Transcriptome profiling based on protein–protein networks provides a core set of genes for understanding blood immune response mechanisms against LPS stress in Amphioctopus fangsiao

Chen, Xipan; Li, Yán; Bao, Xiaokai; Zhang, Enshuo; Cui, Cuiju; Liu, Xiumei; Luo, Qihao; Yang, Jianmin; Li, Zan; Xu, Xiaohui

doi:10.1016/j.dci.2022.104509

Cited by 5 publications

(4 citation statements)

References 62 publications

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“…Amphioctopus fangsiao has important nutritional and economic value, and its immune mechanisms is being extensively investigated in recent years because of the serious disease problems during culture process [ [31] , [32] , [33] ]. With the rapid development of sequencing technologies, RNA-seq has been widely used in the study of immune molecular mechanisms [ [34] , [35] , [36] ].…”

Section: Discussionmentioning

confidence: 99%

Sequencing-based protein–protein interaction analysis provides a core set of immune gene for understanding white body immune response mechanisms against Poly I:C stimulation in Amphioctopus fangsiao

Chen,

Lu,

Wang

et al. 2024

Comparative Immunology Reports

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Section: Discussionmentioning

confidence: 99%

Sequencing-based protein–protein interaction analysis provides a core set of immune gene for understanding white body immune response mechanisms against Poly I:C stimulation in Amphioctopus fangsiao

Chen,

Lu,

Wang

et al. 2024

Comparative Immunology Reports

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“…In contrast to mammals, the innate immune system in fish assumes a more important role in combating pathogenic infections ( 59 – 61 ), with pattern recognition receptors (PRRs) playing a critical role in recognizing microbial pathogens and initiating innate immune responses ( 62 ). TLRs are a type of cell surface PRR with the ability to specifically recognize ligands, mobilize multiple transcription factors (e.g., NF-κB, AP1, and IRFs), and activate intracellular innate immunity ( 63 , 64 ). Notably, TLR5, known for its specific recognition of bacterial flagellin, induces an immune response and plays an important role in protecting fish from disease ( 65 ).…”

Section: Discussionmentioning

confidence: 99%

Role of the Pseudomonas plecoglossicida fliL gene in immune response of infected hybrid groupers (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂)

Shi,

Zhao,

et al. 2024

Front. Immunol.

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Pseudomonas plecoglossicida, a gram-negative bacterium, is the main pathogen of visceral white-point disease in marine fish, responsible for substantial economic losses in the aquaculture industry. The FliL protein, involved in torque production of the bacterial flagella motor, is essential for the pathogenicity of a variety of bacteria. In the current study, the fliL gene deletion strain (ΔfliL), fliL gene complement strain (C-ΔfliL), and wild-type strain (NZBD9) were compared to explore the influence of the fliL gene on P. plecoglossicida pathogenicity and its role in host immune response. Results showed that fliL gene deletion increased the survival rate (50%) and reduced white spot disease progression in the hybrid groupers. Moreover, compared to the NZBD9 strain, the ΔfliL strain was consistently associated with lower bacterial loads in the grouper spleen, head kidney, liver, and intestine, coupled with reduced tissue damage. Transcriptomic analysis identified 2 238 differentially expressed genes (DEGs) in the spleens of fish infected with the ΔfliL strain compared to the NZBD9 strain. Based on Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, the DEGs were significantly enriched in seven immune system-associated pathways and three signaling molecule and interaction pathways. Upon infection with the ΔfliL strain, the toll-like receptor (TLR) signaling pathway was activated in the hybrid groupers, leading to the activation of transcription factors (NF-κB and AP1) and cytokines. The expression levels of proinflammatory cytokine-related genes IL-1β, IL-12B, and IL-6 and chemokine-related genes CXCL9, CXCL10, and CCL4 were significantly up-regulated. In conclusion, the fliL gene markedly influenced the pathogenicity of P. plecoglossicida infection in the hybrid groupers. Notably, deletion of fliL gene in P. plecoglossicida induced a robust immune response in the groupers, promoting defense against and elimination of pathogens via an inflammatory response involving multiple cytokines.

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“…The above experimental procedure and raw data obtained by sequencing were derived from Chen et al [ 25 , 26 ].…”

Section: Methodsmentioning

confidence: 99%

“…This study encompasses the analysis of the transcription profiles of hemolymph tissues at 6 and 24 h under two distinct types of stimulation [ 25 , 26 ]. Employing the union of differentially expressed genes (DEGs) within a 24 h period under both stimulation types, the WGC network was constructed.…”

Section: Introductionmentioning

confidence: 99%

Weighted Gene Co-Expression Network Analysis Based on Stimulation by Lipopolysaccharides and Polyinosinic:polycytidylic Acid Provides a Core Set of Genes for Understanding Hemolymph Immune Response Mechanisms of Amphioctopus fangsiao

Wang,

Chen,

et al. 2023

Animals

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The primary influencer of aquaculture quality in Amphioctopus fangsiao is pathogen infection. Both lipopolysaccharides (LPS) and polyinosinic:polycytidylic acid (Poly I:C) are recognized by the pattern recognition receptor (PRR) within immune cells, a system that frequently serves to emulate pathogen invasion. Hemolymph, which functions as a transport mechanism for immune cells, offers vital transcriptome information when A. fangsiao is exposed to pathogens, thereby contributing to our comprehension of the species’ immune biological mechanisms. In this study, we conducted analyses of transcript profiles under the influence of LPS and Poly I:C within a 24 h period. Concurrently, we developed a Weighted Gene Co-expression Network Analysis (WGCNA) to identify key modules and genes. Further, we carried out Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to investigate the primary modular functions. Co-expression network analyses unveiled a series of immune response processes following pathogen stress, identifying several key modules and hub genes, including PKMYT1 and NAMPT. The invaluable genetic resources provided by our results aid our understanding of the immune response in A. fangsiao hemolymph and will further our exploration of the molecular mechanisms of pathogen infection in mollusks.

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Transcriptome profiling based on protein–protein networks provides a core set of genes for understanding blood immune response mechanisms against LPS stress in Amphioctopus fangsiao

Cited by 5 publications

References 62 publications

Sequencing-based protein–protein interaction analysis provides a core set of immune gene for understanding white body immune response mechanisms against Poly I:C stimulation in Amphioctopus fangsiao

Sequencing-based protein–protein interaction analysis provides a core set of immune gene for understanding white body immune response mechanisms against Poly I:C stimulation in Amphioctopus fangsiao

Role of the Pseudomonas plecoglossicida fliL gene in immune response of infected hybrid groupers (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂)

Weighted Gene Co-Expression Network Analysis Based on Stimulation by Lipopolysaccharides and Polyinosinic:polycytidylic Acid Provides a Core Set of Genes for Understanding Hemolymph Immune Response Mechanisms of Amphioctopus fangsiao

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