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Wei F, Zuo X, Jin F, Yang Q, Cui Y, Zhao M, Cui M, Liang J. Integrated miRNA-mRNA analysis uncovers immediate-early response to salinity stress in gill-derived cell line of Gymnocypris przewalskii. BMC Genomics 2024; 25:965. [PMID: 39407113 PMCID: PMC11481739 DOI: 10.1186/s12864-024-10869-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Accepted: 10/07/2024] [Indexed: 10/19/2024] Open
Abstract
Salinity adaptation is an important issue in aquaculture. Understanding the immediate-early response to salinity stress helps in comprehending this process. In vitro experiments using cell lines can explain cell-independent reactions without the involvement of hormones in vivo. In this study, salinity stress experiments were conducted using cell line derived from the gills of Gymnocypris przewalskii (GPG cell line) to isolate immediate-early response-related genes and miRNAs using transcriptomics, followed by bioinformatics analysis. The results showed that intracellular free Ca2+ appeared to be a key factor in cell sensing and initiating downstream cell signaling in response to external salinity. Additionally, cell apoptosis was the most common feature of salinity stress, with multiple signaling pathways involved in salinity-induced cell apoptosis. Furthermore, MiRNAs played a crucial role in the rapid response to salinity stress by selectively inhibiting the expression of specific genes. Additionally, for the first time in the G. przewalskii genome, Tf2 and TY3 families of transposons were found to have responsive roles to the external salinity stress. This study contributes to a better understanding of osmotic sensing in G. przewalskii and provides theoretical assistance for improving salinity adaptation in aquaculture fish species.
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Affiliation(s)
- Fulei Wei
- College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, 810016, PR China
- State Key Laboratory of Plateau Ecology and Agriculture, College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, 810016, PR China
| | - Xianzhi Zuo
- College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, 810016, PR China
| | - Faxin Jin
- College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, 810016, PR China
| | - Qiangdong Yang
- College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, 810016, PR China
| | - Yanrong Cui
- State Key Laboratory of Plateau Ecology and Agriculture, College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, 810016, PR China
| | - Mingyang Zhao
- College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, 810016, PR China
| | - Mingming Cui
- Qinghai Academy of Agriculture and Forestry sciences, Qinghai University, Xining, 810016, China
| | - Jian Liang
- State Key Laboratory of Plateau Ecology and Agriculture, College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, 810016, PR China.
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Krasnov A, Afanasyev S, Hansen MHS, Bou M, Sveen L, Dessen JE. Smoltification of Atlantic Salmon ( Salmo salar L.) Is Associated with Enhanced Traffic and Renewal of B Cell Repertoire. Genes (Basel) 2024; 15:1220. [PMID: 39336811 PMCID: PMC11431436 DOI: 10.3390/genes15091220] [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: 08/19/2024] [Revised: 09/12/2024] [Accepted: 09/16/2024] [Indexed: 09/30/2024] Open
Abstract
The smoltification of farmed Atlantic salmon is commonly associated with mild immunosuppression. However, B cells may deviate from this trend, showing increased proliferation and migration during this period. This study assessed the effects of smoltification and adaptation to seawater in a controlled experiment. Analyses were conducted on the head kidney, spleen, gill, and both visceral and subcutaneous fat (VAT, SAT) across four time points: parr, early and complete smoltification, and twelve weeks post-seawater transfer. Gene expression analysis was performed to track the distribution and developmental changes in their B cells. Expression profiles of three types of immunoglobulins (ig), including membrane-bound and secreted forms of igm, as well as B cell-specific markers pax1 and cd79, showed strong correlations and contrasted with profiles of other immune cell markers. The highest levels of expression were observed in the lymphatic tissue, followed by the VAT. Enhanced expression in the gill and adipose tissues of smolts suggested an increase in B cell populations. Parallel sequencing of the variable region of the IgM heavy chain was used to track B cell traffic, assessed by the co-occurrence of the most abundant sequences (clonotypes) across different tissues. Smoltification markedly enhanced traffic between all tissues, which returned to initial levels after twelve weeks in the sea. The preferred migration between the head kidney, spleen, and VAT supports the role of abdominal fat as a reservoir of lymphocytes. These findings are discussed in the context of recent studies that suggested the functional significance of B cell traffic in Atlantic salmon. Specifically, the migration of B cells expressing secreted immunoglobulins to virus-infected hearts has been identified as a key factor in the disease recovery and survival of fish challenged with salmon alphavirus (SAV); this process is accelerated by vaccination. Additionally, the study of melanized foci in the skeletal muscles revealed an association between antigen-dependent differentiation and the migration of B cells, indicating a transfer from local to systemic immune responses. Updating the antibody repertoire in the lymphatic and peripheral tissues of smolts may assist in their adaptation to the marine environment and in encountering new pathogens. Emerging evidence highlights B cell migration as an important and previously unrecognized immune mechanism in salmonids.
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Affiliation(s)
- Aleksei Krasnov
- The Norwegian Institute of Aquaculture, Nofima, 9291 Tromsø, Norway
| | - Sergey Afanasyev
- Sechenov Institute of Evolutionary Physiology and Biochemistry, 194233 St. Petersburg, Russia
| | | | - Marta Bou
- The Norwegian Institute of Aquaculture, Nofima, 9291 Tromsø, Norway
| | - Lene Sveen
- The Norwegian Institute of Aquaculture, Nofima, 9291 Tromsø, Norway
| | - Jens-Erik Dessen
- The Norwegian Institute of Aquaculture, Nofima, 9291 Tromsø, Norway
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Liu M, Tang H, Gao K, Zhang X, Ma Z, Jia Y, Yang Z, Inam M, Gao Y, Wang G, Shan X. Poly (I:C)-Induced microRNA-30b-5p Negatively Regulates the JAK/STAT Signaling Pathway to Mediate the Antiviral Immune Response in Silver Carp ( Hypophthalmichthys molitrix) via Targeting CRFB5. Int J Mol Sci 2024; 25:5712. [PMID: 38891899 PMCID: PMC11172372 DOI: 10.3390/ijms25115712] [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: 04/20/2024] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
In aquaculture, viral diseases pose a significant threat and can lead to substantial economic losses. The primary defense against viral invasion is the innate immune system, with interferons (IFNs) playing a crucial role in mediating the immune response. With advancements in molecular biology, the role of non-coding RNA (ncRNA), particularly microRNAs (miRNAs), in gene expression has gained increasing attention. While the function of miRNAs in regulating the host immune response has been extensively studied, research on their immunomodulatory effects in teleost fish, including silver carp (Hyphthalmichthys molitrix), is limited. Therefore, this research aimed to investigate the immunomodulatory role of microRNA-30b-5p (miR-30b-5p) in the antiviral immune response of silver carp (Hypophthalmichthys molitrix) by targeting cytokine receptor family B5 (CRFB5) via the JAK/STAT signaling pathway. In this study, silver carp were stimulated with polyinosinic-polycytidylic acid (poly (I:C)), resulting in the identification of an up-regulated miRNA (miR-30b-5p). Through a dual luciferase assay, it was demonstrated that CRFB5, a receptor shared by fish type I interferon, is a novel target of miR-30b-5p. Furthermore, it was found that miR-30b-5p can suppress post-transcriptional CRFB5 expression. Importantly, this study revealed for the first time that miR-30b-5p negatively regulates the JAK/STAT signaling pathway, thereby mediating the antiviral immune response in silver carp by targeting CRFB5 and maintaining immune system stability. These findings not only contribute to the understanding of how miRNAs act as negative feedback regulators in teleost fish antiviral immunity but also suggest their potential therapeutic measures to prevent an excessive immune response.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yunhang Gao
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China; (M.L.); (H.T.); (K.G.); (X.Z.); (Z.M.); (Y.J.); (Z.Y.); (M.I.); (X.S.)
| | - Guiqin Wang
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China; (M.L.); (H.T.); (K.G.); (X.Z.); (Z.M.); (Y.J.); (Z.Y.); (M.I.); (X.S.)
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Liu M, Tang H, Gao K, Zhang X, Yang Z, Gao Y, Shan X. Identification and Characterization of Immune-Associated MicroRNAs in Silver Carp ( Hypophthalmichthys molitrix) Responding to Aeromonas veronii and LPS Stimulation. Animals (Basel) 2024; 14:285. [PMID: 38254454 PMCID: PMC10812751 DOI: 10.3390/ani14020285] [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: 11/15/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
The ubiquitous Gram-negative bacterial pathogen Aeromonas veronii (A. veronii) can easily cause inflammatory reactions in aquatic organisms, resulting in high mortality and huge economic losses. MicroRNAs (miRNAs) participate in immune regulation and have certain conserved properties. MiRNAs are involved in the immune responses of a variety of teleost fish infected with bacteria, whereas there is no related report in silver carp (Hypophthalmichthys molitrix). Therefore, we identified the expression profiles of miRNA in silver carp stimulated by A. veronii and LPS. Among them, the quantity of differentially expressed miRNAs (DEmiRNAs) obtained in the silver carp challenge group was 73 (A. veronii) and 90 (LPS). The GO enrichment and analysis of KEGG pathways have shown that the predicted target genes are mainly associated with lipid metabolism and the immune response in silver carp. This indicates the possibility that miRNAs play a role in regulating immune-related pathways. In addition, a total of eight DEmiRNAs validated the accuracy of the sequencing result via quantitative real-time PCR (qRT-PCR). Finally, we selected the silver carp head kidney macrophage cells (HKCs) as model cells and proved that miR-30b-5p can regulate the inflammatory response in silver carp HKCs. This study lays the foundation for exploring miRNA regulation in silver carp during pathogenic bacterial infection. In addition, it provides a reference for the future development of non-coding RNA antibacterial drugs.
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Affiliation(s)
| | | | | | | | | | - Yunhang Gao
- College of Veterinary Medicine, Jilin Agricultural University, Changchun 130118, China; (M.L.); (H.T.); (K.G.); (X.Z.); (Z.Y.)
| | - Xiaofeng Shan
- College of Veterinary Medicine, Jilin Agricultural University, Changchun 130118, China; (M.L.); (H.T.); (K.G.); (X.Z.); (Z.Y.)
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Verleih M, Visnovska T, Nguinkal JA, Rebl A, Goldammer T, Andreassen R. The Discovery and Characterization of Conserved and Novel miRNAs in the Different Developmental Stages and Organs of Pikeperch ( Sander lucioperca). Int J Mol Sci 2023; 25:189. [PMID: 38203361 PMCID: PMC10778745 DOI: 10.3390/ijms25010189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Micro RNAs (miRNAs) are short non-coding RNAs that act as post-transcriptional gene expression regulators. Genes regulated in vertebrates include those affecting growth and development or stress and immune response. Pikeperch (Sander lucioperca) is a species that is increasingly being considered for farming in recirculation aquaculture systems. We characterized the pikeperch miRNA repertoire to increase the knowledge of the genomic mechanisms affecting performance and health traits by applying small RNA sequencing to different developmental stages and organs. There were 234 conserved and 8 novel miRNA genes belonging to 104 families. A total of 375 unique mature miRNAs were processed from these genes. Many mature miRNAs showed high relative abundances or were significantly more expressed at early developmental stages, like the miR-10 and miR-430 family, let-7, the miRNA clusters 106-25-93, and 17-19-92. Several miRNAs associated with immune responses (e.g., slu-mir-731-5p, slu-mir-2188-5p, and slu-mir-8159-5p) were enriched in the spleen. The mature miRNAs slu-mir-203a-3p and slu-mir-205-5p were enriched in gills. These miRNAs are similarly abundant in many vertebrates, indicating that they have shared regulatory functions. There was also a significantly increased expression of the disease-associated miR-462/miR-731 cluster in response to hypoxia stress. This first pikeperch miRNAome reference resource paves the way for future functional studies to identify miRNA-associated variations that can be utilized in marker-assisted breeding programs.
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Affiliation(s)
- Marieke Verleih
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (M.V.); (A.R.)
| | - Tina Visnovska
- Bioinformatics Core Facility, Oslo University Hospital, 0424 Oslo, Norway
| | - Julien A. Nguinkal
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany;
| | - Alexander Rebl
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (M.V.); (A.R.)
| | - Tom Goldammer
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (M.V.); (A.R.)
- Faculty of Agriculture and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
| | - Rune Andreassen
- Department of Life Sciences and Health, OsloMet—Oslo Metropolitan University, 0167 Oslo, Norway;
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Zhao T, Zou Y, Yan H, Chang Y, Zhan Y. Non-coding RNAs targeting NF-κB pathways in aquatic animals: A review. Front Immunol 2023; 14:1091607. [PMID: 36825023 PMCID: PMC9941745 DOI: 10.3389/fimmu.2023.1091607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/20/2023] [Indexed: 02/10/2023] Open
Abstract
Nuclear factor-kappa B (NF-κB) pathways have a close relationship with many diseases, especially in terms of the regulation of inflammation and the immune response. Non-coding RNAs (ncRNAs) are a heterogeneous subset of endogenous RNAs that directly affect cellular function in the absence of proteins or peptide products; these include microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), etc. Studies on the roles of ncRNAs in targeting the NF-κB pathways in aquatic animals are scarce. A few research studies have confirmed detailed regulatory mechanisms among ncRNAs and the NF-κB pathways in aquatic animals. This comprehensive review is presented concerning ncRNAs targeting the NF-κB pathway in aquatic animals and provides new insights into NF-κB pathways regulatory mechanisms of aquatic animals. The review discusses new possibilities for developing non-coding-RNA-based antiviral applications in fisheries.
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Affiliation(s)
- Tanjun Zhao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.,College of Life Science, Liaoning Normal University, Dalian, China
| | - Yang Zou
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Hanyu Yan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.,College of Life Science, Liaoning Normal University, Dalian, China
| | - Yaoyao Zhan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
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Nedoluzhko A, Orlova SY, Kurnosov DS, Orlov AM, Galindo-Villegas J, Rastorguev SM. Genomic Signatures of Freshwater Adaptation in Pacific Herring ( Clupea pallasii). Genes (Basel) 2022; 13:genes13101856. [PMID: 36292743 PMCID: PMC9601299 DOI: 10.3390/genes13101856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/04/2022] Open
Abstract
Pacific herring (Clupea pallasii) is an essential target of commercial fishing in the North Pacific Ocean. Previous studies have suggested the existence of marine and lake ecological forms of this species within its range. The lake ecological form of herring has a shortened life cycle, spending the winter and spawning in brackish waters near the shoreline without long migrations for feeding; it also has a relatively smaller body size than the marine form. Genetic-based studies have shown that brackish water Pacific herring not only can be distinguished as a separate lake ecological form but possibly has its genetic legacy. Here, as part of an ongoing study, using ddRAD-sequencing data for marine and lake ecological forms from a total of 54 individuals and methods of comparative bioinformatics, we describe genomic signatures of freshwater adaptivity in Pacific herring. In total, 253 genes containing discriminating SNPs were found, and part of those genes was organized into genome clusters, also known as “genomic islands of divergence”. Moreover, the Tajima’s D test showed that these loci are under directional selection in the lake populations of the Pacific herring. Yet, most discriminating loci between the lake and marine ecological forms of Pacific herring do not intersect (by gene name) with those in other known marine fish species with known freshwater/brackish populations. However, some are associated with the same physiological trait—osmoregulation.
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Affiliation(s)
- Artem Nedoluzhko
- Paleogenomics Laboratory, European University at Saint Petersburg, 191187 Saint Petersburg, Russia
- Limited Liability Company ELGENE, 109029 Moscow, Russia
| | - Svetlana Yu. Orlova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 107140 Moscow, Russia
- Laboratory of Genetic Basis of Identification, Vavilov Institute of General Genetics of the Russian Academy of Sciences, 119991 Moscow, Russia
- Correspondence: (S.Y.O.); (J.G.-V.); (S.M.R.)
| | - Denis S. Kurnosov
- Research Group of Intraspecific Differentiation, Russian Federal Research Institute of Fisheries and Oceanography, Pacific Branch (TINRO), 690091 Vladivostok, Russia
| | - Alexei M. Orlov
- Laboratory of Oceanic Ichthyofauna, Shirshov Institute of Oceanology of the Russian Academy of Sciences, 117218 Moscow, Russia
- Laboratory of Behavior of Lower Vertebrates, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Ichthyology, Dagestan State University, 367000 Makhachkala, Russia
- Department of Ichthyology and Hydrobiology, Tomsk State University, 634050 Tomsk, Russia
- Laboratory of Marine Biology, Caspian Institute of Biological Resources, Russian Academy of Sciences, 367000 Makhachkala, Russia
| | - Jorge Galindo-Villegas
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
- Correspondence: (S.Y.O.); (J.G.-V.); (S.M.R.)
| | - Sergey M. Rastorguev
- Limited Liability Company ELGENE, 109029 Moscow, Russia
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Correspondence: (S.Y.O.); (J.G.-V.); (S.M.R.)
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