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Liu X, Zhao Q, He X, Min J, Yao RSY, Chen Z, Ma J, Hu W, Huang J, Wan H, Guo Y, Zhou M. Clinical characteristics and microbial signatures in the lower airways of diabetic and nondiabetic patients with pneumonia. J Thorac Dis 2024; 16:5262-5273. [PMID: 39268134 PMCID: PMC11388247 DOI: 10.21037/jtd-24-490] [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: 03/25/2024] [Accepted: 07/12/2024] [Indexed: 09/15/2024]
Abstract
Background The microbial signatures in diabetes with pneumonia and the risk factors of severe pneumonia (SP) in diabetic patients are not clear. Our study explored microbial signatures and the association between clinical characteristics and SP then constructed a risk model to find effective biomarkers for predicting pneumonia severity. Methods Our study was conducted among 273 patients with pneumonia diagnosed and treated in our hospital from January 2018 to May 2021. Bronchoalveolar lavage fluid (BALF) samples and clinical data were collected. Metagenomic sequencing was applied after extracting the DNA from samples. Appropriate statistical methods were used to compare the microbial signatures and clinical characteristics in patients with or without diabetes mellitus (DM). Results In total, sixty-one pneumonia patients with diabetes and 212 pneumonia patients without diabetes were included. Sixty-six differential microorganisms were found to be associated with SP in diabetic patients. Some microbes correlated with clinical indicators of SP. The prediction model for SP was established and the receiver operating characteristic (ROC) curve demonstrated its accuracy, with the sensitivity and specificity of 0.82 and 0.91, respectively. Conclusions Some microorganisms affect the severity of pneumonia. We identified the microbial signatures in the lower airways and the association between clinical characteristics and SP. The predictive model was more accurate in predicting SP by combining microbiological indicators and clinical characteristics, which might be beneficial to the early identification and management of patients with SP.
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Affiliation(s)
- Xuefei Liu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qianqian Zhao
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | | | | | | - Jinmin Ma
- PathoGenesis, BGI Genomics, Shenzhen, China
| | - Weiting Hu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingwen Huang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huanying Wan
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Guo
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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2
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Chen X. DISSyphilis and the risk of HIV infection: A Mendelian randomization study. AIDS Res Hum Retroviruses 2024. [PMID: 39086230 DOI: 10.1089/aid.2024.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024] Open
Abstract
OBJECTION To assess the causal effect of syphilis on HIV infection by Mendelian randomization analysis. METHODS The data of syphilis and HIV infection were obtained from genome-wide association studies, Mendelian randomization analyses were conducted using methods such as weighted median, MR Egger, and inverse variance to evaluate the causal relationship between syphilis and HIV infection. Gene expression data of persons living with HIV (PLWH) and single-cell RNA sequencing profiles were obtained from the GEO database. Analysis involved the identification of key molecules and relevant signaling pathways. RESULTS MR analysis showed a significant causal relationship between syphilis and HIV infection (WM, OR: 1.098, 95%CI: 1.033-1.217, P = 0.003; IVW, OR: 1.095, 95%CI: 1.048-1.145, P < 0.001). We discovered that rs138697742, a genetic variant related to the RPAIN gene, is associated with HIV infection, and influences the expression of RPAIN, possibly contributing to the progression of the disease. Moreover, single-cell data analysis revealed the cellular communication patterns within PLWH, with monocytes appearing to play a crucial role. CONCLUSION In summary, our study reveals a direct causal relationship between syphilis and HIV infection. Additionally, the upregulation of RPAIN gene expression resulting from genetic mutations may serve as a key factor in promoting the progression of HIV infection. Targeting the RPAIN/GALECTIN merges as a promising novel therapeutic target for managing HIV infection.
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Affiliation(s)
- Xinye Chen
- Shanghai Licheng Bio-Technique Co Ltd, Lane 2999, Hutai Road, Baoshan District, Shanghai, China, 201900;
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3
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Nguyen THO, Rowntree LC, Chua BY, Thwaites RS, Kedzierska K. Defining the balance between optimal immunity and immunopathology in influenza virus infection. Nat Rev Immunol 2024:10.1038/s41577-024-01029-1. [PMID: 38698083 DOI: 10.1038/s41577-024-01029-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2024] [Indexed: 05/05/2024]
Abstract
Influenza A viruses remain a global threat to human health, with continued pandemic potential. In this Review, we discuss our current understanding of the optimal immune responses that drive recovery from influenza virus infection, highlighting the fine balance between protective immune mechanisms and detrimental immunopathology. We describe the contribution of innate and adaptive immune cells, inflammatory modulators and antibodies to influenza virus-specific immunity, inflammation and immunopathology. We highlight recent human influenza virus challenge studies that advance our understanding of susceptibility to influenza and determinants of symptomatic disease. We also describe studies of influenza virus-specific immunity in high-risk groups following infection and vaccination that inform the design of future vaccines to promote optimal antiviral immunity, particularly in vulnerable populations. Finally, we draw on lessons from the COVID-19 pandemic to refocus our attention to the ever-changing, highly mutable influenza A virus, predicted to cause future global pandemics.
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Affiliation(s)
- Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Brendon Y Chua
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
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Yang Z, Zhou J, Su N, Zhang Z, Chen J, Liu P, Ling P. Insights into the defensive roles of lncRNAs during Mycoplasma pneumoniae infection. Front Microbiol 2024; 15:1330660. [PMID: 38585701 PMCID: PMC10995346 DOI: 10.3389/fmicb.2024.1330660] [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: 11/21/2023] [Accepted: 02/27/2024] [Indexed: 04/09/2024] Open
Abstract
Mycoplasma pneumoniae causes respiratory tract infections, affecting both children and adults, with varying degrees of severity ranging from mild to life-threatening. In recent years, a new class of regulatory RNAs called long non-coding RNAs (lncRNAs) has been discovered to play crucial roles in regulating gene expression in the host. Research on lncRNAs has greatly expanded our understanding of cellular functions involving RNAs, and it has significantly increased the range of functions of lncRNAs. In lung cancer, transcripts associated with lncRNAs have been identified as regulators of airway and lung inflammation in a process involving protein complexes. An excessive immune response and antibacterial immunity are closely linked to the pathogenesis of M. pneumoniae. The relationship between lncRNAs and M. pneumoniae infection largely involves lncRNAs that participate in antibacterial immunity. This comprehensive review aimed to examine the dysregulation of lncRNAs during M. pneumoniae infection, highlighting the latest advancements in our understanding of the biological functions and molecular mechanisms of lncRNAs in the context of M. pneumoniae infection and indicating avenues for investigating lncRNAs-related therapeutic targets.
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Affiliation(s)
- Zhujun Yang
- Department of Critical Care Medicine, The Central Hospital of Shaoyang City and Affiliated Shaoyang Hospital, Hengyang Medical College, University of South China, Shaoyang, China
- Institute of Pathogenic Biology, Basic Medical School, Hengyang Medical School, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang, China
| | - Junjun Zhou
- Department of Critical Care Medicine, The Central Hospital of Shaoyang City and Affiliated Shaoyang Hospital, Hengyang Medical College, University of South China, Shaoyang, China
- Institute of Pathogenic Biology, Basic Medical School, Hengyang Medical School, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang, China
| | - Nana Su
- Department of Critical Care Medicine, The Central Hospital of Shaoyang City and Affiliated Shaoyang Hospital, Hengyang Medical College, University of South China, Shaoyang, China
- Institute of Pathogenic Biology, Basic Medical School, Hengyang Medical School, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang, China
| | - Zifan Zhang
- Department of Critical Care Medicine, The Central Hospital of Shaoyang City and Affiliated Shaoyang Hospital, Hengyang Medical College, University of South China, Shaoyang, China
- Institute of Pathogenic Biology, Basic Medical School, Hengyang Medical School, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang, China
| | - Jiaxin Chen
- Department of Critical Care Medicine, The Central Hospital of Shaoyang City and Affiliated Shaoyang Hospital, Hengyang Medical College, University of South China, Shaoyang, China
- Institute of Pathogenic Biology, Basic Medical School, Hengyang Medical School, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang, China
| | - Peng Liu
- Department of Critical Care Medicine, The Central Hospital of Shaoyang City and Affiliated Shaoyang Hospital, Hengyang Medical College, University of South China, Shaoyang, China
- Institute of Pathogenic Biology, Basic Medical School, Hengyang Medical School, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang, China
| | - Peng Ling
- Department of Critical Care Medicine, The Central Hospital of Shaoyang City and Affiliated Shaoyang Hospital, Hengyang Medical College, University of South China, Shaoyang, China
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Yeyeodu S, Hanafi D, Webb K, Laurie NA, Kimbro KS. Population-enriched innate immune variants may identify candidate gene targets at the intersection of cancer and cardio-metabolic disease. Front Endocrinol (Lausanne) 2024; 14:1286979. [PMID: 38577257 PMCID: PMC10991756 DOI: 10.3389/fendo.2023.1286979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/07/2023] [Indexed: 04/06/2024] Open
Abstract
Both cancer and cardio-metabolic disease disparities exist among specific populations in the US. For example, African Americans experience the highest rates of breast and prostate cancer mortality and the highest incidence of obesity. Native and Hispanic Americans experience the highest rates of liver cancer mortality. At the same time, Pacific Islanders have the highest death rate attributed to type 2 diabetes (T2D), and Asian Americans experience the highest incidence of non-alcoholic fatty liver disease (NAFLD) and cancers induced by infectious agents. Notably, the pathologic progression of both cancer and cardio-metabolic diseases involves innate immunity and mechanisms of inflammation. Innate immunity in individuals is established through genetic inheritance and external stimuli to respond to environmental threats and stresses such as pathogen exposure. Further, individual genomes contain characteristic genetic markers associated with one or more geographic ancestries (ethnic groups), including protective innate immune genetic programming optimized for survival in their corresponding ancestral environment(s). This perspective explores evidence related to our working hypothesis that genetic variations in innate immune genes, particularly those that are commonly found but unevenly distributed between populations, are associated with disparities between populations in both cancer and cardio-metabolic diseases. Identifying conventional and unconventional innate immune genes that fit this profile may provide critical insights into the underlying mechanisms that connect these two families of complex diseases and offer novel targets for precision-based treatment of cancer and/or cardio-metabolic disease.
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Affiliation(s)
- Susan Yeyeodu
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
- Charles River Discovery Services, Morrisville, NC, United States
| | - Donia Hanafi
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
| | - Kenisha Webb
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, United States
| | - Nikia A. Laurie
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
| | - K. Sean Kimbro
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, United States
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6
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Ivanov SM, Tarasova OA, Poroikov VV. Transcriptome-based analysis of human peripheral blood reveals regulators of immune response in different viral infections. Front Immunol 2023; 14:1199482. [PMID: 37795081 PMCID: PMC10546413 DOI: 10.3389/fimmu.2023.1199482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023] Open
Abstract
Introduction There are difficulties in creating direct antiviral drugs for all viruses, including new, suddenly arising infections, such as COVID-19. Therefore, pathogenesis-directed therapy is often necessary to treat severe viral infections and comorbidities associated with them. Despite significant differences in the etiopathogenesis of viral diseases, in general, they are associated with significant dysfunction of the immune system. Study of common mechanisms of immune dysfunction caused by different viral infections can help develop novel therapeutic strategies to combat infections and associated comorbidities. Methods To identify common mechanisms of immune functions disruption during infection by nine different viruses (cytomegalovirus, Ebstein-Barr virus, human T-cell leukemia virus type 1, Hepatitis B and C viruses, human immunodeficiency virus, Dengue virus, SARS-CoV, and SARS-CoV-2), we analyzed the corresponding transcription profiles from peripheral blood mononuclear cells (PBMC) using the originally developed pipeline that include transcriptome data collection, processing, normalization, analysis and search for master regulators of several viral infections. The ten datasets containing transcription data from patients infected by nine viruses and healthy people were obtained from Gene Expression Omnibus. The analysis of the data was performed by Genome Enhancer pipeline. Results We revealed common pathways, cellular processes, and master regulators for studied viral infections. We found that all nine viral infections cause immune activation, exhaustion, cell proliferation disruption, and increased susceptibility to apoptosis. Using network analysis, we identified PBMC receptors, representing proteins at the top of signaling pathways that may be responsible for the observed transcriptional changes and maintain the current functional state of cells. Discussion The identified relationships between some of them and virus-induced alteration of immune functions are new and have not been found earlier, e.g., receptors for autocrine motility factor, insulin, prolactin, angiotensin II, and immunoglobulin epsilon. Modulation of the identified receptors can be investigated as one of therapeutic strategies for the treatment of severe viral infections.
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Affiliation(s)
- Sergey M. Ivanov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
- Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Olga A. Tarasova
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
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Dimka J, van Doren TP, Battles HT. Pandemics, past and present: The role of biological anthropology in interdisciplinary pandemic studies. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022. [PMCID: PMC9082061 DOI: 10.1002/ajpa.24517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Biological anthropologists are ideally suited for the study of pandemics given their strengths in human biology, health, culture, and behavior, yet pandemics have historically not been a major focus of research. The COVID‐19 pandemic has reinforced the need to understand pandemic causes and unequal consequences at multiple levels. Insights from past pandemics can strengthen the knowledge base and inform the study of current and future pandemics through an anthropological lens. In this paper, we discuss the distinctive social and epidemiological features of pandemics, as well as the ways in which biological anthropologists have previously studied infectious diseases, epidemics, and pandemics. We then review interdisciplinary research on three pandemics–1918 influenza, 2009 influenza, and COVID‐19–focusing on persistent social inequalities in morbidity and mortality related to sex and gender; race, ethnicity, and Indigeneity; and pre‐existing health and disability. Following this review of the current state of pandemic research on these topics, we conclude with a discussion of ways biological anthropologists can contribute to this field moving forward. Biological anthropologists can add rich historical and cross‐cultural depth to the study of pandemics, provide insights into the biosocial complexities of pandemics using the theory of syndemics, investigate the social and health impacts of stress and stigma, and address important methodological and ethical issues. As COVID‐19 is unlikely to be the last global pandemic, stronger involvement of biological anthropology in pandemic studies and public health policy and research is vital.
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Affiliation(s)
- Jessica Dimka
- Centre for Research on Pandemics and Society Oslo Metropolitan University Oslo Norway
| | | | - Heather T. Battles
- Anthropology, School of Social Sciences The University of Auckland Auckland New Zealand
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8
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Wei X, Su R, Yang M, Pan B, Lu J, Lin H, Shu W, Wang R, Xu X. Quantitative proteomic profiling of hepatocellular carcinoma at different serum alpha-fetoprotein level. Transl Oncol 2022; 20:101422. [PMID: 35430532 PMCID: PMC9034393 DOI: 10.1016/j.tranon.2022.101422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 11/08/2022] Open
Abstract
Serum AFP equal to 400 ng/mL is a pivotal turning point not only in prognosis but also metabolic and invasion associated pathways. Adjacent noncancerous tissues are not biological normal components at protein level. Four druggable targets (C1QBP, HSPE1, CHDH, ITGAL) are identified as potential prognostic biomarkers in hepatocellular carcinoma.
Purpose Hepatocellular carcinoma (HCC) is characterized by a poor long-term prognosis and high mortality rate. Serum alpha-fetoprotein (AFP) levels show great prognostic value in patients undergoing hepatectomy. This study aims to explore proteomic profiling in HCC samples based on AFP subgroups and identify potential key targets involved in HCC progression. Methods Twelve paired tumor and adjacent noncancerous tissue samples were collected from patients with HCC who underwent primary curative resection from January 2012 to December 2013. Clinical information was curated from four tissue microarrays to conduct survival analysis based on serum AFP levels. TMT-based quantitative proteomic analyses and bioinformatics analyses were performed to comprehensively profile molecular features. Immunohistochemistry was carried out to validate protein expression of identified targets. Kaplan-Meier survival analysis was performed to assess the overall survival and recurrence-free survival based on protein expressions. Results AFP (400 ng/mL) was a turning point in prognosis, metabolic- and invasion-associated pathways. The mass spectrometry analysis yielded a total of 5573 identified proteins. Annotations of 151 differentially expressed proteins in tumors and 95 proteins in paracancerous tissues (1.2-fold) showed similarities in biological processes, cellular components, molecular functions. Furthermore, differentially expressed hub proteins with five innovatively nominated druggable targets (C1QBP, HSPE1, GLUD2 for tumors and CHDH, ITGAL for paracancerous tissues), of which four (C1QBP, HSPE1, CHDH, ITGAL) targets were associated with poor overall survival (all Log-rank P < 0.05). Conclusions Our quantitative proteomics analyses identified four key prognostic biomarkers in HCC and provide opportunities for translational medicine and new treatment.
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9
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Bugaj B, Wielińska J, Bogunia-Kubik K, Świerkot J. Searching for New Genetic Biomarkers of Axial Spondyloarthritis. J Clin Med 2022; 11:jcm11102912. [PMID: 35629038 PMCID: PMC9148009 DOI: 10.3390/jcm11102912] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Axial spondyloarthritis (axSpA) is a chronic inflammatory condition of the spine. In addition to musculoskeletal symptoms, there are also extra-articular manifestations. The aim of this study was to search for new biomarkers associated with the clinical presentation and treatment response in axSpA patients. Methods: In this study, 106 axSpA patients and 110 healthy controls were enrolled. Six single-nucleotide polymorphisms (SNPs) were selected for genotyping: ERAP1 rs2287987, ERAP2 rs2549782, TNF rs1800629, TNFRSF1A rs767455, TNFRSF1B rs1061622, and FCGR2A rs1801274. Participants were examined at baseline and after 12 and 24 weeks of anti-TNF therapy. Results: SNPs associated with high axSpA initial activity were TNFRSF1A rs767455 and TNFRSF1B rs1061622 (p < 0.008). The ERAP1 rs2287987 AA genotype was more frequently observed in patients with enthesitis (AA vs. G+, p = 0.049), while the TNFRSF1B rs1061622 GG genotype was more common in participants with uveitis (GG vs. TT, p = 0.042). Potential in predicting anti-TNF treatment response was demonstrated by ERAP1 rs2287987, ERAP2 rs2549782, TNFRSF1B rs1061622, and FCGR2A rs1801274. Conclusions: SNPs can be used to identify patients at risk of severe disease to initiate treatment earlier. Genetic testing will allow clinicians to choose the right drug for the patient.
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Affiliation(s)
- Bartosz Bugaj
- Department of Rheumatology and Internal Medicine, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland;
- Correspondence:
| | - Joanna Wielińska
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, R. Weigla 12, 53-114 Wroclaw, Poland; (J.W.); (K.B.-K.)
| | - Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, R. Weigla 12, 53-114 Wroclaw, Poland; (J.W.); (K.B.-K.)
| | - Jerzy Świerkot
- Department of Rheumatology and Internal Medicine, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland;
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Flatby HM, Rasheed H, Ravi A, Thomas LF, Liyanarachi KV, Afset JE, DeWan AT, Brumpton BM, Hveem K, Åsvold BO, Simonsen GS, Furberg AS, Damås JK, Solligård E, Rogne T. Risk of lower respiratory tract infections: a genome-wide association study with Mendelian randomization analysis in three independent European populations. Clin Microbiol Infect 2022; 28:732.e1-732.e7. [PMID: 34763054 DOI: 10.1016/j.cmi.2021.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/20/2021] [Accepted: 11/01/2021] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Lower respiratory tract infections (LRTIs) are a leading cause of morbidity and mortality worldwide. Few studies have previously investigated genetic susceptibility and potential risk factors for LRTI. METHODS We used data from the UK Biobank, Trøndelag Health Study (HUNT), and FinnGen to conduct a genome-wide association study (GWAS). Cases were subjects hospitalized with LRTI, and controls were subjects with no such hospitalization. We conducted stratification and interaction analyses to evaluate whether the genetic effect of LRTI differed by sex or smoking. Mendelian randomization (MR) analyses were conducted to identify the unconfounded relationship between cardiometabolic risk factors and LRTI. RESULTS A total of 25 320 cases and 575 294 controls were included. The 15q25.1 locus reached genome-wide significance in the meta-analysis (rs10519203: OR 0.94, p 3.87e-11). The protective effect of effect allele of rs10519203 was present among smokers (OR 0.90, 95%CI 0.87-0.92, p 1.38e-15) but not among never-smokers (OR 1.01, 95%CI 0.97-1.06, p 5.20e-01). In MR analyses, we found that increasing body mass index (OR 1.31, 95%CI 1.24-1.40, p 3.78e-18), lifetime smoking (OR 2.83, 95%CI 2.34-3.42, p 6.56e-27), and systolic blood pressure robustly increased the risk of LRTIs (OR 1.11, 95%CI 1.02-1.22, p 1.48e-02). CONCLUSION A region in 15q25.1 was strongly associated with LRTI susceptibility. Reduction in the prevalence of smoking, overweight, obesity, and hypertension may reduce the disease burden of LRTIs.
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Affiliation(s)
- Helene M Flatby
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Anaesthesia and Intensive Care, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.
| | - Humaira Rasheed
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Anuradha Ravi
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Anaesthesia and Intensive Care, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Laurent F Thomas
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; BioCore-Bioinformatics Core Facility, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Laboratory Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Kristin V Liyanarachi
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Infectious Diseases, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan E Afset
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Laboratory Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway; Department of Medical Microbiology, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Andrew T DeWan
- Department of Chronic Disease Epidemiology and Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, CT, USA; Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ben M Brumpton
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway; HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
| | - Kristian Hveem
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Research, Innovation, and Education, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Bjørn O Åsvold
- Department of Endocrinology, Clinic of Medicine, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway; HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway; K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Gunnar S Simonsen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Research Group for Host-Microbe Interaction, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Anne-Sofie Furberg
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Faculty of Health and Social Sciences, Molde University College, Molde, Norway
| | - Jan K Damås
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Infectious Diseases, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Erik Solligård
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Anaesthesia and Intensive Care, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Tormod Rogne
- Gemini Centre for Sepsis Research, Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Chronic Disease Epidemiology and Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, CT, USA; Clinic of Anaesthesia and Intensive Care, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
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11
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Choudhary ML, Chaudhary U, Salve M, Shinde P, Padbidri V, Sangle SA, Salvi S, Bavdekar AR, D'costa P, Alagarasu K. Functional Single-Nucleotide Polymorphisms in the MBL2 and TLR3 Genes Influence Disease Severity in Influenza A (H1N1)pdm09 Virus-Infected Patients from Maharashtra, India. Viral Immunol 2022; 35:303-309. [PMID: 35196173 DOI: 10.1089/vim.2021.0179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The clinical outcome in influenza A (H1N1)pdm09 virus-infected subjects is determined by several factors, including host genetics. In the present study, single-nucleotide polymorphisms (SNPs) in the IFITM, MBL2, TLR3, TLR8, DDX58, IFIH1, CD55, and FCGR2, genes were investigated in influenza A (H1N1)pdm09 virus-infected subjects to find out their association with disease severity. Influenza A (H1N1)pdm09 virus-infected subjects with severe disease (n = 86) and mild disease (n = 293) from western India were included in the study. The SNPs were investigated by PCR-based methods. The results revealed a higher frequency of TLR3 rs5743313 T/T genotype [odds ratio (OR) with 95% confidence interval (CI) 2.55 (1.08-6.04) p = 0.039] and TLR3 two-locus haplotype rs3775291-rs3775290 T-A [OR with 95% CI 7.94 (2.05-30.68)] in severe cases. Lower frequency of the mutant allele of MBL2 rs1800450 [OR with 95% CI 0.51 (0.27-0.87), p = 0.01] and TLR3 two-locus haplotype rs3775291-rs3775290 T-G [OR with 95% CI 0.48 (0.27-0.85)] was observed in severe cases compared with cases with mild disease. Higher frequency of TLR3 two-locus haplotype rs3775291-rs3775290 T-A was observed in severe cases [OR with 95% CI 7.9 (2.0-30.7)]. The allele and genotype frequencies of other SNPs were not different between the study categories. The results suggest that the functional SNPs in MBL2 and TLR3 are associated with severe disease in influenza A (H1N1)pdm09 virus-infected subjects.
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Affiliation(s)
| | | | | | - Pooja Shinde
- ICMR-National Institute of Virology, Pune, India
| | | | | | - Sonali Salvi
- Department of Medicine, BJ Medical College, Pune, India
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12
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Pollara J, Tay MZ, Edwards RW, Goodman D, Crowley AR, Edwards RJ, Easterhoff D, Conley HE, Hoxie T, Gurley T, Jones C, Machiele E, Tuyishime M, Donahue E, Jha S, Spreng RL, Hope TJ, Wiehe K, He MM, Moody MA, Saunders KO, Ackerman ME, Ferrari G, Tomaras GD. Functional Homology for Antibody-Dependent Phagocytosis Across Humans and Rhesus Macaques. Front Immunol 2021; 12:678511. [PMID: 34093580 PMCID: PMC8174565 DOI: 10.3389/fimmu.2021.678511] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/28/2021] [Indexed: 12/19/2022] Open
Abstract
Analyses of human clinical HIV-1 vaccine trials and preclinical vaccine studies performed in rhesus macaque (RM) models have identified associations between non-neutralizing Fc Receptor (FcR)-dependent antibody effector functions and reduced risk of infection. Specifically, antibody-dependent phagocytosis (ADP) has emerged as a common correlate of reduced infection risk in multiple RM studies and the human HVTN505 trial. This recurrent finding suggests that antibody responses with the capability to mediate ADP are most likely a desirable component of vaccine responses aimed at protecting against HIV-1 acquisition. As use of RM models is essential for development of the next generation of candidate HIV-1 vaccines, there is a need to determine how effectively ADP activity observed in RMs translates to activity in humans. In this study we compared ADP activity of human and RM monocytes and polymorphonuclear leukocytes (PMN) to bridge this gap in knowledge. We observed considerable variability in the magnitude of monocyte and PMN ADP activity across individual humans and RM that was not dependent on FcR alleles, and only modestly impacted by cell-surface levels of FcRs. Importantly, we found that for both human and RM phagocytes, ADP activity of antibodies targeting the CD4 binding site was greatest when mediated by human IgG3, followed by RM and human IgG1. These results demonstrate that there is functional homology between antibody and FcRs from these two species for ADP. We also used novel RM IgG1 monoclonal antibodies engineered with elongated hinge regions to show that hinge elongation augments RM ADP activity. The RM IgGs with engineered hinge regions can achieve ADP activity comparable to that observed with human IgG3. These novel modified antibodies will have utility in passive immunization studies aimed at defining the role of IgG3 and ADP in protection from virus challenge or control of disease in RM models. Our results contribute to a better translation of human and macaque antibody and FcR biology, and may help to improve testing accuracy and evaluations of future active and passive prevention strategies.
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Affiliation(s)
- Justin Pollara
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States.,Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Matthew Zirui Tay
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - R Whitney Edwards
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Derrick Goodman
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Andrew R Crowley
- Thayer School of Engineering, Dartmouth College, Hanover, NH, United States
| | - Robert J Edwards
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - David Easterhoff
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Haleigh E Conley
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Taylor Hoxie
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Thaddeus Gurley
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Caroline Jones
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Emily Machiele
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Marina Tuyishime
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Elizabeth Donahue
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Shalini Jha
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Rachel L Spreng
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Thomas J Hope
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Kevin Wiehe
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Max M He
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - M Anthony Moody
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Kevin O Saunders
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States.,Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | | | - Guido Ferrari
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States.,Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Georgia D Tomaras
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States.,Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
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13
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Lamptey H, Bonney EY, Adu B, Kyei GB. Are Fc Gamma Receptor Polymorphisms Important in HIV-1 Infection Outcomes and Latent Reservoir Size? Front Immunol 2021; 12:656894. [PMID: 34017334 PMCID: PMC8129575 DOI: 10.3389/fimmu.2021.656894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Fc gamma receptors (FcγR) are cell surface glycoproteins which trigger specific effector-cell responses when cross-linked with the Fc portions of immunoglobulin (IgG) antibodies. During HIV-1 infection, the course of disease progression, ART response, and viral reservoir size vary in different individuals. Several factors may account for these differences; however, Fc gamma receptor gene polymorphisms, which influence receptor binding to IgG antibodies, are likely to play a key role. FcγRIIa (CD32) was recently reported as a potential marker for latent HIV reservoir, however, this assertion is still inconclusive. Whether FcγR polymorphisms influence the size of the viral reservoir, remains an important question in HIV cure studies. In addition, potential cure or viral suppression methods such as broadly neutralizing antibody (bNAbs) may depend on FcγRs to control the virus. Here, we discuss the current evidence on the potential role played by FcγR polymorphisms in HIV-1 infection, treatment and vaccine trial outcomes. Importantly, we highlight contrasting findings that may be due to multiple factors and the relatively limited data from African populations. We recommend further studies especially in sub-Saharan Africa to confirm the role of FcγRIIa in the establishment of latent reservoir and to determine their influence in therapies involving bNAbs.
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Affiliation(s)
- Helena Lamptey
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Evelyn Y. Bonney
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Bright Adu
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - George B. Kyei
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Medicine, Washington University School of Medicine in St Louis, St. Louis, MO, United States
- Medical and Scientific Research Centre, University of Ghana Medical Centre, University of Ghana, Accra, Ghana
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14
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Fricke-Galindo I, Falfán-Valencia R. Genetics Insight for COVID-19 Susceptibility and Severity: A Review. Front Immunol 2021; 12:622176. [PMID: 33868239 PMCID: PMC8047200 DOI: 10.3389/fimmu.2021.622176] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/16/2021] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease (COVID-19) presents a broad spectrum of clinical manifestations ranging from an asymptomatic to a severe clinical course. The host genetic background influence on the susceptibility and outcome of multiples infectious diseases has been previously reported. Herein, we aimed to describe relevant identified genetic variants and those potentially related to the inter-individual variability of COVID-19 susceptibility and/or severity considering the physiopathological pathway of the disease The HLA-A*25:01, -B*15:27, -B*46:01, -C*01:02, and -C*07:29 alleles have been associated with COVID-19 susceptibility; while HLA-A*02:02, -B*15:03, and -C*12:03 have been identified as low-risk alleles. Variants in cytokine genes such as IL1B, IL1R1, IL1RN, IL6, IL17A, FCGR2A, and TNF could be related to disease susceptibility and cytokine storm, and/or COVID-19 complications (e.g., venous thrombosis). Several variants in ACE2 and TMPRSS2 affecting the expression of the receptors related to COVID-19 have been associated with the disease susceptibility and risk factors. Finally, two GWAS have identified the loci 3p21.31 (LZTFL1, SLC6A20, CCR9, FYCO1, CXCR6, and XCR1) and 9q34.2 (ABO) with COVID-19 severity. Heterogeneous results in the association of genetic variants with COVID-19 susceptibility and severity were observed. The mechanism of identified risk-genes and studies in different populations are still warranted.
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Affiliation(s)
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
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15
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Mehrbod P, Eybpoosh S, Farahmand B, Fotouhi F, Khanzadeh Alishahi M. Association of the host genetic factors, hypercholesterolemia and diabetes with mild influenza in an Iranian population. Virol J 2021; 18:64. [PMID: 33766078 PMCID: PMC7993858 DOI: 10.1186/s12985-021-01486-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 01/02/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Variation in host genetic factors may result in variation in the host immune response to the infection. Some chronic diseases may also affect individuals' susceptibility to infectious diseases. The aim of this study was to evaluate the association of the host genetic factors mostly involved in inflammation, as well as hypercholesterolemia and diabetes with mild flu in an Iranian population. METHODS In this cross-sectional study, nasopharyngeal swab samples were collected from 93 patients referred to primary care centers of Markazi, Semnan, and Zanjan provinces (central Iran) due to flu-like symptoms between March 2015 and December 2018. Of these, PCR test identified 49 influenza A/H1N1 and 44 flu-negative individuals. Twelve single-nucleotide polymorphisms (SNPs) in RPAIN, FCGR2A, MBL-2, CD55, C1QBP, IL-10, TNF-α and an unknown gene were genotyped using iPLEX GOLD SNP genotyping analysis. Hypercholesterolemia and diabetes status was determined based on the physician diagnosis. Association of the host genetic variants, hypercholesterolemia and diabetes with mild A/H1N1 flu was assessed with univariable and multivariable logistic regression analysis as implemented in Stata software (v.14). Statistical tests were considered as significant at 0.05 levels. RESULTS Frequency of diabetes and hypercholesterolemia, as well as participants mean age was significantly higher in the flu-negative rather than the flu-positive group. Of 12 SNPs, nine did not show any significant association with mild flu in our study (rs1801274, rs1800451, rs2564978, rs361525, rs1800450, rs1800871, rs1800872, rs1800896, rs1800629). Possessing G vs. A allele in two SNPs (rs3786054 and rs8070740) was associated with a threefold increase in the chance of mild flu when compared to flu-negative patients (95% CI: 1.1, 22.0). Possessing C allele (vs. A) in the rs9856661 locus also increased the chance of mild flu up to 2 folds (95% CI: 1.0, 10.0). CONCLUSION The results showed that possessing the G allele in either rs3786054 or rs8070740 loci in C1QBP and RPAIN genes, respectively, increased the risk of H1N1 infection up to 3.3 folds, regardless of the patient's age, BMI, diabetes, and hypercholesterolemia. Complementary functional genomic studies would shed more light on the underlying mechanism of human immunity associated with these genetic markers. The identified genetic factors may have the same role in susceptibility to similar respiratory infections with RNA viruses, like SARS, MERS and COVID-19. Future genetic association studies targeting these RNA viruses, especially COVID-19 is recommended. Studies on other ethnic groups would also shed light on possible ethnic variations in genetic susceptibility to respiratory RNA viruses. Trial registry IR.PII.REC.1399.063.
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Affiliation(s)
- Parvaneh Mehrbod
- Influenza and Respiratory Viruses Department, Pasteur Institute of Iran, Tehran, Iran
| | - Sana Eybpoosh
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Behrokh Farahmand
- Influenza and Respiratory Viruses Department, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Fotouhi
- Influenza and Respiratory Viruses Department, Pasteur Institute of Iran, Tehran, Iran
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16
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Bertrams W, Jung AL, Maxheim M, Schmeck B. [Role of genetic factors in pneumonia and COVID-19]. PNEUMOLOGE 2021; 18:212-217. [PMID: 33716601 PMCID: PMC7934978 DOI: 10.1007/s10405-021-00385-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 11/25/2022]
Abstract
Die Pneumonie ist die Infektionskrankheit mit der weltweit höchsten Mortalität. Die häufigsten Erreger sind Bakterien, es gibt jedoch auch epidemisch oder pandemisch auftretende virale Lungenentzündungen durch Influenza- oder Coronaviren, wie die aktuelle Pandemie durch das SARS Coronavirus 3766 Fälle (SARS-CoV-2). Wichtige Herausforderungen liegen neben dem Auftreten von Antibiotikaresistenzen und Immunpathologien etwa in der Sepsis in der Betrachtung der Suszeptibilität individueller Patienten: Hier werden vor allen Dingen das Lebensalter, Medikamente und Komorbiditäten betrachtet. Es gibt jedoch auch klare Hinweise für genetische Einflüsse auf das individuelle Risiko, an einer Pneumonie zu erkranken oder einen schweren Verlauf der Erkrankung zu entwickeln. In diesem Beitrag wollen wir die genetischen Einflüsse auf die Pneumonie und ihre klinische Bedeutung darstellen.
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Affiliation(s)
- Wilhelm Bertrams
- Institut für Lungenforschung, Universities of Gießen and Marburg Lung Center (UGMLC), Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Deutschland
| | - Anna Lena Jung
- Institut für Lungenforschung, Universities of Gießen and Marburg Lung Center (UGMLC), Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Deutschland
| | - Michael Maxheim
- Klinik für Innere Medizin mit Schwerpunkt Pneumologie, Universitätsklinikum Marburg, Philipps-Universität Marburg, Marburg, Deutschland
| | - Bernd Schmeck
- Institut für Lungenforschung, Universities of Gießen and Marburg Lung Center (UGMLC), Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Deutschland
- Klinik für Innere Medizin mit Schwerpunkt Pneumologie, Universitätsklinikum Marburg, Philipps-Universität Marburg, Marburg, Deutschland
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17
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Pérez-Rubio G, Ponce-Gallegos MA, Domínguez-Mazzocco BA, Ponce-Gallegos J, García-Ramírez RA, Falfán-Valencia R. Role of the Host Genetic Susceptibility to 2009 Pandemic Influenza A H1N1. Viruses 2021; 13:344. [PMID: 33671828 PMCID: PMC7926867 DOI: 10.3390/v13020344] [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: 12/23/2020] [Revised: 02/07/2021] [Accepted: 02/18/2021] [Indexed: 01/05/2023] Open
Abstract
Influenza A virus (IAV) is the most common infectious agent in humans, and infects approximately 10-20% of the world's population, resulting in 3-5 million hospitalizations per year. A scientific literature search was performed using the PubMed database and the Medical Subject Headings (MeSH) "Influenza A H1N1" and "Genetic susceptibility". Due to the amount of information and evidence about genetic susceptibility generated from the studies carried out in the last influenza A H1N1 pandemic, studies published between January 2009 to May 2020 were considered; 119 papers were found. Several pathways are involved in the host defense against IAV infection (innate immune response, pro-inflammatory cytokines, chemokines, complement activation, and HLA molecules participating in viral antigen presentation). On the other hand, single nucleotide polymorphisms (SNPs) are a type of variation involving the change of a single base pair that can mean that encoded proteins do not carry out their functions properly, allowing higher viral replication and abnormal host response to infection, such as a cytokine storm. Some of the most studied SNPs associated with IAV infection genetic susceptibility are located in the FCGR2A, C1QBP, CD55, and RPAIN genes, affecting host immune responses through abnormal complement activation. Also, SNPs in IFITM3 (which participates in endosomes and lysosomes fusion) represent some of the most critical polymorphisms associated with IAV infection, suggesting an ineffective virus clearance. Regarding inflammatory response genes, single nucleotide variants in IL1B, TNF, LTA IL17A, IL8, IL6, IRAK2, PIK3CG, and HLA complex are associated with altered phenotype in pro-inflammatory molecules, participating in IAV infection and the severest form of the disease.
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Affiliation(s)
- Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico; (G.P.-R.); (M.A.P.-G.); (B.A.D.-M.); (R.A.G.-R.)
| | - Marco Antonio Ponce-Gallegos
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico; (G.P.-R.); (M.A.P.-G.); (B.A.D.-M.); (R.A.G.-R.)
| | - Bruno André Domínguez-Mazzocco
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico; (G.P.-R.); (M.A.P.-G.); (B.A.D.-M.); (R.A.G.-R.)
| | - Jaime Ponce-Gallegos
- High Speciality Cardiology Unit “Korazón”, Puerta de Hierro Hospital, Tepic 63173, Nayarit, Mexico;
| | - Román Alejandro García-Ramírez
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico; (G.P.-R.); (M.A.P.-G.); (B.A.D.-M.); (R.A.G.-R.)
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico; (G.P.-R.); (M.A.P.-G.); (B.A.D.-M.); (R.A.G.-R.)
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18
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Chen HH, Shaw DM, Petty LE, Graff M, Bohlender RJ, Polikowsky HG, Zhong X, Kim D, Buchanan VL, Preuss MH, Shuey MM, Loos RJF, Huff CD, Cox NJ, Bastarache JA, Bastarache L, North KE, Below JE. Host genetic effects in pneumonia. Am J Hum Genet 2021; 108:194-201. [PMID: 33357513 PMCID: PMC7820802 DOI: 10.1016/j.ajhg.2020.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/02/2020] [Indexed: 01/05/2023] Open
Abstract
Given the coronavirus disease 2019 (COVID-19) pandemic, investigations into host susceptibility to infectious diseases and downstream sequelae have never been more relevant. Pneumonia is a lung disease that can cause respiratory failure and hypoxia and is a common complication of infectious diseases, including COVID-19. Few genome-wide association studies (GWASs) of host susceptibility and severity of pneumonia have been conducted. We performed GWASs of pneumonia susceptibility and severity in the Vanderbilt University biobank (BioVU) with linked electronic health records (EHRs), including Illumina Expanded Multi-Ethnic Global Array (MEGAEX)-genotyped European ancestry (EA, n= 69,819) and African ancestry (AA, n = 15,603) individuals. Two regions of large effect were identified: the CFTR locus in EA (rs113827944; OR = 1.84, p value = 1.2 × 10-36) and HBB in AA (rs334 [p.Glu7Val]; OR = 1.63, p value = 3.5 × 10-13). Mutations in these genes cause cystic fibrosis (CF) and sickle cell disease (SCD), respectively. After removing individuals diagnosed with CF and SCD, we assessed heterozygosity effects at our lead variants. Further GWASs after removing individuals with CF uncovered an additional association in R3HCC1L (rs10786398; OR = 1.22, p value = 3.5 × 10-8), which was replicated in two independent datasets: UK Biobank (n = 459,741) and 7,985 non-overlapping BioVU subjects, who are genotyped on arrays other than MEGAEX. This variant was also validated in GWASs of COVID-19 hospitalization and lung function. Our results highlight the importance of the host genome in infectious disease susceptibility and severity and offer crucial insight into genetic effects that could potentially influence severity of COVID-19 sequelae.
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Affiliation(s)
- Hung-Hsin Chen
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Douglas M Shaw
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lauren E Petty
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Misa Graff
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Ryan J Bohlender
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Hannah G Polikowsky
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Xue Zhong
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Daeeun Kim
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Victoria L Buchanan
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan M Shuey
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Julie A Bastarache
- Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kari E North
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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19
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Li M, Chen Y, Chen T, Hu S, Chen L, Shen L, Li F, Yang J, Sun Y, Wang D, He L, Qin S, Shu Y. A host-based whole genome sequencing study reveals novel risk loci associated with severity of influenza A(H1N1)pdm09 infection. Emerg Microbes Infect 2021; 10:123-131. [PMID: 33393450 PMCID: PMC7832503 DOI: 10.1080/22221751.2020.1870412] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Influenza A(H1N1)pdm09 virus has remained in a seasonal circulation since being recognized in 2009. Although it followed a mild course in most patients, in others it caused a series of severe clinical illnesses. Epidemiologic studies have implicated that host factors have a major influence on the disease severity of influenza A(H1N1)pdm09 infection. However, an understanding of relevant genetic variations and the underlying mechanisms is still limited. In this present study, we used a host-based whole genome sequencing (WGS) method to comprehensively explore the genetic risk loci associated with severity of influenza A(H1N1)pdm09 infection. From the common single-nucleotide variants (SNVs) analysis, we identified the abnormal nominally significant (P < 1 × 10−4) common SNVs enriched in PTBP3 gene. The results of rare functional SNVs analysis supported that there were several novel candidate genes might confer risk of severe influenza A(H1N1)pdm09 diseases, such as FTSJ3, CPVL, BST2, NOD2 and MAVS. Moreover, our results of gene set based analysis indicated that the HIF-1 transcription factor and IFN-γ pathway might play an important role in the underlying mechanism of severe influenza A(H1N1)pdm09. These findings will increase our knowledge about biological mechanism underlying the severe influenza A(H1N1)pdm09 and facilitate to design novel personalized treatments.
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Affiliation(s)
- Mo Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yongkun Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Tao Chen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Shixiong Hu
- Hunan Provincial Center for Disease Control and Prevention, Changsha, People's Republic of China
| | - Luan Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Lu Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Fangcai Li
- Hunan Provincial Center for Disease Control and Prevention, Changsha, People's Republic of China
| | - Jing Yang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yan Sun
- Changsha Central Hospital, Changsha 410004, People's Republic of China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People's Republic of China.,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
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20
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Holgado MP, Raiden S, Sananez I, Seery V, De Lillo L, Maldonado LL, Kamenetzky L, Geffner J, Arruvito L. Fcγ Receptor IIa (FCGR2A) Polymorphism Is Associated With Severe Respiratory Syncytial Virus Disease in Argentinian Infants. Front Cell Infect Microbiol 2021; 10:607348. [PMID: 33392111 PMCID: PMC7775358 DOI: 10.3389/fcimb.2020.607348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/19/2020] [Indexed: 12/02/2022] Open
Abstract
Background Most patients with respiratory syncytial virus (RSV) infection requiring hospitalization have no risk factors for severe disease. Genetic variation in the receptor for the Fc portion of IgG (FcγR) determines their affinity for IgG subclasses driving innate and adaptive antiviral immunity. We investigated the relationship between FcγRIIa-H131R polymorphism and RSV disease. Methods Blood samples were collected from 182 infants ≤24-month-old (50 uninfected, 114 RSV-infected with moderate course and 18 suffering severe disease). FcγRIIa-H131R SNP genotypic frequencies (HH, HR, RR) and anti-RSV IgG1, IgG2 and IgG3 levels were studied. Results Genotypic frequencies for FcγRIIa-H131R SNP were comparable between uninfected and RSV-infected infants. In contrast, we found a significant higher frequency of HH genotype in severe RSV-infected children compared to moderate patients. Among severe group, HH infants presented more factors associated to severity than HR or RR patients did. Furthermore, compared to moderate RSV-infected infants, severe patients showed higher levels of anti-RSV IgG1 and IgG3. Conclusions We found an association between an FcγRIIa (H131) polymorphism and severe RSV disease, which points towards a critical role for interactions between FcγRs and immune complexes in RSV pathogenesis. This genetic factor could also predict the worse outcome and identify those infants at risk during hospitalization.
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Affiliation(s)
- María Pía Holgado
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, CONICET, Ciudad de Autónoma Buenos Aires, Argentina
| | - Silvina Raiden
- Hospital General de Niños "Pedro de Elizalde", Ciudad Autónoma de Buenos Aires, Argentina
| | - Inés Sananez
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, CONICET, Ciudad de Autónoma Buenos Aires, Argentina
| | - Vanesa Seery
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, CONICET, Ciudad de Autónoma Buenos Aires, Argentina
| | - Leonardo De Lillo
- Hospital General de Niños "Pedro de Elizalde", Ciudad Autónoma de Buenos Aires, Argentina
| | - Lucas L Maldonado
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Laura Kamenetzky
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Jorge Geffner
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, CONICET, Ciudad de Autónoma Buenos Aires, Argentina
| | - Lourdes Arruvito
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, CONICET, Ciudad de Autónoma Buenos Aires, Argentina
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21
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Li M, Li YP, Deng HL, Wang MQ, Wang WJ, Wang J, Wu FP, Dang SS. Association of gene polymorphisms of CD55 with susceptibility to and severity of hand, foot, and mouth disease caused by enterovirus 71 in the Han Chinese population. J Med Virol 2020; 92:3119-3124. [PMID: 32470169 DOI: 10.1002/jmv.26088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 05/23/2020] [Indexed: 12/13/2022]
Abstract
Hand, foot, and mouth disease (HFMD) caused by enterovirus 71 (EV71) can lead to high morbidity and mortality, and genetic background plays an important role during the disease process. We investigated the association between the single-nucleotide polymorphism (SNP) rs2564978 of the CD55 gene and susceptibility to and severity of HFMD using the SNPs can multiple SNP typing methods. Soluble CD55 (sCD55) expression was significantly lower in the EV71 HFMD group than in the control group and lower in severe cases than in mild cases (P < .001). Moreover, CD55 rs2564978 (C vs T OR = 1.300, 95% CI, 1.120-1.509) was associated with the risk of EV71 infection, and genotype TC was related to the severity of the infection (TC vs TT OR = 4.523, 95% CI, 2.033-10.066). Our results suggest that sCD55 expression and the CD55 polymorphism rs2564978 may influence the susceptibility to and severity of EV71 infection.
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Affiliation(s)
- Mei Li
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ya-Ping Li
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Hui-Ling Deng
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Mu-Qi Wang
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Wen-Jun Wang
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jun Wang
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Feng-Ping Wu
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shuang-Suo Dang
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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22
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Polymorphisms in Processing and Antigen Presentation-Related Genes and Their Association with Host Susceptibility to Influenza A/H1N1 2009 Pandemic in a Mexican Mestizo Population. Viruses 2020; 12:v12111224. [PMID: 33138079 PMCID: PMC7692058 DOI: 10.3390/v12111224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/24/2020] [Indexed: 12/14/2022] Open
Abstract
(1) Background: The influenza A/H1N1 pdm09 virus rapidly spread throughout the world. Despite the inflammatory and virus-degradation pathways described in the pathogenesis of influenza A virus (IAV) infection, little is known about the role of the single nucleotide polymorphisms (SNPs) in the genes involved in the processing and antigenic presentation-related mechanisms. (2) Methods: In this case-control study, we evaluated 17 SNPs in five genes (TAP1, TAP2, TAPBP, PSMB8, and PSMB9). One hundred and twenty-eight patients with influenza A/H1N1 infection (INF-P) and 111 healthy contacts (HC) were included; all of them are Mexican mestizo. (3) Results: In allele and genotype comparison, the rs241433/C allele (TAP2), as well as AG haplotype (rs3763365 and rs4148882), are associated with reduced risk for influenza A/H1N1 infection (p < 0.05). On the other hand, the rs2071888G allele (TAPBP) and GG haplotype (rs3763365 and rs9276810) are associated with a higher risk for influenza A/H1N1 infection. In addition, after adjustment for covariates, the association to a reduced risk for influenza A/H1N1 infection remains with rs241433/C allele (p < 0.0001, OR = 0.24, 95% CI = 0.13-0.43), and the association with TAPBP is also maintained with the G allele (p = 0.0095, OR = 1.89, 95% CI = 1.17-3.06) and GG genotype models (p < 0.05, OR = 2.18, 95% CI = 1.27-3.74). (4) Conclusion: The rs241433/C allele and AC genotype (TAP2) and the AG haplotype are associated with a reduced risk for influenza A/H1N1 infection. In addition, the rs2071888/G allele and GG genotype (TAPBP) and the GG haplotype are associated with a higher risk for developing influenza A/H1N1 infection in a Mexican mestizo population.
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23
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Hartshorn KL. Innate Immunity and Influenza A Virus Pathogenesis: Lessons for COVID-19. Front Cell Infect Microbiol 2020; 10:563850. [PMID: 33194802 PMCID: PMC7642997 DOI: 10.3389/fcimb.2020.563850] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022] Open
Abstract
There is abundant evidence that the innate immune response to influenza A virus (IAV) is highly complex and plays a key role in protection against IAV induced infection and illness. Unfortunately it also clear that aspects of innate immunity can lead to severe morbidity or mortality from IAV, including inflammatory lung injury, bacterial superinfection, and exacerbation of reactive airways disease. We review broadly the virus and host factors that result in adverse outcomes from IAV and show evidence that inflammatory responses can become damaging even apart from changes in viral replication per se, with special focus on the positive and adverse effects of neutrophils and monocytes. We then evaluate in detail the role of soluble innate inhibitors including surfactant protein D and antimicrobial peptides that have a potential dual capacity for down-regulating viral replication and also inhibiting excessive inflammatory responses and how these innate host factors could possibly be harnessed to treat IAV infection. Where appropriate we draw comparisons and contrasts the SARS-CoV viruses and IAV in an effort to point out where the extensive knowledge existing regarding severe IAV infection could help guide research into severe COVID 19 illness or vice versa.
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Affiliation(s)
- Kevan L Hartshorn
- Section of Hematology Oncology, Boston University School of Medicine, Boston, MA, United States
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24
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Zhao B, Chen Y, Li M, Zhou J, Teng Z, Chen J, Zhao X, Wu H, Bai T, Mao S, Fang F, Chu W, Huang H, Huai C, Shen L, Zhou W, Sun L, Zheng X, Cheng G, Sun Y, Wang D, He L, Shu Y, Zhang X, Qin S. Novel susceptibility loci for A(H7N9) infection identified by next generation sequencing and functional analysis. Sci Rep 2020; 10:11768. [PMID: 32678187 PMCID: PMC7366728 DOI: 10.1038/s41598-020-68675-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 06/29/2020] [Indexed: 12/23/2022] Open
Abstract
The A(H7N9) virus strain that emerged in 2013 was associated with a high fatality rate and may become a long-term threat to public health. A(H7N9) disease incidence is disproportionate to viral exposure, suggesting that host genetic factors may significantly influence susceptibility to A(H7N9) infection. Human genome variation in conferring risk for A(H7N9) infection in Chinese populations was identified by a two-stage investigation involving 121 A(H7N9) patients and 187 healthy controls using next generation sequencing followed by functional analysis. As a result, a low frequency variant (rs189256251; P = 0.0303, OR = 3.45, 95% CI 1.05–11.35, chi-square test) and three HLA alleles (DQB1*06:01, DQA1*05:05 and C*12:02) were identified in A(H7N9) infected volunteers. In an A549 cell line carrying the rs189256251 variant CT genotype, A(H7N9) infection incidence was elevated 6.665-fold over control cells carrying the CC genotype. Serum levels of interferon alpha were significantly lower in patients with the CT genotype compared to the CC genotype (P = 0.01). The study findings of genetic predisposition to A(H7N9) in the Chinese population may be valuable in systematic investigations of A(H7N9) disease etiology.
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Affiliation(s)
- Baihui Zhao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China.,Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200036, China
| | - Yongkun Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, 510275, China
| | - Mo Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jianfang Zhou
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health Commission, Beijing, 102206, China
| | - Zheng Teng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200036, China
| | - Jian Chen
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200036, China
| | - Xue Zhao
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200036, China
| | - Hao Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Tian Bai
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health Commission, Beijing, 102206, China
| | - Shenghua Mao
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200036, China
| | - Fanghao Fang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200036, China
| | - Wei Chu
- Shanghai Huangpu District Center for Disease Control and Prevention, Shanghai, 200023, China
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Cong Huai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Lu Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wei Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Liangdan Sun
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China
| | - Xiaodong Zheng
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China
| | | | - Ye Sun
- Jinan Infectious Disease Hospital, Jinan, 250021, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention China CDC, Beijing, 102206, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, 510275, China. .,National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health Commission, Beijing, 102206, China.
| | - Xi Zhang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200036, China.
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China. .,Collaborative Innovation Center, Jining Medical University, Jining, 272067, China.
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25
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Noll KE, Whitmore AC, West A, McCarthy MK, Morrison CR, Plante KS, Hampton BK, Kollmus H, Pilzner C, Leist SR, Gralinski LE, Menachery VD, Schäfer A, Miller D, Shaw G, Mooney M, McWeeney S, Pardo-Manuel de Villena F, Schughart K, Morrison TE, Baric RS, Ferris MT, Heise MT. Complex Genetic Architecture Underlies Regulation of Influenza-A-Virus-Specific Antibody Responses in the Collaborative Cross. Cell Rep 2020; 31:107587. [PMID: 32348764 PMCID: PMC7195006 DOI: 10.1016/j.celrep.2020.107587] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/20/2020] [Accepted: 04/08/2020] [Indexed: 02/07/2023] Open
Abstract
Host genetic factors play a fundamental role in regulating humoral immunity to viral infection, including influenza A virus (IAV). Here, we utilize the Collaborative Cross (CC), a mouse genetic reference population, to study genetic regulation of variation in antibody response following IAV infection. CC mice show significant heritable variation in the magnitude, kinetics, and composition of IAV-specific antibody response. We map 23 genetic loci associated with this variation. Analysis of a subset of these loci finds that they broadly affect the antibody response to IAV as well as other viruses. Candidate genes are identified based on predicted variant consequences and haplotype-specific expression patterns, and several show overlap with genes identified in human mapping studies. These findings demonstrate that the host antibody response to IAV infection is under complex genetic control and highlight the utility of the CC in modeling and identifying genetic factors with translational relevance to human health and disease.
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Affiliation(s)
- Kelsey E Noll
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alan C Whitmore
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mary K McCarthy
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Heike Kollmus
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Carolin Pilzner
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vineet D Menachery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Darla Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ginger Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael Mooney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA; OHSU Knight Cancer Center Institute, Oregon Health and Science University, Portland, OR, USA
| | - Shannon McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA; OHSU Knight Cancer Center Institute, Oregon Health and Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany; University of Veterinary Medicine Hannover, Hannover, Germany; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Thomas E Morrison
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ralph S Baric
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark T Heise
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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26
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Shi X, Ma Y, Li H, Yu H. Association between FCGR2A rs1801274 and MUC5B rs35705950 variations and pneumonia susceptibility. BMC MEDICAL GENETICS 2020; 21:71. [PMID: 32252656 PMCID: PMC7137230 DOI: 10.1186/s12881-020-01005-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/19/2020] [Indexed: 12/22/2022]
Abstract
Background Herein, we collected currently published data to comprehensively evaluate the impact of the FCGR2A (Fc fragment of IgG receptor IIa) rs1801274 and MUC5B (mucin 5B, oligomeric mucus/gel-forming) rs35705950 variations on susceptibility to pneumonia diseases. Methods We retrieved case-control studies from three online databases and applied the statistical approach of meta-analysis for a series of pooling analyses. Results A total of fourteen case-control studies were included for FCGR2A rs1801274; while thirty-one case-control studies were included for MUC5B rs35705950. No significant difference between pneumonia cases and controls for FCGR2A rs1801274 was found. However, MUC5B rs35705950 was significantly associated with pneumonia susceptibility in the whole population under the genetic models of allelic T vs. G [OR (odds ratio) =3.78], carrier T vs. G (OR = 3.31), TT vs. GG (OR = 13.66), GT vs. GG (OR = 4.78), GT + TT vs. GG (OR = 5.05), and TT vs. GG + GT (OR = 6.47) (all P < 0.001, Bonferroni-adjusted P < 0.006; false discovery rate-adjusted P < 0.0010). Furthermore, we observed a similar positive result for subgroup analyses of “Caucasian”, “Asian”, “population-based control”, and “idiopathic pulmonary fibrosis”. Conclusions MUC5B rs35705950, but not FCGR2A rs1801274, increases susceptibility to clinical pneumonia, especially to idiopathic pulmonary fibrosis, in both the Caucasian and Asian populations.
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Affiliation(s)
- Xueshu Shi
- Nursing Division, The second affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300150, P.R. China
| | - Yue Ma
- Endoscopic Skull Base Surgery Center, Tianjin Huanhu Hospital, No 6, JiZhao Road, Jinnan District, Tianjin, 300350, P.R. China
| | - Haiyan Li
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin Huanhu Hospital, Tianjin, 300350, P.R. China
| | - Huanxin Yu
- Endoscopic Skull Base Surgery Center, Tianjin Huanhu Hospital, No 6, JiZhao Road, Jinnan District, Tianjin, 300350, P.R. China.
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27
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Cellular signalling pathways mediating the pathogenesis of chronic inflammatory respiratory diseases: an update. Inflammopharmacology 2020; 28:795-817. [PMID: 32189104 DOI: 10.1007/s10787-020-00698-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/02/2020] [Indexed: 02/06/2023]
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28
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Gounder AP, Boon ACM. Influenza Pathogenesis: The Effect of Host Factors on Severity of Disease. THE JOURNAL OF IMMUNOLOGY 2019; 202:341-350. [PMID: 30617115 DOI: 10.4049/jimmunol.1801010] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
Influenza viruses continue to be a major global health threat. Severity and clinical outcome of influenza disease is determined by both viral and host factors. Viral factors have long been the subject of intense research and many molecular determinants have been identified. However, research into the host factors that protect or predispose to severe and fatal influenza A virus infections is lagging. The goal of this review is to highlight the recent insights into host determinants of influenza pathogenesis.
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Affiliation(s)
- Anshu P Gounder
- Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110.,Department of Molecular Microbiology and Microbial Pathogenesis, Washington University School of Medicine in St. Louis, St. Louis, MO 63110; and
| | - Adrianus C M Boon
- Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110; .,Department of Molecular Microbiology and Microbial Pathogenesis, Washington University School of Medicine in St. Louis, St. Louis, MO 63110; and.,Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
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29
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Khadzhieva MB, Kuzovlev AN, Salnikova LE. Pneumonia: host susceptibility and shared genetics with pulmonary function and other traits. Clin Exp Immunol 2019; 198:367-380. [PMID: 31487037 DOI: 10.1111/cei.13367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2019] [Indexed: 12/16/2022] Open
Abstract
Pneumonia is a common and severe infectious lung disease. Host genetics, together with underlying medical and lifestyle conditions, determine pneumonia susceptibility. We performed a secondary analysis of the results of two genome-wide studies for pneumonia in 23andMe participants (40 600 cases/90 039 controls) (Tian et al., 2017) and UK Biobank (BB) participants (12 614 cases/324 585 controls) (via the Global Biobank Engine) and used the GTEx database to correlate the results with expression quantitative trait loci (eQTLs) data in lung and whole blood. In the 23andMe pneumonia single nucleotide polymorphism (SNP) set, 177 genotyped SNPs in the human leukocyte antigen (HLA) region satisfied the genome-wide significance level, P ≤ 5·0E-08. Several target genes (e.g. C4A, VARS2, SFTA2, HLA-C, HLA-DQA2) were unidirectionally regulated by many HLA eSNPs associated with a higher risk of pneumonia. In lung, C4A transcript was up-regulated by 291 pneumonia risk alleles spanning the half the HLA region. Among SNPs correlated with the expression levels of SFTA2 and VARS2, approximately 75% overlapped: all risk alleles were associated with VARS2 up-regulation and SFTA2 down-regulation. To find shared gene loci between pneumonia and pulmonary function (PF), we used data from the Global Biobank Engine and literature on genome-wide association studies (GWAS) of PF in general populations. Numerous gene loci overlapped between pneumonia and PF: 28·8% in the BB data set and 49·2% in the 23andMe data set. Enrichment analysis within the database of Genotypes and Phenotypes (dbGaP) and National Human Genome Research Institute-European Bioinformatics Institute (NHGRI-EBI) Catalog of pneumonia and pneumonia/PF gene sets identified significant overlap between these gene sets and genes related to inflammatory, developmental, neuropsychiatric and cardiovascular and obesity-related traits.
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Affiliation(s)
- M B Khadzhieva
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia.,N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - A N Kuzovlev
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - L E Salnikova
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia.,N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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30
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Host Single Nucleotide Polymorphisms Modulating Influenza A Virus Disease in Humans. Pathogens 2019; 8:pathogens8040168. [PMID: 31574965 PMCID: PMC6963926 DOI: 10.3390/pathogens8040168] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 09/27/2019] [Accepted: 09/28/2019] [Indexed: 12/14/2022] Open
Abstract
A large number of human genes associated with viral infections contain single nucleotide polymorphisms (SNPs), which represent a genetic variation caused by the change of a single nucleotide in the DNA sequence. SNPs are located in coding or non-coding genomic regions and can affect gene expression or protein function by different mechanisms. Furthermore, they have been linked to multiple human diseases, highlighting their medical relevance. Therefore, the identification and analysis of this kind of polymorphisms in the human genome has gained high importance in the research community, and an increasing number of studies have been published during the last years. As a consequence of this exhaustive exploration, an association between the presence of some specific SNPs and the susceptibility or severity of many infectious diseases in some risk population groups has been found. In this review, we discuss the relevance of SNPs that are important to understand the pathology derived from influenza A virus (IAV) infections in humans and the susceptibility of some individuals to suffer more severe symptoms. We also discuss the importance of SNPs for IAV vaccine effectiveness.
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31
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Horwood PF, Tarantola A, Goarant C, Matsui M, Klement E, Umezaki M, Navarro S, Greenhill AR. Health Challenges of the Pacific Region: Insights From History, Geography, Social Determinants, Genetics, and the Microbiome. Front Immunol 2019; 10:2184. [PMID: 31572391 PMCID: PMC6753857 DOI: 10.3389/fimmu.2019.02184] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/29/2019] [Indexed: 02/06/2023] Open
Abstract
The Pacific region, also referred to as Oceania, is a geographically widespread region populated by people of diverse cultures and ethnicities. Indigenous people in the region (Melanesians, Polynesians, Micronesians, Papuans, and Indigenous Australians) are over-represented on national, regional, and global scales for the burden of infectious and non-communicable diseases. Although social and environmental factors such as poverty, education, and access to health-care are assumed to be major drivers of this disease burden, there is also developing evidence that genetic and microbiotic factors should also be considered. To date, studies investigating genetic and/or microbiotic links with vulnerabilities to infectious and non-communicable diseases have mostly focused on populations in Europe, Asia, and USA, with uncertain associations for other populations such as indigenous communities in Oceania. Recent developments in personalized medicine have shown that identifying ethnicity-linked genetic vulnerabilities can be important for medical management. Although our understanding of the impacts of the gut microbiome on health is still in the early stages, it is likely that equivalent vulnerabilities will also be identified through the interaction between gut microbiome composition and function with pathogens and the host immune system. As rapid economic, dietary, and cultural changes occur throughout Oceania it becomes increasingly important that further research is conducted within indigenous populations to address the double burden of high rates of infectious diseases and rapidly rising non-communicable diseases so that comprehensive development goals can be planned. In this article, we review the current knowledge on the impact of nutrition, genetics, and the gut microbiome on infectious diseases in indigenous people of the Pacific region.
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Affiliation(s)
- Paul F. Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | | | - Cyrille Goarant
- Institut Pasteur de Nouvelle-Calédonie, Noumea, New Caledonia
| | - Mariko Matsui
- Institut Pasteur de Nouvelle-Calédonie, Noumea, New Caledonia
| | - Elise Klement
- Institut Pasteur de Nouvelle-Calédonie, Noumea, New Caledonia
- Internal Medicine and Infectious Diseases Department, Centre Hospitalier Territorial, Noumea, New Caledonia
| | - Masahiro Umezaki
- Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Severine Navarro
- Immunology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Andrew R. Greenhill
- School of Health and Life Sciences, Federation University Australia, Churchill, VIC, Australia
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32
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Dela Cruz CS, Wunderink RG, Christiani DC, Cormier SA, Crothers K, Doerschuk CM, Evans SE, Goldstein DR, Khatri P, Kobzik L, Kolls JK, Levy BD, Metersky ML, Niederman MS, Nusrat R, Orihuela CJ, Peyrani P, Prince AS, Ramírez JA, Ridge KM, Sethi S, Suratt BT, Sznajder JI, Tsalik EL, Walkey AJ, Yende S, Aggarwal NR, Caler EV, Mizgerd JP. Future Research Directions in Pneumonia. NHLBI Working Group Report. Am J Respir Crit Care Med 2019; 198:256-263. [PMID: 29546996 DOI: 10.1164/rccm.201801-0139ws] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Pneumonia is a complex pulmonary disease in need of new clinical approaches. Although triggered by a pathogen, pneumonia often results from dysregulations of host defense that likely precede infection. The coordinated activities of immune resistance and tissue resilience then dictate whether and how pneumonia progresses or resolves. Inadequate or inappropriate host responses lead to more severe outcomes such as acute respiratory distress syndrome and to organ dysfunction beyond the lungs and over extended time frames after pathogen clearance, some of which increase the risk for subsequent pneumonia. Improved understanding of such host responses will guide the development of novel approaches for preventing and curing pneumonia and for mitigating the subsequent pulmonary and extrapulmonary complications of pneumonia. The NHLBI assembled a working group of extramural investigators to prioritize avenues of host-directed pneumonia research that should yield novel approaches for interrupting the cycle of unhealthy decline caused by pneumonia. This report summarizes the working group's specific recommendations in the areas of pneumonia susceptibility, host response, and consequences. Overarching goals include the development of more host-focused clinical approaches for preventing and treating pneumonia, the generation of predictive tools (for pneumonia occurrence, severity, and outcome), and the elucidation of mechanisms mediating immune resistance and tissue resilience in the lung. Specific areas of research are highlighted as especially promising for making advances against pneumonia.
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Affiliation(s)
- Charles S Dela Cruz
- 1 Pulmonary, Critical Care and Sleep Medicine, Center for Pulmonary Infection Research and Treatment, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Richard G Wunderink
- 2 Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - David C Christiani
- 3 Department of Environmental Health, Harvard T. H. Chan School of Public Health, and.,4 Pulmonary and Critical Care Division, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Stephania A Cormier
- 5 Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
| | - Kristina Crothers
- 6 Department of Medicine, University of Washington, Seattle, Washington
| | - Claire M Doerschuk
- 7 Marsico Lung Institute and.,8 Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Scott E Evans
- 9 Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel R Goldstein
- 10 Department of Internal Medicine.,11 Department of Microbiology and Immunology, and.,12 Institute of Gerontology, University of Michigan, Ann Arbor, Michigan
| | - Purvesh Khatri
- 13 Center for Biomedical Information Research, Stanford University, Stanford, California
| | - Lester Kobzik
- 3 Department of Environmental Health, Harvard T. H. Chan School of Public Health, and
| | - Jay K Kolls
- 14 Center for Translational Research in Infection and Inflammation, Tulane School of Medicine, New Orleans, Louisiana
| | - Bruce D Levy
- 15 Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Mark L Metersky
- 16 Division of Pulmonary, Critical Care and Sleep Medicine, University of Connecticut School of Medicine, Farmington, Connecticut
| | - Michael S Niederman
- 17 Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Roomi Nusrat
- 18 Department of Medicine, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, New Jersey
| | - Carlos J Orihuela
- 19 Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Paula Peyrani
- 20 Division of Infectious Diseases, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Alice S Prince
- 21 Department of Pediatrics, Columbia University, New York, New York
| | - Julio A Ramírez
- 20 Division of Infectious Diseases, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Karen M Ridge
- 2 Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Sanjay Sethi
- 22 Pulmonary, Critical Care and Sleep Medicine, Jacobs School of Medicine, University at Buffalo, State University of New York, Buffalo, New York
| | - Benjamin T Suratt
- 23 Pulmonary and Critical Care Medicine, University of Vermont College of Medicine, Burlington, Vermont
| | - Jacob I Sznajder
- 2 Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ephraim L Tsalik
- 24 Emergency Medicine Service, Durham Veterans Affairs Health Care System, Durham, North Carolina.,25 Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Allan J Walkey
- 26 Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
| | - Sachin Yende
- 27 Department of Critical Care Medicine, Clinical Research, Investigation, and Systems Modeling of Acute Illness Center, University of Pittsburgh, Pittsburgh, Pennsylvania.,28 Center for Health Equity Research and Promotion, VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania; and
| | - Neil R Aggarwal
- 29 Division of Lung Diseases, NHLBI, NIH, Bethesda, Maryland
| | | | - Joseph P Mizgerd
- 26 Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
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Zhou J, Wang D, Wong BHY, Li C, Poon VKM, Wen L, Zhao X, Chiu MC, Liu X, Ye Z, Yuan S, Sze KH, Chan JFW, Chu H, To KKW, Yuen KY. Identification and characterization of GLDC as host susceptibility gene to severe influenza. EMBO Mol Med 2019; 11:emmm.201809528. [PMID: 30498026 PMCID: PMC6328914 DOI: 10.15252/emmm.201809528] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Glycine decarboxylase (GLDC) was prioritized as a candidate susceptibility gene to severe influenza in humans. The higher expression of GLDC derived from genetic variations may confer a higher risk to H7N9 and severe H1N1 infection. We sought to characterize GLDC as functional susceptibility gene that GLDC may intrinsically regulate antiviral response, thereby impacting viral replication and disease outcome. We demonstrated that GLDC inhibitor AOAA and siRNA depletion boosted IFNβ‐ and IFN‐stimulated genes (ISGs) in combination with PolyI:C stimulation. GLDC inhibition and depletion significantly amplified antiviral response of type I IFNs and ISGs upon viral infection and suppressed the replication of H1N1 and H7N9 viruses. Consistently, GLDC overexpression significantly promoted viral replication due to the attenuated antiviral responses. Moreover, GLDC inhibition in H1N1‐infected BALB/c mice recapitulated the amplified antiviral response and suppressed viral growth. AOAA provided potent protection to the infected mice from lethal infection, comparable to a standard antiviral against influenza viruses. Collectively, GLDC regulates cellular antiviral response and orchestrates viral growth. GLDC is a functional susceptibility gene to severe influenza in humans.
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Affiliation(s)
- Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Dong Wang
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Bosco Ho-Yin Wong
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Cun Li
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | | | - Lei Wen
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Xiaoyu Zhao
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Man Chun Chiu
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Xiaojuan Liu
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ziwei Ye
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Shuofeng Yuan
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kong-Hung Sze
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong.,The Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong.,The Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Kwok Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong .,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong.,The Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
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Eisfeld AJ, Kawaoka Y. Calculated risk: a new single-nucleotide polymorphism linked to severe influenza disease. Nat Med 2019; 23:911-912. [PMID: 28777788 DOI: 10.1038/nm.4383] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amie J Eisfeld
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan, and the International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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35
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Tay MZ, Wiehe K, Pollara J. Antibody-Dependent Cellular Phagocytosis in Antiviral Immune Responses. Front Immunol 2019; 10:332. [PMID: 30873178 PMCID: PMC6404786 DOI: 10.3389/fimmu.2019.00332] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/08/2019] [Indexed: 12/20/2022] Open
Abstract
Antiviral activities of antibodies may either be dependent only on interactions between the antibody and cognate antigen, as in binding and neutralization of an infectious virion, or instead may require interactions between antibody-antigen immune complexes and immunoproteins or Fc receptor expressing immune effector cells. These Fc receptor-dependent antibody functions provide a direct link between the innate and adaptive immune systems by combining the potent antiviral activity of innate effector cells with the diversity and specificity of the adaptive humoral response. The Fc receptor-dependent function of antibody-dependent cellular phagocytosis (ADCP) provides mechanisms for clearance of virus and virus-infected cells, as well as for stimulation of downstream adaptive immune responses by facilitating antigen presentation, or by stimulating the secretion of inflammatory mediators. In this review, we discuss the properties of Fc receptors, antibodies, and effector cells that influence ADCP. We also provide and interpret evidence from studies that support a potential role for ADCP in either inhibiting or enhancing viral infection. Finally, we describe current approaches used to measure antiviral ADCP and discuss considerations for the translation of studies performed in animal models. We propose that additional investigation into the role of ADCP in protective viral responses, the specific virus epitopes targeted by ADCP antibodies, and the types of phagocytes and Fc receptors involved in ADCP at sites of virus infection will provide insight into strategies to successfully leverage this important immune response for improved antiviral immunity through rational vaccine design.
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Affiliation(s)
- Matthew Zirui Tay
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Kevin Wiehe
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Justin Pollara
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
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36
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Rojas-Quintero J, Wang X, Tipper J, Burkett PR, Zuñiga J, Ashtekar AR, Polverino F, Rout A, Yambayev I, Hernández C, Jimenez L, Ramírez G, Harrod KS, Owen CA. Matrix metalloproteinase-9 deficiency protects mice from severe influenza A viral infection. JCI Insight 2018; 3:99022. [PMID: 30568032 DOI: 10.1172/jci.insight.99022] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 11/06/2018] [Indexed: 02/06/2023] Open
Abstract
Matrix metalloproteinase-9 (MMP-9) cleaves various proteins to regulate inflammatory and injury responses. However, MMP-9's activities during influenza A viral (IAV) infections are incompletely understood. Herein, plasma MMP-9 levels were increased in patients with pandemic H1N1 and seasonal IAV infections. MMP-9 lung levels were increased and localized to airway epithelial cells and leukocytes in H1N1-infected WT murine lungs. H1N1-infected Mmp-9-/- mice had lower mortality rates, reduced weight loss, lower lung viral titers, and reduced lung injury, along with lower E-cadherin shedding in bronchoalveolar lavage fluid (BALF) samples than WT mice. H1N1-infected Mmp-9-/- mice had an altered immune response to IAV with lower BALF PMN and macrophage counts, higher Th1-like CD4+ and CD8+ T cell subsets, lower T regulatory cell counts, reduced lung type I interferon levels, and higher lung interferon-γ levels. Mmp-9 bone marrow-chimera studies revealed that Mmp-9 deficiency in lung parenchymal cells protected mice from IAV-induced mortality. H1N1-infected Mmp-9-/- lung epithelial cells had lower viral titers than H1N1-infected WT cells in vitro. Thus, H1N1-infected Mmp-9-/- mice are protected from IAV-induced lung disease due to a more effective adaptive immune response to IAV and reduced epithelial barrier injury due partly to reduced E-cadherin shedding. Thus, we believe that MMP-9 is a novel therapeutic target for IAV infections.
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Affiliation(s)
- Joselyn Rojas-Quintero
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaoyun Wang
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer Tipper
- Department of Anesthesiology and Perioperative Medicine, Division of Molecular and Translational Biomedicine, School of Medicine, University of Alabama-Birmingham, Birmingham, Alabama, USA
| | - Patrick R Burkett
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA
| | - Joaquin Zuñiga
- Laboratory of Immunobiology and Genetics, and Intensive Care Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Amit R Ashtekar
- Department of Anesthesiology and Perioperative Medicine, Division of Molecular and Translational Biomedicine, School of Medicine, University of Alabama-Birmingham, Birmingham, Alabama, USA
| | - Francesca Polverino
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA.,Lovelace Respiratory Research Institute, Albuquerque, New Mexico, USA
| | - Amit Rout
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA
| | - Ilyas Yambayev
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA
| | - Carmen Hernández
- Laboratory of Immunobiology and Genetics, and Intensive Care Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico.,Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Mexico City, Mexico
| | - Luis Jimenez
- Laboratory of Immunobiology and Genetics, and Intensive Care Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Gustavo Ramírez
- Laboratory of Immunobiology and Genetics, and Intensive Care Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Kevin S Harrod
- Department of Anesthesiology and Perioperative Medicine, Division of Molecular and Translational Biomedicine, School of Medicine, University of Alabama-Birmingham, Birmingham, Alabama, USA
| | - Caroline A Owen
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA.,Lovelace Respiratory Research Institute, Albuquerque, New Mexico, USA
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37
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Verhein KC, Vellers HL, Kleeberger SR. Inter-individual variation in health and disease associated with pulmonary infectious agents. Mamm Genome 2018; 29:38-47. [PMID: 29353387 PMCID: PMC5851710 DOI: 10.1007/s00335-018-9733-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Respiratory infectious diseases resulting from bacterial or viral pathogens such as Mycobacterium tuberculosis, Streptococcus pneumoniae, respiratory syncytial virus (RSV), or influenza, are major global public health concerns. Lower respiratory tract infections are leading causes of morbidity and mortality, only behind ischemic heart disease and stroke (GBD 2015 LRI Collaborators in Lancet Infect Dis 17(11):1133–1161, 2017). Developing countries are particularly impacted by these diseases. However, while many are infected with viruses such as RSV (> 90% of all individuals are infected by age 2), only sub-populations develop severe disease. Many factors may contribute to the inter-individual variation in response to respiratory infections, including gender, age, socioeconomic status, nutrition, and genetic background. Association studies with functional single nucleotide polymorphisms in biologically plausible gene candidates have been performed in human populations to provide insight to the molecular genetic contribution to pulmonary infections and disease severity. In vitro cell models and genome-wide association studies in animal models of genetic susceptibility to respiratory infections have also identified novel candidate susceptibility genes, some of which have also been found to contribute to disease susceptibility in human populations. Genetic background may also contribute to differential efficacy of vaccines against respiratory infections. Development of new genetic mouse models such as the collaborative cross and diversity outbred mice should provide additional insight to the mechanisms of genetic susceptibility to respiratory infections. Continued investigation of susceptibility factors should provide insight to novel strategies to prevent and treat disease that contributes to global morbidity and mortality attributed to respiratory infections.
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Affiliation(s)
- Kirsten C Verhein
- Inflammation, Immunity, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
- Inflammation, Immunity, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Dr., Building 101, Rm. D240, Research Triangle Park, NC, 27709, USA.
| | - Heather L Vellers
- Inflammation, Immunity, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Steven R Kleeberger
- Inflammation, Immunity, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
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Identification of complement-related host genetic risk factors associated with influenza A(H1N1)pdm09 outcome: challenges ahead. Med Microbiol Immunol 2018; 208:631-640. [PMID: 30306260 PMCID: PMC7102177 DOI: 10.1007/s00430-018-0567-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 10/03/2018] [Indexed: 10/28/2022]
Abstract
Influenza remains an important threat for human health, despite the extensive study of influenza viruses and the production of effective vaccines. In contrast to virus genetics determinants, host genetic factors with clinical impact remained unexplored until recently. The association between three single nucleotide polymorphisms (SNPs) and influenza outcome in a European population was investigated in the present study. All samples were collected during the influenza A(H1N1)pdm09 post-pandemic period 2010-11 and a sufficient number of severe and fatal cases was included. Host genomic DNA was isolated from pharyngeal samples of 110 patients from northern Greece with severe (n = 59) or mild (n = 51) influenza A(H1N1)pdm09 disease, at baseline, and the genotype of CD55 rs2564978, C1QBP rs3786054 and FCGR2A rs1801274 SNPs was investigated. Our findings suggest a relationship between the two complement-related SNPs, namely, the rare TT genotype of CD55 and the rare AA genotype of C1QBP with increased death risk. No significant differences were observed for FCGR2A genotypes neither with fatality nor disease severity. Additional large-scale genetic association studies are necessary for the identification of reliable host genetic risk factors associated with influenza A(H1N1)pdm09 outcome. Prophylactic intervention of additional high-risk populations, according to their genetic profile, will be a key achievement for the fight against influenza viruses.
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Short KR, Kedzierska K, van de Sandt CE. Back to the Future: Lessons Learned From the 1918 Influenza Pandemic. Front Cell Infect Microbiol 2018; 8:343. [PMID: 30349811 PMCID: PMC6187080 DOI: 10.3389/fcimb.2018.00343] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 09/10/2018] [Indexed: 01/02/2023] Open
Abstract
2018 marks the 100-year anniversary of the 1918 influenza pandemic, which killed ~50 million people worldwide. The severity of this pandemic resulted from a complex interplay between viral, host, and societal factors. Here, we review the viral, genetic and immune factors that contributed to the severity of the 1918 pandemic and discuss the implications for modern pandemic preparedness. We address unresolved questions of why the 1918 influenza H1N1 virus was more virulent than other influenza pandemics and why some people survived the 1918 pandemic and others succumbed to the infection. While current studies suggest that viral factors such as haemagglutinin and polymerase gene segments most likely contributed to a potent, dysregulated pro-inflammatory cytokine storm in victims of the pandemic, a shift in case-fatality for the 1918 pandemic toward young adults was most likely associated with the host's immune status. Lack of pre-existing virus-specific and/or cross-reactive antibodies and cellular immunity in children and young adults likely contributed to the high attack rate and rapid spread of the 1918 H1N1 virus. In contrast, lower mortality rate in in the older (>30 years) adult population points toward the beneficial effects of pre-existing cross-reactive immunity. In addition to the role of humoral and cellular immunity, there is a growing body of evidence to suggest that individual genetic differences, especially involving single-nucleotide polymorphisms (SNPs), contribute to differences in the severity of influenza virus infections. Co-infections with bacterial pathogens, and possibly measles and malaria, co-morbidities, malnutrition or obesity are also known to affect the severity of influenza disease, and likely influenced 1918 H1N1 disease severity and outcomes. Additionally, we also discuss the new challenges, such as changing population demographics, antibiotic resistance and climate change, which we will face in the context of any future influenza virus pandemic. In the last decade there has been a dramatic increase in the number of severe influenza virus strains entering the human population from animal reservoirs (including highly pathogenic H7N9 and H5N1 viruses). An understanding of past influenza virus pandemics and the lessons that we have learnt from them has therefore never been more pertinent.
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Affiliation(s)
- Kirsty R. Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Carolien E. van de Sandt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, Netherlands
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Feng C, Huang H, Huang S, Zhai YZ, Dong J, Chen L, Huang Z, Zhou X, Li B, Wang LL, Chen W, Lv FQ, Li TS. Identification of potential key genes associated with severe pneumonia using mRNA-seq. Exp Ther Med 2018; 16:758-766. [PMID: 30112034 PMCID: PMC6090384 DOI: 10.3892/etm.2018.6262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 04/11/2017] [Indexed: 01/24/2023] Open
Abstract
This study aimed to identify the potential key genes associated with severe pneumonia using mRNA-seq. Nine peripheral blood samples from patients with severe pneumonia alone (SP group, n=3) and severe pneumonia accompanied with chronic obstructive pulmonary disease (COPD; CSP group, n=3), as well as volunteers without pneumonia (control group, n=3) underwent mRNA-seq. Based on the sequencing data, differentially expressed genes (DEGs) were identified by Limma package. Following the pathway enrichment analysis of DEGs, the genes that were differentially expressed in the SP and CSP groups were selected for pathway enrichment analysis and coexpression analysis. In addition, potential genes related to pneumonia were identified based on the information in the Comparative Toxicogenomics Database. In total, 645 and 528 DEGs were identified in the SP and CSP groups, respectively, compared with the normal controls. Among these DEGs, 88 upregulated genes and 80 downregulated genes were common between the two groups. The functions of the common DEGs were similar to those of the DEGs in the SP group. In the coexpression network, the commonly downregulated genes (including ND1, ND3, ND4L, and ND6) and the commonly upregulated genes (including TSPY6P and CDY10P) exhibited a higher degree. In addition, 131 DEGs (including ND1, ND3, ND6, MIR449A and TAS2R43) were predicted to be potential pneumonia-related genes. In conclusion, the present study demonstrated that the common DEGs may be associated with the progression of severe pneumonia.
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Affiliation(s)
- Cong Feng
- Department of Emergency, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - He Huang
- Department of Critical Care Medicine, General Hospital of Jinan Command, Jinan, Shandong 250031, P.R. China
| | - Sai Huang
- Department of Emergency, Chinese PLA General Hospital, Beijing 100853, P.R. China.,Department of Hematology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Yong-Zhi Zhai
- Department of Emergency, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Jing Dong
- Department of Emergency, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Li Chen
- Department of Emergency, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Zhi Huang
- Department of Electrical and Computer Engineering, Purdue University, Indianapolis, IN 46202, USA
| | - Xuan Zhou
- Department of Emergency, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Bei Li
- Department of Emergency, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Li-Li Wang
- Department of Emergency, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Wei Chen
- Department of Emergency, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Fa-Qin Lv
- Department of Ultrasound, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Tan-Shi Li
- Department of Emergency, Chinese PLA General Hospital, Beijing 100853, P.R. China
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Liu M, Han T, Shi S, Chen E. Long noncoding RNA HAGLROS regulates cell apoptosis and autophagy in lipopolysaccharides-induced WI-38 cells via modulating miR-100/NF-κB axis. Biochem Biophys Res Commun 2018; 500:589-596. [PMID: 29673591 DOI: 10.1016/j.bbrc.2018.04.109] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 04/13/2018] [Indexed: 11/17/2022]
Abstract
Pneumonia is a lower respiratory disease caused by pathogens or other factors. This study aimed to explore the roles and mechanism of long noncoding RNA HAGLROS in lipopolysaccharides (LPS)-induced inflammatory injury in pneumonia. The HAGLROS expression in serum of patients with acute stage pneumonia was detected. To induce pulmonary injury, WI-38 human lung fibroblasts were stimulated with lipopolysaccharides (LPS). The HAGLROS expressions in LPS-treated WI-38 cells and the effects of HAGLROS knockdown on the viability, apoptosis, and autophagy of LPS-induced cells were detected. Moreover, the regulatory relationship between HAGLROS and miR-100 was explored as well as the functional targets of miR-100 were identified. Furthermore, the regulatory relationship between miR-100 and PI3K/AKT/NF-κB pathway was elucidated. LncRNA HAGLROS was higher expressed in serum of patients with acute stage pneumonia compared with that in serum of healthy control. LPS caused WI-38 cell injury and increased HAGLROS levels. Downregulation of HAGLROS alleviated LPS-induced cell injury via increasing cell viability, and inhibiting apoptosis and autophagy. Moreover, there was a negative correlation between HAGLROS and miR-100, and the effects of HAGLROS downregulation on LPS-induced apoptosis and autophagy in WI-38 cells were by regulation of miR-100. Furthermore, NFΚB3 was verified as a functional target of miR-100 and effects of miR-100 inhibition on LPS-induced WI-38 cell injury were alleviated by knockdown of NFΚB3. Besides, Knockdown of HAGLROS inhibited the activation of PI3K/AKT/NF-κB pathway. Our findings reveal that downregulation of HAGLROS may alleviate LPS-induced inflammatory injury in WI-38 cells via modulating miR-100/NF-κB axis. HAGLROS/miR-100/NF-κB axis may provide a new strategy for treating acute stage of pneumonia.
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Affiliation(s)
- Meihan Liu
- Department of Ultrasonography, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130033, China
| | - Tao Han
- Department of Vascular Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130033, China
| | - Shaomin Shi
- Department of Respiratory, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130033, China.
| | - Enqi Chen
- Department of Ultrasonography, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130033, China
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An Increased Frequency in HLA Class I Alleles and Haplotypes Suggests Genetic Susceptibility to Influenza A (H1N1) 2009 Pandemic: A Case-Control Study. J Immunol Res 2018; 2018:3174868. [PMID: 29682588 PMCID: PMC5845504 DOI: 10.1155/2018/3174868] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/26/2017] [Accepted: 01/11/2018] [Indexed: 01/16/2023] Open
Abstract
Background The influenza A H1N1/09 pandemic infected a small number of exposed individuals, which suggests the involvement of genetic factors. There are scarce data available on classical HLA class I association with the influenza A H1N1/09 pandemic. Methods We analyzed the frequency of classical HLA class I alleles and haplotypes in A H1N1/09 influenza in a case-control study including 138 influenza patients (INF-P) and 225 asymptomatic healthy contacts (INF-C) simultaneously recruited. HLA class I typing was performed by high-resolution sequence-based typing method. Results Our analysis revealed higher frequency of C∗07:02:01, B∗39:06:02, C∗03:02:01, B∗44:03:01, B∗51:01:05, and B∗73:01 (p < 0.05; OR = 1.84–9.98) and of two haplotypes—A∗68:01:02-C∗07:02:01 (p = 1.05E − 05; OR = 23.99) and B∗35:01:01-C∗07:02.01 (p = 4.15E − 04, OR = 2.15)—in A H1N1/09 influenza subjects. A∗68:01:01 was exclusively present only in the INF-P group (5/138). A decrease in the frequency of C∗03:03:01, A∗11:01:01, B∗39:01:01, A∗24:02:01, C∗03:04:01, B∗51:01:01, and C∗07:01:01 (p < 0.05; OR = 0.12–0.52) and of haplotypes A∗02:01:01-B∗35:01:01-C∗04:01:01, A∗24:02:01-B∗35:01:01, B∗39:01:01-C∗07:02:01, and B∗40:02:01-C∗03:04:01 (p < 0.05; OR = 0.08–0.22) were observed in INF-P group. Conclusion Selective classical HLA class I allele and haplotype combinations predispose individuals towards susceptibility or protection against the influenza A H1N1/09 pandemic. This work has significant implications for accessing population transmission risk for A H1N1/09 or a similar strain breakout in the future.
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van Sluijs L, Pijlman GP, Kammenga JE. Why do Individuals Differ in Viral Susceptibility? A Story Told by Model Organisms. Viruses 2017; 9:E284. [PMID: 28973976 PMCID: PMC5691635 DOI: 10.3390/v9100284] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/22/2017] [Accepted: 09/26/2017] [Indexed: 01/30/2023] Open
Abstract
Viral susceptibility and disease progression is determined by host genetic variation that underlies individual differences. Genetic polymorphisms that affect the phenotype upon infection have been well-studied for only a few viruses, such as HIV-1 and Hepatitis C virus. However, even for well-studied viruses the genetic basis of individual susceptibility differences remains elusive. Investigating the effect of causal polymorphisms in humans is complicated, because genetic methods to detect rare or small-effect polymorphisms are limited and genetic manipulation is not possible in human populations. Model organisms have proven a powerful experimental platform to identify and characterize polymorphisms that underlie natural variations in viral susceptibility using quantitative genetic tools. We summarize and compare the genetic tools available in three main model organisms, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans, and illustrate how these tools can be applied to detect polymorphisms that determine the viral susceptibility. Finally, we analyse how candidate polymorphisms from model organisms can be used to shed light on the underlying mechanism of individual variation. Insights in causal polymorphisms and mechanisms underlying individual differences in viral susceptibility in model organisms likely provide a better understanding in humans.
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Affiliation(s)
- Lisa van Sluijs
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands.
- Laboratory of Virology, Wageningen University, 6708 PB Wageningen, The Netherlands.
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, 6708 PB Wageningen, The Netherlands.
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands.
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44
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Lee N, Cao B, Ke C, Lu H, Hu Y, Tam CHT, Ma RCW, Guan D, Zhu Z, Li H, Lin M, Wong RYK, Yung IMH, Hung TN, Kwok K, Horby P, Hui DSC, Chan MCW, Chan PKS. IFITM3, TLR3, and CD55 Gene SNPs and Cumulative Genetic Risks for Severe Outcomes in Chinese Patients With H7N9/H1N1pdm09 Influenza. J Infect Dis 2017; 216:97-104. [PMID: 28510725 PMCID: PMC7107409 DOI: 10.1093/infdis/jix235] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/11/2017] [Indexed: 12/30/2022] Open
Abstract
Background. We examined associations between single-nucleotide polymorphisms (SNPs) of IFITM3, TLR3, and CD55 genes and influenza clinical outcomes in Chinese. Methods. A multicenter study was conducted on 275 adult cases of avian (H7N9) and pandemic (H1N1pdm09) influenza. Host DNA was extracted from diagnostic respiratory samples; IFITM3 rs12252, TLR3 rs5743313, CD55 rs2564978, and TLR4 rs4986790/4986791 were targeted for genotyping (Sanger sequencing). The primary outcome analyzed was death. Results. IFITM3 and TLR3 SNPs were in Hardy–Weinberg equilibrium; their allele frequencies (IFITM3/C-allele 0.56, TLR3/C-allele 0.88) were comparable to 1000 Genomes Han Chinese data. We found over-representation of homozygous IFITM3 CC (54.5% vs 33.2%; P = .02) and TLR3 CC (93.3% vs 76.9%; P = .04) genotypes among fatal cases. Recessive genetic models showed their significant independent associations with higher death risks (adjusted hazard ratio [aHR] 2.78, 95% confidence interval [CI] 1.29–6.02, and aHR 4.85, 95% CI 1.11−21.06, respectively). Cumulative effects were found (aHR 3.53, 95% CI 1.64−7.59 per risk genotype; aHR 9.99, 95% CI 1.27−78.59 with both). Results were consistent for each influenza subtype and other severity indicators. The CD55 TT genotype was linked to severity. TLR4 was nonpolymorphic. Conclusions. Host genetic factors may influence clinical outcomes of avian and pandemic influenza infections. Such findings have important implications on disease burden and patient care in at-risk populations.
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Affiliation(s)
- Nelson Lee
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong
| | - Bin Cao
- Centre for Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, and National Clinical Research Centre for Respiratory Disease, Capital Medical University, Beijing
| | - Changwen Ke
- Institute of Pathogenic Microbiology, Guangdong Provincial Centre for Disease Control and Prevention, Guangzhou
| | - Hongzhou Lu
- Department of Infectious Diseases, Huashan Hospital Affiliated to Fudan University, Shanghai
| | - Yunwen Hu
- Key Laboratory of Medical Molecular Virology of the Ministries of Education, Shanghai Medical College, Fudan University
| | - Claudia Ha Ting Tam
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong
| | - Ronald Ching Wan Ma
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong
| | - Dawei Guan
- Institute of Pathogenic Microbiology, Guangdong Provincial Centre for Disease Control and Prevention, Guangzhou
| | - Zhaoqin Zhu
- Key Laboratory of Medical Molecular Virology of the Ministries of Education, Shanghai Medical College, Fudan University
| | - Hui Li
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chaoyang Hospital, Capital Medical University
| | - Mulei Lin
- Southern Medical University, Guangzhou
| | - Rity Y K Wong
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong
| | - Irene M H Yung
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong
| | - Tin-Nok Hung
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, People's Republic of China
| | - Kirsty Kwok
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, People's Republic of China
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | - David Shu Cheong Hui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong
| | - Martin Chi Wai Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, People's Republic of China
| | - Paul Kay Sheung Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, People's Republic of China
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Dreshaj S, Alija AJ, Schlagenhauf P, Doda T, Geca N, Bajraktari I, Bresgen N, Eckl PM. Is there a relationship between genetic factors and the incidence and severity of H1N1 in Kosova?: A preliminary investigation and pointers for further research. Travel Med Infect Dis 2017; 18:53-56. [PMID: 28302522 DOI: 10.1016/j.tmaid.2017.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 10/20/2022]
Abstract
BACKGROUND Host genetic factors may impact susceptibility to infection. A small number of studies have investigated the association between factors such as ABO blood groups and selected phenotypes on the incidence and severity of H1N1 infections with inconclusive results. METHODS Using data from the Clinic of Infectious Diseases - University Clinical Centre Prishtina and based on the examination of 125 patients hospitalized with H1N1 in the period 2009-2014, the frequency of blood groups from ABO and Rhesus (Rh) systems as phenotypical markers were evaluated. In addition, other phenotypes such as ear lobe free/ear lobe attached, normal chin/cleft chin, tongue roller/non roller, hand clasping right thumb over/hand clasping left thumb over, right-handed/left-handed, dark eyes/light eyes were also analyzed. The data obtained from the 125 hospitalized patients were compared with the data from the Kosovar population (n = 2000) as a reference group. RESULTS A total of 303 patients with H1N1 were hospitalized in the period 2009-2015. Blood group and phenotype data available from 125 hospitalized H1N1 patients showed significant differences in the frequencies of the blood groups from Rh system as well as in two (out of six) phenotypes of the selected morphological traits compared to reference groups. CONCLUSIONS The findings from this preliminary study indicate that these Rh system and phenotype differences may be linked to H1N1 susceptibility and may guide identification of risk groups and populations.
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Affiliation(s)
- Shemsedin Dreshaj
- University of Prishtina, Faculty of Medicine, Clinic of Infectious Diseases, Prishtina University Clinical Centre, Kosovo.
| | - Avdulla J Alija
- University of Prishtina, Department of Biology, Nena Tereze, n.n., Prishtina, Kosova
| | - Patricia Schlagenhauf
- University of Zurich, Centre for Travel Medicine, Epidemiology, Biostatistics and Prevention Institute, Hirschengraben 84, 8032 Switzerland
| | - Teuta Doda
- University of Prishtina, Faculty of Medicine, Clinic of Infectious Diseases, Prishtina University Clinical Centre, Kosovo
| | - Njomeza Geca
- University of Prishtina, Faculty of Medicine, Clinic of Infectious Diseases, Prishtina University Clinical Centre, Kosovo
| | - Ismet Bajraktari
- University of Prishtina, Department of Biology, Nena Tereze, n.n., Prishtina, Kosova
| | - Nikolaus Bresgen
- University of Salzburg, Department of Cell Biology, Hellbrunnerstr. 34, A-5020 Salzburg, Austria
| | - Peter M Eckl
- University of Salzburg, Department of Cell Biology, Hellbrunnerstr. 34, A-5020 Salzburg, Austria
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Protein profiling of nasopharyngeal aspirates of hospitalized and outpatients revealed cytokines associated with severe influenza A(H1N1)pdm09 virus infections: A pilot study. Cytokine 2016; 86:10-14. [DOI: 10.1016/j.cyto.2016.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/04/2016] [Accepted: 07/05/2016] [Indexed: 12/19/2022]
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Huang S, Feng C, Chen L, Huang Z, Zhou X, Li B, Wang LL, Chen W, Lv FQ, Li TS. Identification of Potential Key Long Non-Coding RNAs and Target Genes Associated with Pneumonia Using Long Non-Coding RNA Sequencing (lncRNA-Seq): A Preliminary Study. Med Sci Monit 2016; 22:3394-3408. [PMID: 27663962 PMCID: PMC5040222 DOI: 10.12659/msm.900783] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background This study aimed to identify the potential key long non-coding RNAs (lncRNAs) and target genes associated with pneumonia using lncRNA sequencing (lncRNA-seq). Material/Methods A total of 9 peripheral blood samples from patients with mild pneumonia (n=3) and severe pneumonia (n=3), as well as volunteers without pneumonia (n=3), were received for lncRNA-seq. Based on the sequencing data, differentially expressed lncRNAs (DE-lncRNAs) were identified by the limma package. After the functional enrichment analysis, target genes of DE-lncRNAs were predicted, and the regulatory network was constructed. Results In total, 99 DE-lncRNAs (14 upregulated and 85 downregulated ones) were identified in the mild pneumonia group and 85 (72 upregulated and 13 downregulated ones) in the severe pneumonia group, compared with the control group. Among these DE-lncRNAs, 9 lncRNAs were upregulated in both the mild and severe pneumonia groups. A set of 868 genes were predicted to be targeted by these 9 DE-lncRNAs. In the network, RP11-248E9.5 and RP11-456D7.1 targeted the majority of genes. RP11-248E9.5 regulated several genes together with CTD-2300H10.2, such as QRFP and EPS8. Both upregulated RP11-456D7.1 and RP11-96C23.9 regulated several genes, such as PDK2. RP11-456D7.1 also positively regulated CCL21. Conclusions These novel lncRNAs and their target genes may be closely associated with the progression of pneumonia.
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Affiliation(s)
- Sai Huang
- Department of Hematology, Chinese PLA General Hospital, Beijing, China (mainland)
| | - Cong Feng
- Department of Emergency, General Hospital of the PLA, Beijing, China (mainland)
| | - Li Chen
- Department of Emergency, General Hospital of the PLA, Beijing, China (mainland)
| | - Zhi Huang
- Department of Electrical and Computer Engineering, Purdue University, Indianapolis, IN, USA
| | - Xuan Zhou
- Department of Emergency, General Hospital of the PLA, Beijing, China (mainland)
| | - Bei Li
- Department of Emergency, General Hospital of the PLA, Beijing, China (mainland)
| | - Li-Li Wang
- Department of Emergency, General Hospital of the PLA, Beijing, China (mainland)
| | - Wei Chen
- Department of Emergency, General Hospital of the PLA, Beijing, China (mainland)
| | - Fa-Qin Lv
- Department of Ultrasound, General Hospital of the PLA, Beijing, China (mainland)
| | - Tan-Shi Li
- Department of Emergency, General Hospital of the PLA, Beijing, China (mainland)
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Maestri A, Sortica VA, Ferreira DL, de Almeida Ferreira J, Amador MAT, de Mello WA, Santos SEB, Sousa RCM. The His131Arg substitution in the FCGR2A gene (rs1801274) is not associated with the severity of influenza A(H1N1)pdm09 infection. BMC Res Notes 2016; 9:296. [PMID: 27267995 PMCID: PMC4897956 DOI: 10.1186/s13104-016-2096-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The virulence and pathogenicity of different influenza strains are responsible for a more or less severe disease. Recent studies have attempted to understand how host genetic factors may influence the clinical presentation of the disease. In the present study, the His131Arg (rs1801274) polymorphism was investigated in individuals from a Brazilian admixed population with a diagnosis of influenza A(H1N1)pdm09 infection. METHODS In the present study, the influence of the His131Arg (rs1801274) polymorphism, a variant of the FCGR2A gene, was investigated in 436 patients with a diagnosis of influenza A(H1N1)pdm09, evaluated at health services in the northern and northeastern regions of Brazil between June 2009 and August 2010. Patients were divided into a group of non-hospitalized patients (n = 192) and a group of hospitalized patients (n = 244; 100 of them died). RESULTS No significant difference in the allele or genotype frequencies of the rs1801274 polymorphism was observed between groups (p = 0.952 and p = 0.388). Multinomial logistic regression showed no effect of the rs1801274 polymorphism on severity or death of patients from the Brazilian admixed population (p = 0.368 and p = 0.469). CONCLUSIONS The rs1801274 polymorphism is not associated with severe disease in patients infected with influenza A(H1N1)pdm09.
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Affiliation(s)
- Alvino Maestri
- />Alvino Maestri Neto, Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Cidade Universitária Prof. José da Silveira Neto, Rua Augusto Corrêa, 01, BOX 8615, CEP 66.075-970 Belém, Pará Brazil
| | | | - Deimy Lima Ferreira
- />Laboratório de Vírus Respiratórios, Seção de Virologia Instituto Evandro Chagas, Ananindeua, Pará Brazil
| | | | | | - Wyller Alencar de Mello
- />Laboratório de Vírus Respiratórios, Seção de Virologia Instituto Evandro Chagas, Ananindeua, Pará Brazil
| | - Sidney Emanuel Batista Santos
- />Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Pará Brazil
- />Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém, Pará Brazil
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Multiple gene mutations identified in patients infected with influenza A (H7N9) virus. Sci Rep 2016; 6:25614. [PMID: 27156515 PMCID: PMC4860572 DOI: 10.1038/srep25614] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 04/18/2016] [Indexed: 11/20/2022] Open
Abstract
Influenza A (H7N9) virus induced high mortality since 2013. It is important to elucidate the potential genetic variations that contribute to virus infection susceptibilities. In order to identify genetic mutations that might increase host susceptibility to infection, we performed exon sequencing and validated the SNPS by Sanger sequencing on 18 H7N9 patients. Blood samples were collected from 18 confirmed H7N9 patients. The genomic DNA was captured with the Agilent SureSelect Human All Exon kit, sequenced on the Illumina Hiseq 2000, and the resulting data processed and annotated with Genome analysis Tool. SNPs were verified by independent Sanger sequencing. The DAVID database and the DAPPLE database were used to do bioinformatics analysis. Through exon sequencing and Sanger sequencing, we identified 21 genes that were highly associated with H7N9 influenza infection. Protein-protein interaction analysis showed that direct interactions among genetic products were significantly higher than expected (p = 0.004), and DAVID analysis confirmed the defense-related functions of these genes. Gene mutation profiles of survived and non-survived patients were similar, suggesting some of genes identified in this study may be associated with H7N9 influenza susceptibility. Host specific genetic determinants of disease severity identified by this approach may provide new targets for the treatment of H7N9 influenza.
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Use of systems biology to decipher host-pathogen interaction networks and predict biomarkers. Clin Microbiol Infect 2016; 22:600-6. [PMID: 27113568 DOI: 10.1016/j.cmi.2016.04.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 02/06/2023]
Abstract
In systems biology, researchers aim to understand complex biological systems as a whole, which is often achieved by mathematical modelling and the analyses of high-throughput data. In this review, we give an overview of medical applications of systems biology approaches with special focus on host-pathogen interactions. After introducing general ideas of systems biology, we focus on (1) the detection of putative biomarkers for improved diagnosis and support of therapeutic decisions, (2) network modelling for the identification of regulatory interactions between cellular molecules to reveal putative drug targets and (3) module discovery for the detection of phenotype-specific modules in molecular interaction networks. Biomarker detection applies supervised machine learning methods utilizing high-throughput data (e.g. single nucleotide polymorphism (SNP) detection, RNA-seq, proteomics) and clinical data. We demonstrate structural analysis of molecular networks, especially by identification of disease modules as a novel strategy, and discuss possible applications to host-pathogen interactions. Pioneering work was done to predict molecular host-pathogen interactions networks based on dual RNA-seq data. However, currently this network modelling is restricted to a small number of genes. With increasing number and quality of databases and data repositories, the prediction of large-scale networks will also be feasible that can used for multidimensional diagnosis and decision support for prevention and therapy of diseases. Finally, we outline further perspective issues such as support of personalized medicine with high-throughput data and generation of multiscale host-pathogen interaction models.
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