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Yang C, Chen W, Huang Y. Long non-coding RNA SUN2-AS1 acts as a negative regulator of ISGs transcription to promote flavivirus infection. Virology 2024; 600:110245. [PMID: 39288611 DOI: 10.1016/j.virol.2024.110245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 09/04/2024] [Accepted: 09/12/2024] [Indexed: 09/19/2024]
Abstract
Recent studies highlight the critical involvement of long non-coding RNAs (lncRNAs) in modulating viral replication and immune responses, yet their specific roles in flavivirus infections remain underexplored. Our study has identified lncRNA SUN2-AS1, which is significantly upregulated in response to flavivirus infection in A549, Huh7 cells, and monocyte-differentiated macrophages (MDMs). SUN2-AS1 interacts with the transcription factors NF-κB and STAT1, andits expression is induced by ZIKV RNA via the type I interferon (IFN) pathway. Notably, SUN2-AS1 enhances the infection of flaviviruses, including ZIKV, DENV2, and JEV, while showing no effect on VSV or HSV-1 infections. Mechanistically, SUN2-AS1 exerts a proviral effect by inhibiting the transcription of interferon-stimulated genes (ISGs). These findings uncover a novel mechanism by which lncRNAs facilitate flavivirus propagation and highlight SUN2-AS1 as a potential target for antiviral therapeutic strategies.
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Affiliation(s)
- Chao Yang
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China; Guangxi Hospital Division of the First Affiliated Hospital, Sun Yat-sen University, Nanning, 530022, China
| | - Weikang Chen
- Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.
| | - Yanxia Huang
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.
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2
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Berglund G, Lennon CD, Badu P, Berglund JA, Pager CT. Transcriptomic Signatures of Zika Virus Infection in Patients and a Cell Culture Model. Microorganisms 2024; 12:1499. [PMID: 39065267 PMCID: PMC11278784 DOI: 10.3390/microorganisms12071499] [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: 05/27/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
Zika virus (ZIKV), a re-emerging flavivirus, is associated with devasting developmental and neurological disease outcomes particularly in infants infected in utero. Towards understanding the molecular underpinnings of the unique ZIKV disease pathologies, numerous transcriptome-wide studies have been undertaken. Notably, these studies have overlooked the assimilation of RNA-seq analysis from ZIKV-infected patients with cell culture model systems. In this study we find that ZIKV-infection of human lung adenocarcinoma A549 cells, mirrored both the transcriptional and alternative splicing profiles from previously published RNA-seq data of peripheral blood mononuclear cells collected from pediatric patients during early acute, late acute, and convalescent phases of ZIKV infection. Our analyses show that ZIKV infection in cultured cells correlates with transcriptional changes in patients, while the overlap in alternative splicing profiles was not as extensive. Overall, our data indicate that cell culture model systems support dissection of select molecular changes detected in patients and establishes the groundwork for future studies elucidating the biological implications of alternative splicing during ZIKV infection.
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Affiliation(s)
- Gillian Berglund
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Claudia D. Lennon
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Pheonah Badu
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - John Andrew Berglund
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Cara T. Pager
- The RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
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3
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Huo Z, Zhu X, Peng Q, Chen C, Yang X, Huang C, Xiang Y, Tian Q, Liu J, Liu C, Zhang P. LINC08148 promotes the caveola-mediated endocytosis of Zika virus through upregulating transcription of Src. J Virol 2024; 98:e0170523. [PMID: 38742902 PMCID: PMC11237476 DOI: 10.1128/jvi.01705-23] [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: 11/07/2023] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) represent a new group of host factors involved in viral infection. Current study identified an intergenic lncRNA, LINC08148, as a proviral factor of Zika virus (ZIKV) and Dengue virus 2 (DENV2). Knockout (KO) or silencing of LINC08148 decreases the replication of ZIKV and DENV2. LINC08148 mainly acts at the endocytosis step of ZIKV but at a later stage of DENV2. RNA-seq analysis reveals that LINC08148 knockout downregulates the transcription levels of five endocytosis-related genes including AP2B1, CHMP4C, DNM1, FCHO1, and Src. Among them, loss of Src significantly decreases the uptake of ZIKV. Trans-complementation of Src in the LINC08148KO cells largely restores the caveola-mediated endocytosis of ZIKV, indicating that the proviral effect of LINC08148 is exerted through Src. Finally, LINC08148 upregulates the Src transcription through associating with its transcription factor SP1. This work establishes an essential role of LINC08148 in the ZIKV entry, underscoring a significance of lncRNAs in the viral infection. IMPORTANCE Long non-coding RNAs (lncRNAs), like proteins, participate in viral infection. However, functions of most lncRNAs remain unknown. In this study, we performed a functional screen based on microarray data and identified a new proviral lncRNA, LINC08148. Then, we uncovered that LINC08148 is involved in the caveola-mediated endocytosis of ZIKV, rather than the classical clathrin-mediated endocytosis. Mechanistically, LINC08148 upregulates the transcription of Src, an initiator of caveola-mediated endocytosis, through binding to its transcription factor SP1. This study identifies a new lncRNA involved in the ZIKV infection, suggesting lncRNAs and cellular proteins are closely linked and cooperate to regulate viral infection.
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Affiliation(s)
- Zhiting Huo
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xuanfeng Zhu
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Qinyu Peng
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Cancan Chen
- Department of Pathology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaoyi Yang
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Changbai Huang
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yincheng Xiang
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Qingju Tian
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jingyu Liu
- Food and Cosmetics Institute, Guangzhou Customs Technology Center, Guangzhou, China
| | - Chao Liu
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ping Zhang
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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4
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Berglund G, Lennon CD, Badu P, Berglund JA, Pager CT. Zika virus infection in a cell culture model reflects the transcriptomic signatures in patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595842. [PMID: 38826459 PMCID: PMC11142252 DOI: 10.1101/2024.05.25.595842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Zika virus (ZIKV), a re-emerging flavivirus, is associated with devasting developmental and neurological disease outcomes particularly in infants infected in utero. Towards understanding the molecular underpinnings of the unique ZIKV disease pathologies, numerous transcriptome-wide studies have been undertaken. Notably, these studies have overlooked the assimilation of RNA-seq analysis from ZIKV-infected patients with cell culture model systems. In this study we find that ZIKV-infection of human lung adenocarcinoma A549 cells, mirrored both the transcriptional and alternative splicing profiles from previously published RNA-seq data of peripheral blood mononuclear cells collected from pediatric patients during early acute, late acute, and convalescent phases of ZIKV infection. Our analyses show that ZIKV infection in cultured cells correlates with transcriptional changes in patients, while the overlap in alternative splicing profiles was not as extensive. Overall, our data indicate that cell culture model systems support dissection of select molecular changes detected in patients and establishes the groundwork for future studies elucidating the biological implications of alternative splicing during ZIKV infection.
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Affiliation(s)
- Gillian Berglund
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Claudia D. Lennon
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Pheonah Badu
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - J. Andrew Berglund
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Cara T. Pager
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
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5
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Tripathi SK, Aneja A, Borgaonkar T, Das S. PSPC1 Binds to HCV IRES and Prevents Ribosomal Protein S5 Binding, Inhibiting Viral RNA Translation. Viruses 2024; 16:738. [PMID: 38793620 PMCID: PMC11126058 DOI: 10.3390/v16050738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Hepatitis C virus (HCV) infects the human liver, and its chronic infection is one of the major causes of Hepatocellular carcinoma. Translation of HCV RNA is mediated by an Internal Ribosome Entry Site (IRES) element located in the 5'UTR of viral RNA. Several RNA Binding proteins of the host interact with the HCV IRES and modulate its function. Here, we demonstrate that PSPC1 (Paraspeckle Component 1), an essential paraspeckle component, upon HCV infection is relocalized and interacts with HCV IRES to prevent viral RNA translation. Competition UV-crosslinking experiments showed that PSPC1 interacts explicitly with the SLIV region of the HCV IRES, which is known to play a vital role in ribosomal loading to the HCV IRES via interaction with Ribosomal protein S5 (RPS5). Partial silencing of PSPC1 increased viral RNA translation and, consequently, HCV replication, suggesting a negative regulation by PSPC1. Interestingly, the silencing of PSPC1 protein leads to an increased interaction of RPS5 at the SLIV region, leading to an overall increase in the viral RNA in polysomes. Overall, our results showed how the host counters viral infection by relocalizing nuclear protein to the cytoplasm as a survival strategy.
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Affiliation(s)
- Sachin Kumar Tripathi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Ashish Aneja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Teji Borgaonkar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
- National Institute of Biomedical Genomics, Kalyani 741251, West Bengal, India
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6
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Lee SG, Furth PA, Hennighausen L, Lee HK. Variant- and vaccination-specific alternative splicing profiles in SARS-CoV-2 infections. iScience 2024; 27:109177. [PMID: 38414855 PMCID: PMC10897911 DOI: 10.1016/j.isci.2024.109177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/28/2023] [Accepted: 02/06/2024] [Indexed: 02/29/2024] Open
Abstract
The COVID-19 pandemic, driven by the SARS-CoV-2 virus and its variants, highlights the important role of understanding host-viral molecular interactions influencing infection outcomes. Alternative splicing post-infection can impact both host responses and viral replication. We analyzed RNA splicing patterns in immune cells across various SARS-CoV-2 variants, considering immunization status. Using a dataset of 190 RNA-seq samples from our prior studies, we observed a substantial deactivation of alternative splicing and RNA splicing-related genes in COVID-19 patients. The alterations varied significantly depending on the infecting variant and immunization history. Notably, Alpha or Beta-infected patients differed from controls, while Omicron-infected patients displayed a splicing profile closer to controls. Particularly, vaccinated Omicron-infected individuals showed a distinct dynamic in alternative splicing patterns not widely shared among other groups. Our findings underscore the intricate interplay between SARS-CoV-2 variants, vaccination-induced immunity, and alternative splicing, emphasizing the need for further investigations to deepen understanding and guide therapeutic development.
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Affiliation(s)
- Sung-Gwon Lee
- Section of Genetics and Physiology, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Priscilla A Furth
- Section of Genetics and Physiology, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Lothar Hennighausen
- Section of Genetics and Physiology, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Hye Kyung Lee
- Section of Genetics and Physiology, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
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7
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Camacho-Concha N, Santana-Román ME, Sánchez NC, Velasco I, Pando-Robles V, Pedraza-Alva G, Pérez-Martínez L. Insights into Zika Virus Pathogenesis and Potential Therapeutic Strategies. Biomedicines 2023; 11:3316. [PMID: 38137537 PMCID: PMC10741857 DOI: 10.3390/biomedicines11123316] [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: 10/01/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 12/24/2023] Open
Abstract
Zika virus (ZIKV) has emerged as a significant public health threat, reaching pandemic levels in 2016. Human infection with ZIKV can manifest as either asymptomatic or as an acute illness characterized by symptoms such as fever and headache. Moreover, it has been associated with severe neurological complications in adults, including Guillain-Barre syndrome, and devastating fetal abnormalities, like microcephaly. The primary mode of transmission is through Aedes spp. mosquitoes, and with half of the world's population residing in regions where Aedes aegypti, the principal vector, thrives, the reemergence of ZIKV remains a concern. This comprehensive review provides insights into the pathogenesis of ZIKV and highlights the key cellular pathways activated upon ZIKV infection. Additionally, we explore the potential of utilizing microRNAs (miRNAs) and phytocompounds as promising strategies to combat ZIKV infection.
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Affiliation(s)
- Nohemi Camacho-Concha
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (N.C.-C.); (M.E.S.-R.); (N.C.S.); (G.P.-A.)
| | - María E. Santana-Román
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (N.C.-C.); (M.E.S.-R.); (N.C.S.); (G.P.-A.)
| | - Nilda C. Sánchez
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (N.C.-C.); (M.E.S.-R.); (N.C.S.); (G.P.-A.)
| | - Iván Velasco
- Instituto de Fisiología Celular-Neurociencias, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
- Laboratorio de Reprogramación Celular, Instituto Nacional de Neurología y Neurocirugía “Manuel Velasco Suárez”, Ciudad de México 14269, Mexico
| | - Victoria Pando-Robles
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca 62100, Morelos, Mexico;
| | - Gustavo Pedraza-Alva
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (N.C.-C.); (M.E.S.-R.); (N.C.S.); (G.P.-A.)
| | - Leonor Pérez-Martínez
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (N.C.-C.); (M.E.S.-R.); (N.C.S.); (G.P.-A.)
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8
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Lee SG, Furth PA, Hennighausen L, Lee HK. Variant- and Vaccination-Specific Alternative Splicing Profiles in SARS-CoV-2 Infections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.24.568603. [PMID: 38076812 PMCID: PMC10705549 DOI: 10.1101/2023.11.24.568603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, and its subsequent variants has underscored the importance of understanding the host-viral molecular interactions to devise effective therapeutic strategies. A significant aspect of these interactions is the role of alternative splicing in modulating host responses and viral replication mechanisms. Our study sought to delineate the patterns of alternative splicing of RNAs from immune cells across different SARS-CoV-2 variants and vaccination statuses, utilizing a robust dataset of 190 RNA-seq samples from our previous studies, encompassing an average of 212 million reads per sample. We identified a dynamic alteration in alternative splicing and genes related to RNA splicing were highly deactivated in COVID-19 patients and showed variant- and vaccination-specific expression profiles. Overall, Omicron-infected patients exhibited a gene expression profile akin to healthy controls, unlike the Alpha or Beta variants. However, significantly, we found identified a subset of infected individuals, most pronounced in vaccinated patients infected with Omicron variant, that exhibited a specific dynamic in their alternative splicing patterns that was not widely shared amongst the other groups. Our findings underscore the complex interplay between SARS-CoV-2 variants, vaccination-induced immune responses, and alternative splicing, emphasizing the necessity for further investigations into these molecular cross-talks to foster deeper understanding and guide strategic therapeutic development.
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Affiliation(s)
- Sung-Gwon Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, USA
| | - Priscilla A. Furth
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, USA
| | - Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, USA
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9
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Leal Y, Valenzuela-Muñoz V, Gallardo-Escárate C. Alternative splicing in Atlantic salmon head kidney and SHK-1 cell line during the Piscirickettsia salmonis infection: A comparative transcriptome survey. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109127. [PMID: 37813155 DOI: 10.1016/j.fsi.2023.109127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Abstract
Piscirickettsia salmonis, an intracellular bacterium in salmon aquaculture, is a big challenge because it is responsible for 54.2% of Atlantic salmon mortalities. In recent years, the high relevance of Alternative Splicing (AS) as a molecular mechanism associated with infectious conditions and host-pathogen interaction processes, especially in host immune activation, has been observed. Several studies have highlighted the role of AS in the host's immune response during viral, bacterial, and endoparasite infection. In the present study, we evaluated AS transcriptome profiles during P. salmonis infection in the two most used study models, SHK-1 cell line and salmon head kidney tissue. First, the SHK-1 cell line was exposed to P. salmonis infection at 0-, 7-, and 14-days post-infection (dpi). Following, total RNA was extracted for Illumina sequencing. On the other hand, RNA-Seq datasets of Atlantic salmon head kidney infected with the same P. salmonis strayingwase used. For both study models, the highest number of differentially alternative splicing (DAS) events was observed at 7 dpi, 16,830 DAS events derived from 9213 DAS genes in SHK-1 cells, and 13,820 DAS events from 7684 DAS genes in salmon HK. Alternative first exon (AF) was the most abundant AS type in the three infection times analyzed, representing 31% in SHK-1 cells and 228.6 in salmon HK; meanwhile, mutually exclusive exon (MX) was the least abundant. Notably, functional annotation of DAS genes in SHK-1 cells infected with P. salmonis showed a high presence of genes related to nucleotide metabolism. In contrast, the salmon head kidney exhibited many GO terms associated with immune response. Our findings reported the role of AS during P. salmonis infection in Atlantic salmon. These studies would contribute to a better understanding of the molecular bases that support the pathogen-host interaction, evidencing the contribution of AS regulating the transcriptional host response.
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Affiliation(s)
- Yeny Leal
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción, 4030000, Chile
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción, 4030000, Chile
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción, 4030000, Chile.
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10
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Rahni Z, Hosseini SM, Shahrokh S, Saeedi Niasar M, Shoraka S, Mirjalali H, Nazemalhosseini-Mojarad E, Rostami-Nejad M, Malekpour H, Zali MR, Mohebbi SR. Long non-coding RNAs ANRIL, THRIL, and NEAT1 as potential circulating biomarkers of SARS-CoV-2 infection and disease severity. Virus Res 2023; 336:199214. [PMID: 37657511 PMCID: PMC10502354 DOI: 10.1016/j.virusres.2023.199214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
The current outbreak of coronavirus disease 2019 (COVID-19) is a global emergency, as its rapid spread and high mortality rate, which poses a significant threat to public health. Innate immunity plays a crucial role in the primary defense against infections, and recent studies have highlighted the pivotal regulatory function of long non-coding RNAs (lncRNAs) in innate immune responses. This study aims to assess the circulating levels of lncRNAs namely ANRIL, THRIL, NEAT1, and MALAT1 in the blood of moderate and severe SARS-CoV-2 infected patients, in comparison to healthy individuals. Additionally, it aims to explore the potential of these lncRNAs as biomarkers for determining the severity of the disease. The blood samples were collected from a total of 38 moderate and 25 severe COVID-19 patients, along with 30 healthy controls. The total RNA was extracted and qPCR was performed to evaluate the blood levels of the lncRNAs. The results indicate significantly higher expression levels of lncRNAs ANRIL and THRIL in severe patients when compared to moderate patients (P value = 0.0307, P value = 0.0059, respectively). Moreover, the expression levels of lncRNAs ANRIL and THRIL were significantly up-regulated in both moderate and severe patients in comparison to the control group (P value < 0.001, P value < 0.001, P value = 0.001, P value < 0.001, respectively). The expression levels of lncRNA NEAT1 were found to be significantly higher in both moderate and severe COVID-19 patients compared to the healthy group (P value < 0.001, P value < 0.001, respectively), and there was no significant difference in the expression levels of NEAT1 between moderate and severe patients (P value = 0.6979). The expression levels of MALAT1 in moderate and severe patients did not exhibit a significant difference compared to the control group (P value = 0.677, P value = 0.764, respectively). Furthermore, the discriminative power of ANRIL and THRIL was significantly higher in the severe patient group than the moderate group (Area under curve (AUC) = 0.6879; P-value = 0.0122, AUC = 0.6947; P-value = 0.0093, respectively). In conclusion, the expression levels of the lncRNAs ANRIL and THRIL are correlated with the severity of COVID-19 and can be regarded as circulating biomarkers for disease progression.
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Affiliation(s)
- Zeynab Rahni
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Seyed Masoud Hosseini
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahsa Saeedi Niasar
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahrzad Shoraka
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamed Mirjalali
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rostami-Nejad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Habib Malekpour
- Research and Development Center, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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11
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Su CF, Das D, Muhammad Aslam M, Xie JQ, Li XY, Chen MX. Eukaryotic splicing machinery in the plant-virus battleground. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1793. [PMID: 37198737 DOI: 10.1002/wrna.1793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/24/2023] [Accepted: 04/19/2023] [Indexed: 05/19/2023]
Abstract
Plant virual infections are mainly caused by plant-virus parasitism which affects ecological communities. Some viruses are highly pathogen specific that can infect only specific plants, while some can cause widespread harm, such as tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV). After a virus infects the host, undergoes a series of harmful effects, including the destruction of host cell membrane receptors, changes in cell membrane components, cell fusion, and the production of neoantigens on the cell surface. Therefore, competition between the host and the virus arises. The virus starts gaining control of critical cellular functions of the host cells and ultimately affects the fate of the targeted host plants. Among these critical cellular processes, alternative splicing (AS) is an essential posttranscriptional regulation process in RNA maturation, which amplify host protein diversity and manipulates transcript abundance in response to plant pathogens. AS is widespread in nearly all human genes and critical in regulating animal-virus interactions. In particular, an animal virus can hijack the host splicing machinery to re-organize its compartments for propagation. Changes in AS are known to cause human disease, and various AS events have been reported to regulate tissue specificity, development, tumour proliferation, and multi-functionality. However, the mechanisms underlying plant-virus interactions are poorly understood. Here, we summarize the current understanding of how viruses interact with their plant hosts compared with humans, analyze currently used and putative candidate agrochemicals to treat plant-viral infections, and finally discussed the potential research hotspots in the future. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Chang-Feng Su
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
| | - Mehtab Muhammad Aslam
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ji-Qin Xie
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
| | - Xiang-Yang Li
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Mo-Xian Chen
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
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12
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Thatai AKS, Ammankallu S, Devasahayam Arokia Balaya R, Soman SP, Nisar M, Babu S, John L, George A, Anto CK, Sanjeev D, Kandiyil MK, Raj SS, Awasthi K, Vinodchandra SS, Prasad TSK, Raju R. VirhostlncR: A comprehensive database to explore lncRNAs and their targets in viral infections. Comput Biol Med 2023; 164:107279. [PMID: 37572440 DOI: 10.1016/j.compbiomed.2023.107279] [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: 11/25/2022] [Revised: 07/11/2023] [Accepted: 07/16/2023] [Indexed: 08/14/2023]
Abstract
Long non-coding-RNAs (lncRNAs) are an expanding set of cis-/trans-regulatory RNA genes that outnumber the protein-coding genes. Although being increasingly discovered, the functional role of the majority of lncRNAs in diverse biological conditions is undefined. Increasing evidence supports the critical role of lncRNAs in the emergence, regulation, and progression of various viral infections including influenza, hepatitis, coronavirus, and human immunodeficiency virus. Hence, the identification of signature lncRNAs would facilitate focused analysis of their functional roles accounting for their targets and regulatory mechanisms associated with infections. Towards this, we compiled 2803 lncRNAs identified to be modulated by 33 viral strains in various mammalian cell types and are provided through the resource named VirhostlncR (http://ciods.in/VirhostlncR/). The information on each of the viral strains, their multiplicity of infection, duration of infection, host cell name and cell types, fold change of lncRNA expression, and their specific identification methods are integrated into VirhostlncR. Based on the current datasets, we report 150 lncRNAs including differentiation antagonizing non-protein coding RNA (DANCR), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), maternally expressed gene 3 (MEG3), nuclear paraspeckle assembly transcript 1 (NEAT1), and plasmacytoma variant translocation 1 (PVT1) to be perturbed by two or more viruses. Analysis of viral protein interactions with human transcription factors (TFs) or TF-containing protein complexes identified that distinct viruses can transcriptionally regulate many of these lncRNAs through multiple protein complexes. Together, we believe that the current dataset will enable priority selection of lncRNAs for identification of their targets and serve as an effective platform for the analysis of noncoding RNA-mediated regulations in viral infections.
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Affiliation(s)
- Arun Kumar Sumaithangi Thatai
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Shruthi Ammankallu
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Rex Devasahayam Arokia Balaya
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Sreelakshmi Pathappillil Soman
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India; Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Mahammad Nisar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Sreeranjini Babu
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India; Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Anju George
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Christy Kallely Anto
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Diya Sanjeev
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India.
| | - Mrudula Kinarulla Kandiyil
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Sini S Raj
- Department of Computer Science, University of Kerala, Thiruvananthapuram, 695 581, Kerala, India.
| | - Kriti Awasthi
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - S S Vinodchandra
- Department of Computer Science, University of Kerala, Thiruvananthapuram, 695 581, Kerala, India.
| | - Thottethodi Subrahmanya Keshava Prasad
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India; Omics Analytics Pvt. Ltd., Yenepoya Incubator, Deralakatte, Mangalore, 575 018, Karnataka, India.
| | - Rajesh Raju
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575 018, Karnataka, India; Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Manjanade, Mangalore, 575 018, Karnataka, India; Omics Analytics Pvt. Ltd., Yenepoya Incubator, Deralakatte, Mangalore, 575 018, Karnataka, India.
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13
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Feng Y, Yang M, Fan Z, Zhao W, Kim P, Zhou X. COVIDanno, COVID-19 annotation in human. Front Microbiol 2023; 14:1129103. [PMID: 37497545 PMCID: PMC10366449 DOI: 10.3389/fmicb.2023.1129103] [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: 12/21/2022] [Accepted: 06/26/2023] [Indexed: 07/28/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 19 (COVID-19), has caused a global health crisis. Despite ongoing efforts to treat patients, there is no universal prevention or cure available. One of the feasible approaches will be identifying the key genes from SARS-CoV-2-infected cells. SARS-CoV-2-infected in vitro model, allows easy control of the experimental conditions, obtaining reproducible results, and monitoring of infection progression. Currently, accumulating RNA-seq data from SARS-CoV-2 in vitro models urgently needs systematic translation and interpretation. To fill this gap, we built COVIDanno, COVID-19 annotation in humans, available at http://biomedbdc.wchscu.cn/COVIDanno/. The aim of this resource is to provide a reference resource of intensive functional annotations of differentially expressed genes (DEGs) among different time points of COVID-19 infection in human in vitro models. To do this, we performed differential expression analysis for 136 individual datasets across 13 tissue types. In total, we identified 4,935 DEGs. We performed multiple bioinformatics/computational biology studies for these DEGs. Furthermore, we developed a novel tool to help users predict the status of SARS-CoV-2 infection for a given sample. COVIDanno will be a valuable resource for identifying SARS-CoV-2-related genes and understanding their potential functional roles in different time points and multiple tissue types.
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Affiliation(s)
- Yuzhou Feng
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
- Med-X Center for Informatics, Sichuan University, Chengdu, China
| | - Mengyuan Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhiwei Fan
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States
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14
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Li R, Gao S, Chen H, Zhang X, Yang X, Zhao J, Wang Z. Virus usurps alternative splicing to clear the decks for infection. Virol J 2023; 20:131. [PMID: 37340420 DOI: 10.1186/s12985-023-02098-9] [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: 04/03/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023] Open
Abstract
Since invasion, there will be a tug-of-war between host and virus to scramble cellular resources, for either restraining or facilitating infection. Alternative splicing (AS) is a conserved and critical mechanism of processing pre-mRNA into mRNAs to increase protein diversity in eukaryotes. Notably, this kind of post-transcriptional regulatory mechanism has gained appreciation since it is widely involved in virus infection. Here, we highlight the important roles of AS in regulating viral protein expression and how virus in turn hijacks AS to antagonize host immune response. This review will widen the understandings of host-virus interactions, be meaningful to innovatively elucidate viral pathogenesis, and provide novel targets for developing antiviral drugs in the future.
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Affiliation(s)
- Ruixue Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Shenyan Gao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Huayuan Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Xiaozhan Zhang
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, People's Republic of China
| | - Xia Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Jun Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Zeng Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China.
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15
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Zhang L, Liang R, Raheem A, Liang L, Zhang X, Cui S. Transcriptomics analysis reveals key lncRNAs and genes related to the infection of feline kidney cell line by panleukopenia virus. Res Vet Sci 2023; 158:203-214. [PMID: 37031469 DOI: 10.1016/j.rvsc.2023.03.027] [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: 09/05/2022] [Revised: 03/16/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023]
Abstract
Feline panleukopenia virus (FPV) can cause a viral disease and is responsible for severe leukopenia, gastroenteritis, and nervous signs with significant economic losses. Biochemically long non-coding RNAs (lncRNAs) can regulate the expression of mRNA in different ways, thereby causing the functional changes in host cells in response to viral infection. However, no attention has been paid until now to investigate the link between FPV pathogenesis and lncRNA. Here, through RNA sequencing, we performed a comprehensive analysis of lncRNA and mRNA in F81 cells after FPV-BJ04 strain infection. Consistent with previous studies, our data showed that lncRNAs have distinct features from mRNA. A total of 291 lncRNAs and 873 mRNAs were differentially expressed in F81 cells after FPV-BJ04 infection. GO and KEGG enrichment analysis showed that the differentially upregulated lncRNAs target genes were mainly involved in the positive regulation of transcription by RNA polymerase II and MAPK signaling pathway. The differentially downregulated lncRNAs target genes were mainly involved in the mRNA splicing and endocytosis. In addition, the differentially expressed immune pathway related genes that are targeted by lncRNA were also screened out to construct a lncRNA-miRNA-mRNA axes as a potential novel biomarkers in regulating the immune response of feline against FPV infection. Our results contribute to understand the basic role of lncRNA in F81 cells during FPV infection and lay the foundation for following research.
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Affiliation(s)
- Lingling Zhang
- Institute of Microbe and Host Health, Linyi University, Linyi, Shandong 276000, China.
| | - Ruiying Liang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing 100193, China
| | - Abdul Raheem
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing 100193, China
| | - Lin Liang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing 100193, China
| | - Xinglin Zhang
- Institute of Microbe and Host Health, Linyi University, Linyi, Shandong 276000, China
| | - Shangjin Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing 100193, China.
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16
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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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17
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Sotcheff SL, Chen JYC, Elrod N, Cao J, Jaworski E, Kuyumcu-Martinez MN, Shi PY, Routh AL. Zika Virus Infection Alters Gene Expression and Poly-Adenylation Patterns in Placental Cells. Pathogens 2022; 11:pathogens11080936. [PMID: 36015056 PMCID: PMC9414685 DOI: 10.3390/pathogens11080936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 11/25/2022] Open
Abstract
Flaviviruses are small RNA viruses that are mainly transmitted via arthropod vectors and are found in tropic and sub-tropical regions. Most infections are asymptomatic (90-95%), but symptoms can be as severe as hemorrhagic fever and encephalitis. One recently emerged flavivirus is Zika virus (ZIKV), which was originally isolated from rhesus monkeys in Uganda roughly 70 years ago but has recently spread east, reaching S. America in 2015-2016. This outbreak was associated with the development of Guillain-Barré syndrome in adults and microcephaly in infants born to expectant mothers infected early in pregnancy. ZIKV must traverse the placenta to impact the development of the fetus, but the mechanisms responsible are unknown. While flaviviruses are known to disrupt splicing patterns in host cells, little is known about how flaviviruses such as ZIKV impact the alternative polyadenylation (APA) of host transcripts. This is important as APA is well-established as a mechanism in the regulation of mRNA metabolism and translation. Thus, we sought to characterize transcriptomic changes including APA in human placental (JEG3) cells in response to ZIKV infection using Poly(A)-ClickSeq (PAC-Seq). We used our differential Poly(A)-cluster (DPAC) analysis pipeline to characterize changes in differential gene expression, alternative poly-adenylation (APA) and the use of alternative terminal exons. We identified 98 upregulated genes and 28 downregulated genes. Pathway enrichment analysis indicated that many RNA processing and immune pathways were upregulated in ZIKV-infected JEG3 cells. We also updated DPAC to provide additional metrics of APA including the percentage-distal usage index (PDUI), which revealed that APA was extensive and the 3' UTRs of 229 genes were lengthened while 269 were shortened. We further found that there were 214 upregulated and 59 downregulated poly(A)-clusters (PACs). We extracted the nucleotide sequences surrounding these PACs and found that the canonical signals for poly-adenylation (binding site for poly-A binding protein (PABP) upstream and a GU-rich region down-stream of the PAC) were only enriched in the downregulated PACs. These results indicate that ZIKV infection makes JEG3 cells more permissive to non-canonical poly-adenylation signals.
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Affiliation(s)
- Stephanea L. Sotcheff
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - John Yun-Chung Chen
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Nathan Elrod
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jun Cao
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Elizabeth Jaworski
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mugé N. Kuyumcu-Martinez
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Pei-Yong Shi
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Andrew L. Routh
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
- Correspondence:
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18
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Huang Y, Su Y, Shen L, Huo Z, Chen C, Sun T, Tian X, Li N, Yang C. A novel IFNbeta-induced long non-coding RNA ZAP-IT1 interrupts Zika virus replication in A549 cells. Virol Sin 2022; 37:904-912. [PMID: 35985476 PMCID: PMC9797370 DOI: 10.1016/j.virs.2022.08.003] [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] [Received: 12/29/2021] [Accepted: 08/09/2022] [Indexed: 01/01/2023] Open
Abstract
Zika virus (ZIKV) infection can cause severe neurological diseases including neonatal microcephaly and Guillain-Barre syndrome. Long noncoding RNAs (lncRNAs) are the by-products of the transcription process, which are considered to affect viral infection. However, it remains largely unexplored whether host lncRNAs play a role in ZIKV infection. Here, we identified a group of human lncRNAs that were up-regulated upon ZIKV infection and were dependent on the type I interferon (IFN) signaling. Overexpression of lncRNA ZAP-IT1 leads to an impairment of ZIKV infection. Correspondently, deficiency of ZAP-IT1 led to an enhancement of ZIKV infection. We further confirmed that ZAP-IT1, an intronic lncRNA with total 551 nt in length, is mainly located in the nuclear upon ZIKV infection. Knockout of ZAP-IT1 also led to the increase of dengue virus (DENV), Japanese encephalitis virus (JEV), or vesicular stomatitis virus (VSV) infection. Mechanically, we found that the antiviral effect of ZAP-IT1 was independent of the type I IFN signaling pathway. Therefore, our data unveiled that host lncRNA ZAP-IT1 induced by the type I IFN signaling, showed robust restriction on ZIKV infection, and even on DENV, JEV, and VSV infection, which may benefit the development of antiviral therapeutics.
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Affiliation(s)
- Yanxia Huang
- Department of Neurosurgery, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yu Su
- Department of Neurosurgery, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Li Shen
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Zhiting Huo
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Cancan Chen
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Tao Sun
- Department of Neurosurgery, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xu Tian
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Ning Li
- Department of Neurosurgery, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Chao Yang
- Department of Neurosurgery, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China,Corresponding author.
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19
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The Isolation and Full-Length Transcriptome Sequencing of a Novel Nidovirus and Response of Its Infection in Japanese Flounder (Paralichthys olivaceus). Viruses 2022; 14:v14061216. [PMID: 35746687 PMCID: PMC9230003 DOI: 10.3390/v14061216] [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: 04/29/2022] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 02/01/2023] Open
Abstract
A novel nidovirus, CSBV Bces-Po19, was isolated from the marine fish, Japanese flounder (Paralichthys olivaceus). The viral genome was 26,597 nucleotides long and shared 98.62% nucleotide identity with CSBV WHQSR4345. PacBio Sequel and Illumina sequencing were used to perform full-length transcriptome sequencing on CSBV Bces-Po19-sensitive (S) and -resistant (R) Japanese flounder. The results of negative staining revealed bacilliform and spherical virions. There were in total 1444 different genes between CSBV Bces-Po19 S and R groups, with 935 being up-regulated and 513 being down-regulated. Metabolism-, immune-, and RNA-related pathways were significantly enriched. Furthermore, CSBV Bces-Po19 infection induced alternative splicing (AS) events in Japanese flounder; the S group had a higher numbers of AS events (12,352) than the R group (11,452). The number of long non-coding RNA (lncRNA) in the S group, on the other hand, was significantly lower than in the R group. In addition to providing valuable information that sheds more light on CSBV Bces-Po19 infection, these research findings provide further clues for CSBV Bces-Po19 prevention and treatment.
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20
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Lin S, Zhang SL, Yin HT, Zhao ZM, Chen ZK, Shen MM, Zhang ZD, Guo XJ, Wu P. Cellular Lnc_209997 suppresses Bombyx mori nucleopolyhedrovirus replication by targeting miR-275-5p in B. mori. INSECT MOLECULAR BIOLOGY 2022; 31:308-316. [PMID: 35060217 DOI: 10.1111/imb.12760] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/07/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Long non-coding RNA (lncRNA) is a type of non-coding RNA molecule, which exceeds 200 nucleotides in length and participates in the regulation of a variety of life activities. Recent studies showed that lncRNAs play important roles in viral infection and host immunity. At present, the researches on insect lncRNAs are relatively few. In this study, we found the expression of Lnc_209997 was significantly down-regulated in silkworm fat body infected with Bombyx mori nucleopolyhedrosis virus (BmNPV). Inhibition of Lnc_209997 promoted BmNPV replication. Enhancing the expression of Lnc_209997 inhibited the proliferation of BmNPV. miR-275-5p was up-regulated in silkworm fat body infected with BmNPV. Dual luciferase reporter gene system confirmed the interaction between Lnc_209997 and miR-275-5p. Over-expression of Lnc_209997 inhibited the expression of miR-275-5p, while inhibition of Lnc_209997 enhanced the expression of miR-275-5p. Further, over-expression of miR-275-5p can facilitate the replication of BmNPV. These results suggested that BmNPV could increase the expression of miR-275-5p by inhibiting cellular Lnc_209997 expression to promote their own proliferation. Our results are helpful for better understanding the role of lncRNAs in BmNPV infection, and provide insights into elucidating the molecular mechanism of interaction between Bombyx mori and virus.
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Affiliation(s)
- Su Lin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Shao Lun Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Hao Tong Yin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Zhi Meng Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Zi Kang Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Man Man Shen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Zheng Dong Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Xi Jie Guo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Ping Wu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
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21
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Wang C, Chen L, Chen Y, Jia W, Cai X, Liu Y, Ji F, Xiong P, Liang A, Liu R, Guan Y, Cheng Z, Weng Y, Wang W, Duan Y, Kuang D, Xu S, Cai H, Xia Q, Yang D, Wang MW, Yang X, Zhang J, Cheng C, Liu L, Liu Z, Liang R, Wang G, Li Z, Xia H, Xia T. Abnormal global alternative RNA splicing in COVID-19 patients. PLoS Genet 2022; 18:e1010137. [PMID: 35421082 PMCID: PMC9089920 DOI: 10.1371/journal.pgen.1010137] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 05/10/2022] [Accepted: 03/08/2022] [Indexed: 12/25/2022] Open
Abstract
Viral infections can alter host transcriptomes by manipulating host splicing machinery. Despite intensive transcriptomic studies on SARS-CoV-2, a systematic analysis of alternative splicing (AS) in severe COVID-19 patients remains largely elusive. Here we integrated proteomic and transcriptomic sequencing data to study AS changes in COVID-19 patients. We discovered that RNA splicing is among the major down-regulated proteomic signatures in COVID-19 patients. The transcriptome analysis showed that SARS-CoV-2 infection induces widespread dysregulation of transcript usage and expression, affecting blood coagulation, neutrophil activation, and cytokine production. Notably, CD74 and LRRFIP1 had increased skipping of an exon in COVID-19 patients that disrupts a functional domain, which correlated with reduced antiviral immunity. Furthermore, the dysregulation of transcripts was strongly correlated with clinical severity of COVID-19, and splice-variants may contribute to unexpected therapeutic activity. In summary, our data highlight that a better understanding of the AS landscape may aid in COVID-19 diagnosis and therapy.
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Affiliation(s)
- Changli Wang
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lijun Chen
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaobin Chen
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Wenwen Jia
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xunhui Cai
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Yufeng Liu
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Fenghu Ji
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Xiong
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Anyi Liang
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Ren Liu
- Department of Research and Development, Hugobiotech Co. Ltd., Beijing, China
| | - Yuanlin Guan
- Department of Research and Development, Hugobiotech Co. Ltd., Beijing, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, China
| | - Yejing Weng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, China
| | - Weixin Wang
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, China
| | - Yaqi Duan
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Dong Kuang
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Sanpeng Xu
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Hanghang Cai
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Qin Xia
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dehua Yang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ming-Wei Wang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiangping Yang
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Liang Liu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhongmin Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ren Liang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guopin Wang
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | | | - Han Xia
- Department of Research and Development, Hugobiotech Co. Ltd., Beijing, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
| | - Tian Xia
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
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22
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Schuler-Faccini L, Del Campo M, García-Alix A, Ventura LO, Boquett JA, van der Linden V, Pessoa A, van der Linden Júnior H, Ventura CV, Leal MC, Kowalski TW, Rodrigues Gerzson L, Skilhan de Almeida C, Santi L, Beys-da-Silva WO, Quincozes-Santos A, Guimarães JA, Garcez PP, Gomes JDA, Vianna FSL, Anjos da Silva A, Fraga LR, Vieira Sanseverino MT, Muotri AR, Lopes da Rosa R, Abeche AM, Marcolongo-Pereira C, Souza DO. Neurodevelopment in Children Exposed to Zika in utero: Clinical and Molecular Aspects. Front Genet 2022; 13:758715. [PMID: 35350244 PMCID: PMC8957982 DOI: 10.3389/fgene.2022.758715] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 01/27/2022] [Indexed: 12/15/2022] Open
Abstract
Five years after the identification of Zika virus as a human teratogen, we reviewed the early clinical manifestations, collectively called congenital Zika syndrome (CZS). Children with CZS have a very poor prognosis with extremely low performance in motor, cognitive, and language development domains, and practically all feature severe forms of cerebral palsy. However, these manifestations are the tip of the iceberg, with some children presenting milder forms of deficits. Additionally, neurodevelopment can be in the normal range in the majority of the non-microcephalic children born without brain or eye abnormalities. Vertical transmission and the resulting disruption in development of the brain are much less frequent when maternal infection occurs in the second half of the pregnancy. Experimental studies have alerted to the possibility of other behavioral outcomes both in prenatally infected children and in postnatal and adult infections. Cofactors play a vital role in the development of CZS and involve genetic, environmental, nutritional, and social determinants leading to the asymmetric distribution of cases. Some of these social variables also limit access to multidisciplinary professional treatment.
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Affiliation(s)
- Lavínia Schuler-Faccini
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | - Miguel Del Campo
- Department of Pediatrics, School of Medicine, University of California San Diego, and Rady Children's Hospital San Diego, San Diego, CA, United States
| | | | - Liana O Ventura
- Department of Ophthalmology, Fundação Altino Ventura, FAV, Recife, Brazil
| | | | | | - André Pessoa
- Hospital Infantil Albert Sabin, Fortaleza, Brazil.,Universidade Estadual do Ceará, Fortaleza, Brazil
| | | | - Camila V Ventura
- Department of Ophthalmology, Fundação Altino Ventura, FAV, Recife, Brazil
| | | | - Thayne Woycinck Kowalski
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,CESUCA-Centro Universitário, Cachoeirinha, Brazil
| | | | | | - Lucélia Santi
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | - Walter O Beys-da-Silva
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | | | - Jorge A Guimarães
- Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | | | | | - Fernanda Sales Luiz Vianna
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | - André Anjos da Silva
- School of Medicine, Graduate Program in Medical Sciences-Universidade do Vale do Taquari-UNIVATES, Lajeado, Brazil.,School of Medicine, Universidade do Vale do Rio dos Sinos-UNISINOS, São Leopoldo, Brazil
| | - Lucas Rosa Fraga
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | - Maria Teresa Vieira Sanseverino
- Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Alysson R Muotri
- Department of Pediatrics, School of Medicine, University of California San Diego, and Rady Children's Hospital San Diego, San Diego, CA, United States
| | | | - Alberto Mantovani Abeche
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | | | - Diogo O Souza
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil
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23
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White LA, Bisom TC, Grimes HL, Hayashi M, Lanchy JM, Lodmell JS. Tra2beta-Dependent Regulation of RIO Kinase 3 Splicing During Rift Valley Fever Virus Infection Underscores the Links Between Alternative Splicing and Innate Antiviral Immunity. Front Cell Infect Microbiol 2022; 11:799024. [PMID: 35127560 PMCID: PMC8807687 DOI: 10.3389/fcimb.2021.799024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022] Open
Abstract
Rift Valley fever virus (RVFV) is an emerging pathogen that has potential to cause severe disease in humans and domestic livestock. Propagation of RVFV strain MP-12 is negatively impacted by the actions of RIOK3, a protein involved in the cellular immune response to viral infection. During RVFV infection, RIOK3 mRNA is alternatively spliced to produce an isoform that correlates with the inhibition of interferon β signaling. Here, we identify splicing factor TRA2-β (also known as TRA2beta and hTRA2-β) as a key regulator governing the relative abundance of RIOK3 splicing isoforms. Using RT-PCR and minigenes, we determined that TRA2-β interaction with RIOK3 pre-mRNA was necessary for constitutive splicing of RIOK3 mRNA, and conversely, lack of TRA2-β engagement led to increased alternative splicing. Expression of TRA2-β was found to be necessary for RIOK3's antiviral effect against RVFV. Intriguingly, TRA2-β mRNA is also alternatively spliced during RVFV infection, leading to a decrease in cellular TRA2-β protein levels. These results suggest that splicing modulation serves as an immune evasion strategy by RVFV and/or is a cellular mechanism to prevent excessive immune response. Furthermore, the results suggest that TRA2-β can act as a key regulator of additional steps of the innate immune response to viral infection.
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Affiliation(s)
- Luke Adam White
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Thomas C. Bisom
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, United States
| | - Hunter L. Grimes
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Miyuki Hayashi
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, United States
| | - Jean-Marc Lanchy
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - J. Stephen Lodmell
- Division of Biological Sciences, University of Montana, Missoula, MT, United States,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, United States,*Correspondence: J. Stephen Lodmell,
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24
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Ren G, Xu L, Zhao J, Shao Y, Lu T, Zhang Q. Comparative transcriptome analysis of long non coding RNA (lncRNA) in RTG-2 cells infected by infectious hematopoietic necrosis virus. FISH & SHELLFISH IMMUNOLOGY 2022; 120:314-324. [PMID: 34890776 DOI: 10.1016/j.fsi.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/09/2021] [Accepted: 12/05/2021] [Indexed: 06/13/2023]
Abstract
Infectious hematopoietic necrosis virus (IHNV) is the vital pathogen that has caused the great economic loss in salmonid fisheries. To date, there is limited information concerning the changes of lncRNAs in RTG-2 cells infected by IHNV. In this study, a comparative transcriptome analysis of lncRNAs was performed in RTG-2 cells with and without IHNV infection to determine their changes and the effects on IHNV infection. The results showed that IHNV infection significantly changed the expression levels of lncRNAs and mRNAs, including 3693 differentially expressed lncRNAs (DE-lncRNAs) and 3503 differentially expressed mRNAs (DE-mRNAs) respectively. These DE-lncRNAs and DE-mRNAs induced by IHNV were mostly associated with immune response, RNA processing, and viral diseases related pathways. Further analysis found that some DE-lncRNAs might participate in the regulation of extracellular matrix metabolism, apoptosis, lipid synthesis, autophagy, and immune responses referring to the functions of their target genes. Afterwards, 349 co-expression relationships were constructed by 223 DE-lncRNAs and 271 DE-mRNAs, of which LTCONS_00146935 was the pivotal node in the interaction networks, and was together with its target genes modulated the immune responses under the IHNV infection. RT-qPCR results showed that the changes of the selected immune-related DEGs were in consistent with the RNA-seq data, suggesting that the sequencing data was relatively reliable. In summary, this is the first study to determine the changes and interactions of lncRNA-mRNA in RTG-2 cells under the IHNV infection. The results provided the valuable information concerning the lncRNAs in salmonid fish, which will benefit for future study on uncovering the roles of lncRNAs-mRNAs during the viral infection.
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Affiliation(s)
- Guangming Ren
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Liming Xu
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China
| | - Jingzhuang Zhao
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China
| | - Yizhi Shao
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China
| | - Tongyan Lu
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.
| | - Qiya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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25
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Integrative RNA profiling of TBEV-infected neurons and astrocytes reveals potential pathogenic effectors. Comput Struct Biotechnol J 2022; 20:2759-2777. [PMID: 35685361 PMCID: PMC9167876 DOI: 10.1016/j.csbj.2022.05.052] [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: 02/13/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 12/30/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV), the most medically relevant tick-transmitted flavivirus in Eurasia, targets the host central nervous system and frequently causes severe encephalitis. The severity of TBEV-induced neuropathogenesis is highly cell-type specific and the exact mechanism responsible for such differences has not been fully described yet. Thus, we performed a comprehensive analysis of alterations in host poly-(A)/miRNA/lncRNA expression upon TBEV infection in vitro in human primary neurons (high cytopathic effect) and astrocytes (low cytopathic effect). Infection with severe but not mild TBEV strain resulted in a high neuronal death rate. In comparison, infection with either of TBEV strains in human astrocytes did not. Differential expression and splicing analyses with an in silico prediction of miRNA/mRNA/lncRNA/vd-sRNA networks found significant changes in inflammatory and immune response pathways, nervous system development and regulation of mitosis in TBEV Hypr-infected neurons. Candidate mechanisms responsible for the aforementioned phenomena include specific regulation of host mRNA levels via differentially expressed miRNAs/lncRNAs or vd-sRNAs mimicking endogenous miRNAs and virus-driven modulation of host pre-mRNA splicing. We suggest that these factors are responsible for the observed differences in the virulence manifestation of both TBEV strains in different cell lines. This work brings the first complex overview of alterations in the transcriptome of human astrocytes and neurons during the infection by two TBEV strains of different virulence. The resulting data could serve as a starting point for further studies dealing with the mechanism of TBEV-host interactions and the related processes of TBEV pathogenesis.
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26
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Liu W, Sun Y, Qiu X, Meng C, Song C, Tan L, Liao Y, Liu X, Ding C. Genome-Wide Analysis of Alternative Splicing during Host-Virus Interactions in Chicken. Viruses 2021; 13:v13122409. [PMID: 34960678 PMCID: PMC8703359 DOI: 10.3390/v13122409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
The chicken is a model animal for the study of evolution, immunity and development. In addition to their use as a model organism, chickens also represent an important agricultural product. Pathogen invasion has already been shown to modulate the expression of hundreds of genes, but the role of alternative splicing in avian virus infection remains unclear. We used RNA-seq data to analyze virus-induced changes in the alternative splicing of Gallus gallus, and found that a large number of alternative splicing events were induced by virus infection both in vivo and in vitro. Virus-responsive alternative splicing events preferentially occurred in genes involved in metabolism and transport. Many of the alternatively spliced transcripts were also expressed from genes with a function relating to splicing or immune response, suggesting a potential impact of virus infection on pre-mRNA splicing and immune gene regulation. Moreover, exon skipping was the most frequent AS event in chickens during virus infection. This is the first report describing a genome-wide analysis of alternative splicing in chicken and contributes to the genomic resources available for studying host-virus interaction in this species. Our analysis fills an important knowledge gap in understanding the extent of genome-wide alternative splicing dynamics occurring during avian virus infection and provides the impetus for the further exploration of AS in chicken defense signaling and homeostasis.
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Affiliation(s)
- Weiwei Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Yingjie Sun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Xusheng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Chunchun Meng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Cuiping Song
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Lei Tan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Ying Liao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Xiufan Liu
- School of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Chan Ding
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-21-3429-3441
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27
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Alternative splicing landscape of small brown planthopper and different response of JNK2 isoforms to rice stripe virus infection. J Virol 2021; 96:e0171521. [PMID: 34757837 DOI: 10.1128/jvi.01715-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alternative splicing (AS) is a frequent posttranscriptional regulatory event occurring in response to various endogenous and exogenous stimuli in most eukaryotic organisms. However, little is known about the effects of insect-transmitted viruses on AS events in insect vectors. The present study used third-generation sequencing technology and RNA sequencing (RNA-Seq) to evaluate the AS response in the small brown planthopper Laodelphax striatellus to rice stripe virus (RSV). The full-length transcriptome of L. striatellus was obtained using single-molecule real-time sequencing technology (SMRT). Posttranscriptional regulatory events, including AS, alternative polyadenylation, and fusion transcripts, were analyzed. A total of 28,175 nonredundant transcript isoforms included 24,950 transcripts assigned to 8,500 annotated genes of L. striatellus, and 5,000 of these genes (58.8%) had AS events. RNA-Seq of the gut samples of insects infected by RSV for 8 d identified 3,458 differentially expressed transcripts (DETs); 2,185 of these DETs were transcribed from 1,568 genes that had AS events, indicating that 31.4% of alternatively spliced genes responded to RSV infection of the gut. One of the c-Jun N-terminal kinase (JNK) genes, JNK2, experienced exon skipping, resulting in three transcript isoforms. These three isoforms differentially responded to RSV infection during development and in various organs. Injection of double-stranded RNAs targeting all or two isoforms indicated that three or at least two JNK2 isoforms facilitated RSV accumulation in planthoppers. These results implied that AS events could participate in the regulation of complex relationships between viruses and insect vectors. Importance Alternative splicing (AS) is a regulatory mechanism that occurs after gene transcription. AS events can enrich protein diversity to promote the reactions of the organisms to various endogenous and exogenous stimulations. It is not known how insect vectors exploit AS events to cope with transmitted viruses. The present study used third-generation sequencing technology to obtain the profile of AS events in the small brown planthopper Laodelphax striatellus, which is an efficient vector for rice stripe virus (RSV). The results indicated that 31.4% of alternatively spliced genes responded to RSV infection in the gut of planthoppers. One of the c-Jun N-terminal kinase (JNK) genes, JNK2, produced three transcript isoforms by AS. These three isoforms showed different responses to RSV infection, and at least two isoforms facilitated viral accumulation in planthoppers. These results implied that AS events could participate in the regulation of complex relationships between viruses and insect vectors.
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Yan JM, Zhang WK, Li F, Zhou CM, Yu XJ. Integrated transcriptome profiling in THP-1 macrophages infected with bunyavirus SFTSV. Virus Res 2021; 306:198594. [PMID: 34637813 DOI: 10.1016/j.virusres.2021.198594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 09/10/2021] [Accepted: 10/06/2021] [Indexed: 10/20/2022]
Abstract
Severe fever with thrombocytopenia syndrome virus (SFTSV) is a tick-borne bunyavirus that causes an emerging hemorrhagic fever termed SFTS with high mortality. However, knowledge of SFTSV-host interactions is largely limited. Here, we performed a global transcriptome analysis of mRNAs and lncRNAs in THP-1 macrophages infected with SFTSV for 24 and 48 h. A total of 2,334 differentially expressed mRNAs and 154 differentially expressed lncRNAs were identified with 577 mRNAs and 31 lncRNAs commonly changed at both time points. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that differentially expressed mRNAs were mainly associated with innate immune, cytokine signaling, systemic lupus erythematosus, and alcoholism. Differentially expressed lncRNAs were enriched in systemic lupus erythematosus, alcoholism, and ribosome. Bioinformatic analysis also revealed hub regulatory mRNAs including IL6, TNF, UBA52, SRC, IL10, CXCL10, and CDK1 and core regulatory lncRNAs including XLOC_083027 and XLOC_113317. Transcription factor analysis of the differentially expressed mRNAs revealed that IRF1, SPI1, SPIB, ELF5, and FEV were enriched during SFTSV infection. Taken together, our studies illustrate the complex interaction between THP-1 macrophages and SFTSV.
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Affiliation(s)
- Jia-Min Yan
- State Key Laboratory of Virology, School of Health Sciences, Wuhan University, Wuhan, 430071, China
| | - Wen-Kang Zhang
- State Key Laboratory of Virology, School of Health Sciences, Wuhan University, Wuhan, 430071, China
| | - Fei Li
- School of Public Health, Shandong University, Jinan, Shandong 250012, China
| | - Chuan-Min Zhou
- State Key Laboratory of Virology, School of Health Sciences, Wuhan University, Wuhan, 430071, China; Zhongnan hospital of Wuhan University, Wuhan, 430071, China.
| | - Xue-Jie Yu
- State Key Laboratory of Virology, School of Health Sciences, Wuhan University, Wuhan, 430071, China.
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Bhagat R, Kaur G, Seth P. Molecular mechanisms of zika virus pathogenesis: An update. Indian J Med Res 2021; 154:433-445. [PMID: 35345069 PMCID: PMC9131805 DOI: 10.4103/ijmr.ijmr_169_20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Indexed: 01/04/2023] Open
Abstract
Zika virus (ZIKV), member of the family Flaviviridae belonging to genus Flavivirus, is an arthropod-borne virus. The ZIKV is known to cause severe congenital birth defects in neonates. Due to a large number of worldwide outbreaks and associated neurological complications with ZIKV, a public health emergency was declared by the World Health Organization on February 1, 2016. The virus exhibits neurotropism and has a specific propensity towards neural precursor cells of the developing brain. In utero ZIKV infection causes massive cell death in the developing brain resulting in various motor and cognitive disabilities in newborns. The virus modulates cell machinery at several levels to replicate itself and inhibits toll like receptors-3 signalling, deregulates microRNA circuitry and induces a chronic inflammatory response in affected cells. Several significant advances have been made to understand the mechanisms of neuropathogenesis, its prevention and treatment. The current review provides an update on cellular and molecular mechanisms of ZIKV-induced alterations in the function of various brain cells.
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Affiliation(s)
- Reshma Bhagat
- Department of Cellular & Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, India
- Department of Genetics, Washington University in Saint Louis, Missouri, United States of America
| | - Guneet Kaur
- Department of Cellular & Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, India
| | - Pankaj Seth
- Department of Cellular & Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, India
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Wang Y, Huo Z, Lin Q, Lin Y, Chen C, Huang Y, Huang C, Zhang J, He J, Liu C, Zhang P. Positive Feedback Loop of Long Noncoding RNA OASL-IT1 and Innate Immune Response Restricts the Replication of Zika Virus in Epithelial A549 Cells. J Innate Immun 2021; 13:179-193. [PMID: 33626545 PMCID: PMC8138224 DOI: 10.1159/000513606] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022] Open
Abstract
Expression of host noncoding RNAs and coding mRNAs is significantly altered by viral infection. In the current study, we screened the transcriptional profile of human lung epithelial A549 cells infected with Zika virus (ZIKV) by microarray assay. Seventy-nine long noncoding RNAs (lncRNAs) and 140 mRNAs were differentially expressed (DE). The bioinformatics analysis revealed that the mRNAs adjacent to the DE lncRNAs were closely related to the host responses to viral infection. We selected 7 lncRNAs from the top 50 hits for validation. The quantitative real-time PCR data confirmed that expression of selected lncRNAs was induced by ZIKV infection. Moreover, the expression of 7 lncRNAs was induced by infection of dengue virus, Japanese encephalitis virus, or vesicular stomatitis virus, or by treatment of poly(I:C) and IFN-β. Furthermore, loss of innate immune adaptor IPS-1 or receptor IFNAR1 resulted in lower induction levels of several lncRNAs by ZIKV. Overexpression of 3 lncRNAs (RPL27-OT1, OASL-IT1, and REC8-OT3) reduced the virus yields of ZIKV. Knockout of OASL-IT1 significantly enhanced ZIKV replication. In OASL-IT1 knockout cells, the levels of interferons (IFNs) and the activation of 3 innate immune signaling pathways triggered by ZIKV were dramatically reduced. Collectively, our work found a positive feedback loop in the IFN system, in which IFNs and OASL-IT1 regulate each other, thereby promoting establishment of antiviral defense.
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Affiliation(s)
- Yi Wang
- Key Laboratory of Tropical Disease Control, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhiting Huo
- Key Laboratory of Tropical Disease Control, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Quanshi Lin
- Key Laboratory of Tropical Disease Control, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuxia Lin
- Key Laboratory of Tropical Disease Control, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Cancan Chen
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanxia Huang
- Key Laboratory of Tropical Disease Control, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Changbai Huang
- Key Laboratory of Tropical Disease Control, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Junsong Zhang
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Junfang He
- Key Laboratory of Tropical Disease Control, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chao Liu
- Key Laboratory of Tropical Disease Control, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ping Zhang
- Key Laboratory of Tropical Disease Control, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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31
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Thompson MG, Dittmar M, Mallory MJ, Bhat P, Ferretti MB, Fontoura BM, Cherry S, Lynch KW. Viral-induced alternative splicing of host genes promotes influenza replication. eLife 2020; 9:55500. [PMID: 33269701 PMCID: PMC7735754 DOI: 10.7554/elife.55500] [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: 01/27/2020] [Accepted: 12/02/2020] [Indexed: 12/17/2022] Open
Abstract
Viral infection induces the expression of numerous host genes that impact the outcome of infection. Here, we show that infection of human lung epithelial cells with influenza A virus (IAV) also induces a broad program of alternative splicing of host genes. Although these splicing-regulated genes are not enriched for canonical regulators of viral infection, we find that many of these genes do impact replication of IAV. Moreover, in several cases, specific inhibition of the IAV-induced splicing pattern also attenuates viral infection. We further show that approximately a quarter of the IAV-induced splicing events are regulated by hnRNP K, a host protein required for efficient splicing of the IAV M transcript in nuclear speckles. Finally, we find an increase in hnRNP K in nuclear speckles upon IAV infection, which may alter accessibility of hnRNP K for host transcripts thereby leading to a program of host splicing changes that promote IAV replication.
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Affiliation(s)
- Matthew G Thompson
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, United States
| | - Mark Dittmar
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Michael J Mallory
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, United States
| | - Prasanna Bhat
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, United States
| | - Max B Ferretti
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, United States.,Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Beatriz Ma Fontoura
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, United States
| | - Sara Cherry
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, United States.,Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Kristen W Lynch
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, United States
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Ashraf U, Benoit-Pilven C, Navratil V, Ligneau C, Fournier G, Munier S, Sismeiro O, Coppée JY, Lacroix V, Naffakh N. Influenza virus infection induces widespread alterations of host cell splicing. NAR Genom Bioinform 2020; 2:lqaa095. [PMID: 33575639 PMCID: PMC7680258 DOI: 10.1093/nargab/lqaa095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/24/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022] Open
Abstract
Influenza A viruses (IAVs) use diverse mechanisms to interfere with cellular gene expression. Although many RNA-seq studies have documented IAV-induced changes in host mRNA abundance, few were designed to allow an accurate quantification of changes in host mRNA splicing. Here, we show that IAV infection of human lung cells induces widespread alterations of cellular splicing, with an overall increase in exon inclusion and decrease in intron retention. Over half of the mRNAs that show differential splicing undergo no significant changes in abundance or in their 3' end termination site, suggesting that IAVs can specifically manipulate cellular splicing. Among a randomly selected subset of 21 IAV-sensitive alternative splicing events, most are specific to IAV infection as they are not observed upon infection with VSV, induction of interferon expression or induction of an osmotic stress. Finally, the analysis of splicing changes in RED-depleted cells reveals a limited but significant overlap with the splicing changes in IAV-infected cells. This observation suggests that hijacking of RED by IAVs to promote splicing of the abundant viral NS1 mRNAs could partially divert RED from its target mRNAs. All our RNA-seq datasets and analyses are made accessible for browsing through a user-friendly Shiny interface (http://virhostnet.prabi.fr:3838/shinyapps/flu-splicing or https://github.com/cbenoitp/flu-splicing).
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Affiliation(s)
- Usama Ashraf
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 75013 Paris, France
| | - Clara Benoit-Pilven
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR5292, 69675 Bron, France
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Lyon 1, 69622 Villeurbanne, France
- EPI ERABLE, INRIA Grenoble Rhône-Alpes, 38330 Montbonnot-Saint-Martin France
| | - Vincent Navratil
- PRABI, Rhône-Alpes Bioinformatics Center, Université Lyon 1, 69622 Villeurbanne, France
- European Virus Bioinformatics Center, 07743 Jena, Germany
- Institut Français de Bioinformatique, IFB-core, UMS 3601, 91057 Évry, France
| | - Cécile Ligneau
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
| | - Guillaume Fournier
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
| | - Sandie Munier
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
| | - Odile Sismeiro
- Institut Pasteur, Pôle BIOMICS, Plateforme Transcriptome et Epigenome, 75015 Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Pôle BIOMICS, Plateforme Transcriptome et Epigenome, 75015 Paris, France
| | - Vincent Lacroix
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Lyon 1, 69622 Villeurbanne, France
- EPI ERABLE, INRIA Grenoble Rhône-Alpes, 38330 Montbonnot-Saint-Martin France
| | - Nadia Naffakh
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
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Ram DR, Kroll K, Reeves RK. Skipped Over: Tuning Natural Killer Cells Toward HIV Through Alternative Splicing. AIDS Res Hum Retroviruses 2020; 36:969-972. [PMID: 32862656 PMCID: PMC7703092 DOI: 10.1089/aid.2020.0116] [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] [Indexed: 11/12/2022] Open
Abstract
Natural killer (NK) cells provide some of the earliest immune responses to infection, but when viruses manipulate or perturb the immune environment to alter NK cell function, this places the host at a disadvantage. Indeed, others and we observe that in the context of HIV/simian immunodeficiency virus (SIV) infection, although NK cells are not infected, they can become dysfunctional over time. Several studies have characterized protein and transcriptional profiles of NK cells during HIV/SIV infection, but none have examined whether the production of alternative transcripts and corresponding isoforms is modulated. This phenomenon occurs broadly in normal biology and in other disease states, and could provide a novel avenue of investigation that may yield better targets to restore or augment NK cell responses to HIV/SIV. Herein, we briefly summarize published and new data that may provide a perspective on how to target NK cell splice variants.
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Affiliation(s)
- Daniel R. Ram
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Kyle Kroll
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - R. Keith Reeves
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, Massachusetts, USA
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Affiliation(s)
- Lucy Ginn
- Transcriptional Networks in Lung Cancer Group Cancer Research UK Manchester Institute University of Manchester Manchester UK
- Cancer Research UK Lung Cancer Centre of Excellence At Manchester and University College London England UK
| | - Manuela La Montagna
- Transcriptional Networks in Lung Cancer Group Cancer Research UK Manchester Institute University of Manchester Manchester UK
- Cancer Research UK Lung Cancer Centre of Excellence At Manchester and University College London England UK
| | - Qinghua Wu
- College of Life Science Yangtze University Jingzhou Hubei China
- Department of Chemistry Faculty of Science University of Hradec Kralove Hradec Kralove East Bohemia Czech Republic
| | - Lei Shi
- Transcriptional Networks in Lung Cancer Group Cancer Research UK Manchester Institute University of Manchester Manchester UK
- Cancer Research UK Lung Cancer Centre of Excellence At Manchester and University College London England UK
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35
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Leblanc S, Brunet MA. Modelling of pathogen-host systems using deeper ORF annotations and transcriptomics to inform proteomics analyses. Comput Struct Biotechnol J 2020; 18:2836-2850. [PMID: 33133425 PMCID: PMC7585943 DOI: 10.1016/j.csbj.2020.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 01/08/2023] Open
Abstract
The Zika virus is a flavivirus that can cause fulminant outbreaks and lead to Guillain-Barré syndrome, microcephaly and fetal demise. Like other flaviviruses, the Zika virus is transmitted by mosquitoes and provokes neurological disorders. Despite its risk to public health, no antiviral nor vaccine are currently available. In the recent years, several studies have set to identify human host proteins interacting with Zika viral proteins to better understand its pathogenicity. Yet these studies used standard human protein sequence databases. Such databases rely on genome annotations, which enforce a minimal open reading frame (ORF) length criterion. An ever-increasing number of studies have demonstrated the shortcomings of such annotation, which overlooks thousands of functional ORFs. Here we show that the use of a customized database including currently non-annotated proteins led to the identification of 4 alternative proteins as interactors of the viral capsid and NS4A proteins. Furthermore, 12 alternative proteins were identified in the proteome profiling of Zika infected monocytes, one of which was significantly up-regulated. This study presents a computational framework for the re-analysis of proteomics datasets to better investigate the viral-host protein interplays upon infection with the Zika virus.
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Key Words
- AP-MS, affinity-purification mass spectrometry
- Alternative ORFs
- DEP, differentially expressed proteins
- FDR, false discovery rate
- FPKM, fragments per kilobase of exon model per million reads mapped
- Flavivirus
- HCIP, highly confident interacting proteins
- HCMV, human cytomegalovirus
- LFQ, label free quantification
- MS, mass spectrometry
- ORF, open reading frame
- PSM, peptide spectrum match
- Protein network
- Proteogenomics
- Proteome profiling
- ZIKV, Zika virus
- Zika
- altProt, alternative protein
- ncRNA, non-coding RNA
- sORF, small open reading frame
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Affiliation(s)
- Sebastien Leblanc
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
| | - Marie A. Brunet
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
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Li D, Su M, Sun PP, Guo WP, Wang CY, Wang JL, Wang H, Zhang Q, Du LY, Xie GC. Global profiling of the alternative splicing landscape reveals transcriptomic diversity during the early phase of enterovirus 71 infection. Virology 2020; 548:213-225. [PMID: 32763492 DOI: 10.1016/j.virol.2020.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/17/2020] [Accepted: 06/17/2020] [Indexed: 02/04/2023]
Abstract
The alteration of host cell splicing is a major strategy favouring viral replication; however, the interaction between human tonsillar epithelial cells (HTECs) and enterovirus 71 (EV71) has not been fully elucidated. Here, a total of 201 differentially expressed genes (DEGs) and 3266 novel genes with coding potential were identified. A total of 3479 skipped exons (SEs), 515 alternative 3' splice sites (A3SSs), 391 alternative 5' splice sites (A5SSs), 531 mutually exclusive exons (MXEs) and 825 retained introns (RIs) were identified as significantly altered alternative splicing (AS) events. The enriched DEGs were mainly related to the cell cycle, spliceosome, and Toll-like receptor (TLR) signalling pathways. Finally, the replication of EV71 was significantly inhibited by TLR2 heterodimers. Our findings suggest that AS events induced by EV71 increase the transcriptomic diversity of HTECs in response to EV71 infection. Additionally, TLR2 heterodimers have the potential to protect HTECs against EV71.
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Affiliation(s)
- Dan Li
- Department of Pathogenic Biology, Chengde Medical University, Chengde, 067000, China
| | - Meng Su
- Department of Pathogenic Biology, Chengde Medical University, Chengde, 067000, China
| | - Ping-Ping Sun
- Department of Pathogenic Biology, Chengde Medical University, Chengde, 067000, China
| | - Wen-Ping Guo
- Department of Pathogenic Biology, Chengde Medical University, Chengde, 067000, China
| | - Chun-Yang Wang
- Clinical Medical College, Xi'an Medical University, Xi'an, 710021, China
| | - Jiang-Li Wang
- Department of Microbiology Laboratory, Chengde Center for Disease Control and Prevention, Chengde, 067000, China
| | - Hong Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Qing Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Luan-Ying Du
- Department of Pathogenic Biology, Chengde Medical University, Chengde, 067000, China
| | - Guang-Cheng Xie
- Department of Pathogenic Biology, Chengde Medical University, Chengde, 067000, China.
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Asian Zika Virus Isolate Significantly Changes the Transcriptional Profile and Alternative RNA Splicing Events in a Neuroblastoma Cell Line. Viruses 2020; 12:v12050510. [PMID: 32380717 PMCID: PMC7290316 DOI: 10.3390/v12050510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/27/2020] [Indexed: 12/18/2022] Open
Abstract
The alternative splicing of pre-mRNAs expands a single genetic blueprint to encode multiple, functionally diverse protein isoforms. Viruses have previously been shown to interact with, depend on, and alter host splicing machinery. The consequences, however, incited by viral infection on the global alternative slicing (AS) landscape are under-appreciated. Here, we investigated the transcriptional and alternative splicing profile of neuronal cells infected with a contemporary Puerto Rican Zika virus (ZIKVPR) isolate, an isolate of the prototypical Ugandan ZIKV (ZIKVMR), and dengue virus 2 (DENV2). Our analyses revealed that ZIKVPR induced significantly more differential changes in expressed genes compared to ZIKVMR or DENV2, despite all three viruses showing equivalent infectivity and viral RNA levels. Consistent with the transcriptional profile, ZIKVPR induced a higher number of alternative splicing events compared to ZIKVMR or DENV2, and gene ontology analyses highlighted alternative splicing changes in genes associated with mRNA splicing. In summary, we show that ZIKV affects cellular RNA homeostasis not only at the transcriptional levels but also through the alternative splicing of cellular transcripts. These findings could provide new molecular insights into the neuropathologies associated with this virus.
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38
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Teixeira FME, Pietrobon AJ, Oliveira LDM, Oliveira LMDS, Sato MN. Maternal-Fetal Interplay in Zika Virus Infection and Adverse Perinatal Outcomes. Front Immunol 2020; 11:175. [PMID: 32117303 PMCID: PMC7033814 DOI: 10.3389/fimmu.2020.00175] [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] [Received: 09/20/2019] [Accepted: 01/22/2020] [Indexed: 12/26/2022] Open
Abstract
During pregnancy, the organization of complex tolerance mechanisms occurs to assure non-rejection of the semiallogeneic fetus. Pregnancy is a period of vulnerability to some viral infections, mainly during the first and second trimesters, that may cause congenital damage to the fetus. Recently, Zika virus (ZIKV) infection has gained great notoriety due to the occurrence of congenital ZIKV syndrome, characterized by fetal microcephaly, which results from the ability of ZIKV to infect placental cells and neural precursors in the fetus. Importantly, in addition to the congenital effects, studies have shown that perinatal ZIKV infection causes a number of disorders, including maculopapular rash, conjunctivitis, and arthralgia. In this paper, we contextualize the immunological aspects involved in the maternal-fetal interface and vulnerability to ZIKV infection, especially the alterations resulting in perinatal outcomes. This highlights the need to develop protective maternal vaccine strategies or interventions that are capable of preventing fetal or even neonatal infection.
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Affiliation(s)
- Franciane Mouradian Emidio Teixeira
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, School of Medicine and Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil.,Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Anna Julia Pietrobon
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, School of Medicine and Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil.,Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Luana de Mendonça Oliveira
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, School of Medicine and Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil.,Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Luanda Mara da Silva Oliveira
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, School of Medicine and Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Maria Notomi Sato
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, School of Medicine and Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil.,Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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39
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Global Analysis of Alternative Splicing Difference in Peripheral Immune Organs between Tongcheng Pigs and Large White Pigs Artificially Infected with PRRSV In Vivo. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4045204. [PMID: 32083129 PMCID: PMC7011390 DOI: 10.1155/2020/4045204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/13/2019] [Indexed: 11/17/2022]
Abstract
Alternative splicing (AS) plays a significant role in regulating gene expression at the transcriptional level in eukaryotes. Flexibility and diversity of transcriptome and proteome can be significantly increased through alternative splicing of genes. In the present study, transcriptome data of peripheral immune organs including spleen and inguinal lymph nodes (ILN) were used to identify AS difference between PRRSV-resistant Tongcheng (TC) pigs and PRRSV-susceptible Large White (LW) pigs artificially infected with porcine reproductive and respiratory syndrome virus (PRRSV) in vivo. The results showed that PRRSV infection induced global alternative splicing events (ASEs) with different modes. Among them, 373 genes and 595 genes in the spleen and ILN of TC pigs, while 458 genes and 560 genes in the spleen and ILN of LW pigs had significantly differential ASEs. Alternative splicing was subject to tissue-specific and lineage-specific regulation in response to PRRSV infection. Enriched GO terms and pathways showed that genes with differential ASEs played important roles in transcriptional regulation, immune response, metabolism, and apoptosis. Furthermore, a splicing factor associated with apoptosis, SRSF4, was significantly upregulated in LW pigs. Functional analysis on apoptosis associated genes was validated by RT-PCR and DNA sequencing. These findings revealed different response to PRRSV between PRRSV-resistant TC pigs and PRRSV-susceptible LW pigs at the level of alternative splicing, suggesting the potential relationship between AS and disease resistance to PRRSV.
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40
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Michalski D, Ontiveros JG, Russo J, Charley PA, Anderson JR, Heck AM, Geiss BJ, Wilusz J. Zika virus noncoding sfRNAs sequester multiple host-derived RNA-binding proteins and modulate mRNA decay and splicing during infection. J Biol Chem 2019; 294:16282-16296. [PMID: 31519749 DOI: 10.1074/jbc.ra119.009129] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/19/2019] [Indexed: 12/17/2022] Open
Abstract
Insect-borne flaviviruses produce a 300-500-base long noncoding RNA, termed subgenomic flavivirus RNA (sfRNA), by stalling the cellular 5'-3'-exoribonuclease 1 (XRN1) via structures located in their 3' UTRs. In this study, we demonstrate that sfRNA production by Zika virus represses XRN1 analogous to what we have previously shown for other flaviviruses. Using protein-RNA reconstitution and a stringent RNA pulldown assay with human choriocarcinoma (JAR) cells, we demonstrate that the sfRNAs from both dengue type 2 and Zika viruses interact with a common set of 21 RNA-binding proteins that contribute to the regulation of post-transcriptional processes in the cell, including splicing, RNA stability, and translation. We found that four of these sfRNA-interacting host proteins, DEAD-box helicase 6 (DDX6) and enhancer of mRNA decapping 3 (EDC3) (two RNA decay factors), phosphorylated adaptor for RNA export (a regulator of the biogenesis of the splicing machinery), and apolipoprotein B mRNA-editing enzyme catalytic subunit 3C (APOBEC3C, a nucleic acid-editing deaminase), inherently restrict Zika virus infection. Furthermore, we demonstrate that the regulations of cellular mRNA decay and RNA splicing are compromised by Zika virus infection as well as by sfRNA alone. Collectively, these results reveal the large extent to which Zika virus-derived sfRNAs interact with cellular RNA-binding proteins and highlight the potential for widespread dysregulation of post-transcriptional control that likely limits the effective response of these cells to viral infection.
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Affiliation(s)
- Daniel Michalski
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - J Gustavo Ontiveros
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80523
| | - Joseph Russo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Phillida A Charley
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - John R Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Adam M Heck
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80523
| | - Brian J Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80523
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523 .,Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80523
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41
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Rosa RL, Santi L, Berger M, Tureta EF, Quincozes-Santos A, Souza DO, Guimarães JA, Beys-da-Silva WO. ZIKAVID-Zika virus infection database: a new platform to analyze the molecular impact of Zika virus infection. J Neurovirol 2019; 26:77-83. [PMID: 31512145 DOI: 10.1007/s13365-019-00799-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/06/2019] [Accepted: 08/22/2019] [Indexed: 12/11/2022]
Abstract
The recent outbreak of Zika virus (ZIKV) in Brazil and other countries globally demonstrated the relevance of ZIKV studies. During and after this outbreak, there was an intense increase in scientific production on ZIKV infections, especially toward alterations promoted by the infection and related to clinical outcomes. Considering this massive amount of new data, mainly thousands of genes and proteins whose expression is impacted by ZIKV infection, the ZIKA Virus Infection Database (ZIKAVID) was created. ZIKAVID is an online database that comprises all genes or proteins, and associated information, for which expression was experimentally measured and found to be altered after ZIKV infection. The database, available at https://zikavid.org, contains 16,984 entries of gene expression measurements from a total of 7348 genes. It allows users to easily perform searches for different experimental hosts (cell lines, tissues, and animal models), ZIKV strains (African, Asian, and Brazilian), and target molecules (messenger RNA [mRNA] and protein), among others, used in differential expression studies regarding ZIKV infection. In this way, the ZIKAVID will serve as an additional and important resource to improve the characterization of the molecular impact and pathogenesis associated with ZIKV infection.
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Affiliation(s)
- Rafael L Rosa
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752 suit 709, Porto Alegre, RS, Brazil.,Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Lucélia Santi
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752 suit 709, Porto Alegre, RS, Brazil.,Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Markus Berger
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Emanuela F Tureta
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752 suit 709, Porto Alegre, RS, Brazil
| | - André Quincozes-Santos
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Diogo O Souza
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jorge A Guimarães
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Walter O Beys-da-Silva
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752 suit 709, Porto Alegre, RS, Brazil. .,Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.
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42
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Dang JW, Tiwari SK, Qin Y, Rana TM. Genome-wide Integrative Analysis of Zika-Virus-Infected Neuronal Stem Cells Reveals Roles for MicroRNAs in Cell Cycle and Stemness. Cell Rep 2019; 27:3618-3628.e5. [PMID: 31216479 PMCID: PMC6687627 DOI: 10.1016/j.celrep.2019.05.059] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 01/16/2019] [Accepted: 05/16/2019] [Indexed: 12/11/2022] Open
Abstract
Zika virus (ZIKV) infection is implicated in severe fetal developmental disorders, including microcephaly. MicroRNAs (miRNAs) post-transcriptionally regulate numerous processes associated with viral infection and neurodegeneration, but their contribution to ZIKV pathogenesis is unclear. We analyzed the mRNA and miRNA transcriptomes of human neuronal stem cells (hNSCs) during infection with ZIKV MR766 and Paraiba strains. Integration of the miRNA and mRNA expression data into regulatory interaction networks showed that ZIKV infection resulted in miRNA-mediated repression of genes regulating the cell cycle, stem cell maintenance, and neurogenesis. Bioinformatics analysis of Argonaute-bound RNAs in ZIKV-infected hNSCs identified a number of miRNAs with predicted involvement in microcephaly, including miR-124-3p, which dysregulates NSC maintenance through repression of the transferrin receptor (TFRC). Consistent with this, ZIKV infection upregulated miR-124-3p and downregulated TFRC mRNA in ZIKV-infected hNSCs and mouse brain tissue. These data provide insights into the roles of miRNAs in ZIKV pathogenesis, particularly the microcephaly phenotype.
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Affiliation(s)
- Jason W Dang
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA; Division of Genetics, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, MC 0412, La Jolla, CA 92093, USA
| | - Shashi Kant Tiwari
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA; Division of Genetics, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA
| | - Yue Qin
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA; Division of Genetics, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology, University of California, San Diego, 9500 Gilman Drive, MC 0419, La Jolla, CA 92093, USA
| | - Tariq M Rana
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA; Division of Genetics, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA; Program in Immunology, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA.
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43
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Xu D, Li C, Qin CF, Xu Z. Update on the Animal Models and Underlying Mechanisms for ZIKV-Induced Microcephaly. Annu Rev Virol 2019; 6:459-479. [PMID: 31206355 DOI: 10.1146/annurev-virology-092818-015740] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The circulation of Zika virus (ZIKV) in nearly 80 countries and territories poses a significant global threat to public health. ZIKV is causally linked to severe developmental defects in the brain, recognized as congenital Zika syndrome (CZS), which includes microcephaly and other serious congenital neurological complications. Since the World Health Organization declared the ZIKV outbreak a public health emergency of international concern, remarkable progress has been made in the generation of different ZIKV infection animal models to gain insight into cellular targets and pathogenesis and to explore the associated underlying mechanisms. Here we focus on summarizing our current understanding of the effects of ZIKV on mammalian brain development in different developmental stages and discuss the potential underlying mechanisms of ZIKV-induced CZS, as well as future perspectives.
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Affiliation(s)
- Dan Xu
- College of Biological Science and Engineering, Institute of Life Sciences, Fuzhou University, Fuzhou 350108, China;
| | - Cui Li
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Cheng-Feng Qin
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China;
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; .,Parkinson's Disease Center, Beijing Institute for Brain Disorders, Beijing 100069, China
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44
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Nithiyanantham SF, Badawi A. Maternal infection with Zika virus and prevalence of congenital disorders in infants: systematic review and meta-analysis. Canadian Journal of Public Health 2019; 110:638-648. [PMID: 31077071 DOI: 10.17269/s41997-019-00215-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/04/2019] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Zika virus (ZIKV) infection is a vector-borne disease that can be transmitted sexually and vertically. The vertical transmission of the virus may lead to congenital Zika syndrome in infants. The aim of this study is to conduct a systematic review and meta-analysis of published reports documenting the prevalence of congenital Zika-related disorders in infants of mothers infected with ZIKV during pregnancy. METHODS We conducted a comprehensive search in Ovid MEDLINE, Ovid MEDLINE (R) Epub ahead of print, Embase, Embase Classic and Web of Science databases to identify human studies reporting prevalence of congenital disorders in infants of ZIKV-infected mothers. RESULTS We identified 25 reports selected for inclusion in the current study (n = 4683 subjects). The majority of the studies were from South American high-risk countries. Only one third of the identified studies were conducted in the United States. Clinical maternal symptoms included maculopapular rash (76.9%), arthralgia (46.4%), fever (45.5%) and headache (31.8%) with myalgia and conjunctivitis only presented in 25% of the cases. The most prevalent congenital disorder in the newborns was brain calcifications (42.6; 95% CI, 30.8-54.4), followed by ventriculomegaly (21.8; 95% CI, 15.2-28.4), joint abnormalities (13.2; 95% CI, 9.4-18.2), ocular abnormalities (4.2; 95% CI, 1.0-7.5) and microcephaly (3.9; 95% CI, 2.4-5.4). CONCLUSION The current study highlights the high prevalence of a range of congenital disorders in newborns of mothers infected with ZIKV. It warrants developing studies to further clarify the mechanisms by which each of these disorders occurs in response to the viral infection during pregnancy and its vertical transmission to the infants.
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Affiliation(s)
| | - Alaa Badawi
- Public Health Risk Sciences Division, Public Health Agency of Canada, 180 Queen Street West, Rm 8-15, Toronto, ON, M5V 3L7, Canada. .,Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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45
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Boudreault S, Roy P, Lemay G, Bisaillon M. Viral modulation of cellular RNA alternative splicing: A new key player in virus-host interactions? WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1543. [PMID: 31034770 PMCID: PMC6767064 DOI: 10.1002/wrna.1543] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 12/26/2022]
Abstract
Upon viral infection, a tug of war is triggered between host cells and viruses to maintain/gain control of vital cellular functions, the result of which will ultimately dictate the fate of the host cell. Among these essential cellular functions, alternative splicing (AS) is an important RNA maturation step that allows exons, or parts of exons, and introns to be retained in mature transcripts, thereby expanding proteome diversity and function. AS is widespread in higher eukaryotes, as it is estimated that nearly all genes in humans are alternatively spliced. Recent evidence has shown that upon infection by numerous viruses, the AS landscape of host‐cells is affected. In this review, we summarize recent advances in our understanding of how virus infection impacts the AS of cellular transcripts. We also present various molecular mechanisms allowing viruses to modulate cellular AS. Finally, the functional consequences of these changes in the RNA splicing signatures during virus–host interactions are discussed. This article is categorized under:RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing
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Affiliation(s)
- Simon Boudreault
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Patricia Roy
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Guy Lemay
- Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada
| | - Martin Bisaillon
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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46
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Liu S, Liu X, Li J, Zhou H, Carr MJ, Zhang Z, Shi W. Long noncoding RNAs: Novel regulators of virus-host interactions. Rev Med Virol 2019; 29:e2046. [PMID: 31016795 PMCID: PMC7169114 DOI: 10.1002/rmv.2046] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/16/2022]
Abstract
Long noncoding RNAs (lncRNAs) represent a key class of cellular regulators, involved in the modulation and control of multiple biological processes. Distinct classes of lncRNAs are now known to be induced by host cytokines following viral infections. Current evidence demonstrates that lncRNAs play essential roles at the host‐pathogen interface regulating viral infections by either innate immune responses at various levels including activation of pathogen recognition receptors or by epigenetic, transcriptional, and posttranscriptional effects. We review the newly described mechanisms underlying the interactions between lncRNAs, cytokines, and metabolites differentially expressed following viral infections; we highlight the regulatory networks of host antiviral responses and emphasize the need for interdisciplinary research between lncRNA biology and immunology to deepen understanding of viral pathogenesis.
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Affiliation(s)
- Shaoqiong Liu
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong Province, Taishan Medical University, Taian, China
| | - Xia Liu
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong Province, Taishan Medical University, Taian, China
| | - Juan Li
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong Province, Taishan Medical University, Taian, China
| | - Hong Zhou
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong Province, Taishan Medical University, Taian, China
| | - Michael J Carr
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan.,National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Zhenjie Zhang
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong Province, Taishan Medical University, Taian, China
| | - Weifeng Shi
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong Province, Taishan Medical University, Taian, China
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47
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Chauhan K, Kalam H, Dutt R, Kumar D. RNA Splicing: A New Paradigm in Host-Pathogen Interactions. J Mol Biol 2019; 431:1565-1575. [PMID: 30857970 DOI: 10.1016/j.jmb.2019.03.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 02/26/2019] [Accepted: 03/02/2019] [Indexed: 12/21/2022]
Abstract
RNA splicing brings diversity to the eukaryotic proteome. Different spliced variants of a gene may differ in their structure, function, localization, and stability influencing protein stoichiometry and physiological outcomes. Alternate spliced variants of different genes are known to associate with various chronic pathologies including cancer. Emerging evidence suggests precise regulation of splicing as fundamental to normal well-being. In this context, infection-induced alternative splicing has emerged as a new pivot of host function, which pathogenic microbes can alter-directly or indirectly-to tweak the host immune responses against the pathogen. The implications of these findings are vast, and although not explored much in the case of pathogenic infections, we present here examples from splicing mediated regulation of immune responses across a variety of conditions and explore how this fascinating finding brings a new paradigm to host-pathogen interactions.
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Affiliation(s)
- Komal Chauhan
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Haroon Kalam
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ravi Dutt
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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48
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Boudreault S, Armero VES, Scott MS, Perreault JP, Bisaillon M. The Epstein-Barr virus EBNA1 protein modulates the alternative splicing of cellular genes. Virol J 2019; 16:29. [PMID: 30832682 PMCID: PMC6399920 DOI: 10.1186/s12985-019-1137-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/25/2019] [Indexed: 12/13/2022] Open
Abstract
Background Alternative splicing (AS) is an important mRNA maturation step that allows increased variability and diversity of proteins in eukaryotes. AS is dysregulated in numerous diseases, and its implication in the carcinogenic process is well known. However, progress in understanding how oncogenic viruses modulate splicing, and how this modulation is involved in viral oncogenicity has been limited. Epstein-Barr virus (EBV) is involved in various cancers, and its EBNA1 oncoprotein is the only viral protein expressed in all EBV malignancies. Methods In the present study, the ability of EBNA1 to modulate the AS of cellular genes was assessed using a high-throughput RT-PCR approach to examine AS in 1238 cancer-associated genes. RNA immunoprecipitation coupled to RNA sequencing (RIP-Seq) assays were also performed to identify cellular mRNAs bound by EBNA1. Results Upon EBNA1 expression, we detected modifications to the AS profiles of 89 genes involved in cancer. Moreover, we show that EBNA1 modulates the expression levels of various splicing factors such as hnRNPA1, FOX-2, and SF1. Finally, RNA immunoprecipitation coupled to RIP-Seq assays demonstrate that EBNA1 immunoprecipitates specific cellular mRNAs, but not the ones that are spliced differently in EBNA1-expressing cells. Conclusion The EBNA1 protein can modulate the AS profiles of numerous cellular genes. Interestingly, this modulation protein does not require the RNA binding activity of EBNA1. Overall, these findings underline the novel role of EBNA1 as a cellular splicing modulator. Electronic supplementary material The online version of this article (10.1186/s12985-019-1137-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simon Boudreault
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Victoria E S Armero
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Jean-Pierre Perreault
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Martin Bisaillon
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada.
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49
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Enhanced single-cell viability using 30Kc6 for efficient expansion of human induced pluripotent stem cells. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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50
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Hu B, Huo Y, Yang L, Chen G, Luo M, Yang J, Zhou J. Correction to: ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells. Virol J 2019; 16:17. [PMID: 30717754 PMCID: PMC6360699 DOI: 10.1186/s12985-019-1122-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 01/21/2019] [Indexed: 11/10/2022] Open
Abstract
In the original publication of this article [1], two grants from National Science Foundation of China and Yunnan Provincial Government (U1602226) and by National Science Foundation of China (2016YFC1200404) were omitted in the 'Funding' section. The correct 'Funding' section is below.
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Affiliation(s)
- Benxia Hu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Yongxia Huo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, China
| | - Liping Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, China
| | - Guijun Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, China
| | - Minhua Luo
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of Virology, Wuhan, 430071, China
| | - Jinlong Yang
- BGI-Yunnan, BGI-Shenzhen, Kunming, 650000, China.,College of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Jumin Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, China.
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