Identification and analysis of lncRNA50877, which is involved in KRT8-mediated mitochondrial homeostasis and GCRV replication in grass carp (Ctenopharyngodon idella).
Aug 2026· Developmental and Comparative Immunology· Vol 183, pp.
105718
· 0 citations· 50 references
Medicine
TL;DR
It is demonstrated that lncRNA50877 disrupts mitochondrial homeostasis by negatively regulating KRT8 expression, thereby modulating ROS levels, apoptosis, and autophagy; promoting oxidative stress-induced cell injury; and providing favorable conditions for GCRV replication.
Abstract
Grass carp (Ctenopharyngodon idella) reovirus (GCRV), the causative agent of hemorrhagic disease, causes substantial economic losses in the grass carp industry every year. However, the biological regulatory roles of long non-coding RNAs (lncRNAs) during GCRV infection remain largely unclear. In this study, high-throughput sequencing technology was used to analyze the expression profiles of lncRNAs in GCRV-infected and mock-infected liver and intestinal tissues of grass carp. In this study, compared with those in the control group, the transcriptomic profiles of grass carp after GCRV genotype II (HZ08 strain) infection revealed 742 upregulated and 1,259 downregulated lncRNA transcripts in the intestines, whereas 709 upregulated and 1,513 downregulated lncRNA transcripts were identified in the liver. GO and KEGG pathway analyses indicated that these lncRNAs were enriched primarily in pathways associated with biological process regulation, including "Pyruvate metabolism" and the "AMPK signaling pathway". Notably, we revealed that lncRNA50877 (PX600394) was upregulated in grass carp tissues and CIK cells following GCRV infection. CIK cells infected with equal titers of GCRV in vitro for 24 h exhibited aggravated cytopathic effect (CPE) upon lncRNA50877 overexpression. Furthermore, ChIRP-MS and RNA pull-down assays confirmed its direct interaction with KRT8 (keratin 8, PX531115). Our results demonstrated that lncRNA50877 disrupts mitochondrial homeostasis by negatively regulating KRT8 expression, thereby modulating ROS levels, apoptosis, and autophagy; promoting oxidative stress-induced cell injury; and providing favorable conditions for GCRV replication. In summary, lncRNA50877 may act as an autophagy-related lncRNA that regulates mitochondrial function and contributes to innate immune responses, offering new insights into the crosstalk between autophagy and innate immunity.
Findings suggest that NEAT1 and SNHG17, which have been reported to regulate inflammatory responses in multiple pathological conditions, may play important roles in the host response to L. donovani infection and could serve as potential targets for the prevention and treatment of leishmaniasis.
Ctenopharyngodon idella (grass carp) is the dominant species in freshwater aquaculture, but its farming industry is severely threatened by grass carp haemorrhagic disease (GCHD) caused by grass carp reovirus (GCRV). Autophagy plays a crucial role in viral infection, and ATG13 is a core factor for autophagy initiation. However, the functional mechanism of grass carp ATG13 (CiATG13) during GCRV-I/II infection remains unclear. In this study, the CiATG13 gene was cloned and characterized by bioinformatics analysis. The results showed that CiATG13 sequence is highly conserved in evolution, sharing the highest homology and closest evolutionary relationship with Chanodichthys erythropterus. The expression and function of CiATG13 were investigated using RT-qPCR, Western blotting, fluorescence microscopy, and CRISPR-Cas13d knockdown techniques at both cellular and individual levels. The key findings are summarized below: tissue distribution analysis revealed that CiATG13 is widely expressed in various tissues of healthy grass carp, with the highest expression in the liver, brain, and heart, and it responds actively to stimulation by pathogen-associated molecular patterns (PAMPs), such as poly (I:C) and lipopolysaccharide (LPS). GCRV-I/II infection induces the expression of CiATG13. Overexpression of CiATG13 significantly promotes GCRV-I replication, whereas knockdown of CiATG13 inhibits GCRV-I replication. Further mechanistic studies indicated that CiATG13 can induce autophagy and upregulate the expression of heat shock protein 70 (CiHSP70) through this pathway. CiHSP70 promotes GCRV-I replication, and quercetin (Qu) can block its pro-viral effect on GCRV-I/II replication by inhibiting CiHSP70. Moreover, treatment with the autophagy inhibitors chloroquine (CQ) and Spautin-1 suppressed GCRV-I replication and the associated cytopathic effect (CPE), accompanied by reduced CiHSP70 expression, overexpression of CiATG13 partially rescued these inhibitory effects.. This study reveals the molecular mechanism that CiATG13 mediates autophagy to regulate CiHSP70 expression and promote GCRV-I/II replication, enriches the understanding of the interaction between fish viruses and autophagic molecules, and provides the potential strategy targeting CiATG13 for the prevention and control of GCHD.
Yanxia Jiang, Li Wu, Yingqi Gao et al.· Fish and Shellfish Immunolog...· 0 citations
Grass carp reovirus genotype II (GCRV-II) is still a major threat to grass carp aquaculture and causes huge economic losses. Viral replication relies on host metabolic resources and metabolic reprogramming is key to virus-host interactions. However, the dynamic hepatic lipid remodeling associated with GCRV-II infection remains poorly understood. Here, the effect of GCRV-II infection on damage condition of liver from grass carp was evaluated and integrated lipidomic and transcriptomic was analyzed. Obviously, GCRV-II infection caused evident hepatic injury, significantly increased viral load and promoted hepatic lipid droplet accumulation. Lipidomic profiling revealed clear stage-dependent remodeling, characterized by broad glycerophospholipid perturbation at the early stage of infection, a sphingolipid- and acylcarnitine-dominant response at the middle stage, and persistent sphingolipid dysregulation with depletion of mitochondria-associated lipids at the late stage of infection. Meanwhile, LPE (20:4), Cer (43:2), and MePC (36:7e) were identified as the potential lipid biomarker corresponding to above three infected stages, respectively. Transcriptomic analysis also showed progressive disruption of lipid metabolism-related pathways, particularly glycerophospholipid metabolism, arachidonic acid metabolism, and sphingolipid metabolism, while fatty acid degradation became more prominent at the middle and late stages. Integrated analysis further revealed sustained glycerophospholipid remodeling and stage-specific sphingolipid dysregulation. These findings reveal temporally coordinated hepatic lipid metabolic reprogramming during GCRV-II infection and provide a foundation for further studies on how host lipid metabolism contributes to viral replication and pathogenesis.
Minxuan Yang, Hai-Bin Luo, Zhen-Yang Qiu et al.· Fish and Shellfish Immunolog...· 0 citations
Piscirickettsia salmonis is one of the most significant pathogens affecting salmon farming. Besides liver, head kidney and spleen, skeletal muscle has shown transcriptional immune responses to these bacteria, but the contribution of non-coding RNAs remains poorly understood. This study investigates the role of long non-coding RNAs (lncRNAs) in the immune response of rainbow trout skeletal muscle and primary myotube cultures infected with P. salmonis. Using RNA-seq data from both in vivo and in vitro muscle under control and infected conditions, the analysis identified 4263 candidate lncRNAs through a stringent bioinformatics pipeline. These lncRNAs were mostly classified as exonic and intergenic, showing distinct genomic distributions and structural differences depending on the source. Expression analyses revealed that cell type had a stronger effect on lncRNA profiles than infection status. From 764 differentially expressed lncRNAs, 191 were uniquely associated with infected and 180 with control conditions, mainly unannotated. Functional predictions based on co-expression and proximity to coding genes suggest that lncRNAs are primarily involved in downregulation of structural-cellular maintenance under control conditions, whereas during infection, they are related to immunity, signaling, and apoptosis. Overall, the findings indicate that lncRNAs exhibit origin-specific regulatory roles and are modulated by P. salmonis infection, highlighting their potential importance in fish immune responses.
Rodrigo Zuloaga, Luciano Ahumada-Langer, P. Dettleff et al.· Fishes· 0 citations
Simple Summary Cephalopholis sonnerati is an economically new aquaculture species in China. The red-spotted grouper nervous necrosis virus (RGNNV) exhibits high pathogenicity in larval C. sonnerati, but its immune response mechanisms remain unexplored, impeding the development of aquaculture. In the present study, we profiled brain transcriptome from healthy and naturally RGNNV-infected larvae. Many differentially expressed microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and fewer circular RNAs were identified. Enrichment analysis demonstrated that these targeted genes of differentially expressed ncRNAs were markedly enriched in innate immune defense, inflammatory, and cell death related pathways, such as JAK-STAT signaling pathway, NF-κB signaling pathway, apoptosis, and necroptosis. Furthermore, a lncRNA–miRNA–mRNA regulatory network focused on miR-93 was established, which may provide a valuable candidate target for future antiviral strategies in C. sonnerati. This study offers the first ncRNA transcriptome landscape of C. sonnerati during RGNNV infection, establishing a theoretical basis for elucidating host-RGNNV interaction mechanism in groupers.
Glaesserella parasuis (G. parasuis) is a major respiratory pathogen in piglets, but the regulatory mechanisms underlying its induced pulmonary inflammation remain poorly understood. In this study, whole-transcriptome sequencing was carried out on lung tissues from colostrum-deprived piglets with mild and severe serotype 5 G. parasuis infection and healthy controls. Differential expression (DE) analysis revealed 299 nominally DE mRNAs and 408 nominally DE lncRNAs in the mild group, increasing to 625 and 1193, respectively, in the severe group. Ingenuity Pathway Analysis identified the S100 family signaling pathway as a core inflammatory module predicted to be activated across both infection grades, with its transcriptional involvement expanding from 8 genes in mild infection to 42 genes in severe infection. Notably, G-protein-coupled receptors (GPCRs) accounted for nearly half (19/42) of the S100-associated DE genes in severe infection, covering multiple functional categories including chemokine receptors, lipid mediator receptors, and metabotropic receptors, suggesting systemic activation of the GPCR family in severe inflammation. Weighted gene co-expression network analysis identified multiple lncRNA candidates, among which two—LOC110256217 and LOC110259349—showed severity-associated connectivity patterns and were selected for further validation. Following G. parasuis infection, time-series RT-qPCR in 3D4/21 cells confirmed their co-expression with corresponding mRNAs and revealed distinct temporal patterns, suggesting their potential differential involvement at early and late stages of the inflammatory response. Collectively, these findings identify a putative lncRNA-S100-GPCR-associated inflammatory module linked to pulmonary inflammation in G. parasuis infection, providing a transcriptomic resource and candidate lncRNA-mRNA pairs for further functional studies and investigation into host resilience. Given the limited sample size (n = 3 per group), these findings should be considered exploratory and warrant validation in larger cohorts.
Jiayi Zeng, Xinqi Zeng, Xiangwei Deng et al.· Animals· 0 citations