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Husain M. Influenza Virus Host Restriction Factors: The ISGs and Non-ISGs. Pathogens 2024; 13:127. [PMID: 38392865 PMCID: PMC10893265 DOI: 10.3390/pathogens13020127] [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: 12/19/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Influenza virus has been one of the most prevalent and researched viruses globally. Consequently, there is ample information available about influenza virus lifecycle and pathogenesis. However, there is plenty yet to be known about the determinants of influenza virus pathogenesis and disease severity. Influenza virus exploits host factors to promote each step of its lifecycle. In turn, the host deploys antiviral or restriction factors that inhibit or restrict the influenza virus lifecycle at each of those steps. Two broad categories of host restriction factors can exist in virus-infected cells: (1) encoded by the interferon-stimulated genes (ISGs) and (2) encoded by the constitutively expressed genes that are not stimulated by interferons (non-ISGs). There are hundreds of ISGs known, and many, e.g., Mx, IFITMs, and TRIMs, have been characterized to restrict influenza virus infection at different stages of its lifecycle by (1) blocking viral entry or progeny release, (2) sequestering or degrading viral components and interfering with viral synthesis and assembly, or (3) bolstering host innate defenses. Also, many non-ISGs, e.g., cyclophilins, ncRNAs, and HDACs, have been identified and characterized to restrict influenza virus infection at different lifecycle stages by similar mechanisms. This review provides an overview of those ISGs and non-ISGs and how the influenza virus escapes the restriction imposed by them and aims to improve our understanding of the host restriction mechanisms of the influenza virus.
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Affiliation(s)
- Matloob Husain
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
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2
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Liao Q, Shen J, Chen Y, Shu Y. Mendelian randomization study on the causal effect of serum IgA levels on H7N9 avian influenza A virus susceptibility. J Med Virol 2023; 95:e29266. [PMID: 38009617 DOI: 10.1002/jmv.29266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/13/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
Avian influenza A viruses (IAVs) that cross the species barrier to infect humans have the potential to initiate a new pandemic. However, the host factors influencing avian IAV infection remain poorly understood. To address this knowledge gap, we conducted a two-sample Mendelian randomization (MR) analysis by integrating our in-house genome-wide association study (GWAS) of avian IAV H7N9 susceptibility (with 217 cases and 116 controls) with the largest GWAS of serum IgA levels to date (sample size 41 263). Using the inverse-variance weighted (IVW) method, we discovered that genetically decreased serum IgA levels were associated with an increased risk of H7N9 infection (β = -2.528, 95% confidence interval [CI]: -4.572 to -0.484; p = 0.015). Consistent results were obtained from three other MR methods, including robust IVW estimation (β = -2.506, 95% CI: -4.109 to -0.902; p = 0.002), generalized summary-data-based MR (GSMR) (β = -2.238, 95% CI: -4.106 to -0.602; p = 0.019), and MR-pleiotropy residual sum and outlier (MR-PRESSO) (β = -2.528, 95% CI: -4.396 to -0.892; p = 0.026). In conclusion, our analysis provided compelling evidence support a causal relationship between genetically predicted serum IgA levels and avian IAV H7N9 susceptibility.
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Affiliation(s)
- Qijun Liao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen, People's Republic of China
- BGI Research, Shenzhen, People's Republic of China
| | - Juan Shen
- BGI Research, Shenzhen, People's Republic of China
| | - Yongkun Chen
- Department of Pathogen Biology, Shenzhen University Health Science Center, Shenzhen, People's Republic of China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Shenzhen, People's Republic of China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
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3
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Yang ZS, Lin CY, Khan MB, Hsu MC, Assavalapsakul W, Thitithanyanont A, Wang SF. Understanding the role of galectins toward influenza A virus infection. Expert Opin Ther Targets 2023; 27:927-937. [PMID: 37747065 DOI: 10.1080/14728222.2023.2263912] [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: 05/10/2023] [Accepted: 09/24/2023] [Indexed: 09/26/2023]
Abstract
INTRODUCTION Influenza A virus (IAV) is highly contagious and causes respiratory diseases in birds, mammals, and humans. Some strains of IAV, whether from human or avian sources, have developed resistance to existing antiviral drugs. Therefore, the discovery of new influenza antiviral drugs and therapeutic approaches is crucial. Recent studies have shown that galectins (Gal), a group of β-galactose-binding lectins, play a role in regulating various viral infections, including IAVs. AREAS COVERED This review provides an overview of the roles of different galectins in IAV infection. We discuss the characteristics of galectins, their impact on IAV infection and spread, and highlight their positive or negative regulatory functions and potential mechanisms during IAV infection. Furthermore, we explore the potential application of galectins in IAV therapy. EXPERT OPINION Galectins were first identified in the mid-1970s, and currently, 15 mammalian galectins have been identified. While all galectin members possess the carbohydrate recognition domain (CRD) that interacts with β-galactoside, their regulatory functions vary in different DNA or RNA virus infections. Certain galectin members have been found to regulate IAV infection through diverse mechanisms. Therefore, a comprehensive understanding of their roles in IAV infection is essential, as it may pave the way for novel therapeutic strategies.
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Affiliation(s)
- Zih-Syuan Yang
- Center for Tropical Medicine and Infectious Disease Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chih-Yen Lin
- Center for Tropical Medicine and Infectious Disease Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Muhammad Bilal Khan
- Center for Tropical Medicine and Infectious Disease Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Cheng Hsu
- Center for Tropical Medicine and Infectious Disease Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wanchai Assavalapsakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Sheng-Fan Wang
- Center for Tropical Medicine and Infectious Disease Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Program in Tropical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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4
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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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Genetic LGALS1 Variants Are Associated with Heterogeneity in Galectin-1 Serum Levels in Patients with Early Arthritis. Int J Mol Sci 2022; 23:ijms23137181. [PMID: 35806182 PMCID: PMC9266574 DOI: 10.3390/ijms23137181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 11/17/2022] Open
Abstract
Galectin 1 (Gal1) exerts immunomodulatory effects leading to therapeutic effects in autoimmune animal models. Patients with rheumatoid arthritis have been reported to show higher Gal1 serum levels than the healthy population. Our study aimed to find genetic variants on the Gal1 gene (LGALS1) modulating its expression and/or clinical features in patients with early arthritis (EA). LGALS1 was sequenced in 53 EA patients to characterize all genetic variants. Then, we genotyped rs9622682, rs929039, and rs4820293, which covered the main genetic variation in LGALS1, in 532 EA patients. Gal1 and IL-6 serum levels were measured by ELISA and Gal1 also by western blot (WB) in lymphocytes from patients with specific genotypes. Once disease activity improved with treatment, patients with at least one copy of the minor allele in rs9622682 and rs929039 or those with GG genotype in rs4820293 showed significantly higher Gal1 serum levels (p < 0.05). These genotypic combinations were also associated with higher Gal1 expression in lymphocytes by WB and lower IL-6 serum levels in EA patients. In summary, our study suggests that genetic variants studied in LGALS1 can explain heterogeneity in Gal1 serum levels showing that patients with higher Gal1 levels have lower serum IL-6 levels.
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Verkerke H, Dias-Baruffi M, Cummings RD, Arthur CM, Stowell SR. Galectins: An Ancient Family of Carbohydrate Binding Proteins with Modern Functions. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2442:1-40. [PMID: 35320517 DOI: 10.1007/978-1-0716-2055-7_1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Galectins are a large family of carbohydrate binding proteins with members in nearly every lineage of multicellular life. Through tandem and en-mass genome duplications, over 15 known vertebrate galectins likely evolved from a single common ancestor extant in pre-chordate lineages. While galectins have divergently evolved numerous functions, some of which do not involve carbohydrate recognition, the vast majority of the galectins have retained the conserved ability to bind variably modified polylactosamine (polyLacNAc) residues on glycans that modify proteins and lipids on the surface of host cells and pathogens. In addition to their direct role in microbial killing, many proposed galectin functions in the immune system and cancer involve crosslinking glycosylated receptors and modifying signaling pathways or sensitivity to antigen from the outside in. However, a large body of work has uncovered intracellular galectin functions mediated by carbohydrate- and non-carbohydrate-dependent interactions. In the cytoplasm, galectins can tune intracellular kinase and G-protein-coupled signaling cascades important for nutrient sensing, cell cycle progression, and transformation. Particularly, but interconnected pathways, cytoplasmic galectins serve the innate immune system as sensors of endolysosomal damage, recruiting and assembling the components of autophagosomes during intracellular infection through carbohydrate-dependent and -independent activities. In the nucleus, galectins participate in pre-mRNA splicing perhaps through interactions with non-coding RNAs required for assembly of spliceosomes. Together, studies of galectin function paint a picture of a functionally dynamic protein family recruited during eons of evolution to regulate numerous essential cellular processes in the context of multicellular life.
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Affiliation(s)
- Hans Verkerke
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Harvard Glycomics Center, Harvard Medical School, Boston, MA, USA
| | - Marcelo Dias-Baruffi
- Department of Clinical Analysis, Toxicological and Bromatological, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Connie M Arthur
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Harvard Glycomics Center, Harvard Medical School, Boston, MA, USA
| | - Sean R Stowell
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,Harvard Glycomics Center, Harvard Medical School, Boston, MA, USA.
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7
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Wang D, Li C, Chiu MC, Yu Y, Liu X, Zhao X, Huang J, Cheng Z, Yuan S, Poon V, Cai J, Chu H, Chan JF, To KK, Yuen KY, Zhou J. SPINK6 inhibits human airway serine proteases and restricts influenza virus activation. EMBO Mol Med 2022; 14:e14485. [PMID: 34826211 PMCID: PMC9976594 DOI: 10.15252/emmm.202114485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 11/06/2021] [Accepted: 11/10/2021] [Indexed: 11/09/2022] Open
Abstract
SPINK6 was identified in human skin as a cellular inhibitor of serine proteases of the KLK family. Airway serine proteases are required to cleave hemagglutinin (HA) of influenza A viruses (IAVs) to initiate an infection in the human airway. We hypothesized that SPINK6 may inhibit common airway serine proteases and restrict IAV activation. We demonstrate that SPINK6 specifically suppresses the proteolytic activity of HAT and KLK5, HAT- and KLK5-mediated HA cleavage, and restricts virus maturation and replication. SPINK6 constrains the activation of progeny virions and impairs viral growth; and vice versa, blocking endogenous SPINK6 enhances HA cleavage and viral growth in physiological-relevant human airway organoids where SPINK6 is intrinsically expressed. In IAV-infected mice, SPINK6 significantly suppresses viral growth and improves mouse survival. Notably, individuals carrying the higher SPINK6 expression allele were protected from human H7N9 infection. Collectively, SPINK6 is a novel host inhibitor of serine proteases in the human airway and restricts IAV activation.
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Affiliation(s)
- Dong Wang
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Cun Li
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Man Chun Chiu
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Yifei Yu
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Xiaojuan Liu
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Xiaoyu Zhao
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Jingjing Huang
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Zhongshan Cheng
- Applied Bioinformatics CenterSt Jude Children’s Research HospitalMemphisTNUSA
| | - Shuofeng Yuan
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Vincent Poon
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Jian‐Piao Cai
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Hin Chu
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina,State Key Laboratory of Emerging Infectious DiseasesThe University of Hong KongHong KongChina
| | - Jasper Fuk‐Woo Chan
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina,State Key Laboratory of Emerging Infectious DiseasesThe University of Hong KongHong KongChina,Carol Yu Centre for InfectionThe University of Hong KongHong KongChina
| | - Kelvin Kai‐Wang To
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina,State Key Laboratory of Emerging Infectious DiseasesThe University of Hong KongHong KongChina,Carol Yu Centre for InfectionThe University of Hong KongHong KongChina
| | - Kwok Yung Yuen
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina,State Key Laboratory of Emerging Infectious DiseasesThe University of Hong KongHong KongChina,Carol Yu Centre for InfectionThe University of Hong KongHong KongChina
| | - Jie Zhou
- Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina,State Key Laboratory of Emerging Infectious DiseasesThe University of Hong KongHong KongChina
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Staller E, Sheppard CM, Baillon L, Frise R, Peacock TP, Sancho-Shimizu V, Barclay WS. A natural variant in ANP32B impairs influenza virus replication in human cells. J Gen Virol 2021; 102. [PMID: 34524075 PMCID: PMC8567425 DOI: 10.1099/jgv.0.001664] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Viruses require host factors to support their replication, and genetic variation in such factors can affect susceptibility to infectious disease. Influenza virus replication in human cells relies on ANP32 proteins, which are involved in assembly of replication-competent dimeric influenza virus polymerase (FluPol) complexes. Here, we investigate naturally occurring single nucleotide variants (SNV) in the human Anp32A and Anp32B genes. We note that variant rs182096718 in Anp32B is found at a higher frequency than other variants in either gene. This SNV results in a D130A substitution in ANP32B, which is less able to support FluPol activity than wild-type ANP32B and binds FluPol with lower affinity. Interestingly, ANP32B-D130A exerts a dominant negative effect over wild-type ANP32B and interferes with the functionally redundant paralogue ANP32A. FluPol activity and virus replication are attenuated in CRISPR-edited cells expressing wild-type ANP32A and mutant ANP32B-D130A. We propose a model in which the D130A mutation impairs FluPol dimer formation, thus resulting in compromised replication. We suggest that both homozygous and heterozygous carriers of rs182096718 may have some genetic protection against influenza viruses.
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Affiliation(s)
- Ecco Staller
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK.,Present address: Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Carol M Sheppard
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
| | - Laury Baillon
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
| | - Rebecca Frise
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
| | | | - Wendy S Barclay
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
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Feng B, Meng X, Zhou H, Chen L, Zou C, Liang L, Meng Y, Xu N, Wang H, Zou D. Identification of Dysregulated Mechanisms and Potential Biomarkers in Ischemic Stroke Onset. Int J Gen Med 2021; 14:4731-4744. [PMID: 34456585 PMCID: PMC8390889 DOI: 10.2147/ijgm.s327594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/13/2021] [Indexed: 12/16/2022] Open
Abstract
Objective Ischemic stroke (IS) is a major cause of severe disability. This study aimed to identify potential biomarkers closely related to IS diagnosis and treatment. Methods Profiles of gene expression were obtained from datasets GSE16561, GSE22255, GSE112801 and GSE110993. Differentially expressed mRNAs between IS and controls were then subjected to weighted gene co-expression network analysis as well as multiscale embedded gene co-expression network analysis. The intersection of the two sets of module genes was subjected to analyses of functional enrichment and of microRNAs (miRNAs) regulation. Then, the area under receiver operating characteristic curves (AUC) was calculated to assess the ability of genes to discriminate IS patients from controls. IS diagnostic signatures were constructed using least absolute shrinkage and selection operator regression. Results A total of 234 common co-expression network genes were found to be potentially associated with IS. Enrichment analysis found that these genes were mainly associated with inflammation and immune response. The aberrantly expressed miRNAs (hsa-miR-651-5p, hsa-miR-138-5p, hsa-miR-9-3p and hsa-miR-374a-3p) in IS had regulatory effects on IS-related genes and were involved in brain-related diseases. We used the criterion AUC > 0.7 to screen out 23 hub genes from IS-related genes in the GSE16561 and GSE22255 datasets. We obtained an 8-gene signature (ADCY4, DUSP1, ATP5F1, DCTN5, EIF3G, ELAVL1, EXOSC7 and PPIE) from the training set of GSE16561 dataset, which we confirmed in the validation set of GSE16561 dataset and in the GSE22255 dataset. The genes in this signature were highly accurate for diagnosing IS. In addition, the 8-gene signature significantly correlated with infiltration by immune cells. Conclusion These findings provide new clues to molecular mechanisms and treatment targets in IS. The genes in the signature may be candidate markers and potential gene targets for treatments.
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Affiliation(s)
- Bing Feng
- Department of Neurology, The People's Hospital of Guiping, Guigang, Guangxi, 537200, People's Republic of China
| | - Xinling Meng
- Department of Endocrinology, The People's Hospital of Guiping, Guigang, Guangxi, 537200, People's Republic of China
| | - Hui Zhou
- Department of Neurology, The People's Hospital of Guiping, Guigang, Guangxi, 537200, People's Republic of China
| | - Liechun Chen
- Department of Neurology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People's Republic of China
| | - Chun Zou
- Department of Neurology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People's Republic of China
| | - Lucong Liang
- Department of Neurology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People's Republic of China
| | - Youshi Meng
- Department of Neurology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People's Republic of China.,Department of Neurology, The First People's Hospital of Nanning, Nanning, Guangxi, 530022, People's Republic of China
| | - Ning Xu
- Department of Neurology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People's Republic of China.,Department of Neurology, The First People's Hospital of Nanning, Nanning, Guangxi, 530022, People's Republic of China
| | - Hao Wang
- Department of Neurology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People's Republic of China.,Department of Neurology, The First People's Hospital of Nanning, Nanning, Guangxi, 530022, People's Republic of China
| | - Donghua Zou
- Department of Neurology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People's Republic of China.,Department of Neurology, The First People's Hospital of Nanning, Nanning, Guangxi, 530022, People's Republic of China
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10
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Chen Y, Graf L, Chen T, Liao Q, Bai T, Petric PP, Zhu W, Yang L, Dong J, Lu J, Chen Y, Shen J, Haller O, Staeheli P, Kochs G, Wang D, Schwemmle M, Shu Y. Rare variant MX1 alleles increase human susceptibility to zoonotic H7N9 influenza virus. Science 2021; 373:918-922. [PMID: 34413236 DOI: 10.1126/science.abg5953] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/19/2021] [Indexed: 12/14/2022]
Abstract
Zoonotic avian influenza A virus (IAV) infections are rare. Sustained transmission of these IAVs between humans has not been observed, suggesting a role for host genes. We used whole-genome sequencing to compare avian IAV H7N9 patients with healthy controls and observed a strong association between H7N9 infection and rare, heterozygous single-nucleotide variants in the MX1 gene. MX1 codes for myxovirus resistance protein A (MxA), an interferon-induced antiviral guanosine triphosphatase known to control IAV infections in transgenic mice. Most of the MxA variants identified lost the ability to inhibit avian IAVs, including H7N9, in transfected human cell lines. Nearly all of the inactive MxA variants exerted a dominant-negative effect on the antiviral function of wild-type MxA, suggesting an MxA null phenotype in heterozygous carriers. Our study provides genetic evidence for a crucial role of the MX1-based antiviral defense in controlling zoonotic IAV infections in humans.
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Affiliation(s)
- Yongkun Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Laura Graf
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tao Chen
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qijun Liao
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Tian Bai
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Philipp P Petric
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Wenfei Zhu
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lei Yang
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Dong
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jian Lu
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | | | | | - Otto Haller
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Peter Staeheli
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Georg Kochs
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dayan Wang
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Martin Schwemmle
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany. .,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China. .,Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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11
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Lin CY, Yang ZS, Wang WH, Urbina AN, Lin YT, Huang JC, Liu FT, Wang SF. The Antiviral Role of Galectins toward Influenza A Virus Infection-An Alternative Strategy for Influenza Therapy. Pharmaceuticals (Basel) 2021; 14:490. [PMID: 34065500 PMCID: PMC8160607 DOI: 10.3390/ph14050490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 12/27/2022] Open
Abstract
Animal lectins are proteins with carbohydrate recognition activity. Galectins, the β-galactoside binding lectins, are expressed in various cells and have been reported to regulate several immunological and physiological responses. Recently, some galectins have been reported to regulate some viral infections, including influenza A virus (IAV); however, the mechanism is still not fully understood. Thus, we aim to review systemically the roles of galectins in their antiviral functions against IAVs. The PRISMA guidelines were used to select the eligible articles. Results indicated that only Galectin-1, Galectin-3, and Galectin-9 were reported to play a regulatory role in IAV infection. These regulatory effects occur extracellularly, through their carbohydrate recognition domain (CRD) interacting with glycans expressed on the virus surface, as well as endogenously, in a cell-cell interaction manner. The inhibition effects induced by galectins on IAV infection were through blocking virus-host receptors interaction, activation of NLRP-3 inflammasome, augment expression of antiviral genes and related cytokines, as well as stimulation of Tim-3 related signaling to enhance virus-specific T cells and humoral immune response. Combined, this study concludes that currently, only three galectins have reported antiviral capabilities against IAV infection, thereby having the potential to be applied as an alternative anti-influenza therapeutic strategy.
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Affiliation(s)
- Chih-Yen Lin
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-Y.L.); (Z.-S.Y.); (W.-H.W.); (A.N.U.)
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Zih-Syuan Yang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-Y.L.); (Z.-S.Y.); (W.-H.W.); (A.N.U.)
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Wen-Hung Wang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-Y.L.); (Z.-S.Y.); (W.-H.W.); (A.N.U.)
- Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Medical, University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Aspiro Nayim Urbina
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-Y.L.); (Z.-S.Y.); (W.-H.W.); (A.N.U.)
| | - Yu-Ting Lin
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Jason C. Huang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei 112304, Taiwan;
| | - Fu-Tong Liu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan;
| | - Sheng-Fan Wang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-Y.L.); (Z.-S.Y.); (W.-H.W.); (A.N.U.)
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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12
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Yang ZS, Lin CY, Huang SW, Wang WH, Urbina AN, Tseng SP, Lu PL, Chen YH, Wang SF. Regulatory roles of galectins on influenza A virus and their potential as a therapeutic strategy. Biomed Pharmacother 2021; 139:111713. [PMID: 34243634 DOI: 10.1016/j.biopha.2021.111713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/19/2022] Open
Abstract
Galectins, are β-galactoside binding lectins expressed in numerous cells and are known to regulate various immune responses and cellular physiological functions. Galectins have been reported to participate in the regulation of several viral infections via carbohydrate‑dependent/independent manner. Galectins have displayed various regulatory functions on viral infection, however, the detailed mechanism remains unclear. More recently, some members of galectins have been reported to regulate influenza A virus (IAV) infection. In this review, we aim to analyze and summarize current findings regarding the role of galectins in IAV infection and their antiviral potential therapeutic application in the treatment of IAVs. The eligible articles were selected according to the PRISMA guidelines. Results indicate that Galectin-1(Gal-1), Galectin-3(Gal-3) and Galectin-9 (Gal-9) were found as the predominant galectins reported to participate in the regulation of IAVs infection. The inhibitory regulation of IAVs by these galectins occurred mainly through extracellular binding to glycosylated envelope proteins, further blocking the interaction between influenza envelope and sialic acid receptor, interacting with ligands or receptors on immune cells to trigger immunol or cellular response against IAVs, and endogenously interacting cellular components in the cytoplasm to activate inflammasome and autophagy. This study offers information regarding the multiple roles of galectins observed in IAVs infection and suggest that galectins has the potential to be used as therapeutic agents for IAVs.
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Affiliation(s)
- Zih-Syuan Yang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chih-Yen Lin
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Szu-Wei Huang
- Model Development Section, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Wen-Hung Wang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Medical, University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Aspiro Nayim Urbina
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Sung-Pin Tseng
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Po-Liang Lu
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Medical, University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yen-Hsu Chen
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Medical, University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Sheng-Fan Wang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
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13
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Wang D, Zhu W, Yang L, Shu Y. The Epidemiology, Virology, and Pathogenicity of Human Infections with Avian Influenza Viruses. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038620. [PMID: 31964651 DOI: 10.1101/cshperspect.a038620] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Influenza is a global challenge, and future pandemics of influenza are inevitable. One of the lessons learned from past pandemics is that all pandemic influenza viruses characterized to date possess viral genes originating from avian influenza viruses (AIVs). During the past decades, a wide range of AIVs have overcome the species barrier and infected humans with different clinical manifestations ranging from mild illness to severe disease and even death. Understanding the mechanisms of infection in the context of clinical outcomes, the mechanism of interspecies transmission, and the molecular determinants that confer interspecies transmission is important for pandemic preparedness. Here, we summarize the epidemiology, virology, and pathogenicity of human infections with AIVs to further our understanding of interspecies transmission.
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Affiliation(s)
- Dayan Wang
- 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 of the People's Republic of China, Beijing 102206, P.R. China
| | - Wenfei Zhu
- 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 of the People's Republic of China, Beijing 102206, P.R. China
| | - Lei Yang
- 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 of the People's Republic of China, Beijing 102206, P.R. China
| | - Yuelong Shu
- 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 of the People's Republic of China, Beijing 102206, P.R. China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong 510275, P.R. China
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14
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Nain Z, Rana HK, Liò P, Islam SMS, Summers MA, Moni MA. Pathogenetic profiling of COVID-19 and SARS-like viruses. Brief Bioinform 2021; 22:1175-1196. [PMID: 32778874 PMCID: PMC7454314 DOI: 10.1093/bib/bbaa173] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/23/2020] [Accepted: 07/08/2020] [Indexed: 12/15/2022] Open
Abstract
The novel coronavirus (2019-nCoV) has recently emerged, causing COVID-19 outbreaks and significant societal/global disruption. Importantly, COVID-19 infection resembles SARS-like complications. However, the lack of knowledge about the underlying genetic mechanisms of COVID-19 warrants the development of prospective control measures. In this study, we employed whole-genome alignment and digital DNA-DNA hybridization analyses to assess genomic linkage between 2019-nCoV and other coronaviruses. To understand the pathogenetic behavior of 2019-nCoV, we compared gene expression datasets of viral infections closest to 2019-nCoV with four COVID-19 clinical presentations followed by functional enrichment of shared dysregulated genes. Potential chemical antagonists were also identified using protein-chemical interaction analysis. Based on phylogram analysis, the 2019-nCoV was found genetically closest to SARS-CoVs. In addition, we identified 562 upregulated and 738 downregulated genes (adj. P ≤ 0.05) with SARS-CoV infection. Among the dysregulated genes, SARS-CoV shared ≤19 upregulated and ≤22 downregulated genes with each of different COVID-19 complications. Notably, upregulation of BCL6 and PFKFB3 genes was common to SARS-CoV, pneumonia and severe acute respiratory syndrome, while they shared CRIP2, NSG1 and TNFRSF21 genes in downregulation. Besides, 14 genes were common to different SARS-CoV comorbidities that might influence COVID-19 disease. We also observed similarities in pathways that can lead to COVID-19 and SARS-CoV diseases. Finally, protein-chemical interactions suggest cyclosporine, resveratrol and quercetin as promising drug candidates against COVID-19 as well as other SARS-like viral infections. The pathogenetic analyses, along with identified biomarkers, signaling pathways and chemical antagonists, could prove useful for novel drug development in the fight against the current global 2019-nCoV pandemic.
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Affiliation(s)
- Zulkar Nain
- Department of Genetic Engineering and Biotechnology, East West University, Bangladesh
| | - Humayan Kabir Rana
- Department of Computer Science and Engineering, Green University of Bangladesh
| | - Pietro Liò
- Artificial Intelligence Group at the University of Cambridge
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15
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Ayona D, Fournier PE, Henrissat B, Desnues B. Utilization of Galectins by Pathogens for Infection. Front Immunol 2020; 11:1877. [PMID: 32973776 PMCID: PMC7466766 DOI: 10.3389/fimmu.2020.01877] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/13/2020] [Indexed: 12/22/2022] Open
Abstract
Galectins are glycan-binding proteins which are expressed by many different cell types and secreted extracellularly. These molecules are well-known regulators of immune responses and involved in a broad range of cellular and pathophysiological functions. During infections, host galectins can either avoid or facilitate infections by interacting with host cells- and/or pathogen-derived glycoconjugates and less commonly, with proteins. Some pathogens also express self-produced galectins to interfere with host immune responses. This review summarizes pathogens which take advantage of host- or pathogen-produced galectins to establish the infection.
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Affiliation(s)
- Diyoly Ayona
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | | | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
- USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Benoit Desnues
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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16
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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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17
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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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18
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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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19
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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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20
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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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21
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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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22
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Machala EA, McSharry BP, Rouse BT, Abendroth A, Slobedman B. Gal power: the diverse roles of galectins in regulating viral infections. J Gen Virol 2019; 100:333-349. [PMID: 30648945 DOI: 10.1099/jgv.0.001208] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Viruses, as a class of pathogenic microbe, remain a significant health burden globally. Viral infections result in significant morbidity and mortality annually and many remain in need of novel vaccine and anti-viral strategies. The development of effective novel anti-viral therapeutics, in particular, requires detailed understanding of the mechanism of viral infection, and the host response, including the innate and adaptive arms of the immune system. In recent years, the role of glycans and lectins in pathogen-host interactions has become an increasingly relevant issue. This review focuses on the interactions between a specific lectin family, galectins, and the broad range of viral infections in which they play a role. Discussed are the diverse activities that galectins play in interacting directly with virions or the cells they infect, to promote or inhibit viral infection. In addition we describe how galectin expression is regulated both transcriptionally and post-transcriptionally by viral infections. We also compare the contribution of known galectin-mediated immune modulation, across a range of innate and adaptive immune anti-viral responses, to the outcome of viral infections.
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Affiliation(s)
- Emily A Machala
- 1Discipline of Infectious Diseases and Immunology, University of Sydney, Camperdown, New South Wales, Australia
| | - Brian P McSharry
- 1Discipline of Infectious Diseases and Immunology, University of Sydney, Camperdown, New South Wales, Australia
| | - Barry T Rouse
- 2Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, Tennessee, USA
| | - Allison Abendroth
- 1Discipline of Infectious Diseases and Immunology, University of Sydney, Camperdown, New South Wales, Australia
| | - Barry Slobedman
- 1Discipline of Infectious Diseases and Immunology, University of Sydney, Camperdown, New South Wales, Australia
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23
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Influenza virus N-linked glycosylation and innate immunity. Biosci Rep 2019; 39:BSR20171505. [PMID: 30552137 PMCID: PMC6328934 DOI: 10.1042/bsr20171505] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/03/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022] Open
Abstract
Influenza viruses cause seasonal epidemics and sporadic pandemics in humans. The virus’s ability to change its antigenic nature through mutation and recombination, and the difficulty in developing highly effective universal vaccines against it, make it a serious global public health challenge. Influenza virus’s surface glycoproteins, hemagglutinin and neuraminidase, are all modified by the host cell’s N-linked glycosylation pathways. Host innate immune responses are the first line of defense against infection, and glycosylation of these major antigens plays an important role in the generation of host innate responses toward the virus. Here, we review the principal findings in the analytical techniques used to study influenza N-linked glycosylation, the evolutionary dynamics of N-linked glycosylation in seasonal versus pandemic and zoonotic strains, its role in host innate immune responses, and the prospects for lectin-based therapies. As the efficiency of innate immune responses is a critical determinant of disease severity and adaptive immunity, the study of influenza glycobiology is of clinical as well as research interest.
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24
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Casals C, Campanero-Rhodes MA, García-Fojeda B, Solís D. The Role of Collectins and Galectins in Lung Innate Immune Defense. Front Immunol 2018; 9:1998. [PMID: 30233589 PMCID: PMC6131309 DOI: 10.3389/fimmu.2018.01998] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 08/14/2018] [Indexed: 12/16/2022] Open
Abstract
Different families of endogenous lectins use complementary defense strategies against pathogens. They may recognize non-self glycans typically found on pathogens and/or host glycans. The collectin and galectin families are prominent examples of these two lectin categories. Collectins are C-type lectins that contain a carbohydrate recognition domain and a collagen-like domain. Members of this group include surfactant protein A (SP-A) and D (SP-D), secreted by the alveolar epithelium to the alveolar fluid. Lung collectins bind to several microorganisms, which results in pathogen aggregation and/or killing, and enhances phagocytosis of pathogens by alveolar macrophages. Moreover, SP-A and SP-D influence macrophage responses, contributing to resolution of inflammation, and SP-A is essential for tissue-repair functions of macrophages. Galectins also function by interacting directly with pathogens or by modulating the immune system in response to the infection. Direct binding may result in enhanced or impaired infection of target cells, or can have microbicidal effects. Immunomodulatory effects of galectins include recruitment of immune cells to the site of infection, promotion of neutrophil function, and stimulation of the bactericidal activity of infected macrophages. Moreover, intracellular galectins can serve as danger receptors, promoting autophagy of the invading pathogen. This review will focus on the role of collectins and galectins in pathogen clearance and immune response activation in infectious diseases of the respiratory system.
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Affiliation(s)
- Cristina Casals
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid, Madrid, Spain
| | - María A Campanero-Rhodes
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Química Física Rocasolano, CSIC, Madrid, Spain
| | - Belén García-Fojeda
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid, Madrid, Spain
| | - Dolores Solís
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Química Física Rocasolano, CSIC, Madrid, Spain
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25
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Jørgensen SE, Christiansen M, Ryø LB, Gad HH, Gjedsted J, Staeheli P, Mikkelsen JG, Storgaard M, Hartmann R, Mogensen TH. Defective RNA sensing by RIG-I in severe influenza virus infection. Clin Exp Immunol 2018; 192:366-376. [PMID: 29453856 PMCID: PMC5980616 DOI: 10.1111/cei.13120] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2018] [Indexed: 12/25/2022] Open
Abstract
Influenza virus infection causes worldwide seasonal epidemics. Although influenza is usually a mild disease, a minority of patients experience very severe fulminating disease courses. Previous studies have demonstrated a role for type I interferon (IFN) in anti-viral responses during influenza. So far, however, IFN regulatory factor (IRF)7 deficiency is the only genetic cause of severe influenza described in humans. In this study we present a patient with severe influenza A virus (IAV) H1N1 infection during the 2009 swine flu pandemic. By whole exome sequencing we identified two variants, p.R71H and p.P885S, located in the caspase activation and recruitment domain (CARD) and RNA binding domains, respectively, of DExD/H-box helicase 58 (DDX58) encoding the RNA sensor retinoic acid inducible gene 1 (RIG-I). These variants significantly impair the signalling activity of RIG-I. Similarly, patient cells demonstrate decreased antiviral responses to RIG-I ligands as well as increased proinflammatory responses to IAV, suggesting dysregulation of the innate immune response with increased immunopathology. We suggest that these RIG-I variants may have contributed to severe influenza in this patient and advocate that RIG-I variants should be sought in future studies of genetic factors influencing single-stranded RNA virus infections.
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Affiliation(s)
- S. E. Jørgensen
- Department of Infectious DiseasesAarhus University HospitalAarhusDenmark
| | - M. Christiansen
- Department of Clinical ImmunologyAarhus University HospitalAarhusDenmark
| | - L. B. Ryø
- Department of BiomedicineAarhus UniversityAarhusDenmark
| | - H. H. Gad
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - J. Gjedsted
- Department of Intensive CareAarhus University HospitalAarhusDenmark
| | - P. Staeheli
- Institute of VirologyMedical Center University of FreiburgBreisgauGermany
| | | | - M. Storgaard
- Department of Infectious DiseasesAarhus University HospitalAarhusDenmark
| | - R. Hartmann
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - T. H. Mogensen
- Department of Infectious DiseasesAarhus University HospitalAarhusDenmark
- Department of BiomedicineAarhus UniversityAarhusDenmark
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26
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Bao S, Jia L, Zhou X, Zhang ZG, Wu HWL, Yu Z, Ng G, Fan Y, Wong DSM, Huang S, Wang To KK, Yuen KY, Yeung ML, Song YQ. Integrated analysis of mRNA-seq and miRNA-seq for host susceptibilities to influenza A (H7N9) infection in inbred mouse lines. Funct Integr Genomics 2018; 18:411-424. [PMID: 29564647 DOI: 10.1007/s10142-018-0602-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 03/12/2018] [Indexed: 02/05/2023]
Abstract
Host genetic factors play an important role in diverse host outcomes after influenza A (H7N9) infection. Studying differential responses of inbred mouse lines with distinct genetic backgrounds to influenza virus infection could substantially increase our understanding of the contributory roles of host genetic factors to disease severity. Here, we utilized an integrated approach of mRNA-seq and miRNA-seq to investigate the transcriptome expression and regulation of host genes in C57BL/6J and DBA/2J mouse strains during influenza virus infection. The differential pathogenicity of influenza virus in C57BL/6J and DBA/2J has been fully demonstrated through immunohistochemical staining, histopathological analyses, and viral replication assessment. A transcriptional molecular signature correlates to differential host response to infection has been uncovered. With the introduction of temporal expression pattern analysis, we demonstrated that host factors responsible for influenza virus replication and host-virus interaction were significantly enriched in genes exhibiting distinct temporal dynamics between different inbred mouse lines. A combination of time-series expression analysis and temporal expression pattern analysis has provided a list of promising candidate genes for future studies. An integrated miRNA regulatory network from both mRNA-seq and miRNA-seq revealed several regulatory modules responsible for regulating host susceptibilities and disease severity. Overall, a comprehensive framework for analyzing host susceptibilities to influenza infection was established by integrating mRNA-seq and miRNA-seq data of inbred mouse lines. This work suggests novel putative molecular targets for therapeutic interventions in seasonal and pandemic influenza.
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Affiliation(s)
- Suying Bao
- Schoolof Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Lilong Jia
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Xueya Zhou
- Department of Psychiatry, The University of Hong Kong, Hong Kong, China
| | - Zhi-Gang Zhang
- Schoolof Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Hazel Wai Lan Wu
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Zhe Yu
- Schoolof Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Gordon Ng
- Schoolof Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Yanhui Fan
- Schoolof Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Dana S M Wong
- Schoolof Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Shishu Huang
- Department of Orthopedic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Kelvin Kai Wang To
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Man Lung Yeung
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.
| | - You-Qiang Song
- Schoolof Biomedical Sciences, The University of Hong Kong, Hong Kong, China. .,Department of Psychiatry, The University of Hong Kong, Hong Kong, China. .,HKU-SIRI/ZIRI, The University of Hong Kong, Hong Kong, China. .,HKU-SUSTech Joint Laboratories of Matrix Biology and Diseases, The University of Hong Kong, Hong Kong, China.
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27
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Tsui NBY, Cheng G, Chung T, Lam CWK, Yee A, Chung PKC, Kwan TK, Ko E, He D, Wong WT, Lau JYN, Lau LT, Fok M. Population-Wide Genetic Risk Prediction of Complex Diseases: A Pilot Feasibility Study in Macau Population for Precision Public Healthcare Planning. Sci Rep 2018; 8:1853. [PMID: 29382849 PMCID: PMC5789865 DOI: 10.1038/s41598-017-19017-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 12/20/2017] [Indexed: 02/01/2023] Open
Abstract
The genetic bases of many common diseases have been identified through genome-wide association studies in the past decade. However, the application of this approach on public healthcare planning has not been well established. Using Macau with population of around 650,000 as a basis, we conducted a pilot study to evaluate the feasibility of population genomic research and its potential on public health decisions. By performing genome-wide SNP genotyping of over a thousand Macau individuals, we evaluated the population genetic risk profiles of 47 non-communicable diseases and traits, as well as two traits associated with influenza infection. We found that for most of the diseases, the genetic risks of Macau population were different from those of Caucasian, but with similar profile with mainland Chinese. We also identified a panel of diseases that Macau population may have a high or elevated genetic risks. This pilot study showed that (1) population genomic study is feasible in Asian regions like Macau; (2) Macau may have different profile of population-based genetic risks than Caucasians, (3) the different prevalence of genetic risk profile indicates the importance of Asian-specific studies for Asian populations; and (4) the results generated may have an impact for going forward healthcare planning.
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Affiliation(s)
- Nancy B Y Tsui
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong.,Avalon Genomics (Hong Kong) Limited, Shatin, Hong Kong
| | - Gregory Cheng
- Faculty of Health Sciences, Macau University of Science and Technology, Taipa, Macau
| | - Teresa Chung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Christopher W K Lam
- Faculty of Health Sciences, Macau University of Science and Technology, Taipa, Macau
| | - Anita Yee
- Avalon Genomics (Hong Kong) Limited, Shatin, Hong Kong
| | | | - Tsz-Ki Kwan
- Avalon Genomics (Hong Kong) Limited, Shatin, Hong Kong
| | - Elaine Ko
- Avalon Genomics (Hong Kong) Limited, Shatin, Hong Kong
| | - Daihai He
- Department of Applied Mathematics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Wing-Tak Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Johnson Y N Lau
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Lok Ting Lau
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong.
| | - Manson Fok
- Faculty of Health Sciences, Macau University of Science and Technology, Taipa, Macau.
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28
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Wen F, Guo J, Tong G, Bi D, Wang Q, Liu X, Wang S, Shan T, Tong W, Zhou Y, Li G, Yu H. A meta-analysis of transcriptomic characterization revealed extracellular matrix pathway involved in the H5N1 and H7N9 infections. Oncotarget 2017; 8:62561-62572. [PMID: 28977969 PMCID: PMC5617529 DOI: 10.18632/oncotarget.19315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/16/2017] [Indexed: 11/25/2022] Open
Abstract
Avian-origin H5N1 and H7N9 influenza A viruses are capable of causing lethal infection in humans, with serious lung pathology and leading to acute respiratory distress syndrome. The contribution of host response associated with the poor prognosis of H5N1 and H7N9 infections remains unclear. The aim of this study was to identify the host factors involved in the high pathogenicity of H5N1 and H7N9 by a systematical meta-analysis. The RNA-seq datasets related to H5N1, H7N9, and H1N1 infections with time series were retrieved from GEO. After merging the data from different series, ComBat was used to adjust the known variances from different batches. The transcription factors binding the genes in each cluster were predicted by PASTAA. We figured out the genes that were differentially expressed at any time point in samples infected with H5N1, H7N9, or H1N1. The analysis of biological function showed that genes related with cytokine were up-regulated in all three viruses. However, genes associated with carbon metabolism were found exclusively down-regulated in H7N9 and the extracellular matrix pathway were only enriched in H5N1 and H7N9. To summary, our study suggested that the extracellular matrix might be associated with the high fatality of H5N1 and H7N9 viruses in humans.
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Affiliation(s)
- Feng Wen
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Jinyue Guo
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangzhi Tong
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Dingren Bi
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Wang
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Xiaomin Liu
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Shuaiyong Wang
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Tonglin Shan
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Wu Tong
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yanjun Zhou
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Guoxin Li
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Hai Yu
- Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
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29
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Detecting Perturbed Subpathways towards Mouse Lung Regeneration Following H1N1 Influenza Infection. COMPUTATION 2017. [DOI: 10.3390/computation5020020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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30
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Söderholm S, Fu Y, Gaelings L, Belanov S, Yetukuri L, Berlinkov M, Cheltsov AV, Anders S, Aittokallio T, Nyman TA, Matikainen S, Kainov DE. Multi-Omics Studies towards Novel Modulators of Influenza A Virus-Host Interaction. Viruses 2016; 8:v8100269. [PMID: 27690086 PMCID: PMC5086605 DOI: 10.3390/v8100269] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 09/13/2016] [Accepted: 09/22/2016] [Indexed: 12/20/2022] Open
Abstract
Human influenza A viruses (IAVs) cause global pandemics and epidemics. These viruses evolve rapidly, making current treatment options ineffective. To identify novel modulators of IAV–host interactions, we re-analyzed our recent transcriptomics, metabolomics, proteomics, phosphoproteomics, and genomics/virtual ligand screening data. We identified 713 potential modulators targeting 199 cellular and two viral proteins. Anti-influenza activity for 48 of them has been reported previously, whereas the antiviral efficacy of the 665 remains unknown. Studying anti-influenza efficacy and immuno/neuro-modulating properties of these compounds and their combinations as well as potential viral and host resistance to them may lead to the discovery of novel modulators of IAV–host interactions, which might be more effective than the currently available anti-influenza therapeutics.
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Affiliation(s)
- Sandra Söderholm
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland.
- Finnish Institute of Occupational Health, Helsinki 00250, Finland.
| | - Yu Fu
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Lana Gaelings
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Sergey Belanov
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Laxman Yetukuri
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Mikhail Berlinkov
- Institute of Mathematics and Computer Science, Ural Federal University, Yekaterinburg 620083, Russia.
| | - Anton V Cheltsov
- Q-Mol L.L.C. in Silico Pharmaceuticals, San Diego, CA 92037, USA.
| | - Simon Anders
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
- Department of Mathematics and Statistics, University of Turku, Turku 20014, Finland.
| | | | - Sampsa Matikainen
- Finnish Institute of Occupational Health, Helsinki 00250, Finland.
- Department of Rheumatology, Helsinki University Hospital, University of Helsinki, Helsinki 00015, Finland.
| | - Denis E Kainov
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
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31
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Abstract
Seasonal and pandemic influenza are the two faces of respiratory infections caused by influenza viruses in humans. As seasonal influenza occurs on an annual basis, the circulating virus strains are closely monitored and a yearly updated vaccination is provided, especially to identified risk populations. Nonetheless, influenza virus infection may result in pneumonia and acute respiratory failure, frequently complicated by bacterial coinfection. Pandemics are, in contrary, unexpected rare events related to the emergence of a reassorted human-pathogenic influenza A virus (IAV) strains that often causes increased morbidity and spreads extremely rapidly in the immunologically naive human population, with huge clinical and economic impact. Accordingly, particular efforts are made to advance our knowledge on the disease biology and pathology and recent studies have brought new insights into IAV adaptation mechanisms to the human host, as well as into the key players in disease pathogenesis on the host side. Current antiviral strategies are only efficient at the early stages of the disease and are challenged by the genomic instability of the virus, highlighting the need for novel antiviral therapies targeting the pulmonary host response to improve viral clearance, reduce the risk of bacterial coinfection, and prevent or attenuate acute lung injury. This review article summarizes our current knowledge on the molecular basis of influenza infection and disease progression, the key players in pathogenesis driving severe disease and progression to lung failure, as well as available and envisioned prevention and treatment strategies against influenza virus infection.
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Affiliation(s)
- Christin Peteranderl
- Department of Internal Medicine II, University of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
| | - Susanne Herold
- Department of Internal Medicine II, University of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
| | - Carole Schmoldt
- Department of Internal Medicine II, University of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
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32
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Abstract
Seasonal and pandemic influenza are the two faces of respiratory infections caused by influenza viruses in humans. As seasonal influenza occurs on an annual basis, the circulating virus strains are closely monitored and a yearly updated vaccination is provided, especially to identified risk populations. Nonetheless, influenza virus infection may result in pneumonia and acute respiratory failure, frequently complicated by bacterial coinfection. Pandemics are, in contrary, unexpected rare events related to the emergence of a reassorted human-pathogenic influenza A virus (IAV) strains that often causes increased morbidity and spreads extremely rapidly in the immunologically naive human population, with huge clinical and economic impact. Accordingly, particular efforts are made to advance our knowledge on the disease biology and pathology and recent studies have brought new insights into IAV adaptation mechanisms to the human host, as well as into the key players in disease pathogenesis on the host side. Current antiviral strategies are only efficient at the early stages of the disease and are challenged by the genomic instability of the virus, highlighting the need for novel antiviral therapies targeting the pulmonary host response to improve viral clearance, reduce the risk of bacterial coinfection, and prevent or attenuate acute lung injury. This review article summarizes our current knowledge on the molecular basis of influenza infection and disease progression, the key players in pathogenesis driving severe disease and progression to lung failure, as well as available and envisioned prevention and treatment strategies against influenza virus infection.
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Affiliation(s)
- Christin Peteranderl
- Department of Internal Medicine II, University of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
| | - Susanne Herold
- Department of Internal Medicine II, University of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
| | - Carole Schmoldt
- Department of Internal Medicine II, University of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
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33
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Multiple gene mutations identified in patients infected with influenza A (H7N9) virus. Sci Rep 2016; 6:25614. [PMID: 27156515 PMCID: PMC4860572 DOI: 10.1038/srep25614] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 04/18/2016] [Indexed: 11/20/2022] Open
Abstract
Influenza A (H7N9) virus induced high mortality since 2013. It is important to elucidate the potential genetic variations that contribute to virus infection susceptibilities. In order to identify genetic mutations that might increase host susceptibility to infection, we performed exon sequencing and validated the SNPS by Sanger sequencing on 18 H7N9 patients. Blood samples were collected from 18 confirmed H7N9 patients. The genomic DNA was captured with the Agilent SureSelect Human All Exon kit, sequenced on the Illumina Hiseq 2000, and the resulting data processed and annotated with Genome analysis Tool. SNPs were verified by independent Sanger sequencing. The DAVID database and the DAPPLE database were used to do bioinformatics analysis. Through exon sequencing and Sanger sequencing, we identified 21 genes that were highly associated with H7N9 influenza infection. Protein-protein interaction analysis showed that direct interactions among genetic products were significantly higher than expected (p = 0.004), and DAVID analysis confirmed the defense-related functions of these genes. Gene mutation profiles of survived and non-survived patients were similar, suggesting some of genes identified in this study may be associated with H7N9 influenza susceptibility. Host specific genetic determinants of disease severity identified by this approach may provide new targets for the treatment of H7N9 influenza.
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34
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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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35
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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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36
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Cheng Z, Zhou J, To KKW, Chu H, Li C, Wang D, Yang D, Zheng S, Hao K, Bossé Y, Obeidat M, Brandsma CA, Song YQ, Chen Y, Zheng BJ, Li L, Yuen KY. Identification of TMPRSS2 as a Susceptibility Gene for Severe 2009 Pandemic A(H1N1) Influenza and A(H7N9) Influenza. J Infect Dis 2015; 212:1214-21. [PMID: 25904605 PMCID: PMC7107393 DOI: 10.1093/infdis/jiv246] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/27/2015] [Indexed: 01/25/2023] Open
Abstract
The genetic predisposition to severe A(H1N1)2009 (A[H1N1]pdm09) influenza was evaluated in 409 patients, including 162 cases with severe infection and 247 controls with mild infection. We prioritized candidate variants based on the result of a pilot genome-wide association study and a lung expression quantitative trait locus data set. The GG genotype of rs2070788, a higher-expression variant of TMPRSS2, was a risk variant (odds ratio, 2.11; 95% confidence interval, 1.18-3.77; P = .01) to severe A(H1N1)pdm09 influenza. A potentially functional single-nucleotide polymorphism, rs383510, accommodated in a putative regulatory region was identified to tag rs2070788. Luciferase assay results showed the putative regulatory region was a functional element, in which rs383510 regulated TMPRSS2 expression in a genotype-specific manner. Notably, rs2070788 and rs383510 were significantly associated with the susceptibility to A(H7N9) influenza in 102 patients with A(H7N9) influenza and 106 healthy controls. Therefore, we demonstrate that genetic variants with higher TMPRSS2 expression confer higher risk to severe A(H1N1)pdm09 influenza. The same variants also increase susceptibility to human A(H7N9) influenza.
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Affiliation(s)
| | - Jie Zhou
- Department of Microbiology Research Centre of Infection and Immunology State Key Laboratory of Emerging Infectious Diseases
| | - Kelvin Kai-Wang To
- Department of Microbiology Research Centre of Infection and Immunology State Key Laboratory of Emerging Infectious Diseases Carol Yu Centre for Infection
| | - Hin Chu
- Department of Microbiology Research Centre of Infection and Immunology State Key Laboratory of Emerging Infectious Diseases
| | - Cun Li
- Department of Microbiology
| | | | | | - Shufa Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University, China
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York
| | - Yohan Bossé
- Department of Molecular Medicine, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University
| | - Ma'en Obeidat
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, Canada
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, The Netherlands
| | - You-Qiang Song
- Department of Biochemistry, The University of Hong Kong, Pok Fu Lam
| | - Yu Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University, China
| | - Bo-Jian Zheng
- Department of Microbiology Research Centre of Infection and Immunology State Key Laboratory of Emerging Infectious Diseases
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University, China
| | - Kwok-Yung Yuen
- Department of Microbiology Research Centre of Infection and Immunology State Key Laboratory of Emerging Infectious Diseases Carol Yu Centre for Infection
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