Transcriptomic analysis and discovery of genes involving in enhanced immune protection of Pacific abalone (Haliotis discus hannai) in response to the re-infection of Vibrio parahaemolyticus

Transcriptomic signatures related to the immune priming of Ruditapes philippinarum in response to the re-infection of Vibrio anguillarum

Manila clam (Ruditapes philippinarum) is a commercially valuable bivalve species, but its susceptibility to pathogenic microorganisms in aquaculture limits the development of the shellfish industry. Immune priming has been previously found in other invertebrates, but not in the unique immune system of the R. philippinarum. In the present study, the survival rate of R. philippinarum after two consecutive injections of Vibrio anguillarum was recorded, and the mechanisms of immune priming was studied by transcriptome analysis of R. philippinarum after two consecutive stimulations of V. anguillarum. R. philippinarum was first injected with V. anguillarum with PBS control group (SA), and then injected with V. anguillarum again after seven days (AA) with PBS control group (SS). The log-rank test showed that the survival rate of the AA group after the second injection was significantly higher than that of the other control groups (P < 0.05). The analysis of hepatopancreatic bacterial load showed that the pathogen clearance efficiency of the AA group was significantly enhanced. The activities of alkaline phosphatase (AKP), acid phosphatase (ACP), antioxidant enzymes (SOD) and malondialdehyde (MDA) were significantly increased after V. anguillarum infection, and the secondary stimulation was significantly higher than the primary stimulation. In addition, transcriptome analysis results showed that a common 84 differentially expressed genes (DEGs) were up-regulated after the primary stimulation and secondary stimulation compared with the SS control group, including C-type mannose receptor 2 (MRC2), Ubiquitin-like protein ATG12 (Atg12) and Toll-like receptor 4 (TLR4). The results of transcriptome analysis were verified by qRT-PCR of fifteen immune-related DEGs. The results showed that the pattern recognition receptors (PRR)-related genes are involved in immune priming. This study provides novel insights into physiological and molecular evidences of the immune priming response in R. philippinarum.

Deleted in malignant brain tumors 1 (DMBT1) gene relate to immune priming and phagocytosis modulation in the small abalone Haliotis diversicolor

The small abalone (Haliotis diversicolor) is an economic shellfish cultured in the south coast of China. In recent years, the frequent occurrence of the disease has led to significant mortality in abalone farms. Deleted in malignant brain tumors 1 (DMBT1), a member of the scavenger receptor cysteine-rich (SRCR) protein family, plays an important role in host defense. However, its function in H. diversicolor remains unknown. In order to evaluate the immune priming effect after secondary infection and elucidate possible regulatory mechanism, a novel DMBT1 from the small abalone H. diversicolor (designated as HdDMBT1) was cloned and characterized in this study. The open reading frame of HdDMBT1 was 2331 bp encoding 776 amino acids with a molecular weight of 84.73 kDa. HdDMBT1 contained conserved active sites with DMBT1 from other species, detected in all tested tissues and had higher expression levels in hepatopancreas. The temporal expression profiles of HdDMBT1 after two challenges of Vibrio harveyi were examined to evaluate priming response in the small abalone. The expression level of HdDMBT1 mRNA in hepatopancreas increased significantly after V. harveyi challenge. Meanwhile, the expression level of HdDMBT1 after the second challenge was significantly higher than that after the first challenge (4.23-fold). RNA interference (RNAi) experiments were conducted to examine the role of HdDMBT1 in response to V. harveyi infection. Knocking down HdDMBT1 decreased the hemocytes phagocytosis (0.48-fold). In addition, the bacterial density in hemolymph and the mortality of abalone raised, when infected with V. harveyi after dsHdDMBT1 injection. These results indicated that HdDMBT1 might play an important role in tolerance to bacterial infection.

Preliminary analysis of pathways and their implications during salinity stress in abalone

Transcriptome sequencing has offered immense opportunities to study non-model organisms. Abalone is an important marine mollusk that encounters harsh environmental conditions in its natural habitat and under aquaculture conditions; hence, research that increases molecular information to understand abalone physiology and stress response is noteworthy. Accordingly, the study used transcriptome sequencing of the gill tissues of abalone exposed to low salinity stress. The aim is to explore some enriched pathways during salinity stress and the crosstalk and functions of the genes involved in the candidate biological processes for future further analysis of their expression patterns. The data suggest that abalone genes such as YAP/TAZ, Myc, Nkd, and Axin (involved in the Hippo signaling pathway) and PI3K/Akt, SHC, and RTK (involved in the Ras signaling pathways) might mediate growth and development. Thus, deregulation of the Hippo and Ras pathways by salinity stress could be a possible mechanism by which unfavorable salinities influence growth in abalone. Furthermore, PEPCK, GYS, and PLC genes (mediating the Glucagon signaling pathway) might be necessary for glucose homeostasis, reproduction, and abalone meat sensory qualities; hence, a need to investigate how they might be influenced by environmental stress. Genes such as MYD88, IRAK1/4, JNK, AP-1, and TRAF6 (mediating the MAPK signaling pathway) could be useful in understanding abalone's innate immune response to environmental stresses. Finally, the aminoacyl-tRNA biosynthesis pathway hints at the mechanism by which new raw materials for protein biosynthesis are mobilized for physiological processes and how abalone might respond to this process during salinity stress. Low salinity clearly regulated genes in these pathways in a time-dependent manner, as hinted by the heat maps. In the future, qRT-PCR verification and in-depth study of the various genes and proteins discussed would provide enormous molecular information resources for the abalone biology.

The plasticity of immune memory in invertebrates

Whether specific immune protection after initial pathogen exposure (immune memory) occurs in invertebrates has long been uncertain. The absence of antibodies, B-cells and T-cells, and the short lifespans of invertebrates led to the hypothesis that immune memory does not occur in these organisms. However, research in the past two decades has supported the existence of immune memory in several invertebrate groups, including Ctenophora, Cnidaria, Nematoda, Mollusca and Arthropoda. Interestingly, some studies have demonstrated immune memory that is specific to the parasite strain. Nonetheless, other work does not provide support for immune memory in invertebrates or offers only partial support. Moreover, the expected biphasic immune response, a characteristic of adaptive immune memory in vertebrates, varies within and between invertebrate species. This variation may be attributed to the influence of biotic or abiotic factors, particularly parasites, on the outcome of immune memory. Despite its critical importance for survival, the role of phenotypic plasticity in immune memory has not been systematically examined in the past two decades. Additionally, the features of immune responses occurring in diverse environments have yet to be fully characterized.

Identification of a potential antigen stimulating immune response against Vibrio parahaemolyticus infection in hybrid tilapia (Oreochromis aureus♂ × Oreochromis niloticus♀)

Vibrio parahaemolyticus (V. parahaemolyticus) is a major pathogen that causes substantial losses in the marine fishery. With the emergence of antibiotic resistance, vaccines have become the most effective approach against V. parahaemolyticus infection. Adhesion factors on the cell surface are pivotal in the colonization and pathogenesis of V. parahaemolyticus within the host, highlighting their potential as vaccine candidates. This study aims to assess the immunogenicity and potential of recombinant V. parahaemolyticus MAM7 (rMAM7) as a vaccine candidate. Initially, we cloned and purified the MAM7 protein of V. parahaemolyticus. Moreover, after 4 weeks of vaccination, the fish were challenged with V. parahaemolyticus. rMAM7 demonstrated a certain protective effect. Immunological analysis revealed that rMAM7 immunization-induced antibody production and significantly increased acid phosphatase (ACP) and alkaline phosphatase (AKP) activity in hybrid tilapia. Furthermore, serum bactericidal tests demonstrated a lower bacterial survival rate in the rMAM7 group compared to PBS and rTrxa. qRT-PCR results indicated that rMAM7 significantly upregulated CD4, CD8 and IgM gene expression, suggesting the induction of Th1 and Th2 responses in hybrid tilapia. Overall, these findings highlight the potential application of MAM7 from V. parahaemolyticus in the development of protein vaccines.

The Modification of H3K4me3 Enhanced the Expression of CgTLR3 in Hemocytes to Increase CgIL17-1 Production in the Immune Priming of Crassostrea gigas

Increasing evidence confirms that histone modification plays a critical role in preserving long-term immunological memory. Immune priming is a novel form of immunological memory recently verified in invertebrates. Toll-like receptor (TLR) signaling and cytokines have been reported to be involved in the immune priming of the Pacific oyster Crassostrea gigas. In the present study, the expression of Toll-like receptor 3 (CgTLR3), myeloid differentiation factor 88-2 (CgMyd88-2) and interleukin 17-1 (CgIL17-1) was found to be elevated in the hemocytes of C. gigas at 6 h after the secondary stimulation with Vibrio splendidus, which was significantly higher than that at 6 h after the primary stimulation (p < 0.05). A significant increase in histone H3 lysine 4 trimethylation (H3K4me3) enrichment was detected in the promoter region of the CgTLR3 gene at 7 d after the primary stimulation with inactivated V. splendidus (p < 0.05). After the treatment with a histone methyltransferase inhibitor (5'-methylthioadenosine, MTA), the level of H3K4me3 at the promoter of the CgTLR3 gene decreased significantly at 7 d after the primary stimulation with inactivated V. splendidus (p < 0.05), and the expression of CgTLR3, CgMyD88-2 and CgIL17-1 was significantly repressed at 6 h after the secondary stimulation with V. splendidus (p < 0.05). Conversely, the treatment with monomethyl fumarate (MEF, an inhibitor of histone demethylases) resulted in a significant increase in H3K4me3 enrichment levels at the CgTLR3 promoter at 7 d after the primary stimulation (p < 0.05), and the expression of CgTLR3, CgMyD88-2 and CgIL17-1 was observed to increase significantly at 6 h after the secondary stimulation (p < 0.05). These results suggested that H3K4me3 regulated MyD88-dependent TLR signaling in the hemocytes of C. gigas, which defined the role of histone modifications in invertebrate immune priming.

Transcriptome analysis of digestive diverticula of Hong Kong oyster (Crassostrea hongkongesis) infected with Vibrio harveyi

The Hong Kong oyster (Crassostrea hongkongesis), as the main marine aquaculture shellfish in the South China Sea, not only has high economic and ecological value, but also is an ideal model for conducting research on pathogen host interaction. However, diseases caused by Vibrio pose a serious impediment to the culture of C. hongkongesis. In this study, we performed transcriptome analysis of digestive diverticula of C. hongkongesis infected with V. harveyi. A total of 977, 689, 912 high quality reads and 955, 208, 562 valid reads were obtained. At 12, 24, 48 and 72 h post-infection, 1402, 2168, 2727 and 1398 differentially expressed genes (DEGs) were captured, respectively. GO enrichment analysis showed that DEGs were significantly enriched in cellular processes, catalytic activity, cell part and other terms. KEGG enrichment analysis revealed that these DEGs were mainly closely related to Necroptosis, RIG-I-like receptor signaling pathway, NF-kappa B signaling pathway, Toll-like receptor signaling pathway and other pathways are related. The results of WGCNA analysis indicated that THBS1, CA10, Trpm2, THAP12, PTPRT, HSPA12A, and ADAM10 were the hub genes in the gene co-expression network. This study will provide new ideas at the transcriptome level for the immune regulatory mechanisms and adaptability of the C. hongkongesis to V. infection, as well as for achieving selective breeding for Vibrio resistance in the C. hongkongesis.

Investigating the Mechanism of Low-Salinity Environmental Adaptation in Sepia esculenta Larvae through Transcriptome Profiling

Sepia esculenta is an economically important mollusk distributed in the coastal waters of China. Juveniles are more susceptible to stimulation by the external environment than mature individuals. The ocean salinity fluctuates due to environmental changes. However, there is a lack of research on the salinity adaptations of S. esculenta. Therefore, in this study, we investigated the differential expression of genes in S. esculenta larvae after stimulation by low salinity. RNA samples were sequenced and 1039 differentially expressed genes (DEGs) were identified. Then, enrichment analysis was performed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Finally, a protein-protein interaction network (PPI) was constructed, and the functions of key genes in S. esculenta larvae after low-salinity stimulation were explored. We suggest that low salinity leads to an excess proliferation of cells in S. esculenta larvae that, in turn, affects normal physiological activities. The results of this study can aid in the artificial incubation of S. esculenta and reduce the mortality of larvae.

A member of the immunoglobulin superfamily lrig-1 might be involved in the immune priming of Scylla paramamosain in response to the infection and re-infection by Vibrio parahaemolyticus

A member of the immunoglobulin superfamily designated leucine-rich repeats and immunoglobulin-like domains protein-1 (lrig-1) encoding a protein with 1109 amino acids with a characteristic IGc2 domain was identified from the transcriptome data of mud crab Scylla paramamosain. Lrig-1 contained: one signaling peptide; one LRR_NT domain; nine LRR domains; three LRR_TYP domains; one LRR_CT domain; three IGc2 regions; one transmembrane region; C-terminal cytoplasmic tail. lrig-1 was widely expressed in all tissues of mud crab and was responsive in hemocytes to first and second Vibrio parahaemolyticus infections. lrig-1 knockdown mediated by RNAi repressed expression of several antimicrobial peptides significantly. Its orthologs in 19 crustacean species were identified and showed high conservation. These results suggest that lrig-1 have a vital role in mud crabs against V. parahaemolyticus infection through expression of multiple antimicrobial peptides. The results obtained in the present study imply the potential roles the lrig-1 played in immune priming in crabs.

Molecular mechanisms underlying the vulnerability of Pacific abalone (Haliotis discus hannai) to Vibrio harveyi infection at higher water temperature

Climate change is one of the most important threats to farmed abalone worldwide. Although abalone is more susceptible to vibriosis at higher water temperatures, the molecular mode of action underlying this has not been fully elucidated. Therefore, this study aimed to address the high susceptibility of Halitotis discus hannai to V. harveyi infection using abalone hemocytes exposed to low and high temperatures. Abalone hemocytes were divided into four groups, 20C, 20V, 25C, and 25V, depending on co-culture with (V)/without (C) V. harveyi (MOI = 12.8) and incubation temperature (20 °C or 25 °C). After 3 h of incubation, hemocyte viability and phagocytic activity were measured, and RNA sequencing was performed using Illumina Novaseq. The expression of several virulence-related genes in V. harveyi was analyzed using real-time PCR. The viability of hemocytes was significantly decreased in the 25V group compared to cells in the other groups, whereas phagocytic activity at 25 °C was significantly higher than at 20 °C. Although a number of immune-associated genes were commonly upregulated in abalone hemocyte exposed to V. harveyi, regardless of temperature, pathways and genes regarding pro-inflammatory responses (interleukin-17 and tumor necrosis factor) and apoptosis were significantly overexpressed in the 25V group compared to the 25C group. Notably, in the apoptosis pathway, genes encoding executor caspases (casp3 and casp7) and pro-apoptotic factor, bax were significantly up-regulated only in the 25V group, while the apoptosis inhibitor, bcl2L1 was significantly up-regulated only in the 20V group compared to the control group at the respective temperatures. The co-culture of V. harveyi with abalone hemocytes at 25 °C up-regulated several virulence-related genes involved in quorum sensing (luxS), antioxidant activity (katA, katB, and sodC), motility (flgI), and adherence/invasion (ompU) compared to those at 20 °C. Therefore, our results showed that H. discus hannai hemocytes exposed to V. harveyi at 25 °C were highly stressed by vigorously activated inflammatory responses and that the bacterial pathogen overexpressed several virulence-related genes at the high temperature tested. The transcriptomic profile of both abalone hemocytes and V. harveyi in the present study provide insight into differential host-pathogen interactions depending on the temperature conditions and the molecular backgrounds related to increased abalone vulnerability upon global warming.

Acclimatory gene expression of primed clams enhances robustness to elevated pCO2

Sub-lethal exposure to environmental challenges may enhance ability to cope with chronic or repeated change, a process known as priming. In a previous study, pre-exposure to seawater enriched with pCO₂ improved growth and reduced antioxidant capacity of juvenile Pacific geoduck Panopea generosa, suggesting that transcriptional shifts may drive phenotypic modifications post-priming. To this end, juvenile clams were sampled and TagSeq gene expression data analyzed after 1) a 110-day acclimation under ambient (921 μatm, naïve) and moderately-elevated pCO₂ (2870 μatm, pre-exposed); then following 2) a second 7-day exposure to three pCO₂ treatments (ambient: 754 μatm; moderately-elevated: 2750 μatm; severely-elevated: 4940 μatm), a 7-day return to ambient pCO₂ , and a third 7-day exposure to two pCO₂ treatments (ambient: 967 μatm; moderately-elevated: 3030 μatm). Pre-exposed geoducks frontloaded genes for stress and apoptosis/innate immune response, homeostatic processes, protein degradation, and transcriptional modifiers. Pre-exposed geoducks were also responsive to subsequent encounters, with gene sets enriched for mitochondrial recycling and immune defense under elevated pCO₂ and energy metabolism and biosynthesis under ambient recovery. In contrast, gene sets with higher expression in naïve clams were enriched for fatty-acid degradation and glutathione components, suggesting naïve clams could be depleting endogenous fuels, with unsustainable energetic requirements if changes in carbonate chemistry persist. Collectively, our transcriptomic data indicates pCO₂ priming during post-larval periods could, via gene expression regulation, enhance robustness in bivalves to environmental change. Such priming approaches may be beneficial for aquaculture, as seafood demand intensifies concurrent with increasing climate change in marine systems.