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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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Djuric O, Andjelkovic M, Vreca M, Skakic A, Pavlovic S, Novakovic I, Jovanovic B, Skodric-Trifunovic V, Markovic-Denic L. Genetic variants in TNFA, LTA, TLR2 and TLR4 genes and risk of sepsis in patients with severe trauma: nested case-control study in a level-1 trauma centre in SERBIA. Injury 2021; 52:419-425. [PMID: 33436266 DOI: 10.1016/j.injury.2020.12.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/20/2020] [Accepted: 12/29/2020] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Single nucleotide variants (SNVs) represent important genetic risk factors for susceptibility to posttraumatic sepsis and a potential target for immunotherapy. We aimed to evaluate the association between 8 different SNVs within tumor necrosis factor alpha (TNFA), lymphotoxin alpha (LTA) and Toll-like receptor (TLR2 and TLR4) genes and the risk of posttraumatic sepsis. METHODS Nested case-control study was conducted in the emergency department of the Clinical Centre of Serbia including 228 traumatized patients (44 with sepsis and 184 without sepsis). To compare the results of trauma subjects with the data from the general population, a control group of 101 healthy persons was included in the study. Genotyping of TNFA (rs1800629 and rs361525), LTA (rs909253), TLR2 (rs3804099, rs4696480 and rs3804100), and TLR4 (rs4986790 and rs4986791) was performed for all patients within all three groups using the real-time PCR method. MutationTaster database and in silico software SIFT were used to predict the variant pathogenic effect. RESULTS Carriage of the G allele of the TNFA rs1800629 gene variant (OR 2.1, 95%CI 1.06-4.16) and T allele-carriage of the TLR4 rs4986791 genetic variant (OR 3.02, 95%CI 1.31-6.57) were associated with significantly higher risk of sepsis in trauma patients when compared to the general population prone to sepsis and traumatized patients without developing a sepsis, respectively. Of these two variants, only variant in TLR4 gene (rs4986791) has been labeled as disease causing by both the MutationTaster database and the in-silico software SIFT, which further supports the role of this variant in various pathologies including sepsis. For the remaining six variants no significant association with the susceptibility to sepsis was detected. CONCLUSIONS Carriage of the G allele of the TNFA rs1800629 gene variant and T allele-carriage of the TLR4 rs4986791 genetic variant confer significant risk of posttraumatic sepsis. TLR4 gene variants (rs4986790 and rs4986791) has been labelled as disease causing.
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Affiliation(s)
- Olivera Djuric
- Institute of Epidemiology, Faculty of medicine, University of Belgrade, Belgrade, Serbia.
| | - Marina Andjelkovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Serbia
| | - Misa Vreca
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Serbia
| | - Anita Skakic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Serbia
| | - Sonja Pavlovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Serbia
| | - Ivana Novakovic
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Bojan Jovanovic
- Department of Surgery and Anesthesia, School of Medicine, University of Belgrade, Belgrade, Serbia; Center for Anesthesia and Resuscitation, Clinical Center of Serbia, Belgrade, Serbia
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Chomkatekaew C, Boonklang P, Sangphukieo A, Chewapreecha C. An Evolutionary Arms Race Between Burkholderia pseudomallei and Host Immune System: What Do We Know? Front Microbiol 2021; 11:612568. [PMID: 33552023 PMCID: PMC7858667 DOI: 10.3389/fmicb.2020.612568] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
A better understanding of co-evolution between pathogens and hosts holds promise for better prevention and control strategies. This review will explore the interactions between Burkholderia pseudomallei, an environmental and opportunistic pathogen, and the human host immune system. B. pseudomallei causes "Melioidosis," a rapidly fatal tropical infectious disease predicted to affect 165,000 cases annually worldwide, of which 89,000 are fatal. Genetic heterogeneities were reported in both B. pseudomallei and human host population, some of which may, at least in part, contribute to inter-individual differences in disease susceptibility. Here, we review (i) a multi-host-pathogen characteristic of the interaction; (ii) selection pressures acting on B. pseudomallei and human genomes with the former being driven by bacterial adaptation across ranges of ecological niches while the latter are driven by human encounter of broad ranges of pathogens; (iii) the mechanisms that generate genetic diversity in bacterial and host population particularly in sequences encoding proteins functioning in host-pathogen interaction; (iv) reported genetic and structural variations of proteins or molecules observed in B. pseudomallei-human host interactions and their implications in infection outcomes. Together, these predict bacterial and host evolutionary trajectory which continues to generate genetic diversity in bacterium and operates host immune selection at the molecular level.
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Affiliation(s)
| | | | - Apiwat Sangphukieo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Wellcome Sanger Institute, Hinxton, United Kingdom
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Harcourt J, Tamin A, Lu X, Kamili S, Sakthivel SK, Murray J, Queen K, Tao Y, Paden CR, Zhang J, Li Y, Uehara A, Wang H, Goldsmith C, Bullock HA, Wang L, Whitaker B, Lynch B, Gautam R, Schindewolf C, Lokugamage KG, Scharton D, Plante JA, Mirchandani D, Widen SG, Narayanan K, Makino S, Ksiazek TG, Plante KS, Weaver SC, Lindstrom S, Tong S, Menachery VD, Thornburg NJ. Isolation and characterization of SARS-CoV-2 from the first US COVID-19 patient. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.03.02.972935. [PMID: 32511316 PMCID: PMC7239045 DOI: 10.1101/2020.03.02.972935] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The etiologic agent of the outbreak of pneumonia in Wuhan China was identified as severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) in January, 2020. The first US patient was diagnosed by the State of Washington and the US Centers for Disease Control and Prevention on January 20, 2020. We isolated virus from nasopharyngeal and oropharyngeal specimens, and characterized the viral sequence, replication properties, and cell culture tropism. We found that the virus replicates to high titer in Vero-CCL81 cells and Vero E6 cells in the absence of trypsin. We also deposited the virus into two virus repositories, making it broadly available to the public health and research communities. We hope that open access to this important reagent will expedite development of medical countermeasures.
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Affiliation(s)
| | - Azaibi Tamin
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Xiaoyan Lu
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | | | - Krista Queen
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ying Tao
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Clinton R Paden
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Yan Li
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | | | | | | | - Brett Whitaker
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Rashi Gautam
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Craig Schindewolf
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
| | - Kumari G Lokugamage
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
| | - Dionna Scharton
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
| | - Jessica A Plante
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
| | - Divya Mirchandani
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
| | - Steven G Widen
- Department of Biochemistry & Molecular Biology, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
| | - Krishna Narayanan
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
| | - Shinji Makino
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
| | - Thomas G Ksiazek
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Pathology, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
| | - Kenneth S Plante
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Pathology, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
| | | | - Suxiang Tong
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Vineet D Menachery
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Pathology, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA
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NOD2 inhibits tumorigenesis and increases chemosensitivity of hepatocellular carcinoma by targeting AMPK pathway. Cell Death Dis 2020; 11:174. [PMID: 32144252 PMCID: PMC7060316 DOI: 10.1038/s41419-020-2368-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 02/07/2023]
Abstract
Nucleotide binding oligomerization domain 2 (NOD2) is a recognized innate immune sensor which can initiate potent immune response against pathogens. Many innate immune sensors have been reported to be of great importance in carcinogenesis. However, the role of NOD2 in cancer is not well understood. Here we investigated the role of NOD2 in the development of hepatocellular carcinoma (HCC). We demonstrated that NOD2 deficiency promoted hepatocarcinogenesis in N-nitrosodiethylamine (DEN)/carbon tetrachloride (CCl4) induced HCC mice model and xenograft tumor model. In vitro investigation showed that NOD2 acted as a tumor suppressor and inhibited proliferation, colony formation and invasion of HCC cells. Clinical investigation showed that NOD2 expression was completely lost or significantly downregulated in clinical HCC tissues, and loss of NOD2 expression was significantly correlated with advanced disease stages. Further investigation showed that NOD2 exerted its anti-tumor effect through activating adenosine 5'-monophosphate (AMP) -activated protein kinase (AMPK) signaling pathway, and NOD2 significantly enhanced the sensitivity of HCC cells to sorafenib, lenvatinib and 5-FU treatment through activating AMPK pathway induced apoptosis. Moreover, we demonstrated that NOD2 activated AMPK pathway by directly binding with AMPKα-LKB1 complex, which led to autophagy-mediated apoptosis of HCC cells. Altogether, this study showed that NOD2 acted as a tumor suppressor as well as a chemotherapeutic regulator in HCC cells by directly activating AMPK pathway, which indicated a potential therapeutic strategy for HCC treatment by upregulating NOD2-AMPK signaling axis.
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Polymorphisms in Receptors Involved in Opsonic and Nonopsonic Phagocytosis, and Correlation with Risk of Infection in Oncohematology Patients. Infect Immun 2018; 86:IAI.00709-18. [PMID: 30275011 DOI: 10.1128/iai.00709-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 09/26/2018] [Indexed: 01/27/2023] Open
Abstract
High-risk hematological malignancies are a privileged setting for infection by opportunistic microbes, with invasive mycosis being one of the most serious complications. Recently, genetic background has emerged as an unanticipated risk factor. For this reason, polymorphisms for genes encoding archetypal receptors involved in the opsonic and nonopsonic clearance of microbes, pentraxin-3 (PTX3) and Dectin-1, respectively, were studied and correlated with the risk of infection. Fungal, bacterial, and viral infections were registered for a group of 198 patients with high-risk hematological malignancies. Polymorphisms for the pentraxin-3 gene (PTX3) showed a significant association with the risk of fungal infection by Candida spp. and, especially, by Aspergillus spp. This link remained even for patients undergoing antifungal prophylaxis, thus demonstrating the clinical relevance of PTX3 in the defense against fungi. CLEC7A polymorphisms did not show any definite correlation with the risk of invasive mycosis, nor did they influence the expression of Dectin-1 isoforms generated by alternative splicing. The PTX3 mRNA expression level was significantly lower in samples from healthy volunteers who showed these polymorphisms, although no differences were observed in the extents of induction elicited by bacterial lipopolysaccharide and heat-killed Candida albicans, thus suggesting that the expression of PTX3 at the start of infection may influence the clinical outcome. PTX3 mRNA expression can be a good biomarker to establish proper antifungal prophylaxis in immunodepressed patients.
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Dickerson F, Stallings C, Origoni A, Schroeder J, Katsafanas E, Schweinfurth L, Savage C, Khushalani S, Yolken R. Inflammatory Markers in Recent Onset Psychosis and Chronic Schizophrenia. Schizophr Bull 2016; 42:134-41. [PMID: 26294704 PMCID: PMC4681560 DOI: 10.1093/schbul/sbv108] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Immune markers have been associated with schizophrenia, but few studies have examined multiple markers in both recent onset and chronic schizophrenia patients. METHODS The sample of 588 individuals included 79 with recent onset psychosis, 249 with chronic schizophrenia, and 260 controls. A combined inflammation score was calculated by principal components factor analysis of the levels of C-reactive protein, Pentraxin 3, and IgG antibodies to gliadin, casein, and Saccharomyces cerevisiae measured in blood samples. Inflammation scores among groups were compared by multivariate analyses. RESULTS The chronic schizophrenia group showed significant elevations in the combined inflammation score compared with controls. The recent onset group surprisingly showed a reduction in the combined inflammation score. Consistent with these findings, the chronic schizophrenia group had significantly increased odds of a combined inflammation score greater than the 75th and the 90th percentile of that of the controls. The recent onset group had significantly increased odds of a combined inflammation score less than the 10th and the 25th percentile level of the controls. CONCLUSIONS The recent onset of psychosis may be associated with inherent deficits in innate immunity. Individuals later in the course of disease may have increased levels of innate immunity. The reasons for these changes are not known with certainty but may be related to compensatory increases as the disease progresses. Longitudinal studies are needed to determine the course of immune abnormalities in schizophrenia and their role in the clinical manifestations of the disorder.
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Affiliation(s)
- Faith Dickerson
- The Stanley Research Program at Sheppard Pratt, Baltimore, MD;
| | | | - Andrea Origoni
- The Stanley Research Program at Sheppard Pratt, Baltimore, MD
| | | | | | | | | | | | - Robert Yolken
- The Stanley Neurovirology Laboratory, Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD
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8
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Bronkhorst MWGA, Patka P, Lieshout EMMV. Multiple Infectious Complications in a Severely Injured Patient with Single Nucleotide Polymorphisms in Important Innate Immune Response Genes. Open Orthop J 2015; 9:367-71. [PMID: 26312121 PMCID: PMC4541467 DOI: 10.2174/1874325001509010367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 04/26/2015] [Accepted: 05/18/2015] [Indexed: 11/22/2022] Open
Abstract
Trauma is a major public health problem worldwide. Infectious complications, sepsis, and multiple organ
dysfunction syndrome (MODS) remain important causes for morbidity and mortality in patients who survive the initial
trauma. There is increasing evidence for the role of genetic variation in the innate immune system on infectious
complications in severe trauma patients. We describe a trauma patient with multiple infectious complications caused by
multiple micro-organisms leading to prolonged hospital stay with numerous treatments. This patient had multiple single
nucleotide polymorphisms (SNPs) in the MBL2, MASP2, FCN2 and TLR2 genes, most likely contributing to increased
susceptibility and severity of infectious disease.
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Affiliation(s)
- Maarten W G A Bronkhorst
- Trauma Research Unit Department of Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter Patka
- Department of Accident & Emergency, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Esther M M Van Lieshout
- Trauma Research Unit Department of Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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Patel S, Shukla R, Goyal A. Probiotics in valorization of innate immunity across various animal models. J Funct Foods 2015. [DOI: 10.1016/j.jff.2015.02.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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Unravelling the complex genetic background of atopic dermatitis: from genetic association results towards novel therapeutic strategies. Arch Dermatol Res 2015; 307:659-70. [PMID: 25693656 DOI: 10.1007/s00403-015-1550-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/14/2015] [Accepted: 01/31/2015] [Indexed: 02/06/2023]
Abstract
Atopic dermatitis (AD) is a chronic inflammatory skin disease arising from complex interaction between genetic and environmental factors. As the starting point of the so-called "atopic march", e.g. the progression towards allergic asthma in some but not all affected children, AD has come into focus for potential disease-modifying strategies. To elucidate the genetic factors influencing AD development, linkage, association as well as genome-wide association studies have been performed over the last two decades. The results suggest that besides variation in immune-mediated pathways, an intact skin barrier function plays a key role in AD development. Mutations in the gene encoding filaggrin, a major structural protein in the epidermis, have been consistently associated with AD, especially the early-onset persistent form of disease, and are regarded as the most significant known risk factor for AD development to date. Additionally, variation in some other genes involved in skin integrity and barrier function have shown association with AD. However, the known genetic risk factors can only explain a small part of the heritability at the moment. Whole-exome or whole-genome sequencing studies have not been reported yet, but will probably soon evaluate the influence of rare variations for AD development. Additionally, large multi-centre studies comprehensively incorporating gene-gene and gene-environment interactions as well as epigenetic mechanisms might further elucidate the genetic factors underlying AD pathogenesis and, thus, open the way for a more individualized treatment in the future.
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Emerging and Reemerging Infectious Disease Threats. MANDELL, DOUGLAS, AND BENNETT'S PRINCIPLES AND PRACTICE OF INFECTIOUS DISEASES 2015. [PMCID: PMC7151803 DOI: 10.1016/b978-1-4557-4801-3.00014-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Mandl JN, Ahmed R, Barreiro LB, Daszak P, Epstein JH, Virgin HW, Feinberg MB. Reservoir host immune responses to emerging zoonotic viruses. Cell 2014; 160:20-35. [PMID: 25533784 PMCID: PMC4390999 DOI: 10.1016/j.cell.2014.12.003] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Indexed: 12/26/2022]
Abstract
Zoonotic viruses, such as HIV, Ebola virus, coronaviruses, influenza A viruses, hantaviruses, or henipaviruses, can result in profound pathology in humans. In contrast, populations of the reservoir hosts of zoonotic pathogens often appear to tolerate these infections with little evidence of disease. Why are viruses more dangerous in one species than another? Immunological studies investigating quantitative and qualitative differences in the host-virus equilibrium in animal reservoirs will be key to answering this question, informing new approaches for treating and preventing zoonotic diseases. Integrating an understanding of host immune responses with epidemiological, ecological, and evolutionary insights into viral emergence will shed light on mechanisms that minimize fitness costs associated with viral infection, facilitate transmission to other hosts, and underlie the association of specific reservoir hosts with multiple emerging viruses. Reservoir host studies provide a rich opportunity for elucidating fundamental immunological processes and their underlying genetic basis, in the context of distinct physiological and metabolic constraints that contribute to host resistance and disease tolerance.
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Affiliation(s)
- Judith N Mandl
- Lymphocyte Biology Section, Laboratory of Systems Biology, NIAID, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Luis B Barreiro
- Sainte-Justine Hospital Research Centre, Department of Pediatrics, University of Montreal, Montreal, QC H3T 1J4, Canada
| | | | | | - Herbert W Virgin
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
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Tulloch F, Atkinson NJ, Evans DJ, Ryan MD, Simmonds P. RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies. eLife 2014; 3:e04531. [PMID: 25490153 PMCID: PMC4383024 DOI: 10.7554/elife.04531] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 12/08/2014] [Indexed: 12/20/2022] Open
Abstract
Mutating RNA virus genomes to alter codon pair (CP) frequencies and reduce translation efficiency has been advocated as a method to generate safe, attenuated virus vaccines. However, selection for disfavoured CPs leads to unintended increases in CpG and UpA dinucleotide frequencies that also attenuate replication. We designed and phenotypically characterised mutants of the picornavirus, echovirus 7, in which these parameters were independently varied to determine which most influenced virus replication. CpG and UpA dinucleotide frequencies primarily influenced virus replication ability while no fitness differences were observed between mutants with different CP usage where dinucleotide frequencies were kept constant. Contrastingly, translation efficiency was unaffected by either CP usage or dinucleotide frequencies. This mechanistic insight is critical for future rational design of live virus vaccines and their safety evaluation; attenuation is mediated through enhanced innate immune responses to viruses with elevated CpG/UpA dinucleotide frequencies rather the viruses themselves being intrinsically defective.
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Affiliation(s)
- Fiona Tulloch
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Nicky J Atkinson
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - David J Evans
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Martin D Ryan
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Peter Simmonds
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
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Bharti D, Kumar A, Mahla RS, Kumar S, Ingle H, Shankar H, Joshi B, Raut AA, Kumar H. The role of TLR9 polymorphism in susceptibility to pulmonary tuberculosis. Immunogenetics 2014; 66:675-81. [PMID: 25248338 DOI: 10.1007/s00251-014-0806-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/09/2014] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis (MTB) is the causative agent of pulmonary tuberculosis (PTB), a major health problem that leads to 1.5 million deaths annually. Host genetic factors play a significant role in disease resistance/susceptibility by altering immunity against MTB. Toll-like receptor (TLR) sensors such as TLR2, TLR4, TLR8, and TLR9 are known to play a pivotal role in PTB via modulating sensor expression and/or effector responses. Single-nucleotide polymorphism (SNP) rs187084 (T-1486C) of the TLR9 promoter is associated with various autoimmune disorders and cancers. A recent bioinformatic analysis predicted that the T-1486C SNP is involved in PTB, although its potential role is unclear. To investigate the role of T-1486C in PTB, we stimulated PBMCs with the H37Rv whole cell lysate. We found that the presence of the "C" allele increases the transcriptional activity of the TLR9, which in turn induces high levels of Interferon gamma-induced protein 10 (IP-10), a biomarker for PTB. However, the expression of protective cytokines such as IFNγ and TNFα was observed significantly less with "C" allele in comparison to "T" allele. We further selected three different tribe populations showing differential susceptibility to PTB and performed genotypic analyses for the TLR9 promoter. We found a significantly lower minor allele frequency (MAF) of T-1486C in the Baiga tribe, wherein fewer PTB cases were reported, than that in the Gond and Korku tribes. Collectively, these data suggest that the minor "C" allele at rs187084 locus may be associated with susceptibility to PTB, which may explain the relatively lower PTB rates observed in Baiga tribe members.
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Affiliation(s)
- Deepak Bharti
- Laboratory of Immunology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Indore-Bypass Road, Bhauri, Bhopal, 460023, Madhya Pradesh, India
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15
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Gutte PGM, Jurt S, Grütter MG, Zerbe O. Unusual structural features revealed by the solution NMR structure of the NLRC5 caspase recruitment domain. Biochemistry 2014; 53:3106-17. [PMID: 24815518 DOI: 10.1021/bi500177x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The cytosolic nucleotide-binding domain and leucine-rich repeat-containing receptors (NLRs) are key sensors for bacterial and viral invaders and endogenous stress signals. NLRs contain a varying N-terminal effector domain that regulates the downstream signaling events upon its activation and determines the subclass to which a NLR member belongs. NLRC5 contains an unclassified N-terminal effector domain that has been reported to interact downstream with the tandem caspase recruitment domain (CARD) of retinoic acid-inducible gene I (RIG-I). Here we report the solution structure of the N-terminal effector domain of NLRC5 and in vitro interaction experiments with the tandem CARD of RIG-I. The N-terminal effector domain of NLRC5 adopts a six α-helix bundle with a general death fold, though it displays specific structural features that are strikingly different from the CARD. Notably, α-helix 3 is replaced by an ordered loop, and α-helix 1 is devoid of the characteristic interruption. Detailed structural alignments between the N-terminal effector domains of NLRC5 with a representative of each death-fold subfamily showed that NLRC5 fits best to the CARD subfamily and can be called an atypical CARD. Due to the specific structural features, the atypical CARD also displays a different electrostatic surface. Because the shape and charge of the surface is crucial for the establishment of a homotypic CARD-CARD interaction, these specific structural features seem to have a significant effect on the interaction between the atypical CARD of NLRC5 and the tandem RIG-I CARD.
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Affiliation(s)
- Petrus G M Gutte
- Institute of Biochemistry, University of Zurich , Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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16
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Bergmann-Leitner ES, Leitner WW. Adjuvants in the Driver's Seat: How Magnitude, Type, Fine Specificity and Longevity of Immune Responses Are Driven by Distinct Classes of Immune Potentiators. Vaccines (Basel) 2014; 2:252-96. [PMID: 26344620 PMCID: PMC4494256 DOI: 10.3390/vaccines2020252] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 03/20/2014] [Accepted: 03/28/2014] [Indexed: 12/16/2022] Open
Abstract
The mechanism by which vaccine adjuvants enhance immune responses has historically been considered to be the creation of an antigen depot. From here, the antigen is slowly released and provided to immune cells over an extended period of time. This "depot" was formed by associating the antigen with substances able to persist at the injection site, such as aluminum salts or emulsions. The identification of Pathogen-Associated Molecular Patterns (PAMPs) has greatly advanced our understanding of how adjuvants work beyond the simple concept of extended antigen release and has accelerated the development of novel adjuvants. This review focuses on the mode of action of different adjuvant classes in regards to the stimulation of specific immune cell subsets, the biasing of immune responses towards cellular or humoral immune response, the ability to mediate epitope spreading and the induction of persistent immunological memory. A better understanding of how particular adjuvants mediate their biological effects will eventually allow them to be selected for specific vaccines in a targeted and rational manner.
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Affiliation(s)
- Elke S Bergmann-Leitner
- US Military Malaria Research Program, Malaria Vaccine Branch, 503 Robert Grant Ave, 3W65, Silver Spring, MD 20910, USA.
| | - Wolfgang W Leitner
- Division on Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 6610 Rockledge Drive, Bethesda, MD 20892, USA.
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17
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Yi G, Brendel VP, Shu C, Li P, Palanathan S, Cheng Kao C. Single nucleotide polymorphisms of human STING can affect innate immune response to cyclic dinucleotides. PLoS One 2013; 8:e77846. [PMID: 24204993 PMCID: PMC3804601 DOI: 10.1371/journal.pone.0077846] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 09/04/2013] [Indexed: 01/08/2023] Open
Abstract
The STING (stimulator of interferon genes) protein can bind cyclic dinucleotides to activate the production of type I interferons and inflammatory cytokines. The cyclic dinucleotides can be bacterial second messengers c-di-GMP and c-di-AMP, 3’5’-3’5’ cyclic GMP-AMP (3’3’ cGAMP) produced by Vibrio cholerae and metazoan second messenger 2’5’-3’5’ Cyclic GMP-AMP (2’3’ cGAMP). Analysis of single nucleotide polymorphism (SNP) data from the 1000 Genome Project revealed that R71H-G230A-R293Q (HAQ) occurs in 20.4%, R232H in 13.7%, G230A-R293Q (AQ) in 5.2%, and R293Q in 1.5% of human population. In the absence of exogenous ligands, the R232H, R293Q and AQ SNPs had only modest effect on the stimulation of IFN-β and NF-κB promoter activities in HEK293T cells, while HAQ had significantly lower intrinsic activity. The decrease was primarily due to the R71H substitution. The SNPs also affected the response to the cyclic dinucleotides. In the presence of c-di-GMP, the R232H variant partially decreased the ability to activate IFN-βsignaling, while it was defective for the response to c-di-AMP and 3’3’ cGAMP. The R293Q dramatically decreased the stimulatory response to all bacterial ligands. Surprisingly, the AQ and HAQ variants maintained partial abilities to activate the IFN-β signaling in the presence of ligands due primarily to the G230A substitution. Biochemical analysis revealed that the recombinant G230A protein could affect the conformation of the C-terminal domain of STING and the binding to c-di-GMP. Comparison of G230A structure with that of WT revealed that the conformation of the lid region that clamps onto the c-di-GMP was significantly altered. These results suggest that hSTING variation can affect innate immune signaling and that the common HAQ haplotype expresses a STING protein with reduced intrinsic signaling activity but retained the ability to response to bacterial cyclic dinucleotides.
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Affiliation(s)
- Guanghui Yi
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Volker P. Brendel
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America
| | - Chang Shu
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Pingwei Li
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Satheesh Palanathan
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
| | - C. Cheng Kao
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
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