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.
Abstract
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.
By damaging target tissues and compromising the host immune system, Myxobolus cerebralis and Tetracapsuloides bryosalmonae remain persistent threats to salmonids. RNA sequencing was used to assess transcriptome modulation in the kidney and head cartilage (HC) of rainbow trout during single and co-infections with these two myxozoan parasites. Fish were exposed to M. cerebralis (Mc) and T. bryosalmonae (Tb), and 30 days later, half of the fish from each group were subjected to sequential co-infections (Mc+ and Tb+). This assessment aimed to evaluate the combined effects of both pathogens. Transcriptomic analysis was conducted using kidney and HC tissues collected 60 days post-co-infection. The results showed that infection order altered host transcriptional profiles in a tissue-dependent manner. In the kidney, Tb fish showed pronounced transcriptional alterations linked to chronic inflammation, immune complex clearance, and IL-8-mediated responses. Tb+ fish exhibited broad immune activation in the kidney, suggesting dysregulated inflammatory responses likely associated with subsequent infection with M. cerebralis. In the kidney of Mc+ fish, the immune response was characterized by macrophage and IL signaling pathways. In HC, Mc fish activated Th17, IL-23, phagolysosome, and IL-6 cytokine pathways. In contrast, Mc+ fish showed increased pathogen processing and enhanced metabolic responses accompanied by suppression of cytokines and tissue repair processes. HC responses in Tb+ fish shifted toward IL-23, Th17-driven responses, alongside reduced developmental and extracellular matrix processes. The study establishes that host responses to myxozoan co-infection are shaped by tissue tropism and infection sequence, with distinct immune and tissue remodeling pathways activated in the target organs. These findings enhance the understanding of sequential T. bryosalmonae and M. cerebralis infections and provide a basis for identifying tissue-specific biomarkers and key immune targets. The findings may help identify methods for improved monitoring and management of myxozoan infections in salmonids.
Naveed Akram, Reinhard Ertl, R. Ghanei-Motlagh et al.· International Journal of Mol...· 0 citations
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.
Yexuan Zhang, Shuai Liu, Zhiwei Sun et al.· Developmental and Comparativ...· 0 citations
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.
Long non-coding RNAs (lncRNAs) stand as newly-arisen molecular types that exert regulatory effects, able to operate as competitive endogenous RNAs (ceRNAs) to engage microRNAs (miRNAs) in interaction, resulting in the recovery of target mRNA expression and activity. Increasing evidences indicate that the ceRNA network affects various biological processes in mammals, including development, cellular differentiation, metabolism, immune response, and disease pathogenesis. In teleost fish, the lncRNA-miRNA-mRNA regulatory networks have been reported occasionally. However, up to now, the roles of lncRNAs in the big-belly seahorse (Hippocampus abdominalis) remains unclear. In this study, we reported for the first time, via whole-transcriptome RNA sequencing, the lncRNA mediated ceRNA regulatory network in Vibrio harveyi-infected H. abdominalis. A total of 4197 differentially expressed mRNAs (DE-mRNAs), 1317 DE-lncRNAs, and 183 DE-miRNAs were identified. Furthermore, the crosstalk between miRNAs and lncRNAs as well as between miRNAs and mRNAs was inferred based on the negative correlations between miRNAs and their target lncRNAs/mRNAs. A core immune associated lncRNA-miRNA-mRNA putative regulatory network was thus constructed, comprising 211 lncRNA-miRNA and 224 mRNA-miRNA pairs. In conclusion, our findings provide an integrative overview of the ceRNA regulatory networks on the underlying immune responses to V. harveyi infection in the big-belly seahorse, and offer a solid theoretical foundation for the comparative immunological research of teleost fish.
Qing Chu, Jiale Zhou, Yuxin Bai et al.· Comparative Biochemistry and...· 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
