Potential immune regulatory role of miR-146a upon Aeromonas hydrophila and Edwardsiella piscicida infections in zebrafish

MicroRNA-203-3p participates in antiviral immune response by negatively regulating TRAF3 in the rainbow trout (Oncorhynchus mykiss)

MicroRNAs (miRNAs) are highly conserved endogenous non-coding RNAs that play a crucial role in fish immune response by regulating gene expression at the post-transcriptional level. In recent years, the viral diseases caused by infectious hematopoietic necrosis virus (IHNV) have caused significant economic losses in rainbow trout (Oncorhynchus mykiss) aquaculture, whereas the immune regulatory mechanisms of miRNAs involved in rainbow trout resistance to IHNV infection remains largely undefined. In this study, we analyzed the structural characteristics of Oncorhynchus mykiss tumor necrosis factor receptor-associated factor 3 (OmTRAF3) by bioinformatics software and explored the molecular mechanism of miR-203-3p in rainbow trout resistance to IHNV by regulating OmTRAF3 in vivo and in vitro. The open reading frame (ORF) of OmTRAF3 gene was 1731 bp and encoded 576 amino acids including an N-terminal RING finger domain, two zinc finger domains, a coiled-coil domain, and a C-terminal MATH domain. The expression pattern analysis showed that the expression of miR-203-3p and OmTRAF3 in immune-related tissues (head kidney, spleen, and liver) and liver cells of rainbow trout infected with IHNV varied with certain regularity and had opposite trends at key time points, and a targeting relationship between miR-203-3p and OmTRAF3 was confirmed using a dual luciferase reporter gene assay. Further, we found that in vivo and in vitro overexpression of miR-203-3p significantly reduced the expression of OmTRAF3, downstream immune-related genes (OmTANK, OmIKKε, OmIFN1, and OmISG15) and promoted IHNV copy number replication, while silencing of miR-203-3p yielded opposite results. More importantly, OmTRAF3 and downstream genes as well as IHNV copy number changed accordingly with the silencing of OmTRAF3. The above results revealed that miR-203-3p participates in the immune response against IHNV by targeting OmTRAF3, and provides a theoretical basis for the screening of antiviral drugs in rainbow trout.

SIGIRR plays a dual role in zebrafish infected with Edwardsiella piscicida: Boosting digestive system wellness and mitigating inflammation

Single immunoglobulin interleukin-1 receptor-associated protein (SIGIRR) negatively regulates the inflammatory response induced by bacterial infection by inhibiting the excessive synthesis of inflammatory mediators and overactivation. This inhibitory mechanism reduces the fish's susceptibility to pathogens and enhances survival rates. Zebrafish lacking the SIGIRR gene were generated using CRISPR/Cas9 gene knockout technology. In a zebrafish model infected with Edwardsiella piscicida, researchers found that SIGIRR gene deletion led to a significant increase in the activation of both inflammatory and anti-inflammatory factors. This deletion also resulted in intestinal villus epithelium damage, epithelial shedding, separation of the epithelium and lamina propria, and a severe reduction in goblet cells. After E. piscicida infection, the survival rate of SIGIRR-/- zebrafish was significantly reduced, and the number of E. piscicida in the body was also significantly increased. Intestinal acid phosphatase activity in SIGIRR-/- zebrafish was markedly elevated compared to wild-type (WT) zebrafish. Furthermore, the intestinal mucosal layer and villus thickness in SIGIRR-/- zebrafish were reduced compared to WT zebrafish. The enzymatic activities of lipase and lysozyme in the intestines of SIGIRR-/- zebrafish were significantly lower than in WT zebrafish. This study reveals the detrimental effects of SIGIRR gene deletion on the intestinal health of zebrafish, leading to decreased innate immune capacity and increased susceptibility to bacterial infections.

Micro-and nano-plastics induce kidney damage and suppression of innate immune function in zebrafish (Danio rerio) larvae

Aquatic environments serve as critical repositories for pollutants and have significantly accumulated micro- and nanoplastics (MNPs) due to the extensive production and application of plastic products. While the disease resistance and immunity of fish are closely linked to the condition of their aquatic habitats, the specific effects of nanoplastics (NPs) and microplastics (MPs) within these environments on fish immune functions are still not fully understood. The present study utilized zebrafish (Danio rerio) embryos and larvae as model organisms to examine the impacts of polystyrene NPs (100 nm) and MPs (5 μm) on fish immune responses. Our findings reveal that NPs and MPs tend to accumulate on the surfaces of embryos and within the intestines of larvae, triggering oxidative stress and significantly increasing susceptibility to Edwardsiella piscicida infection in zebrafish larvae. Transmission electron microscopy examined that both NPs and MPs inflicted damage to the kidney, an essential immune organ, with NPs predominantly inducing endoplasmic reticulum stress and MPs causing lipid accumulation. Transcriptomic analysis further demonstrated that both NPs and MPs significantly suppress the expression of key innate immune pathways, notably the C-type lectin receptor signaling pathway and the cytosolic DNA-sensing pathway. Within these pathways, the immune factor interleukin-1 beta (il1b) was consistently downregulated in both exposure groups. Furthermore, exposure to E. piscicida resulted in restricted upregulation of il1b mRNA and protein levels, likely contributing to diminished disease resistance in zebrafish larvae exposed to MNPs. Our findings suggest that NPs and MPs similarly impair the innate immune function of zebrafish larvae and weaken their disease resistance, highlighting the significant environmental threat posed by these pollutants.

Integrated time-series biochemical, transcriptomic, and metabolomic analyses reveal key metabolites and signaling pathways in the liver of the Chinese soft-shelled turtle (Pelodiscus sinensis) against Aeromonas hydrophila infection

Introduction

Aeromonas hydrophila, a bacterium widely distributed in the natural environment, causes multiple diseases in various animals. Exploring the mechanism of the host defense against A. hydrophila can help develop efficient strategies against Aeromonas infection.

Methods

Herein, we investigated the temporal influence of A. hydrophila on the Chinese soft-shelled turtle, an economically important species, at the biochemical, transcriptomic, and metabolomic levels. Plasma parameters were detected with the test kits. Transcriptome and metabolome were respectively applied to screen the differentially expressed genes and metabolites.

Results

The contents or activities of these plasma parameters were significantly increased at 24 hpi and declined at 96 hpi, indicating that 24 and 96 hpi were two important time points during infection. Totals of 3121 and 274 differentially expressed genes (DEGs) from the transcriptome while 74 and 91 differentially abundant metabolites (DAMs) from the metabolome were detected at 24 and 96 hpi. The top DEGs at 24 hpi included Ccl2, Ccl3, Ccl4, Il1β, Il6, Il7, Il15, Tnf, and Tnfr1 while Zap70, Cd3g, Cd8a, Itk, Pik3r3, Cd247, Malt1, and Cd4 were the most abundant at 96 hpi. The predominant DAMs included O-phospho-L-serine, γ-Aminobutyric acid, orotate, L-tyrosine, and L-tryptophan at 24 hpi, as well as L-glutamic acid, L-arginine, glutathione, glutathione disulfide, and citric acid at 96 hpi.

Discussion

The combined analysis of DEGs and DAMs revealed that tryptophan metabolism, nicotinate and nicotinamide metabolism, as well as starch and sucrose metabolism, were the most important signaling pathways at the early infective stage while tyrosine metabolism, pyrimidine metabolism, as well as alanine, aspartate and glutamate metabolism were the most crucial pathways at the later stage. In general, our results indicated that the Chinese soft-shelled turtle displays stage-specific physiological responses to resist A. hydrophila infection.

Characteristics of conserved microRNAome and their evolutionary adaptation to regulation of immune defense functions in the spleen of silver carp and bighead carp

Immune defense functions of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) have shown obvious evolutionary divergence. MiRNAs participate in the fine regulation of immune function. However, the evolutionary adaptation of miRNAs in the regulation of immune defense function is still poorly understood in silver carp and bighead carp. Here, small RNA libraries were constructed from the spleen tissue of one-year-old and three-year-old healthy silver carp and bighead carp, 424 and 422 known conserved miRNAs were respectively identified from the spleen of silver carp and bighead carp by bioinformatic analysis, which 398 were shared between the two species. These conserved miRNAs showed highly similar expression patterns between silver carp and bighead carp, but the abundance in spleen varied greatly in different species. Family analysis showed that miRNA families including mir-8, mir-7, mir-23, mir-338, mir-30, mir-27, mir-221, mir-19, mir-181, mir-17, mir-15, mir-148, mir-130, mir-10 and let-7 were the main miRNAs in the spleen of silver carp and bighead carp. 27 and 51 significant differentially expressed (SDE) miRNAs were identified from silver carp and bighead carp, respectively. Evolution analysis for the predicted target genes of SDE-miRNAs showed that ten biological processes such as blood coagulation, cell adhesion mediated by integrin and adaptive immune response were positively selected. In addition, immune genes including TLR3, NFATC3, MALT1, B2M, GILT and MHCII were positively selected only in silver carp, and they were specifically targeted by the SDE-miRNAs including miR-9-5p, miR-196a-5p, miR-375, miR-122, miR-722, miR-132-3p, miR-727-5p, miR-724, miR-19d-5p and miR-138-5p, respectively. PLA2G4 in Fc epsilon RI signaling pathway was positively selected only in bighead carp and was specifically targeted by the SDE-miRNAs including miR-222b, miR-22b-5p, miR-15c, miR-146a, miR-125c-3p, miR-221-5p, miR-2188-5p, miR-142a-3p, miR-212, miR-138-5p and miR-15b-5p. In particular, SDE-miRNAs such as miR-144-3p, miR-2188-3p, miR-731, miR-363-3p and miR-218b could simultaneously target multiple evolutionarily differentiated immune-related genes. These results indicated that in the spleen of silver carp and bighead carp, conserved miRNAs have obvious evolutionary adaptations in the regulation of immune defense function. The results of this study can provide valuable resources for further revealing themechanism of miRNA in the formation of resistance traits evolution between silver carp and bighead carp.

Potential Role of microRNAs in Response to Aeromonas Infection in Fish

The genus Aeromonas is a widespread pathogen that includes more than 30 Gram-negative species, many of which are opportunistic bacteria. Aeromonas species are naturally distributed in various aquatic sources. Infectious processes in marine animals such as fish usually develop under stressful conditions, and when their immune systems are weakened. MicroRNAs (miRNAs/miRs) are short, non-coding RNAs that post-transcriptionally regulate gene expression. Their diverse biological functions, such as influencing cell development, proliferation, differentiation, tumorigenesis, metabolism, and apoptosis have been studied in various animals. Fish is the most important source of aquatic nutrients throughout the world, and its market is constantly growing. Overpopulation in aquaculture brings infectious diseases that threaten the development of aquaculture around the world. There is extensive evidence that microRNAs are involved in modulating infectious processes and regulating the inflammatory response to major bacterial fish infections, including Aeromonas. Here, we review the current literature on the fish microRNA repertoire and outline the physiological roles assigned to microRNAs to provide a foundation for future research during Aeromonas infection. Understanding the interaction between microRNAs and Aeromonas may provide clues to a remarkable strategy for preventing Aeromonas infections in fish.

Metabolomic and transcriptomic profiles after immune stimulation in the zebrafish testes

Fish farms are prone to disease outbreaks and stress due to high-density rearing conditions in tanks and sea cages, adversely affecting growth, reproduction, and metabolism. To understand the molecular mechanisms affected in the gonads of breeder fish after an immune challenge, we investigated the metabolome and the transcriptome profiles in zebrafish testes after inducing an immune response. After 48 h of the immune challenge, ultra-high-performance liquid chromatography (LC-MS) and transcriptomic analysis by RNA-seq (Illumina) resulted in 20 different released metabolites and 80 differentially expressed genes. Among these, glutamine and succinic acid were the most abundant metabolites released and 27,5% of the genes belong to either the immune or reproduction systems. Pathway analysis based on metabolomic and transcriptomic crosstalk identified cad and iars genes that act simultaneously with succinate metabolite. This study deciphers interactions between reproduction and immune systems and provides a basis to improve protocols in generating more resistant broodstock.

Characterization of the MMP9 Gene and Its Association with Cryptocaryon irritans Resistance Traits in Trachinotus ovatus (Linnaeus, 1758)

The MMPs are endogenous proteolytic enzymes that require zinc and calcium as cofactors. MMP9 is one of the most complex matrix metalloproteinases in the gelatinase family and has many biological functions. In mammals, mmp9 is thought to be closely associated with cancer. However, studies in fish have rarely been reported. In this study, to understand the expression pattern of the ToMMP9 gene and its association with the resistance of Trachinotus ovatus to Cryptocaryon irritans, the sequence of the MMP9 gene was obtained from the genome database. The expression profiles were measured by qRT-PCR, the SNPs were screened by direct sequencing, and genotyping was performed. The ToMMP9 gene contained a 2058 bp ORF encoding a putative amino acid sequence of 685 residues. The homology of the ToMMP9 in teleosts was more than 85%, and the genome structure of ToMMP9 was conserved in chordates. The ToMMP9 gene was expressed in different tissues of healthy individuals and was highly expressed in the fin, the gill, the liver and the skin tissues. The ToMMP9 expression in the skin of the infected site and its adjacent sites increased significantly after C. irritans infection. Two SNPs were identified in the ToMMP9 gene, and the SNP (+400A/G) located in the first intron was found to be significantly associated with the susceptibility/resistance to C. irritans. These findings suggest that ToMMP9 may play an important role in the immune response of T. ovatus against C. irritans.

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.

Identification of two interleukin 17 receptor C (IL-17RC) genes and their binding activities to three IL-17A/F ligands in the Japanese medaka, Oryzias latipes

In mammals, interleukin (IL)-17 receptor C (IL-17RC) and IL-17RA mediate IL-17A and IL-17F signaling to produce mucin, antimicrobial peptides, and maintain healthy intestinal flora. However, IL-17RC signaling in fish remains unclear. In this study, three il17rc transcripts (il17rca1, il17rca2, and il17rcb) from the Japanese medaka (Oryzias latipes) were cloned; il17rca1 and il17rca2 mRNAs were alternatively spliced from il17rca pre-mRNA as transcript variants. The il17rca and il17rcb genes were located on chromosomes 7 and 5, respectively. Teleost clades containing medaka il17rca and il17rcb clustered separately from the tetrapod clade. In adult tissues, il17rca1 expression was significantly higher than il17rca2 and il17rcb. Conversely, il17rcb expression was significantly higher in embryos and larvae. These expression patterns changed following infection with Edwardsiella piscicida and Aeromonas hydrophila. Furthermore, an immunoprecipitation assay using recombinant IL-17RCs and rIL-17A/Fs suggested that, in teleosts, three ligands could function in signaling through two IL-17RCs.

Expression of ssa-miR-155 during ISAV infection in vitro: Putative role as a modulator of the immune response in Salmo salar

Multiple cellular components are involved in pathogen-host interaction during viral infection; in this context, the role of miRNAs have become highly relevant. We assessed the expression of selected miRNAs during an in vitro infection of a Salmo salar cell line with Infectious Salmon Anemia Virus (ISAV), the causative agent of a severe disease by the same name. Salmon orthologs for miRNAs that regulate antiviral responses were measured using RT-qPCR in an in vitro time-course assay. We observed a modulation of specific miRNAs expression, where ssa-miR-155-5p was differentially over-expressed. Using in silico analysis, we identified the putative mRNA targets for ssa-miR-155-5p, finding a high prevalence of hosts immune response-related genes; moreover, several mRNAs involved in the viral infective process were also identified as targets for this miRNA. Our results suggest a relevant role for miR-155-5p in Salmo salar during an ISAV infection as a regulator of the immune response to the virus.

Lipopolysaccharide-induced TNFα factor (LITAF) promotes inflammatory responses and activates apoptosis in zebrafish Danio rerio

Lipopolysaccharide-induced TNFα factor (LITAF) is an important transcription factor which activates the transcription of TNFα and regulates cell apoptosis and inflammatory response. In the present study, a LITAF gene homologue was identified in zebrafish (Danio rerio) and was shown to be well conserved in the protein sequence, genomic organization and synteny with human LITAF. DrLITAF was constitutively expressed in tissues, with the highest expression detected in the gills. Its expression could be modulated by LPS, poly(I:C), and infection with Edwardsiella tarda, Aeromonus hydrophila and septicemia viremia of carp virus (SVCV). DrLITAF, when overexpressed, was shown to be located on the cellular membrane and nuclear membrane of HEK293T and ZF4 cells and was associated with the endoplasmic reticulum. Stimulation with LPS resulted in rapid translocation of DrLITAF into the nucleus. In addition, DrLITAF was able to induce cell apoptosis and the expression of caspase 3. The results demonstrate that DrLITAF is involved in the immune defence against bacterial and viral infection and plays a role in regulating inflammation and apoptosis.