Toll-Like Receptor 9 Alternatively Spliced Isoform Negatively Regulates TLR9 Signaling in Teleost Fish

Effects of Gene Alternative Splicing Events on Resistance to Cryptocaryonosis of Large Yellow Croaker (Larimichthys crocea)

Large yellow croaker (L. crocea) is a productive species in marine aquaculture with great economic value in China. However, the sustainable development of large yellow croaker is hampered by various diseases including cryptocaryonosis caused by Cryptocaryon irritans. The genetic regulation processes for cryptocaryonosis in large yellow croaker are still unclear. In this present study, we analyzed differential alternative splicing events between a C. irritans resistance strain (RS) and a commercial strain (CS). We identified 678 differential alternative splicing (DAS) events from 453 genes in RS and 719 DAS events from 500 genes in CS. A set of genes that are specifically alternatively spliced in RS was identified including mfap5, emp1, and trim33. Further pathway analysis revealed that the specifically alternative spliced genes in RS were involved in innate immune responses through the PRR pathway and the Toll and Imd pathway, suggesting their important roles in the genetic regulation processes for cryptocaryonosis in large yellow croaker. This study would be helpful for the studies of the pathogenesis of cryptocaryonosis and dissection of C. irritans resistance for L. crocea.

Role of alternative splicing in fish immunity

Alternative splicing serves as a pivotal source of complexity in the transcriptome and proteome, selectively connecting various coding elements to generate a diverse array of mRNAs. This process encodes multiple proteins with either similar or distinct functions, contributing significantly to the intricacies of cellular processes. The role of alternative splicing in mammalian immunity has been well studied. Remarkably, the immune system of fish shares substantial similarities with that of humans, and alternative splicing also emerges as a key player in the immune processes of fish. In this review, we offer an overview of alternative splicing and its associated functions in the immune processes of fish, and summarize the research progress on alternative splicing in the fish immunity. Furthermore, we review the impact of alternative splicing on the fish immune system's response to external stimuli. Finally, we present our perspectives on future directions in this field. Our aim is to provide valuable insights for the future investigations into the role of alternative splicing in immunity.

Nile tilapia Toll-like receptor 7 subfamily: Intracellular TLRs that recruit MyD88 as an adaptor and activate the NF-κB pathway in the immune response

Toll-like receptor 7 (TLR7) subfamily members are important pattern recognition receptors that participate in the recognition of pathogen-associated molecular patterns. In the present study, three TLR family members, OnTLR7, OnTLR8 and OnTLR9, were identified in the Nile tilapia Oreochromis niloticus. TLR7-, TLR8-and TLR9-deduced proteins have typical structural characteristics of TLRs, including Toll/interleukin-1 receptor (TIR), leucine-rich repeat (LRR) and transmembrane region (TM). OnTLR7, OnTLR8 and OnTLR9 were broadly expressed in all of the tissues tested, with the highest expression levels in the brain (TLR7) and spleen (TLR8 and TLR9). Moreover, the expression levels of OnTLR7, OnTLR8 and OnTLR9 were significantly increased in most tested tissues after Streptococcus agalactiae infection in vivo. After LPS stimulation, OnTLR7 and OnTLR9 mRNA expression levels were downregulated in the intestine and upregulated in the liver, spleen and kidney; however, OnTLR8 mRNA expression levels were upregulated in the kidney only after LPS stimulation for 5 d. After Poly I:C stimulation, OnTLR7 and OnTLR9 mRNA expression levels were upregulated in the intestine, liver, spleen and kidney, and the highest expression was found in the liver, while OnTLR8 mRNA expression levels were upregulated in the intestine, liver and kidney and downregulated in the spleen. Subcellular localization of OnTLR7, OnTLR8, and OnTLR9 in 293T cells showed that OnTLR9 was distributed in both the cytoplasm and nucleus while OnTLR8 and OnTLR7 were distributed mainly in the cytoplasm. Overexpression of OnTLR7, OnTLR8 and OnTLR9 in 293T cells had no significant effect on the activity of NF-κB, but they could significantly enhance MyD88-mediated NF-κB activity after cotransfection with MyD88. Pulldown assays showed that OnTLR7, OnTLR8, and OnTLR9 could interact with OnMyD88. Taken together, these results indicate that TLR7 subfamily genes play a role in the immune response to pathogen invasion of Nile tilapia.

Avian Toll-like receptor 3 isoforms and evaluation of Toll-like receptor 3-mediated immune responses using knockout quail fibroblast cells

Toll-like receptor 3 (TLR3) induces host innate immune response on recognition of viral double-stranded RNA (dsRNA). Although several studies of avian TLR3 have been reported, none of these studies used a gene knockout (KO) model to directly assess its role in inducing the immune response and effect on other dsRNA receptors. In this study, we determined the coding sequence of quail TLR3, identified isoforms, and generated TLR3 KO quail fibroblast (QT-35) cells using a CRISPR/Cas9 system optimized for avian species. The TLR3-mediated immune response was studied by stimulating the wild-type (WT) and KO QT-35 cells with synthetic dsRNA or polyinosinic:polycytidylic acid [poly(I:C)] or infecting the cells with different RNA viruses such as influenza A virus, avian reovirus, and vesicular stomatitis virus. The direct poly(I:C) treatment significantly increased IFN-β and IL-8 gene expression along with the cytoplasmic dsRNA receptor, melanoma differentiation-associated gene 5 (MDA5), in WT cells, whereas no changes in all corresponding genes were observed in KO cells. We further confirmed the antiviral effects of poly(I:C)-induced TLR3-mediated immunity by demonstrating significant reduction of virus titer in poly(I:C)-treated WT cells, but not in TLR3 KO cells. On virus infection, varying levels of IFN-β, IL-8, TLR3, and MDA5 gene upregulation were observed depending on the viruses. No major differences in gene expression level were observed between WT and TLR3 KO cells, which suggests a relatively minor role of TLR3 in sensing and exerting immune response against the viruses tested in vitro. Our data show that quail TLR3 is an important endosomal dsRNA receptor responsible for regulation of type I interferon and proinflammatory cytokine, and affect the expression of MDA5, another dsRNA receptor, most likely through cytokine-mediated communication.

Immune sensing of DNA and strategies for fish DNA vaccine development

Studies of DNA vaccines have shown that understanding the mechanism of DNA vaccine-mediated action is the key for vaccine development. Current knowledge has shown the presence of antigen presenting cells (APCs) involving in B and T cells at the muscle injection site and the upregulation of type I interferon (IFN-I) that initiates antiviral response and benefits adaptive immunity in fish DNA vaccines. IFN-I may be triggered by expressed antigen such as the rhabdovirus G protein encoded DNA vaccine or by plasmid DNA itself through cytosolic DNA sensing. The investigating of Toll-like receptor 9, and 21 are the CpG-motif sensors in many fish species, and the cytosolic DNA receptors DDX41 and downstream STING signaling revealed the mechanisms for IFN-I production. This review article describes the recent finding of receptors for cytosolic DNA, the STING-TBK1-IRF signaling, and the possibility of turning these findings into strategies for the future development of DNA vaccines.

Trained Innate Immunity of Fish Is a Viable Approach in Larval Aquaculture

The general understanding has been that only adaptive immunity is capable of immunological memory, but this concept has been challenged in recent years by studies showing that innate immune systems can mount resistance to reinfection-as the innate immune system can adapt its function following an insult. Innate immune training offers an attractive approach in intensive fish larval rearing, especially since the adaptive immune system is not fully developed. Trained innate immunity will potentially favor robust fish in terms of resistance to viral and bacterial diseases. So-called immunostimulants such as ß-glucans have for decades been used both in laboratories and in intensive fish aquaculture. Treatment of fish by ß-glucans (and by other substances with pathogen-associated molecular patterns) often induces activation of non-specific/innate immune mechanisms and induces higher disease resistance. The reported effects of e.g., ß-glucans fit nicely into the concept "trained innate immunity," but the research on fish does not yet include analysis of epigenetic changes that may be a prerequisite for long-lasting trained innate immunity. In this "perspective," we will discuss how in practical terms and based on prior knowledge one can introduce innate immune training in brood stock fish, and their offspring, and whether innate immune training by ß-glucans is a viable approach in larval aquaculture.

Alternatively spliced variants in Atlantic cod (Gadus morhua) support response to variable salinity environment

Analysis of gill transcriptome of the Atlantic cod from the Baltic Sea demonstrated that alternatively spliced (AS) variants may be actively involved in the process of adaptation to altered salinity. Some AS variants of different genes, like phospholipase A2 group IVC (PLA2G4C), appeared only in fish exposed to altered salinity, while other isoforms of the same genes were present in all experimental groups. Novel sequence arrangements represent 89% of all AS in the Baltic cod compared to the Atlantic population. Profiles of modified pathways suggest that regulation by AS can afford specific changes of genes expressed in response to the environment. The AS variants appear to be involved in the response to stress by modifications of signalling in apoptosis pathways, an innate immunological response and pro-inflammatory process. Present results support the hypothesis that developing new AS variants could support genome complexity and reinforce the ability to fast adapt to local environments.

Interleukin-1β secreted from betanodavirus-infected microglia caused the death of neurons in giant grouper brains

High interleukin (IL)-1β gene expression was observed in dead giant grouper brains after nervous necrosis virus (NNV) infection. To investigate the neuronal death caused by NNV infection, primary tissue culture of giant grouper brains (pGB) was performed. In NNV-infected pGB cells, the viral capsid protein was detected in both neurons and microglia; furthermore, microglial proliferation and neuronal death were observed. The culture supernatant (CS) of NNV-infected pGB cells contained IL-1β and tumor necrosis factor-α, which were mainly released from the microglia. A new batch of pGB cells was treated with CS, resulting in neuronal death, which could be prevented by blocking the IL-1β in the CS by using anti-IL-1β polyclonal antibodies. Moreover, pGB cells treated with recombinant IL-1β showed microglial proliferation and neuronal death. Thus, NNV infection may activate microglial proliferation and stimulate microglial secretion of IL-1β, which is a critical cytokine responsible for neuronal death in NNV-infected grouper brains.

Alternative Splicing of Toll-Like Receptor 9 Transcript in Teleost Fish Grouper Is Regulated by NF-κB Signaling via Phosphorylation of the C-Terminal Domain of the RPB1 Subunit of RNA Polymerase II

Similar to its mammalian counterparts, teleost Toll-like receptor 9 (TLR9) recognizes unmethylated CpG DNA presented in the genome of bacteria or DNA viruses and initiates signaling pathway(s) for immune responses. We have previously shown that the TLR9 pathway in grouper, an economically important teleost, can be debilitated by an inhibitory gTLR9B isoform, whose production is mediated by RNA alternative splicing. However, how does grouper TLR9 (gTLR9) signaling impinge on the RNA splicing machinery to produce gTlr9B is unknown. Here we show that the gTlr9 alternative splicing is regulated through ligand-induced phosphorylation of the C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II). We first observed that ligand-activated NF- κB pathway biased the production of the gTlr9B isoform. Because NF- κB is known to recruit p-TEFb kinase, which phosphorylates the Pol II CTD at Ser2 residues, we examined p-TEFb’s role in alternative splicing. We found that promoting p-TEFb kinase activity significantly favored the production of the gTlr9B isoform, whereas inhibiting p-TEFb yielded an opposite result. We further showed that p-TEFb-mediated production of the gTlr9B isoform down-regulates its own immune responses, suggesting a self-limiting mechanism. Taken together, our data indicate a feedback mechanism of the gTLR9 signaling pathway to regulate the alternative splicing machinery, which in turn produces an inhibitor to the pathway.