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Wang NN, Song Y, Yan X, Liu X, Wu R, Cao M, Li C. Regulatory roles of miRNA-530 in the post-transcriptional regulation of NF-κB signaling pathway through targeted modulation of IκBα in Sebastesschlegelii. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109604. [PMID: 38710343 DOI: 10.1016/j.fsi.2024.109604] [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: 01/22/2024] [Revised: 04/17/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024]
Abstract
MicroRNAs (miRNAs) are a crucial type of non-coding RNAs involved in post-transcriptional regulation. The playing essential regulatory roles in the NF-κB signaling pathway and modulate the host immune response to diverse pathogens by targeting IκBα. However, the regulatory mechanism of miRNAs in relation with IκBα in Sebastes schlegelii remains unclear. In our study, we identified two copies of IkBα gene in black rockfish (Sebastes schlegelii), namely IkBα1 and IkBα2. Moreover, we have discovered that miRNA-530 can activate the NF-κB signaling pathway by inhibiting the expression of IκBα, thereby inducing the inflammatory response. This project comprehensively investigated the interactive regulatory roles of miRNA-530 in the NF-κB signaling pathway at both cellular and in vivo levels, while also elucidating the regulatory relationships between miRNA-530 and IκBα. In conclusion, our research confirmed that miRNA-530 can target the 3'UTR region of IκBα, resulting in a decrease in the expression of IκBα at the post-transcriptional level and inhibiting its translation. The findings contribute to the understanding of the regulatory network of non-coding RNA in teleosts and its subsequent regulation of the NF-κB signaling pathway by miRNAs.
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Affiliation(s)
- Ning Ning Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yize Song
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xu Yan
- College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Xiantong Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ruixue Wu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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2
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Zhang X, Jiang Y, Yu H, Wang N, Liu X, Cao M, Li C. Comprehensive analysis of circRNA-miRNA-mRNA networks in the kidney of snakehead (Channa argus) response to Nocardia seriolae challenge. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 151:105099. [PMID: 38007095 DOI: 10.1016/j.dci.2023.105099] [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: 05/26/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/27/2023]
Abstract
Non-coding RNAs (ncRNAs) play vital roles in regulating the expression levels of genes that control essential biological functions, including immune response to bacterial infections in teleost. To dissect the roles of ncRNAs in the Channa argus (snakehead), a systematic analysis of the expression profiles of circRNA, miRNA and mRNA, as well as competing endogenous RNAs (ceRNA) regulatory networks in the kidney of snakehead following Nocardia seriolae infection were performed in the present study. A total of 111 differentially expressed circRNAs, 706 differentially expressed miRNAs, and 2548 differentially expressed mRNAs were identified in the N. seriolae infected snakehead. Based on these differently expressed RNAs, we identified 55 circRNA-mRNA pairs, 124 miRNA-mRNA pairs, and 35 circRNA-miRNA-mRNA regulatory networks, including dre-miR-103-CD302, dre-miR-27e-IGSF3, novel_circ_0005462/novel_403-IGKC, novel_circ_0001750/novel_circ_0002162-novel_477-OCLN, and novel_circ_0003847-novel_4-KCNAB3. In addition, luciferase reporter assay was employed to detect the target relationships of several circRNA-miRNA-mRNA pairs. Taken together, this study demonstrates that the genes associated with immunity and structures in the kidney of snakehead can be regulated by circRNAs and miRNAs at post-transcription levels, and provided theoretical guidance for ncRNAs studies for other teleost. However, further studies are still in great need to validate the regulatory mechanisms of ncRNAs in snakehead.
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Affiliation(s)
- Xiaoyan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yanliang Jiang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Chinese Academy of Fishery Sciences, Beijing, China
| | - Haohui Yu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ningning Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiantong Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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3
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Gao C, Cai X, Lymbery AJ, Ma L, Li C. The evolution of NLRC3 subfamily genes in Sebastidae teleost fishes. BMC Genomics 2023; 24:683. [PMID: 37964222 PMCID: PMC10648357 DOI: 10.1186/s12864-023-09785-5] [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: 04/16/2023] [Accepted: 11/05/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND With more than 36,000 valid fish species, teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. NLRC3 subfamily genes, which are specific to fishes, play vital roles in the immune system of teleosts. The evolution of teleosts has been impacted by several whole-genome duplication (WGD) events, which might be a key reason for the expansions of the NLRC3 subfamily, but detailed knowledge of NLRC3 subfamily evolution in the family Sebastidae is still limited. RESULTS Phylogenetic inference of NLRC3 subfamily protein sequences were conducted to evaluate the orthology of NLRC3 subfamily genes in black rockfish (Sebastes schlegilii), 13 other fish species from the families Sebastidae, Serranidae, Gasterosteidae and Cyclopteridae, and three species of high vertebrates (bird, reptile and amphibian). WGD analyses were used to estimate expansions and contractions of the NLRC3 subfamily, and patterns of expression of NLRC3 subfamily genes in black rockfish following bacterial infections were used to investigate the functional roles of these genes in the traditional and mucosal immune system of the Sebastidae. Different patterns of gene expansions and contractions were observed in 17 fish and other species examined, and one and two whole-genome duplication events were observed in two members of family Sebastidae (black rockfish and honeycomb rockfish, Sebastes umbrosus), respectively. Subsequently, 179 copy numbers of NLRC3 genes were found in black rockfish and 166 in honeycomb rockfish. Phylogenetic analyses corroborated the conservation and evolution of NLRC3 orthologues between Sebastidae and other fish species. Finally, differential expression analyses provided evidence of the immune roles of NLRC3 genes in black rockfish during bacterial infections and gene ontology analysis also indicated other functional roles. CONCLUSIONS We hypothesize that NLRC3 genes have evolved a variety of different functions, in addition to their role in the immune response, as a result of whole genome duplication events during teleost diversification. Importantly, this study had underscored the importance of sampling across taxonomic groups, to better understand the evolutionary patterns of the innate immunity system on which complex immunological novelties arose. Moreover, the results in this study could extend current knowledge of the plasticity of the immune system.
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Affiliation(s)
- Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, 266109, Qingdao, China
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 6150, Murdoch, WA, Australia
| | - Xin Cai
- School of Marine Science and Engineering, Qingdao Agricultural University, 266109, Qingdao, China
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 6150, Murdoch, WA, Australia
| | - Alan J Lymbery
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 6150, Murdoch, WA, Australia
| | - Le Ma
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 6150, Murdoch, WA, Australia
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, 266109, Qingdao, China.
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Zeng C, Tao W, Fu X, Li C, Guo M. CircRNA254 functions as the miR-375 sponge to inhibit coelomocyte apoptosis via targeting BAG2 in V. splendidus-challenged Apostichopus japonicus. FISH & SHELLFISH IMMUNOLOGY 2023; 141:109073. [PMID: 37709179 DOI: 10.1016/j.fsi.2023.109073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/15/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Circular RNAs (circRNAs) function as immune regulators in many biological processes in mammals, while their function and underlying mechanisms in invertebrates are largely unexplored. In this study, the competing endogenous RNA (ceRNA) mechanism of circRNA that sponges miR-375 and thus regulates AjBAG2-mediated coelomocyte apoptosis was evaluated in Apostichopus japonicus. The results showed that circRNA254 (circ254) was significantly down-regulated in the intestines and coelomocytes after Vibrio splendidus challenge or Lipopolysaccharide exposure, which matched the RNA-seq results in A. japonicus within skin ulceration syndrome. Dual-luciferase and RNA FISH assays indicated that circ254 could directly combine with miR-375, in which circ254 possesses three binding sites of miR-375. Moreover, circ254 knockdown significantly promoted the coelomocyte apoptosis levels upon pathogen infection in vivo and in vitro. Furthermore, circ254 silencing could also down-regulate AjBAG2 expression and thereby promoting the levels of coelomocyte apoptosis levels and the expression of caspase 3, which the phenomenon could be reversed by treatment with miR-375 inhibitors. Taken together, our results confirmed that circ254 functions as a ceRNA of AjBAG2 by sponging miR-375, resulting in the inhibition of coelomocyte apoptosis in A. japonicus.
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Affiliation(s)
- Chuili Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Wenjun Tao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Xianmu Fu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
| | - Ming Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.
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Cao M, Xue T, Huo H, Zhang X, Wang NN, Yan X, Li C. Spatial transcriptomes and microbiota reveal immune mechanism that respond to pathogen infection in the posterior intestine of Sebastes schlegelii. Open Biol 2023; 13:220302. [PMID: 36974664 PMCID: PMC9944294 DOI: 10.1098/rsob.220302] [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] [Indexed: 02/25/2023] Open
Abstract
The intestine is a site of immune cell priming at birth. Therefore, spatial transcriptomes were performed to define how the transcriptomic landscape was spatially organized in the posterior intestine of Sebastes schlegelii following Edwardsiella piscicida infection. In the healthy condition, we identified a previously unappreciated molecular regionalization of the posterior intestine. Following bacterial infection, most immune-related genes were identified in mucosa layer. Moreover, investigation of immune-related genes and genes in immune-related KEGG pathways based on spatial transcriptomes shed light on which sections of these genes are in the posterior intestine. Meanwhile, the high expression of genes related to regeneration also indicated that the posterior intestine was responding to the invasion of pathogens by constantly proliferating new cells. In addition, the increasing microbiota communities indicated that these bacteria maintained posterior intestine integrity and shaped the mucosal immune system. Taken together, spatial transcriptomes and microbiota compositions have significant implications for understanding the immune mechanism that responds to E. piscicida infection in the posterior intestine of S. schlegelii, which also provides a theoretical basis for the spatial distribution of immune genes and changes in bacterial flora in other teleosts in the process of resisting pathogens.
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Affiliation(s)
- Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Ting Xue
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Huijun Huo
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Xiaoyan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Ning Ning Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Xu Yan
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
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6
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Sun H, Ma Y, Yang Y, Sun C, Li H. Genome-wide characterization of circRNA expression profile in overexpression of RIP2 chicken macrophages associated with avian pathogenic E.coli infection. Avian Pathol 2023; 52:62-77. [PMID: 36399118 DOI: 10.1080/03079457.2022.2144132] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Avian pathogenic E. coli (APEC) can cause localized and systemic diseases in poultry, threatening human health via meat or egg contamination and resulting in considerable economic losses to the poultry industry globally. Increasing evidence shows circRNAs were widely involved in various biological processes. However, the role of circRNAs in the host response against APEC infection, especially correlated with the regulation of RIP2, remains unclear. Herein, the RNAseq technology was used to identify the circRNA expression profiles in the overexpression of RIP2 macrophages with or without APEC infection. A total of 256 and 287 differentially expressed (DE) circRNAs were identified in the overexpression of RIP2 group (oeRIP2) vs. the wild-type group (WT) and oeRIP2 + APEC vs. APEC, respectively, whose parental genes were involved in MAPK signalling pathway, Wnt signalling pathway, focal adhesion, tight junction, and VEGF signalling pathways. Specifically, the key circRNAs, such as 5:814443-825127, 10:18922360-18928461, 2:8746306-8750639, and 2:124177751-124184063 might play a critical role in APEC infection and the regulation of RIP2. As a whole, these findings will facilitate understanding the molecular mechanism underlying circRNAs, especially related to the regulation of the RIP2 gene. Meanwhile, the study may offer new ideas to improve host immune and inflammatory response against APEC infection.
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Affiliation(s)
- Hongyan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, People's Republic of China.,Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, People's Republic of China
| | - Yuyi Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou, People's Republic of China
| | - Yexin Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, People's Republic of China
| | - Changhua Sun
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou University, Yangzhou, People's Republic of China
| | - Huan Li
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou University, Yangzhou, People's Republic of China
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7
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Guan X, Zhang B, Sun L. TNFR2 is a regulatory target of pol-miR-194a and promotes the antibacterial immunity of Japanese flounder Paralichthys olivaceus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 135:104477. [PMID: 35752347 DOI: 10.1016/j.dci.2022.104477] [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: 04/20/2022] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) are regulatory RNAs that modulate target gene expression after transcription. Pol-miR-194a had been reported to be a miRNA of Japanese flounder (Paralichthys olivaceus) involved in Edwardsiella tarda infection. Here, we identified tumor necrosis factor receptor 2 (TNFR2) as a target gene of pol-miR-194a. Pol-miR-194a markedly repressed the protein expression of flounder TNFR2 (PoTNFR2) via specific interaction with the 3'UTR of PoTNFR2. PoTNFR2 responded to E. tarda infection in a manner that was opposite to that of pol-miR-194a and inhibited E. tarda invasion by activating the NF-κB pathway. Consistently, dysregulation of PoTNFR2 had a significant impact on E. tarda dissemination in flounder tissues. Together, these results add new insights into the regulation mechanism and immune function of fish TNFR2 and pol-miR-194a.
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Affiliation(s)
- Xiaolu Guan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Baocun Zhang
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
| | - Li Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China.
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8
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Xie Y, Cao Y, Guo CJ, Guo XY, He YF, Xu QY, Shen F, Pan Q. Profile analysis and functional modeling identify circular RNAs in nonalcoholic fatty liver disease as regulators of hepatic lipid metabolism. Front Genet 2022; 13:884037. [PMID: 36186461 PMCID: PMC9520628 DOI: 10.3389/fgene.2022.884037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the leading cause of chronic liver disease, associated with an outcome of hepatic fibrosis/cirrhosis and hepatocellular carcinoma. However, limited exploration of the underlying mechanisms hinders its prevention and treatment. To investigate the mechanisms of epigenetic regulation in NAFLD, the expression profile of circular RNA (circRNA) of rodents in which NAFLD was induced by a high-fat, high-cholesterol (HFHC) diet was studied. Modeling of the circRNA-microRNA (miRNA) -mRNA regulatory network revealed the functional characteristics of NAFLD-specific circRNAs. The targets and effects in the liver of such NAFLD-specific circRNAs were further assessed. Our results uncovered that the downregulation of 28 annotated circRNAs characterizes HFHC diet-induced NAFLD. Among the downregulated circRNAs, long intergenic non-protein coding RNA, P53 induced transcript (LNCPINT) -derived circRNAs (circ_0001452, circ_0001453, and circ_0001454) targeted both miR-466i-3p and miR-669c-3p. Their deficiency in NAFLD abrogated the circRNA-based inhibitory effect on both miRNAs, which further inactivated the AMPK signaling pathway via AMPK-α1 suppression. Inhibition of the AMPK signaling pathway promotes hepatic steatosis, depending on the transcriptional and translational upregulation of lipogenic genes, such as those encoding sterol regulatory element-binding protein 1 (SREBP1) and fatty acid synthase (FASN) in hepatocytes. The levels of LNCPINT-derived circRNAs displayed a negative association with hepatic triglyceride (TG) concentration. These findings suggest that loss of LNCPINT-derived circRNAs may underlie NAFLD via miR-466i-3p- and miR-669c-3p-dependent inactivation of the AMPK signaling pathway.
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Affiliation(s)
- Yang Xie
- Department of Gastroenterology, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Cao
- Department of Pediatric Digestion and Nutrition, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Can-Jie Guo
- Department of Gastroenterology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xing-Ya Guo
- Department of Gastroenterology, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ya-Fang He
- Department of Pediatric Respiratory, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qing-Yang Xu
- Department of Gastroenterology, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Shen
- Endoscopy Center, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Feng Shen, ; Qin Pan,
| | - Qin Pan
- Department of Gastroenterology, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
- Research Center, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- *Correspondence: Feng Shen, ; Qin Pan,
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9
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Sun H, Yang Y, Ma Y, Li N, Tan J, Sun C, Li H. Analysis of circRNA expression in chicken HD11 cells in response to avian pathogenic E.coli. Front Vet Sci 2022; 9:1005899. [PMID: 36187840 PMCID: PMC9521048 DOI: 10.3389/fvets.2022.1005899] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
Avian pathogenic E. coli (APEC), one of the widespread zoonotic-pathogen, can cause a series of diseases collectively known as colibacillosis. This disease can cause thousands of million dollars economic loss each year in poultry industry and threaten to human health via meat or egg contamination. However, the detailed molecular mechanism underlying APEC infection is still not fully understood. Circular RNAs, a new type of endogenous noncoding RNA, have been demonstrated to involve in various biological processes. However, it is still not clear whether the circRNAs participate in host response against APEC infection. Herein, we utilized the high-throughput sequence technology to identify the circRNA expression profiles in APEC infected HD11 cells. A total of 49 differentially expressed (DE) circRNAs were detected in the comparison of APEC infected HD11 cells vs. wild type HD11 cells, which were involved in MAPK signaling pathway, Endocytosis, Focal adhesion, mTOR signaling pathway, and VEGF signaling pathway. Specifically, the source genes (BRAF, PPP3CB, BCL2L13, RAB11A, and TSC2) and their corresponding DE circRNAs may play a significant role in APEC infection. Moreover, based on ceRNA regulation, we constructed the circRNA-miRNA network and identified a couple of important regulatory relationship pairs related to APEC infection, including circRAB11A-gga-miR-125b-3p, circRAB11A-gga-miR-1696, and circTSC2-gga-miR-1649-5p. Results indicate that the aforementioned specific circRNAs and circRNA-miRNA network might have important role in regulating host immune response against APEC infection. This study is the first time to investigate the circRNAs expression profile and the biological function of the source genes of the identified DE circRNAs after APEC infection of chicken HD11 cells. These results would contribute to a better understanding of the molecular mechanisms in host response against APEC infection.
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Affiliation(s)
- Hongyan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
- *Correspondence: Hongyan Sun
| | - Yexin Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yuyi Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Nayin Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jishuang Tan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Changhua Sun
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou University, Yangzhou, China
| | - Huan Li
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou University, Yangzhou, China
- Huan Li
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10
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Qiao X, Lu Y, Xu J, Deng N, Lai W, Wu Z, Lin H, Zhang Y, Lu D. Integrative analyses of mRNA and microRNA expression profiles reveal the innate immune mechanism for the resistance to Vibrio parahaemolyticus infection in Epinephelus coioides. Front Immunol 2022; 13:982973. [PMID: 36059501 PMCID: PMC9437975 DOI: 10.3389/fimmu.2022.982973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Vibrio parahaemolyticus, as one of the main pathogens of marine vibriosis, has brought huge losses to aquaculture. However, the interaction mechanism between V. parahaemolyticus and Epinephelus coioides remains unclear. Moreover, there is a lack of comprehensive multi-omics analysis of the immune response of grouper spleen to V. parahaemolyticus. Herein, E. coioides was artificially injected with V. parahaemolyticus, and it was found that the mortality was 16.7% in the early stage of infection, and accompanied by obvious histopathological lesions in the spleen. Furthermore, 1586 differentially expressed genes were screened by mRNA-seq. KEGG analysis showed that genes were significantly enriched in immune-related pathways, Acute-phase immune response, Apoptosis, Complement system and Cytokine-cytokine receptor interaction. As for miRNA-seq analysis, a total of 55 significantly different miRNAs were identified. Further functional annotation analysis indicated that the target genes of differentially expressed miRNAs were enriched in three important pathways (Phosphatidylinositol signaling system, Lysosome and Focal adhesions). Through mRNA-miRNA integrated analysis, 1427 significant miRNA–mRNA pairs were obtained and “p53 signaling pathway”, “Intestinal immune network for IgA production” were considered as two crucial pathways. Finally, miR-144-y, miR-497-x, novel-m0459-5p, miR-7133-y, miR-378-y, novel-m0440-5p and novel-m0084-3p may be as key miRNAs to regulate immune signaling pathways via the miRNA-mRNA interaction network. The above results suggest that the mRNA-miRNA integrated analysis not only sheds new light on the molecular mechanisms underlying the interaction between host and V. parahaemolyticus but also provides valuable and new insights into resistance to vibrio infection.
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Affiliation(s)
- Xifeng Qiao
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou, China
| | - Yuyou Lu
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou, China
| | - Jiachang Xu
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou, China
| | - Niuniu Deng
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou, China
| | - Wenjie Lai
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou, China
| | - Ziyi Wu
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou, China
| | - Haoran Lin
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Ocean, Haikou, China
| | - Yong Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou, China
- *Correspondence: Yong Zhang, ; Danqi Lu,
| | - Danqi Lu
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Guangzhou, China
- *Correspondence: Yong Zhang, ; Danqi Lu,
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Huo HJ, Yang TZ, Gao CB, Cao M, Xue T, Fu Q, Li C. Molecular characterization, antibacterial activity and mechanism analyzation of three different piscidins from black rockfish, Sebastes schlegelii. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 131:104394. [PMID: 35283164 DOI: 10.1016/j.dci.2022.104394] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/08/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Sebastes schlegelii (black rockfish) is a popular and economically important fish species in aquaculture. However, disease outbreaks have hindered the development of its cultivation. Antimicrobial peptides (AMPs) are a group of important components in fish innate immune system, that are active in the first line of defense against pathogens. The piscidin family, which are a group of fish-specific AMPs, have been isolated in a part of teleost but still poorly understood in S. schlegelii. In this study, three piscidin genes (Ss-piscidin1, 2, 3) are identified in S. schlegelii and their antibacterial activities and related mechanisms are analyzed. Three Ss-piscidins have conserved signal peptides but highly variable mature peptides and prodomains, and their mature regions all have predicted amphipathic and α-helical structures. Phylogenetic analysis shows that three Ss-piscidins cluster with different fish piscidin sequences into three sister clades, which correspond to three groups of fish piscidin family, respectively. Ss-piscidins have constitutive expressions in different tissues of healthy fish and enhanced expressions after Aeromonas salmonicida challenge. All three piscidins exhibit antibacterial activities, and are able to enhance bacterial membrane permeability and change bacterial morphology to different degrees, with a positive correlation observed among these activities. This suggests that three peptides exert their antibacterial activity through a "membrane-attack" mechanism. Moreover, hemolytic activities of three piscidins are also analyzed, and Ss-piscidin1, with low hemolytic ability and high antibacterial activity, is considered to be a possible candidate template for design of AMP drugs. Results in this study can promote a better understanding of immune responses in black rockfish and facilitate the future development of strategies in fish disease control in aquaculture.
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Affiliation(s)
- Hui Jun Huo
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Tian Zhen Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Cheng Bin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Ting Xue
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China.
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Liu X, Wang B, Gao C, Xue T, Liu Z, Su B, Li C, Yang N. Characterization and the potential immune role of class A scavenger receptor member 4 (SCARA4) in bacterial infection in turbot (Scophthalmus maximus L.). FISH & SHELLFISH IMMUNOLOGY 2022; 120:590-598. [PMID: 34965442 DOI: 10.1016/j.fsi.2021.12.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/23/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
The class A scavenger receptors play important roles in innate immunity and are distributed on plasma membrane of macrophages and other cell types. Notably, the class A scavenger receptor 4 (SCARA4) contains a typical C-type (calcium-dependent) lectin domain, which belongs to the collectin family of pattern recognition receptors and is involved in the immune response against infection. Here, one turbot SCARA4 gene was identified with a 2,292 bp open reading frame (ORF) encoding 763 amino acid residues. Multiple sequence analysis and phylogenetic analysis confirmed that SmSCARA4 gene was more close to that of P. olivaceus. Gene structure and syntenic analysis showed conserved exon/intron organization pattern and syntenic pattern across selected vertebrate species. Tissue distribution analysis showed SmSCARA4 was expressed in all the tested healthy tissues with the relative high expression levels in skin, gill and spleen. Following both E. tarda and V. anguillarum challenge in vivo, SmSCARA4 was significantly repressed in gill and intestine. Remarkably, SmSCARA4 showed the strongest binding ability to LPS and strongest upregulation in turbot head kidney macrophages in response to LPS. Knockdown and overexpression of SmSCARA4 revealed its interactions with the two pro-inflammatory cytokines, TNF-α and IL-1β. Finally, repression of SmSCARA4 via combined treatment of LPS and overexpression of SmSCARA4 construct in turbot head kidney macrophages further indicated an inhibitory role of SmSCARA4 in LPS-stimulated inflammation. Taken together, turbot SmSCARA4 plays an important role in turbot immunity, especially in the mucosa-related systems; SmSCARA4 possesses strong binding specificity to LPS, and exerts protective roles in response to LPS infection by reducing the release of pro-inflammatory cytokines. The mechanisms of inhibitory role of SmSCARA4 in LPS-elicited inflammation await further investigation.
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Affiliation(s)
- Xiaoli Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Beibei Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ting Xue
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhe Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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Identification of Antimicrobial Peptide Genes in Black Rockfish Sebastes schlegelii and Their Responsive Mechanisms to Edwardsiella tarda Infection. BIOLOGY 2021; 10:biology10101015. [PMID: 34681113 PMCID: PMC8533284 DOI: 10.3390/biology10101015] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/18/2021] [Accepted: 09/20/2021] [Indexed: 01/01/2023]
Abstract
The black rockfish, Sebastes schlegelii, is a typical viviparous teleost, which belongs to the family Scorpaenidae. Due to its high economic and ecological values, S. schlegelii has been widely cultured in East Asian countries. With the enlargement of cultivation scale, bacterial and viral diseases have become the main threats to the farming industry of S. schlegelii, which have resulted in significant economic losses. In this study, Illumina shotgun sequencing, single-molecule real-time (SMRT) sequencing, 10× genomics and high-throughput chromosome conformation capture (Hi-C) technologies were collectively applied to assemble the genome of S. schlegelii. Then, we identified the antimicrobial peptide genes (AMPs) in the S. schlegelii genome. In total, 214 AMPs were identified in the S. schlegelii genome, which can be divided into 33 classes according to the annotation and cataloging of the Antimicrobial Peptides Database (APD3). Among these AMPs, thrombin-derived C-terminal peptide (TCP) was the dominant type, followed by RegIIIgamma and chemokine. The amino acid sequences of the TCP, cgUbiquitin, RegIIIalpha, RegIIIgamma, chemokine shared 32.55%, 42.63%, 29.87%, 28.09%, and 32.15% similarities among the same type in S. schlegelii. Meanwhile, the expression patterns of these AMPs in nine healthy tissues and at different infection time points in intestine were investigated. The results showed that the numbers and types of AMPs that responded to Edwardsiella tarda infection gradually increased as the infection progressed. In addition, we analyzed the phylogenetic relationships of hepcidins in teleost. The identification of AMPs based on the whole genome could provide a comprehensive database of potential AMPs, and benefit for the understanding of the molecular mechanisms of immune responses to E. tarda infection in S. schlegelii. This would further offer insights into an accurate and effective design and development of AMP for aquaculture therapy in the future.
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Xue T, Liu Y, Cao M, Tian M, Zhang L, Wang B, Liu X, Li C. Revealing New Landscape of Turbot ( Scophthalmus maximus) Spleen Infected with Aeromonas salmonicida through Immune Related circRNA-miRNA-mRNA Axis. BIOLOGY 2021; 10:biology10070626. [PMID: 34356481 PMCID: PMC8301059 DOI: 10.3390/biology10070626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/12/2022]
Abstract
Simple Summary In this study, the expression of circRNAs, miRNAs, and mRNA in the immune organs spleen of turbot (Scophthalmus maximus) infected with Aeromonas salmonicida was analyzed by high-throughput sequencing, and circRNA-miRNA-mRNA network was constructed, so as to explore the function of non-coding RNA in the immune system of teleost. A total of 119, 140, and 510 differential expressed circRNAs, miRNAs, and mRNAs were identified in the infected groups compared with the uninfected group. The qRT-PCR verified the reliability and accuracy of the Illumina sequencing data. Fifteen triple networks of circRNA-miRNA-mRNA were presented in the form of “up (circRNA)-down (miRNA)-up (mRNA)” or “down-up-down”. Immune-related genes were also found in these networks. These results indicate that circRNAs and miRNAs may regulate the expression of immune-related genes through the circRNA-miRNA-mRNA regulatory network and thus participate in the immune response of turbot spleen after pathogen infection. Abstract Increasing evidence suggests that non-coding RNAs (ncRNA) play an important role in a variety of biological life processes by regulating gene expression at the transcriptional and post-transcriptional levels. Turbot (Scophthalmus maximus) has been threatened by various pathogens. In this study, the expression of circular RNAs (circRNAs), microRNAs (miRNAs), and mRNA in the immune organs spleen of turbot infected with Aeromonas salmonicida was analyzed by high-throughput sequencing, and a circRNA-miRNA-mRNA network was constructed, so as to explore the function of non-coding RNA in the immune system of teleost. Illumina sequencing was performed on the uninfected group and infected group. A total of 119 differential expressed circRNAs (DE-circRNAs), 140 DE-miRNAs, and 510 DE-mRNAs were identified in the four infected groups compared with the uninfected group. Most DE-mRNAs and the target genes of DE-ncRNAs were involved in immune-related pathways. The quantitative real-time PCR (qRT-PCR) results verified the reliability and accuracy of the high-throughput sequencing data. Ninety-six differentially expressed circRNA-miRNA-mRNA regulatory networks were finally constructed. Among them, 15 circRNA-miRNA-mRNA were presented in the form of “up (circRNA)-down (miRNA)-up (mRNA)” or “down-up-down”. Immune-related genes gap junction CX32.2, cell adhesion molecule 3, and CC chemokine were also found in these networks. These results indicate that ncRNA may regulate the expression of immune-related genes through the circRNA-miRNA-mRNA regulatory network and thus participate in the immune response of turbot spleen after pathogen infection.
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