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Chen M, Kang L, Zhang T, Zheng J, Chen D, Shao D, Li Z, Li B, Wei J, Qiu Y, Feng X, Ma Z, Liu K. Circular RNA network plays a potential antiviral role in the early stage of JEV infection in mouse brain. Front Microbiol 2024; 14:1165378. [PMID: 38249464 PMCID: PMC10797004 DOI: 10.3389/fmicb.2023.1165378] [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: 02/14/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Japanese encephalitis is one of the most important insect-borne infectious disease with public health concern. The virus can break the blood-brain barrier and cause death or long-term sequela in infected humans or animals. Viral encephalitis is an important clinical feature of JEV infection. In recent studies, CircRNAs and related ceRNAs data illustrated the regulative role in many aspects of biological process and disease duration. It is believed that CircRNA regulates JEV infection in a ceRNA-dependent mechanism. In this study, brain tissues of experimental mice were sequenced and analysised. 61 differentially expressed circRNAs, 172 differentially expressed miRNAs and 706 differentially expressed mRNAs were identified by RNA-Sequencing and statistical analysis. CX3CR1 was determined as a key host factor impact JEV infection by microRNA interference measurement. CX3CR1 interaction network indicated circStrbp/miR709/CX3CR1 as a functional regulation axis. Further sequencing in BV2 cell shown CX3CR1 is a special target of miR-709 only during JEV infection. In summary, our study presented a new ceRNA pathway that impact JEV infection in vivo and in vitro, which could be a therapeutic target to fight against JEV.
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Affiliation(s)
- Mengli Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
- Key Laboratory of Animal Disease Diagnostic and Immunology, Department of Veterinary Medicine College, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Lei Kang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
- Key Laboratory of Animal Disease Diagnostic and Immunology, Department of Veterinary Medicine College, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Tong Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Jiayang Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Dishi Chen
- Sichuan Animal Disease Prevention and Control Center, Chengdu, China
| | - Donghua Shao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Zongjie Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Xiuli Feng
- Key Laboratory of Animal Disease Diagnostic and Immunology, Department of Veterinary Medicine College, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
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Fan L, Ren J, Wang Y, Chen Y, Chen Y, Chen L, Lin Q, Liao M, Ding C, Xiang B, Ren T. Circular RNAs are associated with the resistance to Newcastle disease virus infection in duck cells. Front Vet Sci 2023; 10:1181916. [PMID: 37841466 PMCID: PMC10570413 DOI: 10.3389/fvets.2023.1181916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/18/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction Newcastle disease virus (NDV) is prevalent worldwide with an extensive host range. Among birds infected with velogenic NDV strains, chickens experience high pathogenicity and mortality, whereas ducks mostly experience mild symptoms or are asymptomatic. Ducks have a unique, innate immune system hypothesized to induce antiviral responses. Circular RNAs (circRNAs) are among the most abundant and conserved eukaryotic transcripts. These participate in innate immunity and host antiviral response progression. Methods In this study, circRNA expression profile differences post-NDV infection in duck embryo fibroblast (DEF) cells were analyzed using circRNA transcriptome sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to reveal significant enrichment of differentially expressed (DE) circRNAs. The circRNA-miRNA-mRNA interaction networks were used to predict the related functions of circRNAs. Moreover, circ-FBXW7 was selected to determine its effect on NDV infection in DEFs. Results NDV infection altered circRNA expression profiles in DEF cells, and 57 significantly differentially expressed circRNAs were identified post-NDV infection. DEF responded to NDV by forming circRNAs to regulate apoptosis-, cell growth-, and protein degradation-related pathways via GO and KEGG enrichment analyses. circRNA-miRNA-mRNA interaction networks demonstrated that DEF cells combat NDV infection by regulating cellular pathways or apoptosis through circRNA-targeted mRNAs and miRNAs. circ-FBXW7 overexpression and knockdown inhibited and promoted viral replication, respectively. DEF cells mainly regulated cell cycle alterations or altered cellular sensing to combat NDV infection. Conclusion These results demonstrate that DEF cells exert antiviral responses by forming circRNAs, providing novel insights into waterfowl antiviral responses.
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Affiliation(s)
- Lei Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Jinlian Ren
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Yinchu Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Yiyi Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Yichun Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Libin Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Qiuyan Lin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Ming Liao
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chan Ding
- Shanghai Veterinary Research Institute (SHVRI), Chinese Academy of Agricultural Sciences (CAAS), Shanghai, China
| | - Bin Xiang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Tao Ren
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
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Maarouf M, Wang L, Wang Y, Rai KR, Chen Y, Fang M, Chen JL. Functional Involvement of circRNAs in the Innate Immune Responses to Viral Infection. Viruses 2023; 15:1697. [PMID: 37632040 PMCID: PMC10458642 DOI: 10.3390/v15081697] [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: 07/13/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Effective viral clearance requires fine-tuned immune responses to minimize undesirable inflammatory responses. Circular RNAs (circRNAs) are a class of non-coding RNAs that are abundant and highly stable, formed by backsplicing pre-mRNAs, and expressed ubiquitously in eukaryotic cells, emerging as critical regulators of a plethora of signaling pathways. Recent progress in high-throughput sequencing has enabled a better understanding of the physiological and pathophysiological functions of circRNAs, overcoming the obstacle of the sequence overlap between circRNAs and their linear cognate mRNAs. Some viruses also encode circRNAs implicated in viral replication or disease progression. There is increasing evidence that viral infections dysregulate circRNA expression and that the altered expression of circRNAs is critical in regulating viral infection and replication. circRNAs were shown to regulate gene expression via microRNA and protein sponging or via encoding small polypeptides. Recent studies have also highlighted the potential role of circRNAs as promising diagnostic and prognostic biomarkers, RNA vaccines and antiviral therapy candidates due to their higher stability and lower immunogenicity. This review presents an up-to-date summary of the mechanistic involvement of circRNAs in innate immunity against viral infections, the current understanding of their regulatory roles, and the suggested applications.
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Affiliation(s)
- Mohamed Maarouf
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China;
- Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Lulu Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yiming Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kul Raj Rai
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Microbiology, ShiGan International College of Science and Technology/ShiGan Health Foundation, Narayangopal Chowk, Kathmandu 44600, Nepal
| | - Yuhai Chen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China;
| | - Min Fang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China;
| | - Ji-Long Chen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Liu XN, Guo XR, Han Y, Tian T, Sun J, Lei BS, Zhang WC, Yuan WZ, Zhao K. The Cellular and Viral circRNAs Induced by Fowl Adenovirus Serotype 4 Infection. Front Microbiol 2022; 13:925953. [PMID: 35722302 PMCID: PMC9201442 DOI: 10.3389/fmicb.2022.925953] [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: 04/22/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Circular RNAs (circRNAs) are a new class of noncoding RNAs that play vital roles in many biological processes. Virus infection induces modifications in cellular circRNA transcriptomes and expresses viral circRNAs. The outbreaks of Hydropericardium-hepatitis syndrome (HHS) caused by fowl adenovirus serotype 4 (FAdV-4) have resulted in huge economic losses to the poultry industry worldwide. To investigate the expression of circRNAs during FAdV-4 infection, we performed transcriptome analysis of FAdV-4-infected leghorn male hepatoma (LMH) cells. In total, 19,154 cellular circRNAs and 135 differentially expressed (DE) cellular circRNAs were identified. The characteristics of the DE cellular circRNAs were analyzed and most of them were related to multiple biological processes according to GO and KEGG enrichment analysis. The accuracy of 10 cellular circRNAs were verified by semiquantitative RT-PCR and sequencing. The change trend was consistent with the RNA sequencing results. Moreover, 2014 viral circRNAs were identified and 10 circRNAs were verified by the same methods. Our analysis showed that seven circRNAs with the same 3′ terminal and variable 5′ terminal regions were located at pTP protein and DNA pol protein of FAdV-4, which may be generated via alternative splicing events. Moreover, the expression level of viral circRNAs was closely related to the replication efficiency of the virus and partial of the viral circRNAs promoted the replication of FAdV-4. Competing endogenous RNA analysis further showed that the effects of cellular and viral circRNAs on host or viral genes may act via miRNAs. Collectively, our findings first indicate that FAdV-4 infection induced the differential expression of cellular circRNAs and FAdV-4 also expressed viral circRNAs, some of which affected FAdV-4 replication. These findings will provide new clues for further understanding FAdV-4 and provide a basis for investigating host-virus interactions.
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Affiliation(s)
- Xiao-Na Liu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Xiao-Ran Guo
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Ying Han
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Tian Tian
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Jian Sun
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Bai-Shi Lei
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Wu-Chao Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Wan-Zhe Yuan
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China.,Hebei Veterinary Biotechnology Innovation Center, Hebei Agricultural University, Baoding, China
| | - Kuan Zhao
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China.,Hebei Veterinary Biotechnology Innovation Center, Hebei Agricultural University, Baoding, China
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Shangguan A, Li J, Sun Y, Liu Z, Zhang S. Host-virus interactions in PK-15 cells infected with Pseudorabies virus Becker strain based on RNA-seq. Virus Res 2022; 318:198829. [DOI: 10.1016/j.virusres.2022.198829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 10/18/2022]
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Guo Y, Yu X, Su N, Shi N, Zhang S, Zhang L, Yang L, Zhao L, Guan Z, Zhang M, Duan M. Identification and characterization of circular RNAs in the A549 cells following Influenza A virus infection. Vet Microbiol 2022; 267:109390. [DOI: 10.1016/j.vetmic.2022.109390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 02/22/2022] [Accepted: 02/27/2022] [Indexed: 01/01/2023]
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Differential host circRNA expression profiles in human lung epithelial cells infected with SARS-CoV-2. INFECTION GENETICS AND EVOLUTION 2021; 93:104923. [PMID: 34004360 PMCID: PMC8123525 DOI: 10.1016/j.meegid.2021.104923] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/20/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging and highly pathogenic coronavirus that causes coronavirus disease (COVID-19), and might even lead to death. Circular RNAs (circRNAs), a new type of RNAs, are implicated in viral pathogenesis and host immune responses. However, their dynamic expression patterns and functions during SARS-CoV-2 infection remain to be unclear. We herein performed genome-wide dynamic analysis of circRNAs in human lung epithelial cells infected with SARS-CoV-2 at four time points. A total of 6118 circRNAs were identified at different genomic locations, including 5641 known and 477 novel circRNAs. Notably, a total of 42 circRNAs were significantly dysregulated, wherein 17 were up-regulated and 25 were down-regulated following infection at multiple phases. The gene ontology and KEGG enrichment analyses revealed that the parental genes of circRNAs were mainly involved in immune and inflammatory responses. Further, the RNA binding protein (RBP) prediction analysis indicated that the dysregulated circRNAs could regulate mRNA stability, immunity, cell death by binding specific proteins. Additionally, the circRNA-miRNA-gene network analysis showed that circRNAs indirectly regulated gene expression by absorbing their targeted miRNAs. Collectively, these results shed light on the roles of circRNAs in virus-host interactions, facilitating future studies on SARS-CoV-2 infection and pathogenesis.
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