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White LA, Havranek KE, Lodmell JS. Using RNAseq to Uncover Transcriptional and Splicing Differences in Host Cells During Rift Valley Fever Virus Infection. Methods Mol Biol 2024; 2824:373-383. [PMID: 39039424 DOI: 10.1007/978-1-0716-3926-9_23] [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: 07/24/2024]
Abstract
RNAseq is a valuable tool that can aid researchers in uncovering the transcriptional changes that occur when a viral pathogen infects a host cell. Viral infection will invariably cause differential expression of many genes, from transcription of mRNA to alternative splicing and degradation. This change in gene expression can be a result of immune activation or a direct activity of the virus to alter the host cell's environment to make it more favorable for viral replication. Studying the innate immune response to a pathogen can reveal which cellular pathways are active, indicating the steps that the host takes to halt viral infection, and detecting virus-mediated mRNA expression changes can help with identifying the pathways which may be exploited by the virus. Gene expression changes-both cell-caused and virus-caused-can be studied through RNAseq, helping to provide a clearer picture of the cellular changes that occur during viral infection. In this protocol, we outline methods to carry out mRNA sequencing in Rift Valley fever virus-infected cell cultures, from infection to library prep and analysis.
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Affiliation(s)
- Luke Adam White
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | | | - J Stephen Lodmell
- Division of Biological Sciences, University of Montana, Missoula, MT, USA.
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Nair N, Osterhaus ADME, Rimmelzwaan GF, Prajeeth CK. Rift Valley Fever Virus-Infection, Pathogenesis and Host Immune Responses. Pathogens 2023; 12:1174. [PMID: 37764982 PMCID: PMC10535968 DOI: 10.3390/pathogens12091174] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/09/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Rift Valley Fever Virus is a mosquito-borne phlebovirus causing febrile or haemorrhagic illness in ruminants and humans. The virus can prevent the induction of the antiviral interferon response through its NSs proteins. Mutations in the NSs gene may allow the induction of innate proinflammatory immune responses and lead to attenuation of the virus. Upon infection, virus-specific antibodies and T cells are induced that may afford protection against subsequent infections. Thus, all arms of the adaptive immune system contribute to prevention of disease progression. These findings will aid the design of vaccines using the currently available platforms. Vaccine candidates have shown promise in safety and efficacy trials in susceptible animal species and these may contribute to the control of RVFV infections and prevention of disease progression in humans and ruminants.
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Bisom TC, Smelser H, Lanchy JM, Lodmell JS. Alternative Splicing of RIOK3 Engages the Noncanonical NFκB Pathway during Rift Valley Fever Virus Infection. Viruses 2023; 15:1566. [PMID: 37515252 PMCID: PMC10383813 DOI: 10.3390/v15071566] [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: 07/01/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Although the noncanonical NFκB pathway was originally identified as a cellular pathway contributing to lymphoid organogenesis, in the past 20 years, its involvement in innate immunity has become more appreciated. In particular, the noncanonical NFκB pathway has been found to be activated and even exploited by some RNA viruses during infection. Intriguingly, activation of this pathway has been shown to have a role in disrupting transcription of type 1 interferon (IFN), suggesting a rationale for why this response could be co-opted by some viruses. Rift Valley fever virus (RVFV) is a trisegmented ambisense RNA virus that poses a considerable threat to domestic livestock and human health. Previously, we showed the atypical kinase RIOK3 is important for mounting an IFN response to RVFV infection of human epithelial cells, and shortly following infection with RVFV (MP12 strain), RIOK3 mRNA is alternatively spliced to its X2 isoform that encodes a truncated RIOK3 protein. Alternative splicing of RIOK3 mRNA has an inhibitory effect on the IFN response but also stimulates an NFκB-mediated inflammatory response. Here, we demonstrate alternative splicing of RIOK3 mRNA is associated with activation of the noncanonical NFκB pathway and suggest this pathway is co-opted by RVFV (MP12) to enhance viral success during infection.
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Affiliation(s)
- Thomas Charles Bisom
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59801, USA
| | - Hope Smelser
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59801, USA
| | - Jean-Marc Lanchy
- Division of Biological Sciences, University of Montana, Missoula, MT 59801, USA
| | - J Stephen Lodmell
- Division of Biological Sciences, University of Montana, Missoula, MT 59801, USA
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59801, USA
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Bhattacharjee S, Ghosh D, Saha R, Sarkar R, Kumar S, Khokhar M, Pandey RK. Mechanism of Immune Evasion in Mosquito-Borne Diseases. Pathogens 2023; 12:pathogens12050635. [PMID: 37242305 DOI: 10.3390/pathogens12050635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
In recent decades, mosquito-borne illnesses have emerged as a major health burden in many tropical regions. These diseases, such as malaria, dengue fever, chikungunya, yellow fever, Zika virus infection, Rift Valley fever, Japanese encephalitis, and West Nile virus infection, are transmitted through the bite of infected mosquitoes. These pathogens have been shown to interfere with the host's immune system through adaptive and innate immune mechanisms, as well as the human circulatory system. Crucial immune checkpoints such as antigen presentation, T cell activation, differentiation, and proinflammatory response play a vital role in the host cell's response to pathogenic infection. Furthermore, these immune evasions have the potential to stimulate the human immune system, resulting in other associated non-communicable diseases. This review aims to advance our understanding of mosquito-borne diseases and the immune evasion mechanisms by associated pathogens. Moreover, it highlights the adverse outcomes of mosquito-borne disease.
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Affiliation(s)
| | - Debanjan Ghosh
- Department of Biotechnology, Pondicherry University, Puducherry 605014, India
| | - Rounak Saha
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India
| | - Rima Sarkar
- DBT Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Saurav Kumar
- DBT Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Manoj Khokhar
- Department of Biochemistry, AIIMS, Jodhpur 342005, India
| | - Rajan Kumar Pandey
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Solna, Sweden
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Mann JT, Riley BA, Baker SF. All differential on the splicing front: Host alternative splicing alters the landscape of virus-host conflict. Semin Cell Dev Biol 2023; 146:40-56. [PMID: 36737258 DOI: 10.1016/j.semcdb.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
Alternative RNA splicing is a co-transcriptional process that richly increases proteome diversity, and is dynamically regulated based on cell species, lineage, and activation state. Virus infection in vertebrate hosts results in rapid host transcriptome-wide changes, and regulation of alternative splicing can direct a combinatorial effect on the host transcriptome. There has been a recent increase in genome-wide studies evaluating host alternative splicing during viral infection, which integrates well with prior knowledge on viral interactions with host splicing proteins. A critical challenge remains in linking how these individual events direct global changes, and whether alternative splicing is an overall favorable pathway for fending off or supporting viral infection. Here, we introduce the process of alternative splicing, discuss how to analyze splice regulation, and detail studies on genome-wide and splice factor changes during viral infection. We seek to highlight where the field can focus on moving forward, and how incorporation of a virus-host co-evolutionary perspective can benefit this burgeoning subject.
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Affiliation(s)
- Joshua T Mann
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Brent A Riley
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Steven F Baker
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA.
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Wang X, Yuan Y, Liu Y, Zhang L. Arm race between Rift Valley fever virus and host. Front Immunol 2022; 13:1084230. [PMID: 36618346 PMCID: PMC9813963 DOI: 10.3389/fimmu.2022.1084230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Rift Valley fever (RVF) is a zoonotic disease caused by Rift Valley fever virus (RVFV), an emerging arbovirus within the Phenuiviridae family of Bunyavirales that has potential to cause severe diseases in both humans and livestock. It increases the incidence of abortion or foetal malformation in ruminants and leads to clinical manifestations like encephalitis or haemorrhagic fever in humans. Upon virus invasion, the innate immune system from the cell or the organism is activated to produce interferon (IFN) and prevent virus proliferation. Meanwhile, RVFV initiates countermeasures to limit antiviral responses at transcriptional and protein levels. RVFV nonstructural proteins (NSs) are the key virulent factors that not only perform immune evasion but also impact the cell replication cycle and has cytopathic effects. In this review, we summarize the innate immunity host cells employ depending on IFN signal transduction pathways, as well as the immune evasion mechanisms developed by RVFV primarily with the inhibitory activity of NSs protein. Clarifying the arms race between host innate immunity and RVFV immune evasion provides new avenues for drug target screening and offers possible solutions to current and future epidemics.
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Affiliation(s)
- Xiao Wang
- Department of Infectious Diseases, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Yupei Yuan
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Yihan Liu
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Leiliang Zhang
- Department of Infectious Diseases, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
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Bisom TC, White LA, Lanchy JM, Lodmell JS. RIOK3 and Its Alternatively Spliced Isoform Have Disparate Roles in the Innate Immune Response to Rift Valley Fever Virus (MP12) Infection. Viruses 2022; 14:2064. [PMID: 36146870 PMCID: PMC9502082 DOI: 10.3390/v14092064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 12/14/2022] Open
Abstract
Rift Valley fever virus (RVFV) is a pathogenic human and livestock RNA virus that poses a significant threat to public health and biosecurity. During RVFV infection, the atypical kinase RIOK3 plays important roles in the innate immune response. Although its exact functions in innate immunity are not completely understood, RIOK3 has been shown to be necessary for mounting an antiviral interferon (IFN) response to RVFV in epithelial cells. Furthermore, after immune stimulation, the splicing pattern for RIOK3 mRNA changes markedly, and RIOK3's dominant alternatively spliced isoform, RIOK3 X2, exhibits an opposite effect on the IFN response by dampening it. Here, we further investigate the roles of RIOK3 and its spliced isoform in other innate immune responses to RVFV, namely the NFκB-mediated inflammatory response. We find that while RIOK3 is important for negatively regulating this inflammatory pathway, its alternatively spliced isoform, RIOK3 X2, stimulates it. Overall, these data demonstrate that both RIOK3 and its X2 isoform have unique roles in separate innate immune pathways that respond to RVFV infection.
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Affiliation(s)
- Thomas C. Bisom
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59801, USA
| | - Luke A. White
- Division of Biological Sciences, University of Montana, Missoula, MT 59801, USA
| | - Jean-Marc Lanchy
- Division of Biological Sciences, University of Montana, Missoula, MT 59801, USA
| | - J. Stephen Lodmell
- Division of Biological Sciences, University of Montana, Missoula, MT 59801, USA
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59801, USA
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