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Uvarova AN, Tkachenko EA, Stasevich EM, Zheremyan EA, Korneev KV, Kuprash DV. Methods for Functional Characterization of Genetic Polymorphisms of Non-Coding Regulatory Regions of the Human Genome. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:1002-1013. [PMID: 38981696 DOI: 10.1134/s0006297924060026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 07/11/2024]
Abstract
Currently, numerous associations between genetic polymorphisms and various diseases have been characterized through the Genome-Wide Association Studies. Majority of the clinically significant polymorphisms are localized in non-coding regions of the genome. While modern bioinformatic resources make it possible to predict molecular mechanisms that explain influence of the non-coding polymorphisms on gene expression, such hypotheses require experimental verification. This review discusses the methods for elucidating molecular mechanisms underlying dependence of the disease pathogenesis on specific genetic variants within the non-coding sequences. A particular focus is on the methods for identification of transcription factors with binding efficiency dependent on polymorphic variations. Despite remarkable progress in bioinformatic resources enabling prediction of the impact of polymorphisms on the disease pathogenesis, there is still the need for experimental approaches to investigate this issue.
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Affiliation(s)
- Aksinya N Uvarova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - Elena A Tkachenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ekaterina M Stasevich
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141700, Russia
| | - Elina A Zheremyan
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Kirill V Korneev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Dmitry V Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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2
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Bos JW, Groen EJN, Otten HG, Budding K, van Eijk RPA, Curial C, Kardol-Hoefnagel T, Goedee HS, van den Berg LH, van der Pol WL. A 21-bp deletion in the complement regulator CD55 promotor region is associated with multifocal motor neuropathy and its disease course. J Peripher Nerv Syst 2024; 29:193-201. [PMID: 38528725 DOI: 10.1111/jns.12620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND AND AIMS To further substantiate the role of antibody-mediated complement activation in multifocal motor neuropathy (MMN) immunopathology, we investigated the distribution of promotor polymorphisms of genes encoding the membrane-bound complement regulators CD46, CD55, and CD59 in patients with MMN and controls, and evaluated their association with disease course. METHODS We used Sanger sequencing to genotype five common polymorphisms in the promotor regions of CD46, CD55, and CD59 in 133 patients with MMN and 380 controls. We correlated each polymorphism to clinical parameters. RESULTS The genotype frequencies of rs28371582, a 21-bp deletion in the CD55 promotor region, were altered in patients with MMN as compared to controls (p .009; Del/Del genotype 16.8% vs. 7.7%, p .005, odds ratio: 2.43 [1.27-4.58]), and patients carrying this deletion had a more favorable disease course (mean difference 0.26 Medical Research Council [MRC] points/year; 95% confidence interval [CI]: 0.040-0.490, p .019). The presence of CD59 rs141385724 was associated with less severe pre-diagnostic disease course (mean difference 0.940 MRC point/year; 95% CI: 0.083-1.80, p .032). INTERPRETATION MMN susceptibility is associated with a 21-bp deletion in the CD55 promotor region (rs2871582), which is associated with lower CD55 expression. Patients carrying this deletion may have a more favorable long-term disease outcome. Taken together, these results point out the relevance of the pre-C5 level of the complement cascade in the inflammatory processes underlying MMN.
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Affiliation(s)
- Jeroen W Bos
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Ewout J N Groen
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Henny G Otten
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kevin Budding
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Ruben P A van Eijk
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
- Biostatistics & Research Support, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Chantall Curial
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Tineke Kardol-Hoefnagel
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - H Stephan Goedee
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - W Ludo van der Pol
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
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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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Escudero-Pérez B, Lalande A, Mathieu C, Lawrence P. Host–Pathogen Interactions Influencing Zoonotic Spillover Potential and Transmission in Humans. Viruses 2023; 15:v15030599. [PMID: 36992308 PMCID: PMC10060007 DOI: 10.3390/v15030599] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Emerging infectious diseases of zoonotic origin are an ever-increasing public health risk and economic burden. The factors that determine if and when an animal virus is able to spill over into the human population with sufficient success to achieve ongoing transmission in humans are complex and dynamic. We are currently unable to fully predict which pathogens may appear in humans, where and with what impact. In this review, we highlight current knowledge of the key host–pathogen interactions known to influence zoonotic spillover potential and transmission in humans, with a particular focus on two important human viruses of zoonotic origin, the Nipah virus and the Ebola virus. Namely, key factors determining spillover potential include cellular and tissue tropism, as well as the virulence and pathogenic characteristics of the pathogen and the capacity of the pathogen to adapt and evolve within a novel host environment. We also detail our emerging understanding of the importance of steric hindrance of host cell factors by viral proteins using a “flytrap”-type mechanism of protein amyloidogenesis that could be crucial in developing future antiviral therapies against emerging pathogens. Finally, we discuss strategies to prepare for and to reduce the frequency of zoonotic spillover occurrences in order to minimize the risk of new outbreaks.
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Affiliation(s)
- Beatriz Escudero-Pérez
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
| | - Alexandre Lalande
- CIRI (Centre International de Recherche en Infectiologie), Team Neuro-Invasion, TROpism and VIRal Encephalitis, INSERM U1111, CNRS UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Cyrille Mathieu
- CIRI (Centre International de Recherche en Infectiologie), Team Neuro-Invasion, TROpism and VIRal Encephalitis, INSERM U1111, CNRS UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Philip Lawrence
- CONFLUENCE: Sciences et Humanités (EA 1598), Université Catholique de Lyon (UCLy), 69002 Lyon, France
- Correspondence:
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Schott BH, Wang L, Zhu X, Harding AT, Ko ER, Bourgeois JS, Washington EJ, Burke TW, Anderson J, Bergstrom E, Gardener Z, Paterson S, Brennan RG, Chiu C, McClain MT, Woods CW, Gregory SG, Heaton NS, Ko DC. Single-cell genome-wide association reveals that a nonsynonymous variant in ERAP1 confers increased susceptibility to influenza virus. CELL GENOMICS 2022; 2:100207. [PMID: 36465279 PMCID: PMC9718543 DOI: 10.1016/j.xgen.2022.100207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/26/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
During pandemics, individuals exhibit differences in risk and clinical outcomes. Here, we developed single-cell high-throughput human in vitro susceptibility testing (scHi-HOST), a method for rapidly identifying genetic variants that confer resistance and susceptibility. We applied this method to influenza A virus (IAV), the cause of four pandemics since the start of the 20th century. scHi-HOST leverages single-cell RNA sequencing (scRNA-seq) to simultaneously assign genetic identity to cells in mixed infections of cell lines of European, African, and Asian origin, reveal associated genetic variants for viral burden, and identify expression quantitative trait loci. Integration of scHi-HOST with human challenge and experimental validation demonstrated that a missense variant in endoplasmic reticulum aminopeptidase 1 (ERAP1; rs27895) increased IAV burden in cells and human volunteers. rs27895 exhibits population differentiation, likely contributing to greater permissivity of cells from African populations to IAV. scHi-HOST is a broadly applicable method and resource for decoding infectious-disease genetics.
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Affiliation(s)
- Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- These authors contributed equally
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- These authors contributed equally
| | - Xinyu Zhu
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Alfred T Harding
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Emily R Ko
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Hospital Medicine, Division of General Internal Medicine, Department of Medicine, Duke Regional Hospital, Durham, NC 27705, USA
| | - Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Erica J Washington
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Jack Anderson
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Emma Bergstrom
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Zoe Gardener
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Suzanna Paterson
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Richard G Brennan
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Christopher Chiu
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Micah T McClain
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
- Lead contact
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Zhao X, Li C, Chiu MC, Qiao R, Jiang S, Wang P, Zhou J. Rock1 is a novel host dependency factor of human enterovirus A71: Implication as a drug target. J Med Virol 2022; 94:5415-5424. [PMID: 35791459 DOI: 10.1002/jmv.27975] [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: 05/28/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 12/15/2022]
Abstract
Human enterovirus A71 (EV-A71) is the major causative agent of hand-foot-and-mouth disease (HFMD) commonly associated with severe neurological diseases, particularly in children under 5 years of age. Several investigational therapeutic agents and vaccine candidates are being developed. However, no approved drug against EV-A71 infection is available, and no proven drug target has been identified. Since host kinases are key regulators of multiple signaling pathways in response to viral infections, here we screened a kinase inhibitor library and identified potent inhibitors against EV-A71 infection. Among the hits, GSK269962A, a Rho Associated Coiled-Coil Containing Protein Kinase (Rock) inhibitor with potent antiviral activity, was selected for further analysis. We found that this Rock inhibitor not only efficiently suppressed the replication of EV-A71 in RD cells, but also in human intestinal organoids, in a dose-dependent manner. Interestingly, small interfering RNA depletion of Rock1, but not Rock2, significantly restricted viral replication in RD cells, indicating that Rock1 is a novel host dependency factor for EV-A71 replication and can serve as a target for the development of anti-EV-A71 therapeutics.
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Affiliation(s)
- Xiaoyu Zhao
- State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai, China.,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Cun Li
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Man Chun Chiu
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Rui Qiao
- State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Pengfei Wang
- State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai, China
| | - Jie Zhou
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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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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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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9
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Lage SL, Rocco JM, Laidlaw E, Rupert A, Galindo F, Kellogg A, Kumar P, Poon R, Wortmann GW, Lisco A, Manion M, Sereti I. Activation of Complement Components on Circulating Blood Monocytes From COVID-19 Patients. Front Immunol 2022; 13:815833. [PMID: 35250994 PMCID: PMC8892247 DOI: 10.3389/fimmu.2022.815833] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/25/2022] [Indexed: 12/13/2022] Open
Abstract
The coronavirus disease-2019 (COVID-19) caused by the SARS-CoV-2 virus may vary from asymptomatic to severe infection with multi-organ failure and death. Increased levels of circulating complement biomarkers have been implicated in COVID-19-related hyperinflammation and coagulopathy. We characterized systemic complement activation at a cellular level in 49-patients with COVID-19. We found increases of the classical complement sentinel C1q and the downstream C3 component on circulating blood monocytes from COVID-19 patients when compared to healthy controls (HCs). Interestingly, the cell surface-bound complement inhibitor CD55 was also upregulated in COVID-19 patient monocytes in comparison with HC cells. Monocyte membrane-bound C1q, C3 and CD55 levels were associated with plasma inflammatory markers such as CRP and serum amyloid A during acute infection. Membrane-bounds C1q and C3 remained elevated even after a short recovery period. These results highlight systemic monocyte-associated complement activation over a broad range of COVID-19 disease severities, with a compensatory upregulation of CD55. Further evaluation of complement and its interaction with myeloid cells at the membrane level could improve understanding of its role in COVID-19 pathogenesis.
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Affiliation(s)
- Silvia Lucena Lage
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Silvia Lucena Lage, ; Joseph M. Rocco,
| | - Joseph M. Rocco
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Silvia Lucena Lage, ; Joseph M. Rocco,
| | - Elizabeth Laidlaw
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Adam Rupert
- AIDS Monitoring Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - Frances Galindo
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Anela Kellogg
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - Princy Kumar
- Division of Infectious Diseases and Tropical Medicine, Georgetown University Medical Center, Washington, DC, United States
| | - Rita Poon
- Division of Hospital Medicine at MedStar Georgetown University Hospital, Washington, DC, United States
| | - Glenn W. Wortmann
- Section of Infectious Diseases, MedStar Washington Hospital Center, Washington, DC, United States
| | - Andrea Lisco
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Maura Manion
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Irini Sereti
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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10
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Van Goethem N, Danwang C, Bossuyt N, Van Oyen H, Roosens NHC, Robert A. A systematic review and meta-analysis of host genetic factors associated with influenza severity. BMC Genomics 2021; 22:912. [PMID: 34930124 PMCID: PMC8686082 DOI: 10.1186/s12864-021-08240-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/07/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The severity of influenza disease can range from mild symptoms to severe respiratory failure and can partly be explained by host genetic factors that predisposes the host to severe influenza. Here, we aimed to summarize the current state of evidence that host genetic variants play a role in the susceptibility to severe influenza infection by conducting a systematic review and performing a meta-analysis for all markers with at least three or more data entries. RESULTS A total of 34 primary human genetic association studies were identified that investigated a total of 20 different genes. The only significant pooled ORs were retrieved for the rs12252 polymorphism: an overall OR of 1.52 (95% CI [1.06-2.17]) for the rs12252-C allele compared to the rs12252-T allele. A stratified analysis by ethnicity revealed opposite effects in different populations. CONCLUSION With exception for the rs12252 polymorphism, we could not identify specific genetic polymorphisms to be associated with severe influenza infection in a pooled meta-analysis. This advocates for the use of large, hypothesis-free, genome-wide association studies that account for the polygenic nature and the interactions with other host, pathogen and environmental factors.
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Affiliation(s)
- Nina Van Goethem
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Brussels, Belgium
| | - Célestin Danwang
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Brussels, Belgium
| | - Nathalie Bossuyt
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Herman Van Oyen
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Public Health and Primary Care, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Annie Robert
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Brussels, Belgium
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11
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Alagarasu K, Kaushal H, Shinde P, Kakade M, Chaudhary U, Padbidri V, Sangle SA, Salvi S, Bavdekar AR, D’costa P, Choudhary ML. TNFA and IL10 Polymorphisms and IL-6 and IL-10 Levels Influence Disease Severity in Influenza A(H1N1)pdm09 Virus Infected Patients. Genes (Basel) 2021; 12:genes12121914. [PMID: 34946862 PMCID: PMC8700762 DOI: 10.3390/genes12121914] [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: 08/27/2021] [Revised: 11/20/2021] [Accepted: 11/26/2021] [Indexed: 12/05/2022] Open
Abstract
Cytokines are key modulators of immune response, and dysregulated production of proinflammatory and anti-inflammatory cytokines contributes to the pathogenesis of influenza A(H1N1)pdm09 virus infection. Cytokine production is impacted by single nucleotide polymorphisms (SNPs) in the genes coding for them. In the present study, SNPs in the IL6, TNFA, IFNG, IL17A, IL10, and TGFB were investigated for their association with disease severity and fatality in influenza A(H1N1)pdm09-affected patients with mild disease (n = 293) and severe disease (n = 86). Among those with severe disease, 41 patients had fatal outcomes. In a subset of the patients, levels of IL-2, IL-4, IL-6, IL-10, TNF, IFN-γ, and IL-17 were assayed in the plasma for their association with severe disease. The frequency of TNFA rs1800629 G/A allele was significantly higher in severe cases and survived severe cases group compared to that of those with mild infection (OR with 95% for mild vs. severe cases 2.95 (1.52–5.73); mild vs. survived severe cases 4.02 (1.84–8.82)). IL10 rs1800896-rs1800872 G-C haplotype was significantly lower (OR with 95% 0.34 (0.12–0.95)), while IL10 rs1800896-rs1800872 G-A haplotype was significantly higher (OR with 95% 12.11 (2.23–76.96)) in fatal cases group compared to that of the mild group. IL-6 and IL-10 levels were significantly higher in fatal cases compared to that of survived severe cases. IL-6 levels had greater discriminatory power than IL-10 to predict progression to fatal outcome in influenza A(H1N1)pdm09 virus-infected patients. To conclude, the present study reports the association of TNFA and IL10 SNPs with severe disease in Influenza A(H1N1)pdm09 virus-infected subjects. Furthermore, IL-6 levels can be a potential biomarker for predicting fatal outcomes in Influenza A(H1N1)pdm09 virus infected subjects.
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Affiliation(s)
- Kalichamy Alagarasu
- ICMR-National Institute of Virology, Pune 411001, India; (K.A.); (H.K.); (P.S.); (M.K.); (U.C.)
| | - Himanshu Kaushal
- ICMR-National Institute of Virology, Pune 411001, India; (K.A.); (H.K.); (P.S.); (M.K.); (U.C.)
| | - Pooja Shinde
- ICMR-National Institute of Virology, Pune 411001, India; (K.A.); (H.K.); (P.S.); (M.K.); (U.C.)
| | - Mahadeo Kakade
- ICMR-National Institute of Virology, Pune 411001, India; (K.A.); (H.K.); (P.S.); (M.K.); (U.C.)
| | - Urmila Chaudhary
- ICMR-National Institute of Virology, Pune 411001, India; (K.A.); (H.K.); (P.S.); (M.K.); (U.C.)
| | | | - Shashikala A. Sangle
- Department of Medicine, BJ Medical College, Pune 411001, India; (S.A.S.); (S.S.)
| | - Sonali Salvi
- Department of Medicine, BJ Medical College, Pune 411001, India; (S.A.S.); (S.S.)
| | | | - Pradeep D’costa
- KEM Hospital Research Center, Pune 411001, India; (A.R.B.); (P.D.)
| | - Manohar Lal Choudhary
- ICMR-National Institute of Virology, Pune 411001, India; (K.A.); (H.K.); (P.S.); (M.K.); (U.C.)
- Correspondence: ; Tel.: +91-020-26006270
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12
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Adams K, Tenforde MW, Chodisetty S, Lee B, Chow EJ, Self WH, Patel MM. A literature review of severity scores for adults with influenza or community-acquired pneumonia - implications for influenza vaccines and therapeutics. Hum Vaccin Immunother 2021; 17:5460-5474. [PMID: 34757894 DOI: 10.1080/21645515.2021.1990649] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Influenza vaccination and antiviral therapeutics may attenuate disease, decreasing severity of illness in vaccinated and treated persons. Standardized assessment tools, definitions of disease severity, and clinical endpoints would support characterizing the attenuating effects of influenza vaccines and antivirals. We review potential clinical parameters and endpoints that may be useful for ordinal scales evaluating attenuating effects of influenza vaccines and antivirals in hospital-based studies. In studies of influenza and community-acquired pneumonia, common physiologic parameters that predicted outcomes such as mortality, ICU admission, complications, and duration of stay included vital signs (hypotension, tachypnea, fever, hypoxia), laboratory results (blood urea nitrogen, platelets, serum sodium), and radiographic findings of infiltrates or effusions. Ordinal scales based on these parameters may be useful endpoints for evaluating attenuating effects of influenza vaccines and therapeutics. Factors such as clinical and policy relevance, reproducibility, and specificity of measurements should be considered when creating a standardized ordinal scale for assessment.
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Affiliation(s)
- Katherine Adams
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mark W Tenforde
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Shreya Chodisetty
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Benjamin Lee
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Eric J Chow
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wesley H Self
- Department of Emergency Medicine and Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Manish M Patel
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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13
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Complement Decay-Accelerating Factor is a modulator of influenza A virus lung immunopathology. PLoS Pathog 2021; 17:e1009381. [PMID: 34197564 PMCID: PMC8248730 DOI: 10.1371/journal.ppat.1009381] [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: 02/12/2021] [Accepted: 05/26/2021] [Indexed: 12/13/2022] Open
Abstract
Clearance of viral infections, such as SARS-CoV-2 and influenza A virus (IAV), must be fine-tuned to eliminate the pathogen without causing immunopathology. As such, an aggressive initial innate immune response favors the host in contrast to a detrimental prolonged inflammation. The complement pathway bridges innate and adaptive immune system and contributes to the response by directly clearing pathogens or infected cells, as well as recruiting proinflammatory immune cells and regulating inflammation. However, the impact of modulating complement activation in viral infections is still unclear. In this work, we targeted the complement decay-accelerating factor (DAF/CD55), a surface protein that protects cells from non-specific complement attack, and analyzed its role in IAV infections. We found that DAF modulates IAV infection in vivo, via an interplay with the antigenic viral proteins hemagglutinin (HA) and neuraminidase (NA), in a strain specific manner. Our results reveal that, contrary to what could be expected, DAF potentiates complement activation, increasing the recruitment of neutrophils, monocytes and T cells. We also show that viral NA acts on the heavily sialylated DAF and propose that the NA-dependent DAF removal of sialic acids exacerbates complement activation, leading to lung immunopathology. Remarkably, this mechanism has no impact on viral loads, but rather on the host resilience to infection, and may have direct implications in zoonotic influenza transmissions. Exacerbated complement activation and immune deregulation are at the basis of several pathologies induced by respiratory viruses. Here, we report that complement decay-accelerating factor (DAF), which inhibits complement activation in healthy cells, increases disease severity upon influenza A virus (IAV) infection. Remarkably, DAF interaction with IAV proteins, hemagglutinin (HA) and neuraminidase (NA), resulted in excessive complement activation and recruitment of innate and adaptive immune cells, without affecting viral loads. Furthermore, we observed that viral NA directly cleaves DAF and promotes complement activation, providing a possible link between IAV-DAF interaction and pathology. Therefore, our results unveil a novel pathway that could modulate disease severity, which may help to understand the increased pathogenicity of zoonotic and pandemic IAV infections.
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14
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Cotroneo CE, Mangano N, Dragani TA, Colombo F. Lung expression of genes putatively involved in SARS-CoV-2 infection is modulated in cis by germline variants. Eur J Hum Genet 2021; 29:1019-1026. [PMID: 33649539 PMCID: PMC7917374 DOI: 10.1038/s41431-021-00831-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/09/2020] [Accepted: 02/09/2021] [Indexed: 01/10/2023] Open
Abstract
Germline variants in genes involved in SARS-CoV-2 cell entry and in host innate immune responses to viruses may influence the susceptibility to infection. This study used whole-genome analyses of lung tissue to identify polymorphisms acting as expression quantitative trait loci (eQTLs) for 60 genes of relevance to SARS-CoV-2 infection susceptibility. The expression of genes with confirmed or possible roles in viral entry-replication and in host antiviral responses was studied in the non-diseased lung tissue of 408 lung adenocarcinoma patients. No gene was differently expressed by sex, but APOBEC3H levels were higher and PARP12 levels lower in older individuals. A total of 125 cis-eQTLs (false discovery rate < 0.05) was found to modulate mRNA expression of 15 genes (ABO, ANPEP, AP2A2, APOBEC3D, APOBEC3G, BSG, CLEC4G, DDX58, DPP4, FURIN, FYCO1, RAB14, SERINC3, TRIM5, ZCRB1). eQTLs regulating ABO and FYCO1 were found in COVID-19 susceptibility loci. No trans-eQTLs were identified. Genetic control of the expression of these 15 genes, which encode putative virus receptors, proteins required for vesicle trafficking, enzymes that interfere with viral replication, and other restriction factors, may underlie interindividual differences in risk or severity of infection with SARS-CoV-2 or other viruses.
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Affiliation(s)
- Chiara E Cotroneo
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Nunzia Mangano
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Tommaso A Dragani
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
| | - Francesca Colombo
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate, MI, Italy
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15
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Mettelman RC, Thomas PG. Human Susceptibility to Influenza Infection and Severe Disease. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038711. [PMID: 31964647 PMCID: PMC8091954 DOI: 10.1101/cshperspect.a038711] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Influenza viruses are a persistent threat to global human health. Increased susceptibility to infection and the risk factors associated with progression to severe influenza-related disease are determined by a multitude of viral, host, and environmental conditions. Decades of epidemiologic research have broadly defined high-risk groups, while new genomic association studies have identified specific host factors impacting an individual's response to influenza. Here, we review and highlight both human susceptibility to influenza infection and the conditions that lead to severe influenza disease.
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Affiliation(s)
- Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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16
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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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17
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Darbeheshti F, Mahdiannasser M, Uhal BD, Ogino S, Gupta S, Rezaei N. Interindividual immunogenic variants: Susceptibility to coronavirus, respiratory syncytial virus and influenza virus. Rev Med Virol 2021; 31:e2234. [PMID: 33724604 PMCID: PMC8250219 DOI: 10.1002/rmv.2234] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/28/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022]
Abstract
The coronavirus disease (Covid‐19) pandemic is the most serious event of the year 2020, causing considerable global morbidity and mortality. The goal of this review is to provide a comprehensive summary of reported associations between inter‐individual immunogenic variants and disease susceptibility or symptoms caused by the coronavirus strains severe acute respiratory syndrome‐associated coronavirus, severe acute respiratory syndrome‐associated coronavirus‐2, and two of the main respiratory viruses, respiratory syncytial virus and influenza virus. The results suggest that the genetic background of the host could affect the levels of proinflammatory and anti‐inflammatory cytokines and might modulate the progression of Covid‐19 in affected patients. Notably, genetic variations in innate immune components such as toll‐like receptors and mannose‐binding lectin 2 play critical roles in the ability of the immune system to recognize coronavirus and initiate an early immune response to clear the virus and prevent the development of severe symptoms. This review provides promising clues related to the potential benefits of using immunotherapy and immune modulation for respiratory infectious disease treatment in a personalized manner.
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Affiliation(s)
- Farzaneh Darbeheshti
- Department of Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Medical Genetics Network (MeGeNe), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Mojdeh Mahdiannasser
- Department of Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, Michigan, USA
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Cancer Immunology and Cancer Epidemiology Programs, Dana-Farber Harvard Cancer Center, Boston, Massachusetts, USA
| | - Sudhir Gupta
- Division of Basic and Clinical Immunology, Department of Medicine, University of California, Irvine, California, USA
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
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18
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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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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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de Boer ECW, van Mourik AG, Jongerius I. Therapeutic Lessons to be Learned From the Role of Complement Regulators as Double-Edged Sword in Health and Disease. Front Immunol 2020; 11:578069. [PMID: 33362763 PMCID: PMC7758290 DOI: 10.3389/fimmu.2020.578069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
The complement system is an important part of the innate immune system, providing a strong defense against pathogens and removing apoptotic cells and immune complexes. Due to its strength, it is important that healthy human cells are protected against damage induced by the complement system. To be protected from complement, each cell type relies on a specific combination of both soluble and membrane-bound regulators. Their importance is indicated by the amount of pathologies associated with abnormalities in these complement regulators. Here, we will discuss the current knowledge on complement regulatory protein polymorphisms and expression levels together with their link to disease. These diseases often result in red blood cell destruction or occur in the eye, kidney or brain, which are tissues known for aberrant complement activity or regulation. In addition, complement regulators have also been associated with different types of cancer, although their mechanisms here have not been elucidated yet. In most of these pathologies, treatments are limited and do not prevent the complement system from attacking host cells, but rather fight the consequences of the complement-mediated damage, using for example blood transfusions in anemic patients. Currently only few drugs targeting the complement system are used in the clinic. With further demand for therapeutics rising linked to the wide range of complement-mediated disease we should broaden our horizon towards treatments that can actually protect the host cells against complement. Here, we will discuss the latest insights on how complement regulators can benefit therapeutics. Such therapeutics are currently being developed extensively, and can be categorized into full-length complement regulators, engineered complement system regulators and antibodies targeting complement regulators. In conclusion, this review provides an overview of the complement regulatory proteins and their links to disease, together with their potential in the development of novel therapeutics.
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Affiliation(s)
- Esther C W de Boer
- Sanquin Research, Department of Immunopathology, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands.,Department of Pediatric Immunology, Rheumatology, and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Anouk G van Mourik
- Sanquin Research, Department of Immunopathology, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands
| | - Ilse Jongerius
- Sanquin Research, Department of Immunopathology, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands.,Department of Pediatric Immunology, Rheumatology, and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, Netherlands
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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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Ghafouri-Fard S, Noroozi R, Vafaee R, Branicki W, Poṡpiech E, Pyrc K, Łabaj PP, Omrani MD, Taheri M, Sanak M. Effects of host genetic variations on response to, susceptibility and severity of respiratory infections. Biomed Pharmacother 2020; 128:110296. [PMID: 32480226 PMCID: PMC7258806 DOI: 10.1016/j.biopha.2020.110296] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/16/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
The recent outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a global crisis, necessitating the identification of genetic factors that modulate the risk of disorder or its severity. The current data about the role of genetic risk factors in determination of rate of SARS-CoV-2 infection in each ethnic group and the severity of disorder is limited. Moreover, several confounding parameters such as the number of tests performed in each country, the structure of the population especially the age distribution, the presence of risk factors for respiratory disorders such as smoking and other environmental factors might be involved in the variability in disease course or prevalence of infection among different ethnic groups. However, assessment of the role of genetic variants in determination of the course of other respiratory infections might help in recognition of possible candidate for further analysis in patients affected with SARS-CoV-2. In the current review, we summarize the data showing the association between genomic variants and risk of acute respiratory distress syndrome, respiratory infections or severity of these conditions with an especial focus on the SARS-CoV-2.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Reza Vafaee
- Proteomics Research Center, Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Ewelina Poṡpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Krzysztof Pyrc
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Paweł P Łabaj
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Mir Davood Omrani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Marek Sanak
- Department of Internal Medicine, Jagiellonian University Medical College, Krakow, Poland.
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23
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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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24
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Martins JSC, Oliveira MLA, Garcia CC, Siqueira MM, Matos AR. Investigation of Human IFITM3 Polymorphisms rs34481144A and rs12252C and Risk for Influenza A(H1N1)pdm09 Severity in a Brazilian Cohort. Front Cell Infect Microbiol 2020; 10:352. [PMID: 32754450 PMCID: PMC7366732 DOI: 10.3389/fcimb.2020.00352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
Influenza is a major public health problem that causes acute respiratory infection in humans. Identification of host factors influencing in disease outcome is critical for recognition of individuals with increased risk. Investigations on the role of rs34481144A and rs12252C IFITM3 polymorphisms in influenza A(H1N1)pdm09 severity is not yet conclusively determined. This study aimed to evaluate such polymorphisms frequencies and IFITM3 levels in an infected Brazilian cohort of 314 influenza A(H1N1)pdm09 cases and its putative association with clinical, epidemiological and virological data. Individuals were clinically classified into mild, severe and fatal cases. IFITM3 polymorphisms were detected by specific Taqman probes in real time PCR reactions. IFITM3 levels were determined by quantitative real time PCR. Thus, the different clinical groups presented similar distribution of rs34481144 and rs12252 genotypes and allelic frequencies. There was no significant association between the polymorphisms with severity of disease by using distinct genetic models. Additionally, geographic distribution of mutants showed that rs34481144A allele was more predominant in Brazilian Southern region. In contrast, rs12252C allele presented similar frequencies in all regions. Individuals with the distinct rs34481144 and rs12252 genotypes showed similar levels of IFITM3 and viral load in their respiratory specimens. Furthermore, IFITM3 levels were comparable in the distinct clinical groups and were not correlated with influenza viral load in analyzed samples. Thereby, rs34481144A and rs12252C polymorphisms were not associated with severity or mortality of influenza A(H1N1)pdm09 infection nor with IFITM3 transcript levels and influenza viral load in upper respiratory tract samples in a Brazilian cohort.
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Affiliation(s)
- Jéssica S. C. Martins
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Maria L. A. Oliveira
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Cristiana C. Garcia
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Marilda M. Siqueira
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Aline R. Matos
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
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25
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Zhao X, Chu H, Wong BHY, Chiu MC, Wang D, Li C, Liu X, Yang D, Poon VKM, Cai J, Chan JFW, To KKW, Zhou J, Yuen KY. Activation of C-Type Lectin Receptor and (RIG)-I-Like Receptors Contributes to Proinflammatory Response in Middle East Respiratory Syndrome Coronavirus-Infected Macrophages. J Infect Dis 2020; 221:647-659. [PMID: 31562757 PMCID: PMC7107474 DOI: 10.1093/infdis/jiz483] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/20/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human infection with Middle East respiratory syndrome coronavirus (MERS-CoV) poses an ongoing threat to public health worldwide. The studies of MERS patients with severe disease and experimentally infected animals showed that robust viral replication and intensive proinflammatory response in lung tissues contribute to high pathogenicity of MERS-CoV. We sought to identify pattern recognition receptor (PRR) signaling pathway(s) that mediates the inflammatory cascade in human macrophages upon MERS-CoV infection. METHODS The potential signaling pathways were manipulated individually by pharmacological inhibition, small interfering ribonucleic acid (siRNA) depletion, and antibody blocking. The MERS-CoV-induced proinflammatory response was evaluated by measuring the expression levels of key cytokines and/or chemokines. Reverse transcription-quantitative polymerase chain reaction assay, flow cytometry analysis, and Western blotting were applied to evaluate the activation of related PRRs and engagement of adaptors. RESULTS MERS-CoV replication significantly upregulated C-type lectin receptor (CLR) macrophage-inducible Ca2+-dependent lectin receptor (Mincle). The role of Mincle for MERS-CoV-triggered cytokine/chemokine induction was established based on the results of antibody blockage, siRNA depletion of Mincle and its adaptor spleen tyrosine kinase (Syk), and Syk pharmacological inhibition. The cytokine and/or chemokine induction was significantly attenuated by siRNA depletion of retinoic acid-inducible-I-like receptors (RLR) or adaptor, indicating that RLR signaling also contributed to MERS-CoV-induced proinflammatory response. CONCLUSIONS The CLR and RLR pathways are activated and contribute to the proinflammatory response in MERS-CoV-infected macrophages.
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Affiliation(s)
- Xiaoyu Zhao
- State Key Laboratory of Emerging Infectious Diseases, Pokfulam, Hong Kong
- Department of Microbiology, Pokfulam, Hong Kong
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Pokfulam, Hong Kong
- Department of Microbiology, Pokfulam, Hong Kong
| | - Bosco Ho-Yin Wong
- State Key Laboratory of Emerging Infectious Diseases, Pokfulam, Hong Kong
| | | | - Dong Wang
- Department of Microbiology, Pokfulam, Hong Kong
| | - Cun Li
- Department of Microbiology, Pokfulam, Hong Kong
| | | | - Dong Yang
- Department of Microbiology, Pokfulam, Hong Kong
| | | | | | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Pokfulam, Hong Kong
- Department of Microbiology, Pokfulam, Hong Kong
- Carol Yu Centre for Infection, Pokfulam, Hong Kong
- The Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, Pokfulam, Hong Kong
- Department of Microbiology, Pokfulam, Hong Kong
- Carol Yu Centre for Infection, Pokfulam, Hong Kong
- The Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, Pokfulam, Hong Kong
- Department of Microbiology, Pokfulam, Hong Kong
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Pokfulam, Hong Kong
- Department of Microbiology, Pokfulam, Hong Kong
- Carol Yu Centre for Infection, Pokfulam, Hong Kong
- The Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
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26
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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: 59] [Impact Index Per Article: 11.8] [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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27
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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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28
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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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29
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Clohisey S, Baillie JK. Host susceptibility to severe influenza A virus infection. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2019; 23:303. [PMID: 31488196 PMCID: PMC6729070 DOI: 10.1186/s13054-019-2566-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/13/2019] [Indexed: 11/30/2022]
Abstract
Most people exposed to a new flu virus do not notice any symptoms. A small minority develops critical illness. Some of this extremely broad variation in susceptibility is explained by the size of the initial inoculum or the influenza exposure history of the individual; some is explained by generic host factors, such as frailty, that decrease resilience following any systemic insult. Some demographic factors (pregnancy, obesity, and advanced age) appear to confer a more specific susceptibility to severe illness following infection with influenza viruses. As with other infectious diseases, a substantial component of susceptibility is determined by host genetics. Several genetic susceptibility variants have now been reported with varying levels of evidence. Susceptible hosts may have impaired intracellular controls of viral replication (e.g. IFITM3, TMPRS22 variants), defective interferon responses (e.g. GLDC, IRF7/9 variants), or defects in cell-mediated immunity with increased baseline levels of systemic inflammation (obesity, pregnancy, advanced age). These mechanisms may explain the prolonged viral replication reported in critically ill patients with influenza: patients with life-threatening disease are, by definition, abnormal hosts. Understanding these molecular mechanisms of susceptibility may in the future enable the design of host-directed therapies to promote resilience.
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Affiliation(s)
- Sara Clohisey
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - John Kenneth Baillie
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK. .,Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.
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30
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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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31
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Abstract
Pneumonia is a highly prevalent disease with considerable morbidity and mortality. However, diagnosis and therapy still rely on antiquated methods, leading to the vast overuse of antimicrobials, which carries risks for both society and the individual. Furthermore, outcomes in severe pneumonia remain poor. Genomic techniques have the potential to transform the management of pneumonia through deep characterization of pathogens as well as the host response to infection. This characterization will enable the delivery of selective antimicrobials and immunomodulatory therapy that will help to offset the disorder associated with overexuberant immune responses.
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Affiliation(s)
- Samir Gautam
- Pulmonary Critical Care and Sleep Medicine, Center for Pulmonary Infection Research and Treatment, Yale University, 300 Cedar Street, TACS441, New Haven, CT 06520-8057, USA
| | - Lokesh Sharma
- Pulmonary Critical Care and Sleep Medicine, Center for Pulmonary Infection Research and Treatment, Yale University, 300 Cedar Street, TACS441, New Haven, CT 06520-8057, USA
| | - Charles S Dela Cruz
- Pulmonary Critical Care and Sleep Medicine, Center for Pulmonary Infection Research and Treatment, Yale University, 300 Cedar Street, TACS441, New Haven, CT 06520-8057, USA.
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32
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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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33
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Wellington D, Laurenson-Schafer H, Abdel-Haq A, Dong T. IFITM3: How genetics influence influenza infection demographically. Biomed J 2019; 42:19-26. [PMID: 30987701 PMCID: PMC6468115 DOI: 10.1016/j.bj.2019.01.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/06/2018] [Accepted: 01/07/2019] [Indexed: 12/18/2022] Open
Abstract
The role of host genetics in influenza infection is unclear despite decades of interest. Confounding factors such as age, sex, ethnicity and environmental factors have made it difficult to assess the role of genetics without influence. In recent years a single nucleotide polymorphism, interferon-induced transmembrane protein 3 (IFITM3) rs12252, has been shown to alter the severity of influenza infection in Asian populations. In this review we investigate this polymorphism as well as several others suggested to alter the host's defence against influenza infection. In addition, we highlight the open questions surrounding the viral restriction protein IFITM3 with the hope that by answering some of these questions we can elucidate the mechanism of IFITM3 viral restriction and therefore how this restriction is altered due to the rs12252 polymorphism.
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Affiliation(s)
- Dannielle Wellington
- MRC Human Immunology Unit, WIMM, University of Oxford, OX3 9DS, UK; CAMS Oxford Institute, Nuffield Department of Medicine, Oxford University, OX3 9FZ, UK.
| | - Henry Laurenson-Schafer
- MRC Human Immunology Unit, WIMM, University of Oxford, OX3 9DS, UK; CAMS Oxford Institute, Nuffield Department of Medicine, Oxford University, OX3 9FZ, UK
| | - Adi Abdel-Haq
- MRC Human Immunology Unit, WIMM, University of Oxford, OX3 9DS, UK; Martin-Luther-University, Halle-Wittenberg, Germany
| | - Tao Dong
- MRC Human Immunology Unit, WIMM, University of Oxford, OX3 9DS, UK; CAMS Oxford Institute, Nuffield Department of Medicine, Oxford University, OX3 9FZ, UK.
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34
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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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35
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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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36
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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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37
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Cockrell AS, Leist SR, Douglas MG, Baric RS. Modeling pathogenesis of emergent and pre-emergent human coronaviruses in mice. Mamm Genome 2018; 29:367-383. [PMID: 30043100 PMCID: PMC6132729 DOI: 10.1007/s00335-018-9760-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 07/17/2018] [Indexed: 12/21/2022]
Abstract
The emergence of highly pathogenic human coronaviruses (hCoVs) in the last two decades has illuminated their potential to cause high morbidity and mortality in human populations and disrupt global economies. Global pandemic concerns stem from their high mortality rates, capacity for human-to-human spread by respiratory transmission, and complete lack of approved therapeutic countermeasures. Limiting disease may require the development of virus-directed and host-directed therapeutic strategies due to the acute etiology of hCoV infections. Therefore, understanding how hCoV–host interactions cause pathogenic outcomes relies upon mammalian models that closely recapitulate the pathogenesis of hCoVs in humans. Pragmatism has largely been the driving force underpinning mice as highly effective mammalian models for elucidating hCoV–host interactions that govern pathogenesis. Notably, tractable mouse genetics combined with hCoV reverse genetic systems has afforded the concomitant manipulation of virus and host genetics to evaluate virus–host interaction networks in disease. In addition to assessing etiologies of known hCoVs, mouse models have clinically predictive value as tools to appraise potential disease phenotypes associated with pre-emergent CoVs. Knowledge of CoV pathogenic potential before it crosses the species barrier into the human population provides a highly desirable preclinical platform for addressing global pathogen preparedness, an overarching directive of the World Health Organization. Although we recognize that results obtained in robust mouse models require evaluation in non-human primates, we focus this review on the current state of hCoV mouse models, their use as tractable complex genetic organisms for untangling complex hCoV–host interactions, and as pathogenesis models for preclinical evaluation of novel therapeutic interventions.
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Affiliation(s)
- Adam S Cockrell
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Madeline G Douglas
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599, USA. .,Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599, USA.
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38
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Wen L, Chu H, Wong BHY, Wang D, Li C, Zhao X, Chiu MC, Yuan S, Fan Y, Chen H, Zhou J, Yuen KY. Large-scale sequence analysis reveals novel human-adaptive markers in PB2 segment of seasonal influenza A viruses. Emerg Microbes Infect 2018; 7:47. [PMID: 29593225 PMCID: PMC5874250 DOI: 10.1038/s41426-018-0050-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/09/2018] [Accepted: 02/18/2018] [Indexed: 12/12/2022]
Abstract
To elucidate the adaptive strategies of influenza A viruses (IAVs) to human, we proposed a computational approach to identify human-adaptive mutations in seasonal IAVs, which have not been analyzed comprehensively. We compared representative PB2 sequences of 1425 avian IAVs and 2176 human IAVs and identified a total of 42 human-adaptive markers, including 28 and 31 markers in PB2 proteins of seasonal viruses H1N1 and H3N2, respectively. Notably, this comprehensive list encompasses almost all the markers identified in prior computational studies and 21 novel markers including an experimentally verified mutation K526R, suggesting the predictive power of our method. The strength of our analysis derives from the enormous amount of recently available sequences as well as the recognition that human-adaptive mutations are not necessarily conserved across subtypes. We also utilized mutual information to profile the inter-residue coevolution in PB2 protein. A total of 35 and 46 coevolving site pairs are identified in H1N1 and H3N2, respectively. Interestingly, 13 out of the 28 (46.4%) identified markers in H1N1 and 16 out of the 31 (51.6%) in H3N2 are embraced in the coevolving pairs. Many of them are paired with well-characterized human-adaptive mutations, indicating potential epistatic effect of these coevolving residues in human adaptation. Additionally, we reconstructed the PB2 evolutionary history of seasonal IAVs and demonstrated the distinct adaptive pathway of PB2 segment after reassortment from H1 to H3 lineage. Our study may provide clues for further experimental validation of human-adaptive mutations and shed light on the human adaptation process of seasonal IAVs.
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Affiliation(s)
- Lei Wen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Hin Chu
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
| | - Bosco Ho-Yin Wong
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
| | - Dong Wang
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Cun Li
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Xiaoyu Zhao
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Man-Chun Chiu
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Shuofeng Yuan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Yanhui Fan
- Department of Biochemistry, The University of Hong Kong, Hong Kong, China
| | - Honglin Chen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Jie Zhou
- Department of Microbiology, The University of Hong Kong, Hong Kong, China. .,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China. .,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
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39
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Zhang Y, Zhang Z, Cao L, Lin J, Yang Z, Zhang X. A common CD55 rs2564978 variant is associated with the susceptibility of non-small cell lung cancer. Oncotarget 2018; 8:6216-6221. [PMID: 28008159 PMCID: PMC5351625 DOI: 10.18632/oncotarget.14053] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/12/2016] [Indexed: 11/25/2022] Open
Abstract
CD55, as one of key membrane-bound complement-regulatory proteins (mCRPs), is crucial for the progression of various cancers. This study aims to investigate the role of CD55 variants in the development of non-small cell lung cancer (NSCLC). A case-control study, including 706 lung cancer cases and 706 health controls, was conducted in a Chinese population. The odds ratio (OR) and 95% confidence interval (95% CI) were estimated by unconditional logistic regression. We found that significantly higher lung cancer risk was linked with CD55 rs2564978 CC genotype (OR = 1.52, 95% CI = 1.11−2.07) or CT genotypes (OR = 1.34, 95% CI = 1.05−1.71), compared to the TT genotype. Stratified analysis showed that rs2564978 CC was associated with NSCLC risk among males (OR = 1.69, 95% CI = 1.14−2.49) and older subjects (OR = 1.75, 95% CI = 1.08−2.82). When stratified by smoking status, the risk effect of rs2564978 CC was more evident among smokers (OR = 2.01, 95% CI = 1.18−3.43) than non-smokers (OR = 1.30, 95% CI = 0.88−1.90). We also conducted the stratified analysis by NSCLC histological types and found that CD55 rs2564978 CC increased the risk of adenocarcinoma with OR (95% CI) of 1.35 (1.01−1.80). The reporter gene expression driven by rs2564978T-containing CD55 promoter was respectively 1.48-fold, 1.96-fold and 1.93-fold higher than those driven by the rs2564978C-containing CD55 promoter in A549, NCI-H2030 and NCI-H23 cells (P = 0.045, 0.010 and < 0.001). These findings indicate that CD55 rs2564978 polymorphism may contribute to an increased risk of NSCLC in Chinese population.
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Affiliation(s)
- Yanyan Zhang
- Institute of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China.,Institute of Epidemiology, School of Public Health, North China University of Science and Technology, Tangshan, China
| | - Zhi Zhang
- Affiliated Tangshan Gongren Hospital, North China University of Science and Technology, Tangshan, China
| | - Lei Cao
- Institute of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China
| | - Jia Lin
- Institute of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China
| | - Zhenbang Yang
- Institute of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China
| | - Xuemei Zhang
- Institute of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China
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40
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Kulkarni HS, Liszewski MK, Brody SL, Atkinson JP. The complement system in the airway epithelium: An overlooked host defense mechanism and therapeutic target? J Allergy Clin Immunol 2018; 141:1582-1586.e1. [PMID: 29339260 DOI: 10.1016/j.jaci.2017.11.046] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 11/02/2017] [Accepted: 11/13/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Hrishikesh S Kulkarni
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University in St Louis, St Louis, Mo; Division of Rheumatology, Department of Medicine, Washington University in St Louis, St Louis, Mo
| | - M Kathryn Liszewski
- Division of Rheumatology, Department of Medicine, Washington University in St Louis, St Louis, Mo
| | - Steven L Brody
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University in St Louis, St Louis, Mo
| | - John P Atkinson
- Division of Rheumatology, Department of Medicine, Washington University in St Louis, St Louis, Mo.
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41
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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: 45] [Impact Index Per Article: 6.4] [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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Mizuno M, Suzuki Y, Ito Y. Complement regulation and kidney diseases: recent knowledge of the double-edged roles of complement activation in nephrology. Clin Exp Nephrol 2017; 22:3-14. [DOI: 10.1007/s10157-017-1405-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/14/2017] [Indexed: 12/28/2022]
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Chan-Hui PY, Swiderek KM. Immunological considerations for developing antibody therapeutics for Influenza A. Hum Vaccin Immunother 2016; 12:474-7. [PMID: 26325257 DOI: 10.1080/21645515.2015.1079676] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Influenza infection can give rise to serious illness leading to complications and hospitalization of patients. The efficacy of current standard of care is very limited and provides little relief for patients hospitalized with serious flu. Human monoclonal antibodies (mAb) against influenza are being developed as new treatment options for this patient population. When developing antibody therapeutics, it is important to consider all possible immunologic effects of the antibodies on viral infection and disease progression including those other than the postulated therapeutic mechanisms. An area of concern is the potential of antibody-dependent enhancement (ADE) of illness. ADE of viral infections has been extensively described for Dengue virus (DENV) but not for influenza. Recently, preliminary results from clinical viral challenge studies of anti-HA-stalk mAbs suggested the possibility of enhanced viral shedding, raising concerns for ADE when utilizing mAbs as therapeutic intervention for influenza although viral shedding was not enhanced in the clinical viral challenge of anti-M2 mAb TCN-032. We herein discuss the known mechanisms of ADE and their relevance to developing mAbs such as anti-HA and anti-M2 for influenza disease.
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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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45
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Ciancanelli MJ, Abel L, Zhang SY, Casanova JL. Host genetics of severe influenza: from mouse Mx1 to human IRF7. Curr Opin Immunol 2016; 38:109-20. [PMID: 26761402 PMCID: PMC4733643 DOI: 10.1016/j.coi.2015.12.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/30/2015] [Accepted: 12/03/2015] [Indexed: 12/22/2022]
Abstract
Influenza viruses cause mild to moderate respiratory illness in most people, and only rarely devastating or fatal infections. The virulence factors encoded by viral genes can explain seasonal or geographic differences at the population level but are unlikely to account for inter-individual clinical variability. Inherited or acquired immunodeficiencies may thus underlie severe cases of influenza. The crucial role of host genes was first demonstrated by forward genetics in inbred mice, with the identification of interferon (IFN)-α/β-inducible Mx1 as a canonical influenza susceptibility gene. Reverse genetics has subsequently characterized the in vivo role of other mouse genes involved in IFN-α/β and -λ immunity. A series of in vitro studies with mouse and human cells have also refined the cell-intrinsic mechanisms of protection against influenza viruses. Population-based human genetic studies have not yet uncovered variants with a significant impact. Interestingly, human primary immunodeficiencies affecting T and B cells were also not found to predispose to severe influenza. Recently however, human IRF7 was shown to be essential for IFN-α/β- and IFN-λ-dependent protective immunity against primary influenza in vivo, as inferred from a patient with life-threatening influenza revealed to be IRF7-deficient by whole exome sequencing. Next generation sequencing of human exomes and genomes will facilitate the analysis of the human genetic determinism of severe influenza.
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Affiliation(s)
- Michael J Ciancanelli
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM-U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Shen-Ying Zhang
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM-U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM-U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Howard Hughes Medical Institute, New York, NY, USA; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris, France
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PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs. Sci Rep 2015; 5:17302. [PMID: 26612672 PMCID: PMC4661514 DOI: 10.1038/srep17302] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/28/2015] [Indexed: 12/22/2022] Open
Abstract
Expression quantitative trait loci (eQTLs) mapping and linkage disequilibrium (LD) analysis have been widely employed to interpret findings of genome-wide association studies (GWAS). With the availability of deep sequencing data of 423 lymphoblastoid cell lines (LCLs) from six global populations and the microarray expression data, we performed eQTL analysis, identified more than 228 K SNP cis-eQTLs and 21 K indel cis-eQTLs and generated a LCL cis-eQTL database. We demonstrate that the percentages of population-shared and population-specific cis-eQTLs are comparable; while indel cis-eQTLs in the population-specific subsection make more contribution to gene expression variations than those in the population-shared subsection. We found cis-eQTLs, especially the population-shared cis-eQTLs are significantly enriched toward transcription start site. Moreover, the National Human Genome Research Institute cataloged GWAS SNPs are enriched for LCL cis-eQTLs. Specifically, 32.8% GWAS SNPs are LCL cis-eQTLs, among which 12.5% can be tagged by indel cis-eQTLs, suggesting the fundamental contribution of indel cis-eQTLs to GWAS association signals. To search for functional indels and SNPs tagging GWAS SNPs, a pipeline Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) has been developed, integrating LD analysis, functional annotation from public databases, cis-eQTL mapping with our LCL cis-eQTL database and other published cis-eQTL datasets.
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47
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Influenza virus polymerase: Functions on host range, inhibition of cellular response to infection and pathogenicity. Virus Res 2015; 209:23-38. [DOI: 10.1016/j.virusres.2015.03.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 03/25/2015] [Accepted: 03/26/2015] [Indexed: 01/06/2023]
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48
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No Major Host Genetic Risk Factor Contributed to A(H1N1)2009 Influenza Severity. PLoS One 2015; 10:e0135983. [PMID: 26379185 PMCID: PMC4574704 DOI: 10.1371/journal.pone.0135983] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/28/2015] [Indexed: 11/19/2022] Open
Abstract
While most patients affected by the influenza A(H1N1) pandemic experienced mild symptoms, a small fraction required hospitalization, often without concomitant factors that could explain such a severe course. We hypothesize that host genetic factors could contribute to aggravate the disease. To test this hypothesis, we compared the allele frequencies of 547,296 genome-wide single nucleotide polymorphisms (SNPs) between 49 severe and 107 mild confirmed influenza A cases, as well as against a general population sample of 549 individuals. When comparing severe vs. mild influenza A cases, only one SNP was close to the conventional p = 5×10−8. This SNP, rs28454025, sits in an intron of the GSK233 gene, which is involved in a neural development, but seems not to have any connections with immunological or inflammatory functions. Indirectly, a previous association reported with CD55 was replicated. Although sample sizes are low, we show that the statistical power in our design was sufficient to detect highly-penetrant, quasi-Mendelian genetic factors. Hence, and assuming that rs28454025 is likely to be a false positive, no major genetic factor was detected that could explain poor influenza A course.
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Abstract
Blood group antigens represent polymorphic traits inherited among individuals and populations. At present, there are 34 recognized human blood groups and hundreds of individual blood group antigens and alleles. Differences in blood group antigen expression can increase or decrease host susceptibility to many infections. Blood groups can play a direct role in infection by serving as receptors and/or coreceptors for microorganisms, parasites, and viruses. In addition, many blood group antigens facilitate intracellular uptake, signal transduction, or adhesion through the organization of membrane microdomains. Several blood groups can modify the innate immune response to infection. Several distinct phenotypes associated with increased host resistance to malaria are overrepresented in populations living in areas where malaria is endemic, as a result of evolutionary pressures. Microorganisms can also stimulate antibodies against blood group antigens, including ABO, T, and Kell. Finally, there is a symbiotic relationship between blood group expression and maturation of the gastrointestinal microbiome.
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Affiliation(s)
- Laura Cooling
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
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50
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To KKW, Zhou J, Chan JFW, Yuen KY. Host genes and influenza pathogenesis in humans: an emerging paradigm. Curr Opin Virol 2015; 14:7-15. [PMID: 26079652 PMCID: PMC7102748 DOI: 10.1016/j.coviro.2015.04.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 04/29/2015] [Indexed: 12/13/2022]
Abstract
The emergence of the pandemic influenza virus A(H1N1)pdm09 in 2009 and avian influenza virus A(H7N9) in 2013 provided unique opportunities for assessing genetic predispositions to severe disease because many patients did not have any underlying risk factor or neutralizing antibody against these agents, in contrast to seasonal influenza viruses. High-throughput screening platforms and large human or animal databases from international collaborations allow rapid selection of potential candidate genes for confirmatory functional studies. In the last 2 years, at least seven new human susceptibility genes have been identified in genetic association studies. Integration of knowledge from genetic and phenotypic studies is essential to identify important gene targets for treatment and prevention of influenza virus infection.
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Affiliation(s)
- Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Research Centre of Infection and Immunology, Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Jie Zhou
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Research Centre of Infection and Immunology, Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Research Centre of Infection and Immunology, Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Research Centre of Infection and Immunology, Department of Microbiology, The University of Hong Kong, Hong Kong, China.
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