine development. By contrast, the enormous interindividual variability in susceptibility to influenza has received very little attention. One interesting hypothesis is that interindividual variability is driven largely by the genetic makeup of the infected patients. Unbiased genomic approaches have been used to search for genetic lesions in children with life-threatening pulmonary influenza. Four monogenic causes of severe influenza pneumonitis—deficiencies of GATA2, IRF7, IRF9, and TLR3—have provided evidence that severe influenza pneumonitis can be genetic and often in patients with no other severe infections. These deficiencies highlight the importance of human type I and III IFN-mediated immunity for host defense against influenza. Clinical penetrance is incomplete, and the underlying mechanisms are not yet understood. However, human genetic studies have clearly revealed that seemingly sporadic and isolated life-threatening influenza pneumonitis in otherwise healthy individuals can be genetic.
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202
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Human inborn errors of immunity to herpes viruses. Curr Opin Immunol 2020; 62:106-122. [PMID: 32014647 DOI: 10.1016/j.coi.2020.01.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/16/2019] [Accepted: 01/07/2020] [Indexed: 12/16/2022]
Abstract
Infections with any of the nine human herpes viruses (HHV) can be asymptomatic or life-threatening. The study of patients with severe diseases caused by HHVs, in the absence of overt acquired immunodeficiency, has led to the discovery or diagnosis of various inborn errors of immunity. The related inborn errors of adaptive immunity disrupt α/β T-cell rather than B-cell immunity. Affected patients typically develop HHV infections in the context of other infectious diseases. However, this is not always the case, as illustrated by inborn errors of SAP-dependent T-cell immunity to EBV-infected B cells. The related inborn errors of innate immunity disrupt leukocytes other than T and B cells, non-hematopoietic cells, or both. Patients typically develop only a single type of infection due to HHV, although, again, this is not always the case, as illustrated by inborn errors of TLR3 immunity resulting in HSV1 encephalitis in some patients and influenza pneumonitis in others. Most severe HHV infections in otherwise healthy patients remains unexplained. The forward human genetic dissection of isolated and syndromic HHV-driven illnesses will establish the molecular and cellular basis of protective immunity to HHVs, paving the way for novel diagnosis and management strategies.
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203
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Recent human genetic errors of innate immunity leading to increased susceptibility to infection. Curr Opin Immunol 2020; 62:79-90. [PMID: 31935567 DOI: 10.1016/j.coi.2019.12.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 12/17/2022]
Abstract
The germline encoded innate immunity governs eukaryotic host defense through both hematopoietic and non-hematopoietic cells, whereas adaptive immunity actions mainly via T cells and B cells characterized by their somatic genetic diversification of antigen-specific responses. Human inborn errors of innate immunity typically underlie infectious diseases. Disturbed innate immunity can additionally result in auto-inflammation. Here, we review inborn errors of innate immunity that have been recently discovered as well as new insights into previously described inborn errors of innate immunity.
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204
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Benam KH, Denney L, Ho LP. How the Respiratory Epithelium Senses and Reacts to Influenza Virus. Am J Respir Cell Mol Biol 2019; 60:259-268. [PMID: 30372120 DOI: 10.1165/rcmb.2018-0247tr] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The human lung is constantly exposed to the environment and potential pathogens. As the interface between host and environment, the respiratory epithelium has evolved sophisticated sensing mechanisms as part of its defense against pathogens. In this review, we examine how the respiratory epithelium senses and responds to influenza A virus, the biggest cause of respiratory viral deaths worldwide.
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Affiliation(s)
- Kambez H Benam
- 1 Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, Colorado.,2 Department of Bioengineering, University of Colorado Denver, Aurora, Colorado; and
| | - Laura Denney
- 3 Translational Lung Immunology Programme, MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Ling-Pei Ho
- 3 Translational Lung Immunology Programme, MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
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205
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Regulatory genome variants in human susceptibility to infection. Hum Genet 2019; 139:759-768. [PMID: 31807864 DOI: 10.1007/s00439-019-02091-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022]
Abstract
Genome studies have accelerated the discovery of common and rare genetic variants associated with susceptibility to infection and with disease severity. Genome-wide association studies identified many common genetic variants associated with modest risk for infection. Over 80% of these common variants map to the non-coding genome and are thought to modulate the regulatory networks. Exome sequencing has rapidly expanded the number of recognized primary immunodeficiencies through the identification of rare coding variants. In contrast, less than 29 primary immunodeficiencies have causative rare variation mapped outside protein-coding regions. In the future, whole genome sequencing will accelerate the identification of rare variants of substantial phenotypic impact that disrupt essential regulatory elements and the three-dimensional structure of chromatin.
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206
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Abstract
PURPOSE OF REVIEW Studying primary immunodeficiencies (PIDs) provides insights into human antiviral immunity in the natural infectious environment. This review describes new PIDs with genetic defects that impair innate antiviral responses. RECENT FINDINGS New genetic defects in the interferon (IFN) signaling pathway include IFNAR1 deficiency, which causes uncontrolled infections with measles-mumps-rubella or yellow fever vaccines, and possibly also cytomegalovirus (CMV); and IRF9 deficiency, which results in influenza virus susceptibility. Genetic defects in several pattern recognition receptors include MDA5 deficiency, which impairs viral RNA sensing and confers human rhinovirus susceptibility; RNA polymerase III haploinsufficiency, which impairs sensing of A:T-rich virus DNA and confers VZV susceptibility; and TLR3 deficiency, which causes HSV-1 encephalitis (HSE) or influenza virus pneumonitis. Defects in RNA metabolism, such as that caused by Debranching enzyme 1 deficiency, can cause virus meningoencephalitis. Finally, defects in host restriction factors for virus replication, such as in CIB1 deficiency, contribute to uncontrolled β-HPV infections. SUMMARY Several new PIDs highlight the role of type I/III IFN signaling pathway, virus sensors, and host virus restriction factors in human antiviral immunity.
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Affiliation(s)
- Huie Jing
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Helen C. Su
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health
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207
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Haller O, Kochs G. Mx genes: host determinants controlling influenza virus infection and trans-species transmission. Hum Genet 2019; 139:695-705. [PMID: 31773252 PMCID: PMC7087808 DOI: 10.1007/s00439-019-02092-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/19/2019] [Indexed: 12/13/2022]
Abstract
The human MxA protein, encoded by the interferon-inducible MX1 gene, is an intracellular influenza A virus (IAV) restriction factor. It can protect transgenic mice from severe IAV-induced disease, indicating a key role of human MxA for host survival and suggesting that natural variations in MX1 may account for inter-individual differences in disease severity among humans. MxA also provides a robust barrier against zoonotic transmissions of avian and swine IAV strains. Therefore, zoonotic IAV must acquire MxA escape mutations to achieve sustained human-to-human transmission. Here, we discuss recent progress in the field.
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Affiliation(s)
- Otto Haller
- Institute of Virology, Medical Center, University of Freiburg, Freiburg, Germany. .,Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
| | - Georg Kochs
- Institute of Virology, Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
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208
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Rogers LRK, de Los Campos G, Mias GI. Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination. Front Immunol 2019; 10:2616. [PMID: 31787983 PMCID: PMC6854009 DOI: 10.3389/fimmu.2019.02616] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/21/2019] [Indexed: 12/18/2022] Open
Abstract
Influenza, a communicable disease, affects thousands of people worldwide. Young children, elderly, immunocompromised individuals and pregnant women are at higher risk for being infected by the influenza virus. Our study aims to highlight differentially expressed genes in influenza disease compared to influenza vaccination, including variability due to age and sex. To accomplish our goals, we conducted a meta-analysis using publicly available microarray expression data. Our inclusion criteria included subjects with influenza, subjects who received the influenza vaccine and healthy controls. We curated 18 microarray datasets for a total of 3,481 samples (1,277 controls, 297 influenza infection, 1,907 influenza vaccination). We pre-processed the raw microarray expression data in R using packages available to pre-process Affymetrix and Illumina microarray platforms. We used a Box-Cox power transformation of the data prior to our down-stream analysis to identify differentially expressed genes. Statistical analyses were based on linear mixed effects model with all study factors and successive likelihood ratio tests (LRT) to identify differentially-expressed genes. We filtered LRT results by disease (Bonferroni adjusted p < 0.05) and used a two-tailed 10% quantile cutoff to identify biologically significant genes. Furthermore, we assessed age and sex effects on the disease genes by filtering for genes with a statistically significant (Bonferroni adjusted p < 0.05) interaction between disease and age, and disease and sex. We identified 4,889 statistically significant genes when we filtered the LRT results by disease factor, and gene enrichment analysis (gene ontology and pathways) included innate immune response, viral process, defense response to virus, Hematopoietic cell lineage and NF-kappa B signaling pathway. Our quantile filtered gene lists comprised of 978 genes each associated with influenza infection and vaccination. We also identified 907 and 48 genes with statistically significant (Bonferroni adjusted p < 0.05) disease-age and disease-sex interactions, respectively. Our meta-analysis approach highlights key gene signatures and their associated pathways for both influenza infection and vaccination. We also were able to identify genes with an age and sex effect. This gives potential for improving current vaccines and exploring genes that are expressed equally across ages when considering universal vaccinations for influenza.
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Affiliation(s)
- Lavida R K Rogers
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States
| | - Gustavo de Los Campos
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States.,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States.,Department of Statistics and Probability, Michigan State University, East Lansing, MI, United States
| | - George I Mias
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States.,Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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209
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Seifert LL, Si C, Saha D, Sadic M, de Vries M, Ballentine S, Briley A, Wang G, Valero-Jimenez AM, Mohamed A, Schaefer U, Moulton HM, García-Sastre A, Tripathi S, Rosenberg BR, Dittmann M. The ETS transcription factor ELF1 regulates a broadly antiviral program distinct from the type I interferon response. PLoS Pathog 2019; 15:e1007634. [PMID: 31682641 PMCID: PMC6932815 DOI: 10.1371/journal.ppat.1007634] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 12/26/2019] [Accepted: 10/11/2019] [Indexed: 12/20/2022] Open
Abstract
Induction of vast transcriptional programs is a central event of innate host responses to viral infections. Here we report a transcriptional program with potent antiviral activity, driven by E74-like ETS transcription factor 1 (ELF1). Using microscopy to quantify viral infection over time, we found that ELF1 inhibits eight diverse RNA and DNA viruses after multi-cycle replication. Elf1 deficiency results in enhanced susceptibility to influenza A virus infections in mice. ELF1 does not feed-forward to induce interferons, and ELF1’s antiviral effect is not abolished by the absence of STAT1 or by inhibition of JAK phosphorylation. Accordingly, comparative expression analyses by RNA-seq revealed that the ELF1 transcriptional program is distinct from interferon signatures. Thus, ELF1 provides an additional layer of the innate host response, independent from the action of type I interferons. After decades of research on the innate immune system, we still struggle to understand exactly how this first line of defense protects cells against viral infections. Our gap in knowledge stems, on one hand, from the sheer number of effector genes, few of which have been characterized in mechanistic detail. On the other hand, our understanding of innate gene transcription is constantly evolving. We know that different regulatory mechanisms greatly influence the quality, magnitude, and timing of gene expression, all of which may contribute to the antiviral power of the innate response. Deciphering these regulatory mechanisms is indispensable for harnessing the power of innate immunity in novel antiviral therapies. Here, we report a novel transcriptional program as part of the cell-intrinsic immune system, raised by E74-like ETS transcription factor 1 (ELF1). ELF1 potently restricts multi-cycle propagation of all viruses tested in our study. Reduced levels of ELF1 significantly diminish host defenses against influenza A virus in vitro and in vivo, suggesting a critical but previously overlooked role of this ETS transcription factor. The ELF1 program is complex and comprises over 300 potentially antiviral genes, which are almost entirely distinct from those known to be induced by interferon. Taken together, our data provide evidence for a program of antiviral protection that expands the previously known arsenal of the innate immune response.
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Affiliation(s)
- Leon Louis Seifert
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Clara Si
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Debjani Saha
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Mohammad Sadic
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Maren de Vries
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Sarah Ballentine
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Aaron Briley
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Guojun Wang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ana M. Valero-Jimenez
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Adil Mohamed
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Uwe Schaefer
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, New York, United States of America
| | - Hong M. Moulton
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Shashank Tripathi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Microbiology and Cell Biology Department, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Brad R. Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Meike Dittmann
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
- * E-mail:
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210
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Thomsen MM, Jørgensen SE, Storgaard M, Kristensen LS, Gjedsted J, Christiansen M, Gad HH, Hartmann R, Mogensen TH. Identification of an IRF3 variant and defective antiviral interferon responses in a patient with severe influenza. Eur J Immunol 2019; 49:2111-2114. [PMID: 31250433 DOI: 10.1002/eji.201848083] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/30/2019] [Accepted: 06/25/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Michelle M Thomsen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus N, Denmark
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Sofie E Jørgensen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus N, Denmark
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Merete Storgaard
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus N, Denmark
| | | | - Jakob Gjedsted
- Department of Intensive Care, Aarhus University Hospital, Aarhus N, Denmark
| | - Mette Christiansen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus N, Denmark
| | - Hans Henrik Gad
- Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Rune Hartmann
- Department of Molecular Biology and Genetics, Aarhus C, Denmark
| | - Trine H Mogensen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus N, Denmark
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus N, Denmark
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211
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Lormeau B, Foulongne V, Baccino E, Adriansen A, Pidoux O, Prodhomme O, Haquet A, Guyon G, Jeziorski E. Epidemiological survey in a day care center following toddler sudden death due to human metapneumovirus infection. Arch Pediatr 2019; 26:479-482. [PMID: 31685408 PMCID: PMC7125678 DOI: 10.1016/j.arcped.2019.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/26/2019] [Accepted: 10/06/2019] [Indexed: 01/15/2023]
Abstract
We report the sudden death of a 33-month-old child owing to acute respiratory distress syndrome due to human metapneumovirus (hMPV) infection. Of 30 children attending the same day care centre, 26% and 59% had hMPV and multiple infections, respectively; three of six children with pneumonia had a diagnosis of hMPV. hMPV infection is common in childhood viral co-infections but it can cause sudden death.
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Affiliation(s)
- B Lormeau
- Département urgences post-urgences pédiatriques, CHU de Montpellier, 34295 Montpellier, France; Département de médecine légale, CHU de Montpellier, 34295 Montpellier, France.
| | - V Foulongne
- Inserm, Pathogenesis and control of chronic infections, université Montpellier 1, 34295 Montpellier, France; Département de bacteriologie-virologie, CHU de Montpellier, 34295 Montpellier, France
| | - E Baccino
- Département de médecine légale, CHU de Montpellier, 34295 Montpellier, France
| | - A Adriansen
- Département de médecine légale, CHU de Montpellier, 34295 Montpellier, France
| | - O Pidoux
- Département de pédiatrie néonatale et de réanimation, CHU de Montpellier, 34295 Montpellier, France
| | - O Prodhomme
- Département d'imagerie pédiatrique, CHU de Montpellier, 34295 Montpellier, France
| | - A Haquet
- Département urgences post-urgences pédiatriques, CHU de Montpellier, 34295 Montpellier, France
| | - G Guyon
- Département urgences post-urgences pédiatriques, CHU de Montpellier, 34295 Montpellier, France
| | - E Jeziorski
- Département urgences post-urgences pédiatriques, CHU de Montpellier, 34295 Montpellier, France
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212
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Gounder AP, Boon ACM. Influenza Pathogenesis: The Effect of Host Factors on Severity of Disease. THE JOURNAL OF IMMUNOLOGY 2019; 202:341-350. [PMID: 30617115 DOI: 10.4049/jimmunol.1801010] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
Influenza viruses continue to be a major global health threat. Severity and clinical outcome of influenza disease is determined by both viral and host factors. Viral factors have long been the subject of intense research and many molecular determinants have been identified. However, research into the host factors that protect or predispose to severe and fatal influenza A virus infections is lagging. The goal of this review is to highlight the recent insights into host determinants of influenza pathogenesis.
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Affiliation(s)
- Anshu P Gounder
- Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110.,Department of Molecular Microbiology and Microbial Pathogenesis, Washington University School of Medicine in St. Louis, St. Louis, MO 63110; and
| | - Adrianus C M Boon
- Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110; .,Department of Molecular Microbiology and Microbial Pathogenesis, Washington University School of Medicine in St. Louis, St. Louis, MO 63110; and.,Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
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213
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Lacko LA, Chen S. Organoid-based chemical approach to dissect the mechanism controlling cellular dynamics. J Mol Cell Biol 2019; 12:mjz100. [PMID: 31638141 PMCID: PMC7683014 DOI: 10.1093/jmcb/mjz100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 09/16/2019] [Indexed: 11/16/2022] Open
Affiliation(s)
- Lauretta A Lacko
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, US
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, US
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214
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Bougarn S, Boughorbel S, Chaussabel D, Marr N. A curated transcriptome dataset collection to investigate inborn errors of immunity. F1000Res 2019; 8:188. [PMID: 31559014 PMCID: PMC6749933 DOI: 10.12688/f1000research.18048.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/28/2019] [Indexed: 01/10/2023] Open
Abstract
Primary immunodeficiencies (PIDs) are a heterogeneous group of inherited disorders, frequently caused by loss-of-function and less commonly by gain-of-function mutations, which can result in susceptibility to a broad or a very narrow range of infections but also in inflammatory, allergic or malignant diseases. Owing to the wide range in clinical manifestations and variability in penetrance and expressivity, there is an urgent need to better understand the underlying molecular, cellular and immunological phenotypes in PID patients in order to improve clinical diagnosis and management. Here we have compiled a manually curated collection of public transcriptome datasets mainly obtained from human whole blood, peripheral blood mononuclear cells (PBMCs) or fibroblasts of patients with PIDs and of control subjects for subsequent meta-analysis, query and interpretation. A total of eighteen (18) datasets derived from studies of PID patients were identified and retrieved from the NCBI Gene Expression Omnibus (GEO) database and loaded in GXB, a custom web application designed for interactive query and visualization of integrated large-scale data. The dataset collection includes samples from well characterized PID patients that were stimulated
ex vivo under a variety of conditions to assess the molecular consequences of the underlying, naturally occurring gene defects on a genome-wide scale. Multiple sample groupings and rank lists were generated to facilitate comparisons of the transcriptional responses between different PID patients and control subjects. The GXB tool enables browsing of a single transcript across studies, thereby providing new perspectives on the role of a given molecule across biological systems and PID patients. This dataset collection is available at
http://pid.gxbsidra.org/dm3/geneBrowser/list.
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Affiliation(s)
- Salim Bougarn
- Systems Biology and Immunology, Sidra Medicine, Doha, Qatar
| | | | | | - Nico Marr
- Systems Biology and Immunology, Sidra Medicine, Doha, Qatar
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215
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Host Single Nucleotide Polymorphisms Modulating Influenza A Virus Disease in Humans. Pathogens 2019; 8:pathogens8040168. [PMID: 31574965 PMCID: PMC6963926 DOI: 10.3390/pathogens8040168] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 09/27/2019] [Accepted: 09/28/2019] [Indexed: 12/14/2022] Open
Abstract
A large number of human genes associated with viral infections contain single nucleotide polymorphisms (SNPs), which represent a genetic variation caused by the change of a single nucleotide in the DNA sequence. SNPs are located in coding or non-coding genomic regions and can affect gene expression or protein function by different mechanisms. Furthermore, they have been linked to multiple human diseases, highlighting their medical relevance. Therefore, the identification and analysis of this kind of polymorphisms in the human genome has gained high importance in the research community, and an increasing number of studies have been published during the last years. As a consequence of this exhaustive exploration, an association between the presence of some specific SNPs and the susceptibility or severity of many infectious diseases in some risk population groups has been found. In this review, we discuss the relevance of SNPs that are important to understand the pathology derived from influenza A virus (IAV) infections in humans and the susceptibility of some individuals to suffer more severe symptoms. We also discuss the importance of SNPs for IAV vaccine effectiveness.
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216
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Clohisey S, Baillie JK. Host susceptibility to severe influenza A virus infection. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2019; 23:303. [PMID: 31488196 PMCID: PMC6729070 DOI: 10.1186/s13054-019-2566-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/13/2019] [Indexed: 11/30/2022]
Abstract
Most people exposed to a new flu virus do not notice any symptoms. A small minority develops critical illness. Some of this extremely broad variation in susceptibility is explained by the size of the initial inoculum or the influenza exposure history of the individual; some is explained by generic host factors, such as frailty, that decrease resilience following any systemic insult. Some demographic factors (pregnancy, obesity, and advanced age) appear to confer a more specific susceptibility to severe illness following infection with influenza viruses. As with other infectious diseases, a substantial component of susceptibility is determined by host genetics. Several genetic susceptibility variants have now been reported with varying levels of evidence. Susceptible hosts may have impaired intracellular controls of viral replication (e.g. IFITM3, TMPRS22 variants), defective interferon responses (e.g. GLDC, IRF7/9 variants), or defects in cell-mediated immunity with increased baseline levels of systemic inflammation (obesity, pregnancy, advanced age). These mechanisms may explain the prolonged viral replication reported in critically ill patients with influenza: patients with life-threatening disease are, by definition, abnormal hosts. Understanding these molecular mechanisms of susceptibility may in the future enable the design of host-directed therapies to promote resilience.
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Affiliation(s)
- Sara Clohisey
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - John Kenneth Baillie
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK. .,Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.
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217
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Homozygous NLRP1 gain-of-function mutation in siblings with a syndromic form of recurrent respiratory papillomatosis. Proc Natl Acad Sci U S A 2019; 116:19055-19063. [PMID: 31484767 DOI: 10.1073/pnas.1906184116] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Juvenile-onset recurrent respiratory papillomatosis (JRRP) is a rare and debilitating childhood disease that presents with recurrent growth of papillomas in the upper airway. Two common human papillomaviruses (HPVs), HPV-6 and -11, are implicated in most cases, but it is still not understood why only a small proportion of children develop JRRP following exposure to these common viruses. We report 2 siblings with a syndromic form of JRRP associated with mild dermatologic abnormalities. Whole-exome sequencing of the patients revealed a private homozygous mutation in NLRP1, encoding Nucleotide-Binding Domain Leucine-Rich Repeat Family Pyrin Domain-Containing 1. We find the NLRP1 mutant allele to be gain of function (GOF) for inflammasome activation, as demonstrated by the induction of inflammasome complex oligomerization and IL-1β secretion in an overexpression system. Moreover, patient-derived keratinocytes secrete elevated levels of IL-1β at baseline. Finally, both patients displayed elevated levels of inflammasome-induced cytokines in the serum. Six NLRP1 GOF mutations have previously been described to underlie 3 allelic Mendelian diseases with differing phenotypes and modes of inheritance. Our results demonstrate that an autosomal recessive, syndromic form of JRRP can be associated with an NLRP1 GOF mutation.
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218
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Zhang SY, Jouanguy E, Zhang Q, Abel L, Puel A, Casanova JL. Human inborn errors of immunity to infection affecting cells other than leukocytes: from the immune system to the whole organism. Curr Opin Immunol 2019; 59:88-100. [PMID: 31121434 PMCID: PMC6774828 DOI: 10.1016/j.coi.2019.03.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/29/2019] [Indexed: 01/19/2023]
Abstract
Studies of vertebrate immunity have traditionally focused on professional cells, including circulating and tissue-resident leukocytes. Evidence that non-professional cells are also intrinsically essential (i.e. not via their effect on leukocytes) for protective immunity in natural conditions of infection has emerged from three lines of research in human genetics. First, studies of Mendelian resistance to infection have revealed an essential role of DARC-expressing erythrocytes in protection against Plasmodium vivax infection, and an essential role of FUT2-expressing intestinal epithelial cells for protection against norovirus and rotavirus infections. Second, studies of inborn errors of non-hematopoietic cell-extrinsic immunity have shown that APOL1 and complement cascade components secreted by hepatocytes are essential for protective immunity to trypanosome and pyogenic bacteria, respectively. Third, studies of inborn errors of non-hematopoietic cell-intrinsic immunity have suggested that keratinocytes, pulmonary epithelial cells, and cortical neurons are essential for tissue-specific protective immunity to human papillomaviruses, influenza virus, and herpes simplex virus, respectively. Various other types of genetic resistance or predisposition to infection in human populations are not readily explained by inborn variants of genes operating in leukocytes and may, therefore, involve defects in other cells. The probing of this unchartered territory by human genetics is reshaping immunology, by scaling immunity to infection up from the immune system to the whole organism.
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Affiliation(s)
- Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris Descartes University, Imagine Institute, 75015 Paris, France
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris Descartes University, Imagine Institute, 75015 Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris Descartes University, Imagine Institute, 75015 Paris, France
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris Descartes University, Imagine Institute, 75015 Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris Descartes University, Imagine Institute, 75015 Paris, France; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, 75015 Paris, France; Howard Hughes Medical Institute, New York, NY 10065, USA.
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219
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Sun Y, Jiang J, Tien P, Liu W, Li J. IFN-λ: A new spotlight in innate immunity against influenza virus infection. Protein Cell 2019; 9:832-837. [PMID: 29332267 PMCID: PMC6160391 DOI: 10.1007/s13238-017-0503-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Yeping Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jingwen Jiang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Po Tien
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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220
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Li N, Xie T, Sun Y. Towards organogenesis and morphogenesis in vitro: harnessing engineered microenvironment and autonomous behaviors of pluripotent stem cells. Integr Biol (Camb) 2019; 10:574-586. [PMID: 30225509 DOI: 10.1039/c8ib00116b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recently, researchers have been attempting to control pluripotent stem cell fate or generate self-organized tissues from stem cells. Advances in bioengineering enable generation of organotypic structures, which capture the cellular components, spatial cell organization and even some functions of tissues or organs in development. However, only a few engineering tools have been utilized to regulate the formation and organization of spatially complex tissues derived from stem cells. Here, we provide a review of recent progress in the culture of organotypic structures in vitro, focusing on how microengineering approaches including geometric confinement, extracellular matrix (ECM) property modulation, spatially controlled biochemical factors, and external forces, can be utilized to generate organotypic structures. Moreover, we will discuss potential technologies that can be applied to further control both soluble and insoluble factors spatiotemporally in vitro. In summary, advanced engineered approaches have a great promise in generating miniaturized tissues and organs in a reproducible fashion, facilitating the cellular and molecular understanding of embryogenesis and morphogenesis processes.
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Affiliation(s)
- Ningwei Li
- Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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221
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Hernandez N, Bucciol G, Moens L, Le Pen J, Shahrooei M, Goudouris E, Shirkani A, Changi-Ashtiani M, Rokni-Zadeh H, Sayar EH, Reisli I, Lefevre-Utile A, Zijlmans D, Jurado A, Pholien R, Drutman S, Belkaya S, Cobat A, Boudewijns R, Jochmans D, Neyts J, Seeleuthner Y, Lorenzo-Diaz L, Enemchukwu C, Tietjen I, Hoffmann HH, Momenilandi M, Pöyhönen L, Siqueira MM, de Lima SMB, de Souza Matos DC, Homma A, Maia MDLS, da Costa Barros TA, de Oliveira PMN, Mesquita EC, Gijsbers R, Zhang SY, Seligman SJ, Abel L, Hertzog P, Marr N, Martins RDM, Meyts I, Zhang Q, MacDonald MR, Rice CM, Casanova JL, Jouanguy E, Bossuyt X. Inherited IFNAR1 deficiency in otherwise healthy patients with adverse reaction to measles and yellow fever live vaccines. J Exp Med 2019; 216:2057-2070. [PMID: 31270247 PMCID: PMC6719432 DOI: 10.1084/jem.20182295] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/18/2019] [Accepted: 06/11/2019] [Indexed: 01/31/2023] Open
Abstract
We describe two unrelated patients with inherited IFNAR1 deficiency who suffered from life-threatening infections following measles or yellow fever virus vaccination and were otherwise healthy. Vaccination against measles, mumps, and rubella (MMR) and yellow fever (YF) with live attenuated viruses can rarely cause life-threatening disease. Severe illness by MMR vaccines can be caused by inborn errors of type I and/or III interferon (IFN) immunity (mutations in IFNAR2, STAT1, or STAT2). Adverse reactions to the YF vaccine have remained unexplained. We report two otherwise healthy patients, a 9-yr-old boy in Iran with severe measles vaccine disease at 1 yr and a 14-yr-old girl in Brazil with viscerotropic disease caused by the YF vaccine at 12 yr. The Iranian patient is homozygous and the Brazilian patient compound heterozygous for loss-of-function IFNAR1 variations. Patient-derived fibroblasts are susceptible to viruses, including the YF and measles virus vaccine strains, in the absence or presence of exogenous type I IFN. The patients’ fibroblast phenotypes are rescued with WT IFNAR1. Autosomal recessive, complete IFNAR1 deficiency can result in life-threatening complications of vaccination with live attenuated measles and YF viruses in previously healthy individuals.
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Affiliation(s)
- Nicholas Hernandez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Giorgia Bucciol
- Laboratory of Inborn Errors of Immunity, Department of Immunology, Microbiology and Transplantation, KU Leuven, Leuven, Belgium
| | - Leen Moens
- Laboratory of Inborn Errors of Immunity, Department of Immunology, Microbiology and Transplantation, KU Leuven, Leuven, Belgium
| | - Jérémie Le Pen
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Mohammad Shahrooei
- Specialized Immunology Laboratory of Dr. Shahrooei, Sina Medical Complex, Ahvaz, Iran.,Department of Microbiology and Immunology, Clinical and Diagnostic Immunology, KU Leuven, Leuven, Belgium
| | | | - Afshin Shirkani
- Allergy and Clinical Immunology Department, Bushehr University of Medical Science, School of Medicine, Bushehr, Iran
| | | | - Hassan Rokni-Zadeh
- Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Esra Hazar Sayar
- Department of Pediatrics, Division of Pediatric Immunology and Allergy, Necmettin Erbakan University, Meram Medical Faculty, Konya, Turkey
| | - Ismail Reisli
- Department of Pediatrics, Division of Pediatric Immunology and Allergy, Necmettin Erbakan University, Meram Medical Faculty, Konya, Turkey
| | - Alain Lefevre-Utile
- Pediatrics Department, Jean Verdier Hospital, Assistance Publique des Hôpitaux de Paris, Paris 13 University, Bondy, France
| | - Dick Zijlmans
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Andrea Jurado
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Ruben Pholien
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Scott Drutman
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Serkan Belkaya
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Aurelie Cobat
- Pediatric Immunology-Hematology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France
| | - Robbert Boudewijns
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Dirk Jochmans
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Yoann Seeleuthner
- Paris Descartes University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
| | - Lazaro Lorenzo-Diaz
- Paris Descartes University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
| | - Chibuzo Enemchukwu
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Ian Tietjen
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | | | - Mana Momenilandi
- Specialized Immunology Laboratory of Dr. Shahrooei, Sina Medical Complex, Ahvaz, Iran
| | - Laura Pöyhönen
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Marilda M Siqueira
- National Reference Laboratory for Respiratory Viruses, Institute Oswaldo Cruz, Fiocruz, Ministry of Health, Rio de Janeiro, Brazil
| | - Sheila M Barbosa de Lima
- Laboratory of Virological Techniques, Bio-Manguinhos, Fiocruz, Ministry of Health, Rio de Janeiro, Brazil
| | - Denise C de Souza Matos
- Laboratory of Immunological Techniques, Bio-Manguinhos, Fiocruz, Ministry of Health, Rio de Janeiro, Brazil
| | - Akira Homma
- Bio-Manguinhos, Fiocruz, Ministry of Health, Rio de Janeiro, Brazil
| | | | | | | | | | - Rik Gijsbers
- Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium.,Leuven Viral Vector Core, Leuven, Belgium
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY.,Paris Descartes University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
| | - Stephen J Seligman
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY.,Department of Microbiology and Immunology, New York Medical College, Valhalla, NY
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY.,Paris Descartes University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
| | - Paul Hertzog
- Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Nico Marr
- Division of Translational Medicine, Sidra Medicine, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Isabelle Meyts
- Laboratory of Inborn Errors of Immunity, Department of Immunology, Microbiology and Transplantation, KU Leuven, Leuven, Belgium.,Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium.,Precision Immunology Institute and Mindich Child Health and Development Institute at the Icahn School of Medicine at Mount Sinai, New York, NY
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Margaret R MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY .,Pediatric Immunology-Hematology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France.,Howard Hughes Medical Institute, New York, NY
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY.,Paris Descartes University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
| | - Xavier Bossuyt
- Department of Microbiology, Immunology and Transplantation, Clinical and Diagnostic Immunology, KU Leuven, Leuven, Belgium.,Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
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222
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Lim HK, Huang SXL, Chen J, Kerner G, Gilliaux O, Bastard P, Dobbs K, Hernandez N, Goudin N, Hasek ML, García Reino EJ, Lafaille FG, Lorenzo L, Luthra P, Kochetkov T, Bigio B, Boucherit S, Rozenberg F, Vedrinne C, Keller MD, Itan Y, García-Sastre A, Celard M, Orange JS, Ciancanelli MJ, Meyts I, Zhang Q, Abel L, Notarangelo LD, Snoeck HW, Casanova JL, Zhang SY. Severe influenza pneumonitis in children with inherited TLR3 deficiency. J Exp Med 2019; 216:2038-2056. [PMID: 31217193 PMCID: PMC6719423 DOI: 10.1084/jem.20181621] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 04/10/2019] [Accepted: 05/09/2019] [Indexed: 12/20/2022] Open
Abstract
Autosomal recessive IRF7 and IRF9 deficiencies impair type I and III IFN immunity and underlie severe influenza pneumonitis. We report three unrelated children with influenza A virus (IAV) infection manifesting as acute respiratory distress syndrome (IAV-ARDS), heterozygous for rare TLR3 variants (P554S in two patients and P680L in the third) causing autosomal dominant (AD) TLR3 deficiency. AD TLR3 deficiency can underlie herpes simplex virus-1 (HSV-1) encephalitis (HSE) by impairing cortical neuron-intrinsic type I IFN immunity to HSV-1. TLR3-mutated leukocytes produce normal levels of IFNs in response to IAV. In contrast, TLR3-mutated fibroblasts produce lower levels of IFN-β and -λ, and display enhanced viral susceptibility, upon IAV infection. Moreover, the patients' iPSC-derived pulmonary epithelial cells (PECs) are susceptible to IAV. Treatment with IFN-α2b or IFN-λ1 rescues this phenotype. AD TLR3 deficiency may thus underlie IAV-ARDS by impairing TLR3-dependent, type I and/or III IFN-mediated, PEC-intrinsic immunity. Its clinical penetrance is incomplete for both IAV-ARDS and HSE, consistent with their typically sporadic nature.
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Affiliation(s)
- Hye Kyung Lim
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Sarah X L Huang
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY.,Department of Medicine, Columbia University Medical Center, New York, NY.,Center for Stem Cell and Regenerative Medicine, University of Texas Health Science Center at Texas, Houston, TX
| | - Jie Chen
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Department of Infectious Diseases, Shanghai Sixth Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Gaspard Kerner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Olivier Gilliaux
- Laboratory of Experimental Medicine (ULB222), Medicine Faculty, Libre de Bruxelles University, Brussels, Belgium.,Department of Pediatrics, University Hospital Center of Charleroi, Charleroi, Belgium
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Nicholas Hernandez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Nicolas Goudin
- Cell Imaging Platform Structure Fédérative de Recherche Necker, Institut National de la Santé et de la Recherche Médicale US 24, Paris, France
| | - Mary L Hasek
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Eduardo Javier García Reino
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Fabien G Lafaille
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Priya Luthra
- Department of Microbiology, Global Health and Emerging Pathogens Institute, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Tatiana Kochetkov
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Soraya Boucherit
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Flore Rozenberg
- Virology, Cochin-Saint-Vincent de Paul Hospital, Paris Descartes University, Paris, France
| | - Catherine Vedrinne
- Department of Anesthesia and Intensive Care Medicine in Cardiovascular Surgery, Louis Pradel Cardiological Hospital, Lyon, France
| | - Michael D Keller
- Division of Allergy and Immunology, Center for Cancer and Immunology Research, Children's National Health System, Washington, DC
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Adolfo García-Sastre
- Department of Microbiology, Global Health and Emerging Pathogens Institute, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Marie Celard
- National Center for Staphylococcus, Lyon Civil Hospital, Lyon, France
| | - Jordan S Orange
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX
| | - Michael J Ciancanelli
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Isabelle Meyts
- Laboratory for Inborn Errors of Immunity, Department of Immunology, Microbiology, and Transplantation, Katholieke Universiteit Leuven, Leuven, Belgium.,Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium.,Precision Immunology Institute and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Hans-Willem Snoeck
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY.,Department of Medicine, Columbia University Medical Center, New York, NY
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,Pediatric Immuno-Hematology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris, Paris, France.,Howard Hughes Medical Institute, New York, NY
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY .,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
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223
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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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Innate antiviral responses are induced by TLR3 and TLR4 ligands in chicken tracheal epithelial cells: Communication between epithelial cells and macrophages. Virology 2019; 534:132-142. [PMID: 31255797 DOI: 10.1016/j.virol.2019.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/26/2019] [Accepted: 06/06/2019] [Indexed: 01/31/2023]
Abstract
The chicken upper respiratory tract is the portal of entry for respiratory pathogens including avian influenza virus (AIV). There is a paucity of information about the role of airway epithelial cells in the induction of antiviral responses in the chicken trachea. A better understanding of the role of these cells in the initiation of innate responses may improve prophylactic or therapeutic strategies for control of viral infections. The present study aimed to characterize antiviral innate responses in chicken tracheal epithelial cells (cTECs) induced by TLR ligands. The results demonstrated that stimulation of cTECs with TLR ligands induced antiviral responses, and subsequently reduced the replication of AIV in cTECs. Additionally, stimulated cTECs were able to influence the function of other cells such as macrophages. Overall, these results provided evidence that cTECs mount antiviral responses after stimulation with TLR ligands through IRF7 and NF-κB signaling pathways, leading to activation of other cells, such as macrophages.
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225
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Thomsen MM, Jørgensen SE, Gad HH, Storgaard M, Gjedsted J, Christiansen M, Hartmann R, Mogensen TH. Defective interferon priming and impaired antiviral responses in a patient with an IRF7 variant and severe influenza. Med Microbiol Immunol 2019; 208:869-876. [PMID: 31172279 DOI: 10.1007/s00430-019-00623-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 05/25/2019] [Indexed: 12/19/2022]
Abstract
Influenza infection is common worldwide with many individuals affected each year during epidemics and occasionally pandemics. Previous studies in animal models and a few human cases have established an important role of innate type I and III interferon (IFN) for viral elimination and mounting of antiviral responses. However, genetic and immunological determinants of very severe disseminated influenza virus infection in humans remain incompletely understood. Here, we describe an adult patient with severe influenza virus A (IAV) infection, in whom we identified a rare variant E331V in IFN regulatory factor (IRF)7 by whole-exome sequencing. Examination of patient cells demonstrated a cellular phenotype suggesting functional IRF7 impairment, since priming with IFN was almost abolished and IFN responses to IAV were significantly impaired in patient cells. Moreover, IAV replication was significantly higher in patient cells than in controls. Finally, expression of IRF7 E331V in HEK293 cells demonstrated significantly reduced activation of both IFNA7 and IFNB promoters in a luciferase reporter gene expression assay compared to IRF7 wild type. These findings provide further support for the essential role of IRF7 in amplifying antiviral IFN responses to ensure potent and sustained IFN responses during influenza virus infection in humans.
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Affiliation(s)
- Michelle M Thomsen
- Department of Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
- Department of Biomedicine, Aarhus University, CF Møllers Alle 6, 8000, Aarhus C, Denmark
| | - Sofie E Jørgensen
- Department of Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
- Department of Biomedicine, Aarhus University, CF Møllers Alle 6, 8000, Aarhus C, Denmark
| | - Hans Henrik Gad
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Merete Storgaard
- Department of Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Jakob Gjedsted
- Department of Intensive Care, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Mette Christiansen
- Department of Clinical Immunology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Rune Hartmann
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Trine H Mogensen
- Department of Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
- Department of Biomedicine, Aarhus University, CF Møllers Alle 6, 8000, Aarhus C, Denmark.
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark.
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Involvement of Interferon Regulatory Factor 7 in Nicotine's Suppression of Antiviral Immune Responses. J Neuroimmune Pharmacol 2019; 14:551-564. [PMID: 31154625 DOI: 10.1007/s11481-019-09845-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 03/05/2019] [Indexed: 01/16/2023]
Abstract
Nicotine, the active ingredient in tobacco smoke, suppresses antiviral responses. Interferon regulatory factors (IRFs) regulate transcription of type I interferons (IFNs) and IFN-stimulated genes (ISGs) in this response. IRF7 is a key member of the IRF family. Expression of Irf7 is elevated in the brains of virus-infected animals, including human immunodeficiency virus-1 transgenic (HIV-1Tg) rats. We hypothesized that IRF7 affects nicotine's modulation of antiviral responses. Using CRISPR/Cas9 system, IRF7-mutant cell lines were created from human embryonic kidney 293FT cells in which 16 nicotinic acetylcholine receptors (nAChRs) were detected. Decreased expression of IRF7 was confirmed at both the mRNA and protein levels, as was IRF7-regulated cell growth in two IRF7-mutant cell lines, designated IRF7-Δ7 and IRF7-Δ11. In IRF7-Δ7 cells, expression of two nAChR genes, CHRNA3 and CHRNA9, changed modestly. After stimulation with polyinosinic-polycytidylic acid (poly I:C) (0.25 μg/ml) for 4 h to mimic viral infection, 293FT wild-type (WT) and IRF7-Δ7 cells were treated with 0, 1, or 100 μM nicotine for 24 h, which increased IFN-β expression in both types of cells but elevation was higher in WT cells (p < 0.001). Expression was significantly suppressed in WT cells (p < 0.001) but not in IRF7-Δ7 cells by 24-h nicotine exposure. Poly I:C stimulation increased mRNA expression of retinoic-acid-inducible protein I (RIG-I), melanoma-differentiation-associated gene 5 (MDA5), IFN-stimulated gene factor 3 (ISG3) complex, and IFN-stimulated genes (IRF7, ISG15, IFIT1, OAS1); nicotine attenuated mRNA expression only in WT cells. Overall, IRF7 is critical to nicotine's effect on the antiviral immune response. Graphical Abstract Involvement of IRF7 in nicotine's suppression of poly I:C-induced antiviral immune responses. PAMPs, such as a synthetic viral analogue of dsRNA poly I:C attack cells, will be recognized by PRRs, and the host innate immunity against viral infection will be activated. PRRs signaling trigger phosphorylation of IRF7 and IRF3 to induce their translocation to the nucleus and result in the production of type I IFNs. Then IFNs bind to IFNAR to activate the transcription factor ISGF3, a complex consisting of STAT1, STAT2, and IRF9. Further, it induces the expression of ISGs, including IFIT1, OAS1, IRF7, ISG15, etc. Nicotine suppresses the immune responses stimulated by poly I:C. In the IRF7-mutant cells, nicotine's suppressive effects on poly I:C-stimulated immune responses were restrained.
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Pöyhönen L, Bustamante J, Casanova JL, Jouanguy E, Zhang Q. Life-Threatening Infections Due to Live-Attenuated Vaccines: Early Manifestations of Inborn Errors of Immunity. J Clin Immunol 2019; 39:376-390. [PMID: 31123910 DOI: 10.1007/s10875-019-00642-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/02/2019] [Indexed: 02/07/2023]
Abstract
Live-attenuated vaccines (LAVs) can protect humans against 12 viral and three bacterial diseases. By definition, any clinical infection caused by a LAV that is sufficiently severe to require medical intervention attests to an inherited or acquired immunodeficiency that must be diagnosed or identified. Self-healing infections can also result from milder forms of immunodeficiency. We review here the inherited forms of immunodeficiency underlying severe infections of LAVs. Inborn errors of immunity (IEIs) underlying bacille Calmette-Guérin (BCG), oral poliovirus (OPV), vaccine measles virus (vMeV), and oral rotavirus vaccine (ORV) disease have been described from 1951, 1963, 1966, and 2009 onward, respectively. For each of these four LAVs, the underlying IEIs show immunological homogeneity despite genetic heterogeneity. Specifically, BCG disease is due to inborn errors of IFN-γ immunity, OPV disease to inborn errors of B cell immunity, vMeV disease to inborn errors of IFN-α/β and IFN-λ immunity, and ORV disease to adaptive immunity. Severe reactions to the other 11 LAVs have been described yet remain "idiopathic," in the absence of known underlying inherited or acquired immunodeficiencies, and are warranted to be the focus of research efforts. The study of IEIs underlying life-threatening LAV infections is clinically important for the affected patients and their families, as well as immunologically, for the study of the molecular and cellular basis of host defense against both attenuated and parental pathogens.
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Affiliation(s)
- Laura Pöyhönen
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France.,Center for the Study of Primary Immunodeficiencies, AP-HP, Necker Hospital for Sick Children, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France.,Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris, France.,Howard Hughes Medical Institute, New York, NY, USA
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
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228
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Lacoma A, Mateo L, Blanco I, Méndez MJ, Rodrigo C, Latorre I, Villar-Hernandez R, Domínguez J, Prat C. Impact of Host Genetics and Biological Response Modifiers on Respiratory Tract Infections. Front Immunol 2019; 10:1013. [PMID: 31134083 PMCID: PMC6513887 DOI: 10.3389/fimmu.2019.01013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 04/23/2019] [Indexed: 12/26/2022] Open
Abstract
Host susceptibility to respiratory tract infections (RTI) is dependent on both genetic and acquired risk factors. Repeated bacterial and viral RTI, such as pneumonia from encapsulated microorganisms, respiratory tract infections related to respiratory syncytial virus or influenza, and even the development of bronchiectasis and asthma, are often reported as the first symptom of primary immunodeficiencies. In the same way, neutropenia is a well-known risk factor for invasive aspergillosis, as well as lymphopenia for Pneumocystis, and mycobacterial infections. However, in the last decades a better knowledge of immune signaling networks and the introduction of next generation sequencing have increased the number and diversity of known inborn errors of immunity. On the other hand, the use of monoclonal antibodies targeting cytokines, such as tumor necrosis factor alpha has revealed new risk groups for infections, such as tuberculosis. The use of biological response modifiers has spread to almost all medical specialties, including inflammatory diseases and neoplasia, and are being used to target different signaling networks that may mirror some of the known immune deficiencies. From a clinical perspective, the individual contribution of genetics, and/or targeted treatments, to immune dysregulation is difficult to assess. The aim of this article is to review the known and newly described mechanisms of impaired immune signaling that predispose to RTI, including new insights into host genetics and the impact of biological response modifiers, and to summarize clinical recommendations regarding vaccines and prophylactic treatments in order to prevent infections.
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Affiliation(s)
- Alicia Lacoma
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, CIBER Enfermedades Respiratorias, Barcelona, Spain
| | - Lourdes Mateo
- Servei de Reumatologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ignacio Blanco
- Clinical Genetics and Genetic Counseling Program, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Barcelona, Spain
| | - Maria J Méndez
- Servei de Pediatria, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació GermansTrias i Pujol, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Carlos Rodrigo
- Servei de Pediatria, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca, Facultat de Medicina, Unitat Docent Germans Trias i Pujol, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Irene Latorre
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, CIBER Enfermedades Respiratorias, Barcelona, Spain
| | - Raquel Villar-Hernandez
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, CIBER Enfermedades Respiratorias, Barcelona, Spain
| | - Jose Domínguez
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, CIBER Enfermedades Respiratorias, Barcelona, Spain
| | - Cristina Prat
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, CIBER Enfermedades Respiratorias, Barcelona, Spain
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229
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Chandra L, Borcherding DC, Kingsbury D, Atherly T, Ambrosini YM, Bourgois-Mochel A, Yuan W, Kimber M, Qi Y, Wang Q, Wannemuehler M, Ellinwood NM, Snella E, Martin M, Skala M, Meyerholz D, Estes M, Fernandez-Zapico ME, Jergens AE, Mochel JP, Allenspach K. Derivation of adult canine intestinal organoids for translational research in gastroenterology. BMC Biol 2019; 17:33. [PMID: 30975131 PMCID: PMC6460554 DOI: 10.1186/s12915-019-0652-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/26/2019] [Indexed: 12/11/2022] Open
Abstract
Background Large animal models, such as the dog, are increasingly being used for studying diseases including gastrointestinal (GI) disorders. Dogs share similar environmental, genomic, anatomical, and intestinal physiologic features with humans. To bridge the gap between commonly used animal models, such as rodents, and humans, and expand the translational potential of the dog model, we developed a three-dimensional (3D) canine GI organoid (enteroid and colonoid) system. Organoids have recently gained interest in translational research as this model system better recapitulates the physiological and molecular features of the tissue environment in comparison with two-dimensional cultures. Results Organoids were derived from tissue of more than 40 healthy dogs and dogs with GI conditions, including inflammatory bowel disease (IBD) and intestinal carcinomas. Adult intestinal stem cells (ISC) were isolated from whole jejunal tissue as well as endoscopically obtained duodenal, ileal, and colonic biopsy samples using an optimized culture protocol. Intestinal organoids were comprehensively characterized using histology, immunohistochemistry, RNA in situ hybridization, and transmission electron microscopy, to determine the extent to which they recapitulated the in vivo tissue characteristics. Physiological relevance of the enteroid system was defined using functional assays such as optical metabolic imaging (OMI), the cystic fibrosis transmembrane conductance regulator (CFTR) function assay, and Exosome-Like Vesicles (EV) uptake assay, as a basis for wider applications of this technology in basic, preclinical and translational GI research. We have furthermore created a collection of cryopreserved organoids to facilitate future research. Conclusions We establish the canine GI organoid systems as a model to study naturally occurring intestinal diseases in dogs and humans, and that can be used for toxicology studies, for analysis of host-pathogen interactions, and for other translational applications. Electronic supplementary material The online version of this article (10.1186/s12915-019-0652-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lawrance Chandra
- Departments of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA
| | | | - Dawn Kingsbury
- Departments of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA
| | - Todd Atherly
- Departments of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA
| | | | | | - Wang Yuan
- Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Michael Kimber
- Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Yijun Qi
- Departments of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Qun Wang
- Departments of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Michael Wannemuehler
- Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | | | | | | | - Melissa Skala
- Biomedical Engineering, University of Wisconsin, Madison, WI, USA
| | - David Meyerholz
- Division of Comparative Pathology, University of Iowa Carver College of Medicine, Iowa City, USA
| | - Mary Estes
- Baylor College of Medicine, Houston, TX, USA
| | - Martin E Fernandez-Zapico
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
| | - Albert E Jergens
- Departments of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA
| | | | - Karin Allenspach
- Departments of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA.
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230
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Wellington D, Laurenson-Schafer H, Abdel-Haq A, Dong T. IFITM3: How genetics influence influenza infection demographically. Biomed J 2019; 42:19-26. [PMID: 30987701 PMCID: PMC6468115 DOI: 10.1016/j.bj.2019.01.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/06/2018] [Accepted: 01/07/2019] [Indexed: 12/18/2022] Open
Abstract
The role of host genetics in influenza infection is unclear despite decades of interest. Confounding factors such as age, sex, ethnicity and environmental factors have made it difficult to assess the role of genetics without influence. In recent years a single nucleotide polymorphism, interferon-induced transmembrane protein 3 (IFITM3) rs12252, has been shown to alter the severity of influenza infection in Asian populations. In this review we investigate this polymorphism as well as several others suggested to alter the host's defence against influenza infection. In addition, we highlight the open questions surrounding the viral restriction protein IFITM3 with the hope that by answering some of these questions we can elucidate the mechanism of IFITM3 viral restriction and therefore how this restriction is altered due to the rs12252 polymorphism.
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Affiliation(s)
- Dannielle Wellington
- MRC Human Immunology Unit, WIMM, University of Oxford, OX3 9DS, UK; CAMS Oxford Institute, Nuffield Department of Medicine, Oxford University, OX3 9FZ, UK.
| | - Henry Laurenson-Schafer
- MRC Human Immunology Unit, WIMM, University of Oxford, OX3 9DS, UK; CAMS Oxford Institute, Nuffield Department of Medicine, Oxford University, OX3 9FZ, UK
| | - Adi Abdel-Haq
- MRC Human Immunology Unit, WIMM, University of Oxford, OX3 9DS, UK; Martin-Luther-University, Halle-Wittenberg, Germany
| | - Tao Dong
- MRC Human Immunology Unit, WIMM, University of Oxford, OX3 9DS, UK; CAMS Oxford Institute, Nuffield Department of Medicine, Oxford University, OX3 9FZ, UK.
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231
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Yang L, Tu L, Zhao P, Wang Y, Wang S, Lu W, Wang Y, Li X, Yu Y, Hua S, Wang L. Attenuation of interferon regulatory factor 7 activity in local infectious sites of trachea and lung for preventing the development of acute lung injury caused by influenza A virus. Immunology 2019; 157:37-51. [PMID: 30667045 DOI: 10.1111/imm.13045] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 01/14/2019] [Accepted: 01/14/2019] [Indexed: 12/24/2022] Open
Abstract
The excessive activation of interferon regulatory factor 7 (IRF7) promotes the development of acute lung injury (ALI) caused by influenza A virus (IAV). However, the deficiency of IRF7 increases the susceptibility to deadly IAV infection in both humans and mice. To test whether the attenuation rather than the abolishment of IRF7 activity in local infectious sites could alleviate IAV-induced ALI, we established IAV-infected mouse model and trachea/lung-tissue culture systems, and designed two IRF7-interfering oligodeoxynucleotides, IRF7-rODN M1 and IRF7-rODN A1, based on the mouse and human consensus sequences of IRF7-binding sites of Ifna/IFNA genes, respectively. In the model mice, we found a close relationship between the IAV-induced ALI and the level/activity of IRF7 in local infectious sites, and also found that the reduced IRF7 level or activity in the lungs of mice treated with IRF7-rODN M1 led to decreased mRNA levels of Ifna genes, reduced neutrophil infiltration in the lungs and prolonged survival of mice. Furthermore, we found that the effects of IRF7-rODN M1 on alleviating IAV-induced ALI could be correlated to the reduced translocation of IRF7, caused by the IRF7-rODN M1, from cytosol to nucleus in IAV-infected cells. These data suggest that the proper attenuation of IRF7 activity in local infectious sites could be a novel approach for treating IAV-induced ALI.
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Affiliation(s)
- Lei Yang
- Department of Molecular Biology in College of Basic Medical Sciences and Institute of Pediatrics in The First Hospital of Jilin University, Jilin University, Changchun, Jilin, China
| | - Liqun Tu
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Peiyan Zhao
- Department of Molecular Biology in College of Basic Medical Sciences and Institute of Pediatrics in The First Hospital of Jilin University, Jilin University, Changchun, Jilin, China
| | - Ying Wang
- Department of Molecular Biology in College of Basic Medical Sciences and Institute of Pediatrics in The First Hospital of Jilin University, Jilin University, Changchun, Jilin, China
| | - Shengnan Wang
- Department of Molecular Biology in College of Basic Medical Sciences and Institute of Pediatrics in The First Hospital of Jilin University, Jilin University, Changchun, Jilin, China
| | - Wenting Lu
- Department of Molecular Biology in College of Basic Medical Sciences and Institute of Pediatrics in The First Hospital of Jilin University, Jilin University, Changchun, Jilin, China
| | - Yangyang Wang
- Department of Molecular Biology in College of Basic Medical Sciences and Institute of Pediatrics in The First Hospital of Jilin University, Jilin University, Changchun, Jilin, China
| | - Xin Li
- Department of Molecular Biology in College of Basic Medical Sciences and Institute of Pediatrics in The First Hospital of Jilin University, Jilin University, Changchun, Jilin, China
| | - Yongli Yu
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Shucheng Hua
- Department of Respiratory Medicine, The First Hospital of Jilin University, Jilin University, Changchun, Jilin, China
| | - Liying Wang
- Department of Molecular Biology in College of Basic Medical Sciences and Institute of Pediatrics in The First Hospital of Jilin University, Jilin University, Changchun, Jilin, China
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232
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Ilyushina NA, Dickensheets H, Donnelly RP. A comparison of interferon gene expression induced by influenza A virus infection of human airway epithelial cells from two different donors. Virus Res 2019; 264:1-7. [PMID: 30779949 DOI: 10.1016/j.virusres.2019.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 01/26/2019] [Accepted: 02/11/2019] [Indexed: 12/20/2022]
Abstract
Influenza is an acute respiratory disease that can cause local annual epidemics and worldwide pandemics of different morbidity and mortality. Our understanding of host factors that modulate the frequency and severity of influenza virus infections is less than complete. In this study, we examined the inter-individual variations in the innate immune responses to H1N1 and H3N2 influenza A viruses (IAV) using primary cultures of normal human bronchial epithelial (NHBE) cells derived from two different donors (D1 and D2). Although IAV replication kinetics were similar in cultures derived from these two donors, the levels of type III interferons (IFNs) were significantly higher in D1 cells compared to D2 cells (˜31-fold↑ in D1 cells versus D2 cells; P < 0.05). The levels of IFN-λ1 protein at individual time points as well as the total amounts of IFN-λ1 secreted over 72 h were also significantly higher in D1 than in D2 NHBE cells (0.7-7.7-fold↑, P < 0.05). The relative levels of IFN-stimulated gene (ISG) expression also differed significantly between D1 and D2 cells. Our data indicate that donor-specific differences can result in significant differences in IFN and ISG induction by human airway epithelium.
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Affiliation(s)
- Natalia A Ilyushina
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
| | - Harold Dickensheets
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Raymond P Donnelly
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
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233
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Bougarn S, Boughorbel S, Chaussabel D, Marr N. A curated transcriptome dataset collection to investigate inborn errors of immunity. F1000Res 2019; 8:188. [PMID: 31559014 PMCID: PMC6749933 DOI: 10.12688/f1000research.18048.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/28/2019] [Indexed: 08/13/2023] Open
Abstract
Primary immunodeficiencies (PIDs) are a heterogeneous group of inherited disorders, frequently caused by loss-of-function and less commonly by gain-of-function mutations, which can result in susceptibility to a broad or a very narrow range of infections but also in inflammatory, allergic or malignant diseases. Owing to the wide range in clinical manifestations and variability in penetrance and expressivity, there is an urgent need to better understand the underlying molecular, cellular and immunological phenotypes in PID patients in order to improve clinical diagnosis and management. Here we have compiled a manually curated collection of public transcriptome datasets mainly obtained from human whole blood, peripheral blood mononuclear cells (PBMCs) or fibroblasts of patients with PIDs and of control subjects for subsequent meta-analysis, query and interpretation. A total of eighteen (18) datasets derived from studies of PID patients were identified and retrieved from the NCBI Gene Expression Omnibus (GEO) database and loaded in GXB, a custom web application designed for interactive query and visualization of integrated large-scale data. The dataset collection includes samples from well characterized PID patients that were stimulated ex vivo under a variety of conditions to assess the molecular consequences of the underlying, naturally occurring gene defects on a genome-wide scale. Multiple sample groupings and rank lists were generated to facilitate comparisons of the transcriptional responses between different PID patients and control subjects. The GXB tool enables browsing of a single transcript across studies, thereby providing new perspectives on the role of a given molecule across biological systems and PID patients. This dataset collection is available at http://pid.gxbsidra.org/dm3/geneBrowser/list.
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Affiliation(s)
- Salim Bougarn
- Systems Biology and Immunology, Sidra Medicine, Doha, Qatar
| | | | | | - Nico Marr
- Systems Biology and Immunology, Sidra Medicine, Doha, Qatar
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Khoo SK, Read J, Franks K, Zhang G, Bizzintino J, Coleman L, McCrae C, Öberg L, Troy NM, Prastanti F, Everard J, Oo S, Borland ML, Maciewicz RA, Le Souëf PN, Laing IA, Bosco A. Upper Airway Cell Transcriptomics Identify a Major New Immunological Phenotype with Strong Clinical Correlates in Young Children with Acute Wheezing. THE JOURNAL OF IMMUNOLOGY 2019; 202:1845-1858. [PMID: 30745463 DOI: 10.4049/jimmunol.1800178] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 01/08/2019] [Indexed: 01/10/2023]
Abstract
Asthma exacerbations are triggered by rhinovirus infections. We employed a systems biology approach to delineate upper-airway gene network patterns underlying asthma exacerbation phenotypes in children. Cluster analysis unveiled distinct IRF7hi versus IRF7lo molecular phenotypes, the former exhibiting robust upregulation of Th1/type I IFN responses and the latter an alternative signature marked by upregulation of cytokine and growth factor signaling and downregulation of IFN-γ. The two phenotypes also produced distinct clinical phenotypes. For IRF7lo children, symptom duration prior to hospital presentation was more than twice as long from initial symptoms (p = 0.011) and nearly three times as long for cough (p < 0.001), the odds ratio of admission to hospital was increased more than 4-fold (p = 0.018), and time to recurrence was shorter (p = 0.015). In summary, our findings demonstrate that asthma exacerbations in children can be divided into IRF7hi versus IRF7lo phenotypes with associated differences in clinical phenotypes.
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Affiliation(s)
- Siew-Kim Khoo
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - James Read
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Kimberley Franks
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Guicheng Zhang
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,School of Public Health, Curtin University, Perth, Western Australia 6102, Australia.,Centre for Genetic Origins of Health and Disease, The University of Western Australia, Perth, Western Australia 6009, Australia and Curtin University, Perth, Western Australia 6102, Australia
| | - Joelene Bizzintino
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Laura Coleman
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Christopher McCrae
- Respiratory Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Gothenburg, 431 53 Mölndal, Sweden
| | - Lisa Öberg
- Respiratory Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Gothenburg, 431 53 Mölndal, Sweden
| | - Niamh M Troy
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Franciska Prastanti
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Janet Everard
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Stephen Oo
- Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Meredith L Borland
- Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, Western Australia 6009, Australia.,Perth Children's Hospital, Perth, Western Australia 6009, Australia; and.,Division of Emergency Medicine, School of Medicine, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Rose A Maciewicz
- Respiratory Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Gothenburg, 431 53 Mölndal, Sweden
| | - Peter N Le Souëf
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia.,Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Ingrid A Laing
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Anthony Bosco
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia;
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235
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Karagiannis P, Takahashi K, Saito M, Yoshida Y, Okita K, Watanabe A, Inoue H, Yamashita JK, Todani M, Nakagawa M, Osawa M, Yashiro Y, Yamanaka S, Osafune K. Induced Pluripotent Stem Cells and Their Use in Human Models of Disease and Development. Physiol Rev 2019; 99:79-114. [PMID: 30328784 DOI: 10.1152/physrev.00039.2017] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The discovery of somatic cell nuclear transfer proved that somatic cells can carry the same genetic code as the zygote, and that activating parts of this code are sufficient to reprogram the cell to an early developmental state. The discovery of induced pluripotent stem cells (iPSCs) nearly half a century later provided a molecular mechanism for the reprogramming. The initial creation of iPSCs was accomplished by the ectopic expression of four specific genes (OCT4, KLF4, SOX2, and c-Myc; OSKM). iPSCs have since been acquired from a wide range of cell types and a wide range of species, suggesting a universal molecular mechanism. Furthermore, cells have been reprogrammed to iPSCs using a myriad of methods, although OSKM remains the gold standard. The sources for iPSCs are abundant compared with those for other pluripotent stem cells; thus the use of iPSCs to model the development of tissues, organs, and other systems of the body is increasing. iPSCs also, through the reprogramming of patient samples, are being used to model diseases. Moreover, in the 10 years since the first report, human iPSCs are already the basis for new cell therapies and drug discovery that have reached clinical application. In this review, we examine the generation of iPSCs and their application to disease and development.
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Affiliation(s)
- Peter Karagiannis
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Kazutoshi Takahashi
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Megumu Saito
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Yoshinori Yoshida
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Keisuke Okita
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Akira Watanabe
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Haruhisa Inoue
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Jun K Yamashita
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Masaya Todani
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Masato Nakagawa
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Mitsujiro Osawa
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Yoshimi Yashiro
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
| | - Kenji Osafune
- Center for iPS Cell Research and Application, Kyoto University , Kyoto , Japan
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236
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Frankiw L, Majumdar D, Burns C, Vlach L, Moradian A, Sweredoski MJ, Baltimore D. BUD13 Promotes a Type I Interferon Response by Countering Intron Retention in Irf7. Mol Cell 2019; 73:803-814.e6. [DOI: 10.1016/j.molcel.2018.11.038] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/20/2018] [Accepted: 11/29/2018] [Indexed: 01/12/2023]
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237
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Abstract
PURPOSE OF REVIEW Influenza causes a range of illnesses in children, from uncomplicated self-limited illness to severe disease and death. This review provides an update on the severity and burden of influenza in US children over recent seasons. RECENT FINDINGS The 2017-2018 influenza season was widespread and severe across all ages, including children. Disease severity is influenced by influenza virologic characteristics and host factors, as well as public health interventions such as influenza vaccination and antiviral treatment. In recent influenza A (H3N2)-predominant seasons (2016-2017 and 2017-2018), influenza vaccination effectiveness was higher in younger children compared with older children and adolescents, although the reasons for this are unclear. Interestingly, even in seasons when influenza A (H3N2) viruses predominate, influenza A (H1N1)pdm09 and B viruses can play a large role in severe pediatric disease. Although children less than 5 years of age and those with underlying medical conditions are at increased risk for severe disease, influenza-associated hospitalizations and deaths occur every season in healthy children. SUMMARY Influenza causes a substantial burden of outpatient visits, hospitalizations, and deaths among children. Ongoing research is important to better characterize factors that contribute to influenza severity, and to identify strategies to improve the impact of influenza vaccination and treatment.
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238
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Alculumbre S, Raieli S, Hoffmann C, Chelbi R, Danlos FX, Soumelis V. Plasmacytoid pre-dendritic cells (pDC): from molecular pathways to function and disease association. Semin Cell Dev Biol 2019; 86:24-35. [DOI: 10.1016/j.semcdb.2018.02.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 12/28/2017] [Accepted: 02/10/2018] [Indexed: 12/14/2022]
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239
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Mogensen TH. IRF and STAT Transcription Factors - From Basic Biology to Roles in Infection, Protective Immunity, and Primary Immunodeficiencies. Front Immunol 2019; 9:3047. [PMID: 30671054 PMCID: PMC6331453 DOI: 10.3389/fimmu.2018.03047] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/10/2018] [Indexed: 12/11/2022] Open
Abstract
The induction and action of type I interferon (IFN) is of fundamental importance in human immune defenses toward microbial pathogens, particularly viruses. Basic discoveries within the molecular and cellular signaling pathways regulating type I IFN induction and downstream actions have shown the essential role of the IFN regulatory factor (IRF) and the signal transducer and activator of transcription (STAT) families, respectively. However, the exact biological and immunological functions of these factors have been most clearly revealed through the study of inborn errors of immunity and the resultant infectious phenotypes in humans. The spectrum of human inborn errors of immunity caused by mutations in IRFs and STATs has proven very diverse. These diseases encompass herpes simplex encephalitis (HSE) and severe influenza in IRF3- and IRF7/IRF9 deficiency, respectively. They also include Mendelian susceptibility to mycobacterial infection (MSMD) in STAT1 deficiency, through disseminated measles infection associated with STAT2 deficiency, and finally staphylococcal abscesses and chronic mucocutaneous candidiasis (CMC) classically described with Hyper-IgE syndrome (HIES) in the case of STAT3 deficiency. More recently, increasing focus has been on aspects of autoimmunity and autoinflammation playing an important part in many primary immunodeficiency diseases (PID)s, as exemplified by STAT1 gain-of-function causing CMC and autoimmune thyroiditis, as well as a recently described autoinflammatory syndrome with hypogammaglobulinemia and lymphoproliferation as a result of STAT3 gain-of-function. Here I review the infectious, inflammatory, and autoimmune disorders arising from mutations in IRF and STAT transcription factors in humans, highlightning the underlying molecular mechanisms and immunopathogenesis as well as the clinical/therapeutic perspectives of these new insights.
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MESH Headings
- Autoimmunity
- Candidiasis, Chronic Mucocutaneous/genetics
- Candidiasis, Chronic Mucocutaneous/immunology
- Candidiasis, Chronic Mucocutaneous/metabolism
- Encephalitis, Herpes Simplex/genetics
- Encephalitis, Herpes Simplex/immunology
- Encephalitis, Herpes Simplex/metabolism
- Humans
- Immunity, Innate
- Influenza, Human/genetics
- Influenza, Human/immunology
- Influenza, Human/metabolism
- Interferon Regulatory Factors/genetics
- Interferon Regulatory Factors/immunology
- Interferon Regulatory Factors/metabolism
- Interferon Type I/immunology
- Interferon Type I/metabolism
- Janus Kinases/metabolism
- Job Syndrome/genetics
- Job Syndrome/immunology
- Job Syndrome/metabolism
- Mutation
- Mycobacterium Infections/genetics
- Mycobacterium Infections/immunology
- Mycobacterium Infections/metabolism
- Receptor, Interferon alpha-beta/metabolism
- STAT Transcription Factors/genetics
- STAT Transcription Factors/immunology
- STAT Transcription Factors/metabolism
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Affiliation(s)
- Trine H. Mogensen
- Department of Infectious diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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240
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Bustamante J, Zhang SY, Boisson B, Ciancanelli M, Jouanguy E, Dupuis-Boisson S, Puel A, Picard C, Casanova JL. Immunodeficiencies at the Interface of Innate and Adaptive Immunity. Clin Immunol 2019. [DOI: 10.1016/b978-0-7020-6896-6.00036-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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241
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Hong Y, Bai M, Qi X, Li C, Liang M, Li D, Cardona CJ, Xing Z. Suppression of the IFN-α and -β Induction through Sequestering IRF7 into Viral Inclusion Bodies by Nonstructural Protein NSs in Severe Fever with Thrombocytopenia Syndrome Bunyavirus Infection. THE JOURNAL OF IMMUNOLOGY 2018; 202:841-856. [DOI: 10.4049/jimmunol.1800576] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 11/26/2018] [Indexed: 12/12/2022]
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242
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Abstract
Pneumonia is an important cause of morbidity and mortality. However, pneumonia is an unusual outcome of respiratory infection. Most of the time, microbes in the lung can be controlled by a combination of constitutive and recruited defense mechanisms. Inflammation is a key component of recruited defenses. Variations in inflammation that influence pneumonia susceptibility and severity are considered here.
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Affiliation(s)
- Joseph P Mizgerd
- Pulmonary Center, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02115, USA.
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243
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Short KR, Kedzierska K, van de Sandt CE. Back to the Future: Lessons Learned From the 1918 Influenza Pandemic. Front Cell Infect Microbiol 2018; 8:343. [PMID: 30349811 PMCID: PMC6187080 DOI: 10.3389/fcimb.2018.00343] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 09/10/2018] [Indexed: 01/02/2023] Open
Abstract
2018 marks the 100-year anniversary of the 1918 influenza pandemic, which killed ~50 million people worldwide. The severity of this pandemic resulted from a complex interplay between viral, host, and societal factors. Here, we review the viral, genetic and immune factors that contributed to the severity of the 1918 pandemic and discuss the implications for modern pandemic preparedness. We address unresolved questions of why the 1918 influenza H1N1 virus was more virulent than other influenza pandemics and why some people survived the 1918 pandemic and others succumbed to the infection. While current studies suggest that viral factors such as haemagglutinin and polymerase gene segments most likely contributed to a potent, dysregulated pro-inflammatory cytokine storm in victims of the pandemic, a shift in case-fatality for the 1918 pandemic toward young adults was most likely associated with the host's immune status. Lack of pre-existing virus-specific and/or cross-reactive antibodies and cellular immunity in children and young adults likely contributed to the high attack rate and rapid spread of the 1918 H1N1 virus. In contrast, lower mortality rate in in the older (>30 years) adult population points toward the beneficial effects of pre-existing cross-reactive immunity. In addition to the role of humoral and cellular immunity, there is a growing body of evidence to suggest that individual genetic differences, especially involving single-nucleotide polymorphisms (SNPs), contribute to differences in the severity of influenza virus infections. Co-infections with bacterial pathogens, and possibly measles and malaria, co-morbidities, malnutrition or obesity are also known to affect the severity of influenza disease, and likely influenced 1918 H1N1 disease severity and outcomes. Additionally, we also discuss the new challenges, such as changing population demographics, antibiotic resistance and climate change, which we will face in the context of any future influenza virus pandemic. In the last decade there has been a dramatic increase in the number of severe influenza virus strains entering the human population from animal reservoirs (including highly pathogenic H7N9 and H5N1 viruses). An understanding of past influenza virus pandemics and the lessons that we have learnt from them has therefore never been more pertinent.
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Affiliation(s)
- Kirsty R. Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Carolien E. van de Sandt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, Netherlands
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244
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Hernandez N, Melki I, Jing H, Habib T, Huang SSY, Danielson J, Kula T, Drutman S, Belkaya S, Rattina V, Lorenzo-Diaz L, Boulai A, Rose Y, Kitabayashi N, Rodero MP, Dumaine C, Blanche S, Lebras MN, Leung MC, Mathew LS, Boisson B, Zhang SY, Boisson-Dupuis S, Giliani S, Chaussabel D, Notarangelo LD, Elledge SJ, Ciancanelli MJ, Abel L, Zhang Q, Marr N, Crow YJ, Su HC, Casanova JL. Life-threatening influenza pneumonitis in a child with inherited IRF9 deficiency. J Exp Med 2018; 215:2567-2585. [PMID: 30143481 PMCID: PMC6170168 DOI: 10.1084/jem.20180628] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/12/2018] [Accepted: 07/30/2018] [Indexed: 01/10/2023] Open
Abstract
Life-threatening pulmonary influenza can be caused by inborn errors of type I and III IFN immunity. We report a 5-yr-old child with severe pulmonary influenza at 2 yr. She is homozygous for a loss-of-function IRF9 allele. Her cells activate gamma-activated factor (GAF) STAT1 homodimers but not IFN-stimulated gene factor 3 (ISGF3) trimers (STAT1/STAT2/IRF9) in response to IFN-α2b. The transcriptome induced by IFN-α2b in the patient's cells is much narrower than that of control cells; however, induction of a subset of IFN-stimulated gene transcripts remains detectable. In vitro, the patient's cells do not control three respiratory viruses, influenza A virus (IAV), parainfluenza virus (PIV), and respiratory syncytial virus (RSV). These phenotypes are rescued by wild-type IRF9, whereas silencing IRF9 expression in control cells increases viral replication. However, the child has controlled various common viruses in vivo, including respiratory viruses other than IAV. Our findings show that human IRF9- and ISGF3-dependent type I and III IFN responsive pathways are essential for controlling IAV.
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Affiliation(s)
- Nicholas Hernandez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Isabelle Melki
- Pediatric Immunology-Hematology and Rheumatology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France
- General Pediatrics, Infectious Disease and Internal Medicine Department, Assistance Publique-Hôpitaux de Paris, Robert Debré Hospital, Paris, France
- Laboratory of Neurogenetics and Neuroinflammation, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France
| | - Huie Jing
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Tanwir Habib
- Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| | - Susie S Y Huang
- Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| | - Jeffrey Danielson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Tomasz Kula
- Division of Genetics, Department of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Scott Drutman
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Serkan Belkaya
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Vimel Rattina
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | - Lazaro Lorenzo-Diaz
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | - Anais Boulai
- Laboratory of Neurogenetics and Neuroinflammation, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France
| | - Yoann Rose
- Laboratory of Neurogenetics and Neuroinflammation, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France
| | - Naoki Kitabayashi
- Laboratory of Neurogenetics and Neuroinflammation, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France
| | - Mathieu P Rodero
- Laboratory of Neurogenetics and Neuroinflammation, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France
| | - Cecile Dumaine
- Pediatric Immunology-Hematology and Rheumatology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France
- General Pediatrics, Infectious Disease and Internal Medicine Department, Assistance Publique-Hôpitaux de Paris, Robert Debré Hospital, Paris, France
| | - Stéphane Blanche
- Pediatric Immunology-Hematology and Rheumatology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France
| | - Marie-Noëlle Lebras
- Pediatric Pulmonology, Infectious Disease and Internal Medicine Department, Assistance Publique-Hôpitaux de Paris, Robert Debré Hospital, Paris, France
| | - Man Chun Leung
- Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| | | | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | - Stephanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | - Silvia Giliani
- Angelo Nocivelli Institute for Molecular Medicine, University of Brescia, Brescia, Italy
| | | | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Stephen J Elledge
- Division of Genetics, Department of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA
| | - Michael J Ciancanelli
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Nico Marr
- Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| | - Yanick J Crow
- Laboratory of Neurogenetics and Neuroinflammation, Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Department of Genetics, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Pediatric Immunology-Hematology and Rheumatology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
- Howard Hughes Medical Institute, New York, NY
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245
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Lin GL, McGinley JP, Drysdale SB, Pollard AJ. Epidemiology and Immune Pathogenesis of Viral Sepsis. Front Immunol 2018; 9:2147. [PMID: 30319615 PMCID: PMC6170629 DOI: 10.3389/fimmu.2018.02147] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/30/2018] [Indexed: 12/11/2022] Open
Abstract
Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection. Sepsis can be caused by a broad range of pathogens; however, bacterial infections represent the majority of sepsis cases. Up to 42% of sepsis presentations are culture negative, suggesting a non-bacterial cause. Despite this, diagnosis of viral sepsis remains very rare. Almost any virus can cause sepsis in vulnerable patients (e.g., neonates, infants, and other immunosuppressed groups). The prevalence of viral sepsis is not known, nor is there enough information to make an accurate estimate. The initial standard of care for all cases of sepsis, even those that are subsequently proven to be culture negative, is the immediate use of broad-spectrum antibiotics. In the absence of definite diagnostic criteria for viral sepsis, or at least to exclude bacterial sepsis, this inevitably leads to unnecessary antimicrobial use, with associated consequences for antimicrobial resistance, effects on the host microbiome and excess healthcare costs. It is important to understand non-bacterial causes of sepsis so that inappropriate treatment can be minimised, and appropriate treatments can be developed to improve outcomes. In this review, we summarise what is known about viral sepsis, its most common causes, and how the immune responses to severe viral infections can contribute to sepsis. We also discuss strategies to improve our understanding of viral sepsis, and ways we can integrate this new information into effective treatment.
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Affiliation(s)
- Gu-Lung Lin
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Joseph P McGinley
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Simon B Drysdale
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford, United Kingdom.,Department of Paediatrics, St George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford, United Kingdom
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246
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de Jong SJ, Créquer A, Matos I, Hum D, Gunasekharan V, Lorenzo L, Jabot-Hanin F, Imahorn E, Arias AA, Vahidnezhad H, Youssefian L, Markle JG, Patin E, D'Amico A, Wang CQF, Full F, Ensser A, Leisner TM, Parise LV, Bouaziz M, Maya NP, Cadena XR, Saka B, Saeidian AH, Aghazadeh N, Zeinali S, Itin P, Krueger JG, Laimins L, Abel L, Fuchs E, Uitto J, Franco JL, Burger B, Orth G, Jouanguy E, Casanova JL. The human CIB1-EVER1-EVER2 complex governs keratinocyte-intrinsic immunity to β-papillomaviruses. J Exp Med 2018; 215:2289-2310. [PMID: 30068544 PMCID: PMC6122964 DOI: 10.1084/jem.20170308] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/21/2018] [Accepted: 07/02/2018] [Indexed: 02/04/2023] Open
Abstract
Patients with epidermodysplasia verruciformis (EV) and biallelic null mutations of TMC6 (encoding EVER1) or TMC8 (EVER2) are selectively prone to disseminated skin lesions due to keratinocyte-tropic human β-papillomaviruses (β-HPVs), which lack E5 and E8. We describe EV patients homozygous for null mutations of the CIB1 gene encoding calcium- and integrin-binding protein-1 (CIB1). CIB1 is strongly expressed in the skin and cultured keratinocytes of controls but not in those of patients. CIB1 forms a complex with EVER1 and EVER2, and CIB1 proteins are not expressed in EVER1- or EVER2-deficient cells. The known functions of EVER1 and EVER2 in human keratinocytes are not dependent on CIB1, and CIB1 deficiency does not impair keratinocyte adhesion or migration. In keratinocytes, the CIB1 protein interacts with the HPV E5 and E8 proteins encoded by α-HPV16 and γ-HPV4, respectively, suggesting that this protein acts as a restriction factor against HPVs. Collectively, these findings suggest that the disruption of CIB1-EVER1-EVER2-dependent keratinocyte-intrinsic immunity underlies the selective susceptibility to β-HPVs of EV patients.
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Affiliation(s)
- Sarah Jill de Jong
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Amandine Créquer
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Irina Matos
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, The Rockefeller University, New York, NY
| | - David Hum
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | | | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Necker Hospital for Sick Children, Paris, France
- University Paris Descartes, Imagine Institute, Paris, France
| | - Fabienne Jabot-Hanin
- Laboratory of Human Genetics of Infectious Diseases, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Necker Hospital for Sick Children, Paris, France
- University Paris Descartes, Imagine Institute, Paris, France
| | - Elias Imahorn
- Department of Biomedicine, University Hospital Basel and University of Basel, Switzerland
| | - Andres A Arias
- Primary Immunodeficiencies Group, School of Medicine, University of Antioquia, Medellin, Colombia
- School of Microbiology, University of Antioquia, Medellin, Colombia
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
- Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Janet G Markle
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Etienne Patin
- Human Evolutionary Genetics, Pasteur Institute, Paris, France
- National Center for Scientific Research, URA 3012, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Pasteur Institute, Paris, France
| | - Aurelia D'Amico
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Claire Q F Wang
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY
| | - Florian Full
- Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Armin Ensser
- Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Tina M Leisner
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Leslie V Parise
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Matthieu Bouaziz
- Laboratory of Human Genetics of Infectious Diseases, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Necker Hospital for Sick Children, Paris, France
- University Paris Descartes, Imagine Institute, Paris, France
| | | | - Xavier Rueda Cadena
- Dermatology/Oncology - Skin Cancer Unit, National Cancer Institute, Bogota, Colombia
| | - Bayaki Saka
- Department of Dermatology, Sylvanus Olympio Hospital, University of Lomé, Togo
| | - Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Nessa Aghazadeh
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Sirous Zeinali
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Kawsar Human Genetics Research Center, Tehran, Iran
| | - Peter Itin
- Department of Biomedicine, University Hospital Basel and University of Basel, Switzerland
- Dermatology, University Hospital Basel, Basel, Switzerland
| | - James G Krueger
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY
| | - Lou Laimins
- Department of Microbiology-Immunology, Northwestern University, Chicago, IL
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Necker Hospital for Sick Children, Paris, France
- University Paris Descartes, Imagine Institute, Paris, France
| | - Elaine Fuchs
- Robin Chemers Neustein Laboratory of Mammalian Development and Cell Biology, The Rockefeller University, New York, NY
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA
| | - Jose Luis Franco
- Primary Immunodeficiencies Group, School of Medicine, University of Antioquia, Medellin, Colombia
| | - Bettina Burger
- Department of Biomedicine, University Hospital Basel and University of Basel, Switzerland
| | - Gérard Orth
- Department of Virology, Pasteur Institute, Paris, France
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Necker Hospital for Sick Children, Paris, France
- University Paris Descartes, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Necker Hospital for Sick Children, Paris, France
- University Paris Descartes, Imagine Institute, Paris, France
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY
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247
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Denney L, Ho LP. The role of respiratory epithelium in host defence against influenza virus infection. Biomed J 2018; 41:218-233. [PMID: 30348265 PMCID: PMC6197993 DOI: 10.1016/j.bj.2018.08.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/03/2018] [Accepted: 08/03/2018] [Indexed: 12/18/2022] Open
Abstract
The respiratory epithelium is the major interface between the environment and the host. Sophisticated barrier, sensing, anti-microbial and immune regulatory mechanisms have evolved to help maintain homeostasis and to defend the lung against foreign substances and pathogens. During influenza virus infection, these specialised structural cells and populations of resident immune cells come together to mount the first response to the virus, one which would play a significant role in the immediate and long term outcome of the infection. In this review, we focus on the immune defence machinery of the respiratory epithelium and briefly explore how it repairs and regenerates after infection.
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Affiliation(s)
- Laura Denney
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Ling-Pei Ho
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
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248
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Bucciol G, Moens L, Bosch B, Bossuyt X, Casanova JL, Puel A, Meyts I. Lessons learned from the study of human inborn errors of innate immunity. J Allergy Clin Immunol 2018; 143:507-527. [PMID: 30075154 DOI: 10.1016/j.jaci.2018.07.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 07/13/2018] [Accepted: 07/24/2018] [Indexed: 02/07/2023]
Abstract
Innate immunity contributes to host defense through all cell types and relies on their shared germline genetic background, whereas adaptive immunity operates through only 3 main cell types, αβ T cells, γδ T cells, and B cells, and relies on their somatic genetic diversification of antigen-specific responses. Human inborn errors of innate immunity often underlie infectious diseases. The range and nature of infections depend on the mutated gene, the deleteriousness of the mutation, and other ill-defined factors. Most known inborn errors of innate immunity to infection disrupt the development or function of leukocytes other than T and B cells, but a growing number of inborn errors affect cells other than circulating and tissue leukocytes. Here we review inborn errors of innate immunity that have been recently discovered or clarified. We highlight the immunologic implications of these errors.
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Affiliation(s)
- Giorgia Bucciol
- Laboratory of Childhood Immunology, Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium; Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Leen Moens
- Laboratory of Childhood Immunology, Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium
| | - Barbara Bosch
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Xavier Bossuyt
- Experimental Laboratory Immunology, Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium; Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Howard Hughes Medical Institute, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Necker Hospital for Sick Children, INSERM U1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, INSERM U1163, Paris, France
| | - Anne Puel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Necker Hospital for Sick Children, INSERM U1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Isabelle Meyts
- Laboratory of Childhood Immunology, Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium; Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium.
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249
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Hui KPY, Ching RHH, Chan SKH, Nicholls JM, Sachs N, Clevers H, Peiris JSM, Chan MCW. Tropism, replication competence, and innate immune responses of influenza virus: an analysis of human airway organoids and ex-vivo bronchus cultures. THE LANCET RESPIRATORY MEDICINE 2018; 6:846-854. [PMID: 30001996 DOI: 10.1016/s2213-2600(18)30236-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Human airway organoids are three-dimensional cultures derived from stem cells, which self-organise in ex-vivo conditions to form so-called mini-airways. The cellular morphology of these cultures is physiologically similar to the human airway, with cilia, goblet cells, and club cells facing the inner lumen and basal cells situated at the outer layer. The aim of this study was to compare replication competence, tissue tropism, and host responses elicited by human and avian strains of influenza A virus in ex-vivo human bronchus and human airway organoids. METHODS Between Sept 29, 2016, and Jan 4, 2017, we obtained ex-vivo cultures of the human bronchus and cultured human airway organoids from lung stem cells obtained from human lung tissues removed as part of the routine clinical care of patients undergoing surgical resection at the Department of Cardiothoracic Surgery, University of Hong Kong, Queen Mary Hospital, Hong Kong. We compared viral replication competence, tissue tropism, and cytokine and chemokine induction of avian influenza A viruses isolated from humans (Sh2/H7N9, H5N1/483, H5N6/39715), and human H1N1pdm/415742 in airway organoids and ex-vivo bronchus explant cultures. FINDINGS Virus tropism and replication kinetics of human and avian influenza A viruses in human airway organoids mimicked those found in ex-vivo cultures of human bronchus explants. In both airway organoids and bronchus explants, influenza A H1N1 subtype (H1N1) and avian influenza A H7N9 viruses replicated to significantly higher titres than did the highly pathogenic avian influenza (HPAI) H5N1, whereas HPAI H5N6 replication was moderate. H1N1, H7N9, and H5N6 viruses infected ciliated cells and goblet cells, but not basal cells in both airway organoids and bronchus explants. The expression of cytokines, interleukin 6, and interferon β, and the chemokine regulated-on-activation, normal T-cell expressed and secreted, was significantly higher in human airway organoids infected with HPAI H5N1 virus than H1N1pdm/415742, Sh2/H7N9, and H5N6/39715 viruses, and the expression of monocyte chemoattractant protein-1 was significantly higher in human organoids infected with HPAI H5N1 virus than H1N1pdm/415742 and Sh2/H7N9 viruses. INTERPRETATION Human airway organoid cultures provided results that were comparable to those observed in human ex-vivo bronchus cultures, and thus provide an alternative physiologically relevant experimental model for investigating virus tropism and replication competence that could be used to assess the pandemic threat of animal influenza viruses. FUNDING US National Institute of Allergy and Infectious Diseases, Research Grants Council of the Hong Kong Special Administrative Region.
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Affiliation(s)
- Kenrie P Y Hui
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Rachel H H Ching
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Stan K H Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - John M Nicholls
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Norman Sachs
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, Netherlands; Vertex Pharmaceuticals, San Diego, CA, USA
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, Netherlands
| | - J S Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Michael C W Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
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250
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Yip TF, Selim ASM, Lian I, Lee SMY. Advancements in Host-Based Interventions for Influenza Treatment. Front Immunol 2018; 9:1547. [PMID: 30042762 PMCID: PMC6048202 DOI: 10.3389/fimmu.2018.01547] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/22/2018] [Indexed: 12/15/2022] Open
Abstract
Influenza is a major acute respiratory infection that causes mortality and morbidity worldwide. Two classes of conventional antivirals, M2 ion channel blockers and neuraminidase inhibitors, are mainstays in managing influenza disease to lessen symptoms while minimizing hospitalization and death in patients with severe influenza. However, the development of viral resistance to both drug classes has become a major public health concern. Vaccines are prophylaxis mainstays but are limited in efficacy due to the difficulty in matching predicted dominant viral strains to circulating strains. As such, other potential interventions are being explored. Since viruses rely on host cellular functions to replicate, recent therapeutic developments focus on targeting host factors involved in virus replication. Besides controlling virus replication, potential targets for drug development include controlling virus-induced host immune responses such as the recently suggested involvement of innate lymphoid cells and NADPH oxidases in influenza virus pathogenesis and immune cell metabolism. In this review, we will discuss the advancements in novel host-based interventions for treating influenza disease.
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Affiliation(s)
- Tsz-Fung Yip
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong
| | - Aisha Sami Mohammed Selim
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong
| | - Ida Lian
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore, Singapore
| | - Suki Man-Yan Lee
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong
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