1
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Hsu AP. The Known and Unknown "Knowns" of Human Susceptibility to Coccidioidomycosis. J Fungi (Basel) 2024; 10:256. [PMID: 38667927 PMCID: PMC11051025 DOI: 10.3390/jof10040256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/15/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Coccidioidomycosis occurs after inhalation of airborne spores of the endemic, dimorphic fungus, Coccidioides. While the majority of individuals resolve the infection without coming to medical attention, the fungus is a major cause of community-acquired pneumonia in the endemic region, and chronic pulmonary and extrapulmonary disease poses significant personal and economic burdens. This review explores the literature surrounding human susceptibility to coccidioidomycosis, including chronic pulmonary and extrapulmonary dissemination. Over the past century of study, themes have emerged surrounding factors impacting human susceptibility to severe disease or dissemination, including immune suppression, genetic susceptibility, sex, pregnancy, and genetic ancestry. Early studies were observational, frequently with small numbers of cases; several of these early studies are highly cited in review papers, becoming part of the coccidioidomycosis "canon". Specific genetic variants, sex, and immune suppression by TNF inhibitors have been validated in later cohort studies, confirming the original hypotheses. By contrast, some risk factors, such as ABO blood group, Filipino ancestry, or lack of erythema nodosum among black individuals, are repeated in the literature despite the lack of supporting studies or biologic plausibility. Using examination of historical reports coupled with recent cohort and epidemiology studies, evidence for commonly reported risk factors is discussed.
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Affiliation(s)
- Amy P Hsu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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2
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Al-Nakhle HH, Khateb AM. Comprehensive In Silico Characterization of the Coding and Non-Coding SNPs in Human Dectin-1 Gene with the Potential of High-Risk Pathogenicity Associated with Fungal Infections. Diagnostics (Basel) 2023; 13:diagnostics13101785. [PMID: 37238269 DOI: 10.3390/diagnostics13101785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The human C-type lectin domain family 7 member A (CLEC7A) gene encodes a Dectin-1 protein that recognizes beta-1,3-linked and beta-1,6-linked glucans, which form the cell walls of pathogenic bacteria and fungi. It plays a role in immunity against fungal infections through pathogen recognition and immune signaling. This study aimed to explore the impact of nsSNPs in the human CLEC7A gene through computational tools (MAPP, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT, SNAP, and PredictSNP) to identify the most deleterious and damaging nsSNPs. Further, their effect on protein stability was checked along with conservation and solvent accessibility analysis by I-Mutant 2.0, ConSurf, and Project HOPE and post-translational modification analysis using MusiteDEEP. Out of the 28 nsSNPs that were found to be deleterious, 25 nsSNPs affected protein stability. Some SNPs were finalized for structural analysis with Missense 3D. Seven nsSNPs affected protein stability. Results from this study predicted that C54R, L64P, C120G, C120S, S135C, W141R, W141S, C148G, L155P, L155V, I158M, I158T, D159G, D159R, I167T, W180R, L183F, W192R, G197E, G197V, C220S, C233Y, I240T, E242G, and Y3D were the most structurally and functionally significant nsSNPs in the human CLEC7A gene. No nsSNPs were found in the predicted sites for post-translational modifications. In the 5' untranslated region, two SNPs, rs536465890 and rs527258220, showed possible miRNA target sites and DNA binding sites. The present study identified structurally and functionally significant nsSNPs in the CLEC7A gene. These nsSNPs may potentially be used for further evaluation as diagnostic and prognostic biomarkers.
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Affiliation(s)
- Hakeemah H Al-Nakhle
- Department of Medical Laboratory Technology, Collage of Applied Medical Science, Taibah University, Medina 42353, Saudi Arabia
| | - Aiah M Khateb
- Department of Medical Laboratory Technology, Collage of Applied Medical Science, Taibah University, Medina 42353, Saudi Arabia
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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3
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Galgiani JN, Hsu AP, Powell DA, Vyas JM, Holland SM. Genetic and Other Determinants for the Severity of Coccidioidomycosis: A Clinician's Perspective. J Fungi (Basel) 2023; 9:jof9050554. [PMID: 37233265 DOI: 10.3390/jof9050554] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/30/2023] [Accepted: 05/06/2023] [Indexed: 05/27/2023] Open
Abstract
The endemic fungal infection, coccidioidomycosis, occurs after inhalation of one or very few Coccidioides spp. spores. Infections produce diverse clinical manifestations, ranging from insignificant to extremely destructive, even fatal. Approaches to understanding this range of consequences have traditionally categorized patients into a small number of groups (asymptomatic, uncomplicated self-limited, fibro-cavitary, and extra-thoracic disseminated) and then looked for immunologic differences among them. Recently, variants within genes of innate pathways have been found to account, in part, for infections that result in disseminated disease. This discovery raises the very attractive theory that, in patients without severe immunosuppression, much of the disease spectrum can be accounted for by various combinations of such deleterious variants in innate pathways. In this review, we summarize what is known about genetic determinants that are responsible for the severity of coccidioidal infections and how complex innate genetic differences among different people might account for the spectrum of disease observed clinically.
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Affiliation(s)
- John N Galgiani
- Valley Fever Center for Excellence, College of Medicine-Tucson, University of Arizona, Tucson, AZ 85721, USA
- Department of Medicine, College of Medicine-Tucson, University of Arizona, Tucson, AZ 85721, USA
- Department of Immunobiology, College of Medicine-Tucson, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Amy P Hsu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Daniel A Powell
- Valley Fever Center for Excellence, College of Medicine-Tucson, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Jatin M Vyas
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
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4
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Coyne V, Mead HL, Mongini PKA, Barker BM. B Cell Chronic Lymphocytic Leukemia Development in Mice with Chronic Lung Exposure to Coccidioides Fungal Arthroconidia. Immunohorizons 2023; 7:333-352. [PMID: 37195872 PMCID: PMC10579974 DOI: 10.4049/immunohorizons.2300013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
Links between repeated microbial infections and B cell chronic lymphocytic leukemia (B-CLL) have been proposed but not tested directly. This study examines how prolonged exposure to a human fungal pathogen impacts B-CLL development in Eµ-hTCL1-transgenic mice. Monthly lung exposure to inactivated Coccidioides arthroconidia, agents of Valley fever, altered leukemia development in a species-specific manner, with Coccidioides posadasii hastening B-CLL diagnosis/progression in a fraction of mice and Coccidioides immitis delaying aggressive B-CLL development, despite fostering more rapid monoclonal B cell lymphocytosis. Overall survival did not differ significantly between control and C. posadasii-treated cohorts but was significantly extended in C. immitis-exposed mice. In vivo doubling time analyses of pooled B-CLL showed no difference in growth rates of early and late leukemias. However, within C. immitis-treated mice, B-CLL manifests longer doubling times, as compared with B-CLL in control or C. posadasii-treated mice, and/or evidence of clonal contraction over time. Through linear regression, positive relationships were noted between circulating levels of CD5+/B220low B cells and hematopoietic cells previously linked to B-CLL growth, albeit in a cohort-specific manner. Neutrophils were positively linked to accelerated growth in mice exposed to either Coccidioides species, but not in control mice. Conversely, only C. posadasii-exposed and control cohorts displayed positive links between CD5+/B220low B cell frequency and abundance of M2 anti-inflammatory monocytes and T cells. The current study provides evidence that chronic lung exposure to fungal arthroconidia affects B-CLL development in a manner dependent on fungal genotype. Correlative studies suggest that fungal species differences in the modulation of nonleukemic hematopoietic cells are involved.
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Affiliation(s)
- Vanessa Coyne
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, AZ
| | - Heather L. Mead
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, AZ
| | | | - Bridget M. Barker
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, AZ
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5
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Griffiths JS, Orr SJ, Morton CO, Loeffler J, White PL. The Use of Host Biomarkers for the Management of Invasive Fungal Disease. J Fungi (Basel) 2022; 8:jof8121307. [PMID: 36547640 PMCID: PMC9784708 DOI: 10.3390/jof8121307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/03/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Invasive fungal disease (IFD) causes severe morbidity and mortality, and the number of IFD cases is increasing. Exposure to opportunistic fungal pathogens is inevitable, but not all patients with underlying diseases increasing susceptibility to IFD, develop it. IFD diagnosis currently uses fungal biomarkers and clinical risk/presentation to stratify high-risk patients and classifies them into possible, probable, and proven IFD. However, the fungal species responsible for IFD are highly diverse and present numerous diagnostic challenges, which culminates in the empirical anti-fungal treatment of patients at risk of IFD. Recent studies have focussed on host-derived biomarkers that may mediate IFD risk and can be used to predict, and even identify IFD. The identification of novel host genetic variants, host gene expression changes, and host protein expression (cytokines and chemokines) associated with increased risk of IFD has enhanced our understanding of why only some patients at risk of IFD actually develop disease. Furthermore, these host biomarkers when incorporated into predictive models alongside conventional diagnostic techniques enhance predictive and diagnostic results. Once validated in larger studies, host biomarkers associated with IFD may optimize the clinical management of populations at risk of IFD. This review will summarise the latest developments in the identification of host biomarkers for IFD, their use in predictive modelling and their potential application/usefulness for informing clinical decisions.
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Affiliation(s)
- James S. Griffiths
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London WC2R 2LS, UK
| | - Selinda J. Orr
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queen’s University Belfast, Belfast BT9 7BL, UK
| | | | - Juergen Loeffler
- Department of Internal Medicine II, University Hospital of Würzburg, 97070 Würzburg, Germany
| | - P. Lewis White
- Public Health Wales, Microbiology Cardiff, University Hospital of Wales, Heath Park, Cardiff CF14 4XW, UK
- Correspondence:
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Hsu AP, Korzeniowska A, Aguilar CC, Gu J, Karlins E, Oler AJ, Chen G, Reynoso GV, Davis J, Chaput A, Peng T, Sun L, Lack JB, Bays DJ, Stewart ER, Waldman SE, Powell DA, Donovan FM, Desai JV, Pouladi N, Long Priel DA, Yamanaka D, Rosenzweig SD, Niemela JE, Stoddard J, Freeman AF, Zerbe CS, Kuhns DB, Lussier YA, Olivier KN, Boucher RC, Hickman HD, Frelinger J, Fierer J, Shubitz LF, Leto TL, Thompson GR, Galgiani JN, Lionakis MS, Holland SM. Immunogenetics associated with severe coccidioidomycosis. JCI Insight 2022; 7:159491. [PMID: 36166305 PMCID: PMC9746810 DOI: 10.1172/jci.insight.159491] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/21/2022] [Indexed: 12/15/2022] Open
Abstract
Disseminated coccidioidomycosis (DCM) is caused by Coccidioides, pathogenic fungi endemic to the southwestern United States and Mexico. Illness occurs in approximately 30% of those infected, less than 1% of whom develop disseminated disease. To address why some individuals allow dissemination, we enrolled patients with DCM and performed whole-exome sequencing. In an exploratory set of 67 patients with DCM, 2 had haploinsufficient STAT3 mutations, and defects in β-glucan sensing and response were seen in 34 of 67 cases. Damaging CLEC7A and PLCG2 variants were associated with impaired production of β-glucan-stimulated TNF-α from PBMCs compared with healthy controls. Using ancestry-matched controls, damaging CLEC7A and PLCG2 variants were overrepresented in DCM, including CLEC7A Y238* and PLCG2 R268W. A validation cohort of 111 patients with DCM confirmed the PLCG2 R268W, CLEC7A I223S, and CLEC7A Y238* variants. Stimulation with a DECTIN-1 agonist induced DUOX1/DUOXA1-derived hydrogen peroxide [H2O2] in transfected cells. Heterozygous DUOX1 or DUOXA1 variants that impaired H2O2 production were overrepresented in discovery and validation cohorts. Patients with DCM have impaired β-glucan sensing or response affecting TNF-α and H2O2 production. Impaired Coccidioides recognition and decreased cellular response are associated with disseminated coccidioidomycosis.
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Affiliation(s)
- Amy P Hsu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Agnieszka Korzeniowska
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Cynthia C Aguilar
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Jingwen Gu
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Eric Karlins
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Gang Chen
- Marsico Lung Institute and Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Glennys V Reynoso
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Joie Davis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Alexandria Chaput
- Valley Fever Center for Excellence, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA
| | - Tao Peng
- Valley Fever Center for Excellence, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA
| | - Ling Sun
- Marsico Lung Institute and Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Respiratory and Critical Care Medicine, Laboratory of Pulmonary Immunology and Inflammation, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Justin B Lack
- NIAID Collaborative Bioinformatics Resource, NIAID, NIH, Bethesda, Maryland, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Derek J Bays
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Sacramento, California, USA
| | - Ethan R Stewart
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Sacramento, California, USA
| | - Sarah E Waldman
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Sacramento, California, USA
| | - Daniel A Powell
- Valley Fever Center for Excellence, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA.,Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Fariba M Donovan
- Valley Fever Center for Excellence, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA.,Department of Medicine, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA
| | - Jigar V Desai
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Nima Pouladi
- Center for Biomedical Informatics and Biostatistics and.,The Center for Applied Genetics and Genomic Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Debra A Long Priel
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Daisuke Yamanaka
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA.,Laboratory for Immunopharmacology of Microbial Products, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | | | - Julie E Niemela
- Immunology Service, Department of Laboratory Medicine, Clinical Center and
| | - Jennifer Stoddard
- Immunology Service, Department of Laboratory Medicine, Clinical Center and
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Christa S Zerbe
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Douglas B Kuhns
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Yves A Lussier
- Center for Biomedical Informatics and Biostatistics and.,The Center for Applied Genetics and Genomic Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Kenneth N Olivier
- Laboratory of Chronic Airway Infection, Pulmonary Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Richard C Boucher
- Marsico Lung Institute and Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Heather D Hickman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Jeffrey Frelinger
- Valley Fever Center for Excellence, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA.,Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Joshua Fierer
- VA HealthCare San Diego, San Diego, California, USA.,Division of Infectious Diseases, Departments of Pathology and Medicine, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Lisa F Shubitz
- Valley Fever Center for Excellence, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA
| | - Thomas L Leto
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - George R Thompson
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Sacramento, California, USA.,Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, USA
| | - John N Galgiani
- Valley Fever Center for Excellence, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA.,Department of Medicine, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
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Sharma J, Mudalagiriyappa S, Nanjappa SG. T cell responses to control fungal infection in an immunological memory lens. Front Immunol 2022; 13:905867. [PMID: 36177012 PMCID: PMC9513067 DOI: 10.3389/fimmu.2022.905867] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/22/2022] [Indexed: 11/24/2022] Open
Abstract
In recent years, fungal vaccine research emanated significant findings in the field of antifungal T-cell immunity. The generation of effector T cells is essential to combat many mucosal and systemic fungal infections. The development of antifungal memory T cells is integral for controlling or preventing fungal infections, and understanding the factors, regulators, and modifiers that dictate the generation of such T cells is necessary. Despite the deficiency in the clear understanding of antifungal memory T-cell longevity and attributes, in this review, we will compile some of the existing literature on antifungal T-cell immunity in the context of memory T-cell development against fungal infections.
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Spendlove SJ, Bondhus L, Lluri G, Sul JH, Arboleda VA. Polygenic risk scores of endo-phenotypes identify the effect of genetic background in congenital heart disease. HGG ADVANCES 2022; 3:100112. [PMID: 35599848 PMCID: PMC9118152 DOI: 10.1016/j.xhgg.2022.100112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/19/2022] [Indexed: 01/28/2023] Open
Abstract
Congenital heart disease (CHD) is a rare structural defect that occurs in ∼1% of live births. Studies on CHD genetic architecture have identified pathogenic single-gene mutations in less than 30% of cases. Single-gene mutations often show incomplete penetrance and variable expressivity. Therefore, we hypothesize that genetic background may play a role in modulating disease expression. Polygenic risk scores (PRSs) aggregate effects of common genetic variants to investigate whether, cumulatively, these variants are associated with disease penetrance or severity. However, the major limitations in this field have been in generating sufficient sample sizes for these studies. Here we used CHD-phenotype matched genome-wide association study (GWAS) summary statistics from the UK Biobank (UKBB) as our base study and whole-genome sequencing data from the CHD cohort (n1 = 711 trios, n2 = 362 European trios) of the Gabriella Miller Kids First dataset as our target study to develop PRSs for CHD. PRSs estimated using a GWAS for heart valve problems and heart murmur explain 2.5% of the variance in case-control status of CHD (all SNVs, p = 7.90 × 10-3; fetal cardiac SNVs, p = 8.00 × 10-3) and 1.8% of the variance in severity of CHD (fetal cardiac SNVs, p = 6.20 × 10-3; all SNVs, p = 0.015). These results show that common variants captured in CHD phenotype-matched GWASs have a modest but significant contribution to phenotypic expression of CHD. Further exploration of the cumulative effect of common variants is necessary for understanding the complex genetic etiology of CHD and other rare diseases.
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Affiliation(s)
- Sarah J Spendlove
- Interdepartmental Bioinformatics Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Leroy Bondhus
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Gentian Lluri
- Ahmanson/UCLA Adult Congenital Heart Disease Center, Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jae Hoon Sul
- Interdepartmental Bioinformatics Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Valerie A Arboleda
- Interdepartmental Bioinformatics Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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9
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Kohn EM, Taira C, Dobson H, Dias LDS, Okaa U, Wiesner DL, Wüthrich M, Klein BS. Variation in Host Resistance to Blastomyces dermatitidis: Potential Use of Genetic Reference Panels and Advances in Immunophenotyping of Diverse Mouse Strains. mBio 2022; 13:e0340021. [PMID: 35089087 PMCID: PMC8725596 DOI: 10.1128/mbio.03400-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022] Open
Abstract
Host genetic determinants that underpin variation in susceptibility to systemic fungal infection are poorly understood. Genes responsible for complex traits can be identified by correlating variation in phenotype with allele in founder strains of wild mice with known genetic variation, assembled in genetic reference panels. In this work, we describe wide natural variation in both primary and acquired resistance to experimental pulmonary blastomycosis in eight founder strains, including 129, A/J, BL/6, CAST, NOD, NZO, PWK, and WSB of the Collaborative Cross collection, and the inbred DBA strain. These differences in susceptibility across strains were accompanied by sharp differences in the accumulation and function of immune cells in the lungs. Immune perturbations were mapped by identifying reagents that phenotypically mark immune cell populations in the distinct strains of mice. In particular, we uncovered marked differences between BL/6 and DBA/2 mouse strains in the development of acquired resistance. Our findings highlight the potential value in using genetic reference panels of mice, and particularly the BXD (recombinant inbred strains of mice from a cross of C57BL/6J and DBA/2J mice) collection harboring a cross between resistant BL/6 and susceptible DBA/2 mice, for unveiling genes linked with host resistance to fungal infection. IMPORTANCE Host genetic variation significantly impacts vulnerability to infectious diseases. While host variation in susceptibility to fungal infection with dimorphic fungi has long been recognized, genes that underpin this variation are poorly understood. We used a collection of seven mouse strains that represent nearly 90% of the genetic variation in mice to identify genetic variability among the strains in resistance to pulmonary infection with the dimorphic fungus Blastomyces dermatitidis. We analyzed differences between the strains in innate resistance by infecting naive mice and in acquired resistance by infecting vaccinated mice. We identified extreme variations in both innate and acquired resistance among the strains. In particular, we found sharp differences between C57BL/6 and DBA/2 strains in the ability to acquire vaccine-induced resistance. We also identified commercial reagents that allowed the phenotyping of immune cells from this strain collection of mice. Because there are additional mice harboring a genetic cross of the C57BL/6 and DBA/2 strains (BXD collection), such mice will permit future investigations to identify the genes that underlie differences in the ability to acquire resistance to infection.
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Affiliation(s)
- Elaine M. Kohn
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Cleison Taira
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Hanah Dobson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Lucas Dos Santos Dias
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Uju Okaa
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Darin L. Wiesner
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Marcel Wüthrich
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Bruce S. Klein
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Internal Medicine, University of Wisconsin School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
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10
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Willment JA. Fc-conjugated C-type lectin receptors: Tools for understanding host-pathogen interactions. Mol Microbiol 2021; 117:632-660. [PMID: 34709692 DOI: 10.1111/mmi.14837] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 12/24/2022]
Abstract
The use of soluble fusion proteins of pattern recognition receptors (PRRs) used in the detection of exogenous and endogenous ligands has helped resolve the roles of PRRs in the innate immune response to pathogens, how they shape the adaptive immune response, and function in maintaining homeostasis. Using the immunoglobulin (Ig) crystallizable fragment (Fc) domain as a fusion partner, the PRR fusion proteins are soluble, stable, easily purified, have increased affinity due to the Fc homodimerization properties, and consequently have been used in a wide range of applications such as flow cytometry, screening of protein and glycan arrays, and immunofluorescent microscopy. This review will predominantly focus on the recognition of pathogens by the cell membrane-expressed glycan-binding proteins of the C-type lectin receptor (CLR) subgroup of PRRs. PRRs bind to conserved pathogen-associated molecular patterns (PAMPs), such as glycans, usually located within or on the outer surface of the pathogen. Significantly, many glycans structures are identical on both host and pathogen (e.g. the Lewis (Le) X glycan), allowing the use of Fc CLR fusion proteins with known endogenous and/or exogenous ligands as tools to identify pathogen structures that are able to interact with the immune system. Screens of highly purified pathogen-derived cell wall components have enabled identification of many unique PAMP structures recognized by CLRs. This review highlights studies using Fc CLR fusion proteins, with emphasis on the PAMPs found in fungi, bacteria, viruses, and parasites. The structure and unique features of the different CLR families is presented using examples from a broad range of microbes whenever possible.
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Affiliation(s)
- Janet A Willment
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
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11
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Deerhake ME, Shinohara ML. Emerging roles of Dectin-1 in noninfectious settings and in the CNS. Trends Immunol 2021; 42:891-903. [PMID: 34489167 DOI: 10.1016/j.it.2021.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 12/15/2022]
Abstract
Dectin-1 is a C-type lectin receptor (CLR) expressed on the surface of various mammalian myeloid cells. Dectin-1 recognizes β-glucans and elicits antifungal proinflammatory immune responses. Recent studies have begun to examine the biology of Dectin-1 in previously less explored settings, such as homeostasis, sterile inflammation, and in the central nervous system. Indeed, in certain contexts, Dectin-1 is now known to promote tolerance, and anti-inflammatory and neuroprotective responses. In this review, we provide an overview of the current understanding of the roles of Dectin-1 in immunology beyond the context of fungal infections, mainly focusing on in vivo neuroimmunology studies, which could reveal new therapeutic approaches to modify innate immune responses in neurologic disorders.
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Affiliation(s)
- M Elizabeth Deerhake
- Department of Immunology, Duke University School of Medicine, Durham, NC 27705, USA
| | - Mari L Shinohara
- Department of Immunology, Duke University School of Medicine, Durham, NC 27705, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27705, USA.
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12
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Naik B, Ahmed SMQ, Laha S, Das SP. Genetic Susceptibility to Fungal Infections and Links to Human Ancestry. Front Genet 2021; 12:709315. [PMID: 34490039 PMCID: PMC8417537 DOI: 10.3389/fgene.2021.709315] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/13/2021] [Indexed: 12/25/2022] Open
Abstract
Over the ages, fungi have associated with different parts of the human body and established symbiotic associations with their host. They are mostly commensal unless there are certain not so well-defined factors that trigger the conversion to a pathogenic state. Some of the factors that induce such transition can be dependent on the fungal species, environment, immunological status of the individual, and most importantly host genetics. In this review, we discuss the different aspects of how host genetics play a role in fungal infection since mutations in several genes make hosts susceptible to such infections. We evaluate how mutations modulate the key recognition between the pathogen associated molecular patterns (PAMP) and the host pattern recognition receptor (PRR) molecules. We discuss the polymorphisms in the genes of the immune system, the way it contributes toward some common fungal infections, and highlight how the immunological status of the host determines fungal recognition and cross-reactivity of some fungal antigens against human proteins that mimic them. We highlight the importance of single nucleotide polymorphisms (SNPs) that are associated with several of the receptor coding genes and discuss how it affects the signaling cascade post-infection, immune evasion, and autoimmune disorders. As part of personalized medicine, we need the application of next-generation techniques as a feasible option to incorporate an individual’s susceptibility toward invasive fungal infections based on predisposing factors. Finally, we discuss the importance of studying genomic ancestry and reveal how genetic differences between the human race are linked to variation in fungal disease susceptibility.
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Affiliation(s)
- Bharati Naik
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sumayyah M Q Ahmed
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Suparna Laha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Shankar Prasad Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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13
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Diep AL, Tejeda-Garibay S, Miranda N, Hoyer KK. Macrophage and Dendritic Cell Activation and Polarization in Response to Coccidioidesposadasii Infection. J Fungi (Basel) 2021; 7:jof7080630. [PMID: 34436169 PMCID: PMC8397226 DOI: 10.3390/jof7080630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
Coccidioidomycosis is a fungal, respiratory disease caused by Coccidioides immitis and Coccidioides posadasii. The host immune responses that define disease outcome during infection are largely unknown, although T helper responses are required. Adaptive immunity is influenced by innate immunity as antigen-presenting cells activate and educate adaptive responses. Macrophage and dendritic cell (DC) recognition of pathogen surface molecules are critical for Coccidioides clearance. We characterize the broad innate immune responses to Coccidioides by analyzing macrophage and dendritic cell responses to Coccidioides arthroconidia using avirulent, vaccine Coccidioides strain NR-166 (Δcts2/Δard1/Δcts3), developed from parental virulent strain C735. We developed a novel flow cytometry-based method to analyze macrophage phagocytosis to complement traditional image-scoring methods. Our study found that macrophage polarization is blocked at M0 phase and activation reduced, while DCs polarize into proinflammatory DC1s, but not anti-inflammatory DC2, following interaction with Coccidioides. However, DCs exhibit a contact-dependent reduced activation to Coccidioides as defined by co-expression of MHC-II and CD86. In vivo, only modest DC1/DC2 recruitment and activation was observed with avirulent Coccidioides infection. In conclusion, the vaccine Coccidioides strain recruited a mixed DC population in vivo, while in vitro data suggest active innate immune cell inhibition by Coccidioides.
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Affiliation(s)
- Anh L. Diep
- Quantitative Systems Biology Graduate Programme, University of California Merced, Merced, CA 95343, USA; (A.L.D.); (S.T.-G.); (N.M.)
| | - Susana Tejeda-Garibay
- Quantitative Systems Biology Graduate Programme, University of California Merced, Merced, CA 95343, USA; (A.L.D.); (S.T.-G.); (N.M.)
| | - Nadia Miranda
- Quantitative Systems Biology Graduate Programme, University of California Merced, Merced, CA 95343, USA; (A.L.D.); (S.T.-G.); (N.M.)
| | - Katrina K. Hoyer
- Quantitative Systems Biology Graduate Programme, University of California Merced, Merced, CA 95343, USA; (A.L.D.); (S.T.-G.); (N.M.)
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA 95343, USA
- Health Sciences Research Institute, University of California Merced, Merced, CA 95343, USA
- Correspondence: ; Tel.: +1-(209)-228-4229
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14
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Shubitz LF, Powell DA, Butkiewicz CD, Lewis ML, Trinh HT, Frelinger JA, Orbach MJ, Galgiani JN. A Chronic Murine Disease Model of Coccidioidomycosis Using Coccidioides posadasii, Strain 1038. J Infect Dis 2021; 223:166-173. [PMID: 32658292 DOI: 10.1093/infdis/jiaa419] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022] Open
Abstract
Murine infections with most Coccidioides spp. strains are lethal by 3 weeks, limiting the study of immune responses. Coccidioides posadasii, strain 1038 (Cp1038), while slowly lethal, resulted in protracted survival of C57BL/6 (B6) mice. In resistant (B6D2)F1/J mice, lung fungal burdens stabilized by week 4 without progression through week 16, better modeling human coccidioidal infections after their immunologic control. Immunodeficient tumor necrosis factor (Tnf) α knockout (KO) and interferon (Ifn) γ receptor 1 (Ifn-γr1) KO mice survived a median of 22.5 and 34 days, compared with 70 days in B6 mice (P = .001 and P < .01, respectively), though 14-day lung fungal burden studies showed little difference between Ifn-γr1 KO and B6 mice. B6 mice showed peak concentrations of key inflammatory lung cytokines, including interleukin 6, 23, and 17A, Tnf-α, and Ifn-γ, only after 4 weeks of infection. The slower progression in B6 and the acquired fungal burden stability in B6D2 mice after Cp1038 infection greatly increases the array of possible immunologic studies.
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Affiliation(s)
- Lisa F Shubitz
- Valley Fever Center for Excellence, University of Arizona, Tucson, Arizona, USA
| | - Daniel A Powell
- Valley Fever Center for Excellence, University of Arizona, Tucson, Arizona, USA.,Department of Immunobiology, The University of Arizona, Tucson, Arizona, USA
| | | | - M Lourdes Lewis
- Valley Fever Center for Excellence, University of Arizona, Tucson, Arizona, USA
| | - Hien T Trinh
- Valley Fever Center for Excellence, University of Arizona, Tucson, Arizona, USA
| | - Jeffrey A Frelinger
- Valley Fever Center for Excellence, University of Arizona, Tucson, Arizona, USA
| | - Marc J Orbach
- Valley Fever Center for Excellence, University of Arizona, Tucson, Arizona, USA.,School of Plant Sciences, The University of Arizona, Tucson, Arizona, USA
| | - John N Galgiani
- Valley Fever Center for Excellence, University of Arizona, Tucson, Arizona, USA.,Department of Medicine, The University of Arizona, Tucson, Arizona, USA
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15
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Ward RA, Thompson GR, Villani AC, Li B, Mansour MK, Wuethrich M, Tam JM, Klein BS, Vyas JM. The Known Unknowns of the Immune Response to Coccidioides. J Fungi (Basel) 2021; 7:jof7050377. [PMID: 34065016 PMCID: PMC8151481 DOI: 10.3390/jof7050377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/11/2022] Open
Abstract
Coccidioidomycosis, otherwise known as Valley Fever, is caused by the dimorphic fungi Coccidioides immitis and C. posadasii. While most clinical cases present with self-limiting pulmonary infection, dissemination of Coccidioides spp. results in prolonged treatment and portends higher mortality rates. While the structure, genome, and niches for Coccidioides have provided some insight into the pathogenesis of disease, the underlying immunological mechanisms of clearance or inability to contain the infection in the lung are poorly understood. This review focuses on the known innate and adaptive immune responses to Coccidioides and highlights three important areas of uncertainty and potential approaches to address them. Closing these gaps in knowledge may enable new preventative and therapeutic strategies to be pursued.
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Affiliation(s)
- Rebecca A. Ward
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; (R.A.W.); (M.K.M.)
| | - George R. Thompson
- Department of Internal Medicine, University of California Davis Medical Center, Sacramento, CA 96817, USA;
| | - Alexandra-Chloé Villani
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; (A.-C.V.); (B.L.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA;
| | - Bo Li
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; (A.-C.V.); (B.L.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA;
| | - Michael K. Mansour
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; (R.A.W.); (M.K.M.)
- Harvard Medical School, Boston, MA 02115, USA;
| | - Marcel Wuethrich
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.W.); (B.S.K.)
| | - Jenny M. Tam
- Harvard Medical School, Boston, MA 02115, USA;
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Bruce S. Klein
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.W.); (B.S.K.)
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jatin M. Vyas
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; (R.A.W.); (M.K.M.)
- Harvard Medical School, Boston, MA 02115, USA;
- Correspondence: ; Tel.: +1-617-643-6444
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16
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Abstract
Fungi are eukaryotic microorganisms that show complex life cycles, including both anamorph and teleomorph stages. Beta-1,3-1,6-glucans (BGs) are major cell wall components in fungi. BGs are also found in a soluble form and are secreted by fungal cells. Studies of fungal BGs extensively expanded from 1960 to 1990 due to their applications in cancer immunotherapy. However, progress in this field slowed down due to the low efficacy of such therapies. In the early 21st century, the discovery of C-type lectin receptors significantly enhanced the molecular understanding of innate immunity. Moreover, pathogen-associated molecular patterns (PAMPs) and pattern recognition receptors (PRRs) were also discovered. Soon, dectin-1 was identified as the PRR of BGs, whereas BGs were established as PAMPs. Then, studies on fungal BGs focused on their participation in the development of deep-seated mycoses and on their role as a source of functional foods. Fungal BGs may have numerous and complex linkages, making it difficult to systematize them even at the primary structure level. Moreover, elucidating the structure of BGs is largely hindered by the multiplicity of genes involved in cell wall biosynthesis, including those for BGs, and by fungal diversity. The present review mainly focused on the characteristics of fungal BGs from the viewpoint of structure and immunological activities.
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17
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Desamero MJM, Chung SH, Kakuta S. Insights on the Functional Role of Beta-Glucans in Fungal Immunity Using Receptor-Deficient Mouse Models. Int J Mol Sci 2021; 22:4778. [PMID: 33946381 PMCID: PMC8125483 DOI: 10.3390/ijms22094778] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 12/18/2022] Open
Abstract
Understanding the host anti-fungal immunity induced by beta-glucan has been one of the most challenging conundrums in the field of biomedical research. During the last couple of decades, insights on the role of beta-glucan in fungal disease progression, susceptibility, and resistance have been greatly augmented through the utility of various beta-glucan cognate receptor-deficient mouse models. Analysis of dectin-1 knockout mice has clarified the downstream signaling pathways and adaptive effector responses triggered by beta-glucan in anti-fungal immunity. On the other hand, assessment of CR3-deficient mice has elucidated the compelling action of beta-glucans in neutrophil-mediated fungal clearance, and the investigation of EphA2-deficient mice has highlighted its novel involvement in host sensing and defense to oral mucosal fungal infection. Based on these accounts, this review focuses on the recent discoveries made by these gene-targeted mice in beta-glucan research with particular emphasis on the multifaceted aspects of fungal immunity.
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Affiliation(s)
- Mark Joseph Maranan Desamero
- Laboratory of Biomedical Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan;
- Department of Basic Veterinary Sciences, College of Veterinary Medicine, University of the Philippines Los Baños, Laguna 4031, Philippines
| | - Soo-Hyun Chung
- Division of Experimental Animal Immunology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan;
| | - Shigeru Kakuta
- Laboratory of Biomedical Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan;
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18
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Álvarez B, Revilla C, Domínguez J, Ezquerra A. Expression of CLEC4A in porcine tissues and leukocyte populations and characterization of mRNA splice variants. Mol Immunol 2021; 132:157-164. [PMID: 33592571 DOI: 10.1016/j.molimm.2021.01.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/18/2021] [Accepted: 01/23/2021] [Indexed: 10/22/2022]
Abstract
CLECs are a group of molecules of the superfamily of C-type lectin domain containing receptors. Several receptors of this group have been described in humans and mice, as well as in other species. Many of them are expressed in immune cells, and have been shown to be involved in immune response modulation. Several molecules of this family have been proposed as targets for antigen delivery, which is what drew our interest in studying them in the pig. In this species only CLEC7A (also named Dectin-1) had been studied in some detail, and we have characterized two other members, CLEC12A and CLEC12B. Another molecule of interest was CLEC4A, for which we could not find any expression studies in pigs, although up to 5 different mRNA variants had been predicted by bioinformatics analysis of the genomic sequence in databases. Here we present an analysis of the expression of CLEC4A mRNA isoforms in tissues and blood cell subsets by PCR. Cloning and sequencing of cDNA of the different isoforms allowed us to identify all 5 predicted isoforms, in addition to characterizing 5 additional isoforms expressed in alveolar macrophages, of which the form coding for a canonical CLEC4A molecule was apparently the most abundant isoform. Analysis of the sequences of the 10 cDNA cloned allowed us to determine their exon usage and to identify their potential for protein coding. Only 8 of the characterized variants contain a recognizable coding sequence. The sequences of the coded proteins show both proteins with a putative transmembrane segment, and others without this feature, as well as proteins with the complete CLEC domain or with diverse truncated forms. We also prove that most of the cDNA can drive protein expression upon transfection in the CHO cell line. We discuss the relevance that the diversity of products of the porcine CLEC4A gene may have in the regulation of the expression and function of these molecules.
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Affiliation(s)
- Belén Álvarez
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Dpto. Biotecnología, Madrid, Spain
| | - Concepción Revilla
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Dpto. Biotecnología, Madrid, Spain
| | - Javier Domínguez
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Dpto. Biotecnología, Madrid, Spain
| | - Angel Ezquerra
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Dpto. Biotecnología, Madrid, Spain.
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19
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Kalia N, Singh J, Kaur M. The role of dectin-1 in health and disease. Immunobiology 2021; 226:152071. [PMID: 33588306 DOI: 10.1016/j.imbio.2021.152071] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/07/2021] [Accepted: 01/31/2021] [Indexed: 02/08/2023]
Abstract
Dendritic cell-associated C-type lectin-1 (Dectin-1), also known as β-glucan receptor is an emerging pattern recognition receptor (PRR) which belongs to the family of C-type lectin receptor (CLR). This CLR identifies ligands independently of Ca2+ and is majorly involved in coupling of innate with adaptive immunity. Formerly, Dectin-1 was best known for its role in anti-fungal defense only. However, recent explorations suggested its wider role in defense against variety of infectious diseases caused by pathogens including bacteria, parasites and viruses. In fact, Dectin-1 signaling axis has been suggested to be targeted as an effective therapeutic strategy for cancers. Dectin-1 has also been elucidated ascetically in the heart, respiratory, intestinal, neurological and developmental disorders. Being a defensive PRR, Dectin-1 results in optimal immune responses in collaboration with other PRRs, but the overall evaluation reinforces the hypothesis of disease development on dis-regulation of Dectin-1 activity. This underscores the impact of Dectin-1 polymorphisms in modulating protein expression and generation of non-optimal immune responses through defective collaborations, further underlining their therapeutic potential. To add on, Dectin-1 influence autoimmunity and severe inflammation accredited to recognition of self T cells and apoptotic cells through unknown ligands. Few reports have also testified its redundant role in infections, which makes it a complicated molecule to be fully resolved. Thus, Dectin-1 is a hub that runs a complex collaborative network, whose interactive wire connections to different PRRs are still pending to be revealed. Alternatively, so far focus of almost all the researchers was the two major cell surface isoforms of Dectin-1, despite the fact that its soluble functional intracellular isoform (Dectin-1E) has already been dissected but is indefinable. Therefore, this review intensely recommends the need of future research to resolve the un-resolved and treasure the comprehensive role of Dectin-1 in different clinical outcomes, before determining its therapeutic prospective.
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Affiliation(s)
- Namarta Kalia
- Department of Molecular Biology & Biochemistry, Guru Nanak Dev University, Amritsar 143001, India.
| | - Jatinder Singh
- Department of Molecular Biology & Biochemistry, Guru Nanak Dev University, Amritsar 143001, India
| | - Manpreet Kaur
- Department of Human Genetics, Guru Nanak Dev University, Amritsar 143001, India.
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20
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Diep AL, Hoyer KK. Host Response to Coccidioides Infection: Fungal Immunity. Front Cell Infect Microbiol 2020; 10:581101. [PMID: 33262956 PMCID: PMC7686801 DOI: 10.3389/fcimb.2020.581101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/15/2020] [Indexed: 12/22/2022] Open
Abstract
Coccidioidomycosis is a fungal, respiratory disease caused by Coccidioides immitis and Coccidioides posadasii. This emerging infectious disease ranges from asymptomatic to pulmonary disease and disseminated infection. Most infections are cleared with little to no medical intervention whereas chronic disease often requires life-long medication with severe impairment in quality of life. It is unclear what differentiates hosts immunity resulting in disease resolution versus chronic infection. Current understanding in mycology-immunology suggests that chronic infection could be due to maladaptive immune responses. Immunosuppressed patients develop more severe disease and mouse studies show adaptive Th1 and Th17 responses are required for clearance. This is supported by heightened immunosuppressive regulatory responses and lowered anti-fungal T helper responses in chronic Coccidioides patients. Diagnosis and prognosis is difficult as symptoms are broad and overlapping with community acquired pneumonia, often resulting in misdiagnosis and delayed treatment. Furthermore, we lack clear biomarkers of disease severity which could aid prognosis for more effective healthcare. As the endemic region grows and population increases in endemic areas, the need to understand Coccidioides infection is becoming urgent. There is a growing effort to identify fungal virulence factors and host immune components that influence fungal immunity and relate these to patient disease outcome and treatment. This review compiles the known immune responses to Coccidioides spp. infection and various related fungal pathogens to provide speculation on Coccidioides immunity.
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Affiliation(s)
- Anh L. Diep
- Quantitative and Systems Biology, Graduate Program, University of California Merced, Merced, CA, United States
| | - Katrina K. Hoyer
- Quantitative and Systems Biology, Graduate Program, University of California Merced, Merced, CA, United States
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, United States
- Health Sciences Research Institute, University of California Merced, Merced, CA, United States
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21
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Campuzano A, Zhang H, Ostroff GR, Dos Santos Dias L, Wüthrich M, Klein BS, Yu JJ, Lara HH, Lopez-Ribot JL, Hung CY. CARD9-Associated Dectin-1 and Dectin-2 Are Required for Protective Immunity of a Multivalent Vaccine against Coccidioides posadasii Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:3296-3306. [PMID: 32358020 PMCID: PMC7323849 DOI: 10.4049/jimmunol.1900793] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 04/15/2020] [Indexed: 12/11/2022]
Abstract
Coccidioides species are fungal pathogens that can cause a widely varied clinical manifestation from mild pulmonary symptom to disseminated, life-threatening disease. We have previously created a subunit vaccine by encapsulating a recombinant coccidioidal Ag (rCpa1) in glucan-chitin particles (GCPs) as an adjuvant-delivery system. The GCP-rCpa1 vaccine has shown to elicit a mixed Th1 and Th17 response and confers protection against pulmonary coccidioidomycosis in mice. In this study, we further delineated the vaccine-induced protective mechanisms. Depletion of IL-17A in vaccinated C57BL/6 mice prior to challenge abrogated the protective efficacy of GCP-rCpa1 vaccine. Global transcriptome and Ingenuity Pathway Analysis of murine bone marrow-derived macrophages after exposure to this vaccine revealed the upregulation of proinflammatory cytokines (TNF-α, IL-6, and IL-1β) that are associated with activation of C-type lectin receptors (CLR) Dectin-1- and Dectin-2-mediated CARD9 signaling pathway. The GCP formulation of rCpa1 bound soluble Dectin-1 and Dectin-2 and triggered ITAM signaling of corresponding CLR reporter cells. Furthermore, macrophages that were isolated from Dectin-1 -/-, Dectin-2 -/-, and CARD9 -/- mice significantly reduced production of inflammatory cytokines in response to the GCP-rCpa1 vaccine compared with those of wild-type mice. The GCP-rCpa1 vaccine had significantly reduced protective efficacy in Dectin-1 -/-, Dectin-2 -/-, and CARD9 -/- mice that showed decreased acquisition of Th cells in Coccidioides-infected lungs compared with vaccinated wild-type mice, especially Th17 cells. Collectively, we conclude that the GCP-rCpa1 vaccine stimulates a robust Th17 immunity against Coccidioides infection through activation of the CARD9-associated Dectin-1 and Dectin-2 signal pathways.
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Affiliation(s)
- Althea Campuzano
- South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Hao Zhang
- South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Gary R Ostroff
- Program in Molecular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605; and
| | - Lucas Dos Santos Dias
- Department of Pediatrics, University of Wisconsin Medical School, University of Wisconsin Hospital and Clinics, Madison, WI 53792
| | - Marcel Wüthrich
- Department of Pediatrics, University of Wisconsin Medical School, University of Wisconsin Hospital and Clinics, Madison, WI 53792
| | - Bruce S Klein
- Department of Pediatrics, University of Wisconsin Medical School, University of Wisconsin Hospital and Clinics, Madison, WI 53792
| | - Jieh-Juen Yu
- South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Humberto H Lara
- South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Jose L Lopez-Ribot
- South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Chiung-Yu Hung
- South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249;
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22
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Innate Immune Receptors and Defense Against Primary Pathogenic Fungi. Vaccines (Basel) 2020; 8:vaccines8020303. [PMID: 32545735 PMCID: PMC7350247 DOI: 10.3390/vaccines8020303] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023] Open
Abstract
The innate immune system is critical for natural resistance to all pathogenic microorganisms, including fungi. The innate response plays a vital role in resistance to infections before the antigen-specific immune response and also influences antigen-specific adaptive immunity. There are many different receptors for the innate immune response to fungi, and some receptors have been found to play a significant role in the response to human infections with opportunistic fungi. Most human infections are caused by opportunistic fungi, but a small number of organisms are capable of causing infections in normal hosts. The primary pathogenic fungi that cause invasive infections include Blastomyces spp., Cryptococcus gattii, Coccidioides spp., Histoplasma spp., and Paracoccidioides spp. In this review of innate immune receptors that play a role in infections caused by these organisms, we find that innate immunity differs between organisms.
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23
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Bayazid AB, Park SH, Kim JG, Lim BO. Green chicory leaf extract exerts anti-inflammatory effects through suppressing LPS-induced MAPK/NF-κB activation and hepatoprotective activity in vitro. FOOD AGR IMMUNOL 2020. [DOI: 10.1080/09540105.2020.1742667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Al Borhan Bayazid
- Department of Integrated Biosciences, Graduate School of Konkuk University, Chungju, Korea
| | - Seo Hyun Park
- Department of Integrated Biosciences, Graduate School of Konkuk University, Chungju, Korea
| | - Jae Gon Kim
- Ahn-Gook Health, LTD., Seoul, Republic of Korea
| | - Beong Ou Lim
- Department of Integrated Biosciences, Graduate School of Konkuk University, Chungju, Korea
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24
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Heung LJ. Monocytes and the Host Response to Fungal Pathogens. Front Cell Infect Microbiol 2020; 10:34. [PMID: 32117808 PMCID: PMC7031161 DOI: 10.3389/fcimb.2020.00034] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/17/2020] [Indexed: 12/11/2022] Open
Abstract
Monocytes and their derivatives, including macrophages and dendritic cells, play diverse roles in the response to fungal pathogens. Sensing of fungi by monocytes triggers signaling pathways that mediate direct effects like phagocytosis and cytokine production. Monocytes can also present fungal antigens to elicit adaptive immune responses. These monocyte-mediated pathways may be either beneficial or harmful to the host. In some instances, fungi have developed mechanisms to evade the consequences of monocyte activation and subvert these cells to promote disease. Thus, monocytes are critically involved in mediating the outcomes of these often highly fatal infections. This review will highlight the roles of monocytes in the immune response to some of the major fungi that cause invasive human disease, including Aspergillus, Cryptococcus, Candida, Histoplasma, Blastomyces, and Coccidioides, and discuss potential strategies to manipulate monocyte responses in order to enhance anti-fungal immunity in susceptible hosts.
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Affiliation(s)
- Lena J Heung
- Division of Infectious Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
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25
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Abstract
Since its description nearly 130 years ago, hundreds of studies have deepened our understanding of coccidioidomycosis, also known as valley fever (VF), and provided useful diagnostic tests and treatments for the disease caused by the dimorphic fungi Coccidioides spp. In general, most of the literature has addressed well-established infections and has described patients who have experienced major complications. In contrast, little attention has been given to the earliest consequences of the pathogen-host interaction and its implications for disease manifestation, progression, and resolution. The purpose of this review is to highlight published studies on early coccidioidomycosis, identify gaps in our knowledge, and suggest new or former research areas that might be or remain fertile ground for insight into the early stages of this invasive fungal disease.
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26
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Krogstad P, Johnson R, Garcia-Lloret MI, Heidari A, Butte MJ. Host-Pathogen Interactions in Coccidioidomycosis: Prognostic Clues and Opportunities for Novel Therapies. Clin Ther 2019; 41:1939-1954.e1. [PMID: 31648806 PMCID: PMC10482146 DOI: 10.1016/j.clinthera.2019.08.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 01/09/2023]
Abstract
PURPOSE Coccidioidomycosis (CM) is a systemic fungal disease caused by the dimorphic fungi Coccidioides immitis and Coccidioides posadasii. In its endemic areas of the United States, CM is growing as a public health challenge with a marked increase in incidence in the last 15 years. Although Coccidioides infection is asymptomatic in most cases, symptomatic pulmonary disease occurs in ~40% and disseminated coccidioidomycosis (DCM) occurs in ~1% of previously healthy children and adults. DCM is markedly more common in immunocompromised people, who often experience life-threatening disease despite use of antifungal medications. Although options for antifungal therapy have improved, lifelong therapy is needed for those who develop coccidioidal meningitis. The purpose of this article was to review the state of antifungal therapy and recent studies of host-pathogen interactions in CM in light of advances in immunomodulatory therapy. METHODS The study included a review of PubMed and abstracts of the Coccidioidomycosis Study Group (years 2000-2019). FINDINGS Current therapy for CM relies upon azole and polyene antifungal agents. Murine models and studies of DCM in patients with monogenic primary immunodeficiency states and acquired immunodeficiency have revealed the importance of both innate and adaptive immune responses in the control of infections with Coccidioides species. In particular, defects in sensing of fungi and induction of cellular immune responses have been frequently reported. More recently, polymorphisms in key signaling pathways and in the generation of Th17 and Th1 immune responses have been linked with DCM. IMPLICATIONS Antifungal therapy is sufficient to control disease in most cases of CM, but treatment failure occurs in cases of severe pulmonary disease and nonmeningeal disseminated disease. Lifelong therapy is recommended for meningitis in view of the very high risk of recurrence. Corticosteroid therapy is advised by some experts for severe pulmonary disease and for some neurologic complications of DCM. DCM is only rarely the result of a severe monogenic immunodeficiency. Case studies suggest that reorienting cellular immune responses or augmenting effector immune responses may help resolve DCM. Systematic investigation of immunotherapy for coccidioidomycosis is advisable and may help to address the recent marked increase in reports of the disease in endemic areas.
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Affiliation(s)
- Paul Krogstad
- Department of Pediatrics, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, USA; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, USA.
| | - Royce Johnson
- Department of Medicine, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, USA
| | - Maria I Garcia-Lloret
- Department of Pediatrics, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, USA
| | - Arash Heidari
- Department of Medicine, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, USA
| | - Manish J Butte
- Department of Pediatrics, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, USA; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, USA
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27
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Van Dyke MCC, Thompson GR, Galgiani JN, Barker BM. The Rise of Coccidioides: Forces Against the Dust Devil Unleashed. Front Immunol 2019; 10:2188. [PMID: 31572393 PMCID: PMC6749157 DOI: 10.3389/fimmu.2019.02188] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Coccidioidomycosis (Valley fever) is a fungal disease caused by the inhalation of Coccidioides posadasii or C. immitis. This neglected disease occurs in the desert areas of the western United States, most notably in California and Arizona, where infections continue to rise. Clinically, coccidioidomycosis ranges from asymptomatic to severe pulmonary disease and can disseminate to the brain, skin, bones, and elsewhere. New estimates suggest as many as 350,000 new cases of coccidioidomycosis occur in the United States each year. Thus, there is an urgent need for the development of a vaccine and new therapeutic drugs against Coccidioides infection. In this review, we discuss the battle against Coccidioides including the development of potential vaccines, the quest for new therapeutic drugs, and our current understanding of the protective host immune response to Coccidioides infection.
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Affiliation(s)
| | - George R Thompson
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of California Davis Medical Center, Sacramento, CA, United States
| | - John N Galgiani
- Valley Fever Center for Excellence, Department of Medicine, University of Arizona College of Medicine-Tucson, Tucson, AZ, United States
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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28
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Denham ST, Wambaugh MA, Brown JCS. How Environmental Fungi Cause a Range of Clinical Outcomes in Susceptible Hosts. J Mol Biol 2019; 431:2982-3009. [PMID: 31078554 PMCID: PMC6646061 DOI: 10.1016/j.jmb.2019.05.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/18/2019] [Accepted: 05/01/2019] [Indexed: 12/11/2022]
Abstract
Environmental fungi are globally ubiquitous and human exposure is near universal. However, relatively few fungal species are capable of infecting humans, and among fungi, few exposure events lead to severe systemic infections. Systemic infections have mortality rates of up to 90%, cost the US healthcare system $7.2 billion annually, and are typically associated with immunocompromised patients. Despite this reputation, exposure to environmental fungi results in a range of outcomes, from asymptomatic latent infections to severe systemic infection. Here we discuss different exposure outcomes for five major fungal pathogens: Aspergillus, Blastomyces, Coccidioides, Cryptococcus, and Histoplasma species. These fungi include a mold, a budding yeast, and thermal dimorphic fungi. All of these species must adapt to dramatically changing environments over the course of disease. These dynamic environments include the human lung, which is the first exposure site for these organisms. Fungi must defend themselves against host immune cells while germinating and growing, which risks further exposing microbe-associated molecular patterns to the host. We discuss immune evasion strategies during early infection, from disruption of host immune cells to major changes in fungal cell morphology.
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Affiliation(s)
- Steven T Denham
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Morgan A Wambaugh
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Jessica C S Brown
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
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29
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Hung CY, Hsu AP, Holland SM, Fierer J. A review of innate and adaptive immunity to coccidioidomycosis. Med Mycol 2019; 57:S85-S92. [PMID: 30690602 DOI: 10.1093/mmy/myy146] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/28/2018] [Indexed: 12/16/2022] Open
Abstract
Coccidioidomycosis is a human fungal disease cause by inhalation of aerosol spores produced by Coccidioides posadasii or Coccidioides immitis. This disease is a common cause of community-acquired pneumonia in the endemic areas of the Southwestern United States. It also can present as a life-threatening disease as the fungal cells disseminate to skin, bone, and central nervous system. The outcome of coccidioidomycosis is largely determined by the nature of host immune response to the infection. Escalation of symptomatic infections and increased cost of long-term antifungal treatment warrant a concerted effort to better understand the innate and adaptive immune responses and the genetics associated with coccidioidomycosis susceptibility. This knowledge can be harnessed for development of a human vaccine against Coccidioides and advance clinic management of this disease. This review discusses recently reported studies on innate and adaptive immunity to Coccidioides infection, Mendelian susceptibility to disseminated disease and progress toward a human vaccine against this formidable disease.
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Affiliation(s)
- Chiung-Yu Hung
- Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas, San Antonio, Texas, USA
| | - Amy P Hsu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Joshua Fierer
- Infectious Diseases Section, VA Healthcare San Diego, California, USA.,Department of Medicine, Division of Infectious Diseases, University of California San Diego School of Medicine, San Diego, California, USA
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30
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Dendritic cell-based immunization induces Coccidioides Ag2/PRA-specific immune response. Vaccine 2019; 37:1685-1691. [PMID: 30795939 DOI: 10.1016/j.vaccine.2019.01.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 12/08/2018] [Accepted: 01/08/2019] [Indexed: 12/12/2022]
Abstract
Valley Fever, or coccidioidomycosis, is caused by a soil-borne, highly virulent fungal pathogen, Coccidioides spp. Infection with Coccidioides can be life-threatening. Since an effective treatment is not available and the T cell-mediated immune response is protective, vaccine development is of interest. In this study, a primary dendritic cell (DC)-vaccine was evaluated for its ability to stimulate Coccidioides antigen-specific immune response in an extremely susceptible BALB/c mouse model. The DC-vaccine (Ag2-DC) was prepared by non-virally transfecting the primary bone marrow-derived DCs with a plasmid DNA encoding Ag2/PRA (protective epitope of Coccidioides). Mice were intranasally immunized with Ag2-DC on days 2 and 10. Immunized mice were necropsied on days 8, 32, and 44. Major organs and blood samples were harvested. The most common indicators of injury (protein, lactate, and albumin), Ag/PRA-specific cytokine-secreting cells, and IgG and its isotypes were determined by biochemical and immunologic assays, respectively. No signs of sickness were noted. Similarly, no significant changes were observed in the levels of total lung protein, lactate, and albumin, in immunized mice compared with healthy control mice. Interferon (IFN-γ), and interleukin (IL)-4 and IL-17 cytokine-secreting cells were observed in lung and lymph nodes upon Ag2-DC immunization. Our results showed that the levels of serum IgG and its isotypes were increased in Ag2-DC-immunized mice. This report provides evidence of DC immunization-stimulated Ag2/PRA-specific immune responses.
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31
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Park HY, Yoon HK, Kim JY, Park SR. Heat-Killed Saccharomyces cerevisiae, A Dectin-1 Agonist, Selectively Induces IgG4 Production by Human B Cells. Immune Netw 2019; 18:e46. [PMID: 30619632 PMCID: PMC6312892 DOI: 10.4110/in.2018.18.e46] [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] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 12/02/2018] [Accepted: 12/14/2018] [Indexed: 12/24/2022] Open
Abstract
Dectin-1 is a major receptor that recognizes fungal cell wall β-glucan. We previously reported that heat-killed Saccharomyces cerevisiae (HKSC), a Dectin-1 agonist, selectively induces IgG1 class switching in mouse B cells. Dectin-1 is also expressed on human B cells; however, Dectin-1 function in human B cells remains unknown. This study aimed to investigate the direct effect of in vitro stimulation using HKSC on Ig class switching in human B cells. HKSC selectively induced the expression of germline γ4 transcripts (GLTγ4) by human B cell line 2E2, and HKSC significantly augmented GLTγ4 promoter activity. Moreover, HKSC selectively enhanced GLTγ4 expression and IgG4 production by anti-CD40-activated human tonsillar resting B cells. Thus, these results suggest that Dectin-1 maybe involved in selective IgG4 class switching by human B cells.
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Affiliation(s)
- Ha-Yan Park
- Department of Microbiology, College of Medicine, Konyang University, Daejeon 35365, Korea
| | - Hee-Kyung Yoon
- Department of Microbiology, College of Medicine, Konyang University, Daejeon 35365, Korea
| | - Jong-Yeup Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Konyang University, Daejeon 35365, Korea
| | - Seok-Rae Park
- Department of Microbiology, College of Medicine, Konyang University, Daejeon 35365, Korea.,Priority Research Center, Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon 35365, Korea
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32
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Goyal S, Castrillón-Betancur JC, Klaile E, Slevogt H. The Interaction of Human Pathogenic Fungi With C-Type Lectin Receptors. Front Immunol 2018; 9:1261. [PMID: 29915598 PMCID: PMC5994417 DOI: 10.3389/fimmu.2018.01261] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/18/2018] [Indexed: 01/19/2023] Open
Abstract
Fungi, usually present as commensals, are a major cause of opportunistic infections in immunocompromised patients. Such infections, if not diagnosed or treated properly, can prove fatal. However, in most cases healthy individuals are able to avert the fungal attacks by mounting proper antifungal immune responses. Among the pattern recognition receptors (PRRs), C-type lectin receptors (CLRs) are the major players in antifungal immunity. CLRs can recognize carbohydrate ligands, such as β-glucans and mannans, which are mainly found on fungal cell surfaces. They induce proinflammatory immune reactions, including phagocytosis, oxidative burst, cytokine, and chemokine production from innate effector cells, as well as activation of adaptive immunity via Th17 responses. CLRs such as Dectin-1, Dectin-2, Mincle, mannose receptor (MR), and DC-SIGN can recognize many disease-causing fungi and also collaborate with each other as well as other PRRs in mounting a fungi-specific immune response. Mutations in these receptors affect the host response and have been linked to a higher risk in contracting fungal infections. This review focuses on how CLRs on various immune cells orchestrate the antifungal response and on the contribution of single nucleotide polymorphisms in these receptors toward the risk of developing such infections.
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Affiliation(s)
- Surabhi Goyal
- Institute for Microbiology and Hygiene, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Septomics Research Center, Jena University Hospital, Jena, Germany
| | - Juan Camilo Castrillón-Betancur
- Septomics Research Center, Jena University Hospital, Jena, Germany.,International Leibniz Research School for Microbial and Biomolecular Interactions, Leibniz Institute for Natural Product Research and Infection Biology/Hans Knöll Institute, Jena, Germany
| | - Esther Klaile
- Septomics Research Center, Jena University Hospital, Jena, Germany
| | - Hortense Slevogt
- Septomics Research Center, Jena University Hospital, Jena, Germany
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33
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Myeloid Differentiation Factor 88 and Interleukin-1R1 Signaling Contribute to Resistance to Coccidioides immitis. Infect Immun 2018; 86:IAI.00028-18. [PMID: 29610256 DOI: 10.1128/iai.00028-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 03/26/2018] [Indexed: 12/21/2022] Open
Abstract
Rodents are a natural host for the dimorphic pathogenic fungi Coccidioides immitis and Coccidioides posadasii, and mice are a good model for human infection. Humans and rodents both express Dectin-1 and Toll-like receptor 2 (TLR2) on myeloid cells, and those receptors collaborate to maximize the cytokine/chemokine responses to spherules (the tissue form of the fungi) and to formalin-killed spherules (FKS). We showed that Dectin-1 is necessary for resistance to pulmonary coccidioidomycosis, but the importance of TLR2 in vivo is uncertain. Myeloid differentiation factor 88 (MyD88) is the adapter protein for TLR2 and -4, interleukin-1R1 (IL-1R1), and IL-18R1. MyD88/TRIF-/- and MyD88-/- mice were equally susceptible to C. immitis infection, in contrast to C57BL/6 (B6) controls. Of the four surface receptors, only IL-1R1 was required for resistance to C. immitis, partially explaining the susceptibility of MyD88-/- mice. We also found that FKS stimulated production of IL-1Ra by bone marrow-derived dendritic cells (BMDCs), independent of MyD88 and Dectin-1. There also was a very high concentration of IL-1Ra in the lungs of infected B6 mice, supporting the potential importance of this regulatory IL-1 family protein in the largely ineffective response of B6 mice to coccidioidomycosis. These results suggest that IL-1R1 signaling is important for defense against C. immitis infection.
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34
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Kalia N, Kaur M, Sharma S, Singh J. A Comprehensive in Silico Analysis of Regulatory SNPs of Human CLEC7A Gene and Its Validation as Genotypic and Phenotypic Disease Marker in Recurrent Vulvovaginal Infections. Front Cell Infect Microbiol 2018; 8:65. [PMID: 29616193 PMCID: PMC5869923 DOI: 10.3389/fcimb.2018.00065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 02/26/2018] [Indexed: 01/25/2023] Open
Abstract
Recurrent Vulvovaginal infections (RVVI) are the commonly reported microbiological syndrome affecting millions of women globally. Various molecules of innate immune system are instrumental in clearance of these microbial pathogens, thus suggested as one of the most important contributing factor in determining the disease outcome. Dendritic cell-associated C-type lectin-1 (Dectin-1) is an important molecule of innate immunity that is primarily known for its role in antifungal defenses. However, role of dectin-1 in recognition of other pathogens is also documented. The intracellular expression of dectin-1 was shown to be up-regulated by Mannose Binding Lectin (MBL)-mediated opsonophagocytosis of pathogens. Dectin-1 is encoded by CLEC7A, postulated to be a candidate gene in modulating risk of developing RVVI. In this study, we identified CLEC7A causal variants using in silico analysis. To assess their impact on susceptibility to RVVI, these causal variants along with serum dectin-1 levels (sDectin-1) were investigated using polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) and Enzyme Linked Immnosorbent Assay (ELISA) respectively, under a case-control design. Furthermore, effect of these polymorphisms was also assessed on sMBL levels. In silico analysis revealed 9 putative functional conserved SNPs of CLEC7A. Association analysis revealed a significantly lower risk of developing RVVI and its types in carriers of CLEC7A rs3901533 G allele and its homozygous genotypes (p < 0.05). The heterozygous genotype was associated with significant protection against RVVI (p = 0.004). Haplotypes GGG and GTA showed significant protection against RVVI (p < 0.0001; p = 0.0003), Bacterial Vaginosis (p = 0.03; p = 0.002), Vulvovaginal Candidiasis (p = 0.03; p = 0.01) and Mixed Infections (p = 0.007; p = 0.04). Mean sDectin-1 levels were significantly high in RVVI and its types compared to controls (p < 0.05). Further, genotype-phenotype stratification showed significant differences within/between cases groups and controls. The CLEC7A rs3901533 polymorphism was also found to be associated with sMBL levels. The present study contributed novel insights into the role of dectin-1 in RVVI. CLEC7A rs3901533 polymorphism and high sDectin-1 levels along with low sMBL levels were found to be associated with RVVI susceptibility. Thus, screening of women with RVVI for these novel associations may lead to better diagnosis and treatment. Also genotyping method used in this study constitutes a simple and reliable assay, which can be confidently, used as a cheaper alternative for genotyping these variants in clinical settings. Finally, new restorative markers for other infectious diseases might be found by exploring nine functionally identified CLEC7A SNPs.
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Affiliation(s)
- Namarta Kalia
- Department of Molecular Biology & Biochemistry, Guru Nanak Dev University, Amritsar, India
| | - Manpreet Kaur
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, India
| | - Sujata Sharma
- Department of Gynaecology & Obstetrics, Bebe Nanki Mother and Child Care Centre, Government Medical College, Amritsar, India
| | - Jatinder Singh
- Department of Molecular Biology & Biochemistry, Guru Nanak Dev University, Amritsar, India
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35
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Kirkland TN, Fierer J. Coccidioides immitis and posadasii; A review of their biology, genomics, pathogenesis, and host immunity. Virulence 2018; 9:1426-1435. [PMID: 30179067 PMCID: PMC6141143 DOI: 10.1080/21505594.2018.1509667] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/31/2018] [Indexed: 11/24/2022] Open
Abstract
Coccidioides immitis and C. posadasii are two highly pathogenic dimorphic fungal species that are endemic in the arid areas of the new world, including the region from west Texas to southern and central California in the USA that cause coccidioidomycosis (also known as Valley Fever). In highly endemic regions such as southern Arizona, up to 50% of long term residents have been infected. New information about fungal population genetics, ecology, epidemiology, and host-pathogen interactions is becoming available. However, our understanding of some aspects of coccidioidomycosis is still incomplete, including the extent of genetic variability of the fungus, the genes involved in virulence, and how the changes in gene expression during the organism's dimorphic life cycle are related to the transformation from a free-living mold to a parasitic spherule. Unfortunately, efforts to develop an effective subunit vaccine have not yet been productive, although two potential live fungus vaccines have been developed.
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Affiliation(s)
- Theo N. Kirkland
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Joshua Fierer
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, San Diego, CA, USA
- VA Healthcare San Diego, San Diego, CA, USA
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36
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Sinha M, Lowell CA. Immune Defense Protein Expression in Highly Purified Mouse Lung Epithelial Cells. Am J Respir Cell Mol Biol 2017; 54:802-13. [PMID: 26574781 DOI: 10.1165/rcmb.2015-0171oc] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Lung epithelial cells play critical roles in initiating and modulating immune responses during pulmonary infection or injury. To better understand the spectrum of immune response-related proteins present in lung epithelial cells, we developed an improved method of isolating highly pure primary murine alveolar type (AT) II cells and murine tracheal epithelial cells (mTECs) using negative selection for a variety of lineage markers and positive selection for epithelial cell adhesion molecule (EpCAM), a pan-epithelial cell marker. This method yielded 2-3 × 10(6) ATII cells/mouse lung and 1-2 × 10(4) mTECs/trachea that were highly pure (>98%) and viable (>98%). Using these preparations, we found that both ATII cells and mTECs expressed the Lyn tyrosine kinase, which is best studied as an inhibitory kinase in hematopoietic cells. However, we found little or no expression of Syk in either ATII cells or mTECs, which is in contrast to earlier published reports. Both cell types expressed C-type lectin receptors, anaphylatoxin receptors, and various Toll-like receptors (TLRs). In addition, stimulation of ATII cells with TLR ligands led to secretion of various cytokines and chemokines. Interestingly, lyn(-/-) ATII cells were hyperresponsive to TLR3 stimulation, suggesting that, as in hematopoietic cells, Lyn might be playing an inhibitory role in ATII cells. In conclusion, the improved isolation method reported here, along with expression profiles of various immune defense proteins, will help refocus investigations of immune-related signaling events in pulmonary epithelium.
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Affiliation(s)
- Meenal Sinha
- Department of Laboratory Medicine and the Program in Immunology, University of California, San Francisco, San Francisco, California
| | - Clifford A Lowell
- Department of Laboratory Medicine and the Program in Immunology, University of California, San Francisco, San Francisco, California
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Immune Response to Coccidioidomycosis and the Development of a Vaccine. Microorganisms 2017; 5:microorganisms5010013. [PMID: 28300772 PMCID: PMC5374390 DOI: 10.3390/microorganisms5010013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 03/03/2017] [Accepted: 03/14/2017] [Indexed: 02/07/2023] Open
Abstract
Coccidioidomycosis is a fungal infection caused by Coccidioides posadasii and Coccidioides immitis. It is estimated that 150,000 new infections occur in the United States each year. The incidence of this infection continues to rise in endemic regions. There is an urgent need for the development of better therapeutic drugs and a vaccine against coccidioidomycosis. This review discusses the features of host innate and adaptive immune responses to Coccidioides infection. The focus is on the recent advances in the immune response and host-pathogen interactions, including the recognition of spherules by the host and defining the signal pathways that guide the development of the adaptive T-cell response to Coccidioides infection. Also discussed is an update on progress in developing a vaccine against these fungal pathogens.
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Walachowski S, Tabouret G, Foucras G. Triggering Dectin-1-Pathway Alone Is Not Sufficient to Induce Cytokine Production by Murine Macrophages. PLoS One 2016; 11:e0148464. [PMID: 26840954 PMCID: PMC4739705 DOI: 10.1371/journal.pone.0148464] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 01/17/2016] [Indexed: 02/07/2023] Open
Abstract
β-glucans (BG) are abundant polysaccharides of the Saccharomyces cerevisiae cell wall (Sc CW), an industry byproduct. They have immuno-stimulatory properties upon engagement of dectin-1 (Clec7a), their main receptor on particular immune cells, and they actually become of great interest because of their preventive or therapeutic potentials. Zymosan, a crude extract of Sc CW was studied as a prototypic BG, despite its miscellaneous PAMPs content. Here, we examined the response of murine wild type or Clec7a-/- bone marrow-derived macrophages (BMDM) to products with increasing BG content (15, 65 or 75%) and compared their effects with those of other dectin-1 ligands. The enrichment process removed TLR ligands while preserving dectin-1 activity. The most enriched extracts have very low NFκB activity and triggered low amounts of cytokine production in contrast with crude products like zymosan and BG15. Furthermore, MyD88-/- BMDM did not produce TNFα in response to crude Sc CW extracts, whereas their response to BG-enriched extracts was unaffected, suggesting that BG alone are not able to initiate cytokine secretion. Although Sc CW-derived BG stimulated the late and strong expression of Csf2 in a dectin-1-dependent manner, they remain poor inducers of chemokine and cytokine production in murine macrophages.
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Affiliation(s)
- Sarah Walachowski
- Université de Toulouse, INP-ENVT, UMR 1225, IHAP, Toulouse, France
- INRA, UMR1225, IHAP, Toulouse, France
| | - Guillaume Tabouret
- Université de Toulouse, INP-ENVT, UMR 1225, IHAP, Toulouse, France
- INRA, UMR1225, IHAP, Toulouse, France
| | - Gilles Foucras
- Université de Toulouse, INP-ENVT, UMR 1225, IHAP, Toulouse, France
- INRA, UMR1225, IHAP, Toulouse, France
- * E-mail:
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Lee CY, Thompson III GR, Hastey CJ, Hodge GC, Lunetta JM, Pappagianis D, Heinrich V. Coccidioides Endospores and Spherules Draw Strong Chemotactic, Adhesive, and Phagocytic Responses by Individual Human Neutrophils. PLoS One 2015; 10:e0129522. [PMID: 26070210 PMCID: PMC4466529 DOI: 10.1371/journal.pone.0129522] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 05/08/2015] [Indexed: 11/19/2022] Open
Abstract
Coccidioides spp. are dimorphic pathogenic fungi whose parasitic forms cause coccidioidomycosis (Valley fever) in mammalian hosts. We use an innovative interdisciplinary approach to analyze one-on-one encounters between human neutrophils and two forms of Coccidioides posadasii. To examine the mechanisms by which the innate immune system coordinates different stages of the host response to fungal pathogens, we dissect the immune-cell response into chemotaxis, adhesion, and phagocytosis. Our single-cell technique reveals a surprisingly strong response by initially quiescent neutrophils to close encounters with C. posadasii, both from a distance (by complement-mediated chemotaxis) as well as upon contact (by serum-dependent adhesion and phagocytosis). This response closely resembles neutrophil interactions with Candida albicans and zymosan particles, and is significantly stronger than the neutrophil responses to Cryptococcus neoformans, Aspergillus fumigatus, and Rhizopus oryzae under identical conditions. The vigorous in vitro neutrophil response suggests that C. posadasii evades in vivo recognition by neutrophils through suppression of long-range mobilization and recruitment of the immune cells. This observation elucidates an important paradigm of the recognition of microbes, i.e., that intact immunotaxis comprises an intricate spatiotemporal hierarchy of distinct chemotactic processes. Moreover, in contrast to earlier reports, human neutrophils exhibit vigorous chemotaxis toward, and frustrated phagocytosis of, the large spherules of C. posadasii under physiological-like conditions. Finally, neutrophils from healthy donors and patients with chronic coccidioidomycosis display subtle differences in their responses to antibody-coated beads, even though the patient cells appear to interact normally with C. posadasii endospores.
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Affiliation(s)
- Cheng-Yuk Lee
- Department of Biomedical Engineering, University of California Davis, Davis, California, United States of America
| | - George R. Thompson III
- Department of Medical Microbiology and Immunology, Coccidioidomycosis Serology Laboratory, University of California Davis, Davis, California, United States of America
- Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Sacramento, California, United States of America
| | - Christine J. Hastey
- Department of Biomedical Engineering, University of California Davis, Davis, California, United States of America
| | - Gregory C. Hodge
- Department of Medical Microbiology and Immunology, Coccidioidomycosis Serology Laboratory, University of California Davis, Davis, California, United States of America
| | - Jennine M. Lunetta
- Department of Medical Microbiology and Immunology, Coccidioidomycosis Serology Laboratory, University of California Davis, Davis, California, United States of America
| | - Demosthenes Pappagianis
- Department of Medical Microbiology and Immunology, Coccidioidomycosis Serology Laboratory, University of California Davis, Davis, California, United States of America
| | - Volkmar Heinrich
- Department of Biomedical Engineering, University of California Davis, Davis, California, United States of America
- * E-mail:
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Call for a California Coccidioidomycosis Consortium to Face the Top Ten Challenges Posed by a Recalcitrant Regional Disease. Mycopathologia 2014; 179:1-9. [DOI: 10.1007/s11046-014-9816-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 09/17/2014] [Indexed: 10/24/2022]
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Hassan MA, Saeij JPJ. Incorporating alternative splicing and mRNA editing into the genetic analysis of complex traits. Bioessays 2014; 36:1032-40. [PMID: 25171292 DOI: 10.1002/bies.201400079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The nomination of candidate genes underlying complex traits is often focused on genetic variations that alter mRNA abundance or result in non-conservative changes in amino acids. Although inconspicuous in complex trait analysis, genetic variants that affect splicing or RNA editing can also generate proteomic diversity and impact genetic traits. Indeed, it is known that splicing and RNA editing modulate several traits in humans and model organisms. Using high-throughput RNA sequencing (RNA-seq) analysis, it is now possible to integrate the genetics of transcript abundance, alternative splicing (AS) and editing with the analysis of complex traits. We recently demonstrated that both AS and mRNA editing are modulated by genetic and environmental factors, and potentially engender phenotypic diversity in a genetically segregating mouse population. Therefore, the analysis of splicing and RNA editing can expand not only the regulatory landscape of transcriptome and proteome complexity, but also the repertoire of candidate genes for complex traits.
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Affiliation(s)
- Musa A Hassan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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Batbayar S, Lee DH, Kim HW. Immunomodulation of Fungal β-Glucan in Host Defense Signaling by Dectin-1. Biomol Ther (Seoul) 2014; 20:433-45. [PMID: 24009832 PMCID: PMC3762275 DOI: 10.4062/biomolther.2012.20.5.433] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 09/19/2012] [Indexed: 01/23/2023] Open
Abstract
During the course of evolution, animals encountered the harmful effects of fungi, which are strong pathogens. Therefore, they have developed powerful mechanisms to protect themselves against these fungal invaders. β-Glucans are glucose polymers of a linear β(1,3)-glucan backbone with β(1,6)-linked side chains. The immunostimulatory and antitumor activities of β-glucans have been reported; however, their mechanisms have only begun to be elucidated. Fungal and particulate β-glucans, despite their large size, can be taken up by the M cells of Peyer's patches, and interact with macrophages or dendritic cells (DCs) and activate systemic immune responses to overcome the fungal infection. The sampled β-glucans function as pathogen-associated molecular patterns (PAMPs) and are recognized by pattern recognition receptors (PRRs) on innate immune cells. Dectin-1 receptor systems have been incorporated as the PRRs of β-glucans in the innate immune cells of higher animal systems, which function on the front line against fungal infection, and have been exploited in cancer treatments to enhance systemic immune function. Dectin-1 on macrophages and DCs performs dual functions: internalization of β-glucan-containing particles and transmittance of its signals into the nucleus. This review will depict in detail how the physicochemical nature of β-glucan contributes to its immunostimulating effect in hosts and the potential uses of β-glucan by elucidating the dectin-1 signal transduction pathway. The elucidation of β-glucan and its signaling pathway will undoubtedly open a new research area on its potential therapeutic applications, including as immunostimulants for antifungal and anti-cancer regimens.
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Affiliation(s)
- Sainkhuu Batbayar
- Department of Life Sciences, BK21 Cellular Stress Team, University of Seoul, Seoul 130-743, Korea
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Hung CY, Jiménez-Alzate MDP, Gonzalez A, Wüthrich M, Klein BS, Cole GT. Interleukin-1 receptor but not Toll-like receptor 2 is essential for MyD88-dependent Th17 immunity to Coccidioides infection. Infect Immun 2014; 82:2106-14. [PMID: 24614655 PMCID: PMC3993447 DOI: 10.1128/iai.01579-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 03/01/2014] [Indexed: 12/13/2022] Open
Abstract
Interleukin-17A (IL-17A)-producing CD4(+) T helper (Th17) cells have been shown to be essential for defense against pulmonary infection with Coccidioides species. However, we have just begun to identify the required pattern recognition receptors and understand the signal pathways that lead to Th17 cell activation after fungal infection. We previously reported that Card9(-/-) mice vaccinated with formalin-killed spherules failed to acquire resistance to Coccidioides infection. Here, we report that both MyD88(-/-) and Card9(-/-) mice immunized with a live, attenuated vaccine also fail to acquire protective immunity to this respiratory disease. Like Card9(-/-) mice, vaccinated MyD88(-/-) mice revealed a significant reduction in numbers of both Th17 and Th1 cells in their lungs after Coccidioides infection. Both Toll-like receptor 2 (TLR2) and IL-1 receptor type 1 (IL-1r1) upstream of MyD88 have been implicated in Th17 cell differentiation. Surprisingly, vaccinated TLR2(-/-) and wild-type (WT) mice showed similar outcomes after pulmonary infection with Coccidioides, while vaccinated IL-1r1(-/-) mice revealed a significant reduction in the number of Th17 cells in their infected lungs compared to WT mice. Thus, activation of both IL-1r1/MyD88- and Card9-mediated Th17 immunity is essential for protection against Coccidioides infection. Our data also reveal that the numbers of Th17 cells were reduced in IL-1r1(-/-) mice to a lesser extent than in MyD88(-/-) mice, raising the possibility that other TLRs are involved in MyD88-dependent Th17 immunity to coccidioidomycosis. An antimicrobial action of Th17 cells is to promote early recruitment of neutrophils to infection sites. Our data revealed that neutrophils are required for vaccine immunity to this respiratory disease.
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Affiliation(s)
- Chiung-Yu Hung
- Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas, San Antonio, Texas, USA
| | - María del Pilar Jiménez-Alzate
- Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas, San Antonio, Texas, USA
| | - Angel Gonzalez
- Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas, San Antonio, Texas, USA
| | - Marcel Wüthrich
- Department of Pediatrics, University of Wisconsin Medical School, University of Wisconsin Hospital and Clinics, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, USA
| | - Bruce S. Klein
- Department of Pediatrics, University of Wisconsin Medical School, University of Wisconsin Hospital and Clinics, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, USA
- Department of Internal Medicine, University of Wisconsin Medical School, University of Wisconsin Hospital and Clinics, Madison, Wisconsin, USA
| | - Garry T. Cole
- Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas, San Antonio, Texas, USA
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Neither dectin-2 nor the mannose receptor is required for resistance to Coccidioides immitis in mice. Infect Immun 2013; 82:1147-56. [PMID: 24379281 DOI: 10.1128/iai.01355-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We investigated the roles of the mannose receptor (MR) and Dectin-2 in resistance to pulmonary coccidioidomycosis in C57BL/6 (B6) mice and in the interaction of myeloid cells with spherules, using B6 mice with targeted mutations in Mrc1 and Clec4n. Spherules are the tissue form of Coccidioides, and we determined that the MR on bone marrow-derived dendritic cells (BMDC) was important for recognition of spherules (formalin-killed spherules [FKS]) and for secretion of interleukin 10 (IL-10) and proinflammatory cytokines in response to FKS by both elicited macrophages and BMDC. Infected MR knockout (KO) mice produced more IL-10 in their lungs than did B6 mice, and MR KO mice also made more protective Th-17 cytokines. In contrast to the MR, Dectin-2 was not required for recognition of FKS by BMDC or for the production of cytokines by BMDC in response to FKS. However, Dectin-2 KO was required for stimulation of elicited peritoneal macrophages. Despite that, lung cytokine levels were not significantly different in Dectin-2 KO mice and B6 mice 14 days after infection, except for IL-1β, which was higher in Dectin-2 KO lungs. Although both Dectin-2(-/-) and MR(-/-) myeloid cells had reduced proinflammatory cytokine responses to FKS in vitro, neither MR nor Dectin-2 deficiency reduced the resistance of B6 mice to pulmonary coccidioidomycosis.
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Hassan MA, Butty V, Jensen KDC, Saeij JPJ. The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages. Genome Res 2013; 24:377-89. [PMID: 24249727 PMCID: PMC3941103 DOI: 10.1101/gr.166033.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Alternative splicing and mRNA editing are known to contribute to transcriptome diversity. Although alternative splicing is pervasive and contributes to a variety of pathologies, including cancer, the genetic context for individual differences in isoform usage is still evolving. Similarly, although mRNA editing is ubiquitous and associated with important biological processes such as intracellular viral replication and cancer development, individual variations in mRNA editing and the genetic transmissibility of mRNA editing are equivocal. Here, we have used linkage analysis to show that both mRNA editing and alternative splicing are regulated by the macrophage genetic background and environmental cues. We show that distinct loci, potentially harboring variable splice factors, regulate the splicing of multiple transcripts. Additionally, we show that individual genetic variability at the Apobec1 locus results in differential rates of C-to-U(T) editing in murine macrophages; with mouse strains expressing mostly a truncated alternative transcript isoform of Apobec1 exhibiting lower rates of editing. As a proof of concept, we have used linkage analysis to identify 36 high-confidence novel edited sites. These results provide a novel and complementary method that can be used to identify C-to-U editing sites in individuals segregating at specific loci and show that, beyond DNA sequence and structural changes, differential isoform usage and mRNA editing can contribute to intra-species genomic and phenotypic diversity.
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Affiliation(s)
- Musa A Hassan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Abstract
The opportunistic pathogen Pneumocystis jirovecii is a significant cause of disease in HIV-infected patients and others with immunosuppressive conditions. Pneumocystis can also cause complications in treatment following antiretroviral therapy or reversal of immunosuppressive therapy, as the newly reconstituted immune system can develop a pathological inflammatory response to remaining antigens or a previously undetected infection. To target β-(1,3)-glucan, a structural component of the Pneumocystis cell wall with immune-stimulating properties, we have developed immunoadhesins consisting of the carbohydrate binding domain of Dectin-1 fused to the Fc regions of the 4 subtypes of murine IgG (mIgG). These immunoadhesins bind β-glucan with high affinity, and precoating the surface of zymosan with Dectin-1:Fc can reduce cytokine production by macrophages in an in vitro stimulation assay. All Dectin-1:Fc variants showed specificity of binding to the asci of Pneumocystis murina, but effector activity of the fusion molecules varied depending on Fc subtype. Dectin-1:mIgG2a Fc was able to reduce the viability of P. murina in culture through a complement-dependent mechanism, whereas previous studies have shown the mIgG1 Fc fusion to increase macrophage-dependent killing. In an in vivo challenge model, systemic expression of Dectin-1:mIgG1 Fc significantly reduced ascus burden in the lung. When administered postinfection in a model of immune reconstitution inflammatory syndrome (IRIS), both Dectin-1:mIgG1 and Dectin-1:mIgG2a Fc reduced hypoxemia despite minimal effects on fungal burden in the lung. Taken together, these data indicate that molecules targeting β-glucan may provide a mechanism for treatment of fungal infection and for modulation of the inflammatory response to Pneumocystis and other pathogens.
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Marakalala MJ, Vautier S, Potrykus J, Walker LA, Shepardson KM, Hopke A, Mora-Montes HM, Kerrigan A, Netea MG, Murray GI, MacCallum DM, Wheeler R, Munro CA, Gow NAR, Cramer RA, Brown AJP, Brown GD. Differential adaptation of Candida albicans in vivo modulates immune recognition by dectin-1. PLoS Pathog 2013; 9:e1003315. [PMID: 23637604 PMCID: PMC3630191 DOI: 10.1371/journal.ppat.1003315] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 03/05/2013] [Indexed: 12/23/2022] Open
Abstract
The β-glucan receptor Dectin-1 is a member of the C-type lectin family and functions as an innate pattern recognition receptor in antifungal immunity. In both mouse and man, Dectin-1 has been found to play an essential role in controlling infections with Candida albicans, a normally commensal fungus in man which can cause superficial mucocutaneous infections as well as life-threatening invasive diseases. Here, using in vivo models of infection, we show that the requirement for Dectin-1 in the control of systemic Candida albicans infections is fungal strain-specific; a phenotype that only becomes apparent during infection and cannot be recapitulated in vitro. Transcript analysis revealed that this differential requirement for Dectin-1 is due to variable adaptation of C. albicans strains in vivo, and that this results in substantial differences in the composition and nature of their cell walls. In particular, we established that differences in the levels of cell-wall chitin influence the role of Dectin-1, and that these effects can be modulated by antifungal drug treatment. Our results therefore provide substantial new insights into the interaction between C. albicans and the immune system and have significant implications for our understanding of susceptibility and treatment of human infections with this pathogen.
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Affiliation(s)
- Mohlopheni J. Marakalala
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Simon Vautier
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Joanna Potrykus
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Louise A. Walker
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Kelly M. Shepardson
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Alex Hopke
- Molecular and Biomedical Sciences, University of Maine, Orono, Maine, United States of America
| | - Hector M. Mora-Montes
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Ann Kerrigan
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Mihai G. Netea
- Nijmegen Institute for Infection, Inflammation and Immunity (N4i), and University Medical Centre Nijmegen, Nijmegen, The Netherlands
| | - Graeme I. Murray
- Pathology, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Donna M. MacCallum
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Robert Wheeler
- Molecular and Biomedical Sciences, University of Maine, Orono, Maine, United States of America
| | - Carol A. Munro
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Neil A. R. Gow
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Robert A. Cramer
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Alistair J. P. Brown
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Gordon D. Brown
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
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Anti-inflammatory and Immunomodulatory Effect of an Extract of Coccidioides posadasii in Experimental Arthritis. Mycopathologia 2013; 175:193-206. [DOI: 10.1007/s11046-013-9621-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 01/21/2013] [Indexed: 02/03/2023]
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Abstract
We assessed the role of Dectin-1 in the immune response to the pathogenic fungus Coccidioides, both in vitro and in vivo, using mice with a targeted mutation in Clec7a. Elicited peritoneal macrophages responded to formalin-killed spherules (FKS) and alkali-treated FKS by secreting proinflammatory cytokines in a Dectin-1- and β-glucan-dependent manner. The responses of bone marrow-derived dendritic cells (BMDC) to the same stimulants were more complex; interleukin 1β (IL-1β) and tumor necrosis factor alpha (TNF-α) secretion was independent of Dectin-1, while IL-6, IL-10, and granulocyte-macrophage colony-stimulating factor (GM-CSF) were largely but not entirely dependent on Dectin-1. After intranasal infection, Dectin-1(-/-) mice had lower concentrations of IL-12p70, gamma interferon (IFN-γ), IL-1β, and the Th17 cytokines IL-22, IL-23, and 17A in the lung lavage fluid, which may explain why they were significantly more susceptible to pulmonary coccidioidomycosis two weeks after infection. The Dectin-1 mutation was even more deleterious in (B6 × DBA/2)F(2) mice, which are more resistant to coccidioidomycosis than B6 mice by virtue of protective genes from DBA/2, a genetically resistant strain. We also found that two susceptible strains of mice (B6 and BALB/c) expressed much less Dectin-1 in their lungs than did resistant DBA/2 mice. We conclude that Dectin-1 is necessary for resistance to Coccidioides immitis, that Dectin-1 promotes both Th1 and Th17 protective immune responses to this infection, and that there is a correlation between expression of Dectin-1 by the inflammatory infiltrate and resistance to coccidioidomycosis. IMPORTANCE Coccidioidomycosis is a fungal infection endemic in the southwestern United States and neighboring Mexico, causing ~150,000 lung infections in people and resulting in ~17,000 hospitalizations annually in California alone. Very little is known about innate immunity to this fungus. This paper shows that Dectin-1, the primary β-glucan receptor on myeloid cells, is required for resistance to this pathogen. Dectin-1 is part of the innate immune system, and it is needed to direct the acquired immune response toward into a pathway that will lead to macrophage activation. Lungs from infected mice lacking Dectin-1 had lower concentrations of Th1 and Th17 cytokines, two cytokine pathways that are very important for acquired T cell immunity to Coccidioides spp. This is the first demonstration that Dectin-1 is required for host resistance to a dimorphic, primary pathogenic fungus.
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Hassan MA, Melo MB, Haas B, Jensen KDC, Saeij JPJ. De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs. BMC Genomics 2012; 13:696. [PMID: 23231500 PMCID: PMC3543268 DOI: 10.1186/1471-2164-13-696] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 12/04/2012] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, Toxoplasma gondii, are based on computer model predictions without cDNA sequence verification. Additionally, the nature and extent of alternative splicing in Toxoplasma gondii is unknown. In this study, we used de novo transcript assembly and the published type II (ME49) genomic sequence to quantify the extent of alternative splicing in Toxoplasma and to improve the current Toxoplasma gene annotations. RESULTS We used high-throughput RNA-sequencing data to assemble full-length transcripts, independently of a reference genome, followed by gene annotation based on the ME49 genome. We assembled 13,533 transcripts overlapping with known ME49 genes in ToxoDB and then used this set to; a) improve the annotation in the untranslated regions of ToxoDB genes, b) identify novel exons within protein-coding ToxoDB genes, and c) report on 50 previously unidentified alternatively spliced transcripts. Additionally, we assembled a set of 2,930 transcripts not overlapping with any known ME49 genes in ToxoDB. From this set, we have identified 118 new ME49 genes, 18 novel Toxoplasma genes, and putative non-coding RNAs. CONCLUSION RNA-seq data and de novo transcript assembly provide a robust way to update incompletely annotated genomes, like the Toxoplasma genome. We have used RNA-seq to improve the annotation of several Toxoplasma genes, identify alternatively spliced genes, novel genes, novel exons, and putative non-coding RNAs.
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Affiliation(s)
- Musa A Hassan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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