The dynamic immune responses of Mandarin fish (Siniperca chuatsi) to ISKNV in early infection based on full-length transcriptome analysis and weighted gene co-expression network analysis

Zhou, Yu; Fu, Huang-Cui; Wang, Yingying; Huang, He-Zhong; Fu, Xiaozhe; Li, Ningqiu

doi:10.1016/j.fsi.2022.02.017

Cited by 8 publications

(3 citation statements)

References 68 publications

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“…The Infectious Spleen and Kidney Necrosis Virus (ISKNV) is the type species of the Megalocytivirus genus, which is responsible for infecting a variety of marine and freshwater fishes and resulting in significant financial losses to the aquaculture industry worldwide [ 47 ]. ISKNV infections in tissues, like those caused by other megalocytiviruses, result in the enlargement of infected cells, which is much greater than normal cells [ 48 , 49 ].…”

Section: Discussionmentioning

confidence: 99%

High-throughput virtual screening of marine algae metabolites as high-affinity inhibitors of ISKNV major capsid protein: An analysis of in-silico models and DFT calculation to find novel drug molecules for fighting infectious spleen and kidney necrosis virus (ISKNV)

Islam¹,

Ahmed

Habib³

et al. 2023

Heliyon

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Section: Discussionmentioning

confidence: 99%

High-throughput virtual screening of marine algae metabolites as high-affinity inhibitors of ISKNV major capsid protein: An analysis of in-silico models and DFT calculation to find novel drug molecules for fighting infectious spleen and kidney necrosis virus (ISKNV)

Islam¹,

Ahmed

Habib³

et al. 2023

Heliyon

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“…These genes, including col1a1 , col1a2 , col5a1 , col6a2 , col10a1 , and col26a1 , were up-regulated in the fast-growth group and significantly positively correlated with body length/weight. Genes with a high degree of node connection are significantly correlated with proximity to the center of the network ( Zhou et al, 2022 ). Thus, col1a1 , col1a2 , col5a1 , col6a2 , col10a1 , and col26a1 may be crucial genes for S. grahami growth.…”

Section: Discussionmentioning

confidence: 99%

Muscle transcriptome analysis provides new insights into the growth gap between fast- and slow-growing Sinocyclocheilus grahami

Yin

Zhang

Zhong³

et al. 2023

Front. Genet.

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Sinocyclocheilus grahami is an economically valuable and famous fish in Yunnan Province, China. However, given its slow growth (40 g/2 years) and large growth differences among individuals, its growth performance needs to be improved for sustainable future use, in which molecular breeding technology can play an important role. In the current study, we conducted muscle transcriptomic analysis to investigate the growth gaps among individuals and the mechanism underlying growth within 14 fast- and 14 slow-growth S. grahami. In total, 1,647 differentially expressed genes (DEGs) were obtained, including 947 up-regulated and 700 down-regulated DEGs in fast-growth group. Most DEGs were significantly enriched in ECM-receptor interaction, starch and sucrose metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, amino acids biosynthesis and metabolism, peroxisome, and PPAR signaling pathway. Some genes related to glycogen degradation, glucose transport, and glycolysis (e.g., adipoq, prkag1, slc2a1, agl, pygm, pgm1, pfkm, gapdh, aldoa, pgk1, pgam2, bpgm, and eno3) were up-regulated, while some genes related to fatty acid degradation and transport (e.g., acox1, acaa1, fabp1b.1, slc27a1, and slc27a2) and amino acid metabolism (e.g., agxt, shmt1, glula, and cth) were down-regulated in the fast-growth group. Weighted gene co-expression network analysis identified col1a1, col1a2, col5a1, col6a2, col10a1, col26a1, bglap, and krt15 as crucial genes for S. grahami growth. Several genes related to bone and muscle growth (e.g., bmp2, bmp3, tgfb1, tgfb2, gdf10, and myog) were also up-regulated in the fast-growth group. These results suggest that fast-growth fish may uptake adequate energy (e.g., glucose, fatty acid, and amino acids) from fodder, with excess energy substances used to synthesize collagen to accelerate bone and muscle growth after normal life activities are maintained. Moreover, energy uptake may be the root cause, while collagen synthesis may be the direct reason for the growth gap between fast- and slow-growth fish. Hence, improving food intake and collagen synthesis may be crucial for accelerating S. grahami growth, and further research is required to fully understand and confirm these associations.

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“…For enriched KEGG pathways, DE-lncRNAs target 200 genes in co-expression involved in the neuroactive ligand-receptor interaction, and target 16 genes in co-location involved in herpes simplex infection in the compare of OmpA_inf vs FCIA_inf (Fig.5C, 5D). The KEGG pathways of neuroactive ligand-receptor interaction and herpes simplex infection can actively participate in anti-infection at the early stage of bacterial and/or viral infection(Wang et al 2021;Zhou et al 2022), then these DE-lncRNAs elicited by OmpA immunization play an important role in the process of resisting the invasion of E. anguillarum. The 31 and 27 DAS genes between OmpA_inf and FCIA_inf group which involved in viral and bacterial infectious diseases (Fig.7D) also directing the effect of anti-E. anguillarum infection.…”

mentioning

confidence: 99%

The role of outer membrane protein A in OmpA vaccine was revealed by the analysis of alternative splicing and lncRNA after the Edwardsiella anguillarum infected the immunized European eels (Anguilla anguilla)

Guo

Chen

Wan

et al. 2023

Preprint

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Edwardsiella anguillarum is a common bacterial pathogen mainly infected cultivated eel, and outer membrane protein A (OmpA) emulsified with Freund's adjuvant was evaluated as an effective fishery vaccine. However, the role of solo OmpA in the vaccine have not been explored on the molecular mechanism. In this study, we examined the RNA-seq in the liver of European eel (Anguilla anguilla) post the challenge of E. anguillarum in eels injected with the OmpA vaccine, Freund's adjuvant, or PBS to elucidate the alternative splicing (AS) and long noncoding RNA (lncRNA) in the process of E. anguillarum infection and host anti-infection using genome-wide transcriptome. After all eels were challenged by E. anguillarum at 28 d post the injection (dpi), compared to severe pathological changes in the liver of PBS injected eels (Con_inf group), the OmpA immunized eels (OmpA_inf group) showed infiltrated lymphocytes in the liver as well as the Freund's adjuvant inoculated eels (FCIA_inf group) showed slight edema of hepatocytes and blood coagulation. Compared to the Con_inf group, the relative percent survival (RPS) of eels was 77.7% and 44.4% in OmpA_inf and FCIA_inf group. The results of DEGs and DE-transcripts showed 6 samples in the OmpA_inf and FCIA_inf groups were clustered together, which different to 3 samples in the Con_inf group. We found only 35 DEGs between OmpA_inf and FCIA_inf compare to thousands of DEGs in two compares of OmpA_inf vs Con_inf and FCIA_inf Con_inf. GO and KEGG analysis of genes targeted by 37 DE-lncRNAs in co-expression and co-location showed at least 52 GO terms and 2 KEGG pathways were enrichment. The results of AS analysis showed 293 differentially alternative splicing (DAS) genes between OmpA_inf and FCIA_inf were mainly involved in GO terms of catalytic activity, membrane part and biological regulation, and KEGG pathways of signal transduction, immune system and infection disease. Finally, the interaction between proteins expressed by DAS genes and the interaction between DE-lncRNAs and target genes were explored using Cytoscape 3.9.1. The results indicated 66 DAS gene expressed proteins formed total of 50 degrees in 20 networks, and 33 DE-lncRNAs interacted with 194 target genes formed total of 246 and 41 networks in co-expression and co-location. Taken together, after the immunization of OmpA vaccine, compared to Freund's adjuvant inoculation, higher RPS was closely related to DAS genes and DE-lncRNAs in response to E. anguillarum infection in European eels. The OmpA role in vaccine was firstly revealed through AS genes and lncRNAs, and results of this study are of great significance to the development of fishery subunit vaccines.

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The dynamic immune responses of Mandarin fish (Siniperca chuatsi) to ISKNV in early infection based on full-length transcriptome analysis and weighted gene co-expression network analysis

Cited by 8 publications

References 68 publications

High-throughput virtual screening of marine algae metabolites as high-affinity inhibitors of ISKNV major capsid protein: An analysis of in-silico models and DFT calculation to find novel drug molecules for fighting infectious spleen and kidney necrosis virus (ISKNV)

High-throughput virtual screening of marine algae metabolites as high-affinity inhibitors of ISKNV major capsid protein: An analysis of in-silico models and DFT calculation to find novel drug molecules for fighting infectious spleen and kidney necrosis virus (ISKNV)

Muscle transcriptome analysis provides new insights into the growth gap between fast- and slow-growing Sinocyclocheilus grahami

The role of outer membrane protein A in OmpA vaccine was revealed by the analysis of alternative splicing and lncRNA after the Edwardsiella anguillarum infected the immunized European eels (Anguilla anguilla)

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