RNA-Seq Analysis for Assessing the Early Response to DSP Toxins in Mytilus galloprovincialis Digestive Gland and Gill

Analysis of research status and trends on marine benthic dinoflagellate toxins: A bibliometric study based on web of science database and VOSviewer

Marine benthic dinoflagellate toxins, potent bioactive compounds with wide-ranging presence in marine ecosystems, have surged in response to global climate change and human activities, prompting an urgent and imperative inquiry. This study conducts an in-depth review of contemporary research concerning these toxins, employing meticulous bibliometric analysis. Leveraging a dataset of 736 relevant literatures sourced from the Web of Science (spanning from 2000 to May 2023), our analysis delves comprehensively into the scientific discourse surrounding these toxic compounds. Employing tools such as VOSviewer, co-citation analysis, co-occurrence analysis, and cluster analysis, our study yields nuanced insights into the intricate characteristics and trajectories of the field. The co-citation analysis underscores the pivotal role played by benthic and epiphytic dinoflagellates like Ostreopsis and Gambierdiscus in shaping prevailing research trends. Our study identifies four distinct research directions, encompassing the domains of ecology, toxicology, toxin production, and taxonomy. Moreover, it traces the evolutionary journey of research stages, marking the transition from a focus on taxonomy to an emphasis on unraveling molecular mechanisms. The culmination of our comprehensive analysis yields three pertinent research recommendations: a call for widescale global studies, the advancement of rapid toxin monitoring techniques, and a deeper exploration of the factors influencing toxin synthesis and toxicity. These findings provide invaluable insights to researchers grappling with the complex realm of harmful algal blooms and substantially enrich the understanding of this pivotal and pressing field.

Assessment of sulfamethoxazole toxicity to marine mussels (Mytilus galloprovincialis): Combine p38-MAPK signaling pathway modulation with histopathological alterations

Sulfamethoxazole (SMX), is a ubiquitous antibiotic in the aquatic environment and received concerns on its health hazards, especially its sub-lethal effects on non-target organisms which were remained largely unknown. In the present study, in order to investigate SMX induced tissue damages and reveal underlying mechanisms, marine mussels, Mytilus galloprovincialis were challenged to SMX series (0.5, 50 and 500 μg/L) for six-days followed by six-day-recovery. Comprehensive histopathological alteration (including qualitative, semi-quantitative and quantitative indices), together with transcriptional and (post-) translational responses of key factors (p38, NFκB and p53) in the p38-MAPK signaling pathway were analyzed in gills and digestive glands. Tissue-specific responses were clearly investigated with gills showing more prompt responses and digestive glands showing higher tolerance to SMX. The histopathology showed that SMX triggered inflammatory damages in both tissues and quantitative analysis revealed more significant responses, suggesting its potential as a valuable health indicator. SMX activated expressions of p38, NFκB and p53 at transcriptional and (post-) translational levels, especially after exposed to low level SMX, evidenced by p38 coupled with NFκB/p53 regulation on immunity defense in mussels. Less induction of targeted molecules under severe SMX exposure indicated such signaling transduction may not be efficient enough and can result in inflammatory damages. Taken together, this study expanded the understanding of aquatic SMX induced health risk in marine mussels and the underlying regulation mechanism through p38 signaling transduction.

Myticofensin, a novel antimicrobial peptide family identified from Mytilus coruscus

In this study, seven transcripts representing a novel antimicrobial peptide (AMP) family with structural features similar to those of arthropod defensins were identified from Mytilus coruscus. These novel defensins from the Mytilus AMP family were named myticofensins. To explore the possible immune-related functions of these myticofensins, we examined their expression profiles in different tissues and larval stages, as well as in three immune-related tissues under the threat of different microbes. Our data revealed that the seven myticofensins had relatively high expression levels in immune-related tissues. Most myticofensins were undetectable, or had low expression levels, in different larval mussel stages. Additionally, in vivo microbial challenges significantly increased the expression levels of myticofensins in M. coruscus hemocytes, gills, and digestive glands, showing different immune response patterns under challenges from different microbes. Our data indicates that different myticofensins may have different immune functions in different tissues. Furthermore, peptide sequences corresponding to the beta-hairpin, alpha-helix, and N-terminal loop of myticofensin were synthesized and the antimicrobial activities of these peptide fragments were tested. Our data confirms the diversity of defensins in Mytilus and reports the complex regulation of these defensins in the mussel immune response to different microbes in immune-related tissues. The immune system of Mytilus has been studied for years as they are a species with strong environmental adaptations. Our data can be regarded as a step forward in the study of the adaptation of Mytilus spp. to an evolving microbial world.

Transcriptome Analysis Reveals MAPK/AMPK as a Key Regulator of the Inflammatory Response in PST Detoxification in Mytilus galloprovincialis and Argopecten irradians

Paralytic shellfish toxins (PSTs) are an increasingly important source of pollution. Bivalves, as the main transmission medium, accumulate and metabolize PSTs while protecting themselves from damage. At present, the resistance mechanism of bivalves to PSTs is unclear. In this study, Mytilus galloprovincialis and Argopecten irradians were used as experimental shellfish species for in situ monitoring. We compared the inflammatory-related gene responses of the two shellfish during PSTs exposure by using transcriptomes. The results showed that the accumulation and metabolism rate of PSTs in M. galloprovincialis was five-fold higher than that in A. irradians. The inflammatory balance mechanism of M. galloprovincialis involved the co-regulation of the MAPK-based and AMPK-based anti-inflammatory pathways. A. irradians bore a higher risk of death because it did not have the balance system, and the regulation of apoptosis-related pathways such as the PI3K-AKT signaling pathway were upregulated. Taken together, the regulation of the inflammatory balance coincides with the ability of bivalves to cope with PSTs. Inflammation is an important factor that affects the metabolic pattern of PSTs in bivalves. This study provides new evidence to support the studies on the resistance mechanism of bivalves to PSTs.

Toxic Responses of Different Shellfish Species after Exposure to Prorocentrum lima, a DSP Toxins Producing Dinoflagellate

Prorocentrum lima is a global benthic dinoflagellate that produces diarrhetic shellfish poisoning (DSP) toxins, which can be ingested by filter-feeding bivalves, and eventually pose a great threat to human health through food chain. After being exposed to P. lima, different bivalves may accumulate various levels of DSP toxins and display different toxic responses. However, the underlying mechanism remains unclear. Here, we found that the content of okadaic acid-equivalents (OA-eq) varied in the digestive glands of the three bivalves including Crassostrea gigas, Mytilus coruscus and Tegillarca granosa after P. lima exposure. The degree of esterification of OA-eq in the three bivalves were opposite to the accumulation of OA-eq. The digestive gland tissues of the three bivalve species were damaged to different degrees. The transcriptional induction of Nrf2 targeted genes such as ABCB1 and GPx indicates the functionality of Nrf2 pathway against DSP toxins in bivalves. The oyster could protect against DSP toxins mainly through ABC transporters and esterification, while the mussel and clam reduce the damage induced by DSP toxins mainly by regulating the expression of antioxidant genes. Our findings may provide some explanations for the difference in toxic response to DSP toxins in different shellfish.

Transcriptomic Profile of the Cockle Cerastoderma edule Exposed to Seasonal Diarrhetic Shellfish Toxin Contamination

Bivalves constitute an important source of proteins for human consumption, but some accumulate biotoxins such as diarrhetic shellfish toxins (DSTs), constituting a risk to human health. The cockle Cerastoderma edule is one of the most important species harvested in the Portuguese coast but also one of the most affected species due to recurrent DSTs exposure. However, little is known regarding the effects of the toxins produced by blooming dinoflagellates on C. edule. Herein, we explore the Differentially Expressed Genes (DEGs) of two tissues (gills and digestive gland) from wild cockles sampled in Portugal, through their whole transcriptomic response in two different seasons (exposed and not exposed to DSTs). The de novo transcriptome assembly returned 684,723 contigs, N50 of 1049, and 98.53% completeness. Altogether, 1098 DEGs were identified, of which 353 DEGs were exclusive for the digestive gland, 536 unique for the gills and 209 DEGs were common. Among DEGs were identified known DSTs-biomarkers including glutathione peroxidase, glutathione S-transferase, superoxide dismutase, cytochrome P450, ABC transporters, actin and tubulin-related proteins, Heat shock proteins and complement C1Q-like proteins. This study provides the first transcriptomic profile of C. edule, giving new insights about its molecular responses under different environmental conditions of DSTs exposure.

Small RNA analysis of Perna viridis after exposure to Prorocentrum lima, a DSP toxins-producing dinoflagellate

Diarrheic shellfish poisoning toxins (DSP toxins) are a set of the most important phycotoxins produced by some dinoflagellates. Studies have shown that DSP toxins have various toxicities such as genotoxicity, cytotoxicity, and immunotoxicity to bivalve mollusks. However, these toxicities appear decreasing with exposure time and concentration of DSP toxins. The underlying mechanism involved remains unclear. In this study, small RNA sequencing was performed in the digestive gland of the mussel Perna viridis after exposure to DSP toxins-producing dinoflagellate Prorocentrum lima for different time periods. The potential roles of miRNAs in response and detoxification to DSP toxins in the mussel were analyzed. Small RNA sequencing of 12 samples from 72 individuals was conducted by BGISEQ-500. A total of 123 mature miRNAs were identified, including 90 conserved miRNAs and 33 potential novel miRNAs. After exposure to P. lima, multiple important miRNAs displayed some alterations. Further miRNA target prediction revealed some important genes involved in cytoskeleton, apoptosis, complement system and immune stress. qPCR demonstrated that miR-71_5, miR-750_1 and novel_mir4 were significantly up-regulated at 6 h after exposure to P. lima, while miR-100_2 was significantly down-regulated after 96 h of exposure. Accordingly, putative target genes of these differentially expressed miRNAs experienced some changes. After 6 h of DSP toxins exposure, NHLRC2 and C1q-like were significantly down-regulated. After 96 h of DSP toxins exposure, NHLRC2 was significantly up-regulated. It is reasonable to speculate that the mussel P. viridis might respond to DSP toxins through miR-750_1, novel_mir4 and miR-71_5 regulating the expression of relevant target genes involved in apoptosis, cytoskeleton, and immune response, etc. This study might provide new clues to uncover the toxic response of bivalve to DSP toxins and lay a foundation for revealing the roles of miRNAs in the environmental adaptation in shellfish.

Effect of Different Species of Prorocentrum Genus on the Japanese Oyster Crassostrea gigas Proteomic Profile

This paper assesses the effects of exposure to toxic concentrations (1200 to 6000 cells/mL) of the dinoflagellates Prorocentrum lima, Prorocentrum minimum, and Prorocentrum rhathymum and several concentrations of aqueous and organic extracts obtained from the same species (0 to 20 parts per thousand) on the Crassostrea gigas (5-7 mm) proteomic profile. Through comparative proteomic map analyses, several protein spots were detected with different expression levels, of which eight were selected to be identified by liquid chromatography-mass spectrometry (LC-MS/MS) analyses. The proteomic response suggests that, after 72 h of exposure to whole cells, the biological functions of C. gigas affected proteins in the immune system, stress response, contractile systems and cytoskeletal activities. The exposure to organic and aqueous extracts mainly showed effects on protein expressions in muscle contraction and cytoskeleton morphology. These results enrich the knowledge on early bivalve developmental stages. Therefore, they may be considered a solid base for new bioassays and/or generation of specific analytical tools that allow for some of the main effects of algal proliferation phenomena on bivalve mollusk development to be monitored, characterized and elucidated.

Cinnamaldehyde Could Reduce the Accumulation of Diarrhetic Shellfish Toxins in the Digestive Gland of the Mussel Perna viridis under Laboratory Conditions

Diarrhetic shellfish toxins (DSTs), some of the most important phycotoxins, are distributed almost all over the world, posing a great threat to human health through the food chain. Therefore, it is of great significance to find effective methods to reduce toxin accumulation in shellfish. In this paper, we observed the effects of four phytochemicals including cinnamaldehyde (CA), quercetin, oridonin and allicin on the accumulation of DSTs in the digestive gland of Perna viridis after exposure to the DSTs-producing Prorocentrum lima. We found that, among the four phytochemicals, CA could effectively decrease the accumulation of DSTs (okadaic acid-eq) in the digestive gland of P. viridis. Further evidence demonstrated that CA could reduce the histological alterations of the digestive gland of a mussel caused by DSTs. RT-qPCR showed that CA could suppress the CYP3A4 induction by DSTs, suggesting that the DSTs’ decrease induced by CA might be related to the inhibition of CYP3A4 transcription induction. However, further studies on the underlying mechanism, optimal treatment time, ecological safety and cost should be addressed before cinnamaldehyde is used to decrease the accumulation of DSTs in field.

OMICs Approaches in Diarrhetic Shellfish Toxins Research

Diarrhetic shellfish toxins (DSTs) are among the most prevalent marine toxins in Europe's and in other temperate coastal regions. These toxins are produced by several dinoflagellate species; however, the contamination of the marine trophic chain is often attributed to species of the genus Dinophysis. This group of toxins, constituted by okadaic acid (OA) and analogous molecules (dinophysistoxins, DTXs), are highly harmful to humans, causing severe poisoning symptoms caused by the ingestion of contaminated seafood. Knowledge on the mode of action and toxicology of OA and the chemical characterization and accumulation of DSTs in seafood species (bivalves, gastropods and crustaceans) has significantly contributed to understand the impacts of these toxins in humans. Considerable information is however missing, particularly at the molecular and metabolic levels involving toxin uptake, distribution, compartmentalization and biotransformation and the interaction of DSTs with aquatic organisms. Recent contributions to the knowledge of DSTs arise from transcriptomics and proteomics research. Indeed, OMICs constitute a research field dedicated to the systematic analysis on the organisms' metabolisms. The methodologies used in OMICs are also highly effective to identify critical metabolic pathways affecting the physiology of the organisms. In this review, we analyze the main contributions provided so far by OMICs to DSTs research and discuss the prospects of OMICs with regard to the DSTs toxicology and the significance of these toxins to public health, food safety and aquaculture.

Detecting Prognosis Risk Biomarkers for Colon Cancer Through Multi-Omics-Based Prognostic Analysis and Target Regulation Simulation Modeling

Background

Colon cancer is one of the most common health threats for humans since its high morbidity and mortality. Detecting potential prognosis risk biomarkers (PRBs) is essential for the improvement of therapeutic strategies and drug development. Currently, although an integrated prognostic analysis of multi-omics for colon cancer is insufficient, it has been reported to be valuable for improving PRBs’ detection in other cancer types.

Aim

This study aims to detect potential PRBs for colon adenocarcinoma (COAD) samples through the cancer genome atlas (TCGA) by integrating muti-omics.

Materials and Methods

The multi-omics-based prognostic analysis (MPA) model was first constructed to systemically analyze the prognosis of colon cancer based on four-omics data of gene expression, exon expression, DNA methylation and somatic mutations on COAD samples. Then, the essential features related to prognosis were functionally annotated through protein–protein interaction (PPI) network and cancer-related pathways. Moreover, the significance of those essential prognostic features were further confirmed by the target regulation simulation (TRS) model. Finally, an independent testing dataset, as well as the single cell-based expression dataset were utilized to validate the generality and repeatability of PRBs detected in this study.

Results

By integrating the result of MPA modeling, as well the PPI network, integrated pathway and TRS modeling, essential features with gene symbols such as EPB41, PSMA1, FGFR3, MRAS, LEP, C7orf46, LOC285000, LBP, ZNF35, SLC30A3, LECT2, RNF7, and DYNC1I1 were identified as PRBs which provide high potential as drug targets for COAD treatment. Validation on the independent testing dataset demonstrated that these PRBs could be applied to distinguish the prognosis of COAD patients. Moreover, the prognosis of patients with different clinical conditions could also be distinguished by the above PRBs.

Conclusions

The MPA and TRS models constructed in this paper, as well as the PPI network and integrated pathway analysis, could not only help detect PRBs as potential therapeutic targets for COAD patients but also make it a paradigm for the prognostic analysis of other cancers.

De novo transcriptome analysis of the mussel Perna viridis after exposure to the toxic dinoflagellate Prorocentrum lima

Diarrheic shellfish poisoning (DSP) toxins are produced by harmful microalgae and accumulate in bivalve mollusks, causing various toxicity. These toxic effects appear to abate with increasing DSP concentration and longer exposure time, however, the underlying mechanisms remain unclear. To explore the underlying molecular mechanisms, de novo transcriptome analysis of the digestive gland of Perna viridis was performed after Prorocentrum lima exposure. RNA-seq analysis showed that 1886 and 237 genes were up- and down-regulated, respectively after 6 h exposure to P. lima, while 265 genes were up-regulated and 217 genes were down-regulated after 96 h compared to the control. These differentially expressed genes mainly involved in Nrf2 signing pathways, immune stress, apoptosis and cytoskeleton, etc. Combined with qPCR results, we speculated that the mussel P. viridis might mainly rely on glutathione S-transferase (GST) and ABC transporters to counteract DSP toxins during short-term exposure. However, longer exposure of P. lima could activate the Nrf2 signaling pathway and inhibitors of apoptosis protein (IAP), which in turn reduced the damage of DSP toxins to the mussel. DSP toxins could induce cytoskeleton destabilization and had some negative impact on the immune system of bivalves. Collectively, our findings uncovered the crucial molecular mechanisms and the regulatory metabolic nodes that underpin the defense mechanism of bivalves against DSP toxins and also advanced our current understanding of bivalve defense mechanisms.

Solute carriers in scallop genome: Gene expansion and expression regulation after exposure to toxic dinoflagellate

The solute carriers (SLCs) are membrane proteins that transport many endogenous and exogenous substances such as xenobiotic toxins. Bivalve mollusks, mainly feeding on microalgae, show marked capacity to accumulate paralytic shellfish toxins (PSTs), the most common and hazardous marine biotoxins produced by dinoflagellates. Exploring the SLCs related to PST accumulation in bivalve could benefit our understanding about the mechanisms of PST bioavailability in bivalve and the adaptations of these species. Herein, we provided the first systematic analysis of SLC genes in mollusks, which identified 673 SLCs (PySLCs, 48 subfamilies) in Yesso scallop (Patinopecten yessoensis), 510 (48 subfamilies) in Pacific oyster (Crassostrea gigas), and 350 (47 subfamilies) in gastropod owl limpet (Lottia gigantea). Significant expansion of subfamilies SLC5, SLC6, SLC16, and SLC23 in scallop, and SLC46 subfamily in both scallop and oyster were revealed. Different PySLC members were highly expressed in the developmental stages and adult tissues, and hepatopancreas harboured more specifically expressed PySLCs than other tissues/organs. After feeding the scallops with PST-producing dinoflagellate, 131 PySLCs were regulated and more than half of them were from the expanded subfamilies. The trend of expression fold change in regulated PySLCs was consistent with that of PST changes in hepatopancreas, implying the possible involvement of these PySLCs in PST transport and homeostasis. In addition, the PySLCs from the expanded subfamily were revealed to be under positive selection, which might be related to lineage-specific adaptation to the marine environments with algae derived biotoxins.

Genomics and immunity of the Mediterranean mussel Mytilus galloprovincialis in a changing environment

The Mediterranean mussel (Mytilus galloprovincialis) is a marine invasive species cultured all over the world. Mussels are an appreciated resource in local aquaculture enterprises because of their robust production and resilience that translates into a reliable economic value. So far, no massive mortalities have been reported in natural or cultured populations of this species. In the last years, the knowledge about its immune system has greatly improved but there are still many questions to be answered. One of them is why mussels, with their high filtering activity, are able to be exposed to a high number of potential pathogens without getting infected and without developing an elevated inflammatory response. The sequencing of the mussel genome has revealed a very complex organization with high heterozygosity, abundance of repetitive sequences and extreme intraspecific sequence diversity among individuals, mainly in immune related genes. Among those genes, antimicrobial peptides are the most expressed gene families in mussels, highly polymorphic and with antimicrobial effect against molluscs pathogens, but also against pathogens of lower vertebrates and humans. The combination of a complex genome with the adaptation of mussel immune system to a changing environment could explain this high variability, not only in immune-related genes, but also in the functional response among individuals sampled in the same location and date.

RNA-Seq Transcriptome Profiling of the Queen Scallop (Aequipecten opercularis) Digestive Gland after Exposure to Domoic Acid-Producing Pseudo-nitzschia

Some species of the genus Pseudo-nitzschia produce the toxin domoic acid, which causes amnesic shellfish poisoning (ASP). Given that bivalve mollusks are filter feeders, they can accumulate these toxins in their tissues. To elucidate the transcriptional response of the queen scallop Aequipecten opercularis after exposure to domoic acid-producing Pseudo-nitzschia, the digestive gland transcriptome was de novo assembled using an Illumina HiSeq 2000 platform. Then, a differential gene expression analysis was performed. After the assembly, 142,137 unigenes were obtained, and a total of 10,144 genes were differentially expressed in the groups exposed to the toxin. Functional enrichment analysis found that 374 Pfam (protein families database) domains were significantly enriched. The C1q domain, the C-type lectin, the major facilitator superfamily, the immunoglobulin domain, and the cytochrome P450 were among the most enriched Pfam domains. Protein network analysis showed a small number of highly connected nodes involved in specific functions: proteasome components, mitochondrial ribosomal proteins, protein translocases of mitochondrial membranes, cytochromes P450, and glutathione S-transferases. The results suggest that exposure to domoic acid-producing organisms causes oxidative stress and mitochondrial dysfunction. The transcriptional response counteracts these effects with the up-regulation of genes coding for some mitochondrial proteins, proteasome components, and antioxidant enzymes (glutathione S-transferases, thioredoxins, glutaredoxins, and copper/zinc superoxide dismutases).