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Chang D, Zhao Y, Ren Z, Zhu X, Bao X, Wang Y, Wang W, Cui C, Liu X, Li Z, Shan Y, Yang J. Transcriptome analysis reveals the immune response mechanism of golden cuttlefish (Sepia esculenta) larvae exposed to ink. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101355. [PMID: 39541713 DOI: 10.1016/j.cbd.2024.101355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 11/02/2024] [Accepted: 11/03/2024] [Indexed: 11/16/2024]
Abstract
The golden cuttlefish (Sepia esculenta), a significant cephalopod in the Yellow and Bohai Seas of China, is highly esteemed for its exceptional medicinal and commercial value. The natural resources of the S. esculenta are currently facing depletion due to the ongoing environmental degradation and overfishing. Secreted by the ink sac of the S. esculenta, the ink contains a diverse array of nutrients and active ingredients, which can exert a substantial impact on biological immune cells' proliferation and differentiation, the occurrence of inflammation, autophagy, along with other processes pertaining to immune response, and thus affects their survival. In the actual production, the high-density artificial cultivation and transportation process of S. esculenta often leads to large-scale inkjet phenomenon, posing a significant threat to the survival of this species. The present study employed RNA-seq as the basis to investigate the mechanisms of immune response in S. esculenta larvae when exposed to ink. Conduct functional enrichment analysis (GO and KEGG) as well as protein-protein interaction (PPI) network analysis for the 1951 differentially expressed genes (DEGs). In addition, this study is the pioneering attempt to employ a combined analysis of KEGG and PPI network construction and further reveal a set of 20 key genes associated with immunity, which have higher numbers of PPI or KEGG pathway participation. It is evident that the ink exposure has an impact on the inflammatory response, immune cell propagation and specialization, transmission of signals in the immune system, and autophagy in S. esculenta larvae. Through the enrichment analysis of genes and pathway functions, we understood the impact of ink exposure on the larvae of S. esculenta exhibit immune resistance, further improved our overall comprehension regarding the immune functionality exhibited by mollusks, and contributed to improving the survival rate of S. esculenta in factory farming.
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Affiliation(s)
- Deyuan Chang
- Fisheries College, Ludong University, Yantai 264025, China
| | - Yancheng Zhao
- Fisheries College, Ludong University, Yantai 264025, China
| | - Ziwen Ren
- Shandong Yellow River Delta Marine Technology Co., Ltd., Dongying 257200, China
| | - Xueyu Zhu
- Fisheries College, Ludong University, Yantai 264025, China
| | - Xiaokai Bao
- Fisheries College, Ludong University, Yantai 264025, China
| | - Yongjie Wang
- Fisheries College, Ludong University, Yantai 264025, China
| | - Weijun Wang
- Fisheries College, Ludong University, Yantai 264025, China
| | - Cuiju Cui
- Fisheries College, Ludong University, Yantai 264025, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai 264005, China
| | - Zan Li
- Fisheries College, Ludong University, Yantai 264025, China.
| | - Yuan Shan
- National Fisheries Technology Extension Center & China Society of Fisheries, Beijing 100125, China.
| | - Jianmin Yang
- Fisheries College, Ludong University, Yantai 264025, China.
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Koll R, Theilen J, Hauten E, Woodhouse JN, Thiel R, Möllmann C, Fabrizius A. Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 942:173656. [PMID: 38830414 DOI: 10.1016/j.scitotenv.2024.173656] [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: 03/04/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
Coastal and estuarine environments are under endogenic and exogenic pressures jeopardizing survival and diversity of inhabiting biota. Information of possible synergistic effects of multiple (a)biotic stressors and holobiont interaction are largely missing in estuaries like the Elbe but are of importance to estimate unforeseen effects on animals' physiology. Here, we seek to leverage host-transcriptional RNA-seq and gill mucus microbial 16S rRNA metabarcoding data coupled with physiological and abiotic measurements in a network analysis approach to decipher the impact of multiple stressors on the health of juvenile Sander lucioperca along one of the largest European estuaries. We find mesohaline areas characterized by gill tissue specific transcriptional responses matching osmosensing and tissue remodeling. Liver transcriptomes instead emphasized that zander from highly turbid areas were undergoing starvation which was supported by compromised body condition. Potential pathogenic bacteria, including Shewanella, Acinetobacter, Aeromonas and Chryseobacterium, dominated the gill microbiome along the freshwater transition and oxygen minimum zone. Their occurrence coincided with a strong adaptive and innate transcriptional immune response in host gill and enhanced energy demand in liver tissue supporting their potential pathogenicity. Taken together, we show physiological responses of a fish species and its microbiome to abiotic factors whose impact is expected to increase with consequences of climate change. We further present a method for the close-meshed detection of the main stressors and bacterial species with disease potential in a highly productive ecosystem.
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Affiliation(s)
- Raphael Koll
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany.
| | - Jesse Theilen
- University of Hamburg, Department of Biology, Biodiversity Research, Germany
| | - Elena Hauten
- University of Hamburg, Institute of Marine Ecosystem and Fishery Science, Marine ecosystem dynamics, Germany
| | - Jason Nicholas Woodhouse
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Microbial and phytoplankton Ecology, Germany
| | - Ralf Thiel
- Leibniz Institute for the Analysis of Biodiversity Change (LIB) - Hamburg site, Centre for Taxonomy & Morphology, Zoological Museum, Germany; University of Hamburg, Department of Biology, Biodiversity Research, Germany
| | - Christian Möllmann
- University of Hamburg, Institute of Marine Ecosystem and Fishery Science, Marine ecosystem dynamics, Germany
| | - Andrej Fabrizius
- University of Hamburg, Institute of Cell- and Systems Biology of Animals, Molecular Animal Physiology, Germany
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Xie Q, Yao T, Sun X, Liu X, Wang X. Whole genome identification of olive flounder (Paralichthys olivaceus) cathepsin genes: Provides insights into its regulation on biotic and abiotic stresses response. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 266:106783. [PMID: 38064891 DOI: 10.1016/j.aquatox.2023.106783] [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: 08/15/2023] [Revised: 11/10/2023] [Accepted: 11/29/2023] [Indexed: 01/02/2024]
Abstract
Cathepsins are major lysosomal enzymes involved in essential physiological processes, including protein degradation, tissue differentiation, and innate or adaptive responses. Several kinds of cathepsins have been reported in teleost fishes, but no characterization have been performed for the inflammatory response of cathepsin family in olive flounder until now. In our current study, a total of 17 cathepsins in olive flounder were systematically identified and characterized. Phylogenetic analysis clearly indicated that the cathepsin genes was highly conserved. Analysis of structure and motifs exhibited high sequence similarity of cathepsin genes in olive flounder. Expression profiles of cathepsin genes in different tissues and developmental stages showed that cathepsins were temporally and spatially specific. RNA-seq analysis of bacteria and temperature stresses revealed that members of cathepsin were involved in inflammatory responses. Collectively, our findings would provide a further reference for understanding the molecular mechanisms of cathepsins in olive flounder.
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Affiliation(s)
- Qingping Xie
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China
| | - Tingyan Yao
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China
| | - Xuanyang Sun
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, China
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; National Engineering Research Laboratory of marine biotechnology and Engineering, Ningbo University; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China.
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Li Z, Wang H, Bao X, Liu X, Yang J. Gene network analyses of Sepia esculenta larvae exposed to copper and cadmium: A comprehensive investigation of oxidative stress, immune response, and toxicological mechanisms. FISH & SHELLFISH IMMUNOLOGY 2023; 143:109230. [PMID: 37977542 DOI: 10.1016/j.fsi.2023.109230] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/12/2023] [Accepted: 11/11/2023] [Indexed: 11/19/2023]
Abstract
Copper (Cu) and Cadmium (Cd), prevalent heavy metals in marine environments, have known implications in oxidative stress, immune response, and toxicity in marine organisms. Sepia esculenta, a cephalopod of significant economic value along China's eastern coastline, experiences alterations in growth, mobility, and reproduction when subjected to these heavy metals. However, the specific mechanisms resulting from heavy metal exposure in S. esculenta remain largely uncharted. In this study, we utilized transcriptome and four oxidative, immunity, and toxicity indicators to assess the toxicological mechanism in S. esculenta larvae exposed to Cu and Cd. The measurements of Superoxide Dismutase (SOD), Malondialdehyde (MDA), Glutathione S-Transferase (GST), and Metallothioneins (MTs) revealed that Cu and Cd trigger substantial oxidative stress, immune response, and metal toxicity. Further, we performed an analysis on the transcriptome data through Weighted Gene Co-expression Network Analysis (WGCNA) and Protein-Protein Interaction (PPI) network analysis. Our findings indicate that exposure methods and duration influence the type and the extent of toxicity and oxidative stress within the S. esculenta larvae. We took an innovative approach in this research by integrating WGCNA and PPI network analysis with four significant physiological indicators to closely examine the toxicity and oxidative stress profiles of S. esculenta upon exposure to Cu and Cd. This investigation is vital in decoding the toxicological, immunological, and oxidative stress mechanisms within S. esculenta when subjected to heavy metals. It provides foundational insights capable of advancing invertebrate environmental toxicology and informs S. esculenta artificial breeding practices.
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Affiliation(s)
- Zan Li
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Haoyu Wang
- St. John's School, Vancouver, V6K 2J1, Canada
| | - Xiaokai Bao
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai, 264025, China.
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Zhu J, Zou Z, Li D, Xiao W, Yu J, Chen B, Yang H. Comparative transcriptomes reveal different tolerance mechanisms to Streptococcus agalactiae in hybrid tilapia, nile tilapia, and blue tilapia. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109121. [PMID: 37802264 DOI: 10.1016/j.fsi.2023.109121] [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: 06/06/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/08/2023]
Abstract
Tilapia is one of the most economically important freshwater fish farmed in China. Streptococcosis outbreaks have been extensively documented in farmed tilapia species. Hybrid tilapia (Oreochromis niloticus ♀ × O. aureus ♂) exhibit greater disease resistance than Nile tilapia (O. niloticus) and blue tilapia (O. aureus). However, the molecular mechanism underlying the enhanced tolerance of hybrid tilapia is still poorly understood. In this study, comparative transcriptome analysis was performed to reveal the different tolerance mechanisms to Streptococcus agalactiae in the three tilapia lines. In total, 1982, 2355, and 2076 differentially expressed genes were identified at 48 h post-infection in hybrid tilapia, Nile tilapia, and blue tilapia, respectively. Functional enrichment analysis indicated that numerous metabolic and immune-related pathways were activated in all three tilapia lines. The differential expression of specific genes associated with phagosome, focal adhesion, cytokine-cytokine receptor interaction, and toll-like receptor signaling pathways contributed to the resistance of hybrid tilapia. Notably, immune response genes in hybrid tilapia, such as P38, TLR5, CXCR3, CXCL12, PSTPIP1, and TFR, were generally suppressed under normal conditions but selectively induced following pathogen challenge. These results expand our knowledge of the molecular mechanisms underlying S. agalactiae tolerance in hybrid tilapia and provide valuable insights for tilapia breeding programs.
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Affiliation(s)
- Jinglin Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214128, China.
| | - Zhiying Zou
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214128, China.
| | - Dayu Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Wei Xiao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214128, China.
| | - Jie Yu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Binglin Chen
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Hong Yang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
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Liu X, Bao X, Yang J, Zhu X, Li Z. Preliminary study on toxicological mechanism of golden cuttlefish (Sepia esculenta) larvae exposed to cd. BMC Genomics 2023; 24:503. [PMID: 37649007 PMCID: PMC10466719 DOI: 10.1186/s12864-023-09630-9] [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: 06/18/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Cadmium (Cd) flows into the ocean with industrial and agricultural pollution and significantly affects the growth and development of economic cephalopods such as Sepia esculenta, Amphioctopus fangsiao, and Loligo japonica. As of now, the reasons why Cd affects the growth and development of S. esculenta are not yet clear. RESULTS In this study, transcriptome and four oxidation and toxicity indicators are used to analyze the toxicological mechanism of Cd-exposed S. esculenta larvae. Indicator results indicate that Cd induces oxidative stress and metal toxicity. Functional enrichment analysis results suggest that larval ion transport, cell adhesion, and some digestion and absorption processes are inhibited, and the cell function is damaged. Comprehensive analysis of protein-protein interaction network and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was used to explore S. esculenta larval toxicological mechanisms, and we find that among the 20 identified key genes, 14 genes are associated with neurotoxicity. Most of them are down-regulated and enriched to the neuroactive ligand-receptor interaction signaling pathway, suggesting that larval nervous system might be destroyed, and the growth, development, and movement process are significantly affected after Cd exposure. CONCLUSIONS S. esculenta larvae suffered severe oxidative damage after Cd exposure, which may inhibit digestion and absorption functions, and disrupt the stability of the nervous system. Our results lay a function for understanding larval toxicological mechanisms exposed to heavy metals, promoting the development of invertebrate environmental toxicology, and providing theoretical support for S. esculenta artificial culture.
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Affiliation(s)
- Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Xiaokai Bao
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xibo Zhu
- Fishery Technology Service Center of Lanshan District, Rizhao, 276800, China.
| | - Zan Li
- School of Agriculture, Ludong University, Yantai, 264025, China.
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Li Z, Bao X, Liu X, Wang W, Yang J, Zhu X, Wang S. Transcriptome Profiling Based at Different Time Points after Hatching Deepened Our Understanding on Larval Growth and Development of Amphioctopus fangsiao. Metabolites 2023; 13:927. [PMID: 37623871 PMCID: PMC10456336 DOI: 10.3390/metabo13080927] [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: 07/09/2023] [Revised: 07/22/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
As the quality of life improves, there is an increasing demand for nutrition-rich marine organisms like fish, shellfish, and cephalopods. To address this, artificial cultivation of these organisms is being explored along with ongoing research on their growth and development. A case in point is Amphioctopus fangsiao, a highly valued cephalopod known for its tasty meat, nutrient richness, and rapid growth rate. Despite its significance, there is a dearth of studies on the A. fangsiao growth mechanism, particularly of its larvae. In this study, we collected A. fangsiao larvae at 0, 4, 12, and 24 h post-hatching and conducted transcriptome profiling. Our analysis identified 4467, 5099, and 4181 differentially expressed genes (DEGs) at respective intervals, compared to the 0 h sample. We further analyzed the expression trends of these DEGs, noting a predominant trend of continuous upregulation. Functional exploration of this trend entailed GO and KEGG functional enrichment along with protein-protein interaction network analyses. We identified GLDC, DUSP14, DPF2, GNAI1, and ZNF271 as core genes, based on their high upregulation rate, implicated in larval growth and development. Similarly, CLTC, MEF2A, PPP1CB, PPP1R12A, and TJP1, marked by high protein interaction numbers, were identified as hub genes and the gene expression levels identified via RNA-seq analysis were validated through qRT-PCR. By analyzing the functions of key and core genes, we found that the ability of A. fangsiao larvae to metabolize carbohydrates, lipids, and other energy substances during early growth may significantly improve with the growth of the larvae. At the same time, muscle related cells in A. fangsiao larvae may develop rapidly, promoting the growth and development of larvae. Our findings provide preliminary insights into the growth and developmental mechanism of A. fangsiao, setting the stage for more comprehensive understanding and broader research into cephalopod growth and development mechanisms.
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Affiliation(s)
- Zan Li
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Xiaokai Bao
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai 264005, China
| | - Weijun Wang
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Xibo Zhu
- Fishery Technology Service Center of Lanshan District, Rizhao 276800, China
| | - Shuhai Wang
- Ocean and Aquatic Research Center of Hekou District, Dongying 257200, China
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Liu X, Bao X, Li Z, Zhang Q. Investigation of Gene Networks in Three Components of Immune System Provides Novel Insights into Immune Response Mechanisms against Edwardsiella tarda Infection in Paralichthys olivaceus. Animals (Basel) 2023; 13:2542. [PMID: 37570350 PMCID: PMC10417057 DOI: 10.3390/ani13152542] [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: 06/30/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
As a quintessential marine teleost, Paralichthys olivaceus demonstrates vulnerability to a range of pathogens. Long-term infection with Edwardsiella tarda significantly inhibits fish growth and even induces death. Gills, blood, and kidneys, pivotal components of the immune system in teleosts, elicit vital regulatory roles in immune response processes including immune cell differentiation, diseased cell clearance, and other immunity-related mechanisms. This study entailed infecting P. olivaceus with E. tarda for 48 h and examining transcriptome data from the three components at 0, 8, and 48 h post-infection employing weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network analysis. Network analyses revealed a series of immune response processes after infection and identified multiple key modules and key, core, and hub genes including xpo1, src, tlr13, stat1, and mefv. By innovatively amalgamating WGCNA and PPI network methodologies, our investigation facilitated an in-depth examination of immune response mechanisms within three significant P. olivaceus components post-E. tarda infection. Our results provided valuable genetic resources for understanding immunity in P. olivaceus immune-related components and assisted us in further exploring the molecular mechanisms of E. tarda infection in teleosts.
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Affiliation(s)
- Xiumei Liu
- College of Life Sciences, Yantai University, Yantai 264005, China
| | - Xiaokai Bao
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Zan Li
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Quanqi Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
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Xie H, Hu J, Wang Y, Wang X. Identification of the matrix metalloproteinase (MMP) gene family in Japanese flounder (Paralichthys olivaceus): Involved in immune response regulation to temperature stress and Edwardsiella tarda infection. FISH & SHELLFISH IMMUNOLOGY 2023:108878. [PMID: 37271328 DOI: 10.1016/j.fsi.2023.108878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
The Matrix metalloproteinase (MMP) gene family is responsible for regulating the degradation of Extra Cellular Matrix (ECM) proteins, which are important for physiological processes such as wound healing, tissue remodeling, and stress response. Although MMPs have been studied in many species, their role in immune response in Japanese flounder (Paralichthys olivaceus) is still not fully understood. This study conducted a comprehensive analysis of MMPs in flounder, including gene structures, evolutionary relationships, conserved domains, molecular evolution, and expression patterns. Analysis revealed that MMP genes could be grouped into 17 subfamilies and were evolutionarily conserved and functionally-constrained. Meanwhile, MMP genes were found to express in different embryonic and larval stages and might play the role of sentinel in healthy tissues. Furthermore, expression profiling showed that MMPs had diverse functions in environmental stress, with 60% (9/15) and 73% (11/15) of MMPs showing differential expression patterns under temperature stress and Edwardsiella tarda (E. tarda) infection, respectively. These findings provide a useful resource for understanding the immune functions of MMP genes in Japanese flounder.
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Affiliation(s)
- Huihui Xie
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, China; Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Key Laboratory of Green Mariculture (Co-construction By Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, China
| | - Jiabao Hu
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, China; Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Key Laboratory of Green Mariculture (Co-construction By Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, China; School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
| | - Yajun Wang
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, China; Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Key Laboratory of Green Mariculture (Co-construction By Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, China.
| | - Xubo Wang
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, China; Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Key Laboratory of Green Mariculture (Co-construction By Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, China.
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Wang R, Han P, Liu X, Wang X. Genome-wide identification of TNF receptor-associated factors in Japanese flounder (Paralichthys olivaceus) and functional analysis of resistance to temperature and Edwardsiella tarda stress. FISH & SHELLFISH IMMUNOLOGY 2023; 138:108862. [PMID: 37263548 DOI: 10.1016/j.fsi.2023.108862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/16/2023] [Accepted: 05/29/2023] [Indexed: 06/03/2023]
Abstract
Tumor necrosis factor receptor-associated factors (TRAFs), as the signaling mediators of the tumor necrosis factor (TNFR) superfamily, toll-like receptors (TLR) and interleukin-1 receptor (IL-1R) superfamily, can activate downstream signal transduction pathways and play an important role in the body's immune process. In this study, six TRAF genes, namely PoTRAF2a, PoTRAF2b, PoTRAF3, PoTRAF4, PoTRAF6 and PoTRAF7, were identified and annotated in Japanese flounder by using bioinformatics methods. Phylogenetic analysis confirmed that TRAF genes can be divided into seven groups. Analysis of motif composition and gene structure demonstrated that all PoTRAF members were evolutionarily conserved. The expression patterns of PoTRAF genes were then further investigated in six different developmental stages and eleven tissues of healthy fish, and it was found that there were spatial and tissue specificities among the members. To investigate the immune response of Japanese flounder to abiotic and biotic stresses, we further analyzed the expression profile of PoTRAFs after temperature stress and pathogen challenge. The result showed that PoTRAF3 and PoTRAF4 were observably differentially expressed under temperature stress, indicating that they were involved in the immune response after temperature stress. The expression of PoTRAF2a, PoTRAF2b and PoTRAF4 was significantly different after E. tarda infection, suggesting that they might have antibacterial effects. These results would help to clarify the molecular roles of PoTRAF genes in the regulation of immune and inflammatory responses in Japanese flounder.
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Affiliation(s)
- Ruoxin Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China.
| | - Ping Han
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China.
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, China.
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Key Laboratory of Green Mariculture (Co-construction By Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, China.
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Chen J, Han P, Liu X, Wang X. Characterization of Japanese flounder (Paralichthys olivaceus) STAT members: An immune-related gene family involved in Edwardsiella tarda and temperature stress. FISH & SHELLFISH IMMUNOLOGY 2023; 138:108818. [PMID: 37201733 DOI: 10.1016/j.fsi.2023.108818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 05/20/2023]
Abstract
The signal transducer and activator of transcription (STAT) family members are not only the transcriptional activators, but also play important roles in regulating inflammatory response. Some members have been reported to be involved in innate bacterial and antiviral immunity in aquatic organisms. However, no systematic research on STATs has been found in teleost. In this present study, we characterized six STAT genes in Japanese flounder based on bioinformatics methods, namely PoSTAT1, PoSTAT2, PoSTAT3, PoSTAT4, PoSTAT5 and PoSTAT6. The phylogenetic analysis of STATs in fish indicated that STATs were highly conserved and revealed an absence of STAT5 in a few species. Further analysis of gene structures and motifs showed STAT proteins shared a similar structure and probably had similar functionality in Japanese flounder. The expression profiles of different development stages and tissues demonstrated that PoSTATs exhibited specificity in temporality and spatiality as well as PoSTAT4 was highly expressed in gill. The transcriptome data analysis of E. tarda and temperature stress showed that PoSTAT1 and PoSTAT2 were more respective to these two kinds of stress. In addition, the results also demonstrated that these PoSTATs might regulate immune response in different ways, manifested by up-regulation in E. tarda infection and down-regulation in temperature stress. In a word, this systematic analysis of PoSTATs would provide valuable information about the phylogenetic relationship of STATs in fish species and help understand the role of STAT genes in the immune response of Japanese flounder.
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Affiliation(s)
- Jianming Chen
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China.
| | - Ping Han
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China.
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, China.
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China.
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12
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Li Z, Bao X, Liu X, Wang W, Yang J. Gene network analyses of larvae under different egg-protecting behaviors provide novel insights into immune response mechanisms of Amphioctopus fangsiao. FISH & SHELLFISH IMMUNOLOGY 2023; 136:108733. [PMID: 37028690 DOI: 10.1016/j.fsi.2023.108733] [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: 01/06/2023] [Revised: 03/28/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
Amphioctopus fangsiao was a representative economic species in cephalopods, which was vulnerable to marine bacteria. Vibrio anguillarum was a highly infectious pathogen that have recently been found to infect A. fangsiao and inhibit its growth and development. There were significant differences in the immune response mechanisms between egg-protected and egg-unprotected larvae. To explore larval immunity under different egg-protecting behaviors, we infected A. fangsiao larvae with V. anguillarum for 24 h and analyzed the transcriptome data about egg-protected and egg-unprotected larvae infected with 0, 4, 12, and 24 h using weighted gene co-expression networks (WGCNA) and protein-protein interaction (PPI) networks. Network analyses revealed a series of immune response processes after infection, and identified six key modules and multiple immune-related hub genes. Meanwhile, we found that ZNF family, such as ZNF32, ZNF160, ZNF271, ZNF479, and ZNF493 might play significant roles in A. fangsiao immune response processes. We first creatively combined WGCNA and PPI network analysis to deeply explore the immune response mechanisms of A. fangsiao larvae with different egg-protecting behaviors. Our results provided further insights into the immunity of V. anguillarum infected invertebrates, and laid the foundation for exploring the immune differences among cephalopods with different egg protecting behaviors.
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Affiliation(s)
- Zan Li
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiaokai Bao
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Weijun Wang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai, 264025, China.
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13
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Han P, Wang R, Yao T, Liu X, Wang X. Genome-wide identification of olive flounder (Paralichthys olivaceus) SOCS genes: Involvement in immune response regulation to temperature stress and Edwardsiella tarda infection. FISH & SHELLFISH IMMUNOLOGY 2023; 133:108515. [PMID: 36603791 DOI: 10.1016/j.fsi.2023.108515] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/25/2022] [Accepted: 01/01/2023] [Indexed: 06/17/2023]
Abstract
The suppressors of cytokine signaling (SOCS) gene family participates in development and immunity through negative regulation of cytokine signaling pathways. Although the immune response of SOCS gene family members has been extensively characterized in teleost, no similar study has been reported in olive flounder yet. In our present study, a total of 13 SOCSs in olive flounder were identified and characterized systematically. By querying the SOCS sequences of ten teleost fish species, we found there were exactly more members of SOCSs in fish than mammals, which indicated that there were more duplication events occurred in fish than in higher vertebrates. Phylogenetic analysis clearly illuminated that SOCS genes were highly conserved. The analysis of gene structure and motif showed SOCS proteins of olive flounder shared a high level of sequence similarity strikingly. The expression profiles of tissues and developmental stages indicated that SOCS members had a kind of specificity in temporality and spatiality. RNA-Seq analysis of temperature stress and E. Tarda infection demonstrated SOCS members were involved in inflammatory response. In a word, our results would provide a further reference for understanding the mechanism of SOCS genes in olive flounder.
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Affiliation(s)
- Ping Han
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China.
| | - Ruoxin Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China.
| | - Tingyan Yao
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China.
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, 264005, China.
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China.
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14
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Li Z, Qin H, Zhang Y, He X, Bao X, Sun G, Cui C, Xu X, Liu X, Yang J, Zhang G. Transcriptome analysis preliminary reveals the immune response mechanism of golden cuttlefish (Sepia esculenta) larvae exposed to Cd. FISH & SHELLFISH IMMUNOLOGY 2023; 132:108494. [PMID: 36565999 DOI: 10.1016/j.fsi.2022.108494] [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: 10/12/2022] [Revised: 11/18/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
As a well-known marine metal element, Cd can significantly affect bivalve mollusk life processes such as growth and development. However, the effects of Cd on the molecular mechanisms of the economically important cephalopod species Sepia esculenta remain unclear. In this study, S. esculenta larval immunity exposed to Cd is explored based on RNA-Seq. The analyses of GO, KEGG, and protein-protein interaction (PPI) network of 1,471 differentially expressed genes (DEGs) reveal that multiple immune processes are affected by exposure such as inflammatory reaction and cell adhesion. Comprehensive analyses of KEGG signaling pathways and the PPI network are first used to explore Cd-exposed S. esculenta larval immunity, revealing the presence of 16 immune-related key and hub genes involved in exposure response. Results of gene and pathway functional analyses increase our understanding of Cd-exposed S. esculenta larval immunity and improve our overall understanding of mollusk immune functions.
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Affiliation(s)
- Zan Li
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Huimin Qin
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Yining Zhang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiaohua He
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiaokai Bao
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Guohua Sun
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Cuiju Cui
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiaohui Xu
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai, 264025, China.
| | - Guoguang Zhang
- School of Agriculture, Ludong University, Yantai, 264025, China; Laizhou Marine Development and Fishery Service Center, Yantai, 261499, China.
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15
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Xu XW, Zheng W, Yang Y, Hou J, Chen S. High-quality Japanese flounder genome aids in identifying stress-related genes using gene coexpression network. Sci Data 2022; 9:705. [PMID: 36385241 PMCID: PMC9668919 DOI: 10.1038/s41597-022-01821-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/21/2022] [Indexed: 11/17/2022] Open
Abstract
The Japanese flounder is one of the most economically important marine flatfish. However, due to the increased frequency of extreme weather events and high-density industrial farming, an increasing number of environmental stresses have become severe threats to the healthy development of the Japanese flounder culture industry. Herein, we produced a high-quality chromosome-scale Japanese flounder genome using PacBio Circular Consensus Sequencing technologies. The assembled Japanese flounder genome spanned 588.22 Mb with a contig N50 size of 24.35 Mb. In total, 105.89 Mb of repetitive sequences and 22,565 protein-coding genes were identified by genome annotation. In addition, 67 candidate genes responding to distinct stresses were identified by gene coexpression network analysis based on 16 published stress-related RNA-seq datasets encompassing 198 samples. A high-quality chromosome-scale Japanese flounder genome and candidate stress-related gene set will not only serve as key resources for genomics studies and further research on the underlying stress responsive molecular mechanisms in Japanese flounder but will also advance the progress of genetic improvement and comprehensive stress-resistant molecular breeding of Japanese flounder. Measurement(s) | genome assembly | Technology Type(s) | PacBio RS II |
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16
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Wu X, Xing J, Tang X, Sheng X, Chi H, Zhan W. Splenic protection network revealed by transcriptome analysis in inactivated vaccine-immunized flounder ( Paralichthys olivaceus) against Edwardsiella tarda infection. Front Immunol 2022; 13:1058599. [PMID: 36439120 PMCID: PMC9681833 DOI: 10.3389/fimmu.2022.1058599] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/24/2022] [Indexed: 07/01/2024] Open
Abstract
The protective immune response produced by fish after vaccination is crucial for vaccine effectiveness. Our previous studies have shown inactivated vaccine against Edwardsiella tarda can induce immune response in flounder (Paralichthys olivaceus). To elucidate the protective immune response at the genetic level, in this study, flounder was immunized with inactivated E. tarda for 5 weeks, and then they were challenged with E. tarda. The spleen was dissected at 7th day post immunization, 1st and 7th day post challenge, respectively. Transcriptome analysis showed that average of 46 million clean reads were obtained per library, while percentage of clean reads being mapped to reference genome was more than 89% in all cases, which suggested good quality of samples. As for differentially expressed genes (DEGs) identification in inactivated E. tarda groups, at 7th day post immunization, 1422 DEGs were identified and significantly enriched in innate immune-related pathways, such as Phagosome, Cell adhesion molecules and NF-kappa B signaling pathway; At 1st post challenge day, 1210 DEGs were identified and enriched to Antigen processing and presentation and Cell adhesion molecules, indicating that the pathogen was rapidly recognized and delivered; At 7th post challenge day, 1929 DEGs were identified, belonged to Toll-like receptor signaling pathway, Antigen processing and presentation, Th1 and Th2 cell differentiation and Th17 cell differentiation. Compared to 7th post immunization day, 73 immune-associated DEGs were identified at 1st post challenge day. Protein-protein interaction networks analysis revealed 11 hub genes (TLR7, TLR3, CXCR4, IFIH1, TLR8 etc), associated with recognition of pathogens and activation of innate immunity; while for 7th post challenge day, 141 immune-associated DEGs were identified. 30 hub genes (IL6, STAT1, HSP90A.1, TLR7, IL12β etc) were associated with stimulation of lymphocyte differentiation and activation of cellular immunity. Ten immune-related genes were randomly selected for RT-qPCR validation at each time point. In conclusion, data revealed protection of flounder against E. tarda infection by inactivated vaccine is mediated via immediate recognition of pathogen and subsequently activation of cellular immunity. Results give new aspect for vaccine protection cascades, is good references for vaccine evaluation.
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Affiliation(s)
| | - Jing Xing
- Laboratory of Pathology and Immunology of Aquatic Animals, Key Laboratory of Mariculture, MOE, Ocean University of China, Qingdao, China
| | | | | | | | - Wenbin Zhan
- Laboratory of Pathology and Immunology of Aquatic Animals, Key Laboratory of Mariculture, MOE, Ocean University of China, Qingdao, China
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17
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Han P, Qiao Y, He J, Men Y, Liu Y, Liu X, Wang X. Identification and functional analysis of dual-specificity phosphatases (DUSP) genes in Japanese flounder (Paralichthys olivaceus) against temperature and Edwardsiella tarda stress. FISH & SHELLFISH IMMUNOLOGY 2022; 130:453-461. [PMID: 36162775 DOI: 10.1016/j.fsi.2022.09.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Dual-specificity Phosphatases (DUSPs) are not only the key regulators of dephosphorylating and inactivating mitogen-activated protein kinases (MAPKs), but play a crucial role in the immune response. However, the role of DUSP genes in Japanese flounder (PoDUSPs) is still unclear. In this study, 28 DUSP genes in Japanese flounder were identified and classified based on the whole genome database. Phylogenetic analysis and protein structure analysis revealed that DUSPs had highly conserved domains in teleosts. Molecular evolution analysis indicated that the PoDUSP genes were conservative during evolution and were functional-constrained. Meanwhile, PoDUSP genes were found to express in different embryonic and larval stages which might play the role of sentinel in healthy organisms. Furthermore, PoDUSP genes' expression profiles after temperature stress and Edwardsiella tarda (E. tarda) infection were determined in Japanese flounder without precedent, and the results demonstrated that Podusp1, Podusp2 and Podusp16 were more respective to temperature variation whereas Podusp1 and Podusp6 were more respective to E. tarda infection. In summary, our results provide useful resources for understanding the immune responsibilities of DUSP genes in flatfish.
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Affiliation(s)
- Ping Han
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China.
| | - Yingjie Qiao
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China.
| | - Jiayi He
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China.
| | - Yu Men
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China.
| | - Yuxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China.
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, 264005, China.
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China.
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18
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Zhou S, Li Y, Yi J, Zheng X, Huang Q, Su L, Guo B, Yang Z, Xiu Y. Immune responses to Vibrio vulnificus formalin-killed vaccine and ghost vaccine in Scophthalmus maximus. JOURNAL OF FISH DISEASES 2022; 45:1511-1527. [PMID: 35771999 DOI: 10.1111/jfd.13678] [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: 04/09/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
In this research, Vibrio vulnificus formalin-killed (FKCs) vaccine and ghost (VVGs) vaccine were successfully developed, and shown to prevent vibriosis of Scophthalmus maximus resulting from V. vulnificus. The antibody titre of FKCs and VVGs vaccine was 1: 28 and 1: 211 . The RPS of FKCs and VVGs vaccine was 60% and 80%. In order to improve the understanding of vaccine protection mechanism, transcriptome data was used to analyse the immune response of S. maximus infected with V. vulnificus after vaccination with FKCs and VVGs vaccine. In the SmCon and SmIV groups, a series of innate immune-related genes were upregulated (such as, TLR5, Tp12, AP-1 and IL-1β) or downregulated (such as, CASP6 and CASP8), which suggested that the immune protection mechanism induced by inactivated vaccine was similar to that of autoimmune response. In the SmIV and SmGho group, a number of innate and adaptive immune-related genes (such as, STAT1, IFN-γ and MHC Ia) were activated, in which the expression of these genes was higher in SmGho, and VVGs vaccine induced stronger innate and acquired immune responses. In conclusion, the results lay a foundation for further study on the molecular mechanisms of immune protection induced by VVGs vaccine and FKCs vaccine.
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Affiliation(s)
- Shun Zhou
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Ying Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Jingyuan Yi
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Xujia Zheng
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Qing Huang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Lin Su
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Baoshan Guo
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Zongrui Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Yunji Xiu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
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19
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Li R, Qu J, Li H, Zhang Q. Genome-wide identification and analysis of scavenger receptors and their expression profiling in response to Edwardsiella tarda infection in Japanese flounder (Paralichthys olivaceus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 132:104397. [PMID: 35307477 DOI: 10.1016/j.dci.2022.104397] [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: 12/30/2021] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The scavenger receptors (SRs) gene family, as one of pattern recognition receptors, participates in the innate immune response in diverse lineages. However, the systematic identification, characteristics and functions of SRs family are lacking in teleost. Here, we identified all 19 SRs family members in Japanese flounder (Paralichthys olivaceus) based on the genome and transcriptome data. Phylogenetic and Ka/Ks analysis demonstrated that these SRs genes were divided into five classes and all exhibited pronounced purified selection pressures. Whole genome duplication event was found in colec12, scarb2, and lamp1. Gene structure, functional domain and motif distribution analyses indicated that SRs within the different subfamilies are severely conservative. SRs genes showed diverse expression patterns in the embryogenesis and unchanged tissues. The regulations of 14 SRs genes in blood, gill and kidney after E. tarda infection suggested their roles in innate immune response. Meanwhile, ten SRs genes were differentially expressed after E. tarda stimulation in macrophages in vitro. Then we proved that PoSCARA3 could suppress the activity of NF-κB and AP-1 in HEK 293T cells by dual-luciferase assays. In summary, this study provided valuable basis for further functional characterization and immune functions of SRs genes in P. olivaceus.
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Affiliation(s)
- Rui Li
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Jiangbo Qu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Hengshun Li
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, 266003, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, Shandong, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, 572000, Sanya, Hainan, China.
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20
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Bao X, Wang W, Yuan T, Li Y, Chen X, Liu X, Xu X, Sun G, Li B, Yang J, Feng Y, Li Z. Transcriptome profiling based on larvae at different time points after hatching provides a core set of gene resource for understanding the immune response mechanisms of the egg-protecting behavior against Vibrio anguillarum infection in Amphioctopus fangsiao. FISH & SHELLFISH IMMUNOLOGY 2022; 124:430-441. [PMID: 35472401 DOI: 10.1016/j.fsi.2022.04.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 04/17/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Mollusks have recently received increasing attention because of their unique immune systems. Mollusks such as Amphioctopus fangsiao are economically important cephalopods, and the effects of their egg-protecting behavior on the larval immune response are unclear. Meanwhile, little research has been done on the resistance response of cephalopod larvae infected with pathogenic bacteria such as Vibrio anguillarum. In this study, V. anguillarum was used to infect the primary hatching A. fangsiao larvae under different egg-protecting behaviors for 24 h, and a total of 7156 differentially expressed genes (DEGs) were identified at four time points after hatching based on transcriptome analysis. GO and KEGG enrichment analyses showed that multiple immune-related GO terms and KEGG signaling pathways were enriched. Protein-protein interaction networks (PPI networks) were used to search functional relationships between immune-related DEGs. Finally, 20 hub genes related to multiple gene functions or involved in multiple signaling pathways were identified, and their accuracy was verified using quantitative RT-PCR. PPI networks were first used to study the effects A. fangsiao larvae after infection with V. anguillarum under different egg-protecting behaviors. The results provide significant genetic resources for exploring invertebrate larval immune processes. The data lays a foundation for further study the immune response mechanisms for invertebrates after infection.
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Affiliation(s)
- Xiaokai Bao
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Weijun Wang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Tingzhu Yuan
- Marine Economy Promotion Center of Changdao County Marine Ecological Civilization Comprehensive Experimental Zone, Yantai, 265800, China
| | - Yan Li
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xipan Chen
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Xiaohui Xu
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Guohua Sun
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Bin Li
- School of Agriculture, Ludong University, Yantai, 264025, China; Yantai Haiyu Marine Science and Technology Co. Ltd., Yantai, 264004, China
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Yanwei Feng
- School of Agriculture, Ludong University, Yantai, 264025, China.
| | - Zan Li
- School of Agriculture, Ludong University, Yantai, 264025, China.
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21
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Wang L, Xu X, Zhang Z, Li K, Yang Y, Zheng W, Sun H, Chen S. Transcriptome analysis and protein-protein interaction in resistant and susceptible families of Japanese flounder (Paralichthys olivaceus) to understand the mechanism against Edwardsiella tarda. FISH & SHELLFISH IMMUNOLOGY 2022; 123:265-281. [PMID: 35272057 DOI: 10.1016/j.fsi.2022.02.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Edwardsiella tarda is one of the most harmful bacterial pathogens for aquaculture flatfish. After artificial infection of 47 Japanese flounder (Paralichthys olivaceus) families, resistant and susceptible families were identified in this study. High-throughput sequencing was performed on the liver transcriptome of uninfected groups (PoRU and PoSU) and infected groups (PoRC and PoSC). Through assembly and annotation, a total of 3012 and 1386 differentially expressed genes (DEGs) were identified in PoRU vs. PoSU and PoRC vs. PoSC. The significant enrichment pathways between PoRU and PoSU were mainly in metabolic and biosynthesis pathways. A total of thirty dominant enrichment pathways between PoRC and PoSC mainly focused on some immune-related pathways, including the hematopoietic cell lineage, cytokine-cytokine receptor interaction, complement and coagulation cascades, antigen processing and presentation, the intestinal immune network for immunoglobulin A (IgA) production and T/B cell receptor signaling pathway. Under the protein-protein interaction (PPI) analysis, hub genes, including CD molecules, complement component factors and chemokines, were identified in the network, and 16 core genes were differentially expressed in resistant and sustainable families in quantitative polymerase chain reaction (qPCR) validation. This study represents the first transcriptome analysis based on resistant and susceptible families and provides resistant genes to understand the potential molecular mechanisms of antibacterial function in marine fish. The results obtained in this study provide crucial information on gene markers for resistant breeding of Japanese flounder.
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Affiliation(s)
- Lei Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China
| | - Xiwen Xu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China
| | - Ziwei Zhang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Kaimin Li
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Shandong Normal University, Jinan, 250014, China
| | - Yingming Yang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China
| | - Weiwei Zheng
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China
| | - Hejun Sun
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China
| | - Songlin Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China.
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Bao X, Liu X, Yu B, Li Y, Cui M, Wang W, Feng Y, Xu X, Sun G, Li B, Li Z, Yang J. Transcriptome Profiling Based on Larvae at Different Time Points After Hatching Provides a Core Set of Gene Resource for Understanding the Metabolic Mechanisms of the Brood-Care Behavior in Octopus ocellatus. Front Physiol 2022; 12:762681. [PMID: 35069236 PMCID: PMC8777255 DOI: 10.3389/fphys.2021.762681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
The metabolic processes of organisms are very complex. Each process is crucial and affects the growth, development, and reproduction of organisms. Metabolism-related mechanisms in Octopus ocellatus behaviors have not been widely studied. Brood-care is a common behavior in most organisms, which can improve the survival rate and constitution of larvae. Octopus ocellatus carried out this behavior, but it was rarely noticed by researchers before. In our study, 3,486 differentially expressed genes (DEGs) were identified based on transcriptome analysis of O. ocellatus. We identify metabolism-related DEGs using GO and KEGG enrichment analyses. Then, we construct protein-protein interaction networks to search the functional relationships between metabolism-related DEGs. Finally, we identified 10 hub genes related to multiple gene functions or involved in multiple signal pathways and verified them using quantitative real-time polymerase chain reaction (qRT-PCR). Protein-protein interaction networks were first used to study the effects of brood-care behavior on metabolism in the process of growing of O. ocellatus larvae, and the results provide us valuable genetic resources for understanding the metabolic processes of invertebrate larvae. The data lay a foundation for further study the brood-care behavior and metabolic mechanisms of invertebrates.
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Affiliation(s)
- Xiaokai Bao
- School of Agriculture, Ludong University, Yantai, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, China
| | - Benshu Yu
- Shandong Fisheries Development and Resources Conservation Center, Yantai, China
| | - Yan Li
- School of Agriculture, Ludong University, Yantai, China
| | - Mingxian Cui
- School of Agriculture, Ludong University, Yantai, China
| | - Weijun Wang
- School of Agriculture, Ludong University, Yantai, China
| | - Yanwei Feng
- School of Agriculture, Ludong University, Yantai, China
| | - Xiaohui Xu
- School of Agriculture, Ludong University, Yantai, China
| | - Guohua Sun
- School of Agriculture, Ludong University, Yantai, China
| | - Bin Li
- School of Agriculture, Ludong University, Yantai, China
- Yantai Haiyu Marine Science and Technology Co. Ltd., Yantai, China
| | - Zan Li
- School of Agriculture, Ludong University, Yantai, China
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai, China
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OUP accepted manuscript. Brief Funct Genomics 2022; 21:243-269. [DOI: 10.1093/bfgp/elac007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/14/2022] Open
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Qiao Y, Yan W, He J, Liu X, Zhang Q, Wang X. Identification, evolution and expression analyses of mapk gene family in Japanese flounder (Paralichthys olivaceus) provide insight into its divergent functions on biotic and abiotic stresses response. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 241:106005. [PMID: 34731643 DOI: 10.1016/j.aquatox.2021.106005] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Mitogen-activated protein kinase (MAPK) are a series of serine/threonine protein kinases showing evolutionary conservation, which can be activated by many stimulus signals and then transfer them from cell membrane to nucleus. MAPKs regulate a variety of biological processes, such as apoptosis, hormone signaling and immune response. In this study, 14 putative mapk genes in Japanese flounder were identified, and their basic physical and chemical properties were characterized. Phylogenetic analysis showed that mapk genes were divided into three main subfamilies, including ERK, JNK and the p38 MAPK. Selection pressure analysis revealed they were evolutionarily-constrained and undergone strong purifying selection. Gene structure and conserved protein motif comparison suggested high levels of conservation in members of mapk gene family. The expression patterns were further investigated in each embryonic and larval development stages and different tissues. In addition, RNA-seq analyses after bacteria and temperature stresses suggested mapk genes had different expression patterns. Three mapk genes showed significant differences in response to E. tarda challenge and five were induced significantly after temperature stress, indicating their potential functions. This systematic analysis provided valuable information for further understanding of the regulation mechanism of mapk gene family under different stresses in Japanese flounder.
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Affiliation(s)
- Yingjie Qiao
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Weijie Yan
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Jiayi He
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai 264005, China
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Xubo Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China.
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Li Z, Bao X, Liu X, Li Y, Cui M, Liu X, Li B, Feng Y, Xu X, Sun G, Wang W, Yang J. Transcriptome profiling based on protein-protein interaction networks provides a set of core genes for understanding the immune response mechanisms of the egg-protecting behavior in Octopus ocellatus. FISH & SHELLFISH IMMUNOLOGY 2021; 117:113-123. [PMID: 34333127 DOI: 10.1016/j.fsi.2021.07.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Protection via of the immune system is indispensable to the life of organisms. Within an immune network, problems with a given link will affect the normal life activities of the organism. Octopus ocellatus is cephalopod widely distributed throughout the world's oceans. Because of its unique nervous system and locomotive organs, research on this species has gradually increased in recent years. Many immune response mechanisms associated with behaviors of O. ocellatus are still unclear. Moreover, as a factor affecting the normal growth of O. ocellatus, egg protection has rarely been considered in previous behavioral studies. In this study, we analyzed the transcriptome profile of gene expression in O. ocellatus larvae, and identified 5936 differentially expressed genes (DEGs). GO and KEGG enrichment analyses were used to search for immune-related DEGs. Protein-protein interaction networks were constructed to examine the interactions between immune-related genes. Fifteen hub genes involved in multiple KEGG signaling pathways or with multiple protein-protein interaction relationships were obtained and verified by quantitative RT-PCR. We first studied the effects of egg protection on the immunity of O. ocellatus larvae by means of protein-protein interaction networks, and the results provide valuable genetic resources for understanding the immunity of invertebrate larvae. The data serve as a foundation for further research on the egg-protecting behavior of invertebrates.
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Affiliation(s)
- Zan Li
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiaokai Bao
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xintian Liu
- Weihai Oceanic Development Research Institute, Weihai, 264200, China
| | - Yan Li
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Mingxian Cui
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Bin Li
- School of Agriculture, Ludong University, Yantai, 264025, China; Yantai Haiyu Marine Science and Technology Co. Ltd., Yantai, 264004, China
| | - Yanwei Feng
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiaohui Xu
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Guohua Sun
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Weijun Wang
- School of Agriculture, Ludong University, Yantai, 264025, China; Jiangsu Baoyuan Biotechnology Co. Ltd., Lianyungang, 222100, China.
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai, 264025, China.
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Blood Transcriptomics of Turbot Scophthalmus maximus: A Tool for Health Monitoring and Disease Studies. Animals (Basel) 2021; 11:ani11051296. [PMID: 33946507 PMCID: PMC8147184 DOI: 10.3390/ani11051296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/31/2022] Open
Abstract
Simple Summary The analysis of blood gene expression is emerging as a relevant source of information about the health status of an organism. While these investigations are increasingly performed in human and terrestrial animals, their potential is still underexplored in fish pathology. The aim of this work was to analyze the blood transcriptional profile of a commercially important flatfish species, turbot (Scophthalmus maximus), in healthy and diseased specimens. The analysis of the most expressed genes in healthy fish indicated that turbot red blood cells have important immunological functions. In diseased fish, parasitized by a myxozoan, the blood analysis reflected a broad inhibition of the immune response followed by intense inflammatory activation in heavy infections. The results showed that turbot response appears delayed, dysregulated and ineffective in stopping the infection. Particularly, a proper development of the adaptive immune response was lacking. This study points out that blood gene expression profiling is a reliable tool for health monitoring, as well as to advance in the knowledge of fish immunity and diseases. Abstract Blood transcriptomics is emerging as a relevant tool to monitor the status of the immune system and assist in diagnosis, prognosis, treatment and pathogenesis studies of diseases. In fish pathology, the potential of transcriptome profiling of blood is still poorly explored. Here, RNA sequencing was applied to analyze the blood transcriptional profile of turbot (Scophthalmus maximus), the most important farmed flatfish. The study was conducted in healthy specimens and specimens parasitized by the myxozoan Enteromyxum scophthalmi, which causes one of the most devastating diseases in turbot aquaculture. The blood of healthy turbot showed a transcriptomic profile mainly related to erythrocyte gas transportation function, but also to antigen processing and presentation. In moderately infected turbot, the blood reflected a broad inhibition of the immune response. Particularly, down-regulation of the B cell receptor signaling pathway was shared with heavily parasitized fish, which showed larger transcriptomic changes, including the activation of the inflammatory response. Turbot response to enteromyxosis proved to be delayed, dysregulated and ineffective in stopping the infection. The study evinces that blood transcriptomics can contribute to a better understanding of the teleost immune system and serve as a reliable tool to investigate the physiopathological status of fish.
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Seibel H, Baßmann B, Rebl A. Blood Will Tell: What Hematological Analyses Can Reveal About Fish Welfare. Front Vet Sci 2021; 8:616955. [PMID: 33860003 PMCID: PMC8042153 DOI: 10.3389/fvets.2021.616955] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/10/2021] [Indexed: 01/11/2023] Open
Abstract
Blood analyses provide substantial information about the physiological aspects of animal welfare assessment, including the activation status of the neuroendocrine and immune system, acute and long-term impacts due to adverse husbandry conditions, potential diseases, and genetic predispositions. However, fish blood is still not routinely analyzed in research or aquaculture for the assessment of health and/or welfare. Over the years, the investigative techniques have evolved from antibody-based or PCR-based single-parameter analyses to now include transcriptomic, metabolomic, and proteomic approaches and from hematological observations to fluorescence-activated blood cell sorting in high-throughput modes. The range of testing techniques established for blood is now broader than for any other biogenic test material. Evaluation of the particular characteristics of fish blood, such as its cell composition, the nucleation of distinct blood cells, or the multiple isoforms of certain immune factors, requires adapted protocols and careful attention to the experimental designs and interpretation of the data. Analyses of fish blood can provide an integrated picture of the endocrine, immunological, reproductive, and genetic functions under defined environmental conditions and treatments. Therefore, the scarcity of high-throughput approaches using fish blood as a test material for fish physiology studies is surprising. This review summarizes the wide range of techniques that allow monitoring of informative fish blood parameters that are modulated by different stressors, conditions, and/or treatments. We provide a compact overview of several simple plasma tests and of multiparametric analyses of fish blood, and we discuss their potential use in the assessment of fish welfare and pathologies.
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Affiliation(s)
- Henrike Seibel
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Kiel, Germany
- Gesellschaft für Marine Aquakultur mbH (GMA), Büsum, Germany
| | - Björn Baßmann
- Department of Aquaculture and Sea-Ranching, Faculty of Agricultural and Environmental Science, University of Rostock, Rostock, Germany
| | - Alexander Rebl
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
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Zhu TF, Shi YH, Li MY, Chen J. RGD-binding integrins mediated phagocytosis involved in the entry of Edwardsiella tarda into mudskipper MO/MФ. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 116:103960. [PMID: 33301793 DOI: 10.1016/j.dci.2020.103960] [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: 10/17/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
The versatile fish pathogen Edwardsiella tarda is an intracellular pathogen with the ability to invade and replicate in host phagocytes. However, the mechanism mediating the uptake of E. tarda in fish monocytes/macrophages (MO/MΦ) is not yet understood. Generating mudskipper kidney-derived MO/MФ transcriptomic resources from mudskipper challenged by E. tarda is crucial for understanding the molecular mechanisms underlying the mudskipper invasion process. In the present study, a total of 1185 up-regulated and 885 down-regulated differentially expressed genes (DEGs) were identified using RNA-seq. Enrichment and pathway analysis of DEGs revealed the centrality of the phagosome and regulation of actin cytoskeleton pathways in pathogen entry. The progress of phagosome formation was observed by transmission electron microscopy. Eight conserved integrin (ITG) subunit genes, belonging to the phagocytic receptors, were found in the transcriptomic sequence data. Additionally, quantitative real-time PCR showed that the mRNA expressions of most ITG subunit genes were related to the different infection times of E. tarda and the different bacterial pathogens. Further assays demonstrated that phagocytosis of FITC-labeled E. tarda by mudskipper MO/MФ was significantly reduced by the tetrapeptide Asp-Gly-Arg-Ser (RGDS). In summary, phagocytosis is one of the entry pathways into mudskipper MO/MΦ, and RGD-binding ITGs are involved in the phagosome formation process.
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Affiliation(s)
- Ting-Fang Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo, 315832, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Meishan Campus, Ningbo University, Ningbo, 315832, China
| | - Yu-Hong Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo, 315832, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Meishan Campus, Ningbo University, Ningbo, 315832, China.
| | - Ming-Yun Li
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo, 315832, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Meishan Campus, Ningbo University, Ningbo, 315832, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo, 315832, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Meishan Campus, Ningbo University, Ningbo, 315832, China.
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Liu J, Li Z, Wang Y, Zhang Q. Impact of Ringer's Solution Challenge Stress to Immunostimulatory Experiment, Insights From Japanese Flounder. Front Physiol 2020; 11:612036. [PMID: 33343401 PMCID: PMC7746848 DOI: 10.3389/fphys.2020.612036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/11/2020] [Indexed: 11/13/2022] Open
Abstract
Ringer's or phosphate buffer saline (PBS) solution buffer usually was used as dilution butter in intraperitoneal injection. Stress could activate immune response, inflammatory response and glycogen metabolic process. The impact of solution buffer as a stressor to immune system was ignored in immunostimulatory experiment. In this report, we tested the hypothesis that the innate immune response and glycogen metabolic process were altered when it were challenged with Ringer's in Japanese flounder (Paralichthys olivaceus). RNA-seq was performed after challenge with Ringer's at 8 h and 48 h. The data revealed that the expression profiles of blood, gill, and kidney were significantly changed. Differentially expressed genes (DEGs) were identified, and energy metabolic and immune-related genes were up-regulated or down-regulated obviously. GO and KEGG analyses showed that DEGs were mainly enriched in innate immune terms and pathways. Weighted gene co-expression networks analysis (WGCNA) also indicated the highest association module with stress. A total of 16 genes were detected in the gray module, which were immune-related and metabolic-related genes. These results provided fundamental information on intraperitoneal injection with solution buffer. It offered useful clues to further explore the functional mechanism of stress and immunity.
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Affiliation(s)
- Jinxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Zan Li
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yujue Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, China
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
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Transcriptome Analysis of Paralichthys olivaceus Erythrocytes Reveals Profound Immune Responses Induced by Edwardsiella tarda Infection. Int J Mol Sci 2020; 21:ijms21093094. [PMID: 32353932 PMCID: PMC7247156 DOI: 10.3390/ijms21093094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/03/2020] [Accepted: 04/03/2020] [Indexed: 12/12/2022] Open
Abstract
Unlike mammalian red blood cells (RBCs), fish RBCs are nucleated and thus capable of gene expression. Japanese flounder (Paralichthys olivaceus) is a species of marine fish with important economic values. Flounder are susceptible to Edwardsiella tarda, a severe bacterial pathogen that is able to infect and survive in flounder phagocytes. However, the infectivity of and the immune response induced by E. tarda in flounder RBCs are unclear. In the present research, we found that E. tarda was able to invade and replicate inside flounder RBCs in both in vitro and in vivo infections. To investigate the immune response induced by E. tarda in RBCs, transcriptome analysis of the spleen RBCs of flounder challenged with E. tarda was performed. Six sequencing libraries were constructed, and an average of 43 million clean reads per library were obtained, with 85% of the reads being successfully mapped to the genome of flounder. A total of 1720 differentially expressed genes (DEGs) were identified in E. tarda-infected fish. The DEGs were significantly enriched in diverse Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, especially those associated with immunity, disease, and infection. Ninety-one key DEGs involved in 12 immune-related pathways were found to form extensive interaction networks. Twenty-one genes that constituted the hub of the networks were further identified, which were highly regulated by E. tarda and involved in a number of immune processes, notably pathogen recognition and signal transduction, antigen processing and presentation, inflammation, and splicing. These results provide new insights into the immune role of flounder RBCs during bacterial infection.
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Ning X, Sun L. Gene network analysis reveals a core set of genes involved in the immune response of Japanese flounder (Paralichthys olivaceus) against Vibrio anguillarum infection. FISH & SHELLFISH IMMUNOLOGY 2020; 98:800-809. [PMID: 31743762 DOI: 10.1016/j.fsi.2019.11.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/30/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
Japanese flounder (Paralichthys olivaceus) is one of the most economically important marine fish cultured in north Asia. Vibrio anguillarum is a severe bacterial pathogen to Japanese flounder and many other aquaculture species. In order to understand the immune response of flounder during bacterial infection, we systematically examined the transcriptome profiles of flounder spleen at three time points after V. anguillarum challenge. More than one billion high quality reads were obtained, approximately 80.70% of which were successfully mapped to the reference genome of flounder. A total of 6060, 4688 and 4235 differentially expressed genes (DEGs) were captured at 6, 12 and 24-h post-infection, respectively. The DEGs exhibited dynamic changes in expression and were assigned into four different profiles based on expression trend. GO and KEGG analysis showed that the DEGs were enriched in various immune-related terms, including response to stimulation, immune system and pathways of cytokine-cytokine receptor interaction, Jak-STAT signaling and Toll-like receptor signaling. Furthermore, a network of highly interactive DEGs involved in 11 immune-related pathways was detected by utilizing the weighted co-expressing network analysis (WGCNA). Accordingly, 26 hub genes were discovered that constituted an elaborate immune regulatory network and functioned mainly in pathogen recognition, antigen processing, and molecular signaling. The results of this study provided the first systematical transcriptome profile of flounder in association with V. anguillarum infection and can serve as a valuable resource of target genes for future studies on the molecular mechanisms underlying the immune defense of flounder against bacterial infection.
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Affiliation(s)
- Xianhui Ning
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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32
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Lohinai Z, Megyesfalvi Z, Suda K, Harko T, Ren S, Moldvay J, Laszlo V, Rivard C, Dome B, Hirsch FR. Comparative expression analysis in small cell lung carcinoma reveals neuroendocrine pattern change in primary tumor versus lymph node metastases. Transl Lung Cancer Res 2019; 8:938-950. [PMID: 32010572 DOI: 10.21037/tlcr.2019.11.30] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background Recent preclinical data suggest that neuroendocrine (NE) subtype of small cell lung cancer (SCLC) has strong therapeutic relevance. NE high tumors are associated with immune desert and NE low tumors are considered to have an immune oasis phenotype. Our aim was to investigate the NE phenotypes of surgically resected SCLC tumors according to inter-tumor heterogeneity. Methods Expression analysis for 2,560 genes was performed in 32 surgically resected SCLC patients' primary tumors and corresponding lymph node (LN) metastases. To analyze tumor heterogeneity, we examined the differences in the gene expression of primary tumors versus LN metastases. We performed cluster analysis and heat map to divide patients into NE high and low subtypes by using the top NE-associated genes described in preclinical studies. Results We found 6% (n=154) genes with significant differences and only 13.1% (n=336) of all genes in the panel had a strong correlation between the primary tumor and LN metastases. Cluster analysis clearly distinguished SCLC NE high versus low subtypes both in primary tumor (20 vs. 12, respectively) and LNs (23 vs. 9, respectively). As for inter-tumor heterogeneity, in case of five patients, a change in the NE pattern was observed. Specifically, we found significant downregulation of the NE-associated genes CAV1 (P=0.004), CAV2 (P=0.029) and ANXA3 (P=0.035) in their LN metastases compared to their primary tumor. Conclusions Our data confirm the results of preclinical studies and clearly distinguish NE low and high differentiation clusters in SCLC. Moreover, they highlight the gene expression discordance between primary tumors and corresponding LN metastases suggesting that the NE pattern of metastatic LNs might not reflect that of the primary tumor. Altogether, by shedding light on the diversity of SCLC, the current study might help to improve patient selection and treatment in this devastating disease. Keywords Small cell lung cancer (SCLC); neuroendocrine tumor; lymph node metastasis; tumor heterogeneity; RNA sequencing.
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Affiliation(s)
- Zoltan Lohinai
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Zsolt Megyesfalvi
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary.,Division of Thoracic Surgery, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Kenichi Suda
- Division of Thoracic Surgery, Department of Surgery, Faculty of Medicine, Kindai University, Osaka-Sayama, Japan
| | - Tunde Harko
- Department of Pathology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China
| | - Judit Moldvay
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Viktoria Laszlo
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, Budapest, Hungary.,Division of Thoracic Surgery, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Christopher Rivard
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Balazs Dome
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary.,Division of Thoracic Surgery, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Fred R Hirsch
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Tisch Cancer Institute, Center for Thoracic Oncology, Mount Sinai Health System, New York, NY, USA
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33
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A Comparative Analysis of Edwardsiella tarda-Induced Transcriptome Profiles in RAW264.7 Cells Reveals New Insights into the Strategy of Bacterial Immune Evasion. Int J Mol Sci 2019; 20:ijms20225724. [PMID: 31731575 PMCID: PMC6888325 DOI: 10.3390/ijms20225724] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/08/2019] [Accepted: 11/10/2019] [Indexed: 01/15/2023] Open
Abstract
Edwardsiella tarda is a Gram-negative bacterial pathogen with a broad host range, including fish, reptiles, and mammals. One prominent virulence feature of E. tarda is its ability to survive and replicate in host phagocytes, but the relevant molecular mechanism is largely unknown. In this study, we examined the transcriptome profiles of RAW264.7 cells, a murine macrophage cell line, infected with live E. tarda or stimulated with dead E. tarda for 4 h and 8 h. Eighteen libraries were constructed, and an average of 69 million clean reads per library were obtained, with ~81.63% of the reads being successfully mapped to the reference genome. In total, 208 and 232 differentially expressed genes (DEGs) were identified between live and dead E. tarda-treated cells at 4 h and 8 h post-infection, respectively. The DEGs were markedly enriched in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with immunity. Live E. tarda differed strikingly from dead E. tarda in the regulation of immune related genes. Compared with dead E. tarda-treated cells, live E. tarda-treated cells exhibited marked and significant suppression in the induction of a large amount of immune genes, including RIG-I-like receptors, cytokines, and interferon-related genes. Furthermore, some of the immune genes highly regulated by live E. tarda formed complicated interaction networks with each other. Together, the results of this study revealed a transcriptome profile specifically induced by the active virulence elements of live E. tarda during the infection process, thus adding new insights into the intracellular infection mechanism of E. tarda. This study also provided a valuable set of target genes for further study of the immune evasion strategy of E. tarda.
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Liu K, Hao X, Wang Q, Hou J, Lai X, Dong Z, Shao C. Genome-wide identification and characterization of heat shock protein family 70 provides insight into its divergent functions on immune response and development of Paralichthys olivaceus. PeerJ 2019; 7:e7781. [PMID: 31737440 PMCID: PMC6855204 DOI: 10.7717/peerj.7781] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/28/2019] [Indexed: 01/16/2023] Open
Abstract
Flatfish undergo extreme morphological development and settle to a benthic in the adult stage, and are likely to be more susceptible to environmental stress. Heat shock proteins 70 (hsp70) are involved in embryonic development and stress response in metazoan animals. However, the evolutionary history and functions of hsp70 in flatfish are poorly understood. Here, we identified 15 hsp70 genes in the genome of Japanese flounder (Paralichthys olivaceus), a flatfish endemic to northwestern Pacific Ocean. Gene structure and motifs of the Japanese flounder hsp70 were conserved, and there were few structure variants compared to other fish species. We constructed a maximum likelihood tree to understand the evolutionary relationship of the hsp70 genes among surveyed fish. Selection pressure analysis suggested that four genes, hspa4l, hspa9, hspa13, and hyou1, showed signs of positive selection. We then extracted transcriptome data on the Japanese flounder with Edwardsiella tarda to induce stress, and found that hspa9, hspa12b, hspa4l, hspa13, and hyou1 were highly expressed, likely to protect cells from stress. Interestingly, expression patterns of hsp70 genes were divergent in different developmental stages of the Japanese flounder. We found that at least one hsp70 gene was always highly expressed at various stages of embryonic development of the Japanese flounder, thereby indicating that hsp70 genes were constitutively expressed in the Japanese flounder. Our findings provide basic and useful resources to better understand hsp70 genes in flatfish.
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Affiliation(s)
- Kaiqiang Liu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resource, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, QingDao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, QingDao, China
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
| | - Xiancai Hao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resource, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, QingDao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, QingDao, China
| | - Qian Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resource, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, QingDao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, QingDao, China
| | - Jilun Hou
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Beidaihe, China
| | - Xiaofang Lai
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
| | - Zhiguo Dong
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
| | - Changwei Shao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resource, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, QingDao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, QingDao, China
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Zhang K, Liu X, Han M, Liu Y, Wang X, Yu H, Liu J, Zhang Q. Functional differentiation of three phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) in response to Vibrio anguillarum infection in turbot (Scophthalmus maximus). FISH & SHELLFISH IMMUNOLOGY 2019; 92:450-459. [PMID: 31207302 DOI: 10.1016/j.fsi.2019.06.035] [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: 03/14/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 06/09/2023]
Abstract
PIK3CA has been extensively investigated from its molecular mechanism perspective and association with its mutations in different types of cancers. However, little has been reported regarding the pathological significance of PIK3CA expression in teleost. Here, in our present study, three PIK3CA genes termed SmPIK3CAa, SmPIK3CAb and SmPIK3CA-like were firstly identified in the genome of turbot S. maximus. Although these three genes located in different chromosomes, all of them share the same five domains. Phylogenetic and synteny analysis indicated that SmPIK3CAa, SmPIK3CAb and SmPIK3CA-like were three paralogs that may originate from duplication of the same ancestral PIK3CA gene. Subcellular localization analysis confirmed the cytoplasm distribution of these three paralogs. All three SmPIK3CA were ubiquitously expressed in examined tissues in turbot, with the higher expression levels in immune-related tissues such as blood, spleen, kidney, gills and intestines. Upon Vibrio anguillarum challenge, SmPIK3CAa and SmPIK3CA-like transcripts were significantly induced in spleen, intestine and blood despite of differential expression levels and responsive time points. Additionally, individuals in resistant group showed significantly higher expression level of both two genes than in the susceptible group. Moreover, four SNPs (102, 2530, 3027 and 3060) and one haplotype (Hap2) located in exon region of SmPIK3CA-like were identified and confirmed to be associated with V. anguillarum resistance in turbot by association analysis in different populations. Taken together, these results suggested that functional differentiation occurred in three SmPIK3CA paralogs with Vibrio anguillarum resistance and SmPIK3CAa and SmPIK3CA-like probable play potential roles in innate immune response to pathogenic invasions in turbot.
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Affiliation(s)
- Kai Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Xiumei Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China; College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Miao Han
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yuxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Xuangang Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Haiyang Yu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Jinxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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36
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Jiang M, Chen ZG, Zheng J, Peng B. Metabolites-Enabled Survival of Crucian Carps Infected by Edwardsiella tarda in High Water Temperature. Front Immunol 2019; 10:1991. [PMID: 31507599 PMCID: PMC6713922 DOI: 10.3389/fimmu.2019.01991] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/06/2019] [Indexed: 12/20/2022] Open
Abstract
Temperature is one of the major factors that affect the outbreak of infectious disease. Lines of evidences have shown that virulence factors can be controlled by thermo-sensors in bacterial pathogens. However, how temperature influences host's responses to the pathogen is still largely unexplored, and the study of this might pave the way to develop strategies to manage pathogenic bacterial infection. In the present study, we show that finfish Carassius carassius, the crucian carp that is tolerant to a wide range of temperatures, is less susceptible to bacterial infection when grown in 20°C than in 30°C. The different responses of C. carassius to bacterial infection could be partially explained by the distinct metabolisms under the specific temperatures: C. carassius shows elevated tricarboxylic acid cycle (TCA cycle) but decreased taurine and hypotaurine metabolism as well as lower biosynthesis of unsaturated fatty acids at 30°C. The decreased abundance of palmitate, threonine, and taurine represents the most characteristic metabolic feature. Consistently, exogenous palmitate, threonine, or taurine enhances the survival of C. carassius to bacterial infection at 30°C in a dose-dependent manner. This effect could be attributed to the inhibition on the TCA cycle by the three metabolites. This notion is further supported by the fact that low concentration of malonate, a succinate dehydrogenase inhibitor, increases the survival of C. carassius at 30°C as well. On the other hand, addition of the three metabolites rescued the decreased expression of pro-inflammatory cytokines including TNF-α1, TNF-α2, IL-1β1, IL-1β2, and lysozyme at 30°C. Taken together, our results revealed an unexpected relationship between temperature and metabolism that orchestrates the immune regulation against infection by bacterial pathogens. Thus, this study shed light on the modulation of finfish physiology to fight against bacterial infection through metabolism.
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Affiliation(s)
- Ming Jiang
- State Key Laboratory of Bio-Control, Higher Education Mega Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhuang-Gui Chen
- Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jun Zheng
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Bo Peng
- State Key Laboratory of Bio-Control, Higher Education Mega Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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37
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Liu Y, Liu Y, Han M, Du X, Liu X, Zhang Q, Liu J. Edwardsiella tarda-induced miR-7a functions as a suppressor in PI3K/AKT/GSK3β signaling pathway by targeting insulin receptor substrate-2 (IRS2a and IRS2b) in Paralichthys olivaceus. FISH & SHELLFISH IMMUNOLOGY 2019; 89:477-485. [PMID: 30940579 DOI: 10.1016/j.fsi.2019.03.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/29/2019] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
To study the effect of Edwardsiella tarda infection on miRNAs expression profile in Japanese flounder, fish were injected intraperitoneally with E. tarda. The miRNAs involved in regulating immune responses were analyzed by high-throughput sequencing. A total of 164 mature miRNAs were identified, of which 17 miRNAs were differentially expressed (DE miRNAs) after E. tarda infection, indicating that they were immune-related miRNAs. To further examine the relationship between the miRNAs and their predicted target mRNAs, a total of 22 predicted target mRNAs, mainly related to endocytic signaling pathway, NF-κB signaling pathway, and p53 signaling pathway, were detected with miRNA mimics in HEK-293T cells by dual-luciferase reporter experiments. Finally, we confirmed that insulin receptor substrate-2 (IRS2a and IRS2b) were regulated by miR-7a. And the target sites of the 3' untranslated region (UTR) of IRS2a and IRS2b were verified by dual-luciferase reporter experiments. Furthermore, we found that the E. tarda and LPS significantly increased host miR-7a expression. In vivo and in vitro studies revealed that IRS2-mediated PI3K/AKT/GSK3β signaling pathway was suppressed. Taken together, these results implied that miR-7a might be a key regulator of PI3K/AKT/GSK3β signaling pathway via suppressing the IRS2a and IRS2b genes.
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Affiliation(s)
- Yuezhong Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yuxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Miao Han
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Xinxin Du
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China; Department of Life Science and Engineering, Jining University, Jining, China
| | - Xiumei Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China; College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Jinxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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38
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Maekawa S, Wang PC, Chen SC. Comparative Study of Immune Reaction Against Bacterial Infection From Transcriptome Analysis. Front Immunol 2019; 10:153. [PMID: 30804945 PMCID: PMC6370674 DOI: 10.3389/fimmu.2019.00153] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/17/2019] [Indexed: 12/28/2022] Open
Abstract
Transcriptome analysis is a powerful tool that enables a deep understanding of complicated physiological pathways, including immune responses. RNA sequencing (RNA-Seq)-based transcriptome analysis and various bioinformatics tools have also been used to study non-model animals, including aquaculture species for which reference genomes are not available. Rapid developments in these techniques have not only accelerated investigations into the process of pathogenic infection and defense strategies in fish, but also used to identify immunity-related genes in fish. These findings will contribute to fish immunotherapy for the prevention and treatment of bacterial infections through the design of more specific and effective immune stimulants, adjuvants, and vaccines. Until now, there has been little information regarding the universality and diversity of immune reactions against pathogenic infection in fish. Therefore, one of the aims of this paper is to introduce the RNA-Seq technique for examination of immune responses in pathogen-infected fish. This review also aims to highlight comparative studies of immune responses against bacteria, based on our previous findings in largemouth bass (Micropterus salmoides) against Nocardia seriolae, gray mullet (Mugil cephalus) against Lactococcus garvieae, orange-spotted grouper (Epinephelus coioides) against Vibrio harveyi, and koi carp (Cyprinus carpio) against Aeromonas sobria, using RNA-seq techniques. We demonstrated that only 39 differentially expressed genes (DEGs) were present in all species. However, the number of specific DEGs in each species was relatively higher than that of common DEGs; 493 DEGs in largemouth bass against N. seriolae, 819 DEGs in mullets against L. garvieae, 909 in groupers against V. harveyi, and 1471 in carps against A. sobria. The DEGs in different fish species were also representative of specific immune-related pathways. The results of this study will enhance our understanding of the immune responses of fish, and will aid in the development of effective vaccines, therapies, and disease-resistant strains.
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Affiliation(s)
- Shun Maekawa
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Pei-Chi Wang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan.,Southern Taiwan Fish Disease Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Shih-Chu Chen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan.,Southern Taiwan Fish Disease Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan.,International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan.,Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung, Taiwan
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39
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Zhang W, Lv Z, Li C, Sun Y, Jiang H, Zhao M, Zhao X, Shao Y, Chang Y. Transcriptome profiling reveals key roles of phagosome and NOD-like receptor pathway in spotting diseased Strongylocentrotus intermedius. FISH & SHELLFISH IMMUNOLOGY 2019; 84:521-531. [PMID: 30342081 DOI: 10.1016/j.fsi.2018.10.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/13/2018] [Accepted: 10/16/2018] [Indexed: 06/08/2023]
Abstract
Spotting disease is a common disease in the process of aquaculture and restocking of the sea urchin Strongylocentrotus intermedius and leads to mass mortality. To characterize the molecular processes and candidate genes related to spotting disease in S. intermedius, we conducted next-generation sequencing to assess the key genes/pathways in spotting diseased sea urchin (DUG) compared to healthy ones (HUG). A total of 321.1 million clean reads were obtained and assembled into 93,877 Unigenes with an N50 of 1185 bp, in which 86.48% of them matched to the genome sequence of the sea urchin S. purpuratus and 27,456 Unigenes mapped to Nr database. Salmon expression analysis revealed 1557 significantly differently expressed genes (DEGs) between DUG and HUG. These DEGs were enriched into 151 KEGG pathways including a core set of immune correlated pathways notably in phagosome and NOD-like receptor signaling. DUG displayed an obvious downregulation in these immune pathways. The expression patterns of six DEGs were confirmed by RT-qPCR, and the expressions were consistent with the results of RNA-seq. Furthermore, 15,990 SSRs were identified and a total of 235,249 and 295,567 candidate SNPs were identified from DUG and HUG, respectively. All these results provided basic information for our understanding of spotting disease outbreak in sea urchin.
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Affiliation(s)
- Weijie Zhang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang Province, 315211, PR China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, PR China
| | - Zhimeng Lv
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang Province, 315211, PR China
| | - Chenghua Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang Province, 315211, PR China.
| | - Yahui Sun
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, PR China
| | - Huijie Jiang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, PR China
| | - Manxi Zhao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, PR China
| | - Xuelin Zhao
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang Province, 315211, PR China
| | - Yina Shao
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang Province, 315211, PR China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, PR China.
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40
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Shi H, Zhou T, Wang X, Yang Y, Wu C, Liu S, Bao L, Li N, Yuan Z, Jin Y, Tan S, Wang W, Zhong X, Qin G, Geng X, Gao D, Dunham R, Liu Z. Genome-wide association analysis of intra-specific QTL associated with the resistance for enteric septicemia of catfish. Mol Genet Genomics 2018; 293:1365-1378. [PMID: 29967962 DOI: 10.1007/s00438-018-1463-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/19/2018] [Indexed: 02/07/2023]
Abstract
Disease resistance is one of the most important traits for aquaculture industry. For catfish industry, enteric septicemia of catfish (ESC), caused by the bacterial pathogen Edwardsiella ictaluri, is the most severe disease, causing enormous economic losses every year. In this study, we used three channel catfish families with 900 individuals (300 fish per family) and the 690K catfish SNP array, and conducted a genome-wide association study to detect the quantitative trait loci (QTL) associated with ESC resistance. Three significant QTL, with two of located on LG1 and one on LG26, and three suggestive QTL located on LG1, LG3, and LG21, respectively, were identified to be associated with ESC resistance. With a well-assembled- and -annotated reference genome sequence, genes around the involved QTL regions were identified. Among these genes, 37 genes had known functions in immunity, which may be involved in ESC resistance. Notably, nlrc3 and nlrp12 identified here were also found in QTL regions of ESC resistance in the channel catfish × blue catfish interspecific hybrid system, suggesting this QTL was operating within both intra-specific channel catfish populations and interspecific hybrid backcross populations. Many of the genes of the Class I MHC pathway, for mediated antigen processing and presentation, were found in the QTL regions. The positional correlation found in this study and the expressional correlation found in previous studies indicated that Class I MHC pathway was significantly associated with ESC resistance. This study validated one QTL previously identified using the second and fourth generation of the interspecific hybrid backcross progenies, and identified five additional QTL among channel catfish families. Taken together, it appears that there are only a few major QTL for ESC disease resistance, making marker-assisted selection an effective approach for genetic improvements of ESC resistance.
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Affiliation(s)
- Huitong Shi
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xiaozhu Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Chenglong Wu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lisui Bao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ning Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zihao Yuan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yulin Jin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Suxu Tan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Wenwen Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xiaoxiao Zhong
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Guyu Qin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xin Geng
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Dongya Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhanjiang Liu
- Department of Biology, College of Art and Sciences, Syracuse University, Syracuse, NY, 13244, USA.
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