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Bhatnagar P, Bajpai P, Shrinet J, Kaja MK, Chandele A, Sitaraman R. Prediction of human protein interactome of dengue virus non-structural protein 5 (NS5) and its downstream immunological implications. 3 Biotech 2023; 13:180. [PMID: 37193327 PMCID: PMC10182223 DOI: 10.1007/s13205-023-03569-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/19/2023] [Indexed: 05/18/2023] Open
Abstract
The non-structural protein 5 (NS5) is the most conserved protein among flaviviruses, a family that includes the dengue virus. It functions both as an RNA-dependent RNA polymerase and an RNA-methyltransferase and is therefore essential for the replication of viral RNA. The discovery that dengue virus NS5 protein (DENV-NS5) can also localize to the nucleus has resulted in renewed interest in its potential roles at the host-virus interface. In this study, we have used two complementary computational approaches in parallel - one based on linear motifs (ELM) and another based on tertiary structure of the protein (DALI) - to predict the host proteins that DENV-NS5 might interact with. Of the 42 human proteins predicted by both these methods, 34 are novel. Pathway analysis of these 42 human proteins shows that they are involved in key host cellular processes related to cell cycle regulation, proliferation, protein degradation, apoptosis, and immune responses. A focused analysis of transcription factors that directly interact with the predicted DENV-NS5 interacting proteins was performed, followed by the identification of downstream genes that are differentially expressed after dengue infection using previously published RNA-seq data. Our study provides unique insights into the DENV-NS5 interaction network and delineates mechanisms whereby DENV-NS5 could impact the host-virus interface. The novel interactors identified in this study could be potentially targeted by NS5 to modulate the host cellular environment in general, and the immune response in particular, thereby extending the role of DENV-NS5 beyond its known enzymatic functions. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03569-0.
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Affiliation(s)
- Priya Bhatnagar
- Department of Biotechnology, TERI School of Advanced Studies, New Delhi, India
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Prashant Bajpai
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Jatin Shrinet
- Department of Biological Science, Florida State University, Tallahassee, FL 32306 USA
| | - Murali Krishna Kaja
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- Department of Pediatrics and Emory Vaccine Centre, Emory University School of Medicine, Atlanta, GA USA
| | - Anmol Chandele
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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Ramasamy V, Arora U, Shukla R, Poddar A, Shanmugam RK, White LJ, Mattocks MM, Raut R, Perween A, Tyagi P, de Silva AM, Bhaumik SK, Kaja MK, Villinger F, Ahmed R, Johnston RE, Swaminathan S, Khanna N. A tetravalent virus-like particle vaccine designed to display domain III of dengue envelope proteins induces multi-serotype neutralizing antibodies in mice and macaques which confer protection against antibody dependent enhancement in AG129 mice. PLoS Negl Trop Dis 2018; 12:e0006191. [PMID: 29309412 PMCID: PMC5774828 DOI: 10.1371/journal.pntd.0006191] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 01/19/2018] [Accepted: 12/26/2017] [Indexed: 12/29/2022] Open
Abstract
Background Dengue is one of the fastest spreading vector-borne diseases, caused by four antigenically distinct dengue viruses (DENVs). Antibodies against DENVs are responsible for both protection as well as pathogenesis. A vaccine that is safe for and efficacious in all people irrespective of their age and domicile is still an unmet need. It is becoming increasingly apparent that vaccine design must eliminate epitopes implicated in the induction of infection-enhancing antibodies. Methodology/principal findings We report a Pichia pastoris-expressed dengue immunogen, DSV4, based on DENV envelope protein domain III (EDIII), which contains well-characterized serotype-specific and cross-reactive epitopes. In natural infection, <10% of the total neutralizing antibody response is EDIII-directed. Yet, this is a functionally relevant domain which interacts with the host cell surface receptor. DSV4 was designed by in-frame fusion of EDIII of all four DENV serotypes and hepatitis B surface (S) antigen and co-expressed with unfused S antigen to form mosaic virus-like particles (VLPs). These VLPs displayed EDIIIs of all four DENV serotypes based on probing with a battery of serotype-specific anti-EDIII monoclonal antibodies. The DSV4 VLPs were highly immunogenic, inducing potent and durable neutralizing antibodies against all four DENV serotypes encompassing multiple genotypes, in mice and macaques. DSV4-induced murine antibodies suppressed viremia in AG129 mice and conferred protection against lethal DENV-4 virus challenge. Further, neither murine nor macaque anti-DSV4 antibodies promoted mortality or inflammatory cytokine production when passively transferred and tested in an in vivo dengue disease enhancement model of AG129 mice. Conclusions/significance Directing the immune response to a non-immunodominant but functionally relevant serotype-specific dengue epitope of the four DENV serotypes, displayed on a VLP platform, can help minimize the risk of inducing disease-enhancing antibodies while eliciting effective tetravalent seroconversion. DSV4 has a significant potential to emerge as a safe, efficacious and inexpensive subunit dengue vaccine candidate. Dengue is mosquito-borne viral disease which is currently a global public health problem. It is caused by four different types of dengue viruses. Nearly a 100 million people a year suffer from overt sickness, which may range from mild fever to potentially fatal disease. A virus-based dengue vaccine was launched for the first time in late 2015. Unexpectedly, this vaccine mimics the dengue viruses in that it appears to elicit disease-enhancing antibodies. To reduce such risk, safer vaccines that eliminate viral proteins responsible for undesirable antibodies are needed. We focused our attention on a small domain of the dengue virus surface protein known as envelope domain III (EDIII). Humans make only a small amount of antibodies against EDIII, but these antibodies are effective in blocking dengue virus from entering cells. We used a yeast expression system to display EDIIIs of all four types of dengue viruses on the surface of non-infectious virus-like particles (VLPs). These VLPs elicited antibodies, in mice and monkeys, which blocked all four dengue virus types and their variants from entering cells in culture. Importantly, these antibodies did not enhance dengue infection in a mouse model.
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Affiliation(s)
- Viswanathan Ramasamy
- Recombinant Gene Products Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Upasana Arora
- Recombinant Gene Products Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rahul Shukla
- Recombinant Gene Products Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ankur Poddar
- Recombinant Gene Products Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rajgokul K. Shanmugam
- Recombinant Gene Products Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Laura J. White
- Global Vaccines Inc., 801 Capitola Dr., Ste. 11, Durham, NC, United States of America
| | - Melissa M. Mattocks
- Global Vaccines Inc., 801 Capitola Dr., Ste. 11, Durham, NC, United States of America
| | - Rajendra Raut
- Recombinant Gene Products Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, United States of America
| | - Ashiya Perween
- Recombinant Gene Products Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Poornima Tyagi
- Recombinant Gene Products Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Aravinda M. de Silva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, United States of America
| | - Siddhartha K. Bhaumik
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Murali Krishna Kaja
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, United States of America
- ICGEB-Emory Vaccine Center, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - François Villinger
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Robert E. Johnston
- Global Vaccines Inc., 801 Capitola Dr., Ste. 11, Durham, NC, United States of America
| | - Sathyamangalam Swaminathan
- Recombinant Gene Products Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- * E-mail: (SS); , (NK)
| | - Navin Khanna
- Recombinant Gene Products Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, United States of America
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, INDIA
- * E-mail: (SS); , (NK)
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