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Huang J, Zheng S, Li Q, Zhao H, Zhou X, Yang Y, Zhang W, Cao Y. Host miR-146a-3p Facilitates Replication of Infectious Hematopoietic Necrosis Virus by Targeting WNT3a and CCND1. Vet Sci 2024; 11:204. [PMID: 38787176 PMCID: PMC11126136 DOI: 10.3390/vetsci11050204] [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: 04/02/2024] [Revised: 04/28/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Infectious hematopoietic necrosis virus (IHNV) is a serious pathogen that causes great economic loss to the salmon and trout industry. Previous studies showed that IHNV alters the expression patterns of splenic microRNAs (miRNAs) in rainbow trout. Among the differentially expressed miRNAs, miRNA146a-3p was upregulated by IHNV. However, it is unclear how IHNV utilizes miRNA146a-3p to escape the immune response or promote viral replication. The present study suggested that one multiplicity of infection (MOI) of IHNV induced the most significant miR-146a-3p expression at 1 day post infection (dpi). The upregulation of miR-146a-3p by IHNV was due to viral N, P, M, and G proteins and relied on the interferon (IFN) signaling pathway. Further investigation revealed that Wingless-type MMTV integration site family 3a (WNT3a) and G1/S-specific cyclin-D1-like (CCND1) are the target genes of miRNA-146a-3p. The regulation of IHNV infection by miRNA-146a-3p is dependent on WNT3a and CCND1. MiRNA-146a-3p was required for the downregulation of WNT3a and CCND1 by IHNV. Moreover, we also found that WNT3a and CCND1 are novel proteins that induce the type-I IFN response in RTG-2 cells, and both of them could inhibit the replication of IHNV. Therefore, IHNV-induced upregulation of miRNA-146a-3p promotes early viral replication by suppressing the type-I IFN response by targeting WNT3a and CCND1. This work not only reveals the molecular mechanism of miRNA-146a-3p during IHNV infection but also provides new antiviral targets for IHNV.
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Affiliation(s)
- Jingwen Huang
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Street NO.600, Harbin 150030, China
| | - Shihao Zheng
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Street NO.600, Harbin 150030, China
| | - Qiuji Li
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Street NO.600, Harbin 150030, China
| | - Hongying Zhao
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Street NO.600, Harbin 150030, China
| | - Xinyue Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Street NO.600, Harbin 150030, China
| | - Yutong Yang
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Street NO.600, Harbin 150030, China
| | - Wenlong Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Street NO.600, Harbin 150030, China
- Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin 150069, China
| | - Yongsheng Cao
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Street NO.600, Harbin 150030, China
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Yao X, Zhong L, Wang M, Wang M, Han Y, Wang Y, Zhou J, Song J, Li Y, Xu Y. Up-regulated lncRNA CYLD as a ceRNA of miR-2383 facilitates bovine viral diarrhea virus replication by promoting CYLD expression to counteract RIG-I-mediated type-I IFN production. Int J Biol Macromol 2023; 253:127351. [PMID: 37839600 DOI: 10.1016/j.ijbiomac.2023.127351] [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: 04/24/2023] [Revised: 09/17/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
Abstract
Bovine viral diarrhea virus (BVDV) is one of the most important pathogens of cattle, causing numerous economic losses to the cattle industry. To date, many potential mechanisms of BVDV evading or subverting innate immunity are still unknown. In this study, an lnc-CYLD/miR-2383/CYLD axis involved in BVDV-host interactions was screened from RNA-seq-based co-expression networks analysis of long noncoding RNAs, microRNAs and mRNAs in BVDV-infected bovine cells, and underlying mechanisms of lnc-CYLD/miR-2383/CYLD axis regulating BVDV replication were explored. Results showed that BVDV-induced up-regulation of the lnc-CYLD competed for binding to the miR-2383, and then promoted CYLD expression, thereby inhibiting RIG-I-mediated type-I interferon (IFN) production, which was subsequently confirmed by treatment with lnc-CYLD overexpression and miR-2383 inhibitor. However, miR-2383 transfection and small interfering RNA-mediated lnc-CYLD knockdown inhibited CYLD expression and enhanced RIG-I-mediated type-I IFN production, inhibiting BVDV replication. In addition, interaction relationship between lnc-CYLD and miR-2383, and colocalization relationship of lnc-CYLD, miR-2383 and CYLD were confirmed by dual-luciferase assay and in situ hybridization assay. Conclusively, up-regulation of the lnc-CYLD as a competing endogenous RNA binds to the miR-2383 to reduce inhibitory effect of the miR-2383 on the CYLD expression, playing an important role in counteracting type-I IFN-dependent antiviral immunity to facilitate BVDV replication.
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Affiliation(s)
- Xin Yao
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China; Key Laboratory for Animal Disease Control and Pharmaceutical Development of Heilongjiang Province, Northeast Agricultural University, Harbin, China
| | - Linhan Zhong
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Mengmeng Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Mei Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Yanyan Han
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Yixin Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Jiaying Zhou
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Jingge Song
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Yuan Li
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China.
| | - Yigang Xu
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China; Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics and Advanced Technology, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China.
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3
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Sadeghi H, Karimi Dermani F, Gheibi N, Afshar D, Heidarzadeh S, Datta I, Gholamzadeh Khoei S. Potential Role of microRNAs in Response to Aeromonas Infection in Fish. ARCHIVES OF RAZI INSTITUTE 2023; 78:1668-1679. [PMID: 38828176 PMCID: PMC11139387 DOI: 10.32592/ari.2023.78.6.1668] [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: 07/17/2023] [Accepted: 09/06/2023] [Indexed: 06/05/2024]
Abstract
The genus Aeromonas is a widespread pathogen that includes more than 30 Gram-negative species, many of which are opportunistic bacteria. Aeromonas species are naturally distributed in various aquatic sources. Infectious processes in marine animals such as fish usually develop under stressful conditions, and when their immune systems are weakened. MicroRNAs (miRNAs/miRs) are short, non-coding RNAs that post-transcriptionally regulate gene expression. Their diverse biological functions, such as influencing cell development, proliferation, differentiation, tumorigenesis, metabolism, and apoptosis have been studied in various animals. Fish is the most important source of aquatic nutrients throughout the world, and its market is constantly growing. Overpopulation in aquaculture brings infectious diseases that threaten the development of aquaculture around the world. There is extensive evidence that microRNAs are involved in modulating infectious processes and regulating the inflammatory response to major bacterial fish infections, including Aeromonas. Here, we review the current literature on the fish microRNA repertoire and outline the physiological roles assigned to microRNAs to provide a foundation for future research during Aeromonas infection. Understanding the interaction between microRNAs and Aeromonas may provide clues to a remarkable strategy for preventing Aeromonas infections in fish.
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Affiliation(s)
- H Sadeghi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - F Karimi Dermani
- Department of Biological Sciences, Florida State University, USA
| | - N Gheibi
- Cellular and Molecular Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
| | - D Afshar
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - S Heidarzadeh
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - I Datta
- Department of Biological Sciences, Florida State University, USA
| | - S Gholamzadeh Khoei
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
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Eurlaphan C, Nozaki R, Sano M, Koiwai K, Hirono I, Kondo H. Red sea bream iridovirus infection downregulates inflammation-related genes in the spleen of rock bream (Oplegnathus fasciatus). JOURNAL OF FISH DISEASES 2023; 46:1403-1411. [PMID: 37697626 DOI: 10.1111/jfd.13858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/20/2023] [Accepted: 08/26/2023] [Indexed: 09/13/2023]
Abstract
This study investigated the kinetics of red sea bream iridovirus and host gene expression during infection in rock bream (Oplegnathus fasciatus), a species highly sensitive to the virus. After intraperitoneal injection of the viral solution at 104 TCID50/fish, the viral genome copy number in the spleen was 104.7 ± 0.2 and 105.9 ± 0.4 copies/μg DNA at 3 and 5 days post-injection (dpi), respectively. Using transcriptomic analyses via MiSeq, viral gene transcripts were detected at 3 and 5 dpi. Six genes including RING-finger domain-containing protein and laminin-type epidermal growth factor-like domain genes were significantly expressed at 5 dpi. Further, 334 host genes were differentially expressed compared with those before infection. Genes were clustered into four groups based on their expression profiles. Interferon-stimulated genes were more prevalent in groups showing upregulation at 5 dpi and 3 and 5 dpi. In contrast, the group showing downregulation at 3 dpi included inflammation-related genes, such as granzyme and eosinophil peroxidase genes. Downregulation of certain inflammation-related genes may contribute to the susceptibility of this fish to the virus.
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Affiliation(s)
- Chalermkwan Eurlaphan
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Reiko Nozaki
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Motohiko Sano
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Keiichiro Koiwai
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hidehiro Kondo
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
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5
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Gareev I, de Jesus Encarnacion Ramirez M, Goncharov E, Ivliev D, Shumadalova A, Ilyasova T, Wang C. MiRNAs and lncRNAs in the regulation of innate immune signaling. Noncoding RNA Res 2023; 8:534-541. [PMID: 37564295 PMCID: PMC10410465 DOI: 10.1016/j.ncrna.2023.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
The detection and defense against foreign agents and pathogens by the innate immune system is a crucial mechanism in the body. A comprehensive understanding of the signaling mechanisms involved in innate immunity is essential for developing effective diagnostic tools and therapies for infectious diseases. Innate immune response is a complex process involving recognition of pathogens through receptors, activation of signaling pathways, and cytokine production, which are all crucial for deploying appropriate countermeasures. Non-coding RNAs (ncRNAs) are vital regulators of the immune response during infections, mediating the body's defense mechanisms. However, an overactive immune response can lead to tissue damage, and maintaining immune homeostasis is a complex process in which ncRNAs play a significant role. Recent studies have identified microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) as key players in controlling gene expression in innate immune pathways, thereby participating in antiviral defenses, tumor immunity, and autoimmune diseases. MiRNAs act by regulating host defense mechanisms against viruses, bacteria, and fungi by targeting mRNA at the post-transcriptional level, while lncRNAs function as competing RNAs, blocking the binding of miRNAs to mRNA. This review provides an overview of the regulatory role of miRNAs and lncRNAs in innate immunity and its mechanisms, as well as highlights potential future research directions, including the expression and maturation of new ncRNAs and the conservation of ncRNAs in evolution.
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Affiliation(s)
- Ilgiz Gareev
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Manuel de Jesus Encarnacion Ramirez
- Department of Neurosurgery, Рeoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, Moscow, 117198, Russian Federation
| | - Evgeniy Goncharov
- Traumatology and Orthopedics Center, Central Clinical Hospital of the Russian Academy of Sciences, 117593, Moscow, Russia
| | - Denis Ivliev
- Department of Neurosurgery, Smolensk State Medical University of the Ministry of Health of the Russian Federation, Smolensk, Russia
| | - Alina Shumadalova
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Tatiana Ilyasova
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Chunlei Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
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6
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Liu B, San L, Guo H, Zhu K, Zhang N, Yang J, Liu B, Hou J, Zhang D. Transcriptomic Analysis Reveals Functional Interaction of mRNA-lncRNA-miRNA in Trachinotus ovatus Infected by Cryptocaryon irritans. Int J Mol Sci 2023; 24:15886. [PMID: 37958869 PMCID: PMC10648848 DOI: 10.3390/ijms242115886] [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: 08/26/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
The skin of Trachinotus ovatus is a crucial component of the mucosal immune system and serves as the primary site of infection by Cryptocaryon irritans. In order to investigate the significant role of skin in C. irritans infection, a comprehensive transcriptome analysis was conducted on skin tissues from the infection group, infection-adjacent group, and infection group compared with the infection-adjacent group (ATT_vs_PER, ADJ_vs_PER, ATT_vs_ADJ). This study identified differentially expressed long non-coding RNAs (DE lncRNAs), microRNAs (DE miRNAs), and differentially expressed genes (DEGs). The prediction of lncRNA target genes was accomplished by utilizing positional relationship (co-location) and expression correlation (co-expression) with protein-coding genes. Subsequently, functional enrichment analysis was conducted on the target genes of differentially expressed lncRNAs, revealing their involvement in signaling pathways such as tight junction, MAPK, and cell adhesion molecules. This study describes the regulatory network of lncRNA-miRNA-mRNA in T. ovatus skin tissue infected with C. irritans. Functional prediction analysis showed that differentially expressed lncRNA and miRNA may regulate the expression of immune genes such as interleukin-8 (il8) to resist the infection of C. irritans. Conducting additional research on these non-coding RNAs will facilitate a deeper understanding of their immune regulatory function in T. ovatus during C. irritans infection. The study of non-coding RNA in this study laid a foundation for revealing the molecular mechanism of the immune system of T. ovatus to respond to the infection of C. irritans. It provided a choice for the molecular breeding of Trachinotus ovatus against C. irritans.
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Affiliation(s)
- Baosuo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (B.L.); (B.L.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Lize San
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Huayang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (B.L.); (B.L.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Kecheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (B.L.); (B.L.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (B.L.); (B.L.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Jingwen Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (B.L.); (B.L.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Bo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (B.L.); (B.L.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Jilun Hou
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Dianchang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (B.L.); (B.L.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572000, China
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Zhang Z, Guan X. Japanese Flounder pol-miR-155 Is Involved in Edwardsiella tarda Infection via ATG3. Genes (Basel) 2023; 14:genes14050958. [PMID: 37239318 DOI: 10.3390/genes14050958] [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: 03/10/2023] [Revised: 04/08/2023] [Accepted: 04/18/2023] [Indexed: 05/28/2023] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules that function in the post-transcriptionally regulation of the expression of diverse genes, including those involved in immune defense. Edwardsiella tarda can infect a broad range of hosts and cause severe disease in aquatic species, including Japanese flounder (Paralichthys olivaceus). In this study, we examined the regulation mechanism of a flounder miRNA, pol-miR-155, during the infection of E. tarda. Pol-miR-155 was identified to target flounder ATG3. Overexpression of pol-miR-155 or knockdown of ATG3 expression suppressed autophagy and promoted the intracellular replication of E. tarda in flounder cells. Overexpression of pol-miR-155 activated the NF-κB signaling pathway and further promoted the expression of downstream immune related genes of interleukin (IL)-6 and IL-8. These results unraveled the regulatory effect of pol-miR-155 in autophagy and in E. tarda infection.
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Affiliation(s)
- Zhanwei Zhang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaolu Guan
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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8
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Li PH, Wang LQ, He JY, Zhu XL, Huang W, Wang SW, Qin QW, Sun HY. MicroRNA-124 Promotes Singapore Grouper Iridovirus Replication and Negatively Regulates Innate Immune Response. Front Immunol 2021; 12:767813. [PMID: 34858424 PMCID: PMC8631330 DOI: 10.3389/fimmu.2021.767813] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/19/2021] [Indexed: 02/02/2023] Open
Abstract
Viral infections seriously affect the health of organisms including humans. Now, more and more researchers believe that microRNAs (miRNAs), one of the members of the non-coding RNA family, play significant roles in cell biological function, disease occurrence, and immunotherapy. However, the roles of miRNAs in virus infection (entry and replication) and cellular immune response remain poorly understood, especially in low vertebrate fish. In this study, based on the established virus-cell infection model, Singapore grouper iridovirus (SGIV)-infected cells were used to explore the roles of miR-124 of Epinephelus coioides, an economically mariculture fish in southern China and Southeast Asia, in viral infection and host immune responses. The expression level of E. coioides miR-124 was significantly upregulated after SGIV infection; miR-124 cannot significantly affect the entry of SGIV, but the upregulated miR-124 could significantly promote the SGIV-induced cytopathic effects (CPEs), the viral titer, and the expressions of viral genes. The target genes of miR-124 were JNK3/p38α mitogen-activated protein kinase (MAPK). Overexpression of miR-124 could dramatically inhibit the activation of NF-κB/activating protein-1 (AP-1), the transcription of proinflammatory factors, caspase-9/3, and the cell apoptosis. And opposite results happen when the expression of miR-124 was inhibited. The results suggest that E. coioides miR-124 could promote viral replication and negatively regulate host immune response by targeting JNK3/p38α MAPK, which furthers our understanding of virus and host immune interactions.
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Affiliation(s)
- Pin-Hong Li
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Li-Qun Wang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Jia-Yang He
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xiang-Long Zhu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Wei Huang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Shao-Wen Wang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Qi-Wei Qin
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hong-Yan Sun
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
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9
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Su H, Zheng W, Pan J, Lv X, Xin S, Xu T. Circular RNA circSamd4a Regulates Antiviral Immunity in Teleost Fish by Upregulating STING through Sponging miR-29a-3p. THE JOURNAL OF IMMUNOLOGY 2021; 207:2770-2784. [PMID: 34697227 DOI: 10.4049/jimmunol.2100469] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/21/2021] [Indexed: 12/22/2022]
Abstract
Circular RNAs (circRNAs) are a subgroup of endogenous noncoding RNA that is covalently closed rings and widely expressed. In recent years, there is accumulating evidence indicating that circRNAs are a class of important regulators, which play an important role in various biological processes. However, the biological functions and regulation mechanism of circRNAs in lower vertebrates are little known. In this study, we discovered a circRNA Samd4a (circSamd4a) that is related to the antiviral immune response of teleost fish. It can act as a key regulator of the host's antiviral response and play a key role in inhibiting Sininiperca chuatsi rhabdovirus replication. Further studies have shown that circSamd4a may act as a competing endogenous RNA, which can enhance the STING-mediated NF-κB/IRF3 signaling pathway by adsorbing miR-29a-3p, thereby enhancing the antiviral immune response. Therefore, circSamd4a plays an active regulatory role in the antiviral immune response of bony fish. Our research results provide a strong foundation for circular RNA to play a regulatory role in the antiviral immune response of teleost fish.
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Affiliation(s)
- Hui Su
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jiajia Pan
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xing Lv
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Shiying Xin
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; .,Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China; and.,National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
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10
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Li W, Guan X, Sun B, Sun L. A Novel microRNA of Japanese Flounder Regulates Antimicrobial Immunity Involving a Bacteria-Binding CSF3. Front Immunol 2021; 12:723401. [PMID: 34489973 PMCID: PMC8417112 DOI: 10.3389/fimmu.2021.723401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/04/2021] [Indexed: 11/22/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate diverse biological processes including immunity. In a previous high-throughput RNA sequencing study, a novel miRNA, pol-miR-novel_642, was identified from Japanese flounder (Paralichthys olivaceus), a farmed fish species with important economic value. In this study, we investigated the regulatory mechanism and the function of pol-miR-novel_642 and its target gene. We found that pol-miR-novel_642 targeted, in a sequence-specific manner, a flounder gene encoding an uncharacterized protein that is a structural homologue of murine granulocyte colony stimulating factor 3 (CSF3). The expression of pol-miR-novel_642 and its target gene (named PoCSF3-1) was regulated, in different manners, by the bacterial pathogen Edwardsiella tarda and the viral pathogen megalocytivirus. Overexpression of pol-miR-novel_642 or interference with PoCSF3-1 expression in flounder cells strongly potentiated E. tarda infection. Consistently, in vivo knockdown of PoCSF3-1 enhanced bacterial dissemination in flounder tissues but blocked viral replication, whereas in vivo overexpression of PoCSF3-1 inhibited bacterial dissemination and facilitated viral infection. Overexpression/knockdown of PoCSF3-1 and pol-miR-novel_642 also affected the activation of autophagy. Recombinant PoCSF3-1 (rPoCSF3-1) interacted with and inhibited the growth of Gram-negative bacteria in a manner relying on a PoCSF3-1-characteristic structural motif that is absent in mouse CSF3. rPoCSF3-1 also regulated the proliferation, inflammatory response, and immune defense of flounder head kidney leukocytes in a structure-dependent fashion. Together, these results reveal the function of a novel miRNA-CSF3 regulatory system of flounder, and add new insights into the role and mechanism of fish miRNA and CSF3 in antimicrobial immunity.
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Affiliation(s)
- Wenrui Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolu Guan
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Bin Sun
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
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11
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Batool M, Kim MS, Choi S. Structural insights into the distinctive RNA recognition and therapeutic potentials of RIG-I-like receptors. Med Res Rev 2021; 42:399-425. [PMID: 34287999 DOI: 10.1002/med.21845] [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: 12/09/2020] [Revised: 06/11/2021] [Accepted: 07/04/2021] [Indexed: 12/12/2022]
Abstract
RNA viruses, including the coronavirus, develop a unique strategy to evade the host immune response by interrupting the normal function of cytosolic retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs). RLRs rapidly detect atypical nucleic acids, thereby triggering the antiviral innate immune signaling cascade and subsequently activates the interferons transcription and induction of other proinflammatory cytokines and chemokines. Nonetheless, these receptors are manipulated by viral proteins to subvert the host immune system and sustain the infectivity and replication potential of the virus. RIG-I senses the single-stranded, double-stranded, and short double-stranded RNAs and recognizes the key signature, a 5'-triphosphate moiety, at the blunt end of the viral RNA. Meanwhile, the melanoma differentiation-associated gene 5 (MDA5) is triggered by longer double stranded RNAs, messenger RNAs lacking 2'-O-methylation in their 5'-cap, and RNA aggregates. Therefore, structural insights into the nucleic-acid-sensing and downstream signaling mechanisms of these receptors hold great promise for developing effective antiviral therapeutic interventions. This review highlights the critical roles played by RLRs in viral infections as well as their ligand recognition mechanisms. In addition, we highlight the crosstalk between the toll-like receptors and RLRs and provide a comprehensive overview of RLR-associated diseases as well as the therapeutic potential of RLRs for the development of antiviral-drugs. Moreover, we believe that these RLR-based antivirals will serve as a step toward countering the recent coronavirus disease 2019 pandemic.
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Affiliation(s)
- Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon, Korea
- S&K Therapeutics, Campus Plaza 418, Ajou University, Suwon, Korea
| | - Moon Suk Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, Korea
- S&K Therapeutics, Campus Plaza 418, Ajou University, Suwon, Korea
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12
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Zhou W, Xie Y, Li Y, Xie M, Zhang Z, Yang Y, Zhou Z, Duan M, Ran C. Research progress on the regulation of nutrition and immunity by microRNAs in fish. FISH & SHELLFISH IMMUNOLOGY 2021; 113:1-8. [PMID: 33766547 DOI: 10.1016/j.fsi.2021.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/17/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
MicroRNAs (miRNAs) are a class of highly conserved, endogenous non-coding single-stranded small RNA molecules with a length of 18-25 nucleotides. MiRNAs can negatively regulate the target gene through complementary pairing with the mRNA. It has been more than 20 years since the discovery of miRNA molecules, and many achievements have been made in fish research. This paper reviews the research progress in the regulation of fish nutrition and immunity by miRNAs in recent years. MiRNAs regulate the synthesis of long-chain polyunsaturated fatty acids, and are involved in the metabolism of glucose, lipids, as well as cholesterol in fish. Moreover, miRNAs play various roles in antibacterial and antiviral immunity of fish. They can promote the immune response of fish, but may also participate in the immune escape mechanism of bacteria or viruses. One important aspect of miRNAs regulation on fish immunity is mediated by targeting pattern recognition receptors and downstream signaling factors. Together, current results indicate that miRNAs are widely involved in the complex regulatory network of fish. Further studies on fish miRNAs may deepen our understanding of the regulatory network of fish nutrition and immunity, and have the potential to promote the development of microRNA-based products and detection reagents that can be applied in aquaculture industry.
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Affiliation(s)
- Wei Zhou
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Yadong Xie
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Yu Li
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Mingxu Xie
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Zhen Zhang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yalin Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Zhigang Zhou
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Ming Duan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Chao Ran
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
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13
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Chang MX. The negative regulation of retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) signaling pathway in fish. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 119:104038. [PMID: 33548290 DOI: 10.1016/j.dci.2021.104038] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/30/2021] [Accepted: 01/30/2021] [Indexed: 06/12/2023]
Abstract
At each stage of innate immune response, there are stimulatory and inhibitory signals that modulate the strength and character of the response. RIG-I-like receptor (RLR) signaling pathway plays pivotal roles in antiviral innate immune response. Recent studies have revealed the molecular mechanisms that viral infection leads to the activation of RLRs-mediated downstream signaling cascades and the production of type I interferons (IFNs). However, antiviral immune responses must be tightly regulated in order to prevent detrimental type I IFNs production. Previous reviews have highlighted negative regulation of RLR signaling pathway, which mainly target to directly regulate RIG-I, MDA5, MAVS and TBK1 function in mammals. In this review, we summarize recent advances in our understanding of negative regulators of RLR signaling pathway in teleost, with specific focus on piscine and viral regulatory mechanisms that directly or indirectly inhibit the function of RIG-I, MDA5, LGP2, MAVS, TRAF3, TBK1, IRF3 and IRF7 both in the steady state or upon viral infection. We also further discuss important directions for future studies, especially for non-coding RNAs and post-translational modifications via fish specific TRIM proteins. The knowledge of negative regulators of RLR signaling pathway in teleost will shed new light on the critical information for potential therapeutic purposes.
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Affiliation(s)
- Ming Xian Chang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
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14
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Abo-Al-Ela HG. The emerging regulatory roles of noncoding RNAs in immune function of fish: MicroRNAs versus long noncoding RNAs. Mol Genet Genomics 2021; 296:765-781. [PMID: 33904988 DOI: 10.1007/s00438-021-01786-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/12/2021] [Indexed: 02/06/2023]
Abstract
The genome could be considered as raw data expressed in proteins and various types of noncoding RNAs (ncRNAs). However, a large portion of the genome is dedicated to ncRNAs, which in turn represent a considerable amount of the transcriptome. ncRNAs are modulated on levels of type and amount whenever any physiological process occurs or as a response to external modulators. ncRNAs, typically forming complexes with other partners, are key molecules that influence diverse cellular processes. Based on the knowledge of mammalian biology, ncRNAs are known to regulate and control diverse trafficking pathways and cellular activities. Long noncoding RNAs (lncRNAs) notably have diverse and more regulatory roles than microRNAs. Expanding these studies on fish has derived the same conclusion with relevance to other species, including invertebrates, explored the potentials to harness such types of RNA to further understand the biology of such organisms, and opened gates for applying recent technologies, such as RNA interference and delivering micromolecules as microRNAs to living cells and possibly to target organs. These technologies should improve aquaculture productivity and fish health, as well as help understand fish biology.
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Affiliation(s)
- Haitham G Abo-Al-Ela
- Genetics and Biotechnology, Department of Aquaculture, Faculty of Fish Resources, Suez University, 43518, Suez, Egypt.
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15
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Megalocytivirus Induces Complicated Fish Immune Response at Multiple RNA Levels Involving mRNA, miRNA, and circRNA. Int J Mol Sci 2021; 22:ijms22063156. [PMID: 33808870 PMCID: PMC8003733 DOI: 10.3390/ijms22063156] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 12/22/2022] Open
Abstract
Megalocytivirus is an important viral pathogen to many farmed fishes, including Japanese flounder (Paralichthys olivaceus). In this study, we examined megalocytivirus-induced RNA responses in the spleen of flounder by high-throughput sequencing and integrative analysis of various RNA-seq data. A total of 1327 microRNAs (miRNAs), including 368 novel miRNAs, were identified, among which, 171 (named DEmiRs) exhibited significantly differential expressions during viral infection in a time-dependent manner. For these DEmiRs, 805 differentially expressed target mRNAs (DETmRs) were predicted, whose expressions not only significantly changed after megalocytivirus infection but were also negatively correlated with their paired DEmiRs. Integrative analysis of immune-related DETmRs and their target DEmiRs identified 12 hub DEmiRs, which, together with their corresponding DETmRs, formed an interaction network containing 84 pairs of DEmiR and DETmR. In addition to DETmRs, 19 DEmiRs were also found to regulate six key immune genes (mRNAs) differentially expressed during megalocytivirus infection, and together they formed a network consisting of 21 interactive miRNA-messenger RNA (mRNA) pairs. Further analysis identified 9434 circular RNAs (circRNAs), 169 of which (named DEcircRs) showed time-specific and significantly altered expressions during megalocytivirus infection. Integrated analysis of the DETmR-DEmiR and DEcircR-DEmiR interactions led to the identification of a group of competing endogenous RNAs (ceRNAs) constituted by interacting triplets of circRNA, miRNA, and mRNA involved in antiviral immunity. Together these results indicate that complicated regulatory networks of different types of non-coding RNAs and coding RNAs are involved in megalocytivirus infection.
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16
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A Highly Conserved Circular RNA circRasGEF1B Enhances Antiviral Immunity by Regulating miR-21-3p/MITA Pathway in Lower Vertebrates. J Virol 2021; 95:JVI.02145-20. [PMID: 33441345 PMCID: PMC8092700 DOI: 10.1128/jvi.02145-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Circular RNAs (circRNAs) represent a class of widespread, diverse, and covalently closed circRNAs that function as microRNA (miRNA) sponges and crucial regulators of gene expression in mammals. However, the regulation and function of circRNAs in lower vertebrates are still unknown. Here, we first discover a highly conserved circRNA termed circRasGEF1B, which displays a high conservation from mammals to fish and serves as key regulator in eliciting antiviral immunity in teleost fish. Results indicate that circRasGEF1B was highly expressed in Siniperca chuatsi rhabdovirus-infected tissues and cells. Functionally, miR-21-3p could inhibit cellular antiviral responses significantly, whereas circRasGEF1B counteract the effects of miR-21-3p. In mechanism, the results demonstrate that circRasGEF1B acts as a competing endogenous RNA (ceRNA) of miR-21-3p to relieve the repressive effect of miR-21-3p on its target MITA, then enhance the innate antiviral responses. Our results not only provide a novel insight into the functions of circRNAs in lower vertebrates, but broaden our understanding of circRNAs in viral infection.IMPORTANCE Siniperca chuatsi rhabdovirus (SCRV) is a typical fish RNA rhabdovirus, which is one of the most significant viral pathogens in teleost fish and can cause severe hemorrhagic septicemia in freshwater and marine fishes. Here, we discovered a highly conserved circRNAs called circRasGEF1B, which acts as a key regulator for innate antiviral responses upon SCRV infection. circRasGEF1B acts as an endogenous sponge of miR-21-3p that downregulates miR-21-3p expression levels. circRasGEF1B is able to bind to miR-21-3p directly and regulates MITA expression. To our knowledge, this report is the first to characterize circRNA-miRNA regulatory networks that exist in lower vertebrates.
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17
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He J, Gu H, Wang W, Hu Y. Two CD9 tetraspanin family members of Japanese flounder (Paralichthys olivaceus): characterization and comparative analysis of the anti-infectious immune function. Vet Res 2021; 52:28. [PMID: 33597018 PMCID: PMC7890607 DOI: 10.1186/s13567-021-00903-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 01/10/2021] [Indexed: 12/14/2022] Open
Abstract
CD9 is a glycoprotein of the transmembrane 4 superfamily that is involved in various cellular processes. Studies related to the immune functions and activities of CD9 in teleost fish are limited. In this study, we characterized two CD9 homologs, PoCD9.1 and PoCD9.3, from Japanese flounder (Paralichthys olivaceus). Sequence analysis showed that PoCD9.1 and PoCD9.3 possess characteristic transmembrane 4 superfamily (TM4SF) structures. PoCD9.1 shares 70.61% sequence identity with PoCD9.3. The expression of PoCD9.1 and PoCD9.3 in the three main immune tissues was significantly induced in a time-dependent manner by extracellular and intracellular pathogen infection, which indicates that the two CD9 homologs play an important role in the response to pathogenic infection. Following infection with the extracellular pathogen Vibrio anguillarum, the expression profiles of both PoCD9.1 and PoCD9.3 were similar. After infection with the intracellular pathogen Edwardsiella piscicida, the expression levels of PoCD9.1 and PoCD9.3 were different at different stages of infection, especially in the spleen. The spleen was the most important tissue for the PoCD9.1 and PoCD9.3 responses to pathogen infection among the three examined immune tissues. Knockdown of PoCD9.1 and PoCD9.3 attenuated the ability of host cells to eliminate pathogenic bacteria, and PoCD9.1 knockdown was more lethal than PoCD9.3 knockdown for host cells with E. piscicida infection. Overexpression of PoCD9.1 and PoCD9.3 promoted host or host cell defence against E. piscicida infection. These findings suggest that PoCD9.1 and PoCD9.3 serve as immune-related factors, play an important role in the immune defence system of Japanese flounder, and display different functions in response to different pathogens at different stages of infection.
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Affiliation(s)
- Jiaojiao He
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China.,Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou, 571101, China
| | - Hanjie Gu
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou, 571101, China.,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China
| | - Wenqi Wang
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Yonghua Hu
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou, 571101, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, China. .,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China.
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18
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Smith NC, Wajnberg G, Chacko S, Woldemariam NT, Lacroix J, Crapoulet N, Ayre DC, Lewis SM, Rise ML, Andreassen R, Christian SL. Characterization of miRNAs in Extracellular Vesicles Released From Atlantic Salmon Monocyte-Like and Macrophage-Like Cells. Front Immunol 2020; 11:587931. [PMID: 33262769 PMCID: PMC7686242 DOI: 10.3389/fimmu.2020.587931] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/09/2020] [Indexed: 12/18/2022] Open
Abstract
Cell-derived extracellular vesicles (EVs) participate in cell-cell communication via transfer of molecular cargo including genetic material like miRNAs. In mammals, it has previously been established that EV-mediated transfer of miRNAs can alter the development or function of immune cells, such as macrophages. Our previous research revealed that Atlantic salmon head kidney leukocytes (HKLs) change their morphology, phagocytic ability and miRNA profile from primarily “monocyte-like” at Day 1 to primarily “macrophage-like” at Day 5 of culture. Therefore, we aimed to characterize the miRNA cargo packaged in EVs released from these two cell populations. We successfully isolated EVs from Atlantic salmon HKL culture supernatants using the established Vn96 peptide-based pull-down. Isolation was validated using transmission electron microscopy, nanoparticle tracking analysis, and Western blotting. RNA-sequencing identified 19 differentially enriched (DE) miRNAs packaged in Day 1 versus Day 5 EVs. Several of the highly abundant miRNAs, including those that were DE (e.g. ssa-miR-146a, ssa-miR-155 and ssa-miR-731), were previously identified as DE in HKLs and are associated with macrophage differentiation and immune response in other species. Interestingly, the abundance relative of the miRNAs in EVs, including the most abundant miRNA (ssa-miR-125b), was different than the miRNA abundance in HKLs, indicating selective packaging of miRNAs in EVs. Further study of the miRNA cargo in EVs derived from fish immune cells will be an important next step in identifying EV biomarkers useful for evaluating immune cell function, fish health, or response to disease.
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Affiliation(s)
- Nicole C Smith
- Department of Ocean Sciences, Memorial University, St. John's, NL, Canada
| | | | - Simi Chacko
- Atlantic Cancer Research Institute, Moncton, NB, Canada
| | - Nardos T Woldemariam
- Department of Life Sciences and Health, OsloMet-Oslo Metropolitan University, Oslo, Norway
| | | | | | - D Craig Ayre
- Department of Molecular Sciences, University of Medicine and Health Sciences, Basseterre, Saint Kitts and Nevis
| | - Stephen M Lewis
- Atlantic Cancer Research Institute, Moncton, NB, Canada.,Department of Chemistry & Biochemistry, Université de Moncton, Moncton, NB, Canada.,Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University, St. John's, NL, Canada
| | - Rune Andreassen
- Department of Life Sciences and Health, OsloMet-Oslo Metropolitan University, Oslo, Norway
| | - Sherri L Christian
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada.,Department of Biochemistry, Memorial University, St. John's, NL, Canada
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19
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Tang X, Fu J, Tan X, Shi Y, Ye J, Guan W, Shi Y, Xu M. The miR-155 regulates cytokines expression by SOSC1 signal pathways of fish in vitro and in vivo. FISH & SHELLFISH IMMUNOLOGY 2020; 106:28-35. [PMID: 32707297 DOI: 10.1016/j.fsi.2020.07.042] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
MiR-155 is reported as immune regulated miRNA in mammalian corresponding to immunity, antibacterial and antiviral effects regulation. However, the roles and mechanisms of the miRNA have remained largely undefined. We herein comprehensively investigated the functions of miR-155 in vitro and in vivo by miR-155 mimics, agomir and antagomir in Cyprinus carpio and Ictalurus punctatus, with the target genes in the SOSC1 pathway certified in I. punctatus via luciferase reporter assays. Results showed that the miR-155 regulated the expressions of cytokines, including TNF-α, IFN-γ, IL-1β, IL-6 and IL-10. Further research confirmed SOSC1 as one of the targets of the miRNA, and the JAK1/STAT3/SOSC1 signal pathway involved in the miR-155 effects on the expression of immune cytokines as well. Additionally, the changes of TLR2 in fish may also be related to miR-155 along with its target SOCS1, and the TLR2/MyD88 pathway may partly participate in the effects of the miR-155 on the cytokines. The research here confirmed that the miR-155 can regulate cytokines expression by SOSC1 signal pathways of fish in vitro and in vivo, which would provide resources for understanding and studying about immune regulation in fish.
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Affiliation(s)
- Xuelian Tang
- Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jinghua Fu
- Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Xukai Tan
- Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yunfeng Shi
- Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jiawei Ye
- Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wanting Guan
- Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yifu Shi
- Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Minjun Xu
- Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
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20
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Phosphatase and Tensin Homolog (PTEN) of Japanese Flounder-Its Regulation by miRNA and Role in Autophagy, Apoptosis and Pathogen Infection. Int J Mol Sci 2020; 21:ijms21207725. [PMID: 33086544 PMCID: PMC7589652 DOI: 10.3390/ijms21207725] [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: 10/02/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs with important roles in diverse biological processes including immunity. Japanese flounder (Paralichthys olivaceus) is an aquaculture fish species susceptible to the infection of bacterial and viral pathogens including Edwardsiella tarda. In a previous study, pol-miR-novel_547, a novel miRNA of flounder with unknown function, was found to be induced by E. tarda. In the present study, we investigated the regulation and function of pol-miR-novel_547 and its target gene. We found that pol-miR-novel_547 was regulated differently by E. tarda and the viral pathogen megalocytivirus, and pol-miR-novel_547 repressed the expression of PTEN (phosphatase and tensin homolog) of flounder (PoPTEN). PoPTEN is ubiquitously expressed in multiple tissues of flounder and responded to bacterial and viral infections. Interference with PoPTEN expression in flounder cells directly or via pol-miR-novel_547 promoted E. tarda invasion. Consistently, in vivo knockdown of PoPTEN enhanced E. tarda dissemination in flounder tissues, whereas in vivo overexpression of PoPTEN attenuated E. tarda dissemination but facilitated megalocytivirus replication. Further in vitro and in vivo studies showed that PoPTEN affected autophagy activation via the AKT/mTOR pathway and also modulated the process of apoptosis. Together these results reveal for the first time a critical role of fish PTEN and its regulatory miRNA in pathogen infection, autophagy, and apoptosis.
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21
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Sun YL, Guan XL, Zhang P, Li MF, Zhang J, Sun L. Pol-miR-363-3p plays a significant role in the immune defense of Japanese flounder Paralichthys olivaceus against bacterial and viral infection. FISH & SHELLFISH IMMUNOLOGY 2020; 104:439-446. [PMID: 32561457 DOI: 10.1016/j.fsi.2020.06.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
In this study, we examined the function of a Japanese flounder (Paralichthys olivaceus) microRNA (miRNA), pol-miR-363-3p. We found that pol-miR-363-3p targets an ubiquitin-specific protease (USP), USP32. USP is a family of deubiquitinating enzymes essential to the functioning of the ubiquitin proteasome system. In mammals, USP32 is known to be associated with cancer and immunity. In fish, the function of USP32 is unknown. We found that flounder USP32 (PoUSP32) expression was detected in the major tissues of flounder, particularly intestine. In vitro and in vivo studies showed that pol-miR-363-3p directly regulated PoUSP32 in a negative manner by interaction with the 3'UTR of PoUSP32. Overexpression of pol-miR-363-3p or interference with PoUSP32 expression in flounder cells significantly blocked Streptococcus iniae infection. Consistently, in vivo knockdown of pol-miR-363-3p or overexpression of PoUSP32 enhanced dissemination of S. iniae in flounder tissues, whereas in vivo knockdown of PoUSP32 inhibited S. iniae dissemination. In addition, pol-miR-363-3p knockdown also significantly promoted the tissue dissemination of the viral pathogen megalocytivirus, which, as well as S. iniae, regulated pol-miR-363-3p expression. Together these results revealed an important role of pol-miR-363-3p in flounder immune defense against bacterial and viral infection.
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Affiliation(s)
- Yan-Ling Sun
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiao-Lu Guan
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Peng Zhang
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Mo-Fei Li
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Zhang
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Chu Q, Xu T, Zheng W, Chang R, Zhang L. Long noncoding RNA MARL regulates antiviral responses through suppression miR-122-dependent MAVS downregulation in lower vertebrates. PLoS Pathog 2020; 16:e1008670. [PMID: 32678830 PMCID: PMC7390449 DOI: 10.1371/journal.ppat.1008670] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 07/29/2020] [Accepted: 05/31/2020] [Indexed: 12/19/2022] Open
Abstract
Increasing evidence suggests important roles for long noncoding RNAs (lncRNAs) as new gene modulators involved in various biological processes. However, the function roles of lncRNAs in lower vertebrates are still unknown. Here, we firstly identify a lncRNA, named MAVS antiviral-related lncRNA (MARL), as a key regulator for antiviral immunity in teleost fish. The results indicate that fish MAVS play essential roles in host antiviral responses and inhibition of Siniperca chuatsi rhabdovirus (SCRV) replication. miR-122 reduces MAVS expression and suppress MAVS-mediated antiviral responses, which may help viruses evade host antiviral responses. Further, MARL functions as a competing endogenous RNA (ceRNA) for miR-122 to control protein abundance of MAVS, thereby inhibiting SCRV replication and promoting antiviral responses. Our data not only shed new light on understanding the function role of lncRNA in biological processes in lower vertebrates, but confirmed the hypothesis that ceRNA regulatory networks exist widely in vertebrates. Increasing evidence indicates that lncRNAs participate in the regulation of various biological processes, especially innate and adaptive immunity. However, the relationship between lncRNAs and host antiviral responses remains largely unknown, particularly in lower vertebrates. Our results provided the first direct evidence that a lncRNA, termed MAVS antiviral-related lncRNA (MARL), acts as a key regulator for antiviral immunity in lower vertebrates. lncRNAs have been identified to function as competing endogenous RNAs (ceRNAs) and cross-talk with mRNAs by competing shared for miRNAs. Such ceRNAs regulate the distribution of miRNA molecules on their targets and thereby apply an additional level of post-transcriptional regulation. In our study, MARL functions as a ceRNA for miR-122 to control protein abundance of fish MAVS, thereby inhibiting virus replication and promoting antiviral responses. This is the first study to demonstrate ceRNA regulatory networks existing in lower vertebrates, which can provide new insights into understanding the effects of lncRNAs on host-virus interactions.
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Affiliation(s)
- Qing Chu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, China
- * E-mail:
| | - Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, China
| | - Renjie Chang
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Lei Zhang
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
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Li WR, Guan XL, Jiang S, Sun L. The novel fish miRNA pol-miR-novel_171 and its target gene FAM49B play a critical role in apoptosis and bacterial infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 106:103616. [PMID: 31958496 DOI: 10.1016/j.dci.2020.103616] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/12/2020] [Accepted: 01/12/2020] [Indexed: 06/10/2023]
Abstract
MicroRNAs (miRNAs) are a type of small, non-coding RNAs that participate in many cellular and biological processes by regulating mRNA stability. In a previous study, we identified 96 Japanese flounder (Paralichthys olivaceus) miRNAs responsive to the infection of Edwardsiella tarda, a bacterial pathogen to fish as well as humans. In the current study, we examined the regulation and function of one novel miRNA, i.e., pol-miR-novel_171, from the above 96 miRNA pool. We found that pol-miR-novel_171 expression was regulated by E. tarda and megalocytivirus in a pathogen-specific manner, and that pol-miR-novel_171 targeted the gene of FAM49B (family with sequence similarity 49 member B) of flounder (named PoFAM49B) by negative interaction with the 3'-UTR of PoFAM49B. To date, the function fish FAM49B is unknown. We found that PoFAM49B expressed in multiple tissues of flounder, and recombinant PoFAM49B interacted with and inhibited the growth of Gram-negative bacterial pathogens. Interference with PoFAM49B expression in flounder cells promoted E. tarda infection. Similar effects on E. tarda infection were observed with pol-miR-novel_171 overexpression. Consistently, in vivo knockdown of PoFAM49B in flounder enhanced E. tarda dissemination in fish tissues. Furthermore, interference with PoFAM49B expression, or overexpression of pol-miR-novel_171, promoted apoptosis of flounder cells, while in vitro and in vivo knockdown of PoFAM49B augmented the expressions of key apoptosis-associated genes. These results revealed for the first time the immune function of fish FAM49B and the regulatory mechanism of a novel fish miRNA by demonstrating that pol-miR-novel_171, via PoFAM49B, played a critical role in apoptosis and anti-bacterial immunity.
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Affiliation(s)
- Wen-Rui Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Lu Guan
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Shuai Jiang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.
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24
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Wu TS, Lin YT, Huang YT, Yu FY, Liu BH. Ochratoxin A triggered intracerebral hemorrhage in embryonic zebrafish: Involvement of microRNA-731 and prolactin receptor. CHEMOSPHERE 2020; 242:125143. [PMID: 31675585 DOI: 10.1016/j.chemosphere.2019.125143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Ochratoxin A (OTA), a mycotoxin widely found in foodstuffs, reportedly damages multiple brain regions in developing rodents, but the corresponding mechanisms have not been elucidated. In this study, zebrafish embryos at 6 h post fertilization (hpf) were exposed to various concentrations of OTA and the phenomenon associated with intracerebral hemorrhage was observed at 72 hpf. Exposure of embryos to OTA significantly increased their hemorrhagic rate in a dose-dependent manner. Large numbers of extravagated erythrocytes were observed in the midbrain/hindbrain areas of Tg(fli-1a:EGFP; gata1:DsRed) embryos following exposure to OTA. OTA also disrupted the vascular patterning, especially the arch-shaped central arteries (CtAs), in treated embryos. Histological analysis revealed a cavity-like pattern in their hindbrain ventricles, implying the possibility of cerebral edema. OTA-induced intracerebral hemorrhage and CtA vessel defects were partially reversed by the presence of miR-731 antagomir or the overexpression of prolactin receptor a (prlra); prlra is a downstream target of miR-731. These results suggest that exposure to OTA has a negative effect on cerebral vasculature development by interfering with the miR-731/PRLR axis in zebrafish.
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Affiliation(s)
- Ting-Shuan Wu
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Ting Lin
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ying-Tzu Huang
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Feng-Yih Yu
- Department of Biomedical Sciences, Chung Shan Medical University, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan.
| | - Biing-Hui Liu
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan.
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25
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Liu S, Ning XH, Guan XL, Li XP, Sun L. Characterization of Streptococcus iniae-induced microRNA profiles in Paralichthys olivaceus and identification of pol-3p-10740_175 as a regulator of antibacterial immune response. FISH & SHELLFISH IMMUNOLOGY 2020; 98:860-867. [PMID: 31756455 DOI: 10.1016/j.fsi.2019.11.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/29/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
MicroRNAs (miRNAs) are involved in many biological activities including immune defense against pathogens. In this study, we applied high-throughput sequencing technology to examine miRNAs in Japanese flounder (Paralichthys olivaceus) infected with Streptococcus iniae at different times. A total of 1038 miRNAs were identified, of which, 249 were novel miRNAs, and 81 showed differential expression (named DEmiRNAs) after S. iniae infection. Of the 81 DEmiRNAs identified, 34 and 58 occurred at 6 h and 24 h post-infection, respectively; most DEmiRNAs were strongly time-specific, and only 13.6% of the DEmiRNAs were shared between the two time points. A total of 9582 target genes were predicted for the 81 DEmiRNAs. The putative target genes were enriched in various GO and KEGG pathways of biological processes and molecular/cellular functions, in particular endocytosis, regulation of transcription, lysososme, and the signaling pathways of MAPK, ErbB, and AMPK. One of the DEmiRNAs, pol-3p-10740_175, was found to target dual specificity phosphatase 6 (Dusp6) and repress the expression of the latter. Transfection of flounder FG cells with pol-3p-10740_175 caused a significant inhibition on S. iniae invasion. The results of this study provided the first S. iniae-induced miRNA profile in Japanese flounder and indicated that flounder miRNAs play an important role in antibacterial immunity.
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Affiliation(s)
- Shuang Liu
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xian-Hui Ning
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiao-Lu Guan
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xue-Peng Li
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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26
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Im J, Kim HS. Genetic features of Haliotis discus hannai by infection of vibrio and virus. Genes Genomics 2019; 42:117-125. [PMID: 31776802 DOI: 10.1007/s13258-019-00892-w] [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: 10/16/2019] [Accepted: 11/14/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND Haliotis discus hannai more commonly referred to as the Pacific Abalone is of significant commercial and economical value in South Korea, with it being the second largest producer in the world. Despite this significance there is a lack of genetic studies with regards to the species. Most existing studies focused mainly on environmental factors. OBJECTIVE To provide a comprehensive review describing the genetic feature of Haliotis discus hannai by infection of vibrio and virus. METHODS This review summarized the immune response in the Haliotis spp. with regards to immunological genes such as Cathepsin B, C-type lectin and Toll-like receptors. Genetic studies with regards to transposable elements and miRNAs are few and far between. A study identified LTR retrotransposon Ty3/gypsy in the species. As to miRNA, a single study identified numerous miRNAs in the Haliotis discus hannai. CONCLUSION This paper sought to provide an overview of genetic perspective with regards to immune response genes, transposable elements and miRNAs.
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Affiliation(s)
- Jennifer Im
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.,Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea. .,Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea.
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27
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Liu Y, Liu Y, Han M, Du X, Liu X, Zhang Q, Liu J. Edwardsiella tarda-induced miR-7a functions as a suppressor in PI3K/AKT/GSK3β signaling pathway by targeting insulin receptor substrate-2 (IRS2a and IRS2b) in Paralichthys olivaceus. FISH & SHELLFISH IMMUNOLOGY 2019; 89:477-485. [PMID: 30940579 DOI: 10.1016/j.fsi.2019.03.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/29/2019] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
To study the effect of Edwardsiella tarda infection on miRNAs expression profile in Japanese flounder, fish were injected intraperitoneally with E. tarda. The miRNAs involved in regulating immune responses were analyzed by high-throughput sequencing. A total of 164 mature miRNAs were identified, of which 17 miRNAs were differentially expressed (DE miRNAs) after E. tarda infection, indicating that they were immune-related miRNAs. To further examine the relationship between the miRNAs and their predicted target mRNAs, a total of 22 predicted target mRNAs, mainly related to endocytic signaling pathway, NF-κB signaling pathway, and p53 signaling pathway, were detected with miRNA mimics in HEK-293T cells by dual-luciferase reporter experiments. Finally, we confirmed that insulin receptor substrate-2 (IRS2a and IRS2b) were regulated by miR-7a. And the target sites of the 3' untranslated region (UTR) of IRS2a and IRS2b were verified by dual-luciferase reporter experiments. Furthermore, we found that the E. tarda and LPS significantly increased host miR-7a expression. In vivo and in vitro studies revealed that IRS2-mediated PI3K/AKT/GSK3β signaling pathway was suppressed. Taken together, these results implied that miR-7a might be a key regulator of PI3K/AKT/GSK3β signaling pathway via suppressing the IRS2a and IRS2b genes.
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Affiliation(s)
- Yuezhong Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yuxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Miao Han
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Xinxin Du
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China; Department of Life Science and Engineering, Jining University, Jining, China
| | - Xiumei Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China; College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Jinxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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28
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Guan XL, Zhang BC, Sun L. pol-miR-194a of Japanese flounder (Paralichthys olivaceus) suppresses type I interferon response and facilitates Edwardsiella tarda infection. FISH & SHELLFISH IMMUNOLOGY 2019; 87:220-225. [PMID: 30641186 DOI: 10.1016/j.fsi.2019.01.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 06/09/2023]
Abstract
MicroRNAs (miRNAs) are a type of small non-coding RNAs that participate in diverse cellular processes including microbial invasion and immune defense. In a previous study, we identified a large amount of Japanese flounder (Paralichthys olivaceus) miRNAs responsive to megalocytivirus infection. In the present study, we examined the function of one of these miRNAs, pol-miR-194a, in association with the infectivity of Edwardsiella tarda, an intracellular bacterial pathogen to many fish species including flounder. We found that pol-miR-194a was induced in expression to a significant extent in the spleen, liver, and gill of Japanese flounder infected by E. tarda. Transfection of flounder cells with pol-miR-194a mimic significantly enhanced the intracellular replication of E. tarda. pol-miR-194a was able to interact specifically with the 3'UTR of IRF7 in a negative manner, resulting in inhibition of IRF7 expression. Consistently, pol-miR-194a significantly blocked the promoter activity of type Ⅰ interferon. Taken together, these results indicate that pol-miR-194a plays an important role in the regulation of flounder immune response as well as microbial infection, and that pol-miR-194a probably serves as a target for E. tarda to manipulate and escape host immune defense.
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Affiliation(s)
- Xiao-Lu Guan
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Bao-Cun Zhang
- Department of Biomedicine and Aarhus Research Center for Innate Immunity, Aarhus University, Aarhus, Denmark
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Zhang J, Sun L. Global profiling of megalocytivirus-induced proteins in tongue sole (Cynoglossus semilaevis) spleen identifies cellular processes essential to viral infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 92:150-159. [PMID: 30428365 PMCID: PMC7102559 DOI: 10.1016/j.dci.2018.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/06/2018] [Accepted: 11/06/2018] [Indexed: 05/30/2023]
Abstract
Megalocytivirus is a DNA virus with a broad host range among farmed fish including tongue sole (Cynoglossus semilaevis). In this study, label-free proteomics was performed to examine protein expression in tongue sole spleen induced by megalocytivirus at 8 and 12 days post infection (dpi). Compared to uninfected control fish, virus-infected fish displayed 315 up-regulated proteins and 111 down-regulated proteins at 8 dpi, and 48 up-regulated proteins and 43 down-regulated proteins at 12 dpi. The expressions of five differentially expressed proteins were confirmed by Western blot. The differentially expressed proteins were enriched in the pathways and processes associated with innate immune response and viral infection. Interference with the expression of two up-regulated proteins of the ubiquitin proteasome system (UPS), i.e. proteasome assembly chaperone 2 and proteasome maturation protein, significantly reduced viral propagation in fish, whereas overexpression of these two proteins significantly enhanced viral propagation. Consistently, inhibition of the functioning of proteasome significantly impaired viral replication in vivo. This study provided the first global protein profile responsive to megalocytivirus in tongue sole, and revealed an essential role of UPS in viral infection.
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Affiliation(s)
- Jian Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China; Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.
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30
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Wang M, Jiang S, Wu W, Yu F, Chang W, Li P, Wang K. Non-coding RNAs Function as Immune Regulators in Teleost Fish. Front Immunol 2018; 9:2801. [PMID: 30546368 PMCID: PMC6279911 DOI: 10.3389/fimmu.2018.02801] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/13/2018] [Indexed: 12/13/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are functional RNA molecules that are transcribed from DNA but not translated into proteins. ncRNAs function as key regulators of gene expression and chromatin modification. Recently, the functional role of ncRNAs in teleost fish has been extensively studied. Teleost fish are a highly diverse group among the vertebrate lineage. Fish are also important in terms of aquatic ecosystem, food production and human life, being the source of animal proteins worldwide and models of biomedical research. However, teleost fish always suffer from the invasion of infectious pathogens including viruses and bacteria, which has resulted in a tremendous economic loss to the fishing industry worldwide. Emerging evidence suggests that ncRNAs, especially miRNAs and lncRNAs, may serve as important regulators in cytokine and chemokine signaling, antigen presentation, complement and coagulation cascades, and T cell response in teleost fish. In this review, we summarize current knowledge and understanding of the roles of both miRNAs and lncRNAs in immune regulation in teleost fish. Molecular mechanism insights into the function of ncRNAs in fish immune response may contribute to the development of potential biomarkers and therapeutic targets for the prevention and treatment of fish diseases.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Shuai Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Wu
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Fei Yu
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Wenguang Chang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Kun Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
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Zebrafish miR-462-731 regulates hematopoietic specification and pu.1-dependent primitive myelopoiesis. Cell Death Differ 2018; 26:1531-1544. [PMID: 30459392 DOI: 10.1038/s41418-018-0234-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) play significant roles in both embryonic hematopoiesis and hematological malignancy. Zebrafish miR-462-731 cluster is orthologous of miR-191-425 in human which regulates proliferation and tumorigenesis. In our previous work, miR-462-731 was found highly and ubiquitously expressed during early embryogenesis. In this study, by loss-of-function analysis (morpholino knockdown combined with CRISRP/Cas9 knockout) and mRNA profiling, we suggest that miR-462-731 is required for normal embryonic development by regulating cell survival. We found that loss of miR-462/miR-731 caused a remarkable decrease in the number of erythroid cells as well as an ectopic myeloid cell expansion at 48 hpf, suggesting a skewing of myeloid-erythroid lineage differentiation. Mechanistically, miR-462-731 provides an instructive input for pu.1-dependent primitive myelopoiesis through regulating etsrp/scl signaling combined with a novel pu.1/miR-462-731 feedback loop. On the other hand, morpholino (MO) knockdown of miR-462/miR-731 resulted in an expansion of posterior blood islands at 24 hpf, which is a mild ventralization phenotype resulted from elevation of BMP signaling. Rescue experiments with both BMP type I receptor inhibitor dorsomorphin and alk8 MO indicate that miR-462-731 acts upstream of alk8 within the BMP/Smad signaling pathway and functions as a novel endogenous BMP antagonist. Besides, an impairment of angiogenesis was observed in miR-462/miR-731 morphants. The specification of arteries and veins was also perturbed, as characterized by the irregular patterning of efnb2a and flt4 expression. Our study unveils a previously unrecognized role of miR-462-731 in BMP/Smad signaling mediated hematopoietic specification of mesodermal progenitors and demonstrates a miR-462-731 mediated regulatory mechanism driving primitive myelopoiesis in the ALPM. We also show a requirement for miR-462-731 in regulating arterial-venous specification and definitive hematopoietic stem cell (HSC) production. The current findings might provide further insights into the molecular mechanistic basis of miRNA regulation of embryonic hematopoiesis and hematological malignancy.
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Cao Y, Wang D, Li S, Xu L, Zhao J, Liu H, Lu T, Zhang Q. Identification and analysis of differentially expressed microRNAs in rainbow trout (Oncorhynchus mykiss) responding to infectious hematopoietic necrosis virus infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 88:28-36. [PMID: 29990507 DOI: 10.1016/j.dci.2018.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/06/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
MicroRNAs (miRNAs) are a class of regulators essential for numerous biological processes. Infectious hematopoietic necrosis virus (IHNV) is one of the most important viral pathogens in salmon and trout. In this study, the miRNA expression profiles of rainbow trout upon IHNV infection were explored. In total, 392 known miRNAs and 936 novel miRNAs were identified. Twelve known and 13 novel miRNAs were differentially expressed between infected and uninfected fish. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that certain miRNA target genes were associated with biological regulation, the immune system, and signal transduction. In addition, over- and suppressed expression of miR-146a-3p, miR-155-5p, miR-216a-5p, and miR-499b-5p could respectively increase and decrease viral gene expression in cells and viral titers. MiR-146a-3p and miR-216a-5p inhibited the expression of type-I IFN and the Mx1 gene induced by IHNV. These results provide preliminary insights into the IHNV-host interactions mediated by miRNAs.
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Affiliation(s)
- Yongsheng Cao
- Laboratory of Fish Diseases, Department of Aquaculture, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Songfa Street No. 43, Daoli District, Harbin, 150070, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Di Wang
- Laboratory of Fish Diseases, Department of Aquaculture, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Songfa Street No. 43, Daoli District, Harbin, 150070, China.
| | - Shaowu Li
- Laboratory of Fish Diseases, Department of Aquaculture, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Songfa Street No. 43, Daoli District, Harbin, 150070, China.
| | - Liming Xu
- Laboratory of Fish Diseases, Department of Aquaculture, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Songfa Street No. 43, Daoli District, Harbin, 150070, China.
| | - Jingzhuang Zhao
- Laboratory of Fish Diseases, Department of Aquaculture, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Songfa Street No. 43, Daoli District, Harbin, 150070, China.
| | - Hongbai Liu
- Laboratory of Fish Diseases, Department of Aquaculture, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Songfa Street No. 43, Daoli District, Harbin, 150070, China.
| | - Tongyan Lu
- Laboratory of Fish Diseases, Department of Aquaculture, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Songfa Street No. 43, Daoli District, Harbin, 150070, 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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Salazar C, Marshall SH. Involvement of selected cellular miRNAs in the in vitro and in vivo infection of infectious salmon anemia virus (ISAV). Microb Pathog 2018; 123:353-360. [PMID: 30041004 DOI: 10.1016/j.micpath.2018.07.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/16/2022]
Abstract
Infectious salmon anemia virus (ISAV) is the causative agent of infectious salmon anemia (ISA), a relatively novel disease primarily affecting farmed salmon species, primarily in Salmo salar specimens, causing severe outbreaks in most producer countries. Although ISAV has been extensively studied at the molecular level, not much is known about the host/cell interaction at the small RNA level. MicroRNAs (miRNAs) are small, non-coding RNA that regulate mRNA expression at the post-transcriptional level. In recent years, the putative role of these molecules in host-pathogen interactions has drawn particular attention because of their pivotal involvement as regulatory elements in a number of eukaryotic organisms. Given the importance of the salmon industry in Chile, a deep understanding of the interaction between ISAV and its hosts is of importance. In the present work, we studied the kinetic expression of selected miRNAs during ISAV infection, both in vitro and in vivo. Based on initial experimental data derived from a small RNA-Seq analysis, a group of miRNAs that were differentially expressed in infected cells were selected for analysis. As a result, two miRNAs, miR-462a-5p and miR-125 b-5p, showed increased and decreased expression, respectively, during ISAV infection.
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Affiliation(s)
- Carolina Salazar
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Sergio H Marshall
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.
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Discovery of microRNAs associated with the antiviral immune response of Atlantic cod macrophages. Mol Immunol 2017; 93:152-161. [PMID: 29190475 DOI: 10.1016/j.molimm.2017.11.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/13/2017] [Accepted: 11/17/2017] [Indexed: 02/08/2023]
Abstract
MicroRNAs (miRNAs) are known to play important immunoregulatory roles in teleosts, although miRNAs involved in the antiviral immune response of Atlantic cod (Gadus morhua) were previously uncharacterised. Using deep sequencing and qPCR, the present study was conducted to identify miRNAs responsive to the viral mimic, polyriboinosinic polyribocytidylic acid (pIC) in Atlantic cod macrophages. Macrophage samples isolated from Atlantic cod (n=3) and treated with pIC or phosphate buffered saline (PBS control) for 24 and 72h were used for miRNA profiling. Following deep sequencing, DESeq2 analyses identified four (miR-731-3p, miR-125b-3-3p, miR-150-3p and miR-462-3p) and two (miR-2188-3p and miR-462-3p) significantly differentially expressed miRNAs at 24 and 72h post-stimulation (HPS), respectively. Sequencing-identified miRNAs were subjected to qPCR validation using a larger number of biological replicates (n=6) exposed to pIC or PBS over time (i.e. 12, 24, 48 and 72 HPS). As in sequencing, miR-731-3p, miR-462-3p and miR-2188-3p showed significant up-regulation by pIC. The sequencing results were not qPCR-validated for miR-125b-3-3p and miR-150-3p as up- and down-regulated miRNAs at 24 HPS, respectively; however, qPCR results showed significant up-regulation in response to pIC stimulation at later time points (i.e. 48 and/or 72 HPS). We also used qPCR to assess the expression of other miRNAs that were previously shown as immune responsive in other vertebrates. qPCR results at 48 and/or 72 HPS revealed that miR-128-3-5p, miR-214-1-5p and miR-451-3p were induced by pIC, whereas miR-30b-3p and miR-199-1-3p expression were repressed in response to pIC. The present study identified ten pIC-stimulated miRNAs, suggesting them as important in antiviral immune responses of Atlantic cod macrophages. Some pIC-responsive miRNAs identified in this study were predicted to target putative immune-related genes of Atlantic cod (e.g. miR-30b-3p targeting herc4), although the regulatory functions of these miRNAs need to be validated by future studies.
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Andreassen R, Høyheim B. miRNAs associated with immune response in teleost fish. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:77-85. [PMID: 28254620 DOI: 10.1016/j.dci.2017.02.023] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 02/25/2017] [Accepted: 02/26/2017] [Indexed: 06/06/2023]
Abstract
MicroRNAs (miRNAs) have been identified as important post transcriptional regulators of gene expression. In higher vertebrates, a subset of miRNAs has been identified as important regulators of a number of key genes in immune system gene networks, and this paper review recent studies on miRNAs associated with immune response in teleost fish. Challenge studies conducted in several species have identified differently expressed miRNAs associated with viral or bacterial infection. The results from these studies point out several miRNAs that are likely to have evolutionary conserved functions that are related to immune response in teleost fish. Changed expression levels of mature miRNAs from the five miRNA genes miRNA-462, miRNA-731, miRNA-146, miRNA-181 and miRNA-223 are observed following viral as well as bacterial infection in several teleost fish. Furthermore, significant changes in expression of mature miRNAs from the five genes miRNA-21, miRNA-155, miRNA-1388, miRNA-99 and miRNA-100 are observed in multiple studies of virus infected fish while changes in expression of mature miRNA from the three genes miRNA-122, miRNA-192 and miRNA-451 are observed in several studies of fish with bacterial infections. Interestingly, some of these genes are not present in higher vertebrates. The function of the evolutionary conserved miRNAs responding to infection depends on the target gene(s) they regulate. A few target genes have been identified while a large number of target genes have been predicted by in silico analysis. The results suggest that many of the targets are genes from the host's immune response gene networks. We propose a model with expected temporal changes in miRNA expression if they target immune response activators/effector genes or immune response inhibitors, respectively. The best way to understand the function of a miRNA is to identify its target gene(s), but as the amount of genome resources for teleost fish is limited, with less well characterized genomes and transcriptomes, identifying the true target genes of the miRNAs associated with the immune response is a challenge. Identifying such target genes by applying new methods and approaches will likely be the next important step to understand the function of the miRNAs associated with immune response in teleost fish.
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Affiliation(s)
- Rune Andreassen
- Department of Pharmacy and Biomedical and Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Pilestredet 50, N-0130 Oslo, Norway.
| | - Bjørn Høyheim
- Department of Basic Sciences and Aquatic Medicine, School of Veterinary Medicine, Norwegian University of Life Sciences, Ullevålsveien 72, 0454 Oslo, Norway.
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Zhang J, Sun L. Transcriptome analysis reveals temperature-regulated antiviral response in turbot Scophthalmus maximus. FISH & SHELLFISH IMMUNOLOGY 2017; 68:359-367. [PMID: 28735862 DOI: 10.1016/j.fsi.2017.07.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/19/2017] [Accepted: 07/19/2017] [Indexed: 06/07/2023]
Abstract
Megalocytivirus is a severe pathogen to turbot (Scophthalmus maximus), a popular aquaculture species in many countries. In this study, we investigated the effect of temperature on the antiviral response of turbot at transcriptome level. We found that when turbot were infected with megalocytivirus RBIV-C1 at low temperatures (14 °C, 16 °C, and 18 °C), viral replication was undetectable or moderate and no fish mortality occurred; in contrast, when turbot were infected with RBIV-C1 at high temperatures (20 °C, 22 °C, and 24 °C), viral replication was robust and 100% host mortality was observed. During the course of viral infection, downward temperature shift curbed viral replication and augmented host survival, whereas upward temperature shift promoted viral replication and reduced host survival. Comparative transcriptome analyses were conducted to examine the whole-genome transcription of turbot infected with RBIV-C1 at 16 °C and 22 °C for 4 days (samples S16-4d and S22-4d, respectively) and 8 days (samples S16-8d and S22-8d, respectively). The results showed that compared to S22-4d and S22-8d, 1600 and 5927 upregulated unigenes of various functional categories were identified in S16-4d and S16-8d, respectively. Of these genes, 22 were immune-related, most of which were detected in S16-8d and exhibited more genetic subtypes in S16-8d than in S16-4d. In addition, upregulated genes associated with cell junctions and cell membrane were also identified. These results indicate that temperature had a profound effect on the global transcription of turbot, which consequently affects the immune as well as physical resistance of the fish against viral infection.
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Affiliation(s)
- Jian Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Zhou Y, Li R, Yu H, Wang R, Shen Z. microRNA-130a is an oncomir suppressing the expression of CRMP4 in gastric cancer. Onco Targets Ther 2017; 10:3893-3905. [PMID: 28831264 PMCID: PMC5548272 DOI: 10.2147/ott.s139443] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Gastric cancer is one of the most common causes of death worldwide, although its incidence has steadily declined in recent years. There is strong evidence that aberrantly expressed microRNAs (miRNAs) are involved in gastric cancer tumorigenesis. Furthermore, CRMP4 is closely associated with the occurrence and development of gastric cancer, and our predictions suggest that miR-130a, which can promote gastric cancer tumorigenesis, is a potential CRMP4 regulator. In this study, we investigated the expression of CRMP4 and miR-130a in human gastric cancer cell lines by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Western blot (WB) examination and direct interactions between miR-130a and CRMP4 by dual-luciferase reporter assay. We also evaluated the biological roles of miR-130a and CRMP4 in gastric cancer cells by flow cytometry, MTT assay, soft agar colony formation assay, and Transwell tests and confirmed CRMP4 function in vivo, using a tumor xenograft model. Our results demonstrated that CRMP4 expression was significantly decreased at both the gene and protein levels, while miR-130a expression was notably increased, in five human gastric cancer cell lines compared with human gastric epithelial cells. Dual-luciferase reporter assays indicated that CRMP4 was the direct target of miR-130a. Moreover, an inverse regulatory relationship between miR-130a and CRMP4 was verified by qRT-PCR and WB, and overexpression of miR-130a in BGC823 cells enhanced apoptosis and cell proliferation, arrested the cell cycle in G0/G1, and facilitated cell colony formation, invasion, migration, and adhesion, while upregulation of CRMP4 had opposite effects. Finally, the growth and weight of transplanted tumors derived from BGC823 cells in which CRMP4 was knocked down were remarkably reduced. These data indicate that miR-130a is an oncomir targeting CRMP4 and could be developed as a potential prognostic factor and a novel therapeutic target in gastric cancer.
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Affiliation(s)
- Yiran Zhou
- Department of Pharmacy, Kunming Medical University
- Yan’an Hospital Affiliated to Kunming Medical University, Kunming, People’s Republic of China
| | - Ruhong Li
- Yan’an Hospital Affiliated to Kunming Medical University, Kunming, People’s Republic of China
| | - Haidong Yu
- Yan’an Hospital Affiliated to Kunming Medical University, Kunming, People’s Republic of China
| | - Ruotian Wang
- Yan’an Hospital Affiliated to Kunming Medical University, Kunming, People’s Republic of China
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Hu YH, Zhang BC, Zhou HZ, Guan XL, Sun L. Edwardsiella tarda-induced miRNAs in a teleost host: Global profile and role in bacterial infection as revealed by integrative miRNA-mRNA analysis. Virulence 2017; 8:1457-1464. [PMID: 28762875 DOI: 10.1080/21505594.2017.1356541] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- Yong-Hua Hu
- a Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China.,b Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology , Qingdao , China
| | - Bao-Cun Zhang
- a Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China.,b Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology , Qingdao , China
| | - Hai-Zhen Zhou
- a Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China.,b Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology , Qingdao , China.,c University of Chinese Academy of Sciences , Beijing , China
| | - Xiao-Lu Guan
- a Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China.,b Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology , Qingdao , China.,c University of Chinese Academy of Sciences , Beijing , China
| | - Li Sun
- a Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China.,b Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology , Qingdao , China
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Zhang C, Yi L, Feng S, Liu X, Su J, Lin L, Tu J. MicroRNA miR-214 inhibits snakehead vesiculovirus replication by targeting the coding regions of viral N and P. J Gen Virol 2017; 98:1611-1619. [PMID: 28699870 DOI: 10.1099/jgv.0.000854] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Snakeheadvesiculovirus (SHVV), a new member of the family Rhabdoviridae, has caused enormous economic losses in snakehead fish culture during the past years in China; however, little is known about the molecular mechanisms of its pathogenicity. MicroRNAs (miRNAs) are small non-coding RNAs that play important roles in virus infection. In this study, we identified that SHVV infection downregulated miR-214 in striped snakehead (SSN-1) cells in a time- and dose-dependent manner. Notably, transfecting SSN-1 cells with miR-214 mimic significantly inhibitedSHVV replication, whereas miR-214 inhibitor promoted it, suggesting that miR-214 acted as a negative regulator of SHVV replication. Our study further demonstrated that N and P of SHVV were the target genes of miR-214. Over-expression of P, but not N, inhibited IFN-α production in SHVV-infected cells, which could be restored by over-expression of miR-214. Taken together, these results suggest that miR-214 is downregulated during SHVV infection, and the downregulated miR-214 in turn increased N and P expression and decreased IFN-α production, thus facilitating SHVV replication. This study provides a better understanding of the molecular mechanisms on the pathogenesis of SHVV and a potential antiviral strategy against SHVV infection.
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Affiliation(s)
- Chi Zhang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Lizhu Yi
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Shuangshuang Feng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xueqin Liu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Jianguo Su
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Li Lin
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.,College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong 510225, PR China
| | - Jiagang Tu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
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Huang CH, Chen N, Huang CX, Zhang B, Wu M, He L, Liu H, Tang R, Wang WM, Wang HL. Involvement of the miR-462/731 cluster in hypoxia response in Megalobrama amblycephala. FISH PHYSIOLOGY AND BIOCHEMISTRY 2017; 43:863-873. [PMID: 28280952 DOI: 10.1007/s10695-017-0341-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 01/04/2017] [Indexed: 05/20/2023]
Abstract
MicroRNAs (miRNAs) are non-coding small RNAs showing both evolutionarily conserved and unique features and are involved in nearly all biological processes. In the present study, the role played by miR-462/731 cluster miRNAs in hypoxia response in Megalobrama amblycephala, an important freshwater fish, was investigated. The M. amblycephala miR-462/731 cluster locus and their 5' flanking sequences were sequenced and analyzed. In M. amblycephala and other teleost fish species, the mature sequences of miR-462 and miR-731 were identical and hypoxia-responsive elements (HREs) were identified upstream of the miR-462/731 loci. The two miRNAs were significantly induced in the liver, spleen, gill, muscle, and brain after hypoxia treatment. The expression of both miRNAs was also upregulated in cells that received treatment which mimicked hypoxia. Furthermore, reporter assay revealed that M. amblycephala HREs can be activated by hypoxia. Taken together, the 462/731 cluster may play a role in the regulation of the hypoxia response in M. amblycephala.
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Affiliation(s)
- Cui-Hong Huang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Nan Chen
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Chun-Xiao Huang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Bao Zhang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Meng Wu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Lei He
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Hong Liu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, 430070, Wuhan, People's Republic of China
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Rong Tang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, 430070, Wuhan, People's Republic of China
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Wei-Min Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Huan-Ling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China.
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, 430070, Wuhan, People's Republic of China.
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China.
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41
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Andreassen R, Woldemariam NT, Egeland IØ, Agafonov O, Sindre H, Høyheim B. Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection. BMC Genomics 2017; 18:349. [PMID: 28472924 PMCID: PMC5418855 DOI: 10.1186/s12864-017-3741-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 04/27/2017] [Indexed: 02/07/2023] Open
Abstract
Background MicroRNAs (miRNAs) control multiple biological processes including the innate immune responses by negative post-transcriptional regulation of gene expression. As there were no studies on the role(s) of miRNAs in viral diseases in Atlantic salmon, we aimed to identify miRNAs responding to salmonid alphavirus (SAV) infection. Their expression were studied at different time points post infection with SAV isolates associated with different mortalities. Furthermore, the genome sequences of the identified miRNAs were analysed to reveal putative cis-regulatory elements, and, finally, their putative target genes were predicted. Results Twenty differentially expressed miRNAs (DE miRNAs) were identified. The expression of the majority of these increased post infection with maximum levels reached after the viral load were stabilized or decreasing. On the other hand, some miRNAs (e.g. the miRNA-21 family) showed decreased expression at the early time points post infection. There were significant differences in the temporal expression of individual miRNA associated with different SAV isolates. Target gene prediction in SAV responsive immune network genes showed that seventeen of the DE miRNAs could target 24 genes (e.g. IRF3, IRF7). Applying the Atlantic salmon transcriptome as input 28 more immune network genes were revealed as putative targets (e.g. IRF5, IRF4). The majority of the predicted target genes promote inflammatory response. The upstream sequences of the miRNA genes revealed a high density of cis-regulatory sequences known as binding sites for immune network transcription factors (TFs). A high expression in the late phase could therefore be due to increased transcription promoted by immune response activated TFs. Based on the in silico target predictions, we discuss their putative roles as early promotors or late inhibitors of inflammation. We propose that the differences in expressions associated with different SAV isolates could contribute to their differences in mortality rates. Conclusions This study represents the first steps in exploring miRNAs important in viral-host interaction in Atlantic salmon. We identified several miRNAs responding to SAV infection. Some likely to prohibit harmful inflammation while other may promote an early immune response. Their predicted functions need to be validated and further studied in functional assays to fully understand their roles in immune homeostasis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3741-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rune Andreassen
- Department of Pharmacy and Biomedical and Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Pilestredet 50, N-0130, Oslo, Norway.
| | - Nardos Tesfaye Woldemariam
- Department of Pharmacy and Biomedical and Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Pilestredet 50, N-0130, Oslo, Norway
| | - Ine Østråt Egeland
- Department of Pharmacy and Biomedical and Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Pilestredet 50, N-0130, Oslo, Norway
| | - Oleg Agafonov
- Bioinformatics Core Facility, Department of Core Facilities, Institute of Cancer Research, Radium hospital, part of Oslo University Hospital, Oslo, Norway
| | - Hilde Sindre
- Norwegian Veterinary Institute, PB 750 Sentrum, N-106, Oslo, Norway
| | - Bjørn Høyheim
- Department of Basic Sciences and Aquatic Medicine, School of Veterinary Medicine, Norwegian University of Life Sciences, Ullevålsveien 72, 0454, Oslo, Norway
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42
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Schulz KS, Mossman KL. Viral Evasion Strategies in Type I IFN Signaling - A Summary of Recent Developments. Front Immunol 2016; 7:498. [PMID: 27891131 PMCID: PMC5104748 DOI: 10.3389/fimmu.2016.00498] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/26/2016] [Indexed: 12/13/2022] Open
Abstract
The immune system protects the organism against infections and the damage associated with them. The first line of defense against pathogens is the innate immune response. In the case of a viral infection, it induces the interferon (IFN) signaling cascade and eventually the expression of type I IFN, which then causes an antiviral state in the cells. However, many viruses have developed strategies to counteract this mechanism and prevent the production of IFN. In order to modulate or inhibit the IFN signaling cascade in their favor, viruses have found ways to interfere at every single step of the cascade, for example, by inducing protein degradation or cleavage, or by mediate protein polyubiquitination. In this article, we will review examples of viruses that modulate the IFN response and describe the mechanisms they use.
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Affiliation(s)
- Katharina S Schulz
- Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre, Institute for Infectious Disease Research, McMaster University , Hamilton, ON , Canada
| | - Karen L Mossman
- Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre, Institute for Infectious Disease Research, McMaster University , Hamilton, ON , Canada
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