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Sawant S, Nandi SS, Gohil T, Jadhav A, Samudra P, Arora M, Rudra U, Deshpande J. A multiplex SNaPshot assay for the detection of single nucleotide polymorphism associated with clinical severity of enterovirus infections. Gene 2024; 926:148618. [PMID: 38821327 DOI: 10.1016/j.gene.2024.148618] [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: 01/19/2024] [Revised: 05/14/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Non-polio enterovirus infections are known to cause a variety of diseases and neurological complications. It is also known that the severity of these diseases largely differs among individuals with different genotypes and alleles. The Single Nucleotide Polymorphisms (SNPs) within specific genes have a considerable effect on the immune response to enteroviruses and on the outcome of disease, leading to variations in complications and infection susceptibility. Knowing the distribution of such SNPs can be valuable for individual case management and studying epidemiological parameters of enterovirus infections. In this feasibility study, a multiplex version of the primer extension-based technique called the SNaPshot Assay has been developed to examine SNPs in various relevant genes for predicting the clinical severity of enterovirus infections. It is already established that this technique is precise, consistent, scalable, and likely to exhibit high throughput. The multiplex SNaPshot can investigate multiple genetic susceptibility markers simultaneously, and the assay can be used to identify vulnerable populations, understand the epidemiology of infections, and manage the outbreaks of enteroviruses. Based on the literature, 15 SNPs were identified which are suspected for higher susceptibility to the worst outcomes after enterovirus infection and the assay was developed. Blood samples of 100 healthy volunteers were collected and tested for assay feasibility as well as to know the proportions of 15 selected SNPs. After the analysis, seven SNPs have been identified and suggested to be considered for future assays. Based on the pilot test results, it appears that positivity for any three out of the identified seven SNPs might indicate a higher risk, and future studies correlated with clinical studies among patients with and without severe diseases utilizing this assay will provide robust parameters to determine at-risk individuals more accurately.
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Affiliation(s)
- Sonali Sawant
- National Institute of Virology Mumbai Unit, Haffkine Institute Compound, AD Marg, Parel, Mumbai 400012, India.
| | - Shyam Sundar Nandi
- National Institute of Virology Mumbai Unit, Haffkine Institute Compound, AD Marg, Parel, Mumbai 400012, India.
| | - Trupti Gohil
- National Institute of Virology Mumbai Unit, Haffkine Institute Compound, AD Marg, Parel, Mumbai 400012, India.
| | - Abhijeet Jadhav
- Scientist E, National Institute of Virology, Pune 411001, India.
| | - Prasanna Samudra
- National Institute of Virology Mumbai Unit, Haffkine Institute Compound, AD Marg, Parel, Mumbai 400012, India.
| | - Meera Arora
- Dr. Babasaheb Ambedkar Memorial Hospital (Zonal) Byculla, Central Railway, Mumbai 400012, India.
| | - Ujjaini Rudra
- Dr. Balasaheb Vikhe Patil Rural Medical College, Loni 413736, India.
| | - Jagadish Deshpande
- National Institute of Virology Mumbai Unit, Haffkine Institute Compound, AD Marg, Parel, Mumbai 400012, India.
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Harioudh MK, Perez J, Chong Z, Nair S, So L, McCormick KD, Ghosh A, Shao L, Srivastava R, Soveg F, Ebert TS, Atianand MK, Hornung V, Savan R, Diamond MS, Sarkar SN. Oligoadenylate synthetase 1 displays dual antiviral mechanisms in driving translational shutdown and protecting interferon production. Immunity 2024; 57:446-461.e7. [PMID: 38423012 PMCID: PMC10939734 DOI: 10.1016/j.immuni.2024.02.002] [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: 06/15/2023] [Revised: 11/15/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
In response to viral infection, how cells balance translational shutdown to limit viral replication and the induction of antiviral components like interferons (IFNs) is not well understood. Moreover, how distinct isoforms of IFN-induced oligoadenylate synthetase 1 (OAS1) contribute to this antiviral response also requires further elucidation. Here, we show that human, but not mouse, OAS1 inhibits SARS-CoV-2 replication through its canonical enzyme activity via RNase L. In contrast, both mouse and human OAS1 protect against West Nile virus infection by a mechanism distinct from canonical RNase L activation. OAS1 binds AU-rich elements (AREs) of specific mRNAs, including IFNβ. This binding leads to the sequestration of IFNβ mRNA to the endomembrane regions, resulting in prolonged half-life and continued translation. Thus, OAS1 is an ARE-binding protein with two mechanisms of antiviral activity: driving inhibition of translation but also a broader, non-canonical function of protecting IFN expression from translational shutdown.
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Affiliation(s)
- Munesh K Harioudh
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, Pittsburgh, PA, USA
| | - Joseph Perez
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, Pittsburgh, PA, USA
| | - Zhenlu Chong
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sharmila Nair
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lomon So
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA; Division of Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Kevin D McCormick
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, Pittsburgh, PA, USA
| | - Arundhati Ghosh
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, Pittsburgh, PA, USA
| | - Lulu Shao
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, Pittsburgh, PA, USA
| | - Rashmi Srivastava
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, Pittsburgh, PA, USA
| | - Frank Soveg
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Thomas S Ebert
- Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Maninjay K Atianand
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Veit Hornung
- Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Ram Savan
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Saumendra N Sarkar
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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Sarkar SN, Harioudh MK, Shao L, Perez J, Ghosh A. The Many Faces of Oligoadenylate Synthetases. J Interferon Cytokine Res 2023; 43:487-494. [PMID: 37751211 PMCID: PMC10654648 DOI: 10.1089/jir.2023.0098] [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] [Accepted: 08/13/2023] [Indexed: 09/27/2023] Open
Abstract
2'-5' Oligoadenylate synthetases (OAS) are interferon-stimulated genes that are most well-known to protect hosts from viral infections. They are evolutionarily related to an ancient family of Nucleotidyltransferases, which are primarily involved in pathogen-sensing and innate immune response. Classical function of OAS proteins involves double-stranded RNA-stimulated polymerization of adenosine triphosphate in 2'-5' oligoadenylates (2-5A), which can activate the latent RNase (RNase L) to degrade RNA. However, accumulated evidence over the years have suggested alternative mode of antiviral function of several OAS family proteins. Furthermore, recent studies have connected some OAS proteins with wider function beyond viral infection. Here, we review some of the canonical and noncanonical functions of OAS proteins and their mechanisms.
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Affiliation(s)
- Saumendra N. Sarkar
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Munesh K. Harioudh
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lulu Shao
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Joseph Perez
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Arundhati Ghosh
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Gokul A, Arumugam T, Ramsuran V. Genetic Ethnic Differences in Human 2'-5'-Oligoadenylate Synthetase and Disease Associations: A Systematic Review. Genes (Basel) 2023; 14:527. [PMID: 36833454 PMCID: PMC9956131 DOI: 10.3390/genes14020527] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Recently, several studies have highlighted a skewed prevalence of infectious diseases within the African continent. Furthermore, a growing number of studies have demonstrated unique genetic variants found within the African genome are one of the contributing factors to the disease severity of infectious diseases within Africa. Understanding the host genetic mechanisms that offer protection against infectious diseases provides an opportunity to develop unique therapeutic interventions. Over the past two decades, several studies have linked the 2'-5'-oligoadenylate synthetase (OAS) family with a range of infectious diseases. More recently, the OAS-1 gene has also been associated with disease severity caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which led to a global pandemic. The OAS family serves as an antiviral factor through the interaction with Ribonuclease-Latent (RNase-L). This review explores the genetic variants observed within the OAS genes and the associations with various viral infections and how previously reported ethnic-specific polymorphisms drive clinical significance. This review provides an overview of OAS genetic association studies with a particular focus on viral diseases affecting individuals of African descent.
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Affiliation(s)
- Anmol Gokul
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban 4041, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban 4001, South Africa
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Yaping LI, Song Z, Wenjun W, Huiling D, Mei LI, Xiaoli J, Shuangsuo D. [ OAS1 gene polymorphism is associated with central nervous system involvement in children with enterovirus 71 infection]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2019; 39:381-386. [PMID: 31068279 PMCID: PMC6744003 DOI: 10.12122/j.issn.1673-4254.2019.04.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE We investigated the association between OAS1 gene polymorphism and susceptibility to central nervous system (CNS) involvement of enterovirus (EV)71 infection. METHODS This case-control study was conducted among 180 children with EV71 infection, including 72 with mild infections without any complications and 108 with severe infections and CNS involvement; 201 children undergoing routine physical examination served as the healthy controls. For all the participants, the single nucleotide polymorphisms (SNPs) at OAS1 rs2660 and rs1131454 were analyzed using SNPscan multiple SNP typing methods. RESULTS No significant differences were found between the case and control groups in genotype or allele distributions of rs2660 and rs1131454. OAS1 rs2660 polymorphism was significantly different between the children with CNS involvement and those with mild EV71 infection, and the genotype AG frequency was higher and the genotype GG frequency was lower in children with CNS involvement. No significant difference was found in the distribution of genotypes or alleles of rs1131454 between the children with CNS involvement and those with mild EV71 infection. CONCLUSIONS OAS1 gene rs2660 and rs1131454 SNPs are not associated with the susceptibility to or CNS involvement of EV71 infection, but OAS1 rs2660 SNPs are significantly correlated with the susceptibility to CNS involvement in EV71 infection. Children carrying OAS1 rs2660 AG genotype are more likely to have CNS involvement after EV71 infection.
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Affiliation(s)
- L I Yaping
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Zhai Song
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Wang Wenjun
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Deng Huiling
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China.,Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an 710003, China
| | - L I Mei
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Jia Xiaoli
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Dang Shuangsuo
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
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Lee WB, Choi WY, Lee DH, Shim H, Kim-Ha J, Kim YJ. OAS1 and OAS3 negatively regulate the expression of chemokines and interferon-responsive genes in human macrophages. BMB Rep 2019. [PMID: 30078389 PMCID: PMC6443328 DOI: 10.5483/bmbrep.2019.52.2.129] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Upon viral infection, the 2′, 5′-oligoadenylate synthetase (OAS)-ribonuclease L (RNaseL) system works to cleave viral RNA, thereby blocking viral replication. However, it is unclear whether OAS proteins have a role in regulating gene expression. Here, we show that OAS1 and OAS3 act as negative regulators of the expression of chemokines and interferon-responsive genes in human macrophages. Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 nuclease (Cas9) technology was used to engineer human myeloid cell lines in which the OAS1 or OAS3 gene was deleted. Neither OAS1 nor OAS3 was exclusively responsible for the degradation of rRNA in macrophages stimulated with poly(I:C), a synthetic surrogate for viral double-stranded (ds)RNA. An mRNA sequencing analysis revealed that genes related to type I interferon signaling and chemokine activity were increased in OAS1−/− and OAS3−/− macrophages treated with intracellular poly(I:C). Indeed, retinoic-acid-inducible gene (RIG)-I- and interferon-induced helicase C domain-containing protein (IFIH1 or MDA5)-mediated induction of chemokines and interferon-stimulated genes was regulated by OAS3, but Toll-like receptor 3 (TLR3)- and TLR4-mediated induction of those genes was modulated by OAS1 in macrophages. However, stimulation of these cells with type I interferons had no effect on OAS1- or OAS3-mediated chemokine secretion. These data suggest that OAS1 and OAS3 negatively regulate the expression of chemokines and interferon-responsive genes in human macrophages.
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Affiliation(s)
- Wook-Bin Lee
- Korean Institute of Science and Technology (KIST), Gangneung Institute of Natural Products, Gangneung 25451, Korea
| | - Won Young Choi
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Korea
| | - Dong-Hyun Lee
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Korea
| | - Hyeran Shim
- Department of Integrative Bioscience and Biotechnology, College of Life Sciences, Sejong University, Seoul 05006; Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jeongsil Kim-Ha
- Department of Integrative Bioscience and Biotechnology, College of Life Sciences, Sejong University, Seoul 05006, Korea
| | - Young-Joon Kim
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul 03722; Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea Korea
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Yen TY, Shih WL, Huang YC, Lee JT, Huang LM, Chang LY. Polymorphisms in enterovirus 71 receptors associated with susceptibility and clinical severity. PLoS One 2018; 13:e0206769. [PMID: 30395634 PMCID: PMC6218064 DOI: 10.1371/journal.pone.0206769] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/18/2018] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVE To evaluate the association of enterovirus 71 (EV71) susceptibility and clinical severity with polymorphisms in EV71 receptors, including human scavenger receptor class B member 2 (SCARB2), P-selectin glycoprotein ligand-1 (PSGL-1), and annexin II (ANXA2). METHODS We enrolled laboratory-confirmed EV71 cases and healthy age- and gender-matched controls in Taiwan from 2000 to 2012. We detected genetic polymorphisms in SCARB2, PSGL-1, and ANXA2 and correlated the results with EV71 susceptibility and severity. RESULTS We collected 599 EV71 cases and 98 controls. Among EV71 patients, the male to female ratio was 1.61, and the mean age was 2.99±2.47 years. For clinical severity, 117 (19.6%) had severe central nervous system involvement with or without cardiopulmonary failure. For outcomes, 46 (7.7%) had sequelae, and 14 (2.3%) died. SCARB2 polymorphisms (rs6824953 and rs11097262) were associated with susceptibility to EV71 infection (OR 1.60, 95% CI 1.07-2.39; and OR 1.64, 95% CI 1.09-2.47, respectively). PSGL-1 polymorphisms (rs7137098 and rs8179137) were significantly associated with severe EV71 infection (OR 1.46, 95% CI 1.1-1.96; and OR 1.47, 95% CI 1.07-2.03, respectively). CONCLUSIONS SCARB2 polymorphisms (rs6824953 and rs11097262) might be associated with EV71 susceptibility. PSGL-1 polymorphisms (rs7137098 and rs8179137) were associated with severe EV71 infection.
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Affiliation(s)
- Ting-Yu Yen
- Department of Pediatrics, China Medical University Children’s Hospital, China Medical University, Taichung, Taiwan
| | - Wei-Liang Shih
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Yi-Chuan Huang
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Jian-Te Lee
- Department of Pediatrics, National Taiwan University Hospital, Yun-Lin Branch, Yunlin, Taiwan
| | - Li-Min Huang
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Luan-Yin Chang
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
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8
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Polymorphism of OAS2 rs739901 C/A Involves the Susceptibility to EV71 Infection in Chinese Children. Curr Med Sci 2018; 38:640-647. [DOI: 10.1007/s11596-018-1925-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 05/15/2018] [Indexed: 10/28/2022]
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van der Sanden SMG, Sachs N, Koekkoek SM, Koen G, Pajkrt D, Clevers H, Wolthers KC. Enterovirus 71 infection of human airway organoids reveals VP1-145 as a viral infectivity determinant. Emerg Microbes Infect 2018; 7:84. [PMID: 29743570 PMCID: PMC5943241 DOI: 10.1038/s41426-018-0077-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 02/25/2018] [Accepted: 03/17/2018] [Indexed: 11/10/2022]
Abstract
Human enteroviruses frequently cause severe diseases in children. Human enteroviruses are transmitted via the fecal-oral route and respiratory droplets, and primary replication occurs in the gastro-intestinal and respiratory tracts; however, how enteroviruses infect these sites is largely unknown. Human intestinal organoids have recently proven to be valuable tools for studying enterovirus-host interactions in the intestinal tract. In this study, we demonstrated the susceptibility of a newly developed human airway organoid model for enterovirus 71 (EV71) infection. We showed for the first time in a human physiological model that EV71 replication kinetics are strain-dependent. A glutamine at position 145 of the VP1 capsid protein was identified as a key determinant of infectivity, and residues VP1-98K and VP1-104D were identified as potential infectivity markers. The results from this study provide new insights into EV71 infectivity in the human airway epithelia and demonstrate the value of organoid technology for virus research.
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Affiliation(s)
| | - Norman Sachs
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht and Cancer Genomics Netherlands, 3584 CT, Utrecht, The Netherlands
| | - Sylvie M Koekkoek
- Department of Medical Microbiology, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Gerrit Koen
- Department of Medical Microbiology, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Dasja Pajkrt
- Department of Pediatric Infectious Diseases, Emma Children's Hospital, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht and Cancer Genomics Netherlands, 3584 CT, Utrecht, The Netherlands
| | - Katja C Wolthers
- Department of Medical Microbiology, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
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Liu Y, Liu P, Liu S, Guo Y, He H, Yang C, Song J, Zhang N, Cheng J, Chen Z. Oligoadenylate synthetase 3 S381R gene polymorphism is associated with severity of EV71 infection in Chinese children. J Clin Virol 2018; 101:29-33. [PMID: 29414184 DOI: 10.1016/j.jcv.2018.01.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 01/15/2018] [Accepted: 01/24/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Oligoadenylate synthetase 3 (OAS3) is interferon-induced antiviral enzyme, playing a significant role in the innate immune response. Genetic polymorphism in OAS3 gene has been reported to be a susceptibility factor in many infected diseases, but evidence of its effect on enterovirus 71 (EV71) infection is still lacking. OBJECTIVES An attempt study was made to investigate whether genetic polymorphism of OAS3 S381R is associated with the severity of EV71 infection in Chinese children. STUDY DESIGN Retrospectively sumed up the clinical onsets and experimental results for 249 cases with EV71 infection (including 151 mild cases and 98 severe cases) and 243 controls. An improved multiplex ligation detection reaction (iMLDR) technique was carried out to analyze polymorphism in OAS3 S381R G/C gene for genetic association analyses. The plasma levels of IFN-γ were determined by enzyme-linked immunosorbent assays. RESULTS The distribution of OAS3 S381R CC genotype (73.47%) and C allele (85.20%) in severe cases was markedly higher than in mild cases (45.70%, P < .01; 67.88%, P < .01). The blood IFN-γ levels of severe cases were significantly lower in CC genotype (131.66 ± 10.84 pg/mL) compared to GG (183.37 ± 24.50 pg/mL, p < .01) and GC genotype (168.48 ± 26.57 pg/mL, p < .01). CONCLUSIONS Carrying the C allele of the OAS3 S381R gene could be a susceptibility factor in the development of severe EV71 infection in Chinese children.
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Affiliation(s)
- Yedan Liu
- Department of Pediatrics, The Affiliated Hospital of Qingdao University, NO. 16, Jiangsu Road, Qingdao 266000, China.
| | - Peipei Liu
- Department of Pediatrics, The Affiliated Hospital of Qingdao University, NO. 16, Jiangsu Road, Qingdao 266000, China.
| | - Shihai Liu
- Medical Research Center, The Affiliated Hospital of Qingdao University, NO. 1677, Wutaishan Road, Qingdao, 266000, China.
| | - Ya Guo
- Department of Pediatrics, The Affiliated Hospital of Qingdao University, NO. 16, Jiangsu Road, Qingdao 266000, China.
| | - Hongfang He
- Department of Pediatrics, The Affiliated Hospital of Qingdao University, NO. 16, Jiangsu Road, Qingdao 266000, China.
| | - Chengqing Yang
- Department of Pediatrics, The Affiliated Hospital of Qingdao University, NO. 16, Jiangsu Road, Qingdao 266000, China.
| | - Jie Song
- Department of Pediatrics, The Affiliated Hospital of Qingdao University, NO. 16, Jiangsu Road, Qingdao 266000, China.
| | - Na Zhang
- Department of Pediatrics, The Affiliated Hospital of Qingdao University, NO. 16, Jiangsu Road, Qingdao 266000, China.
| | - Jianguo Cheng
- Departments of Pain Management and Neurosciences, Lerner Research Institute, Cleveland Clinic, Euclid Avenue, Cleveland, OH 44195, USA.
| | - Zongbo Chen
- Department of Pediatrics, The Affiliated Hospital of Qingdao University, NO. 16, Jiangsu Road, Qingdao 266000, China.
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11
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Liu G, Xu Y, Wang X, Zhuang X, Liang H, Xi Y, Lin F, Pan L, Zeng T, Li H, Cao X, Zhao G, Xia H. Developing a Machine Learning System for Identification of Severe Hand, Foot, and Mouth Disease from Electronic Medical Record Data. Sci Rep 2017; 7:16341. [PMID: 29180702 PMCID: PMC5703994 DOI: 10.1038/s41598-017-16521-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/13/2017] [Indexed: 11/21/2022] Open
Abstract
Children of severe hand, foot, and mouth disease (HFMD) often present with same clinical features as those of mild HFMD during the early stage, yet later deteriorate rapidly with a fulminant disease course. Our goal was to: (1) develop a machine learning system to automatically identify cases with high risk of severe HFMD at the time of admission; (2) compare the effectiveness of the new system with the existing risk scoring system. Data on 2,532 HFMD children admitted between March 2012 and July 2015, were collected retrospectively from a medical center in China. By applying a holdout strategy and a 10-fold cross validation method, we developed four models with the random forest algorithm using different variable sets. The prediction system HFMD-RF based on the model of 16 variables from both the structured and unstructured data, achieved 0.824 sensitivity, 0.931 specificity, 0.916 accuracy, and 0.916 area under the curve in the independent test set. Most remarkably, HFMD-RF offers significant gains with respect to the commonly used pediatric critical illness score in clinical practice. As all the selected risk factors can be easily obtained, HFMD-RF might prove to be useful for reductions in mortality and complications of severe HFMD.
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Affiliation(s)
- Guangjian Liu
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yi Xu
- Department of Infectious Diseases, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xinming Wang
- School of Computer, South China Normal University, Guangzhou, China
| | - Xutian Zhuang
- School of Computer, South China Normal University, Guangzhou, China
| | - Huiying Liang
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yun Xi
- School of Computer, South China Normal University, Guangzhou, China
| | - Fangqin Lin
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Liyan Pan
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Taishan Zeng
- School of Mathematical Sciences, South China Normal University, Guangzhou, China
| | - Huixian Li
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiaojun Cao
- Department of Research, Education and Data Management, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Gansen Zhao
- School of Computer, South China Normal University, Guangzhou, China.
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
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12
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Fish I, Boissinot S. Functional evolution of the OAS1 viral sensor: Insights from old world primates. INFECTION GENETICS AND EVOLUTION 2016; 44:341-350. [PMID: 27393659 DOI: 10.1016/j.meegid.2016.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 11/26/2022]
Abstract
Infections with viral pathogens impose considerable selective pressure on host defensive genes. Those genes at the forefront, responsible for identifying and binding exogenous molecular viral components, will carry the hallmarks of this struggle. Oligoadenylate synthetase (OAS) enzymes play a major role in the innate defense against a large number of viruses by acting as sensors of viral infections. Following their up-regulation by the interferon pathway, OASs bind viral dsRNA and then signal ribonuclease L (RNase L) to degrade RNA, shutting down viral and host protein synthesis. We have investigated the evolution of OAS1 in twenty-two Old World monkey species. We identified a total of 35 codons with the earmarks of positive selection and we performed a comprehensive analysis of their functional significance using in silico modeling of the OAS1 protein. Subdividing OAS1 into functional domains revealed intense purifying selection in the active domain but significant positive directional selection in the RNA-binding domain (RBD), the region where OAS1 binds viral dsRNA. The modeling analysis revealed a concentration of rapidly evolving residues in one region of the RBD suggestive of the sub-functionalization of different regions of the RBD. This analysis also identified several positively selected residues circumscribing the entry to the active site suggesting adaptive evasion of viral antagonism and/or selection for production of oligoadenylate of different length.
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Affiliation(s)
- Ian Fish
- Biology Department, Queens College, The City University of New York, 65-30 Kissena Boulevard, Flushing, NY 11367, USA; Graduate Center, Sub-program in Molecular, Cellular and Developmental Biology, The City University of New York, 365(th) avenue, New York, NY 10016, USA.
| | - Stéphane Boissinot
- New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates.
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Ong KC, Wong KT. Understanding Enterovirus 71 Neuropathogenesis and Its Impact on Other Neurotropic Enteroviruses. Brain Pathol 2016; 25:614-24. [PMID: 26276025 DOI: 10.1111/bpa.12279] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 06/19/2015] [Indexed: 01/27/2023] Open
Abstract
Enterovirus A71 (EV-A71) belongs to the species group A in the Enterovirus genus within the Picornaviridae family. EV-A71 usually causes self-limiting hand, foot and mouth disease or herpangina but rarely causes severe neurological complications such as acute flaccid paralysis and encephalomyelitis. The pathology and neuropathogenesis of these neurological syndromes is beginning to be understood. EV-A71 neurotropism for motor neurons in the spinal cord and brainstem, and other neurons, is mainly responsible for central nervous system damage. This review on the general aspects, recent developments and advances of EV-A71 infection will focus on neuropathogenesis and its implications on other neurotropic enteroviruses, such as poliovirus and the newly emergent Enterovirus D68. With the imminent eradication of poliovirus, EV-A71 is likely to replace it as an important neurotropic enterovirus of worldwide importance.
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Affiliation(s)
- Kien Chai Ong
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kum Thong Wong
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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14
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A functional polymorphism in IFNAR1 gene is associated with susceptibility and severity of HFMD with EV71 infection. Sci Rep 2015; 5:18541. [PMID: 26679744 PMCID: PMC4683517 DOI: 10.1038/srep18541] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/19/2015] [Indexed: 12/15/2022] Open
Abstract
Enterovirus 71 (EV71), one of the major pathogens of Hand, foot and mouth disease (HFMD), results in millions of infections and hundreds of deaths each year in Southeast Asia. Biased infection and variable clinical manifestations of EV71 HFMD indicated that host genetic background played an important role in the occurrence and development of the disease. We identified the mRNA profiles of EV71 HFMD patients, which type I interferon (IFN) pathway related genes were down-regulated. Four single nucleotide polymorphisms (SNPs) of type I IFN receptor 1 (IFNAR1) were chosen to analyze their relationships to EV71 infection. We found that genotype GG of promoter variant rs2843710 was associated with the susceptibility and severity to EV71 HFMD. In addition, we assessed the regulatory effects of rs2843710 to IFN stimulated genes (ISGs), and found that the expressions of IFNAR1, OAS1 and MX1 were significantly lower in patients with rs2843710 genotype GG. And rs2843710 allele G showed weaker transcriptional activity compared with allele C. Our study indicated that rs2843710 of IFNAR1 was associated with the susceptibility and severity of EV71 HFMD in Chinese Han populations, acting as a functional polymorphism by regulating ISGs expression, such as OAS1 and MX1.
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15
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Abstract
PURPOSE OF REVIEW Hand-foot-and-mouth disease (HFMD) is a common cause of viral rash in children with classic skin findings which are easily recognized by pediatricians. Recently, several atypical cutaneous manifestations of HFMD have been described. Awareness of these patterns may lead providers to appropriate diagnosis and management. This review also highlights the epidemiological patterns of more virulent strains and emerging research in disease prevention. RECENT FINDINGS Classic HFMD presents with tender lesions on the hands, feet, and oral mucosa. Atypical skin findings in HFMD may be seen in children with atopic dermatitis. These include 'eczema coxsackium', in which eczematous skin is superinfected with coxsackie virus, resembling herpes infection. Nail changes, such as shedding, may follow HFMD after a latency period. Enterovirus 71 is responsible for epidemic outbreaks of HFMD in Asia, with systemic manifestations and occasionally neurological sequelae. Research is underway to develop a vaccine which could curb epidemics, but for the present, supportive care and hygiene measures are the standard of care. SUMMARY Atypical manifestations of HFMD in children with atopic dermatitis may mimic herpetic superinfection. In a child presenting with nail changes, consider antecedent HFMD in the differential diagnosis. The mainstay of treatment for HMFD remains supportive care.
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Contrasted patterns of variation and evolutionary convergence at the antiviral OAS1 gene in old world primates. Immunogenetics 2015; 67:487-99. [PMID: 26156123 PMCID: PMC4809017 DOI: 10.1007/s00251-015-0855-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 06/24/2015] [Indexed: 11/13/2022]
Abstract
The oligoadenylate synthetase 1 (OAS1) enzyme acts as an innate sensor of viral infection and plays a major role in the defense against a wide diversity of viruses. Polymorphisms at OAS1 have been shown to correlate with differential susceptibility to several infections of great public health significance, including hepatitis C virus, SARS coronavirus, and West Nile virus. Population genetics analyses in hominoids have revealed interesting evolutionary patterns. In Central African chimpanzee, OAS1 has evolved under long-term balancing selection, resulting in the persistence of polymorphisms since the origin of hominoids, whereas human populations have acquired and retained OAS1 alleles from Neanderthal and Denisovan origin. We decided to further investigate the evolution of OAS1 in primates by characterizing intra-specific variation in four species commonly used as models in infectious disease research: the rhesus macaque, the cynomolgus macaque, the olive baboon, and the Guinea baboon. In baboons, OAS1 harbors a very low level of variation. In contrast, OAS1 in macaques exhibits a level of polymorphism far greater than the genomic average, which is consistent with the action of balancing selection. The region of the enzyme that directly interacts with viral RNA, the RNA-binding domain, contains a number of polymorphisms likely to affect the RNA-binding affinity of OAS1. This strongly suggests that pathogen-driven balancing selection acting on the RNA-binding domain of OAS1 is maintaining variation at this locus. Interestingly, we found that a number of polymorphisms involved in RNA-binding were shared between macaques and chimpanzees. This represents an unusual case of convergent polymorphism.
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Deo S, Patel TR, Chojnowski G, Koul A, Dzananovic E, McEleney K, Bujnicki JM, McKenna SA. Characterization of the termini of the West Nile virus genome and their interactions with the small isoform of the 2' 5'-oligoadenylate synthetase family. J Struct Biol 2015; 190:236-49. [PMID: 25871524 DOI: 10.1016/j.jsb.2015.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/07/2015] [Accepted: 04/08/2015] [Indexed: 02/05/2023]
Abstract
2' 5'-Oligoadenylate synthetases (OAS) are interferon-stimulated proteins that act in the innate immune response to viral infection. Upon binding viral double-stranded RNA, OAS enzymes produce 2'-5'-linked oligoadenylates that stimulate RNase L and ultimately slow viral propagation. Truncations/mutations in the smallest human OAS isoform, OAS1, results in susceptibility to West Nile virus (WNV). We have previously demonstrated in vitro the interaction between OAS1 and the 5'-terminal region of the WNV RNA genome. Here we report that the 3'-terminal region is also able to mediate specific interaction with and activation of OAS1. Binding and kinetic experiments identified a specific stem loop within the 3'-terminal region that is sufficient for activation of the enzyme. The solution conformation of the 3'-terminal region was determined by small angle X-ray scattering, and computational models suggest a conformationally restrained structure comprised of a helix and short stem loop. Structural investigation of the 3'-terminal region in complex with OAS1 is also presented. Finally, we show that genome cyclization by base pairing between the 5'- and 3'-terminal regions, a required step for replication, is not sufficient to protect WNV from OAS1 recognition in vitro. These data provide a physical framework for understanding recognition of the highly structured terminal regions of a flaviviral genome by an innate immune enzyme.
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Affiliation(s)
- Soumya Deo
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Trushar R Patel
- School of Biosciences, University of Birmingham, Birmingham B152TT, UK
| | - Grzegorz Chojnowski
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Amit Koul
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Edis Dzananovic
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Kevin McEleney
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada; Manitoba Institute for Materials, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland; Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada.
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