Identification and characterization of circRNAs in the liver of blunt snout bream (Megalobrama amblycephala) infected with Aeromonas hydrophila

Circular RNA transcriptome across various development periods of Paralichthys olivaceus reveal skeletal muscle-specific circchd6 regulating myogenesis

The Japanese flounder (Paralichthys olivaceus) is greatly influenced in terms of muscle quality and quantity by the development of skeletal muscle. While the mechanisms underlying skeletal muscle development are well-studied, the role of non-coding RNAs, particularly circRNAs, in the skeletal muscle development of Japanese flounder remains unclear. To investigate the expression patterns of circRNAs during different developmental stages (JP1: 7 days, JP2: 90 days, JP3: 24 months (female), JP4: 24 months (male)) in Japanese flounder, we performed transcriptome sequencing analysis. We identified a total of 3523 circRNAs, of which 10.19 % were differentially expressed. These differentially expressed (DE) circRNAs were studied, and their impacts on muscle development were analyzed. The RNA interaction network revealed that skeletal muscle-specific circchd6 targeted novel-miR-508 and further regulated dual specificity tyrosine-phosphorylation regulated kinase 2 (dyrk2). Functional analysis showed that overexpressed circchd6 and dyrk2 promoted myoblast proliferation and differentiation, while novel-miR-508 inhibited both. Our study identified the circchd6-novel-miR-508-dyrk2 axis as a regulatory mechanism and provided new evidence for the use of epigenetic approaches in genetic breeding.

A novel lncRNA MSTRG.59348.1 regulates muscle cells proliferation and innate immunity of Megalobrama amblycephala

In mammals, long non-coding RNAs (lncRNAs) play a regulatory role in gene expression, contribute to immune responses, and aid in pathogen elimination, primarily through interactions with RNA-binding proteins (RBPs). However, the role of lncRNAs in fish innate immunity and their interaction with RBPs remains uncertain. To investigate the immunomodulatory role of lncRNAs in Megalobrama amblycephala, we identified the novel lncRNA MSTRG.59348.1 and examined its function in the innate immune response to Aeromonas hydrophila infection. Localization studies in hepatocytes revealed that MSTRG.59348.1 is primarily located in the nucleus, suggesting its potential involvement in gene regulation, possibly through chromatin modification or other nuclear processes. The expression of MSTRG.59348.1 was significantly up-regulated after lipopolysaccharide (LPS) stimulation in liver cells. RNA-seq analysis of muscle cells revealed that genes differentially expressed following MSTRG.59348.1 overexpression were enriched in immune pathways. MSTRG.59348.1 overexpression significantly inhibited the expression of sting and ifn, and significantly up-regulated muscle cell viability and promoted cell proliferation by targeting sting, ifn, nf-κb1, and bcl2. Screening by RNA pull-down and mass spectrometry identified 57 RBPs interacting with MSTRG.59348.1, with functions enriched in immune pathways. Our results suggest that MSTRG.59348.1 plays a crucial regulatory role in fish antibacterial response, marking it as a significant subject for future research in innate immunity.

Dynamics and regulatory role of circRNAs in Asian honey bee larvae following fungal infection

Non-coding RNA (ncRNA) plays a vital part in the regulation of immune responses, growth, and development in plants and animals. Here, the identification, characteristic analysis, and molecular verification of circRNAs in Apis cerana cerana worker larval guts were conducted, followed by in-depth investigation of the expression pattern of larval circRNAs during Ascosphaera apis infection and exploration of the potential regulatory part of differentially expressed circRNAs (DEcircRNAs) in host immune responses. A total of 3178 circRNAs in the larval guts of A. c. cerana were identified, with a length distribution ranging from 15 to 96,007 nt. Additionally, 155, 95, and 86 DEcircRNAs were identified in the in the 4-, 5-, and 6-day-old larval guts following A. apis infection. These DEcircRNAs were predicted to target 29, 25, and 18 parental genes relevant to 12, 20, and 17 GO terms as well as 144, 114, and 61 KEGG pathways, including 5 cellular and 4 humoral immune pathways. Complex competing endogenous RNA (ceRNA) regulatory networks were detected as being formed among DEcircRNAs, DEmiRNAs, and DEmRNAs. The target DEmRNAs were engaged in 36, 47, and 47 GO terms as well as 331, 332, and 331 pathways, including 6 cellular and 6 humoral immune pathways. Further, 19 DEcircRNAs, 5 DEmiRNAs, and 3 mRNAs were included in the sub-networks relative to 3 antioxidant enzymes. Finally, back-splicing sites within 15 circRNAs and the difference in the 15 DEcircRNAs' expression between uninoculated and A. apis-inoculated larval guts were confirmed based on molecular methods. These findings not only enrich our understanding of bee host-fungal pathogen interactions but also lay a foundation for illuminating the mechanism underlying the DEcircRNA-mediated immune defense of A. c. cerana larvae against A. apis invasion. KEY POINTS: • The expression pattern of circRNAs was altered in the A. cerana worker larval guts following A. apis infection. • Back-splicing sites within 15 A. cerana circRNAs were verified using molecular approaches. DEcircRNAs potentially modulated immune responses and antioxidant enzymes in A. apis-challenged host guts.

Dietary betaine and/or TMAO affect hepatic lipid accumulation and glycometabolism of Megalobrama amblycephala exposed to a high-carbohydrate diet

A 12-week experiment was conducted to explore the effects of betaine and/or TMAO on growth, hepatic health, gut microbiota, and serum metabolites in Megalobrama amblycephala fed with high-carbohydrate diets. The diets were as follows: CD group (control diet, 28.5% carbohydrate), HCD group (high-carbohydrate diet, 38.2% carbohydrate), HBD group (betaine-added diet, 38.3% carbohydrate + 1.2% betaine), HTD group (TMAO-added diet, 38.2% carbohydrate + 0.2% TMAO), and HBT group (diet added with both betaine and TMAO, 38.2% carbohydrate + 1.2% betaine + 0.2% TMAO). The results showed that the hepatosomatic index (HSI); whole-body crude fat; hepatic lipid accumulation; messenger RNA expression levels of gk, fpbase, g6pase, ahas, and bcat; serum branched-chain amino acids (BCAAs); ratio of Firmicutes-to-Bacteroidetes; and abundance of the genus Aeromonas were all significantly increased, while the abundance levels of the genus Lactobacillus and phyla Tenericutes and Bacteroidetes were drastically decreased in the HCD group. Compared with the HCD group, the HSI; whole-body crude fat; hepatic lipid accumulation; expression levels of fbpase, g6pase, pepck, ahas, and bcat; circulating BCAA; ratio of Firmicutes-to-Bacteroidetes; and abundance levels of the genus Aeromonas and phyla Tenericutes and Bacteroidetes were significantly downregulated in the HBD, HTD, and HBT groups. Meanwhile, the expression levels of pk were drastically upregulated in the HBD, HTD, and HBT groups as well as the abundance of Lactobacillus in the HBT group. These results indicated that the supplementation of betaine and/or TMAO in high-carbohydrate diets could affect the hepatic lipid accumulation and glycometabolism of M. amblycephala by promoting glycolysis, inhibiting gluconeogenesis and biosynthesis of BCAA, and mitigating the negative alteration of gut microbiota. Among them, the combination of betaine and TMAO had the best effect.

Comprehensive analysis of circRNA-miRNA-mRNA networks in the kidney of snakehead (Channa argus) response to Nocardia seriolae challenge

Non-coding RNAs (ncRNAs) play vital roles in regulating the expression levels of genes that control essential biological functions, including immune response to bacterial infections in teleost. To dissect the roles of ncRNAs in the Channa argus (snakehead), a systematic analysis of the expression profiles of circRNA, miRNA and mRNA, as well as competing endogenous RNAs (ceRNA) regulatory networks in the kidney of snakehead following Nocardia seriolae infection were performed in the present study. A total of 111 differentially expressed circRNAs, 706 differentially expressed miRNAs, and 2548 differentially expressed mRNAs were identified in the N. seriolae infected snakehead. Based on these differently expressed RNAs, we identified 55 circRNA-mRNA pairs, 124 miRNA-mRNA pairs, and 35 circRNA-miRNA-mRNA regulatory networks, including dre-miR-103-CD302, dre-miR-27e-IGSF3, novel_circ_0005462/novel_403-IGKC, novel_circ_0001750/novel_circ_0002162-novel_477-OCLN, and novel_circ_0003847-novel_4-KCNAB3. In addition, luciferase reporter assay was employed to detect the target relationships of several circRNA-miRNA-mRNA pairs. Taken together, this study demonstrates that the genes associated with immunity and structures in the kidney of snakehead can be regulated by circRNAs and miRNAs at post-transcription levels, and provided theoretical guidance for ncRNAs studies for other teleost. However, further studies are still in great need to validate the regulatory mechanisms of ncRNAs in snakehead.

Identification of immune-responsive circular RNAs in shrimp (Litopenaeus vannamei) upon yellow head virus infection

Circular RNAs (circRNAs) are a subclass of non-coding RNAs (ncRNAs) formed through a process known as back-splicing. They play a crucial role in the genetic regulation of various biological processes. Currently, circRNAs have been identified as participants in the antiviral response within mammalian cells. However, circRNAs in shrimp infected with the yellow head virus (YHV) remain largely unexplored. Therefore, this study aims to identify circRNAs in the hemocytes of Litopenaeus vannamei during YHV infection. We discovered 358 differentially expressed circRNAs (DECs), with 177 of them being up-regulated and 181 down-regulated. Subsequently, eight DECs, including circ_alpha-1-inhibitor 3, circ_CDC42 small effector protein 2, circ_hemicentin 2, circ_integrin alpha V, circ_kazal-type proteinase inhibitor, circ_phenoloxidase 3, circ_related protein rab-8B, and circ_protein toll-like, were randomly selected for analysis of their expression patterns during YHV infection using qRT-PCR. Furthermore, the circRNAs' characteristics were confirmed through PCR, RNase R treatment, and Sanger sequencing, all of which were consistent with the features of circRNAs. These findings contribute to a better understanding of circRNAs' involvement in the antiviral response in shrimp.

CircRNA254 functions as the miR-375 sponge to inhibit coelomocyte apoptosis via targeting BAG2 in V. splendidus-challenged Apostichopus japonicus

Circular RNAs (circRNAs) function as immune regulators in many biological processes in mammals, while their function and underlying mechanisms in invertebrates are largely unexplored. In this study, the competing endogenous RNA (ceRNA) mechanism of circRNA that sponges miR-375 and thus regulates AjBAG2-mediated coelomocyte apoptosis was evaluated in Apostichopus japonicus. The results showed that circRNA254 (circ254) was significantly down-regulated in the intestines and coelomocytes after Vibrio splendidus challenge or Lipopolysaccharide exposure, which matched the RNA-seq results in A. japonicus within skin ulceration syndrome. Dual-luciferase and RNA FISH assays indicated that circ254 could directly combine with miR-375, in which circ254 possesses three binding sites of miR-375. Moreover, circ254 knockdown significantly promoted the coelomocyte apoptosis levels upon pathogen infection in vivo and in vitro. Furthermore, circ254 silencing could also down-regulate AjBAG2 expression and thereby promoting the levels of coelomocyte apoptosis levels and the expression of caspase 3, which the phenomenon could be reversed by treatment with miR-375 inhibitors. Taken together, our results confirmed that circ254 functions as a ceRNA of AjBAG2 by sponging miR-375, resulting in the inhibition of coelomocyte apoptosis in A. japonicus.

Janus kinase 1 in Megalobrama amblycephala: Identification, phylogenetic analysis and expression profiling after Aeromonas hydrophila infection

Janus kinase 1 (JAK1), a member of the JAK family, plays an essential and non-redundant role in the mammalian immune system. However, the potential role of JAK1 in fish immune response remains largely unclear. In the present study, the JAK1 gene of Megalobrama amblycephala (MamJAK1) was identified and characterized. The open reading frame (ORF) of MamJAK1 was 3462 bp, encoding 1153 amino acids. MamJAK1 consists of four common domains of the JAK family, including B41, SH2, STyrKc (a pseudo kinase domain), and TyrKc (a kinase domain). Phylogenetic analysis showed that JAK1s are divided into two evolutionary clades, one containing fish JAK1s, and the other containing JAK1s from other vertebrates. The results of quantitative real-time PCR (qPCR) showed that in healthy M. amblycephala, MamJAK1 mRNA was highest expressed in blood, followed by spleen, intestine and mid-kidney, and lowly expressed in other tissues including gill, liver, head kidney, muscle, brain and heart. After Aeromonas hydrophila infection, the expression of MamJAK1 mRNA was significantly induced in four selected tissues including spleen, mid-kidney, liver and intestine, reaching a peak at 24 hpi (hour post infection) in spleen and mid-kidney, at 12 hpi in liver and at 4 hpi in intestine, and then the expression level was restricted to control levels at 72 or 120 hpi. In addition, the results of Western blot showed that the phosphorylation level of MamJAK1 protein in spleen and mid-kidney increased significantly after A. hydrophila infection, although MamJAK1 protein did not change obviously. Further, the JAK1 phosphorylation in Ctenopharyngodon idellus kidney (CIK) cells was found to be significantly induced by LPS stimulation and IL-6R over-expression. The results above suggest that MamJAK1 may play an essential role in the immune response against bacterial infection through the IL-6R mediated JAK1/STAT signaling pathway, which further deepen our understanding of JAK1 and provides a potential target for the treatment and prevention of bacterial diseases in teleost.

Intelectin enhances the phagocytosis of macrophages via CDC42-WASF2-ARPC2 signaling axis in Megalobrama amblycephala

Intelectin has been identified in various vertebrates and plays an important role in the host immune system. In our previous studies, recombinant Megalobrama amblycephala intelectin (rMaINTL) protein with excellent bacterial binding and agglutination activities enhances the phagocytic and killing activities of macrophages in M. amblycephala; however, the underlying regulatory mechanisms remain unclear. The present study showed that treatment with Aeromonas hydrophila and LPS induced the expression of rMaINTL in macrophages, and its level and distribution in macrophages or kidney tissue markedly increased after incubation or injection with rMaINTL. The cellular structure of macrophages was significantly affected after incubation with rMaINTL, resulting in an increased surface area and pseudopodia extension, which might contribute to enhancing the phagocytic ability of macrophages. Then, digital gene expression profiling analysis of the kidneys from rMaINTL-treated juvenile M. amblycephala identified some phagocytosis-related signaling factors that were enriched in pathways involved in the regulation of the actin cytoskeleton. In addition, qRT-PCR and western blotting verified that rMaINTL upregulated the expression of CDC42, WASF2, and ARPC2 in vitro and in vivo; however, the expression of these proteins was inhibited by a CDC42 inhibitor in macrophages. Moreover, CDC42 mediated the promotion of rMaINTL on actin polymerization by increasing the F-actin/G-actin ratio, which led to the extension of pseudopodia and remodeling of the macrophage cytoskeleton. Furthermore, the enhancement of macrophage phagocytosis by rMaINTL was blocked by the CDC42 inhibitor. These results suggested that rMaINTL induced the expression of CDC42 as well as the downstream signaling molecules WASF2 and ARPC2, thereby facilitating actin polymerization to promote cytoskeletal remodeling and phagocytosis. Overall, MaINTL enhanced the phagocytosis activity of macrophages in M. amblycephala via activation of the CDC42-WASF2-ARPC2 signaling axis.

Identification of four STAT3 isoforms and functional investigation of IL-6/JAK2/STAT3 pathway in blunt snout bream (Megalobrama amblycephala)

Signal transducer and activator of transcription 3 (STAT3) is a major regulator of immune response and chronic inflammatory, which can be activated by interleukin-6 (IL-6). In mammals, STAT3 has multiple isoforms, and its function has been well studied. In teleost, a single stat3 has been cloned and identified in several species, but studies on its function are limited. In the present study, four stat3 isoforms including mastat3α1, mastat3α2, mastat3β1 and mastat3β2 were identified from blunt snout bream (Megalobrama amblycephala). The results of quantitative PCR (qPCR) showed that four mastat3 transcripts were ubiquitously expressed in all 10 tissues examined. After Aeromonas hydrophila challenge, the expression patterns of mastat3a1, mastat3a2 and mastat3β2 were similar, but significantly different from that of mastat3β1. In addition, western blot showed that rmaIL-6+rmasIL-6R (IL-6 trans-signaling) significantly up-regulated phosphorylation levels of the four maSTAT3 isoforms and mRNA levels of the il-10, il-11, tnf-a, socs3a and socs3b genes, while rmaIL-6 (IL-6 classical signaling) only significantly up-regulated phosphorylation levels of the two maSTAT3α isoforms and mRNA levels of the il-10, socs3a and socs3b genes. Meanwhile, overexpression or inhibition of JAK2 could significantly change the STAT3 phosphorylation. Finally, JAK2 and STAT3 inhibitors could significantly inhibit the up-regulation of il-10, il-11, tnf-a, socs3a and socs3b induced by rmaIL-6+rmasIL-6R or rmaIL-6. To sum up, this study reveals the functional distinctions and overlaps among the four maSTAT3 isoforms in blunt snout bream and reveals the differential regulation of IL-6 classical signaling and trans-signaling on downstream immune genes via the JAK2/STAT3 pathway, enriching our knowledge of fish's defense mechanisms against pathogens.

The effects of blunt snout bream (Megalobrama amblycephala) IL-6 trans-signaling on immunity and iron metabolism via JAK/STAT3 pathway

Interleukin-6 (IL-6) is a pleiotropic inflammatory cytokine, which plays a dual role in mammalian inflammation through both classical signaling (IL-6 binds to IL-6 receptor/IL-6R) and trans-signaling (IL-6 binds to soluble IL-6R). However, the function of IL-6, especially the regulatory mechanism of IL-6 trans-signaling in immunity and iron metabolism remains largely unclear in teleost. Here, L8824 cells (Ctenopharyngodon idella hepatic cells) were stimulated with blunt snout bream (Megalobrama amblycephala) IL-6 combination with sIL-6R protein (rmaIL-6+rmasIL-6R/maIL-6 trans-signaling) or STAT3 inhibitor (c188-9), and RNA-sequencing, global transcriptional analyses. The enrichment analysis of GO and KEGG showed that maIL-6 trans-signaling is mainly involved in stress and inflammation response, and the activation of STAT3 is mainly related to cell proliferation, apoptosis and immune regulation. Furthermore, after treated L8824 cells with JAK2 inhibitors, it was found that the induction of IL-6 trans-signaling on the selected immune-related genes could be inhibited. These results implied that in early stage after rmaIL-6+rmasIL-6R treatment, the maIL-6 trans-signaling played an important role in the immune regulation through the JAK2/STAT3 pathway. By extending the rmaIL-6+rmasIL-6R treatment time, it was found that maIL-6 trans-signaling could promote the expression of iron metabolism related genes (ft, tf, tfr1, hamp and fpn1) in L8824 cells, indicating that maIL-6 trans-signaling may be involved in iron metabolism in the non-acute immune phase. Finally, after treated L8824 cells with JAK2 and STAT3 inhibitors, it was found that only tf and fpn1 were regulated by maIL-6 trans-signaling through the JAK2/STAT3 pathway. These findings provided novel insights into IL-6 trans-signaling regulatory mechanism in teleost, enriching our knowledge of fish immunity and iron metabolism.

Evolution and expression analysis of STAT family members in blunt snout bream (Megalobrama amblycephala)

The Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway is involved in regulating the body's immunity, cell proliferation, differentiation, and apoptosis. Members of the STAT family have been extensively studied in different mammalian species. However, there are few studies on the STAT family genes in farmed economic fish. In this study, eight STAT genes including STAT1a, STAT1b, STAT2, STAT3, STAT4, STAT5a, STAT5b and STAT6, in blunt snout bream (Megalobrama amblycephala), an economically important fish in China, were identified and characterized. Analyses of gene location, phylogeny and conserved synteny were conducted to infer the evolutionary origin of these STAT family genes. Furthermore, the evolutionary origin model of STATs was constructed based on the 2R hypothesis and teleost genome duplication (TGD) hypothesis, which clarified the evolutionary origin of the eight STATs in blunt snout bream. Besides, expression of the eight STATs was detected in 10 tissues of healthy blunt snout bream, which showed different expression patterns, and all had the highest level in the blood. In addition, expression of the STATs was significantly induced in the spleen, liver, and kidney after infection of Aeromonas hydrophila, suggesting that they play an important role in protecting the host from pathogens. In general, the evolution of cytokine-related genes parallels that of the immune system, which has likely been a main evolutionary driver. Therefore, the evolutionary model of STAT genes, constructed in the non-model organism pioneeringly, may provide some enlightenment for the evolution of the fish STAT family genes and their involvement in the immune function.