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Eurlaphan C, Nozaki R, Sano M, Koiwai K, Hirono I, Kondo H. Red sea bream iridovirus infection downregulates inflammation-related genes in the spleen of rock bream (Oplegnathus fasciatus). JOURNAL OF FISH DISEASES 2023; 46:1403-1411. [PMID: 37697626 DOI: 10.1111/jfd.13858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/20/2023] [Accepted: 08/26/2023] [Indexed: 09/13/2023]
Abstract
This study investigated the kinetics of red sea bream iridovirus and host gene expression during infection in rock bream (Oplegnathus fasciatus), a species highly sensitive to the virus. After intraperitoneal injection of the viral solution at 104 TCID50/fish, the viral genome copy number in the spleen was 104.7 ± 0.2 and 105.9 ± 0.4 copies/μg DNA at 3 and 5 days post-injection (dpi), respectively. Using transcriptomic analyses via MiSeq, viral gene transcripts were detected at 3 and 5 dpi. Six genes including RING-finger domain-containing protein and laminin-type epidermal growth factor-like domain genes were significantly expressed at 5 dpi. Further, 334 host genes were differentially expressed compared with those before infection. Genes were clustered into four groups based on their expression profiles. Interferon-stimulated genes were more prevalent in groups showing upregulation at 5 dpi and 3 and 5 dpi. In contrast, the group showing downregulation at 3 dpi included inflammation-related genes, such as granzyme and eosinophil peroxidase genes. Downregulation of certain inflammation-related genes may contribute to the susceptibility of this fish to the virus.
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Affiliation(s)
- Chalermkwan Eurlaphan
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Reiko Nozaki
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Motohiko Sano
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Keiichiro Koiwai
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hidehiro Kondo
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
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Lin P, Xu M, Yang Q, Chen M, Guo S. Inoculation of Freund's adjuvant in European eel (Anguilla anguilla) revealed key KEGG pathways and DEGs of host anti-Edwardsiella anguillarum infection. FISH & SHELLFISH IMMUNOLOGY 2023; 136:108708. [PMID: 36997037 DOI: 10.1016/j.fsi.2023.108708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Freund's complete (FCA) and incomplete adjuvants (FIA), generally applied in subunit fishery vaccine, have not been explored on the molecular mechanism of the nonspecific immune enhancement. In this study, we examined the RNA-seq in the spleen of European eel (Anguilla anguilla) inoculated with FCA and FIA (FCIA group) to elucidate the key KEGG pathways and differential expressed genes (DEGs) in the process of Edwardsiella anguillarum infection and A. anguilla anti-E. anguillarum infection using genome-wide transcriptome. After eels were challenged by E. anguillarum at 28 d post the first inoculation (dpi), compared to the control uninfected eels (Con group), the control infected eels (Con_inf group) showed severe pathological changes in the liver, kidney and spleen, although infected eels post the inoculation of FCIA (FCIA_inf group) also formed slight bleeding. Compared to the FCIA_inf group, there was more than 10 times colony forming unit (cfu) in the Con_inf group per 100 μg spleen, kidney or blood, and the relative percent survival (RPS) of eels was 44.4% in FCIA_inf vs Con_inf. Compared to the Con group, the SOD activity in the FCIA group increased significantly in the liver and spleen. Using high-throughput transcriptomics, DEGs were identified and 29 genes were verified using fluorescence real-time polymerase chain reaction (qRT-PCR). The result of DEGs clustering showed 9 samples in 3 groups of Con, FCIA and FCIA_inf were similar, contrast to distinct differences of 3 samples in the Con_inf group. We found 3795 up and 3548 down regulated DEGs in the compare of FCIA_inf vs Con_inf, of which 5 enriched KEGG pathways of "Lysosome", "Autophagy", "Apoptosis", "C-type lectin receptor signaling" and "Insulin signaling" were ascertained, and 26 of 30 top GO terms in the compare were significantly enriched. Finally, protein-protein interactions between the DEGs of the 5 KEGG pathways and other DEGs were explored using Cytoscape 3.9.1. The compare of FCIA_inf vs Con_inf showed 110 DEGs from the 5 pathways and 718 DEGs from other pathways formed total of 9747° in a network, of which 9 hub DEGs play vital roles in anti-infection or apoptosis. Together, the interaction networks revealed that 9 DEGs involved in the 5 pathways underlies the key process of A. anguilla anti-E. anguillarum infection or host cell apoptosis.
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Affiliation(s)
- Peng Lin
- Fisheries College, Jimei University /Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education of PRC, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Xiamen, China
| | - Ming Xu
- Fisheries College, Jimei University /Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education of PRC, Xiamen, China
| | - Qiuhua Yang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Minxia Chen
- Fisheries College, Jimei University /Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education of PRC, Xiamen, China
| | - Songlin Guo
- Fisheries College, Jimei University /Engineering Research Center of the Modern Industry Technology for Eel, Ministry of Education of PRC, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Xiamen, China.
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Zhang L, Yan S, Hong X, Zhao G, Zha J. Integrative time series of cellular, humoral and molecular response revealed immunotoxicity of bifenthrin to Chinese rare minnow (Gobiocypris rarus) following Pseudomonas fluorescens challenge. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 256:106427. [PMID: 36805112 DOI: 10.1016/j.aquatox.2023.106427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Bifenthrin is a common pesticide that is widespread in aquatic environments. Although it has been shown to be toxic to aquatic organisms, its immunotoxicity and mechanism are unclear. Herein, we reported the immunotoxicity of bifenthrin on adult Chinese rare minnow (Gobiocypris rarus) after 28 days of exposure to different concentrations of bifenthrin (0.1, 0.3, and 1.0 μg/L) and 36-h Pseudomonas fluorescens challenge. Bifenthrin inhibited the fish humoral immune response to bacteria by altering the lymphocyte and neutrophil ratios and decreasing the production of lysozyme, complement component 3, immunoglobulin M, and C-reactive protein, particularly were 1.0 μg/L. Bifenthrin caused intestinal damage and significantly reduced the volume of intestinal mucus at 12 and 36 hours postinjection (hpi) (p < 0.05). Moreover, 1.0 μg/L bifenthrin significantly increased the fish mortality and bacterial loads at 12 and 36 hpi (p < 0.05). RNA-seq analysis revealed several enriched genes involved in pathogen attachment and recognition, inflammatory responses, and complement system at the early-to-mid stage of infection (4-12 hpi). Overall, our results corroborated that bifenthrin induced immunotoxicity in Gobiocypris rarus, resulting in immune dysfunction of fish and increasing their sensitivity to bacterial infection and accelerating mortality. Moreover, 4-12 hpi was better than 36 hpi for analyzing immune responses against pathogen infection in fish exposed to bifenthrin.
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Affiliation(s)
- Le Zhang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Saihong Yan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xiangsheng Hong
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Gaofeng Zhao
- Institute of Environment and Sustainable Development in Agriculture, CAAS, Beijing, 100081, China
| | - Jinmiao Zha
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Sánchez-Baizán N, Ribas L, Piferrer F. Improved biomarker discovery through a plot twist in transcriptomic data analysis. BMC Biol 2022; 20:208. [PMID: 36153614 PMCID: PMC9509653 DOI: 10.1186/s12915-022-01398-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 09/02/2022] [Indexed: 11/22/2022] Open
Abstract
Background Transcriptomic analysis is crucial for understanding the functional elements of the genome, with the classic method consisting of screening transcriptomics datasets for differentially expressed genes (DEGs). Additionally, since 2005, weighted gene co-expression network analysis (WGCNA) has emerged as a powerful method to explore relationships between genes. However, an approach combining both methods, i.e., filtering the transcriptome dataset by DEGs or other criteria, followed by WGCNA (DEGs + WGCNA), has become common. This is of concern because such approach can affect the resulting underlying architecture of the network under analysis and lead to wrong conclusions. Here, we explore a plot twist to transcriptome data analysis: applying WGCNA to exploit entire datasets without affecting the topology of the network, followed with the strength and relative simplicity of DEG analysis (WGCNA + DEGs). We tested WGCNA + DEGs against DEGs + WGCNA to publicly available transcriptomics data in one of the most transcriptomically complex tissues and delicate processes: vertebrate gonads undergoing sex differentiation. We further validate the general applicability of our approach through analysis of datasets from three distinct model systems: European sea bass, mouse, and human. Results In all cases, WGCNA + DEGs clearly outperformed DEGs + WGCNA. First, the network model fit and node connectivity measures and other network statistics improved. The gene lists filtered by each method were different, the number of modules associated with the trait of interest and key genes retained increased, and GO terms of biological processes provided a more nuanced representation of the biological question under consideration. Lastly, WGCNA + DEGs facilitated biomarker discovery. Conclusions We propose that building a co-expression network from an entire dataset, and only thereafter filtering by DEGs, should be the method to use in transcriptomic studies, regardless of biological system, species, or question being considered. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01398-w.
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Fu Q, Li Y, Zhang H, Cao M, Zhang L, Gao C, Cai X, Chen D, Yang Z, Li J, Yang N, Li C. Comparative Transcriptome Analysis of Spleen Reveals Potential Regulation of Genes and Immune Pathways Following Administration of Aeromonas salmonicida subsp. masoucida Vaccine in Atlantic Salmon (Salmo salar). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:97-115. [PMID: 35084599 PMCID: PMC8792528 DOI: 10.1007/s10126-021-10089-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Aeromonas salmonicida is a global fish pathogen. Aeromonas salmonicida subsp. masoucida (ASM) is classified as atypical A. salmonicida and caused huge losses to salmonid industry in China. Hence, it is of great significance to develop ASM vaccine and explore its protection mechanism in salmonids. In this regard, we conducted RNA-seq analysis with spleen tissue of Atlantic salmon after ASM vaccination to reveal genes, their expression patterns, and pathways involved in immune protections. In our results, a total of 441.63 million clean reads were obtained, and 389.37 million reads were mapped onto the Atlantic salmon reference genome. In addition, 1125, 2126, 1098, 820, and 1351 genes were significantly up-regulated, and 747, 2626, 818, 254, and 908 genes were significantly down-regulated post-ASM vaccination at 12 h, 24 h, 1 month, 2 months, and 3 months, respectively. Subsequent pathway analysis revealed that many differentially expressed genes (DEGs) following ASM vaccination were involved in cytokine-cytokine receptor interaction (TNFRSF11b, IL-17RA, CCR9, and CXCL11), HTLV-I infection (MR1 and HTLV-1), MAPK signaling pathway (MAPK, IL8, and TNF-α-1), PI3K-Akt signaling pathway (PIK3R3, THBS4, and COL2A1), and TNF signaling pathway (PTGS2, TNFRSF21-l, and CXCL10). Finally, the results of qRT-PCR showed a significant correlation with RNA-seq results, suggesting the reliability of RNA-seq for gene expression analysis. This study provided insights into regulation of gene expression and their involved pathways in Atlantic salmon spleen in responses to vaccine, and set the foundation for further study on the vaccine protective mechanism in Atlantic salmon as well as other teleost species.
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Affiliation(s)
- Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuqing Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hao Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lu Zhang
- Shandong Sinder Technology Co., Ltd, Zhucheng, 262200, China
| | - Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xin Cai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Defeng Chen
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ziying Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jie Li
- Key Laboratory of Maricultural Organism Disease Control, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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Zhang Y, Ding J, Liu C, Luo S, Gao X, Wu Y, Wang J, Wang X, Wu X, Shen W, Zhu J. Genetics Responses to Hypoxia and Reoxygenation Stress in Larimichthys crocea Revealed via Transcriptome Analysis and Weighted Gene Co-Expression Network. Animals (Basel) 2021; 11:ani11113021. [PMID: 34827754 PMCID: PMC8614329 DOI: 10.3390/ani11113021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/26/2021] [Accepted: 09/29/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Hypoxia, which occurs frequently in aquaculture, can cause serious harm to all aspects of the growth, reproduction and metabolism of cultured fish. Due to the intolerance of Larimichthys crocea to hypoxia, Larimichthys crocea often floats head or even dies under hypoxic environment. However, the molecular mechanism of hypoxia tolerance in Larimichthys crocea has not been fully described. Therefore, the aim of this study was to explore the hub regulatory genes under hypoxic stress environment by transcriptome analysis of three key tissues (liver, blood and gill) in Larimichthys crocea. We identified a number of important genes that exercise different regulatory functions. Overall, this study will provide important clues to the molecular mechanisms of hypoxia tolerance in Larimichthys crocea. Abstract The large yellow croaker (Larimichthys crocea) is an important marine economic fish in China; however, its intolerance to hypoxia causes widespread mortality. To understand the molecular mechanisms underlying hypoxia tolerance in L. crocea, the transcriptome gene expression profiling of three different tissues (blood, gills, and liver) of L. crocea exposed to hypoxia and reoxygenation stress were performed. In parallel, the gene relationships were investigated based on weighted gene co-expression network analysis (WGCNA). Accordingly, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that several pathways (e.g., energy metabolism, signal transduction, oxygen transport, and osmotic regulation) may be involved in the response of L. crocea to hypoxia and reoxygenation stress. In addition, also, four key modules (darkorange, magenta, saddlebrown, and darkolivegreen) that were highly relevant to the samples were identified by WGCNA. Furthermore, some hub genes within the association module, including RPS16, EDRF1, KCNK5, SNAT2, PFKL, GSK-3β, and PIK3CD, were found. This is the first study to report the co-expression patterns of a gene network after hypoxia stress in marine fish. The results provide new clues for further research on the molecular mechanisms underlying hypoxia tolerance in L. crocea.
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Affiliation(s)
- Yibo Zhang
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, 169 South Qixing Road, Ningbo 315832, China; (Y.Z.); (J.D.); (C.L.); (S.L.); (X.G.); (Y.W.); (J.W.)
- State Key Laboratory of Large Yellow Croaker Breeding, Ningbo Academy of Oceanology and Fishery, Juxian Road, Ningbo 315103, China; (X.W.); (X.W.)
| | - Jie Ding
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, 169 South Qixing Road, Ningbo 315832, China; (Y.Z.); (J.D.); (C.L.); (S.L.); (X.G.); (Y.W.); (J.W.)
- State Key Laboratory of Large Yellow Croaker Breeding, Ningbo Academy of Oceanology and Fishery, Juxian Road, Ningbo 315103, China; (X.W.); (X.W.)
| | - Cheng Liu
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, 169 South Qixing Road, Ningbo 315832, China; (Y.Z.); (J.D.); (C.L.); (S.L.); (X.G.); (Y.W.); (J.W.)
- State Key Laboratory of Large Yellow Croaker Breeding, Ningbo Academy of Oceanology and Fishery, Juxian Road, Ningbo 315103, China; (X.W.); (X.W.)
| | - Shengyu Luo
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, 169 South Qixing Road, Ningbo 315832, China; (Y.Z.); (J.D.); (C.L.); (S.L.); (X.G.); (Y.W.); (J.W.)
| | - Xinming Gao
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, 169 South Qixing Road, Ningbo 315832, China; (Y.Z.); (J.D.); (C.L.); (S.L.); (X.G.); (Y.W.); (J.W.)
| | - Yuanjie Wu
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, 169 South Qixing Road, Ningbo 315832, China; (Y.Z.); (J.D.); (C.L.); (S.L.); (X.G.); (Y.W.); (J.W.)
| | - Jingqian Wang
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, 169 South Qixing Road, Ningbo 315832, China; (Y.Z.); (J.D.); (C.L.); (S.L.); (X.G.); (Y.W.); (J.W.)
| | - Xuelei Wang
- State Key Laboratory of Large Yellow Croaker Breeding, Ningbo Academy of Oceanology and Fishery, Juxian Road, Ningbo 315103, China; (X.W.); (X.W.)
| | - Xiongfei Wu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningbo Academy of Oceanology and Fishery, Juxian Road, Ningbo 315103, China; (X.W.); (X.W.)
| | - Weiliang Shen
- State Key Laboratory of Large Yellow Croaker Breeding, Ningbo Academy of Oceanology and Fishery, Juxian Road, Ningbo 315103, China; (X.W.); (X.W.)
- Correspondence: (W.S.); (J.Z.); Tel.: +86-153-8137-7660 (W.S.); +86-139-5784-1679 (J.Z.)
| | - Junquan Zhu
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, 169 South Qixing Road, Ningbo 315832, China; (Y.Z.); (J.D.); (C.L.); (S.L.); (X.G.); (Y.W.); (J.W.)
- Correspondence: (W.S.); (J.Z.); Tel.: +86-153-8137-7660 (W.S.); +86-139-5784-1679 (J.Z.)
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Ahn G, Cha JY, Lee JW, Park G, Shin GI, Song SJ, Ryu G, Hwang I, Kim MG, Kim WY. Production of a Bacteria-like Particle Vaccine Targeting Rock Bream ( Oplegnathus fasciatus) Iridovirus Using Nicotiana benthamiana. JOURNAL OF PLANT BIOLOGY = SINGMUL HAKHOE CHI 2021; 65:21-28. [PMID: 34602836 PMCID: PMC8477727 DOI: 10.1007/s12374-021-09328-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Viral diseases are extremely widespread infections that change constantly through mutations. To produce vaccines against viral diseases, transient expression systems are employed, and Nicotiana benthamiana (tobacco) plants are a rapidly expanding platform. In this study, we developed a recombinant protein vaccine targeting the major capsid protein (MCP) of iridovirus fused with the lysine motif (LysM) and coiled-coil domain of coronin 1 (ccCor1) for surface display using Lactococcus lactis. The protein was abundantly produced in N. benthamiana in its N-glycosylated form. Total soluble proteins isolated from infiltrated N. benthamiana leaves were treated sequentially with increasing ammonium sulfate solution, and recombinant MCP mainly precipitated at 40-60%. Additionally, affinity chromatography using Ni-NTA resin was applied for further purification. Native structure analysis using size exclusion chromatography showed that recombinant MCP existed in a large oligomeric form. A minimum OD600 value of 0.4 trichloroacetic acid (TCA)-treated L. lactis was required for efficient recombinant MCP display. Immunogenicity of recombinant MCP was assessed in a mouse model through enzyme-linked immunosorbent assay (ELISA) with serum-injected recombinant MCP-displaying L. lactis. In summary, we developed a plant-based recombinant vaccine production system combined with surface display on L. lactis.
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Affiliation(s)
- Gyeongik Ahn
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Joon-Yung Cha
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Jeong Won Lee
- Department of Agricultural Chemistry and Food Science and Technology, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Gyeongran Park
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Shi-Jian Song
- Department of Life Science, Pohang University of Science and Technology, Pohang, 37673 Republic of Korea
| | - Gyeongryul Ryu
- College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Inhwan Hwang
- Department of Life Science, Pohang University of Science and Technology, Pohang, 37673 Republic of Korea
| | - Min Gab Kim
- College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828 Republic of Korea
- Department of Agricultural Chemistry and Food Science and Technology, Gyeongsang National University, Jinju, 52828 Republic of Korea
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Zhao X, Sun Z, Xu H, Song N, Gao T. Transcriptome and co-expression network analyses reveal the regulatory pathways and key genes associated with temperature adaptability in the yellow drum (Nibea albiflora). J Therm Biol 2021; 100:103071. [PMID: 34503808 DOI: 10.1016/j.jtherbio.2021.103071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/14/2021] [Accepted: 08/03/2021] [Indexed: 12/27/2022]
Abstract
The yellow drum (Nibea albiflora) is an important marine economy fish, that is widely distributed in the coastal waters of the Northwest Pacific. To understand the molecular regulatory mechanism of the yellow drum under temperature stress, transcriptome analysis was performed under five temperature conditions (10 °C, 15 °C, 20 °C, 24 °C, 28 °C) in the present study. Compared with 20 °C, 163, 401, 276, and 372 differentially expressed genes (DEGs) were obtained at 10 °C, 15 °C, 24 °C and 28 °C, respectively. Gene Ontology (GO) analysis indicated that the DEGs were mainly involved in cellular processes, metabolic processes, catalytic activity, membrane and binding. Meanwhile, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the temperature adaptive regulation of the yellow drum was mainly involved in signal transduction, metabolism, genetic information and protein processing. Weighted gene co-expression network analysis (WGCNA) showed that HMGB1, STAT4, Noct, C1q and CRT may be the key hub genes in the response of the yellow drum to temperature stress. In addition, 20 genes that may be associated with temperature stress were identified based on comparative analysis between the KEGG enrichment and the WGCNA results. Ten DEGs were selected for further validation using quantitative real-time PCR (qRT-PCR), and the results were consistent with the RNA-seq data. This study explored the transcriptional patterns of the yellow drum under temperature stress and provided fundamental information on the temperature adaptability of this species.
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Affiliation(s)
- Xiang Zhao
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, 266003, China
| | - Zhicheng Sun
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, 266003, China
| | - Hao Xu
- Qingdao Marine Hazard Mitigation Service, Qingdao, Shandong, 266003, China
| | - Na Song
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, 266003, China.
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, China.
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Ko EJ, Kim H, Lee AR, Jeon KY, Kim A, Kim DH, Park CI, Choi YH, Kim S, Kim HS, Ock MS, Cha HJ. Proteome profile of spleen in rock bream (Oplegnathus fasciatus) naturally infected with rock bream iridovirus (RBIV). Genes Genomics 2021; 43:1259-1268. [PMID: 34427872 DOI: 10.1007/s13258-021-01149-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/04/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Rock bream iridovirus (RBIV) is one of the most dangerous pathogens that causes the highest mortality in the aquaculture of rock bream (Oplegnathus fasciatus). Even though RBIV infection leads to huge economic loss, proteome studies on RBIV-infected rock bream have not been conducted to provide information about the differential protein expression pattern by the host protection system. OBJECTIVE The purpose of this study was to investigate the protein expression patterns in spleens of rock bream olive after infection by RBIV or mixed infection by RBIV and bacteria. METHODS Depending on the infection intensity and sampling time point, fish were divided into five groups: uninfected healthy fish at week 0 as the control (0C), heavily infected fish at week 0 (0H), heavily mixed RBIV and bacterial infected fish at week 0 (0MH), uninfected healthy fish at week 3 (3C), and lightly infected fish at week 3 (3L). Proteins were extracted from the spleens of infected rock bream. We used 2-DE analysis with LC-MS/MS to investigate proteome changes in infected rock bream. RESULTS The results of the LC-MS/MS analyses showed different protein expression profiles after infection. Proteins related to oxygen transport and energy generation, such as hemoglobin, beta-globin, and ATP synthase, were mostly expressed in the infected spleen. Whereas proteins involved in structure and cell movement, such as tubulin, myosin, actin binding proteins, and intermediate filament proteins, were down-regulated in the infected spleens. The protein expression profiles between infection by RBIV and mixed infection by RBIV and bacteria showed similar patterns. CONCLUSIONS Our results indicated that infection by RBIV or mixed infection by RBIV and bacteria triggered energy generation and oxygen-transport, but cell migration and constructional changes in the spleen were extremely decreased.
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Affiliation(s)
- Eun-Ji Ko
- Department of Parasitology and Genetics, Kosin University College of Medicine, Busan, Republic of Korea
| | - Hyunsu Kim
- Department of Parasitology and Genetics, Kosin University College of Medicine, Busan, Republic of Korea
| | - A-Reum Lee
- Department of Parasitology and Genetics, Kosin University College of Medicine, Busan, Republic of Korea
| | - Kyung-Yoon Jeon
- Department of Parasitology and Genetics, Kosin University College of Medicine, Busan, Republic of Korea
| | - Ahran Kim
- Pathology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan, Republic of Korea
| | - Chan-Il Park
- Department of Marine Biology and Aquaculture, College of Marine Science, Gyeongsang National University, Tongyeong, Republic of Korea
| | - Yung Hyun Choi
- Department of Biochemistry, College of Oriental Medicine, Dongeui University, Busan, Republic of Korea
| | - Suhkmann Kim
- Department of Chemistry, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
| | - Mee Sun Ock
- Department of Parasitology and Genetics, Kosin University College of Medicine, Busan, Republic of Korea
| | - Hee-Jae Cha
- Department of Parasitology and Genetics, Kosin University College of Medicine, Busan, Republic of Korea.
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10
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Roh H, Kim N, Lee Y, Park J, Kim BS, Lee MK, Park CI, Kim DH. Dual-Organ Transcriptomic Analysis of Rainbow Trout Infected With Ichthyophthirius multifiliis Through Co-Expression and Machine Learning. Front Immunol 2021; 12:677730. [PMID: 34305907 PMCID: PMC8296305 DOI: 10.3389/fimmu.2021.677730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/31/2021] [Indexed: 01/16/2023] Open
Abstract
Ichthyophthirius multifiliis is a major pathogen that causes a high mortality rate in trout farms. However, systemic responses to the pathogen and its interactions with multiple organs during the course of infection have not been well described. In this study, dual-organ transcriptomic responses in the liver and head kidney and hemato-serological indexes were profiled under I. multifiliis infection and recovery to investigate systemic immuno-physiological characteristics. Several strategies for massive transcriptomic interpretation, such as differentially expressed genes (DEGs), Poisson linear discriminant (PLDA), and weighted gene co-expression network analysis (WGCNA) models were used to investigate the featured genes/pathways while minimizing the disadvantages of individual methods. During the course of infection, 6,097 and 2,931 DEGs were identified in the head kidney and liver, respectively. Markers of protein processing in the endoplasmic reticulum, oxidative phosphorylation, and the proteasome were highly expressed. Likewise, simultaneous ferroptosis and cellular reconstruction was observed, which is strongly linked to multiple organ dysfunction. In contrast, pathways relevant to cellular replication were up-regulated in only the head kidney, while endocytosis- and phagosome-related pathways were notably expressed in the liver. Moreover, interestingly, most immune-relevant pathways (e.g., leukocyte trans-endothelial migration, Fc gamma R-mediated phagocytosis) were highly activated in the liver, but the same pathways in the head kidney were down-regulated. These conflicting results from different organs suggest that interpretation of co-expression among organs is crucial for profiling of systemic responses during infection. The dual-organ transcriptomics approaches presented in this study will greatly contribute to our understanding of multi-organ interactions under I. multifiliis infection from a broader perspective.
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Affiliation(s)
- HyeongJin Roh
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan, South Korea
| | - Nameun Kim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan, South Korea
| | - Yoonhang Lee
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan, South Korea
| | - Jiyeon Park
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan, South Korea
| | - Bo Seong Kim
- Aquatic Disease Control Division, National Institute of Fisheries Science (NIFS), Busan, South Korea
| | - Mu Kun Lee
- Korean Aquatic Organism Disease Inspector Association, Busan, South Korea
| | - Chan-Il Park
- Department of Marine Biology & Aquaculture, College of Marine Science, Gyeongsang National University, Tongyeong, South Korea
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan, South Korea
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11
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Yang J, Zhang J, Fan R, Zhao W, Han T, Duan K, Li X, Zeng P, Deng J, Zhang J, Yang X. Identifying Potential Candidate Hub Genes and Functionally Enriched Pathways in the Immune Responses to Quadrivalent Inactivated Influenza Vaccines in the Elderly Through Co-Expression Network Analysis. Front Immunol 2020; 11:603337. [PMID: 33343577 PMCID: PMC7746648 DOI: 10.3389/fimmu.2020.603337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/06/2020] [Indexed: 11/21/2022] Open
Abstract
Insights into the potential candidate hub genes may facilitate the generation of safe and effective immunity against seasonal influenza as well as the development of personalized influenza vaccines for the elderly at high risk of influenza virus infection. This study aimed to identify the potential hub genes related to the immune induction process of the 2018/19 seasonal quadrivalent inactivated influenza vaccines (QIVs) in the elderly ≥60 years by using weighted gene co-expression network analysis (WGCNA). From 63 whole blood samples from16 elderly individuals, a total of 13,345 genes were obtained and divided into eight co-expression modules, with two modules being significantly correlated with vaccine-induced immune responses. After functional enrichment analysis, genes under GO terms of vaccine-associated immunity were used to construct the sub-network for identification and functional validation of hub genes. MCEMP1 and SPARC were confirmed as the hub genes with an obvious effect on QIVs-induced immunity. The MCEMP1 expression was shown to be negatively correlated with the QIVs-associated reactogenicity within 7 days after vaccination, which could be suppressed by the CXCL 8/IL-8 and exacerbated by the Granzyme-B cytotoxic mediator. Meanwhile, the SPARC expression was found to increase the immune responses to the QIVs and contribute to the persistence of protective humoral antibody titers. These two genes can be used to predict QIVs-induced adverse reaction, the intensity of immune responses, and the persistence of humoral antibody against influenza. This work has shed light on further research on the development of personalized QIVs with appropriate immune responses and long-lasting immunity against the forthcoming seasonal influenza.
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Affiliation(s)
- Jing Yang
- National Institute of Engineering Technology Research in Combination Vaccine, Wuhan, China.,Wuhan Institute of Biological Products Co., Ltd., Wuhan, China
| | - Jiayou Zhang
- National Institute of Engineering Technology Research in Combination Vaccine, Wuhan, China.,Wuhan Institute of Biological Products Co., Ltd., Wuhan, China
| | - Renfeng Fan
- Guangdong Province Institute of Biological Products and Materia Medica, Guangzhou, China
| | - Wei Zhao
- National Institute of Engineering Technology Research in Combination Vaccine, Wuhan, China.,Wuhan Institute of Biological Products Co., Ltd., Wuhan, China
| | - Tian Han
- National Institute of Engineering Technology Research in Combination Vaccine, Wuhan, China.,Wuhan Institute of Biological Products Co., Ltd., Wuhan, China
| | - Kai Duan
- National Institute of Engineering Technology Research in Combination Vaccine, Wuhan, China.,Wuhan Institute of Biological Products Co., Ltd., Wuhan, China
| | - Xinguo Li
- National Institute of Engineering Technology Research in Combination Vaccine, Wuhan, China.,Wuhan Institute of Biological Products Co., Ltd., Wuhan, China
| | - Peiyu Zeng
- Gaozhou Center for Disease Control and Prevention, Maoming City, China
| | - Jinglong Deng
- Gaozhou Center for Disease Control and Prevention, Maoming City, China
| | - Jikai Zhang
- Guangdong Province Institute of Biological Products and Materia Medica, Guangzhou, China
| | - Xiaoming Yang
- National Institute of Engineering Technology Research in Combination Vaccine, Wuhan, China.,China Biotechnology Co., Ltd., Peking, China
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