The long noncoding RNA NARL regulates immune responses via microRNA-mediated NOD1 downregulation in teleost fish

Host long noncoding RNAs in bacterial infections

Bacterial infections remain a significant global health concern, necessitating a comprehensive understanding of the intricate host-pathogen interactions that play a critical role in the outcome of infectious diseases. Recent investigations have revealed that noncoding RNAs (ncRNAs) are key regulators of these complex interactions. Among them, long noncoding RNAs (lncRNAs) have gained significant attention because of their diverse regulatory roles in gene expression, cellular processes and the production of cytokines and chemokines in response to bacterial infections. The host utilizes lncRNAs as a defense mechanism to limit microbial pathogen invasion and replication. On the other hand, some host lncRNAs contribute to the establishment and maintenance of bacterial pathogen reservoirs within the host by promoting bacterial pathogen survival, replication, and dissemination. However, our understanding of host lncRNAs in the context of bacterial infections remains limited. This review focuses on the impact of host lncRNAs in shaping host-pathogen interactions, shedding light on their multifaceted functions in both host defense and bacterial survival, and paving the way for future research aimed at harnessing their regulatory potential for clinical applications.

EFHD2 cooperates with E3 ubiquitin ligase Smurf1 to facilitate virus infection by promoting the degradation of TRAF6 in teleost fish

The ubiquitin-proteasome system is one of the most important protein stability regulation systems. It can precisely regulate host immune responses by targeting signaling proteins. TRAF6 is a crucial E3 ubiquitin ligase in host antiviral signaling pathway. Here, we discovered that EF-hand domain-containing protein D2 (EFHD2) collaborated with the E3 ubiquitin ligase Smurf1 to potentiate the degradation of TRAF6, hence facilitating RNA virus Siniperca chuatsi rhabdovirus infection. The mechanism analysis revealed that EFHD2 interacted with Smurf1 and enhanced its protein stability by impairing K48-linked polyubiquitination of Smurf1, thereby promoting Smurf1-catalyzed degradation of TRAF6. This study initially demonstrated a novel mechanism by which viruses utilize host EFHD2 to achieve immune escape and provided a new perspective on the exploration of mammalian innate immunity.IMPORTANCEViruses induce host cells to activate several antiviral signaling pathways. TNF receptor-associated factor 6 (TRAF6) plays an essential role in these pathways. Numerous studies have been done on the mechanisms of TRAF6-mediated resistance to viral invasion. However, little is known about the strategies that viruses employ to antagonize TRAF6-mediated antiviral signaling pathway. Here, we discovered that EFHD2 functions as a host factor to promote viral replication. Mechanistically, EFHD2 potentiates Smurf1 to catalyze the ubiquitin-proteasomal degradation of TRAF6 by promoting the deubiquitination and stability of Smurf1, which in turn inhibits the production of proinflammatory cytokines and interferons. Our study also provides a new perspective on mammalian resistance to viral invasion.

LncRNA pol-lnc78 as a ceRNA regulates antibacterial responses via suppression of pol-miR-n199-3p-mediated SARM down-regulation in Paralichthys olivaceus

Long non-coding RNAs (lncRNAs) function as key modulators in mammalian immunity, particularly due to their involvement in lncRNA-mediated competitive endogenous RNA (ceRNA) crosstalk. Despite their recognized significance in mammals, research on lncRNAs in lower vertebrates remains limited. In the present study, we characterized the first immune-related lncRNA (pol-lnc78) in the teleost Japanese flounder ( Paralichthys olivaceus). Results indicated that pol-lnc78 acted as a ceRNA for pol-miR-n199-3p to target the sterile alpha and armadillo motif-containing protein (SARM), the fifth discovered member of the Toll/interleukin 1 (IL-1) receptor (TIR) adaptor family. This ceRNA network regulated the antibacterial responses of flounder via the Toll-like receptor (TLR) signaling pathway. Specifically, SARM acted as a negative regulator and exacerbated bacterial infection by inhibiting the expression of inflammatory cytokines IL-1β and tumor necrosis factor-α (TNF-α). Pol-miR-n199-3p reduced SARM expression by specifically interacting with the 3' untranslated region (UTR), thereby promoting SARM-dependent inflammatory cytokine expression and protecting the host against bacterial dissemination. Furthermore, pol-lnc78 sponged pol-miR-n199-3p to ameliorate the inhibition of SARM expression. During infection, the negative regulators pol-lnc78 and SARM were significantly down-regulated, while pol-miR-n199-3p was significantly up-regulated, thus favoring host antibacterial defense. These findings provide novel insights into the mechanisms underlying fish immunity and open new horizons to better understand ceRNA crosstalk in lower vertebrates.

MiRNAs and lncRNAs in the regulation of innate immune signaling

The detection and defense against foreign agents and pathogens by the innate immune system is a crucial mechanism in the body. A comprehensive understanding of the signaling mechanisms involved in innate immunity is essential for developing effective diagnostic tools and therapies for infectious diseases. Innate immune response is a complex process involving recognition of pathogens through receptors, activation of signaling pathways, and cytokine production, which are all crucial for deploying appropriate countermeasures. Non-coding RNAs (ncRNAs) are vital regulators of the immune response during infections, mediating the body's defense mechanisms. However, an overactive immune response can lead to tissue damage, and maintaining immune homeostasis is a complex process in which ncRNAs play a significant role. Recent studies have identified microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) as key players in controlling gene expression in innate immune pathways, thereby participating in antiviral defenses, tumor immunity, and autoimmune diseases. MiRNAs act by regulating host defense mechanisms against viruses, bacteria, and fungi by targeting mRNA at the post-transcriptional level, while lncRNAs function as competing RNAs, blocking the binding of miRNAs to mRNA. This review provides an overview of the regulatory role of miRNAs and lncRNAs in innate immunity and its mechanisms, as well as highlights potential future research directions, including the expression and maturation of new ncRNAs and the conservation of ncRNAs in evolution.

Effect of TRAF6-knockout on gene expression and lncRNA expression in Epithelioma papulosum cyprini (EPC) cells

TRAF6 is a key immune gene that plays a significant role in toll-like receptor signal transduction and activates downstream immune genes involved in antiviral immunity in fish. To explore the role of TRAF6 in Epithelioma papulosum cyprini (EPC) cells, we knocked out the TRAF6 gene using the Clustered Regularly Interspaced Short Palindromic Repeats-Cas9 (CRISPR-Cas9) technique and then analyzed the transcriptomes of the knockout cells. In this study, we identified that 232 transcripts were differentially expressed in naive cells. Using the pipeline, we identified 381 novel lncRNAs in EPC cells, 23 of which were differentially expressed. Gene Ontology enrichment analysis demonstrated that differentially expressed genes (DEG) are implicated in various immune processes, such as neutrophil chemotaxis and mitogen-activated protein kinase binding. In addition, the KEGG pathway analysis revealed enrichment in immune-related pathways (Interleukin-17 signaling pathway, cytokine-cytokine receptor interaction, and TNF signaling pathway). Furthermore, the target genes of the differentially expressed lncRNAs were implicated in the negative regulation of interleukin-6 and tumor necrosis factor production. These results indicate that lncRNAs and protein-coding genes participate in the regulation of immune and metabolic processes in fish.

LILAR, a novel long noncoding RNA regulating autophagy in the liver tissues of endotoxemic mice through a competing endogenous RNA mechanism

Sepsis is an often-deadly complication of infection that can lead to multiple organ failure. Previous studies have demonstrated that autophagy has a protective effect on liver injury in sepsis. Here, we report a novel long noncoding RNA (lncRNA), named lipopolysaccharide (LPS)-induced liver autophagy regulator (LILAR), which was highly induced in the liver tissues of endotoxemic mice. LILAR deficiency significantly increased the susceptibility of mice to LPS. In contrast, LILAR overexpression rescued the liver injury mediated by LILAR deficiency and increased the survival of LILAR knockout mice with endotoxemia. Autophagy-related protein 13 (Atg13) is a potential downstream target gene of LILAR. LILAR deficiency notably decreased Atg13 expression and suppressed autophagy in the livers of mice challenged with LPS. A reporter gene assay showed that LILAR competitively adsorbed miR-705 to increase the expression of Atg13 in cultured cells, indicating that LILAR participates in the regulation of the autophagy in the liver tissues of endotoxemic mice through a competitive endogenous RNA mechanism. In summary, we identified a novel lncRNA, LILAR, as a hepatic autophagy regulator, which not only promotes our understanding of liver pathophysiology but also provides a potential therapeutic target and/or diagnostic biomarker for liver injury in endotoxemia.

The protease calpain2a limits innate immunity by targeting TRAF6 in teleost fish

TNF receptor-associated factor 6 (TRAF6) plays a key signal transduction role in both antibacterial and antiviral signaling pathways. However, the regulatory mechanisms of TRAF6 in lower vertebrates are less reported. In this study, we identify calpain2a, is a member of the calcium-dependent proteases family with unique hydrolytic enzyme activity, functions as a key regulator for antibacterial and antiviral immunity in teleost fish. Upon lipopolysaccharide (LPS) stimulation, knockdown of calpain2a promotes the upregulation of inflammatory cytokines. Mechanistically, calpain2a interacts with TRAF6 and reduces the protein level of TRAF6 by hydrolyzing. After loss of enzymatic activity, mutant calpain2a competitively inhibits dimer formation and auto-ubiquitination of TRAF6. Knockdown of calpain2a also promotes cellular antiviral response. Mutant calpain2a lacking hydrolase activity represses ubiquitination of IFN regulatory factor (IRF) 3/7 from TRAF6. Taken together, these findings classify calpain2a is a negative regulator of innate immune responses by targeting TRAF6 in teleost fish.

Long noncoding RNA TARL promotes antibacterial activity and prevents bacterial escape in Miichthys miiuy through suppression of TAK1 downregulation

Noncoding RNA (ncRNA) is an important regulatory factor that plays a major role in innate immunity. However, most studies on ncRNA have focused on mammals, resulting in a knowledge gap on ncRNA in lower vertebrates such as teleost fish. In this study, we identified a new long noncoding RNA (lncRNA), termed TAK1-related lncRNA (TARL), which can play a positive role in the antibacterial immunity of Miichthys miiuy to Vibrio anguillarum and V. harveyi. We also found a novel microRNA miR-2188-3p that could target TAK1 and inhibit the host antibacterial response and promote bacterial escape. We further found that the antibacterial effect inhibited by miR-2188-3p could be reversed with TARL. Moreover, V. anguillarum and V. harveyi are the two most susceptible Gram-negative pathogens of aquaculture fish, and the economic losses caused by these two bacteria are immeasurable every year. This study is the first to report on the ability of lncRNA to prevent the escape of V. anguillarum and V. harveyi in fish through the competing endogenous RNA (ceRNA) mechanism. Our results not only elucidate the ceRNA mechanism of the lncRNA in antibacterial immune responses but also provide new insights into the impact of lncRNA on host immunity and bacterial escape.

Identification and Expression Analysis of LncRNAs Reveal the Immune Mechanism of Visceral White-Nodules Disease Resistance in Large Yellow Croaker

Long non-coding RNAs (lncRNAs) have several known functions in fish growth processes and signal transduction, but their possible roles in response to bacterial diseases remain largely unresolved. In this study, we report a comprehensive cold-water bacterial disease-responsive lncRNA expression profile for understanding the transcriptional regulatory mechanisms of visceral white-nodules disease resistance in large yellow croaker. A total of 2534 high-confidence lncRNAs were identified by a rigorous filtering pipeline as a basic sequence set for comparative transcriptional analysis. In addition, a total of 10,200 lncRNA-mRNA pairs with high correlation coefficients were identified by expressions level correlation analysis, including non-redundant 381 DE lncRNAs and 2590 differential expressed genes. MSTRG_11084_1 and MSTRG_20402_1 were linked to a large number of target genes and may be involved in important functions in immune regulation. We further revealed the conserved and idiosyncratic features of the disease response process between the technical control strain (TCS) and the resistant strain (RS). Immune-related pathways were enriched in GO terms and KEGG pathways, among which cytokine-cytokine receptor interaction, MAPK signaling pathway, and NF-kappa B signaling pathway may play a key role in VWND resistance in large yellow croaker. Protein-protein interaction network (PPI) analysis revealed that immune-related target genes such as il-10, met, acta2, myc, cav1, and ntrk1, as well as growth and metabolism-related target genes such as pik3r2, igf1, sc5d, hmgcr, and lss were considered the main hub genes. This study represents the first characterization of lncRNAs involved in VWND resistance in large yellow croaker and provides new clues for elucidating the disease response mechanism of large yellow croaker.

Multiomics analysis revealed miRNAs as potential regulators of the immune response in Carassius auratus gills to Aeromonas hydrophila infection

The gill of fish is an important immune organ for pathogen defense, but its microRNA (miRNA) expression and regulatory mechanism remain unclear. In this study, we report on the histopathological and immunohistochemical features of the gills of the crucian carp Carassius auratus challenged with Aeromonas hydrophila. Small RNA libraries of the gills were constructed and sequenced on the Illumina HiSeq 2000 platform. A total of 1,165 differentially expressed miRNAs (DEMs) were identified in gills, of which 539 known and 7 unknown DEMs were significantly screened (p < 0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes/proteins were primarily involved in 33 immune-related pathways, in which the inflammatory responses were focused on the Toll-like receptor (TLR), mitogen-activated protein kinase (MAPK), and nuclear factor kappa B (NF-κB) signaling pathways. Moreover, the expression levels of 14 key miRNAs (e.g., miR-10, miR-17, miR-26a, miR-144, miR-145, and miR-146a) and their target genes (e.g., TNFα, TLR4, NF-κB, TAB1, PI3K, and IRAK1) were verified. In addition, the protein levels based on isobaric tags for relative and absolute quantification (iTRAQ) were significantly associated with the results of the quantitative real-time PCR (qRT-PCR) analysis (p < 0.01). miR-17/pre-miR-17 were identified in the regulation expression of the NF-κB target gene, and the phylogenetic tree analysis showed that the pre-miR-17 of C. auratus with the closest similarity to the zebrafish Danio rerio is highly conserved in teleosts. This is the first report of the multi-omics analysis of the miRNAs and proteins in the gills of C. auratus infected with A. hydrophila, thus enriching knowledge on the regulation mechanism of the local immune response in Cyprinidae fish.

The potential regulatory role of the lncRNA-miRNA-mRNA axis in teleost fish

Research over the past two decades has confirmed that noncoding RNAs (ncRNAs), which are abundant in cells from yeast to vertebrates, are no longer "junk" transcripts but functional regulators that can mediate various cellular and physiological processes. The dysregulation of ncRNAs is closely related to the imbalance of cellular homeostasis and the occurrence and development of various diseases. In mammals, ncRNAs, such as long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), have been shown to serve as biomarkers and intervention targets in growth, development, immunity, and disease progression. The regulatory functions of lncRNAs on gene expression are usually mediated by crosstalk with miRNAs. The most predominant mode of lncRNA-miRNA crosstalk is the lncRNA-miRNA-mRNA axis, in which lncRNAs act as competing endogenous RNAs (ceRNAs). Compared to mammals, little attention has been given to the role and mechanism of the lncRNA-miRNA-mRNA axis in teleost species. In this review, we provide current knowledge about the teleost lncRNA-miRNA-mRNA axis, focusing on its physiological and pathological regulation in growth and development, reproduction, skeletal muscle, immunity to bacterial and viral infections, and other stress-related immune responses. Herein, we also explored the potential application of the lncRNA-miRNA-mRNA axis in the aquaculture industry. These findings contribute to an enhanced understanding of ncRNA and ncRNA-ncRNA crosstalk in fish biology to improve aquaculture productivity, fish health and quality.

Long non‐coding RNA, a supreme post‐transcriptional immune regulator of bacterial or virus‐driven immune evolution in teleost

The global aquaculture boom, fuelled by a reduction in wild population and detection of novel viruses, has created a demanding market, hence, there is a pressing need to investigate the immune system of fish, further. As the most diverse community of vertebrates and a central contributor to the progressing global aquaculture market, teleost continues to draw vast scientific interest. Recent breakthroughs in multi‐omics technologies have provided a platform to understand the role of long non‐coding RNA (lncRNA) in the host immune system during infection. Emerging evidence shows that teleost lncRNA might have a regulatory role in immune responses, mostly through lncRNA–microRNA (miRNA) sponging. Teleost lncRNA shares a functionally active short sequence complement to target the miRNA which is conserved among the several fish species. Recent report suggests that rhabdovirus exploits a lncRNA in teleost and, to dodge the host immune mechanism and negatively regulate the immune system. This observation reveals the essentiality of lncRNA in pathogen‐driven immunity in teleost. Reports available on the function of teleost lncRNA are still in early stages and experimental verifications are a limiting factor. Unravelling the lncRNA‐mediated immune regulation in fishes could be used against the invading pathogens to strengthen the aquaculture production. This review elaborates on the experimentally identified and functionally characterized lncRNA and its regulatory role in the teleost immune response during infection and pathogen‐driven host immune evolution, which could eventually lead to achieving high standards in aquaculture productivity.

Non-coding RNAs targeting NF-κB pathways in aquatic animals: A review

Nuclear factor-kappa B (NF-κB) pathways have a close relationship with many diseases, especially in terms of the regulation of inflammation and the immune response. Non-coding RNAs (ncRNAs) are a heterogeneous subset of endogenous RNAs that directly affect cellular function in the absence of proteins or peptide products; these include microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), etc. Studies on the roles of ncRNAs in targeting the NF-κB pathways in aquatic animals are scarce. A few research studies have confirmed detailed regulatory mechanisms among ncRNAs and the NF-κB pathways in aquatic animals. This comprehensive review is presented concerning ncRNAs targeting the NF-κB pathway in aquatic animals and provides new insights into NF-κB pathways regulatory mechanisms of aquatic animals. The review discusses new possibilities for developing non-coding-RNA-based antiviral applications in fisheries.

Genome-Wide Analysis of Differentially Expressed mRNAs and lncRNAs in Koi Carp Infected with Koi Herpesvirus

Long noncoding RNAs (lncRNAs) constitute an emerging group of ncRNAs that modulate gene expression at the transcriptional or translational level. Koi herpesvirus (KHV), also known as Cyprinus herpesvirus type 3 (CyHV-3) and characterized by high pathogenicity and high mortality, has caused substantial economic losses in the common carp and koi carp fisheries industry. In this work, we sequenced the lncRNA and mRNA of host koi carp infected with KHV. A total of 20,178 DEmRNAs were obtained, of which 5021 mRNAs were upregulated and 15,157 mRNAs were downregulated. Both KEGG pathways and GO terms were enriched in many important immune pathways. The KEGG analysis showed that DEGs were significantly enriched in many important immune pathways, such as apoptosis, NOD-like receptor signaling pathway, Jak-STAT signaling pathway, TNF signaling pathway, IL-17 signaling pathway, NF-kappa B signaling pathway, and so on. Furthermore, a total of 32,697 novel lncRNA transcripts were obtained from koi carp immune tissues; 9459 of these genes were differentially expressed. Through antisense, cis-acting, and trans-acting analyses, the target genes of differentially expressed lncRNAs (DElncRNAs) were predicted. Gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the DElncRNA expression pattern was consistent with the differential mRNA expression pattern. The lncRNA-mRNA network analysis, which included many immune pathways, showed that after KHV infection, the expression of most lncRNAs and their target mRNAs were downregulated, suggesting that these lncRNAs engage in a positive regulatory relationship with their target mRNAs. Considering that many studies have shown that herpesviruses can escape the immune system by negatively regulating these immune pathways, we speculated that these lncRNAs play a significant role in KHV's escape from host immunity. Furthermore, 10 immune-related genes and 20 lncRNAs were subsequently verified through RT-qPCR, to confirm the accuracy of the high-throughput sequencing results. In this study, we aimed to explore lncRNA functions in the immune response of lower vertebrates and provide a theoretical basis for the study of noncoding RNAs in teleosts. Therefore, exploring lncRNA expression in KHV-infected koi carp helped us better understand the biological role played by lncRNA-dependent pathways in aquaculture animal viral infection.

The long noncoding RNA LTCONS5539 up-regulates the TRAF6-mediated immune responses in miiuy croaker (Miichthys miiuy)

With the further study of long noncoding RNAs (lncRNAs), an increasing number of biological studies have demonstrated that lncRNAs are involved in various physiological processes, including cell proliferation, apoptosis, invasion, development and disease states. However, unlike mammals, little is known about the role of lncRNAs in the innate immunity of teleost fish. Here, we identify a lncRNA, named LTCONS5539, as critical role in the antiviral and antibacterial response of miiuy croaker and the results showed that lncRNA LTCONS5539 plays a critical regulatory role on TRAF6. Firstly, we found that LPS and poly(I:C) can up-regulate the expression of lncRNA LTCONS5539. Elevated lncRNA LTCONS5539 is capable of increasing the production of inflammatory factors and antiviral genes. Furthermore, the over-expression of lncRNA LTCONS5539 increases the expression of TRAF6 which was confirmed by qPCR and western blotting. On these foundations, we also proved that lncRNA LTCONS5539 modulates innate immunity through TRAF6-mediated immune responses through dual luciferase reporter assay. These results will help to further understand the immunomodulatory mechanisms of lncRNA in teleost fish.

Competing endogenous RNA-networks reveal key regulatory microRNAs involved in the response of Atlantic salmon to a novel orthomyxovirus

One of the most intriguing discoveries of the genomic era is that only a small fraction of the genome is dedicated to protein coding. The remaining fraction of the genome contains, amongst other elements, a number of non-coding transcripts that regulate the transcription of protein coding genes. Here we used transcriptome sequencing data to explore these gene regulatory networks using RNA derived from gill tissue of Atlantic salmon (Salmo salar) infected with Pilchard orthomyxovirus (POMV), but showing no clinical signs of disease. We examined fish sampled early during the challenge trial (8-12 days after infection) to uncover potential biomarkers of early infection and innate immunity, and fish sampled late during the challenge trial (19 dpi) to elucidate potential markers of resistance to POMV. We analysed total RNA-sequencing data to find differentially expressed messenger RNAs (mRNA) and identify new long-noncoding RNAs (lncRNAs). We also evaluated small RNA sequencing data to find differentially transcribed microRNAs (miRNAs) and explore their role in gene regulatory networks. Whole-genome expression data (both coding and non-coding transcripts) were used to explore the crosstalk between RNA molecules by constructing competing endogenous RNA networks (ceRNA). The teleost specific miR-462/miR-731 cluster was strongly induced in POMV infected fish and deemed a potential biomarker of early infection. Gene networks also identified a selenoprotein (selja), downregulated in fish sampled late during the challenge, which may be associated to viral clearance and the return to homeostasis after infection. This study provides the basis for further investigations using molecular tools to overexpress or inhibit miRNAs to confirm the functional impact of the interactions presented here on gene expression and their potential application at commercial level.

Long non-coding RNA LTCONS7822 positively regulates innate immunity by targeting MITA in miiuy croaker (Miichthys miiuy)

Accumulated studies have shown that long non-coding RNA (lncRNA) is considered a critical regulatory factor in mammals, with a length greater than 200 nucleotides, and it can participate in gene imprinting, dose compensation, transcription enhancement, and antisense regulation. Most of the above studies are carried out in mammals, and there are very few studies on lncRNA of lower vertebrates. Here, we report a novel lncRNA, LTCONS7822, which can play a positive regulatory effect on antiviral immunity in miiuy croaker, Miichthys miiuy. Our results show that the levels of lncRNA LTCONS7822 were significantly increased after poly (I:C) stimulation. Further study, we found that lncRNA LTCONS7822 could positively regulate MITA at the post-transcriptional level. In addition, the dual-luciferase reporter assay analysis showed that the positive regulatory effect of lncRNA LTCONS7822 on NF-κB and IRF3 signaling pathways presented the dose and time-dependent manner. Western blotting experiments proved that lncRNA LTCONS7822 has a positive regulatory effect on MITA. Collectively, our study provided new information to enrich the immune regulation network of lncRNA in teleost fish.

Integrated Analysis of lncRNA and circRNA Mediated ceRNA Regulatory Networks in Skin Reveals Innate Immunity Differences Between Wild-Type and Yellow Mutant Rainbow Trout (Oncorhynchus mykiss)

Fish skin is a vital immune organ that forms the first protective barrier preventing entry of external pathogens. Rainbow trout is an important aquaculture fish species that is farmed worldwide. However, our knowledge of innate immunity differences between wild-type (WR_S) and yellow mutant rainbow trout (YR_S) remains limited. In this study, we performed whole transcriptome analysis of skin from WR_S and YR_S cultured in a natural flowing water pond. A total of 2448 mRNAs, 1630 lncRNAs, 22 circRNAs and 50 miRNAs were found to be differentially expressed (DE). Among these DEmRNAs, numerous key immune-related genes, including ifih1, dhx58, trim25, atp6v1e1, tap1, tap2, cd209, hsp90a.1, nlrp3, nlrc3, and several other genes associated with metabolism (gstp1, nampt, naprt and cd38) were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEmRNAs revealed that many were significantly enriched in innate immune-related GO terms and pathways, including NAD+ADP-ribosyltransferase activity, complement binding, immune response and response to bacterium GO terms, and RIG-I-like receptor signaling, NOD-like receptor signaling and phagosome KEGG pathways. Furthermore, the immune-related competing endogenous RNA networks were constructed, from which we found that lncRNAs MSTRG.11484.2, MSTRG.32014.1 and MSTRG.29012.1 regulated at least three immune-related genes (ifih1, dhx58 and irf3) through PC-5p-43254_34, PC-3p-28352_70 and bta-miR-11987_L-1R-1_1ss8TA, and tap2 was regulated by two circRNAs (circRNA5279 and circRNA5277) by oni-mir-124a-2-p5_1ss13GA. The findings expand our understanding of the innate immune system of rainbow trout, and lay the foundation for further study of immune mechanisms and disease resistance breeding.

lncRNA GAS5 promotes pyroptosis in COPD by functioning as a ceRNA to regulate the miR‑223‑3p/NLRP3 axis

Chronic obstructive pulmonary disease (COPD) is characterized by irreversible and progressive airflow limitation and encompasses a spectrum of diseases, including chronic obstructive bronchitis and emphysema. Pyroptosis is a unique form of inflammatory cell death mediated by the activation of caspase-1 and inflammasomes. The long non-coding RNA (lncRNA) growth arrest-specific 5 (GAS5) is a well-documented tumor suppressor, which is associated with cell proliferation and death in various diseases. The aim of the present study was to evaluate whether lncRNA GAS5 is associated with the pyroptosis in COPD. To create a COPD cell model, MRC-5 cells were treated with 10 µg/ml lipopolysaccharide (LPS) for 48 h. Then the level of pro-caspase 1, caspase 1, IL-1β, IL-18, NLRP3 and cleaved gasdermin D (GSDMD) was examined by western blotting. GAS5 mRNA level was detected by qualitative PCR following LPS treatment in MRC-5 cells. Subsequently, IL-2, IL-6, IL-10 and TNF-α in MRC-5 cells was measured by ELISA. Then the proliferation ability of MRC-5 cells was detected by CCK-8. Cell death was detected by TUNEL assay. LDH release was measured using an LDH Cytotoxicity Assay kit. The Magna RIP kit was used to validate the interaction between GAS5 and miR-223-3p. The present study revealed that increased expression levels of caspase-1, IL-1β, IL-18 and cleaved GSDMD were observed in LPS-treated MRC-5 cells, indicating that pyroptosis is involved in COPD progression. Additionally, LPS induced the increase in GAS5 mRNA expression levels and the release of inflammatory factors (IL-2, IL-6, IL-10 and TNF-α), suggesting that GAS5 is implicated in pyroptosis in COPD. Furthermore, upregulation of GAS5 promoted cell death and inhibited proliferation in the MRC-5 cell line. Additionally, increased GAS5 expression significantly promoted the production of caspase-1, IL-1β, IL-18, cleaved GSDMD and NLR pyrin domain containing protein 3 (NLRP3). A dual-luciferase assay demonstrated that GAS5 could directly bind to microRNA-223-3p (miR-223-3p), and NLRP3 is a direct target of miR-223-3p. Furthermore, GAS5 reduced the expression levels of miR-223-3p, while it increased the expression levels of NLRP3. The present study concluded that lncRNA GAS5 promoted pyroptosis in COPD by targeting the miR-223-3p/NLRP3 axis, implying that GAS5 could be a potential target for COPD.

Long Noncoding RNA MIR122HG Inhibits MAVS-Mediated Antiviral Immune Response by Deriving miR-122 in Miiuy Croaker (Miichthys miiuy)

Long noncoding RNAs (lncRNAs) function as micro regulators to impact gene expression after multiple pathogen infections, which have been largely studied in the last few years. Although lncRNA studies on lower vertebrates have received less attention than those on mammals, current studies suggest that lncRNA plays an important role in the immune response of fish to pathogen infections. Here, we studied the effect of MIR122HG as the host gene of miR-122 and indirectly negatively regulate MAVS-mediated antiviral immune responses in miiuy croaker (Miichthysmiiuy). We found that poly(I:C) significantly increases the host MIR122HG expression. The increased MIR122HG expression inhibited the production of the antiviral immune-related genes IFN-1, ISG15 and Viperin upon SCRV treatment. In addition, MIR122HG can act as a pivotally negative regulator involved in the MAVS-mediated NF-κB and IRF3 signaling pathways, which can effectively avoid an excessive immune response. Additionally, we found that MIR122HG can promote the replication of SCRV. Our study provides evidence about the involvement of lncRNAs in the antiviral immune response of fish and broadens the understanding of the function of lncRNAs as a precursor miRNA in teleost fish.

Inducible MicroRNA-132 Inhibits the Production of Inflammatory Cytokines by Targeting TRAF6, TAK1, and TAB1 in Teleost Fish

The innate immune response is the first line of defense against pathogen infection. Eradication of pathogen infection requires appropriate immune and inflammatory responses, but excessive inflammation may cause inflammatory and autoimmune diseases. MicroRNAs (miRNAs) are a group of small noncoding RNAs, and accumulating evidence has shown that in mammals, they can act as negative regulators that participate in the regulation of inflammation and immune responses. However, the miRNA-mediated immune regulation networks in the inflammatory responses of lower vertebrates are largely unknown. In this study, we report an miRNA, miR-132, identified from miiuy croaker, that acts as a negative regulator in the host's bacterium-induced inflammatory response. We found that miR-132 expression was dramatically increased upon infection by the Gram-negative bacterium Vibrio harveyi and lipopolysaccharide (LPS). Inducible miR-132 inhibits the production of inflammatory cytokines by targeting tumor necrosis factor receptor-associated factor 6 (TRAF6), transforming growth factor-activated protein kinase 1 (TAK1), and TAK1 binding protein 1 (TAB1), thus avoiding an excessive inflammatory response. Furthermore, we demonstrate that miR-132 modulates the inflammatory response through a TRAF6-, TAK1-, and TAB1-mediated NF-κB signaling pathway. These results collectively reveal that miR-132 plays a negative regulatory role in the host antibacterial immune response, which will help to gain insight into the intricate network of host resistance to pathogen infection in lower vertebrates.

Exon-Intron Circular RNA circRNF217 Promotes Innate Immunity and Antibacterial Activity in Teleost Fish by Reducing miR-130-3p Function

Circular RNA (circRNA) is produced by splicing head to tail and is widely distributed in multicellular organisms, and circRNA reportedly can participate in various cell biological processes. In this study, we discovered a novel exon-intron circRNA derived from probable E3 ubiquitin-protein ligase RNF217 (RNF217) gene, namely, circRNF217, which was related to the antibacterial responses in teleost fish. Results indicated that circRNF217 played essential roles in host antibacterial immunity and inhibited the Vibrio anguillarum invasion into cells. Our study also found a microRNA miR-130-3p, which could inhibit antibacterial immune response and promote V. anguillarum invasion into cells by targeting NOD1. Moreover, we also found that the antibacterial effect inhibited by miR-130-3p could be reversed with circRNF217. In mechanism, our data revealed that circRNF217 was a competing endogenous RNA of NOD1 by sponging miR-130-3p, leading to activation of the NF-κB pathway and then enhancing the innate antibacterial responses. In addition, we also found that circRNF217 can promote the antiviral response caused by Siniperca chuatsi rhabdovirus through targeting NOD1. Our study provides new insights for understanding the impact of circRNA on host-pathogen interactions and formulating fish disease prevention to resist the severely harmful V. anguillarum infection.

eIF3k inhibits NF-κB signaling by targeting MyD88 for ATG5-mediated autophagic degradation in teleost fish

Optimal activation of NF-κB signaling is crucial for the initiation of inflammatory responses and eliminating invading bacteria. Bacteria have likewise evolved the ability to evade immunity; however, mechanisms by which bacteria dysregulate host NF-κB signaling are unclear. In this study, we identify eukaryotic translation initiation factor eIF3k, a nonessential member of the eIF3 translation initiation complex, as a suppressor of the NF-κB pathway. Mechanistically, we show that eIF3k expression induced by Vibrio harveyi enhances E3 ligase Nrdp1-mediated K27-linked ubiquitination of MyD88, an upstream regulator of NF-κB pathway activation. Furthermore, we show that eIF3k acts as a bridge linking ubiquitin-tagged MyD88 and ATG5, an important mediator of autophagy. We demonstrate that the MyD88-eIF3k-ATG5 complex is transported to the autophagosome for degradation, and that innate immune signaling is subsequently terminated and does not attack invading V. harveyi. Therefore, our study identifies eIF3k as a specific inhibitor of the MyD88-dependent NF-κB pathway and suggests that eIF3k may act as a selective autophagic receptor that synergizes with ATG5 to promote the autophagic degradation of MyD88, which helps V. harveyi to evade innate immunity. We conclude that V. harveyi can manipulate a host's autophagy process to evade immunity in fish and also provide a new perspective on mammalian resistance to bacterial invasion.

Genomic organization, evolution and functional characterization of caspase-2 and caspase-8 in miiuy croaker (Miichthys miiuy)

As the central link and executor of cell apoptosis, the caspase protease family has received extensive attention in recent years. However, the genetic characteristics and immune functions of some caspases are still unknown in fish. In our study, we cloned the full-length caspase-2 (mmCasp2) and caspase-8 (mmCasp2) of miiuy croaker, then we analyzed characteristics and functions of these two genes which are upstream of the apoptosis cascade reaction. Mmcasp2 and mmCasp8 exhibited a conserved domain (CASc), and the different part is that the mmCasp2 has a CARD domain, while mmCasp8 have two DED domains. Sequence and evolution analysis results showed that caspase-2 is more conservative than caspae-8 in the process of evolution. Cellular localization analysis showed that the distribution of mmCasp2 and mmCasp2 was in cytoplasm. The real-time PCR analysis showed that these two caspases are constitutively expressed in different tissues, and the expression of mmCasp2 and mmCasp8 were up-regulated in the liver, spleen, and kidney after infection with V. anguillarum. Lastly, qRT-PCR and Luciferase assays analysis showed that mmCasp2 and mmCasp8 can inhibit the NF-кB pathway. In general, we systematically analyzed the structure, evolution and related functional experiments of the caspase-2 and caspase-8 in miiuy croaker, which will help further understand the role caspase family plays in the apoptosis and immune response.

microRNA-148 is involved in NF-κB signaling pathway regulation after LPS stimulation by targeting IL-1β in miiuy croaker

The inflammatory response is a protective process to clear detrimental stimuli, constitutes the defense against infectious pathogens. Clearing pathogen infection requires appropriate immune and inflammatory response, but excessive inflammatory response can lead to uncontrolled inflammation, autoimmune disease, or pathogen transmission. Accumulating evidences show that miRNAs are important and multifunctional regulators of innate immunity and inflammation. However, in the inflammatory response of lower vertebrates, the miRNAs regulatory networks are largely unknown. In this study, a combination of bioinformatics and experimental techniques were used to investigate the functions of miR-148. IL-1β is a hypothetical target gene of miR-148 predicted by bioinformatics. In addition, dual-luciferase reporter gene experiment was used to verify the targeting effect of miR-148 on IL-1β-3'UTR. miR-148 inhibits IL-1β expression in a dose-dependent manner at protein and mRNA levels. It is important that miR-148 participates in regulation of LPS-induced the NF-κB signaling pathway by inhibiting IL-1β. These results will improve our understanding of the regulation of miRNAs in fish on the immune response.

Long noncoding RNA MIR2187HG suppresses TBK1-mediated antiviral signaling through deriving miR-2187-3p in teleost fish

Long non-coding RNAs (lncRNAs) function as microregulatory factors that influence gene expression after a variety of pathogenic infection, which have been extensively studied in the past few years. Although less attention has been paid to lncRNAs in lower vertebrates than in mammals, current studies reveals that lncRNAs plays a vital role in fish stimulated by pathogens. Here, we discovered a new lncRNA, termed as MIR2187HG, which can function as a precursor of a small RNA miR-2187-3p with regulatory functions in miiuy croaker (Miichthys miiuy). Upon Siniperca chuatsi rhabdovirus (SCRV) virus infection, the expression levels of MIR2187HG were remarkably enhanced. Elevated MIR2187HG expression can act as a pivotally negative regulator that participates in the innate immune response of teleost fish to inhibit the intracellular TANK-binding kinase 1 (TBK1)-mediated antiviral signaling pathways, which can effectively avoid excessive immunity. In addition, we found that the SCRV virus could also utilize MIR2187HG to enhance its own number. Our results not only provide evidence regarding the involvement of the lncRNAs in response to anti-viruses in fish, but also broaden our understanding of the function of lncRNAs as precursor miRNA in teleost fish for the first time. Importance: SCRV infection upregulates MIR2187HG levels, which in turn suppresses SCRV-triggered type I interferon production, thus promoting viral replication in miiuy croaker. Notably, MIR2187HG regulates the release of miR-2187-3p, and TBK1 is a target of miR-2187-3p. MIR2187HG could obtain the function from miR-2187-3p to inhibit TBK1 expression and subsequently modulate TBK1-mediated NF-κB and IRF3 signaling. The collective results suggest that the novel regulation mechanism of TBK1-mediated antiviral response during RNA viral infection was regulated by MIR2187HG. Therefore, a new regulation mechanism for lncRNAs to regulate antiviral immune responses in fish is proposed.

The circular RNA circBCL2L1 regulates innate immune responses via microRNA-mediated downregulation of TRAF6 in teleost fish

Growing numbers of studies have shown that circular RNAs (circRNAs) can function as regulatory factors to regulate the innate immune response, cell proliferation, cell migration, and other important processes in mammals. However, the function and regulatory mechanism of circRNAs in lower vertebrates are still unclear. Here, we discovered a novel circRNA derived from the gene encoding Bcl-2-like protein 1 (BCL2L1) gene, named circBCL2L1, which was related to the innate immune responses in teleost fish. Results indicated that circBCL2L1 played essential roles in host antiviral immunity and antibacterial immunity. Our study also identified a microRNA, miR-30c-3-3p, which could inhibit the innate immune response by targeting inflammatory mediator TRAF6. And TRAF6 is a key signal transduction factor in innate immune response mediated by TLRs. Moreover, we also found that the antiviral and antibacterial effects inhibited by miR-30c-3-3p could be reversed with the expression of circBCL2L1. Our data revealed that circBCL2L1 functioned as a competing endogenous RNA (ceRNA) of TRAF6 by competing for binding with miR-30c-3-3p, leading to activation of the NF-κB/IRF3 inflammatory pathway and then enhancing the innate immune responses. Our results suggest that circRNAs can play an important role in the innate immune response of teleost fish.

microRNA-132 as a negative regulator in NF-κB signaling pathway via targeting IL-1β in miiuy croaker

The innate immune system is the first line of defense against the invasion of pathogens. It can make a rapid immune response to the invading pathogenic microorganisms, thereby eliminating the invading pathogens and protecting the body from harm. microRNAs are a family of small non-coding ribonucleic acid molecules, which are important and multifunctional regulator of immune response. In this study, we studied the role of miR-132 as a key regulatory factor of IL-1β-mediated inflammation. The seed region of miR-132 can regulate gene expression by binding to the 3'UTR of IL-1β, and inhibit the expression of IL-1β at the post-transcriptional level. More importantly, miR-132 inhibits LPS-induced NF-κB signaling pathway by targeting IL-1β, thereby preventing excessive inflammatory response from causing autoimmune diseases. These results will help to better understand the complex regulatory mechanisms of teleost fishes.