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Vigeveno RM, Han AX, de Vries RP, Parker E, de Haan K, van Leeuwen S, Hulme KD, Lauring AS, te Velthuis AJW, Boons GJ, Fouchier RAM, Russell CA, de Jong MD, Eggink D. Long-term evolution of human seasonal influenza virus A(H3N2) is associated with an increase in polymerase complex activity. Virus Evol 2024; 10:veae030. [PMID: 38808037 PMCID: PMC11131032 DOI: 10.1093/ve/veae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/08/2024] [Indexed: 05/30/2024] Open
Abstract
Since the influenza pandemic in 1968, influenza A(H3N2) viruses have become endemic. In this state, H3N2 viruses continuously evolve to overcome immune pressure as a result of prior infection or vaccination, as is evident from the accumulation of mutations in the surface glycoproteins hemagglutinin (HA) and neuraminidase (NA). However, phylogenetic studies have also demonstrated ongoing evolution in the influenza A(H3N2) virus RNA polymerase complex genes. The RNA polymerase complex of seasonal influenza A(H3N2) viruses produces mRNA for viral protein synthesis and replicates the negative sense viral RNA genome (vRNA) through a positive sense complementary RNA intermediate (cRNA). Presently, the consequences and selection pressures driving the evolution of the polymerase complex remain largely unknown. Here, we characterize the RNA polymerase complex of seasonal influenza A(H3N2) viruses representative of nearly 50 years of influenza A(H3N2) virus evolution. The H3N2 polymerase complex is a reassortment of human and avian influenza virus genes. We show that since 1968, influenza A(H3N2) viruses have increased the transcriptional activity of the polymerase complex while retaining a close balance between mRNA, vRNA, and cRNA levels. Interestingly, the increased polymerase complex activity did not result in increased replicative ability on differentiated human airway epithelial (HAE) cells. We hypothesize that the evolutionary increase in polymerase complex activity of influenza A(H3N2) viruses may compensate for the reduced HA receptor binding and avidity that is the result of the antigenic evolution of influenza A(H3N2) viruses.
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Affiliation(s)
- René M Vigeveno
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Alvin X Han
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Robert P de Vries
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Edyth Parker
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Karen de Haan
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Sarah van Leeuwen
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Katina D Hulme
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Adam S Lauring
- Department of Microbiology and Immunology and Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, MI 48109, USA
| | - Aartjan J W te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Geert-Jan Boons
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Department of Chemistry, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, Dr. Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
| | - Colin A Russell
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Menno D de Jong
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Dirk Eggink
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, The Netherlands
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Serafin B, Kamen A, de Crescenzo G, Henry O. Antibody-independent surface plasmon resonance assays for influenza vaccine quality control. Appl Microbiol Biotechnol 2024; 108:307. [PMID: 38656587 PMCID: PMC11043112 DOI: 10.1007/s00253-024-13145-y] [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: 01/17/2024] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
Surface plasmon resonance (SPR)-based biosensors have emerged as a powerful platform for bioprocess monitoring due to their ability to detect biointeractions in real time, without the need for labeling. Paramount for the development of a robust detection platform is the immobilization of a ligand with high specificity and affinity for the in-solution species of interest. Following the 2009 H1N1 pandemic, much effort has been made toward the development of quality control platforms for influenza A vaccine productions, many of which have employed SPR for detection. Due to the rapid antigenic drift of influenza's principal surface protein, hemagglutinin, antibodies used for immunoassays need to be produced seasonally. The production of these antibodies represents a 6-8-week delay in immunoassay and, thus, vaccine availability. This review focuses on SPR-based assays that do not rely on anti-HA antibodies for the detection, characterization, and quantification of influenza A in bioproductions and biological samples. KEY POINTS: • The single radial immunodiffusion assay (SRID) has been the gold standard for the quantification of influenza vaccines since 1979. Due to antigenic drift of influenza's hemagglutinin protein, new antibody reagents for the SRID assay must be produced each year, requiring 6-8 weeks. The resulting delay in immunoassay availability is a major bottleneck in the influenza vaccine pipeline. This review highlights ligand options for the detection and quantification of influenza viruses using surface plasmon resonance biosensors.
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Affiliation(s)
- Benjamin Serafin
- Department of Chemical Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Amine Kamen
- Department of Bioengineering, McGill University, Montreal, QC, Canada
| | - Gregory de Crescenzo
- Department of Chemical Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Olivier Henry
- Department of Chemical Engineering, Polytechnique Montreal, Montreal, QC, Canada.
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Mu J, Hirayama M, Morimoto K, Hori K. A Complex-Type N-Glycan-Specific Lectin Isolated from Green Alga Halimeda borneensis Exhibits Potent Anti-Influenza Virus Activity. Int J Mol Sci 2024; 25:4345. [PMID: 38673930 PMCID: PMC11050134 DOI: 10.3390/ijms25084345] [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: 03/19/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Marine algal lectins specific for high-mannose N-glycans have attracted attention because they strongly inhibit the entry of enveloped viruses, including influenza viruses and SARS-CoV-2, into host cells by binding to high-mannose-type N-glycans on viral surfaces. Here, we report a novel anti-influenza virus lectin (named HBL40), specific for complex-type N-glycans, which was isolated from a marine green alga, Halimeda borneensis. The hemagglutination activity of HBL40 was inhibited with both complex-type N-glycan and O-glycan-linked glycoproteins but not with high-mannose-type N-glycan-linked glycoproteins or any of the monosaccharides examined. In the oligosaccharide-binding experiment using 26 pyridylaminated oligosaccharides, HBL40 only bound to complex-type N-glycans with bi- and triantennary-branched sugar chains. The sialylation, core fucosylation, and the increased number of branched antennae of the N-glycans lowered the binding activity with HBL40. Interestingly, the lectin potently inhibited the infection of influenza virus (A/H3N2/Udorn/72) into NCI-H292 cells at IC50 of 8.02 nM by binding to glycosylated viral hemagglutinin (KD of 1.21 × 10-6 M). HBL40 consisted of two isolectins with slightly different molecular masses to each other that could be separated by reverse-phase HPLC. Both isolectins shared the same 16 N-terminal amino acid sequences. Thus, HBL40 could be useful as an antivirus lectin specific for complex-type N-glycans.
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Affiliation(s)
- Jinmin Mu
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan; (J.M.); (M.H.)
| | - Makoto Hirayama
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan; (J.M.); (M.H.)
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| | - Kinjiro Morimoto
- Faculty of Pharmacy, Yasuda Women’s University, Yasuhigashi 6-13-1, Asaminami-Ku, Hiroshima 731-0153, Japan;
| | - Kanji Hori
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan; (J.M.); (M.H.)
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
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Roy R. Cancer cells and viruses share common glycoepitopes: exciting opportunities toward combined treatments. Front Immunol 2024; 15:1292588. [PMID: 38495885 PMCID: PMC10940920 DOI: 10.3389/fimmu.2024.1292588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/06/2024] [Indexed: 03/19/2024] Open
Abstract
Aberrant glycosylation patterns of glycoproteins and glycolipids have long been recognized as one the major hallmarks of cancer cells that has led to numerous glycoconjugate vaccine attempts. These abnormal glycosylation profiles mostly originate from the lack of key glycosyltransferases activities, mutations, over expressions, or modifications of the requisite chaperone for functional folding. Due to their relative structural simplicity, O-linked glycans of the altered mucin family of glycoproteins have been particularly attractive in the design of tumor associated carbohydrate-based vaccines. Several such glycoconjugate vaccine formulations have generated potent monoclonal anti-carbohydrate antibodies useful as diagnostic and immunotherapies in the fight against cancer. Paradoxically, glycoproteins related to enveloped viruses also express analogous N- and O-linked glycosylation patterns. However, due to the fact that viruses are not equipped with the appropriate glycosyl enzyme machinery, they need to hijack that of the infected host cells. Although the resulting N-linked glycans are very similar to those of normal cells, some of their O-linked glycan patterns often share the common structural simplicity to those identified on tumor cells. Consequently, given that both cancer cells and viral glycoproteins share both common N- and O-linked glycoepitopes, glycoconjugate vaccines could be highly attractive to generate potent immune responses to target both conditions.
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Affiliation(s)
- René Roy
- Glycosciences and Nanomaterial Laboratory, Université du Québec à Montréal, Montréal, QC, Canada
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Li X, Li Y, Shang X, Kong H. A sequence-based machine learning model for predicting antigenic distance for H3N2 influenza virus. Front Microbiol 2024; 15:1345794. [PMID: 38314434 PMCID: PMC10834737 DOI: 10.3389/fmicb.2024.1345794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
Introduction Seasonal influenza A H3N2 viruses are constantly changing, reducing the effectiveness of existing vaccines. As a result, the World Health Organization (WHO) needs to frequently update the vaccine strains to match the antigenicity of emerged H3N2 variants. Traditional assessments of antigenicity rely on serological methods, which are both labor-intensive and time-consuming. Although numerous computational models aim to simplify antigenicity determination, they either lack a robust quantitative linkage between antigenicity and viral sequences or focus restrictively on selected features. Methods Here, we propose a novel computational method to predict antigenic distances using multiple features, including not only viral sequence attributes but also integrating four distinct categories of features that significantly affect viral antigenicity in sequences. Results This method exhibits low error in virus antigenicity prediction and achieves superior accuracy in discerning antigenic drift. Utilizing this method, we investigated the evolution process of the H3N2 influenza viruses and identified a total of 21 major antigenic clusters from 1968 to 2022. Discussion Interestingly, our predicted antigenic map aligns closely with the antigenic map generated with serological data. Thus, our method is a promising tool for detecting antigenic variants and guiding the selection of vaccine candidates.
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Affiliation(s)
- Xingyi Li
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
- Big Data Storage and Management MIIT Lab, Xi'an, Shaanxi, China
| | - Yanyan Li
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
- Big Data Storage and Management MIIT Lab, Xi'an, Shaanxi, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
- Big Data Storage and Management MIIT Lab, Xi'an, Shaanxi, China
| | - Huihui Kong
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, China
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Le BT, Gallage HC, Kim MH, Park JE. Molecular Characterization of Porcine Epidemic Diarrhea Virus from Field Samples in South Korea. Viruses 2023; 15:2428. [PMID: 38140669 PMCID: PMC10748127 DOI: 10.3390/v15122428] [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: 11/01/2023] [Revised: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric pathogen of swine. PEDV has been a major problem in the pig industry since its first identification in 1992. The aim of this study was to investigate the diversity, molecular characteristics, and phylogenetic relationships of PEDVs in field samples from Korea. Six PEDVs were identified from the field samples, and the full spike (S) glycoprotein gene sequences were analyzed. A phylogenetic analysis of the S gene sequences from the six isolates revealed that they were clustered into the G2b subgroup with genetic distance. The genetic identity of the nucleotide sequences and deduced amino acid sequences of the S genes of those isolates was 97.9-100% and 97.4-100%, respectively. A BLAST search for new PEDVs revealed an identity greater than 99.5% compared to the highest similarity of two different Korean strains. The CO-26K equivalent (COE) epitope had a 521H→Y/Q amino acid substitution compared to the subgroup G2b reference strain (KNU-1305). The CNU-22S11 had 28 amino acid substitutions compared to the KNU-1305 strain, which included two newly identified amino acid substitutions: 562S→F and 763P→L in the COE and SS6 epitopes, respectively. Furthermore, the addition and loss of N-linked glycosylation were observed in the CNU-22S11. The results suggest that various strains of PEDV are prevalent and undergoing evolution at swine farms in South Korea and can affect receptor specificity, virus pathogenicity, and host immune system evasion. Overall, this study provides an increased understanding of the prevalence and control of PEDV in South Korea.
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Affiliation(s)
| | | | | | - Jung-Eun Park
- College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea; (B.T.L.); (H.C.G.); (M.-H.K.)
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7
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Zhang Y, Cui P, Shi J, Chen Y, Zeng X, Jiang Y, Tian G, Li C, Chen H, Kong H, Deng G. Key Amino Acid Residues That Determine the Antigenic Properties of Highly Pathogenic H5 Influenza Viruses Bearing the Clade 2.3.4.4 Hemagglutinin Gene. Viruses 2023; 15:2249. [PMID: 38005926 PMCID: PMC10674173 DOI: 10.3390/v15112249] [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: 10/21/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The H5 subtype highly pathogenic avian influenza viruses bearing the clade 2.3.4.4 HA gene have been pervasive among domestic poultry and wild birds worldwide since 2014, presenting substantial risks to human and animal health. Continued circulation of clade 2.3.4.4 viruses has resulted in the emergence of eight subclades (2.3.4.4a-h) and multiple distinct antigenic groups. However, the key antigenic substitutions responsible for the antigenic change of these viruses remain unknown. In this study, we analyzed the HA gene sequences of 5713 clade 2.3.4.4 viruses obtained from a public database and found that 23 amino acid residues were highly variable among these strains. We then generated a series of single-amino-acid mutants based on the H5-Re8 (a vaccine seed virus) background and tested their reactivity with a panel of eight monoclonal antibodies (mAbs). Six mutants bearing amino acid substitutions at positions 120, 126, 141, 156, 185, or 189 (H5 numbering) led to reduced or lost reactivity to these mAbs. Further antigenic cartography analysis revealed that the amino acid residues at positions 126, 156, and 189 acted as immunodominant epitopes of H5 viruses. Collectively, our findings offer valuable guidance for the surveillance and early detection of emerging antigenic variants.
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Affiliation(s)
- Yuancheng Zhang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Pengfei Cui
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Jianzhong Shi
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yuan Chen
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Xianying Zeng
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Yongping Jiang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Guobin Tian
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Chengjun Li
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Hualan Chen
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Huihui Kong
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Guohua Deng
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
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Macauslane KL, Pegg CL, Short KR, Schulz BL. Modulation of endoplasmic reticulum stress response pathways by respiratory viruses. Crit Rev Microbiol 2023:1-19. [PMID: 37934111 DOI: 10.1080/1040841x.2023.2274840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/15/2023] [Indexed: 11/08/2023]
Abstract
Acute respiratory infections (ARIs) are amongst the leading causes of death and disability, and the greatest burden of disease impacts children, pregnant women, and the elderly. Respiratory viruses account for the majority of ARIs. The unfolded protein response (UPR) is a host homeostatic defence mechanism primarily activated in response to aberrant endoplasmic reticulum (ER) resident protein accumulation in cell stresses including viral infection. The UPR has been implicated in the pathogenesis of several respiratory diseases, as the respiratory system is particularly vulnerable to chronic and acute activation of the ER stress response pathway. Many respiratory viruses therefore employ strategies to modulate the UPR during infection, with varying effects on the host and the pathogens. Here, we review the specific means by which respiratory viruses affect the host UPR, particularly in association with the high production of viral glycoproteins, and the impact of UPR activation and subversion on viral replication and disease pathogenesis. We further review the activation of UPR in common co-morbidities of ARIs and discuss the therapeutic potential of modulating the UPR in virally induced respiratory diseases.
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Affiliation(s)
- Kyle L Macauslane
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
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Tahar AS, Ong EJ, Rahardja A, Mamora D, Lim KT, Ahmed K, Kulai D, Tan CS. Emergence of equine-like G3 and porcine-like G9 rotavirus strains in Sarawak, Malaysia: 2019-2021. J Med Virol 2023; 95:e28987. [PMID: 37501648 DOI: 10.1002/jmv.28987] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023]
Abstract
Rotavirus is the leading causative viral agent of pediatric acute gastroenteritis globally, infecting mostly children 5 years old and below. Data on rotavirus prevalence in Malaysia is scarce, despite the WHO's recommendation for continuous rotavirus surveillance, and has underestimated the need for national rotavirus vaccination. Characteristics of the current rotavirus strains in Malaysia have to be determined to understand the rotavirus epidemiology and vaccine compatibility. This study sought to determine the genetic relatedness of Sarawak rotavirus strains with global strains and to determine the antigenic coverage and epitope compatibility of Rotarix and RotaTeq vaccines with the Sarawak rotavirus strains via in silico analysis. A total of 89 stool samples were collected from pediatric patients (<5 years old) with acute gastroenteritis at private hospitals in Kuching, Sarawak. Rotavirus was detected using reverse transcription-polymerase chain reaction. Positive amplicons were analyzed using nucleotide sequencing before phylogenetic analyses and assessment of epitope compatibility. Genotyping revealed G1P[8] (1/13; 7.7%), G3P[8] (3/13; 23%), G9P[4] (1/13; 7.7%), and G9P[8] (3/13; 23%), G9P[X] (1/13; 7.7%), GXP[4] (1/13; 7.7%), and GXP[8] (3/13; 23%) in samples. All wild-type Sarawak rotavirus strains, with the exception of G1, showed variations in their phylogenetic and antigenic epitope characteristics.
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Affiliation(s)
- Ahmad Syatir Tahar
- Centre for Tropical and Emerging Diseases, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Eng Joe Ong
- Borneo Medical Centre, Kuching, Sarawak, Malaysia
| | | | - Dewi Mamora
- Borneo Medical Centre, Kuching, Sarawak, Malaysia
| | | | - Kamruddin Ahmed
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
- Borneo Medical and Health Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Dorothy Kulai
- Universiti Teknologi Mara Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Cheng Siang Tan
- Centre for Tropical and Emerging Diseases, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
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10
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Wong TL, Mooney BP, Cavallero GJ, Guan M, Li L, Zaia J, Wan XF. Glycoproteomic Analyses of Influenza A Viruses Using timsTOF Pro MS. J Proteome Res 2023; 22:62-77. [PMID: 36480915 DOI: 10.1021/acs.jproteome.2c00469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
N-Linked glycosylation in hemagglutinin and neuraminidase glycoproteins of influenza viruses affects antigenic and receptor binding properties, and precise analyses of site-specific glycoforms in these proteins are critical in understanding the antigenic and immunogenic properties of influenza viruses. In this study, we developed a glycoproteomic approach by using a timsTOF Pro mass spectrometer (MS) to determine the abundance and heterogeneity of site-specific glycosylation for influenza glycoproteins. Compared with a Q Exactive HF MS, the timsTOF Pro MS method without the hydrophilic interaction liquid chromatography column enrichment achieved similar glycopeptide coverage and quantities but was more effective in identifying low-abundance glycopeptides. We quantified the distributions of intact site-specific glycopeptides in hemagglutinin of A/chicken/Wuxi/0405005/2013 (H7N9) and A/mute swan/Rhode Island/A00325125/2008 (H7N3). Results showed that hemagglutinin for both viruses had complex N-glycans at N22, N38, N240, and N483 but only high-mannose glycans at N411 and, however, that the type and quantities of glycans were distinct between these viruses. Collisional cross section (CCS) provided by the ion mobility spectrometry from the timsTOF Pro MS data differentiated sialylation linkages of the glycopeptides. In summary, timsTOF Pro MS method can quantify intact site-specific glycans for influenza glycoproteins without enrichment and thus facilitate influenza vaccine development and production.
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Affiliation(s)
- Tin Long Wong
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri65211, United States.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri65211, United States.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri65211, United States
| | - Brian P Mooney
- Department of Biochemistry and Charles W. Gehrke Proteomics Center, University of Missouri, Columbia, Missouri65211, United States
| | - Gustavo J Cavallero
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts02118, United States
| | - Minhui Guan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri65211, United States.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri65211, United States.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri65211, United States
| | - Lei Li
- Department of Chemistry, Georgia State University, Atlanta, Georgia30302, United States
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts02118, United States
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri65211, United States.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri65211, United States.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri65211, United States.,Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, Missouri65211, United States
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11
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Nainu F, Ophinni Y, Shiratsuchi A, Nakanishi Y. Apoptosis and Phagocytosis as Antiviral Mechanisms. Subcell Biochem 2023; 106:77-112. [PMID: 38159224 DOI: 10.1007/978-3-031-40086-5_3] [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] [Indexed: 01/03/2024]
Abstract
Viruses are infectious entities that make use of the replication machinery of their hosts to produce more progenies, causing disease and sometimes death. To counter viral infection, metazoan hosts are equipped with various defense mechanisms, from the rapid-evoking innate immune responses to the most advanced adaptive immune responses. Previous research demonstrated that cells in fruit flies and mice infected with Drosophila C virus and influenza, respectively, undergo apoptosis, which triggers the engulfment of apoptotic virus-infected cells by phagocytes. This process involves the recognition of eat-me signals on the surface of virus-infected cells by receptors of specialized phagocytes, such as macrophages and neutrophils in mice and hemocytes in fruit flies, to facilitate the phagocytic elimination of virus-infected cells. Inhibition of phagocytosis led to severe pathologies and death in both species, indicating that apoptosis-dependent phagocytosis of virus-infected cells is a conserved antiviral mechanism in multicellular organisms. Indeed, our understanding of the mechanisms underlying apoptosis-dependent phagocytosis of virus-infected cells has shed a new perspective on how hosts defend themselves against viral infection. This chapter explores the mechanisms of this process and its potential for developing new treatments for viral diseases.
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Affiliation(s)
- Firzan Nainu
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar, Indonesia.
| | - Youdiil Ophinni
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
- Laboratory of Host Defense, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Akiko Shiratsuchi
- Center for Medical Education, Sapporo Medical University, Sapporo, Japan
- Division of Biological Function and Regulation, Graduate School of Medicine, Sapporo Medical University, Sapporo, Japan
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12
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Changes in the Hemagglutinin and Internal Gene Segments Were Needed for Human Seasonal H3 Influenza A Virus to Efficiently Infect and Replicate in Swine. Pathogens 2022; 11:pathogens11090967. [PMID: 36145399 PMCID: PMC9501159 DOI: 10.3390/pathogens11090967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 11/16/2022] Open
Abstract
The current diversity of influenza A viruses (IAV) circulating in swine is largely a consequence of human-to-swine transmission events and consequent evolution in pigs. However, little is known about the requirements for human IAVs to transmit to and subsequently adapt in pigs. Novel human-like H3 viruses were detected in swine herds in the U.S. in 2012 and have continued to circulate and evolve in swine. We evaluated the contributions of gene segments on the ability of these viruses to infect pigs by using a series of in vitro models. For this purpose, reassortant viruses were generated by reverse genetics (rg) swapping the surface genes (hemagglutinin-HA and neuraminidase-NA) and internal gene segment backbones between a human-like H3N1 isolated from swine and a seasonal human H3N2 virus with common HA ancestry. Virus growth kinetics in porcine intestinal epithelial cells (SD-PJEC) and in ex-vivo porcine trachea explants were significantly reduced by replacing the swine-adapted HA with the human seasonal HA. Unlike the human HA, the swine-adapted HA demonstrated more abundant attachment to epithelial cells throughout the swine respiratory tract by virus histochemistry and increased entry into SD-PJEC swine cells. The human seasonal internal gene segments improved replication of the swine-adapted HA at 33 °C, but decreased replication at 40 °C. Although the HA was crucial for the infectivity in pigs and swine tissues, these results suggest that the adaptation of human seasonal H3 viruses to swine is multigenic and that the swine-adapted HA alone was not sufficient to confer the full phenotype of the wild-type swine-adapted virus.
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13
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ARHGAP1 Transported with Influenza Viral Genome Ensures Integrity of Viral Particle Surface through Efficient Budozone Formation. mBio 2022; 13:e0072122. [PMID: 35475647 PMCID: PMC9239208 DOI: 10.1128/mbio.00721-22] [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] [Indexed: 11/24/2022] Open
Abstract
Influenza viral particles are assembled at the plasma membrane concomitantly with Rab11a-mediated endocytic transport of viral ribonucleoprotein complexes (vRNPs). The mechanism of spatiotemporal regulation of viral budozone formation and its regulatory molecules on the endocytic vesicles remain unclear. Here, we performed a proximity-based proteomics approach for Rab11a and found that ARHGAP1, a Rho GTPase-activating protein, is transported through the Rab11a-mediated apical transport of vRNP. ARHGAP1 stabilized actin filaments in infected cells for the lateral clustering of hemagglutinin (HA) molecules, a viral surface membrane protein, to the budozone. Disruption of the HA clustering results in the production of virions with low HA content, and such virions were less resistant to protease and had enhanced antigenicity, presumably because reduced clustering of viral membrane proteins exposes hidden surfaces. Collectively, these results demonstrate that Rab11a-mediated endocytic transport of ARHGAP1 with vRNPs stimulates budozone formation to ensure the integrity of virion surface required for viral survival.
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14
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Polasky DA, Geiszler DJ, Yu F, Nesvizhskii AI. Multi-attribute Glycan Identification and FDR Control for Glycoproteomics. Mol Cell Proteomics 2022; 21:100205. [PMID: 35091091 PMCID: PMC8933705 DOI: 10.1016/j.mcpro.2022.100205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/10/2022] [Accepted: 01/20/2022] [Indexed: 11/18/2022] Open
Abstract
Rapidly improving methods for glycoproteomics have enabled increasingly large-scale analyses of complex glycopeptide samples, but annotating the resulting mass spectrometry data with high confidence remains a major bottleneck. We recently introduced a fast and sensitive glycoproteomics search method in our MSFragger search engine, which reports glycopeptides as a combination of a peptide sequence and the mass of the attached glycan. In samples with complex glycosylation patterns, converting this mass to a specific glycan composition is not straightforward; however, as many glycans have similar or identical masses. Here, we have developed a new method for determining the glycan composition of N-linked glycopeptides fragmented by collisional or hybrid activation that uses multiple sources of information from the spectrum, including observed glycan B-type (oxonium) and Y-type ions and mass and precursor monoisotopic selection errors to discriminate between possible glycan candidates. Combined with false discovery rate estimation for the glycan assignment, we show that this method is capable of specifically and sensitively identifying glycans in complex glycopeptide analyses and effectively controls the rate of false glycan assignments. The new method has been incorporated into the PTM-Shepherd modification analysis tool to work directly with the MSFragger glyco search in the FragPipe graphical user interface, providing a complete computational pipeline for annotation of N-glycopeptide spectra with false discovery rate control of both peptide and glycan components that is both sensitive and robust against false identifications. Identifying the glycan on intact glycopeptides remains difficult in glycoproteomics. We developed a method to assign glycan compositions in N-glycoproteomics searches. We demonstrate well-controlled glycan FDR in multiple sample types. The method annotates more glycopeptide spectra than competing tools. The method is included PTM-Shepherd for a full glycoproteomics workflow in FragPipe.
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Affiliation(s)
- Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Daniel J Geiszler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
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15
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Inherent heterogeneity of influenza A virus stability following aerosolization. Appl Environ Microbiol 2022; 88:e0227121. [PMID: 34985975 DOI: 10.1128/aem.02271-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Efficient human-to-human transmission represents a necessary adaptation for a zoonotic influenza A virus (IAV) to cause a pandemic. As such, many emerging IAVs are characterized for transmissibility phenotypes in mammalian models, with an emphasis on elucidating viral determinants of transmission and the role host immune responses contribute to mammalian adaptation. Investigations of virus infectivity and stability in aerosols concurrent with transmission assessments have increased in recent years, enhancing our understanding of this dynamic process. Here, we employ a diverse panel of 17 human and zoonotic IAVs, inclusive of seasonally circulating H1N1 and H3N2 viruses, and avian and swine viruses associated with human infection, to evaluate differences in spray factor (a value that assesses efficiency of the aerosolization process), stability, and infectivity following aerosolization. While most seasonal influenza viruses did not exhibit substantial variability within these parameters, there was more heterogeneity among zoonotic influenza viruses, which possess a diverse range of transmission phenotypes. Aging of aerosols at different relative humidities identified strain-specific levels of stability with different profiles identified between zoonotic H3, H5, and H7 subtype viruses associated with human infection. As studies continue to elucidate the complex components governing virus transmissibility, notably aerosol matrices and environmental parameters, considering the relative role of subtype- and strain-specific factors to modulate these parameters will improve our understanding of the pandemic potential of zoonotic influenza A viruses. Importance Transmission of respiratory pathogens through the air can facilitate the rapid and expansive spread of infection and disease through a susceptible population. While seasonal influenza viruses are quite capable of airborne spread, there is a lack of knowledge regarding how well influenza viruses remain viable after aerosolization, and if influenza viruses capable of jumping species barriers to cause human infection differ in this property from seasonal strains. We evaluated a diverse panel of influenza viruses associated with human infection (originating from human, avian, and swine reservoirs) for their ability to remain viable after aerosolization in the laboratory under a range of conditions. We found greater diversity among avian and swine-origin viruses compared with seasonal influenza viruses; strain-specific stability was also noted. Although influenza virus stability in aerosols is an underreported property, if molecular markers associated with enhanced stability are identified, we will be able to quickly recognize emerging strains of influenza that present the greatest pandemic threat.
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16
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Sun Z, Ren K, Zhang X, Chen J, Jiang Z, Jiang J, Ji F, Ouyang X, Li L. Mass Spectrometry Analysis of Newly Emerging Coronavirus HCoV-19 Spike Protein and Human ACE2 Reveals Camouflaging Glycans and Unique Post-Translational Modifications. ENGINEERING 2021; 7:1441-1451. [PMID: 32904601 PMCID: PMC7456593 DOI: 10.1016/j.eng.2020.07.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/22/2020] [Accepted: 07/05/2020] [Indexed: 05/18/2023]
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17
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Nuwarda RF, Alharbi AA, Kayser V. An Overview of Influenza Viruses and Vaccines. Vaccines (Basel) 2021; 9:1032. [PMID: 34579269 PMCID: PMC8473132 DOI: 10.3390/vaccines9091032] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 01/12/2023] Open
Abstract
Influenza remains one of the major public health concerns because it causes annual epidemics and can potentially instigate a global pandemic. Numerous countermeasures, including vaccines and antiviral treatments, are in use against seasonal influenza infection; however, their effectiveness has always been discussed due to the ongoing resistance to antivirals and relatively low and unpredictable efficiency of influenza vaccines compared to other vaccines. The growing interest in vaccines as a promising approach to prevent and control influenza may provide alternative vaccine development options with potentially increased efficiency. In addition to currently available inactivated, live-attenuated, and recombinant influenza vaccines on the market, novel platforms such as virus-like particles (VLPs) and nanoparticles, and new vaccine formulations are presently being explored. These platforms provide the opportunity to design influenza vaccines with improved properties to maximize quality, efficacy, and safety. The influenza vaccine manufacturing process is also moving forward with advancements relating to egg- and cell-based production, purification processes, and studies into the physicochemical attributes and vaccine degradation pathways. These will contribute to the design of more stable, optimized vaccine formulations guided by contemporary analytical testing methods and via the implementation of the latest advances in the field.
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Affiliation(s)
| | | | - Veysel Kayser
- Faculty of Medicine and Health, Sydney Pharmacy School, The University of Sydney, Sydney, NSW 2006, Australia; (R.F.N.); (A.A.A.)
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18
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Sun Z, Zheng X, Ji F, Zhou M, Su X, Ren K, Li L. Mass Spectrometry Analysis of SARS-CoV-2 Nucleocapsid Protein Reveals Camouflaging Glycans and Unique Post-Translational Modifications. INFECTIOUS MICROBES & DISEASES 2021; 3:149-157. [PMID: 38630108 PMCID: PMC8454284 DOI: 10.1097/im9.0000000000000071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/18/2021] [Accepted: 06/28/2021] [Indexed: 01/08/2023]
Abstract
The devastating coronavirus disease 2019 (COVID-19) pandemic has prompted worldwide efforts to study structural biological traits of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its viral components. Compared to the Spike protein, which is the primary target for currently available vaccines or antibodies, knowledge about other virion structural components is incomplete. Using high-resolution mass spectrometry, we report a comprehensive post-translational modification (PTM) analysis of nucleocapsid phosphoprotein (NCP), the most abundant structural component of the SARS-CoV-2 virion. In addition to phosphoryl groups, we show that the SARS-CoV-2 NCP is decorated with a variety of PTMs, including N-glycans and ubiquitin. Based on newly identified PTMs, refined protein structural models of SARS-CoV-2 NCP were proposed and potential immune recognition epitopes of NCP were aligned with PTMs. These data can facilitate the design of novel vaccines or therapeutics targeting NCP, as valuable alternatives to the current vaccination and treatment paradigm that is under threat of the ever-mutating SARS-CoV-2 Spike protein.
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Affiliation(s)
- Zeyu Sun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaoqin Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Feiyang Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Menghao Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaoling Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Keyi Ren
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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19
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Li X, Guo Y, Song Y, Sun R, Zhu M, Tan Z, Swaiba UE, Zhang L, Huang J. The glycosyltransferase ST3GAL2 modulates virus proliferation and the inflammation response in porcine reproductive and respiratory syndrome virus infection. Arch Virol 2021; 166:2723-2732. [PMID: 34319453 DOI: 10.1007/s00705-021-05180-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/10/2021] [Indexed: 11/27/2022]
Abstract
β-galactoside α-2,3-sialyltransferase 2 (ST3GAL2) is a member of the sialyltransferase family that mediates terminal modification of glycoproteins and glycolipids. ST3GAL2 has been found to play a role in obesity, aging, and malignant diseases. In this study, we cloned porcine ST3GAL2 (pST3GAL2) from porcine alveolar macrophages (PAMs), and its role in porcine reproductive and respiratory syndrome virus (PRRSV) infection was investigated by transcriptome analysis. pST3GAL2 was found to be located in the Golgi apparatus, and it was expressed at high levels in PRRSV-infected PAMs. Overexpression of pST3GAL2 resulted in a slight increase in PRRSV proliferation, and the interaction between pST3GAL2 and GP2a of PRRSV was detected by coimmunoprecipitation and confocal microscopy. The expression of pro-inflammatory cytokines (IFN-β, IL-2, IL-6, IL-18, IL-1β and TNF-α) was significantly inhibited in pST3GAL2-overexpressing, PRRSV-infected cells and upregulated in PRRSV-infected pST3GAL2-knockout cells, while the pattern of expression of anti-inflammatory cytokines (IL-4 and IL-10) was diametrically opposite. Our results demonstrate that the regulation of pST3GAL2 plays an important role in PRRSV proliferation and functional alterations in virus-infected cells. These results contribute to our understanding of the role of β-galactoside α-2,3-sialyltransferase 2 in antiviral immunity.
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Affiliation(s)
- Xiaoyang Li
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Yanyu Guo
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Yinna Song
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Ruiqi Sun
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Min Zhu
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Zheng Tan
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Umm E Swaiba
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Lilin Zhang
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China.
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20
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Abstract
Introduction: As the pathogen that caused the first influenza virus pandemic in this century, the swine-origin A(H1N1) pdm09 influenza virus has caused continuous harm to human public health. The evolution of hemagglutinin protein glycosylation sites, including the increase in number and positional changes, is an important way for influenza viruses to escape host immune pressure. Based on the traditional influenza virus molecular monitoring, special attention should be paid to the influence of glycosylation evolution on the biological characteristics of virus antigenicity, transmission and pathogenicity. The epidemiological significance of glycosylation mutants should be analyzed as a predictive tool for early warning of new outbreaks and pandemics, as well as the design of vaccines and drug targets.Areas covered: We review on the evolutionary characteristics of glycosylation on the HA protein of the A(H1N1)pdm09 influenza virus in the last ten years.Expert opinion: We discuss the crucial impact of evolutionary glycosylation on the biological characteristics of the virus and the host immune responses, summarize studies revealing different roles of glycosylation play during host adaptation. Although these studies show the significance of glycosylation evolution in host-virus interaction, much remains to be discovered about the mechanism.
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Affiliation(s)
- Pan Ge
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA.,Department of Infectious Diseases, University of Georgia, Athens, GA USA
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21
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Pralow A, Hoffmann M, Nguyen-Khuong T, Pioch M, Hennig R, Genzel Y, Rapp E, Reichl U. Comprehensive N-glycosylation analysis of the influenza A virus proteins HA and NA from adherent and suspension MDCK cells. FEBS J 2021; 288:4869-4891. [PMID: 33629527 DOI: 10.1111/febs.15787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 12/25/2022]
Abstract
Glycosylation is considered as a critical quality attribute for the production of recombinant biopharmaceuticals such as hormones, blood clotting factors, or monoclonal antibodies. In contrast, glycan patterns of immunogenic viral proteins, which differ significantly between the various expression systems, are hardly analyzed yet. The influenza A virus (IAV) proteins hemagglutinin (HA) and neuraminidase (NA) have multiple N-glycosylation sites, and alteration of N-glycan micro- and macroheterogeneity can have strong effects on virulence and immunogenicity. Here, we present a versatile and powerful glycoanalytical workflow that enables a comprehensive N-glycosylation analysis of IAV glycoproteins. We challenged our workflow with IAV (A/PR/8/34 H1N1) propagated in two closely related Madin-Darby canine kidney (MDCK) cell lines, namely an adherent MDCK cell line and its corresponding suspension cell line. As expected, N-glycan patterns of HA and NA from virus particles produced in both MDCK cell lines were similar. Detailed analysis of the HA N-glycan microheterogeneity showed an increasing variability and a higher complexity for N-glycosylation sites located closer to the head region of the molecule. In contrast, NA was found to be exclusively N-glycosylated at site N73. Almost all N-glycan structures were fucosylated. Furthermore, HA and NA N-glycan structures were exclusively hybrid- and complex-type structures, to some extent terminated with alpha-linked galactose(s) but also with blood group H type 2 and blood group A epitopes. In contrast to the similarity of the overall glycan pattern, differences in the relative abundance of individual structures were identified. This concerned, in particular, oligomannose-type, alpha-linked galactose, and multiantennary complex-type N-glycans.
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Affiliation(s)
- Alexander Pralow
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Terry Nguyen-Khuong
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Markus Pioch
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - René Hennig
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,glyXera GmbH, Magdeburg, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,glyXera GmbH, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Chair of Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
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22
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In Vitro Characterization of the Carbohydrate-Binding Agents HHA, GNA, and UDA as Inhibitors of Influenza A and B Virus Replication. Antimicrob Agents Chemother 2021; 65:AAC.01732-20. [PMID: 33288640 DOI: 10.1128/aac.01732-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/02/2020] [Indexed: 12/30/2022] Open
Abstract
Here, we report on the anti-influenza virus activity of the mannose-binding agents Hippeastrum hybrid agglutinin (HHA) and Galanthus nivalis agglutinin (GNA) and the (N-acetylglucosamine) n -specific Urtica dioica agglutinin (UDA). These carbohydrate-binding agents (CBA) strongly inhibited various influenza A(H1N1), A(H3N2), and B viruses in vitro, with 50% effective concentration values ranging from 0.016 to 83 nM, generating selectivity indexes up to 125,000. Somewhat less activity was observed against A/Puerto Rico/8/34 and an A(H1N1)pdm09 strain. In time-of-addition experiments, these CBA lost their inhibitory activity when added 30 min postinfection (p.i.). Interference with virus entry processes was also evident from strong inhibition of virus-induced hemolysis at low pH. However, a direct effect on acid-induced refolding of the viral hemagglutinin (HA) was excluded by the tryptic digestion assay. Instead, HHA treatment of HA-expressing cells led to a significant reduction of plasma membrane mobility. Crosslinking of membrane glycoproteins, through interaction with HA, could also explain the inhibitory effect on the release of newly formed virions when HHA was added at 6 h p.i. These CBA presumably interact with one or more N-glycans on the globular head of HA, since their absence led to reduced activity against mutant influenza B viruses and HHA-resistant A(H1N1) viruses. The latter condition emerged only after 33 cell culture passages in the continuous presence of HHA, and the A(H3N2) virus retained full sensitivity even after 50 passages. Thus, these CBA qualify as potent inhibitors of influenza A and B viruses in vitro with a pleiotropic mechanism of action and a high barrier for viral resistance.
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23
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Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. Int J Mol Sci 2021; 22:ijms22020743. [PMID: 33451024 PMCID: PMC7828482 DOI: 10.3390/ijms22020743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 12/11/2022] Open
Abstract
DC-SIGN, a C-type lectin mainly expressed in dendritic cells (DCs), has been reported to mediate several viral infections. We previously reported that DC-SIGN mediated H5N1 influenza A virus (AIVs) infection, however, the important DC-SIGN interaction with N-glycosylation sites remain unknown. This study aims to identify the optimal DC-SIGN interacting N-glycosylation sites in HA proteins of H5N1-AIVs. Results from NetNGlyc program analyzed the H5 hemagglutinin sequences of isolates during 2004–2020, revealing that seven and two conserved N-glycosylation sites were detected in HA1 and HA2 domain, respectively. A lentivirus pseudotyped A/Vietnam/1203/04 H5N1 envelope (H5N1-PVs) was generated which displayed an abundance of HA5 proteins on the virions via immuno-electron microscope observation. Further, H5N1-PVs or reverse-genetics (H5N1-RG) strains carrying a serial N-glycosylated mutation was generated by site-directed mutagenesis assay. Human recombinant DC-SIGN (rDC-SIGN) coated ELISA showed that H5N1-PVs bound to DC-SIGN, however, mutation on the N27Q, N39Q, and N181Q significantly reduced this binding (p < 0.05). Infectivity and capture assay demonstrated that N27Q and N39Q mutations significantly ameliorated DC-SIGN mediated H5N1 infection. Furthermore, combined mutations (N27Q&N39Q) significantly waned the interaction on either H5N1-PVs or -RG infection in cis and in trans (p < 0.01). This study concludes that N27 and N39 are two essential N-glycosylation contributing to DC-SIGN mediating H5N1 infection.
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Chepur SV, Pluzhnikov NN, Chubar OV, Bakulina LS, Litvinenko IV, Makarov VA, Gogolevsky AS, Myasnikov VA, Myasnikova IA, Al-Shehadat RI. Respiratory RNA Viruses: How to Be Prepared for an Encounter with New Pandemic Virus Strains. BIOLOGY BULLETIN REVIEWS 2021; 11. [PMCID: PMC8078390 DOI: 10.1134/s207908642102002x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The characteristics of the biology of influenza viruses and coronavirus that determine the implementation of the infectious process are presented. With provision for pathogenesis of infection possible effects of serine proteinase inhibitors, heparin, and inhibitors of heparan sulfate receptors in the prevention of cell contamination by viruses are examined. It has been determined that chelators of metals of variable valency and antioxidants should be used for the reduction of replicative activity of viruses and anti-inflammatory therapy. The possibility of a pH-dependent impairment of glycosylation of cellular and viral proteins was traced for chloroquine and its derivatives. The use of low-toxicity drugs as part of adjunct therapy increases the effectiveness of synthetic antiviral drugs and interferons and ensures the safety of baseline therapy.
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Affiliation(s)
- S. V. Chepur
- State Scientific Research Test Institute of Military Medicine of the Ministry of Defense of the Russian Federation, 195043 St. Petersburg, Russia
| | - N. N. Pluzhnikov
- State Scientific Research Test Institute of Military Medicine of the Ministry of Defense of the Russian Federation, 195043 St. Petersburg, Russia
| | - O. V. Chubar
- State Scientific Research Test Institute of Military Medicine of the Ministry of Defense of the Russian Federation, 195043 St. Petersburg, Russia
| | - L. S. Bakulina
- Burdenko Voronezh State Medical University, 394036 Voronezh, Russia
| | | | - V. A. Makarov
- Fundamentals of Biotechnology Federal Research Center, 119071 Moscow, Russia
| | - A. S. Gogolevsky
- State Scientific Research Test Institute of Military Medicine of the Ministry of Defense of the Russian Federation, 195043 St. Petersburg, Russia
| | - V. A. Myasnikov
- State Scientific Research Test Institute of Military Medicine of the Ministry of Defense of the Russian Federation, 195043 St. Petersburg, Russia
| | - I. A. Myasnikova
- State Scientific Research Test Institute of Military Medicine of the Ministry of Defense of the Russian Federation, 195043 St. Petersburg, Russia
| | - R. I. Al-Shehadat
- State Scientific Research Test Institute of Military Medicine of the Ministry of Defense of the Russian Federation, 195043 St. Petersburg, Russia
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Zhang J, Peng Q, Zhao W, Sun W, Yang J, Liu N. Proteomics in Influenza Research: The Emerging Role of Posttranslational Modifications. J Proteome Res 2020; 20:110-121. [PMID: 33348980 DOI: 10.1021/acs.jproteome.0c00778] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Influenza viruses continue evolving and have the ability to cause a global pandemic, so it is very important to elucidate its pathogenesis and find new treatment methods. In recent years, proteomics has made important contributions to describing the dynamic interaction between influenza viruses and their hosts, especially in posttranslational regulation of a variety of key biological processes. Protein posttranslational modifications (PTMs) increase the diversity of functionality of the organismal proteome and affect almost all aspects of pathogen biology, primarily by regulating the structure, function, and localization of the modified proteins. Considerable technical achievements in mass spectrometry-based proteomics have been made in a large number of proteome-wide surveys of PTMs in many different organisms. Herein we specifically focus on the proteomic studies regarding a variety of PTMs that occur in both the influenza viruses, mainly influenza A viruses (IAVs), and their hosts, including phosphorylation, ubiquitination and ubiquitin-like modification, glycosylation, methylation, acetylation, and some types of acylation. Integration of these data sets provides a unique scenery of the global regulation and interplay of different PTMs during the interaction between IAVs and their hosts. Various techniques used to globally profiling these PTMs, mostly MS-based approaches, are discussed regarding their increasing roles in mechanical regulation of interaction between influenza viruses and their hosts.
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Affiliation(s)
- Jinming Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Qisheng Peng
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Weizheng Zhao
- Clinical Medical College, Jilin University, Changchun 130021, PR China
| | - Wanchun Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Jingbo Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Ning Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
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Pralow A, Cajic S, Alagesan K, Kolarich D, Rapp E. State-of-the-Art Glycomics Technologies in Glycobiotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 175:379-411. [PMID: 33112988 DOI: 10.1007/10_2020_143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Glycosylation affects the properties of biologics; thus regulatory bodies classified it as critical quality attribute and force biopharma industry to capture and control it throughout all phases, from R&D till end of product lifetime. The shift from originators to biosimilars further increases importance and extent of glycoanalysis, which thus increases the need for technology platforms enabling reliable high-throughput and in-depth glycan analysis. In this chapter, we will first summarize on established glycoanalytical methods based on liquid chromatography focusing on hydrophilic interaction chromatography, capillary electrophoresis focusing on multiplexed capillary gel electrophoresis, and mass spectrometry focusing on matrix-assisted laser desorption; we will then highlight two emerging technologies based on porous graphitized carbon liquid chromatography and on ion-mobility mass spectrometry as both are highly promising tools to deliver an additional level of information for in-depth glycan analysis; additionally we elaborate on the advantages and challenges of different glycoanalytical technologies and their complementarity; finally, we briefly review applications thereof to biopharmaceutical products. This chapter provides an overview of current state-of-the-art analytical approaches for glycan characterization of biopharmaceuticals that can be employed to capture glycoprotein heterogeneity in a biopharmaceutical context.
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Affiliation(s)
- Alexander Pralow
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Samanta Cajic
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Kathirvel Alagesan
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
- ARC Centre of Excellence in Nanoscale Biophotonics, Griffith University, Gold Coast, QLD, Australia
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
- glyXera GmbH, Magdeburg, Germany.
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27
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Makarov V, Riabova O, Ekins S, Pluzhnikov N, Chepur S. The past, present and future of RNA respiratory viruses: influenza and coronaviruses. Pathog Dis 2020; 78:ftaa046. [PMID: 32860686 PMCID: PMC7499567 DOI: 10.1093/femspd/ftaa046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Influenza virus and coronaviruses continue to cause pandemics across the globe. We now have a greater understanding of their functions. Unfortunately, the number of drugs in our armory to defend us against them is inadequate. This may require us to think about what mechanisms to address. Here, we review the biological properties of these viruses, their genetic evolution and antiviral therapies that can be used or have been attempted. We will describe several classes of drugs such as serine protease inhibitors, heparin, heparan sulfate receptor inhibitors, chelating agents, immunomodulators and many others. We also briefly describe some of the drug repurposing efforts that have taken place in an effort to rapidly identify molecules to treat patients with COVID-19. While we put a heavy emphasis on the past and present efforts, we also provide some thoughts about what we need to do to prepare for respiratory viral threats in the future.
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Affiliation(s)
- Vadim Makarov
- Federal Research Center Fundamentals of Biotechnology of the Russian Academy of Sciences, 33-2 Leninsky Prospect, Moscow 119071, Russia
| | - Olga Riabova
- Federal Research Center Fundamentals of Biotechnology of the Russian Academy of Sciences, 33-2 Leninsky Prospect, Moscow 119071, Russia
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
| | - Nikolay Pluzhnikov
- State Research Institute of Military Medicine of the Ministry of Defence of the Russian Federation, St Petersburg 195043, Russia
| | - Sergei Chepur
- State Research Institute of Military Medicine of the Ministry of Defence of the Russian Federation, St Petersburg 195043, Russia
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28
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Engineering anti-cancer nanovaccine based on antigen cross-presentation. Biosci Rep 2020; 39:220729. [PMID: 31652460 PMCID: PMC6822533 DOI: 10.1042/bsr20193220] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/27/2019] [Accepted: 10/01/2019] [Indexed: 01/16/2023] Open
Abstract
Dendritic cells (DCs) present exogenous antigens on major histocompatibility complex (MHC) class I molecules, thereby activating CD8+ T cells, contributing to tumor elimination through a mechanism known as antigen cross-presentation. A variety of factors such as maturation state of DCs, co-stimulatory signals, T-cell microenvironment, antigen internalization routes and adjuvants regulate the process of DC-mediated antigen cross-presentation. Recently, the development of successful cancer immunotherapies may be attributed to the ability of DCs to cross-present tumor antigens. In this review article, we focus on the underlying mechanism of antigen cross-presentation and ways to improve antigen cross-presentation in different DC subsets. We have critically summarized the recent developments in the generation of novel nanovaccines for robust CD8+ T-cell response in cancer. In this context, we have reviewed nanocarriers that have been used for cancer immunotherapeutics based on antigen cross-presentation mechanism. Additionally, we have also expressed our views on the future applications of this mechanism in curing cancer.
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MARCH8 Inhibits Ebola Virus Glycoprotein, Human Immunodeficiency Virus Type 1 Envelope Glycoprotein, and Avian Influenza Virus H5N1 Hemagglutinin Maturation. mBio 2020; 11:mBio.01882-20. [PMID: 32934085 PMCID: PMC7492737 DOI: 10.1128/mbio.01882-20] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Enveloped viruses express three classes of fusion proteins that are required for their entry into host cells via mediating virus and cell membrane fusion. Class I fusion proteins are produced from influenza viruses, retroviruses, Ebola viruses, and coronaviruses. They are first synthesized as a type I transmembrane polypeptide precursor that is subsequently glycosylated and oligomerized. Most of these precursors are cleaved en route to the plasma membrane by a cellular protease furin in the late secretory pathway, generating the trimeric N-terminal receptor-binding and C-terminal fusion subunits. Here, we show that a cellular protein, MARCH8, specifically inhibits the furin-mediated cleavage of EBOV GP, HIV-1 Env, and H5N1 HA. Further analyses uncovered that MARCH8 blocked the EBOV GP glycosylation in the Golgi and inhibited its transport from the Golgi to the plasma membrane. Thus, MARCH8 has a very broad antiviral activity by specifically inactivating different viral fusion proteins. Membrane-associated RING-CH-type 8 (MARCH8) strongly blocks human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) incorporation into virions by downregulating its cell surface expression, but the mechanism is still unclear. We now report that MARCH8 also blocks the Ebola virus (EBOV) glycoprotein (GP) incorporation via surface downregulation. To understand how these viral fusion proteins are downregulated, we investigated the effects of MARCH8 on EBOV GP maturation and externalization via the conventional secretion pathway. MARCH8 interacted with EBOV GP and furin when detected by immunoprecipitation and retained the GP/furin complex in the Golgi when their location was tracked by a bimolecular fluorescence complementation (BiFC) assay. MARCH8 did not reduce the GP expression or affect the GP modification by high-mannose N-glycans in the endoplasmic reticulum (ER), but it inhibited the formation of complex N-glycans on the GP in the Golgi. Additionally, the GP O-glycosylation and furin-mediated proteolytic cleavage were also inhibited. Moreover, we identified a novel furin cleavage site on EBOV GP and found that only those fully glycosylated GPs were processed by furin and incorporated into virions. Furthermore, the GP shedding and secretion were all blocked by MARCH8. MARCH8 also blocked the furin-mediated cleavage of HIV-1 Env (gp160) and the highly pathogenic avian influenza virus H5N1 hemagglutinin (HA). We conclude that MARCH8 has a very broad antiviral activity by prohibiting different viral fusion proteins from glycosylation and proteolytic cleavage in the Golgi, which inhibits their transport from the Golgi to the plasma membrane and incorporation into virions.
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Host Synthesized Carbohydrate Antigens on Viral Glycoproteins as "Achilles' Heel" of Viruses Contributing to Anti-Viral Immune Protection. Int J Mol Sci 2020; 21:ijms21186702. [PMID: 32933166 PMCID: PMC7555091 DOI: 10.3390/ijms21186702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 01/10/2023] Open
Abstract
The glycans on enveloped viruses are synthesized by host-cell machinery. Some of these glycans on zoonotic viruses of mammalian reservoirs are recognized by human natural antibodies that may protect against such viruses. These antibodies are produced mostly against carbohydrate antigens on gastrointestinal bacteria and fortuitously, they bind to carbohydrate antigens synthesized in other mammals, neutralize and destroy viruses presenting these antigens. Two such antibodies are: anti-Gal binding to α-gal epitopes synthesized in non-primate mammals, lemurs, and New World monkeys, and anti-N-glycolyl neuraminic acid (anti-Neu5Gc) binding to N-glycolyl-neuraminic acid (Neu5Gc) synthesized in apes, Old World monkeys, and many non-primate mammals. Anti-Gal appeared in Old World primates following accidental inactivation of the α1,3galactosyltransferase gene 20–30 million years ago. Anti-Neu5Gc appeared in hominins following the inactivation of the cytidine-monophosphate-N-acetyl-neuraminic acid hydroxylase gene, which led to the loss of Neu5Gc <6 million-years-ago. It is suggested that an epidemic of a lethal virus eliminated ancestral Old World-primates synthesizing α-gal epitopes, whereas few mutated offspring lacking α-gal epitopes and producing anti-Gal survived because anti-Gal destroyed viruses presenting α-gal epitopes, following replication in parental populations. Similarly, anti-Neu5Gc protected few mutated hominins lacking Neu5Gc in lethal virus epidemics that eliminated parental hominins synthesizing Neu5Gc. Since α-gal epitopes are presented on many zoonotic viruses it is suggested that vaccines elevating anti-Gal titers may be of protective significance in areas endemic for such zoonotic viruses. This protection would be during the non-primate mammal to human virus transmission, but not in subsequent human to human transmission where the virus presents human glycans. In addition, production of viral vaccines presenting multiple α-gal epitopes increases their immunogenicity because of effective anti-Gal-mediated targeting of vaccines to antigen presenting cells for extensive uptake of the vaccine by these cells.
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31
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Gouma S, Zost SJ, Parkhouse K, Branche A, Topham DJ, Cobey S, Hensley SE. Comparison of Human H3N2 Antibody Responses Elicited by Egg-Based, Cell-Based, and Recombinant Protein-Based Influenza Vaccines During the 2017-2018 Season. Clin Infect Dis 2020; 71:1447-1453. [PMID: 31598646 PMCID: PMC7486837 DOI: 10.1093/cid/ciz996] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/04/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The H3N2 component of egg-based 2017-2018 influenza vaccines possessed an adaptive substitution that alters antigenicity. Several influenza vaccines include antigens that are produced through alternative systems, but a systematic comparison of different vaccines used during the 2017-2018 season has not been completed. METHODS We compared antibody responses in humans vaccinated with Fluzone (egg-based, n = 23), Fluzone High-Dose (egg-based, n = 16), Flublok (recombinant protein-based, n = 23), or Flucelvax (cell-based, n = 23) during the 2017-2018 season. We completed neutralization assays using an egg-adapted H3N2 virus, a cell-based H3N2 virus, wild-type 3c2.A and 3c2.A2 H3N2 viruses, and the H1N1 vaccine strain. We also performed enzyme-linked immunosorbent assays using a recombinant wild-type 3c2.A hemagglutinin. Antibody responses were compared in adjusted analysis. RESULTS Postvaccination neutralizing antibody titers to 3c2.A and 3c2.A2 were higher in Flublok recipients compared with Flucelvax or Fluzone recipients (P < .01). Postvaccination titers to 3c2.A and 3c2.A2 were similar in Flublok and Fluzone High-Dose recipients, though seroconversion rates trended higher in Flublok recipients. Postvaccination titers in Flucelvax recipients were low to all H3N2 viruses tested, including the cell-based H3N2 strain. Postvaccination neutralizing antibody titers to H1N1 were similar among the different vaccine groups. CONCLUSIONS These data suggest that influenza vaccine antigen match and dose are both important for eliciting optimal H3N2 antibody responses in humans. Future studies should be designed to determine if our findings directly impact vaccine effectiveness. CLINICAL TRIALS REGISTRATION NCT03068949.
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Affiliation(s)
- Sigrid Gouma
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Seth J Zost
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kaela Parkhouse
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Angela Branche
- Division of Infectious Diseases, University of Rochester Medical Center, Rochester, New York, USA
| | - David J Topham
- Department of Medicine and Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Sarah Cobey
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, USA
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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32
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Garcia-Revilla J, Deierborg T, Venero JL, Boza-Serrano A. Hyperinflammation and Fibrosis in Severe COVID-19 Patients: Galectin-3, a Target Molecule to Consider. Front Immunol 2020; 11:2069. [PMID: 32973815 PMCID: PMC7461806 DOI: 10.3389/fimmu.2020.02069] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/29/2020] [Indexed: 12/13/2022] Open
Abstract
COVID-19 disease have become so far the most important sanitary crisis in the XXI century. In light of the events, any clinical resource should be considered to alleviate this crisis. Severe COVID-19 cases present a so-called cytokine storm as the most life-threatening symptom accompanied by lung fibrosis. Galectin-3 has been widely described as regulator of both processes. Hereby, we present compelling evidences on the potential role of galectin-3 in COVID-19 in the regulation of the inflammatory response, fibrosis and infection progression. Moreover, we provide a strong rationale of the utility of measuring plasma galectin-3 as a prognosis biomarker for COVID-19 patients and propose that inhibition of galectin-3 represents a feasible and promising new therapeutical approach.
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Affiliation(s)
- Juan Garcia-Revilla
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Tomas Deierborg
- Department of Experimental Medical Science, Experimental Neuroinflammation Laboratory, BMC, Lund University, Lund, Sweden
| | - Jose Luis Venero
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Antonio Boza-Serrano
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Department of Experimental Medical Sciences, Experimental Dementia Research Laboratory, BMC, Lund University, Lund, Sweden
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33
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Hronowski XL, Wang Y, Sosic Z, Wei R. On-MALDI-Target N-Glycan Nonreductive Amination by 2-Aminobenzoic Acid. Anal Chem 2020; 92:10252-10256. [PMID: 32628832 DOI: 10.1021/acs.analchem.0c01748] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
2-Aminobenzoic acid (2-AA) is widely used as a labeling reagent to derivatize released N-glycans at their free reducing terminus by reductive amination. 2-AA-labeled glycans have increased mass spectrometric sensitivity for their identification and enable fluorescence-chromatography-based glycan quantification. Drawbacks are that the labeling process is labor intensive and time consuming. Clean up of labeled glycans via removal of excess of labeling reagents often leads to sample losses. Here, we report use of 2-AA for labeling N-glycans on a MALDI target through nonreductive amination, while simultaneously functioning as a matrix in MALDI-MS glycan analysis. Coupling 2-AA to glycans results in significant increases of glycan anionic signals as compared to that using the traditional 2,5-dihydroxybenzoic acid (2,5-DHB) matrix. The on-MALDI-target sample preparation is a single-step protocol with high derivatization efficiency. It is also noticed that 2-AA-labeled glycan generated dominant deprotonated molecular anions with much fewer and low-intensity sodium adducts and therefore greatly simplified glycan profiles. We further explored its application in the N-glycan profile of a biotherapeutic monoclonal antibody and was able to achieve sensitive glycan identification at a low microgram level of glycoprotein. This 2-AA on-MALDI-target glycan derivatization eliminates tedious sample preparation and avoids sample loss. It is generally applicable for other applications (e.g., glycomics), where limited amounts of glycoproteins are available for analysis.
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Cipollo JF, Parsons LM. Glycomics and glycoproteomics of viruses: Mass spectrometry applications and insights toward structure-function relationships. MASS SPECTROMETRY REVIEWS 2020; 39:371-409. [PMID: 32350911 PMCID: PMC7318305 DOI: 10.1002/mas.21629] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 04/01/2020] [Accepted: 04/05/2020] [Indexed: 05/21/2023]
Abstract
The advancement of viral glycomics has paralleled that of the mass spectrometry glycomics toolbox. In some regard the glycoproteins studied have provided the impetus for this advancement. Viral proteins are often highly glycosylated, especially those targeted by the host immune system. Glycosylation tends to be dynamic over time as viruses propagate in host populations leading to increased number of and/or "movement" of glycosylation sites in response to the immune system and other pressures. This relationship can lead to highly glycosylated, difficult to analyze glycoproteins that challenge the capabilities of modern mass spectrometry. In this review, we briefly discuss five general areas where glycosylation is important in the viral niche and how mass spectrometry has been used to reveal key information regarding structure-function relationships between viral glycoproteins and host cells. We describe the recent past and current glycomics toolbox used in these analyses and give examples of how the requirement to analyze these complex glycoproteins has provided the incentive for some advances seen in glycomics mass spectrometry. A general overview of viral glycomics, special cases, mass spectrometry methods and work-flows, informatics and complementary chemical techniques currently used are discussed. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- John F. Cipollo
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMaryland
| | - Lisa M. Parsons
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMaryland
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35
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Pawestri HA, Nugraha AA, Han AX, Pratiwi E, Parker E, Richard M, van der Vliet S, Fouchier RAM, Muljono DH, de Jong MD, Setiawaty V, Eggink D. Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. Virus Genes 2020; 56:417-429. [PMID: 32483655 PMCID: PMC7262163 DOI: 10.1007/s11262-020-01765-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/07/2020] [Indexed: 01/07/2023]
Abstract
Since the initial detection in 2003, Indonesia has reported 200 human cases of highly pathogenic avian influenza H5N1 (HPAI H5N1), associated with an exceptionally high case fatality rate (84%) compared to other geographical regions affected by other genetic clades of the virus. However, there is limited information on the genetic diversity of HPAI H5N1 viruses, especially those isolated from humans in Indonesia. In this study, the genetic and antigenic characteristics of 35 HPAI H5N1 viruses isolated from humans were analyzed. Full genome sequences were analyzed for the presence of substitutions in the receptor binding site, and polymerase complex, as markers for virulence or human adaptation, as well as antiviral drug resistance substitutions. Only a few substitutions associated with human adaptation were observed, a remarkably low prevalence of the human adaptive substitution PB2-E627K, which is common during human infection with other H5N1 clades and a known virulence marker for avian influenza viruses during human infections. In addition, the antigenic profile of these Indonesian HPAI H5N1 viruses was determined using serological analysis and antigenic cartography. Antigenic characterization showed two distinct antigenic clusters, as observed previously for avian isolates. These two antigenic clusters were not clearly associated with time of virus isolation. This study provides better insight in genetic diversity of H5N1 viruses during human infection and the presence of human adaptive markers. These findings highlight the importance of evaluating virus genetics for HPAI H5N1 viruses to estimate the risk to human health and the need for increased efforts to monitor the evolution of H5N1 viruses across Indonesia.
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Affiliation(s)
- Hana A Pawestri
- National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Arie A Nugraha
- National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Alvin X Han
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Eka Pratiwi
- National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Edyth Parker
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Mathilde Richard
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | | - Menno D de Jong
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Vivi Setiawaty
- National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia.
| | - Dirk Eggink
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
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36
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Tucci P, Portela M, Chetto CR, González-Sapienza G, Marín M. Integrative proteomic and glycoproteomic profiling of Mycobacterium tuberculosis culture filtrate. PLoS One 2020; 15:e0221837. [PMID: 32126063 PMCID: PMC7053730 DOI: 10.1371/journal.pone.0221837] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/10/2020] [Indexed: 12/20/2022] Open
Abstract
Despite being the subject of intensive research, tuberculosis, caused by Mycobacterium tuberculosis, remains at present the leading cause of death from an infectious agent. Secreted and cell wall proteins interact with the host and play important roles in pathogenicity. These proteins are explored as candidate diagnostic markers, potential drug targets or vaccine antigens, and more recently special attention is being given to the role of their post-translational modifications. With the purpose of contributing to the proteomic and glycoproteomic characterization of this important pathogen, we performed a shotgun analysis of culture filtrate proteins of M. tuberculosis based on a liquid nano-HPLC tandem mass spectrometry and a label-free spectral counting normalization approach for protein quantification. We identified 1314 M. tuberculosis proteins in culture filtrate and found that the most abundant proteins belong to the extracellular region or cell wall compartment, and that the functional categories with higher protein abundance factor were virulence, detoxification and adaptation, and cell wall and cell processes. We could identify a group of proteins consistently detected in previous studies, most of which were highly abundant proteins. In culture filtrate, 140 proteins were predicted to contain one of the three types of bacterial N-terminal signal peptides. Besides, various proteins belonging to the ESX secretion systems, and to the PE and PPE families, secreted by the type VII secretion system using nonclassical secretion signals, were also identified. O-glycosylation was identified in 46 proteins, many of them lipoproteins and cell wall associated proteins. Finally, we provide proteomic evidence for 33 novel O-glycosylated proteins, aiding to the glycoproteomic characterization of relevant antigenic membrane and exported proteins. These findings are expected to collaborate with the research on pathogen derived biomarkers, virulence factors and vaccine candidates, and to provide clues to the understanding of the pathogenesis and survival strategies adopted by M. tuberculosis.
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Affiliation(s)
- Paula Tucci
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Madelón Portela
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Carlos Rivas Chetto
- Departamento de Laboratorio, Comisión Honoraria para la Lucha Antituberculosa y Enfermedades Prevalentes, Centro de Referencia Nacional para Micobacterias, Ministerio de Salud Pública, Montevideo, Uruguay
| | - Gualberto González-Sapienza
- Cátedra de Inmunología, DEPBIO, Facultad de Química, Universidad de la Republica Uruguay, Montevideo, Uruguay
| | - Mónica Marín
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Liang Y, Zhang Q, Zhang L, Wang R, Xu X, Hu X. Astragalus Membranaceus Treatment Protects Raw264.7 Cells from Influenza Virus by Regulating G1 Phase and the TLR3-Mediated Signaling Pathway. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2019; 2019:2971604. [PMID: 31975996 PMCID: PMC6955127 DOI: 10.1155/2019/2971604] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 11/24/2019] [Accepted: 12/11/2019] [Indexed: 12/26/2022]
Abstract
Influenza is an acute respiratory infection disease caused by the influenza virus. At present, due to the high mutation rate of influenza virus, it is difficult for the existing antiviral drugs to play an effective antiviral effect continually, so it is urgent to develop a new anti-influenza drug. Recently, more and more studies have been conducted on the antiviral activity of Astragalus membranaceus, but the specific antiviral mechanism of this traditional Chinese medicine is not clear. In this study, the results proved that the Astragalus membranaceus injection showed obvious anti-influenza virus activity. It could improve the survival rate of Raw264.7 cells which were infected with influenza virus, while it improved the blocking effect of influenza virus on cell cycle after infection, increased the SOD activity, and reduced the MDA content. At the same time, the innate immunity was affected by regulating the expression of TLR3, TAK1, TBK1, IRF3, and IFN-β in the TLR3-mediated signaling pathway, thus exerting its antiviral effect in vitro.
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Affiliation(s)
- Yuxi Liang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Qiuyan Zhang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Linjing Zhang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Rufeng Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaoying Xu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Xiuhua Hu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
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Ivan FX, Kwoh CK. Rule-based meta-analysis reveals the major role of PB2 in influencing influenza A virus virulence in mice. BMC Genomics 2019; 20:973. [PMID: 31874643 PMCID: PMC6929465 DOI: 10.1186/s12864-019-6295-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022] Open
Abstract
Background Influenza A virus (IAV) poses threats to human health and life. Many individual studies have been carried out in mice to uncover the viral factors responsible for the virulence of IAV infections. Nonetheless, a single study may not provide enough confident about virulence factors, hence combining several studies for a meta-analysis is desired to provide better views. For this, we documented more than 500 records of IAV infections in mice, whose viral proteins could be retrieved and the mouse lethal dose 50 or alternatively, weight loss and/or survival data, was/were available for virulence classification. Results IAV virulence models were learned from various datasets containing aligned IAV proteins and the corresponding two virulence classes (avirulent and virulent) or three virulence classes (low, intermediate and high virulence). Three proven rule-based learning approaches, i.e., OneR, JRip and PART, and additionally random forest were used for modelling. PART models achieved the best performance, with moderate average model accuracies ranged from 65.0 to 84.4% and from 54.0 to 66.6% for the two-class and three-class problems, respectively. PART models were comparable to or even better than random forest models and should be preferred based on the Occam’s razor principle. Interestingly, the average accuracy of the models was improved when host information was taken into account. For model interpretation, we observed that although many sites in HA were highly correlated with virulence, PART models based on sites in PB2 could compete against and were often better than PART models based on sites in HA. Moreover, PART had a high preference to include sites in PB2 when models were learned from datasets containing the concatenated alignments of all IAV proteins. Several sites with a known contribution to virulence were found as the top protein sites, and site pairs that may synergistically influence virulence were also uncovered. Conclusion Modelling IAV virulence is a challenging problem. Rule-based models generated using viral proteins are useful for its advantage in interpretation, but only achieve moderate performance. Development of more advanced approaches that learn models from features extracted from both viral and host proteins shall be considered for future works.
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Affiliation(s)
- Fransiskus Xaverius Ivan
- Biomedical Informatics Lab, School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore.
| | - Chee Keong Kwoh
- Biomedical Informatics Lab, School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
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A Complex Dance: Measuring the Multidimensional Worlds of Influenza Virus Evolution and Anti-Influenza Immune Responses. Pathogens 2019; 8:pathogens8040238. [PMID: 31731815 PMCID: PMC6963821 DOI: 10.3390/pathogens8040238] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 11/17/2022] Open
Abstract
The human antibody response to influenza virus infection or vaccination is as complicated as it is essential for protection against flu. The constant antigenic changes of the virus to escape human herd immunity hinder the yearly selection of vaccine strains since it is hard to predict which virus strains will circulate for the coming flu season. A "universal" influenza vaccine that could induce broad cross-influenza subtype protection would help to address this issue. However, the human antibody response is intricate and often obscure, with factors such as antigenic seniority or original antigenic sin (OAS), and back-boosting ensuring that each person mounts a unique immune response to infection or vaccination with any new influenza virus strain. Notably, the effects of existing antibodies on cross-protective immunity after repeated vaccinations are unclear. More research is needed to characterize the mechanisms at play, but traditional assays such as hemagglutinin inhibition (HAI) and microneutralization (MN) are excessively limited in scope and too resource-intensive to effectively meet this challenge. In the past ten years, new multiple dimensional assays (MDAs) have been developed to help overcome these problems by simultaneously measuring antibodies against a large panel of influenza hemagglutinin (HA) proteins with a minimal amount of sample in a high throughput way. MDAs will likely be a powerful tool for accelerating the study of the humoral immune response to influenza vaccination and the development of a universal influenza vaccine.
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