1
|
Afroz S, Saul S, Dai J, Surman S, Liu X, Park HS, Le Nouën C, Lingemann M, Dahal B, Coleman JR, Mueller S, Collins PL, Buchholz UJ, Munir S. Human parainfluenza virus 3 vaccine candidates attenuated by codon-pair deoptimization are immunogenic and protective in hamsters. Proc Natl Acad Sci U S A 2024; 121:e2316376121. [PMID: 38861603 PMCID: PMC11194498 DOI: 10.1073/pnas.2316376121] [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: 10/11/2023] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
Human parainfluenza virus type 3 (HPIV3) is a major pediatric respiratory pathogen lacking available vaccines or antiviral drugs. We generated live-attenuated HPIV3 vaccine candidates by codon-pair deoptimization (CPD). HPIV3 open reading frames (ORFs) encoding the nucleoprotein (N), phosphoprotein (P), matrix (M), fusion (F), hemagglutinin-neuraminidase (HN), and polymerase (L) were modified singly or in combination to generate 12 viruses designated Min-N, Min-P, Min-M, Min-FHN, Min-L, Min-NP, Min-NPM, Min-NPL, Min-PM, Min-PFHN, Min-MFHN, and Min-PMFHN. CPD of N or L severely reduced growth in vitro and was not further evaluated. CPD of P or M was associated with increased and decreased interferon (IFN) response in vitro, respectively, but had little effect on virus replication. In Vero cells, CPD of F and HN delayed virus replication, but final titers were comparable to wild-type (wt) HPIV3. In human lung epithelial A549 cells, CPD F and HN induced a stronger IFN response, viral titers were reduced 100-fold, and the expression of F and HN proteins was significantly reduced without affecting N or P or the relative packaging of proteins into virions. Following intranasal infection in hamsters, replication in the nasal turbinates and lungs tended to be the most reduced for viruses bearing CPD F and HN, with maximum reductions of approximately 10-fold. Despite decreased in vivo replication (and lower expression of CPD F and HN in vitro), all viruses induced titers of serum HPIV3-neutralizing antibodies similar to wt and provided complete protection against HPIV3 challenge. In summary, CPD of HPIV3 yielded promising vaccine candidates suitable for further development.
Collapse
Affiliation(s)
- Sharmin Afroz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Sirle Saul
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Jin Dai
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Sonja Surman
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Xueqiao Liu
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Hong-Su Park
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Cyril Le Nouën
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Matthias Lingemann
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Bibha Dahal
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | | | | | - Peter Leon Collins
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Ursula Johanna Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Shirin Munir
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| |
Collapse
|
2
|
Beauvois A, Gazon H, Chauhan PS, Jamakhani M, Jacques JR, Thiry M, Dejardin E, Valentin ED, Twizere JC, Péloponèse JM, Njock MS, Yasunaga JI, Matsuoka M, Hamaïdia M, Willems L. The helicase-like transcription factor redirects the autophagic flux and restricts human T cell leukemia virus type 1 infection. Proc Natl Acad Sci U S A 2023; 120:e2216127120. [PMID: 37487091 PMCID: PMC10400947 DOI: 10.1073/pnas.2216127120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/11/2023] [Indexed: 07/26/2023] Open
Abstract
Retroviruses and their host have coevolved in a delicate balance between viral replication and survival of the infected cell. In this equilibrium, restriction factors expressed by infected cells control different steps of retroviral replication such as entry, uncoating, nuclear import, expression, or budding. Here, we describe a mechanism of restriction against human T cell leukemia virus type 1 (HTLV-1) by the helicase-like transcription factor (HLTF). We show that RNA and protein levels of HLTF are reduced in primary T cells of HTLV-1-infected subjects, suggesting a clinical relevance. We further demonstrate that the viral oncogene Tax represses HLTF transcription via the Enhancer of zeste homolog 2 methyltransferase of the Polycomb repressive complex 2. The Tax protein also directly interacts with HLTF and induces its proteasomal degradation. RNA interference and gene transduction in HTLV-1-infected T cells derived from patients indicate that HLTF is a restriction factor. Restoring the normal levels of HLTF expression induces the dispersal of the Golgi apparatus and overproduction of secretory granules. By synergizing with Tax-mediated NF-κB activation, physiologically relevant levels of HLTF intensify the autophagic flux. Increased vesicular trafficking leads to an enlargement of the lysosomes and the production of large vacuoles containing viral particles. HLTF induction in HTLV-1-infected cells significantly increases the percentage of defective virions. In conclusion, HLTF-mediated activation of the autophagic flux blunts the infectious replication cycle of HTLV-1, revealing an original mode of viral restriction.
Collapse
Affiliation(s)
- Aurélie Beauvois
- Laboratory of Molecular and Cellular Epigenetics, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
- Molecular Biology, Teaching and Research Center, University of Liège, 5030, Gembloux, Belgium
| | - Hélène Gazon
- Laboratory of Molecular and Cellular Epigenetics, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
- Molecular Biology, Teaching and Research Center, University of Liège, 5030, Gembloux, Belgium
| | - Pradeep Singh Chauhan
- Laboratory of Molecular and Cellular Epigenetics, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
- Molecular Biology, Teaching and Research Center, University of Liège, 5030, Gembloux, Belgium
| | - Majeed Jamakhani
- Laboratory of Molecular and Cellular Epigenetics, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
- Molecular Biology, Teaching and Research Center, University of Liège, 5030, Gembloux, Belgium
| | - Jean-Rock Jacques
- Laboratory of Molecular and Cellular Epigenetics, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
- Molecular Biology, Teaching and Research Center, University of Liège, 5030, Gembloux, Belgium
| | - Marc Thiry
- Laboratory of Cell and Tissue Biology, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
| | - Emmanuel Dejardin
- Laboratory of Molecular Immunology & Signal Transduction, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
| | - Emmanuel Di Valentin
- Viral Vectors Platform, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000Liège, Belgium
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000Liège, Belgium
| | - Jean-Marie Péloponèse
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS, 34094, Montpellier, France
| | - Makon-Sébastien Njock
- Laboratory of Pneumology, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, University Hospital of Liège, 4000Liège, Belgium
| | | | - Masao Matsuoka
- Department of Hematology, Kumamoto University, 860-8556, Kumamoto, Japan
| | - Malik Hamaïdia
- Laboratory of Molecular and Cellular Epigenetics, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
- Molecular Biology, Teaching and Research Center, University of Liège, 5030, Gembloux, Belgium
| | - Luc Willems
- Laboratory of Molecular and Cellular Epigenetics, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
- Molecular Biology, Teaching and Research Center, University of Liège, 5030, Gembloux, Belgium
| |
Collapse
|
3
|
Nigos LR, Scott NE, Brooks AG, Ait-Goughoulte M, Londrigan SL, Reading PC, Farrukee R. TRIM16 Overexpression in HEK293T Cells Results in Cell Line-Specific Antiviral Activity. Pathogens 2023; 12:852. [PMID: 37375542 DOI: 10.3390/pathogens12060852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/17/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
Host cell restriction factors are intracellular proteins that can inhibit virus replication. Characterisation of novel host cell restriction factors can provide potential targets for host-directed therapies. In this study, we aimed to assess a member of the Tripartite-motif family protein (TRIM) family, TRIM16, as a putative host cell restriction factor. To this end, we utilized constitutive or doxycycline-inducible systems to overexpress TRIM16 in HEK293T epithelial cells and then tested for its ability to inhibit growth by a range of RNA and DNA viruses. In HEK293T cells, overexpression of TRIM16 resulted in potent inhibition of multiple viruses, however, when TRIM16 was overexpressed in other epithelial cell lines (A549, Hela, or Hep2), virus inhibition was not observed. When investigating the antiviral activity of endogenous TRIM16, we report that siRNA-mediated knockdown of TRIM16 in A549 cells also modulated the mRNA expression of other TRIM proteins, complicating the interpretation of results using this method. Therefore, we used CRISPR/Cas9 editing to knockout TRIM16 in A549 cells and demonstrate that endogenous TRIM16 did not mediate antiviral activity against the viruses tested. Thus, while initial overexpression in HEK293T cells suggested that TRIM16 was a host cell restriction factor, alternative approaches did not validate these findings. These studies highlight the importance of multiple complementary experimental approaches, including overexpression analysis in multiple cell lines and investigation of the endogenous protein, when defining host cell restriction factors with novel antiviral activity.
Collapse
Affiliation(s)
- Lance R Nigos
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St., Melbourne, VIC 3000, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St., Melbourne, VIC 3000, Australia
| | - Andrew G Brooks
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St., Melbourne, VIC 3000, Australia
| | - Malika Ait-Goughoulte
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Sarah L Londrigan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St., Melbourne, VIC 3000, Australia
| | - Patrick C Reading
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St., Melbourne, VIC 3000, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Disease Reference Laboratory, Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St., Melbourne, VIC 3000, Australia
| | - Rubaiyea Farrukee
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St., Melbourne, VIC 3000, Australia
| |
Collapse
|
4
|
Haas GD, Lee B. Paramyxoviruses from bats: changes in receptor specificity and their role in host adaptation. Curr Opin Virol 2023; 58:101292. [PMID: 36508860 PMCID: PMC9974588 DOI: 10.1016/j.coviro.2022.101292] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022]
Abstract
Global metagenomic surveys have revealed that bats host a diverse array of paramyxoviruses, including species from at least five major genera. An essential determinant of successful spillover is the entry of a virus into a new host. We evaluate the role of receptor usage in the zoonotic potential of bat-borne henipaviruses, morbilliviruses, pararubulaviruses, orthorubulaviruses, and jeilongviruses; successful spillover into humans depends upon compatibility of a respective viral attachment protein with its cognate receptor. We also emphasize the importance of postentry restrictions in preventing spillover. Metagenomics and characterization of newly identified paramyxoviruses have greatly improved our understanding of spillover determinants, allowing for better forecasts of which bat-borne viruses may pose the greatest risk for cross-species transmission into humans.
Collapse
Affiliation(s)
- Griffin D Haas
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA.
| |
Collapse
|
5
|
Duan Z, Shi H, Xing J, Zhang Q, Liu M. Mutation of Basic Residues R283, R286, and K288 in the Matrix Protein of Newcastle Disease Virus Attenuates Viral Replication and Pathogenicity. Int J Mol Sci 2023; 24:ijms24020980. [PMID: 36674496 PMCID: PMC9864103 DOI: 10.3390/ijms24020980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/25/2022] [Accepted: 01/02/2023] [Indexed: 01/07/2023] Open
Abstract
The matrix (M) protein of Newcastle disease virus (NDV) contains large numbers of unevenly distributed basic residues, but the precise function of most basic residues in the M protein remains enigmatic. We previously demonstrated that the C-terminus (aa 264-313) of M protein interacted with the extra-terminal (ET) domain of chicken bromodomain-containing protein 2 (chBRD2), which promoted NDV replication by downregulating chBRD2 expression and facilitating viral RNA synthesis and transcription. However, the key amino acid sites determining M's interaction with chBRD2/ET and their roles in the replication and pathogenicity of NDV are not known. In this study, three basic residues-R283, R286, and K288-in the NDV M protein were verified to be responsible for its interaction with chBRD2/ET. In addition, mutation of these basic residues (R283A/R286A/K288A) in the M protein changed its electrostatic pattern and abrogated the decreased expression of endogenic chBRD2. Moreover, a recombinant virus harboring these mutations resulted in a pathotype change of NDV and attenuated viral replication and pathogenicity in chickens due to the decreased viral RNA synthesis and transcription. Our findings therefore provide a better understanding of the crucial biological functions of M's basic residues and also aid in understanding the poorly understood pathogenesis of NDV.
Collapse
Affiliation(s)
- Zhiqiang Duan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
- Correspondence: ; Tel.: +86-(851)-8829-8005
| | - Haiying Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Jingru Xing
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Qianyong Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Menglan Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| |
Collapse
|
6
|
Interaction between the Hepatitis B Virus and Cellular FLIP Variants in Viral Replication and the Innate Immune System. Viruses 2022; 14:v14020373. [PMID: 35215970 PMCID: PMC8874586 DOI: 10.3390/v14020373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/28/2022] [Accepted: 02/08/2022] [Indexed: 12/10/2022] Open
Abstract
During viral evolution and adaptation, many viruses have utilized host cellular factors and machinery as their partners. HBx, as a multifunctional viral protein encoded by the hepatitis B virus (HBV), promotes HBV replication and greatly contributes to the development of HBV-associated hepatocellular carcinoma (HCC). HBx interacts with several host factors in order to regulate HBV replication and evolve carcinogenesis. The cellular FADD-like IL-1β-converting enzyme (FLICE)-like inhibitory protein (c-FLIP) is a major factor that functions in a variety of cellular pathways and specifically in apoptosis. It has been shown that the interaction between HBx and c-FLIP determines HBV fate. In this review, we provide a comprehensive and detailed overview of the interplay between c-FLIP and HBV in various environmental circumstances. We describe strategies adapted by HBV to establish its chronic infection. We also summarize the conventional roles of c-FLIP and highlight the functional outcome of the interaction between c-FLIP and HBV or other viruses in viral replication and the innate immune system.
Collapse
|