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He Y, Ma L, Zeng X, Xie J, Ning X. Systematic identification and analysis of immune-related circRNAs of Pelteobagrus fulvidraco involved in Aeromonas veronii infection. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 51:101256. [PMID: 38797004 DOI: 10.1016/j.cbd.2024.101256] [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: 03/18/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
Circular RNA (circRNA) represents a type of newly discovered non-coding RNA, distinguished by its closed loop structure formed through covalent bonds. Recent studies have revealed that circRNAs have crucial influences on host anti-pathogen responses. Yellow catfish (Pelteobagrus fulvidraco), an important aquaculture fish with great economic value, is susceptible to Aeromonas veronii, a common aquatic pathogen that can cause acute death. Here, we reported the first systematic investigation of circRNAs in yellow catfish, especially those associated with A. veronii infection at different time points. A total of 1205 circRNAs were identified, which were generated from 875 parental genes. After infection, 47 circRNAs exhibited differential expression patterns (named DEcirs). The parental genes of these DEcirs were functionally engaged in immune-related processes. Accordingly, seven DEcirs (novel_circ_000226, 278, 401, 522, 736, 843, and 975) and six corresponding parental genes (ADAMTS13, HAMP1, ANG3, APOA1, FGB, and RALGPS1) associated with immunity were obtained, and their expression was confirmed by RT-qPCR. Moreover, we found that these DEcir-gene pairs likely acted through pathways, such as platelet activation, antimicrobial humoral response, and regulation of Ral protein signal transduction, to influence host immune defenses. Additionally, integrated analysis showed that, of the 7 immune-related DEcirs, three targeted 16 miRNAs, which intertwined into circRNA-miRNA networks. These findings revealed that circRNAs, by targeting genes or miRNAs are highly involved in anti-bacterial responses in yellow catfish. Our study comprehensively illustrates the roles of circRNAs in yellow catfish immune defenses. The identified DEcirs and the circRNA-miRNA network will contribute to the further investigations on the molecular mechanisms underlying yellow catfish immune responses.
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Affiliation(s)
- Yongxin He
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Lina Ma
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Xueyu Zeng
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Jingjing Xie
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Xianhui Ning
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang 222005, China.
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Kang S, Ni Y, Lan K, Lv F. Hsa_circ_0008133 contributes to lung cancer progression by promoting glycolysis metabolism through the miR-760/MEX3A axis. ENVIRONMENTAL TOXICOLOGY 2024; 39:3014-3025. [PMID: 38317294 DOI: 10.1002/tox.24162] [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: 06/21/2023] [Revised: 12/08/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND Lung cancer is a very common cancer with poor prognosis and high mortality. Circular RNAs (circRNAs) have been confirmed to be related to the occurrence of lung cancer, and circ_0008133 has been found to be possibly related to lung cancer. METHODS Expression of circ_0008133, miR-760, and mex-3 RNA binding family member A (MEX3A) messenger RNA (mRNA) was detected using quantitative real-time polymerase chain reaction (qRT-PCR). Cell viability, colony number, migration, and invasion were assessed using cell counting kit-8 (CCK8), colony formation, wound healing, and transwell assays. Glucose consumption and lactate production were detected using commercial kits. Protein expression was measured using western blot. Dual-luciferase reporter assay and RNA pull-down assay were used to analyze the relationships between miR-760 and circ_0008133 or MEX3A. The effects of circ_0008133 knockdown on tumor growth in vivo were examined by the nude mice expriment. Immunohistochemistry (IHC) assay analyzed Ki-67 expression. RESULTS Circ_0008133 and MEX3A were markedly boosted in lung cancer tissues and cells. Circ_0008133 knockdown decreased lung cancer cell viability, glucose consumption, lactate production, colony formation, migration, and invasion. In mechanism, circ_0008133 might positively regulate MEX3A expression by sponging miR-760. Additionally, knockdown of circ_0008133 inhibited tumor growth in vivo. CONCLUSION Circ_0008133 accelerated the progression of lung cancer by promoting glycolysis metabolism through the miR-760/MEX3A axis.
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Affiliation(s)
- Shuhong Kang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, China
| | - Yunfeng Ni
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, China
| | - Ke Lan
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, China
| | - Feng Lv
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, China
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Gao C, Cai X, Ma L, Sun P, Li C. Systematic analysis of circRNA-related ceRNA networks of black rockfish (Sebastes schlegelii) in response to Aeromonas salmonicides infection. FISH & SHELLFISH IMMUNOLOGY 2023; 135:108648. [PMID: 36842642 DOI: 10.1016/j.fsi.2023.108648] [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: 12/26/2022] [Revised: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Aeromonas salmonicides is a type of Gram-negative bacteria and has become the main fish pathogen in aquaculture because of its characteristics of worldwide distribution, broad host range and potentially devastating impacts. In the past years, studies have been focused to explore the regulatory roles of circRNA-miRNA-mRNA network in fish diseases. However, there are only few systematic studies linked to the anti-bacterial roles of circRNA-related ceRNA networks in the spleen immune system of black rockfish (Sebastes schlegelii). In this study, the whole-transcriptome sequencing (RNA-seq) was conducted in the black rockfish spleen with A. salmonicida challenging. The differentially expressed (DE) circRNAs were identified comprehensively for the following enrichment analysis. Interactions of miRNA-circRNA pairs and miRNA-mRNA pairs were predicted for the construction of circRNA-related ceRNA regulatory networks. Then, protein-protein interaction (PPI) analysis of mRNAs from these ceRNA networks were conducted. Finally, a total number of 39 circRNAs exhibited significantly differential expressions during A. salmonicida infection in the black rockfish spleen in 4338 identified circRNAs from 12 samples in 4 libraries. Functional enrichment analysis suggested that they were significantly enriched in several immune-related pathways, including Endocytosis, FoxO signaling pathway, Jak-STST signaling pathway, Herpes simplex infection, etc. Subsequently, 290 circRNA-miRNA-mRNA pathways (91 at 2 h, 142 at 12 h and 65 at 24 h) were constructed including 31 circRNAs, 50 miRNAs, and 156 mRNAs. In conclusion, the circRNA-related ceRNA networks were established, which will provide some novel insights in molecular mechanistic investigations of anti-bacterial immune response in teleost. Also, these findings will propose significant predictive values for the development of methods of treatment and prevention in black rockfish after bacterial infection in the future.
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Affiliation(s)
- Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China; Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Xin Cai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China; Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Le Ma
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Peng Sun
- Shandong Weifang Ecological Environment Monitoring Center, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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Fan Q, Shi K, Zhan M, Xu Q, Liu X, Li Z, Liu H, Xia Y, Chen Y, Shi X, Sha Z. Acute damage from the degradation of Ulva prolifera on the environmental microbiota, intestinal microbiota and transcriptome of Japanese flounder Paralichthys olivaceus. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 302:119022. [PMID: 35219793 DOI: 10.1016/j.envpol.2022.119022] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/30/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Green tide outbreaks caused by overgrowth of Ulva prolifera in the Yellow Sea of China can cause serious ecological stress with concomitant economic hardships, especially to marine fisheries. In this study, short-term effects (14 days) were evaluated using fresh algae U. prolifera (FU), and a 7-day assessment of the effects of decomposing U. prolifera (DU) algal effluent was conducted to determine the effects on the environmental and intestinal microbiota, intestinal transcriptome and mortality of the commercial marine benthic fish, Japanese flounder (Paralichthys olivaceus). The results revealed that algal degradation altered the microbial community structure of fish farm water and fish intestines and increased the relative abundance of the pathogens Flavobacteriaceae in water and Vibrio in fish intestines. Fish intestinal tissue structure appeared to be damaged, as indicated in pathological sections, and transcriptome analysis showed intestinal inflammation after exposure, which may have caused an increase in fish mortality. The degradation of U. prolifera led to a bloom of potential pathogenic bacteria and the inflammation of fish intestines, which resulted in disease in the flounder population that reduced fish harvests and might pose a potential health threat.
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Affiliation(s)
- Qingxin Fan
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Kunpeng Shi
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Min Zhan
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Qian Xu
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Xinbao Liu
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Zhujun Li
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Hongning Liu
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Yanting Xia
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Yadong Chen
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xiaoyong Shi
- National Marine Hazard Mitigation Service, Ministry of Natural Resources, Beijing, 100194, China
| | - Zhenxia Sha
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, 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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Yang J, Liu B, Li X, Li G, Wen H, Qi X, Li Y, He F. Immune correlates of NF-κB and TNFα promoter DNA methylation in Japanese flounder (Paralichthys olivaceus) muscle and immune parameters change response to vibrio anguillarum infection. FISH & SHELLFISH IMMUNOLOGY 2021; 119:578-586. [PMID: 34655738 DOI: 10.1016/j.fsi.2021.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/05/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Vibrio anguillarum infection can activate NF-κB/TNFα pathway in the immune organs of fish. Fish muscle is also an important immune organ, but the research on its immune function is few. Our aim was to study regulating mechanism of NF-κB and TNFα gene expressions in the muscle of Japanese flounder (Paralichthys olivaceus) which was under Vibrio anguillarum infection (0, 24, 48, 72 and 96 h). The results showed that the expressions of NF-κB and TNFα increased significantly at 48 h, and there was a significant positive correlation between them. In situ hybridization confirmed the co-existence of NF-κB and TNFα genes in Japanese flounder muscle. Interestingly, the expression of the TNFα gene was regulated by the DNA methylation and its methylation level was negatively correlated with the expression. The lowest methylation level of TNFα occurred at 48 h under Vibrio anguillarum infection (P < 0.05). And more, when the fragment (-2122 ∼ -730) was deleted on TNFα gene promoter, double luciferase activity was the highest, indicating that fragment (-730-0) was the transcription factor binding region. The site (-78 ~ -69) on the fragment (-730-0) binding NF-κB was mutated, and double luciferase activity decreased significantly. The results confirmed that the site (-78 ~ -69) was indeed an important binding site for NF-κB. In addition, the activity of TNFα in the serum of Japanese flounder changed with the prolongation of vibrio anguillarum infection, and the concentration of other immune factors such as ALP, ALT, AST and LDH also changed in the muscle under vibrio anguillarum infection. They all showed a trend of first increasing and then decreasing. Above studies implied that Japanese flounder responded to Vibrio anguillarum infection at the immune level with the change of its methylation status and the activation of transcription factor. By studying the mechanism of immune pathways, understanding the response to immune stress is great significant to the research of fish breeding for disease resistance.
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Affiliation(s)
- Jun Yang
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, PR China
| | - Binghua Liu
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, PR China
| | - Xiaohui Li
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, PR China
| | - Guangling Li
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, PR China
| | - Haishen Wen
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, PR China
| | - Xin Qi
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, PR China
| | - Yun Li
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, PR China
| | - Feng He
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, PR China.
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Xue T, Liu Y, Cao M, Li J, Tian M, Zhang L, Wang B, Liu X, Li C. Transcriptome analysis reveals deep insights into the early immune response of turbot (Scophthalmus maximus) induced by inactivated Aeromonas salmonicida vaccine. FISH & SHELLFISH IMMUNOLOGY 2021; 119:163-172. [PMID: 34562583 DOI: 10.1016/j.fsi.2021.09.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/15/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Non-coding RNAs are a class of RNAs, including circRNA and miRNA, that cannot be translated into proteins, but play an important role in the regulation of the expression of protein-coding genes. More and more evidences showed that circRNA can regulate the expression of miRNA target genes by adsorbing miRNA and form the circRNA-miRNA-mRNA regulatory network. The inactivated Aeromonas salmonicida vaccine is a commercial vaccine for many teleost. Understanding the role of circRNA and miRNA in the early stage of vaccine injection will provide a new insight for the study of the early immune response process in teleost. In this study, the expression profiles of circRNA, miRNA and mRNA were analyzed by high-throughput sequencing at 6 h, 12 h, 24 h and 96 h after injection of inactivated Aeromonas salmonicida vaccine and normal turbot spleen. Compared with the control group, 111, 141 and 453 differentially expressed circRNAs, miRNAs and mRNAs were identified in the four vaccination groups, respectively. The targeting relationships of differentially expressed miRNA to circRNA and mRNA were predicted by using miRanda software, and the results showed that a variety of differentially expressed immune-related genes were targeted. A total of 53 differentially expressed circRNA-miRNA-mRNA regulatory networks were constructed according to circRNA-miRNA pairs and miRNA-mRNA pairs. Among them, cell adhesion molecule 3 and immunoglobulin superfamily member 21 were regulated by the same miRNA (novel_880) and circRNA (novel_circ_0000311/novel_circ_0005326). These suggest that these circRNA-miRNA-mRNA regulatory networks may be a multi-molecule regulatory network, and its regulatory mechanism needs to be further studied.
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Affiliation(s)
- Ting Xue
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yiping 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
| | - Jie Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266109, China
| | - Mengyu Tian
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lu Zhang
- 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
| | - Xiaoli Liu
- 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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Wang G, Sun Q, Wang H, Liu H. Identification and characterization of circRNAs in the liver of blunt snout bream (Megalobrama amblycephala) infected with Aeromonas hydrophila. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 124:104185. [PMID: 34174243 DOI: 10.1016/j.dci.2021.104185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/21/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Circular RNAs (circRNAs), a class of non-coding RNAs, play an important role in regulating various biological processes. In the present study, circRNAs from the Megalobrama amblycephala liver were identified at five different time points post Aeromonas hydrophila using RNA-seq technology. A total of 250 circRNAs were identified, of which 106 were differentially expressed (DE) in ten pairwise comparisons. GO and KEGG analyses showed that the parental genes of DE circRNAs were enriched in phagocytosis, complement and coagulation cascades, and Fc gamma R-mediated phagocytosis pathways. According to ceRNA hypothesis, the interaction network of circRNAs, miRNAs and mRNAs was constructed. Moreover, WGCNA was conducted, and five specific modules significantly related to bacterial infection were identified. All the above results reveal the important role of circRNAs in immune response, which enriches the information of circRNAs in teleost, and helps to understand the immune response mechanism of M. amblycephala to A. hydrophila.
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Affiliation(s)
- Guowen Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/ Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Qianhui Sun
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/ Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Huanling Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/ Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Hong Liu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/ Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China.
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