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Li X, Lin Y, Li W, Cheng Y, Zhang J, Qiu J, Fu Y. Comparative Analysis of mRNA, microRNA of Transcriptome, and Proteomics on CIK Cells Responses to GCRV and Aeromonas hydrophila. Int J Mol Sci 2024; 25:6438. [PMID: 38928143 PMCID: PMC11204273 DOI: 10.3390/ijms25126438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Grass Carp Reovirus (GCRV) and Aeromonas hydrophila (Ah) are the causative agents of haemorrhagic disease in grass carp. This study aimed to investigate the molecular mechanisms and immune responses at the miRNA, mRNA, and protein levels in grass carp kidney cells (CIK) infected by Grass Carp Reovirus (GCRV, NV) and Aeromonas hydrophilus (Bacteria, NB) to gain insight into their pathogenesis. Within 48 h of infection with Grass Carp Reovirus (GCRV), 99 differentially expressed microRNA (DEMs), 2132 differentially expressed genes (DEGs), and 627 differentially expressed proteins (DEPs) were identified by sequencing; a total of 92 DEMs, 3162 DEGs, and 712 DEPs were identified within 48 h of infection with Aeromonas hydrophila. It is worth noting that most of the DEGs in the NV group were primarily involved in cellular processes, while most of the DEGs in the NB group were associated with metabolic pathways based on KEGG enrichment analysis. This study revealed that the mechanism of a grass carp haemorrhage caused by GCRV infection differs from that caused by the Aeromonas hydrophila infection. An important miRNA-mRNA-protein regulatory network was established based on comprehensive transcriptome and proteome analysis. Furthermore, 14 DEGs and 6 DEMs were randomly selected for the verification of RNA/small RNA-seq data by RT-qPCR. Our study not only contributes to the understanding of the pathogenesis of grass carp CIK cells infected with GCRV and Aeromonas hydrophila, but also serves as a significant reference value for other aquatic animal haemorrhagic diseases.
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Affiliation(s)
- Xike Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yue Lin
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Wenjuan Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yuejuan Cheng
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Junling Zhang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Junqiang Qiu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yuanshuai Fu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
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Zhou X, Liu L, Wang L, Liu T, Wu X. Proteomic study of Chinese black-bone silky fowl and the ring-necked pheasant egg white by iTRAQ technique. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lv W, Jin S, Wang N, Cao D, Jin X, Zhang Y. Identification of important proteins from the gonads and pituitary involved in the gonad development of Amur sturgeon, Acipenser schrenckii, regulated by GnRH-a treatment by iTRAQ-based analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100831. [PMID: 33933834 DOI: 10.1016/j.cbd.2021.100831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/16/2021] [Accepted: 03/26/2021] [Indexed: 11/16/2022]
Affiliation(s)
- Weihua Lv
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Haebin, China
| | - Shubo Jin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Nianmin Wang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Haebin, China
| | - Dingchen Cao
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Haebin, China
| | - Xing Jin
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Haebin, China.
| | - Ying Zhang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Haebin, China.
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Fabre B, Korona D, Lees JG, Lazar I, Livneh I, Brunet M, Orengo CA, Russell S, Lilley KS. Comparison of Drosophila melanogaster Embryo and Adult Proteome by SWATH-MS Reveals Differential Regulation of Protein Synthesis, Degradation Machinery, and Metabolism Modules. J Proteome Res 2019; 18:2525-2534. [DOI: 10.1021/acs.jproteome.9b00076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bertrand Fabre
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, U.K
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge CB2 1GA, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
- Technion Integrated Cancer Center (TICC), The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel
| | - Dagmara Korona
- Department of Genetics, University of Cambridge, University of Cambridge, Cambridge CB2 3EH, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Jonathan G. Lees
- Institute of Structural and Molecular Biology, University College London, London WC1E 7HX, United Kingdom
| | - Ikrame Lazar
- Technion Integrated Cancer Center (TICC), The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel
| | - Ido Livneh
- Technion Integrated Cancer Center (TICC), The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel
| | - Manon Brunet
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, U.K
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge CB2 1GA, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Christine A. Orengo
- Institute of Structural and Molecular Biology, University College London, London WC1E 7HX, United Kingdom
| | - Steven Russell
- Department of Genetics, University of Cambridge, University of Cambridge, Cambridge CB2 3EH, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, U.K
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge CB2 1GA, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
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Wen X, Zhang X, Hu Y, Xu J, Wang T, Yin S. iTRAQ-based quantitative proteomic analysis of Takifugu fasciatus liver in response to low-temperature stress. J Proteomics 2019; 201:27-36. [PMID: 30954612 DOI: 10.1016/j.jprot.2019.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/25/2019] [Accepted: 04/03/2019] [Indexed: 10/27/2022]
Abstract
Low temperatures profoundly influence the physiological and behavioural processes of ectotherms, especially teleosts, which have made them the subjects of strong interest over time. However, the characteristics of fish cold-tolerance at the protein level remain unclear. Therefore, to shed further light on the molecular mechanisms of low temperature adaptation in fish, we conducted quantitative proteomics on the T. fasciatus liver using iTRAQ. Comparing the proteomic profiles of the T. fasciatus liver at 12 °C and 26 °C, a total of 3741 proteins were identified, and 160 were differentially abundant proteins (DAPs). Among the DAPs, the most significant changes were noted in proteins involved in oxidative stress (nine proteins), mitochondrial enzymes (eleven proteins) and signal transduction (thirteen proteins). The KEGG enrichment analysis indicated significant enhancement of D-arginine and D-ornithine metabolism, MAPK signalling, Wnt signalling and Gap junction pathway. Subsequently, three significantly up-regulated proteins (CIRB, HSP90 and GST) and two significantly down-regulated proteins (FLNB and A2ML1) were validated with parallel reaction monitoring (PRM) assays. Furthermore, the changes in abundance of proteins that are involved in oxidative stress, mitochondrial enzymes and signal transduction were validated at the transcriptional level with qPCR. These verification results show that the experimental data of iTRAQ are reliable. Our results not only deepen the understanding of the mechanisms underlying low-temperature tolerance in fish, but they also may contribute to the enhancement of cold tolerance during its breeding process. SIGNIFICANCE OF THE STUDY: The study focused on a comparative quantitative proteomics analysis of the T. fasciatus liver in response to low temperatures using iTRAQ, which has not yet been reported in the literatures. The results showed that the effect of low temperature on T. fasciatus is significant, including a detoxification of metabolic by-products and oxidative stress, an activation of the mitochondrial enzyme to strengthen energy metabolism, and a negative effect on signal transduction, which result in dysfunction or suboptimal performance. These low-temperature-related changes in the liver proteome of T. fasciatus can facilitate the understanding of the low temperature-related response that takes place in similar conditions in the liver and may contribute to the breeding of cold-resistant strains.
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Affiliation(s)
- Xin Wen
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Xinyu Zhang
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Yadong Hu
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Jiejie Xu
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Tao Wang
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China.
| | - Shaowu Yin
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China.
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Liu R, Huang Q, Zhu Z, Zhang Y, Qian D, Duan JA. Further evidence for sustainable alternatives to replace threatened animal horn based on quantitative proteomic analysis. Electrophoresis 2018; 39:3185-3190. [PMID: 30192403 DOI: 10.1002/elps.201800282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/28/2018] [Accepted: 08/31/2018] [Indexed: 01/07/2023]
Abstract
In the present study, a quantitative proteomic approach was used to analyze and compare the proteome in horns from endangered species (rhinoceros, Saiga antelope, and Tibetan antelope) and common species (yak, water buffalo, and goat) based on the isobaric tag for relative and absolute quantification techniques. In total, 591 proteins were identified, and 321 were quantified and categorized based on molecular function, cellular component, and biological process. Principal component analysis and hierarchical clustering analysis results based on differences in the amount of protein identified three major clusters, and proteins including transglutaminase, desmocollin, and elongation factors were selected as trait components from proteomic patterns of horn samples from different species. Quantitative proteomic analysis based strategies can therefore provide further evidence for sustainable alternatives to replace animal horn from threatened species.
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Affiliation(s)
- Rui Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, P. R. China.,Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing University of Chinese Medicine, Nanjing, P. R. China
| | - Qiong Huang
- The First Affiliated Hospital, Nanjing Medical University, Nanjing, P. R. China
| | - Zhenhua Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, P. R. China
| | - Yan Zhang
- School of Public Administration, Nanjing Normal University, Nanjing, P. R. China
| | - Dawei Qian
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, P. R. China
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, P. R. China
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