Transcriptomic analysis of sea cucumber (Holothuria leucospilota) coelomocytes revealed the echinoderm cytokine response during immune challenge

Morpho-functional characterisation of cœlomocytes in the aquacultivated sea cucumber Holothuria scabra: From cell diversity to transcriptomic immune response

Holothuria scabra is one of the most valuable species of sea cucumber owing to its exploitation as a seafood product. This study aims to describe the main molecular and cellular actors in the immunology of this species. First, a detailed description of the immune cells - the cœlomocytes - is provided, highlighting five main cell types including phagocytes, small round cells (SRCs), spherulocytes, fusiform cells, and crystal cells, with a further five subtypes identified using transmission electron microscopy. Cœlomocyte aggregates were also described morphologically, yielding two main types, one comprising three successive maturation stages. A comparison of the concentration and proportion of cell populations was carried out between the two main body fluids, namely the hydrovascular fluid of the Polian vesicle (HF) and the perivisceral fluid of the general cavity (PF), and no clear relation could be highlighted. Next, the cœlomocyte immune response was studied 24 h after lipopolysaccharide (LPS) injection in the two body fluids. Firstly, the fluctuation in cell populations was assessed, and despite a high inter-individual variability, it shows a decrease in the phagocyte proportion and an increase in the SRC proportion. Secondly, the differential gene expression of PF cœlomocytes was studied by de novo RNA-sequencing between LPS-injected and control-injected individuals: 945 genes were differentially expressed, including 673 up-regulated and 272 down-regulated in the LPS-injected individuals. Among these genes, 80 had a presumed function in immunity based on their annotation, covering a wide range of immune mechanisms. Overall, this study reveals a complex immune system at both molecular and cellular levels and constitutes a baseline reference on H. scabra immunity, which may be useful for the development of sustainable aquaculture and provides valuable data for comparative immunology.

Physiological and intestinal microbiota responses of sea cucumber Apostichopus japonicus to various stress and signatures of intestinal microbiota dysbiosis

Identifying the signatures of intestinal dysbiosis caused by common stresses is fundamental to establishing efficient health monitoring strategies for sea cucumber. This study investigated the impact of six common stress experienced frequently in aquaculture on the growth performance, intestinal homeostasis and microbiota of sea cucumber, including thermal (23°C), hypoosmotic (22‰ salinity), ammonium (0.5 mg/L NH4 +-N), and nitrite (0.25 mg/L NO2 --N) stress exposure for 30 days, as well as starvation and crowding (6 kg/m3 density) stress exposure for 60 days. Results demonstrated that all stress led to reduced growth performance and digestive capacity of sea cucumber, along with varying degrees of oxidative stress and immune responses. Various stresses significantly altered the diversity, community structure (except for crowding stress), and composition of intestinal microbiota. The ratios of Bacteroidota: Proteobacteria (B: P) and Firmicutes: Proteobacteria (F: P) declined markedly compared to the control. Potentially pathogenic bacteria of Shewanellaceae, Vibrionaceae, and Moraxellaceae significantly increased under crowding, ammonium, and nitrite stress, respectively, whereas beneficial microbes of Achromobacter and Rhodobacteraceae were, respectively, enriched under hypoosmotic and starvation stresses. The complexity and stability of microbial ecological networks were further altered by these stresses. KEGG predictions revealed the reduced functional pathways of intestinal microbiota involved in host immunity under different stresses. Correlation analysis further confirmed a strong link between microbiota response and host immunity under different stresses. The increased abundance of Verrucomicrobia species could also be identified as the sensitive indicator for diagnosing whether the host was under stressful pressure by random forest analysis.

Genomic and Transcriptional Analysis of the Necroptosis Pathway Elements RIPK and MLKL in Sea Cucumber, Holothuria leucospilota

Background: Receptor-interacting protein kinases (RIPKs) and mixed-lineage kinase domain-like protein (MLKL) are crucial in regulating innate immune responses and cell death signaling (necroptosis and apoptosis), and are potential candidates for genetic improvement in breeding programs. Knowledge about the RIPK family and MLKL in sea cucumber remains limited. Methods: We searched the genomes of sea cucumber Holothuria leucospilota for genes encoding RIPKs and MLKL, performed phylogenetic tree, motif and functional domain analyses, and examined tissue distribution and embryonic development patterns using qPCR. Results: RIPK5 (Hl-RIPK5), RIPK7 (Hl-RIPK7) and MLKL (Hl-MLKL) were identified in sea cucumber H. leucospilota. Hl-RIPK5 and Hl-RIPK7 were mainly expressed in coelomocytes, suggesting that they play a role in innate immunity, whereas Hl-MLKL exhibited relatively low expression across tissues. During embryonic development, Hl-MLKL was highly expressed from the 2-cell stage to the morula stage, while Hl-RIPK5 and Hl-RIPK7 were primarily expressed after the morula stage, indicating different roles in embryonic development. In primary coelomocytes, Hl-RIPK5 transcriptional activity was significantly depressed by LPS, poly(I:C), or pathogen Vibrio harveyi. Hl-RIPK7 expression levels were unchanged following the same challenges. Hl-MLKL mRNA levels were significantly decreased with poly(I:C) or V. harveyi, but did not change with LPS. Conclusions: These findings provide valuable insights into the evolutionary tree and characterization of RIPK and MLKL genes in sea cucumber, contributing to the broader understanding of the RIPK gene family and MLKL in ancient echinoderms.

Transcriptomic analysis reveals the early body wall regeneration mechanism of the sea cucumber Holothuria leucospilota after artificially induced transverse fission

BACKGROUND

Sea cucumbers exhibit a remarkable ability to regenerate damaged or lost tissues and organs, making them an outstanding model system for investigating processes and mechanisms of regeneration. They can also reproduce asexually by transverse fission, whereby the anterior and posterior bodies can regenerate independently. Despite the recent focus on intestinal regeneration, the molecular mechanisms underlying body wall regeneration in sea cucumbers still remain unclear.

RESULTS

In this study, transverse fission was induced in the tropical sea cucumber, Holothuria leucospilota, through constrainment using rubber bands. Histological examination revealed the degradation and loosening of collagen fibers on day-3, followed by increased density but disorganization of the connective tissue on day-7 of regeneration. An Illumina transcriptome analysis was performed on the H. leucospilota at 0-, 3- and 7-days after artificially induced fission. The differential expression genes were classified and enriched by GO terms and KEGG database, respectively. An upregulation of genes associated with extracellular matrix remodeling was observed, while a downregulation of pluripotency factors Myc, Klf2 and Oct1 was detected, although Sox2 showed an upregulation in expression. In addition, this study also identified progressively declining expression of transcription factors in the Wnt, Hippo, TGF-β, and MAPK signaling pathways. Moreover, changes in genes related to development, stress response, apoptosis, and cytoskeleton formation were observed. The localization of the related genes was further confirmed through in situ hybridization.

CONCLUSION

The early regeneration of H. leucospilota body wall is associated with the degradation and subsequent reconstruction of the extracellular matrix. Pluripotency factors participate in the regenerative process. Multiple transcription factors involved in regulating cell proliferation were found to be gradually downregulated, indicating reduced cell proliferation. Moreover, genes related to development, stress response, apoptosis, and cell cytoskeleton formation were also involved in this process. Overall, this study provides new insights into the mechanisms of whole-body regeneration and uncover potential cross-species regenerative-related genes.

de novo transcriptome assembly for discovering gene expressed in Holothuria leucospilota with exposed to copper

Sea cucumber is a bioremediator as it can composite organic matter and excrete inorganic matter. Sea cucumber has the potential to serve as a bioindicator in marine habitat as they provide an integrated insight into the status of their environment over long periods. Sea cucumbers are sensitive to the organic concentration in the marine environment and can effectively provide an early warning system for any organic contamination that can negatively impact the ecosystem. The availability of a reference transcriptome for sea cucumber would constitute an essential tool for identifying genes involved in crucial steps of the defence pathway. De novo assembly of RNA-seq data enables researchers to study the transcriptomes without needing a genome sequence. In this study, sea cucumbers fed with Kappaphycus alvarezii powder were treated with 0.20 mg/L copper concentration comprehensive transcriptome data containing 75,149 Unigenes, with a total length of 20,460,032 bp. A total of 8820 genes were predicted from the unigenes, annotated, and functionally categorized into 25 functional groups with approximately 20% cluster in signal transduction mechanism. The reference transcriptome presented and validated in this study is meaningful for identifying a wide range of gene(s) related to the bioindication of sea cucumber in a high copper environment.

Induced Immune Reaction in the Acorn Worm, Saccoglossus kowalevskii, Informs the Evolution of Antiviral Immunity

Evolutionary perspectives on the deployment of immune factors following infection have been shaped by studies on a limited number of biomedical model systems with a heavy emphasis on vertebrate species. Although their contributions to contemporary immunology cannot be understated, a broader phylogenetic perspective is needed to understand the evolution of immune systems across Metazoa. In our study, we leverage differential gene expression analyses to identify genes implicated in the antiviral immune response of the acorn worm hemichordate, Saccoglossus kowalevskii, and place them in the context of immunity evolution within deuterostomes-the animal clade composed of chordates, hemichordates, and echinoderms. Following acute exposure to the synthetic viral double-stranded RNA analog, poly(I:C), we show that S. kowalevskii responds by regulating the transcription of genes associated with canonical innate immunity signaling pathways (e.g., nuclear factor κB and interferon regulatory factor signaling) and metabolic processes (e.g., lipid metabolism), as well as many genes without clear evidence of orthology with those of model species. Aggregated across all experimental time point contrasts, we identify 423 genes that are differentially expressed in response to poly(I:C). We also identify 147 genes with altered temporal patterns of expression in response to immune challenge. By characterizing the molecular toolkit involved in hemichordate antiviral immunity, our findings provide vital evolutionary context for understanding the origins of immune systems within Deuterostomia.

An Interleukin-17 Isoform from Thick Shell Mussel Mytilus coruscus Serves as a Mediator of Inflammatory Response

The inflammatory cytokine interleukin-17 (IL17) plays an important role in innate immunity by binding to its receptors (IL17Rs) to activate immune defense signals. To date, information on members of the IL17 family is still very limited in molluscan species. Here, a novel member of the IL17 family was identified and characterized from thick shell mussel Mytilus coruscus, and this gene was designated as McIL17-1 by predicting structural domains and phylogenetic analysis. McIL17-1 transcripts existed in all examined tissues with high expression levels in gills, hemocytes and digestive glands. After the stimuli of different pathogen associated molecular patterns (PAMPs) for 72 h, transcriptional expression of McIL17-1 was significantly upregulated, except for poly I:C stimulation. Cytoplasm localization of McIL17-1 was shown in HEK293T cells by fluorescence microscopy. Further, in vivo and in vitro assays were performed to evaluate the potential function of McIL17-1 played in immune response. McIL17-1 was either knocked down or overexpressed in vivo through RNA inference (RNAi) and recombinant protein injection, respectively. With the infection of living Vibrio alginolyticus, a high mortality rate was exhibited in the McIL17-1 overexpressed group compared to the control group, while a lower mortality rate was observed in the McIL17-1 knocked down group than control group. In vitro, the flow cytometric analysis showed that the apoptosis rate of McIL17-1 inhibited hemocytes was significantly lower than that of the control group after lipopolysaccharide stimulation. These results collectively suggested that the newly identified IL17 isoform is involved in the inflammatory response to bacterial infection in M. coruscus.

Evolutionarily Ancient Caspase-9 Sensitizes Immune Effector Coelomocytes to Cadmium-Induced Cell Death in the Sea Cucumber, Holothuria leucospilota

Heavy-metal pollution has increasingly jeopardized the habitats of marine organisms including the sea cucumber, a seafloor scavenger vital to seawater bio-decontamination, ocean de-acidification and coral-reef protection. Normal physiology including immune functions of sea cucumbers is toxicologically modulated by marine metal pollutants such as cadmium (Cd). The processes underpinning Cd's toxic effects on immune systems in the sea cucumber, Holothuria leucospilota, are still poorly understood. To this end, we cloned and characterized a full-length caspase-9 (Hl-CASP9) cDNA in the sea cucumber, Holothuria leucospilota. Hl-CASP9 mRNA levels evolved dynamically during embryonic development. Coelomocytes, a type of phagocytic immune effectors central to H. leucospilota immunity, were found to express Hl-CASP9 mRNA most abundantly. Hl-CASP9 protein structurally resembles caspases-2 and -9 in both invertebrate and vertebrate species, comprising a CARD domain and a CASc domain. Remarkably, Hl-CASP9 was transcriptionally sensitive to abiotic oxidative stress inducers including hydrogen peroxide (H₂O₂), nitric oxide (^•NO) and cadmium (Cd), but insensitive to immunostimulants including lipopolysaccharide (LPS), and poly(I:C). Overexpression of Hl-CASP9 augmented mitochondria-dependent apoptosis in HEK293T cells, while knock-down of Hl-CASP9 blunted Cd-induced coelomocyte apoptosis in vivo. Overall, we illustrate that an evolutionarily ancient caspase-9-dependent pathway exists to sensitize coelomocytes to premature cell death precipitated by heavy metal pollutants, with important implications for negative modulation of organismal immune response in marine invertebrates.

Apoptosis-Inducing Factor 2 (AIF-2) Mediates a Caspase-Independent Apoptotic Pathway in the Tropical Sea Cucumber (Holothuria leucospilota)

Apoptosis, also known as programmed cell death, is a biological process that is critical for embryonic development, organic differentiation, and tissue homeostasis of organisms. As an essential mitochondrial flavoprotein, the apoptosis-inducing factor (AIF) can directly mediate the caspase-independent mitochondrial apoptotic pathway. In this study, we identified and characterized a novel AIF-2 (HlAIF-2) from the tropical sea cucumber Holothuria leucospilota. HlAIF-2 contains a conserved Pyr_redox_2 domain and a putative C-terminal nuclear localization sequence (NLS) but lacks an N-terminal mitochondrial localization sequence (MLS). In addition, both NADH- and FAD-binding domains for oxidoreductase function are conserved in HlAIF-2. HlAIF-2 mRNA was ubiquitously detected in all tissues and increased significantly during larval development. The transcript expression of HlAIF-2 was significantly upregulated after treatment with CdCl₂, but not the pathogen-associated molecular patterns (PAMPs) in primary coelomocytes. In HEK293T cells, HlAIF-2 protein was located in the cytoplasm and nucleus, and tended to transfer into the nucleus by CdCl₂ incubation. Moreover, there was an overexpression of HlAIF-2-induced apoptosis in HEK293T cells. As a whole, this study provides the first evidence for heavy metal-induced apoptosis mediated by AIF-2 in sea cucumbers, and it may contribute to increasing the basic knowledge of the caspase-independent apoptotic pathway in ancient echinoderm species.

Identification and localization of growth factor genes in the sea cucumber, Holothuria scabra

The sea cucumber Holothuria scabra is both an economically important species in Asian countries and an emerging experimental model for research studies in regeneration and medicinal bioactives. Growth factors and their receptors are known to be key components that guide tissue repair and renewal, yet validation of their presence in H. scabra has not been established. We performed a targeted in silico search of H. scabra transcriptome data to elucidate conserved growth factor family and receptor genes. In total, 42 transcripts were identified, of which 9 were validated by gene cloning and sequencing. The H. scabra growth factor genes, such as bone morphogenetic protein 2A (BMP 2A), bone morphogenetic protein 5-like (BMP5-like), neurotrophin (NT) and fibroblast growth factor 18 (FGF18), were selected for further analyses, including phylogenetic comparison and spatial gene expression using RT-PCR and in situ hybridization. Expression of all genes investigated were widespread in multiple tissues. However, BMP 2A, BMP5-like and NT were found extensively in the radial nerve cord cells, while FGF18 was highly expressed in connective tissue layer of the body wall. Our identification and expression analysis of the H. scabra growth factor genes provided the molecular information of growth factors in this species which may ultimately complement the research in regenerative medicine.

Comparative transcriptome analysis reveals changes in gene expression in sea cucumber (Holothuria leucospilota) in response to acute temperature stress

Ambient temperature is an important abiotic factor that influences growth performance and physiological functions in sea cucumbers. To understand the molecular responses of the sea cucumber Holothuria leucospilota to acute temperature stress, we performed a de novo transcriptome analysis of body wall tissue from H. leucospilota exposed to 2 hoursh of acute heat (35 ± 1 °C) and cold stress (15 ± 1 °C). A total of 99,015 unigenes were obtained after assembly of the sequenced reads. Compared with a control group maintained at 25.0 ± 1 °C, 1169 differentially expressed unigenes (DEGs) were identified after heat stress, 781 were up-regulated and 388 were down-regulated. After cold stress, 1464 DEGs were identified; 900 were up-regulated and 564 were down-regulated. The annotation of DEGs revealed that heat shock proteins play important roles in protecting H. leucospilota from high temperature stress. Furthermore, KEGG pathway enrichment analysis showed that the categories: "Ribosome" and "Protein processing in endoplasmic reticulum" were strongly affected by heat stress. These two pathways are associated with biosynthesis and processing of proteins, and refolding of misfolded proteins. The lipid metabolism pathways "Sphingolipid metabolism" and "Ether lipid metabolism", were affected by cold stress. The RNA-Seq results for eight selected DEGs were verified the expression by quantitative real-time PCR analysis. Our results will improve the understanding of the molecular response mechanisms of H. leucospilota to ambient temperature stress.

Current progress on identification of virus pathogens and the antiviral effectors in echinoderms

Echinoderms are important marine organisms that live in a wide range from the intertidal zone to the abyssal zone. Members of this phylum are prone to dramatic population fluctuations that may trigger dramatic shifts in ecosystem structure. Despite the extremely complex nature of the marine environment, the immune systems of echinoderms induce a complex innate immune response to prokaryotic and eukaryotic pathogens. Previous studies showed that many echinoderm disease outbreaks were associated with specific bacteria, whereas recent scientific investigations using newly developed technologies revealed the amazing diversity of viruses in seawater. Viruses are potential pathogens of several infectious diseases of marine echinoderms. We reviewed the discovery of viruses in echinoderms and discussed the relationship between viruses and diseases for the first time. We further summarized the research progress of the potential immune-related genes and signal pathways induced by viruses and poly (I:C). Additionally, numbers of studies showed that active substances extracted from echinoderms, or the compounds synthesized from these substances, have significant antihuman virus ability. This result suggests that the active substances derived from echinoderms provide potential antiviral protection for the organism, which may provide future research directions for the antiviral immunity of echinoderms. Thus, this review also collected information on the antiviral activities of biologically active substances from echinoderms, which may pave the way for new trends in antiviral immunity for echinoderms and antiviral drugs in humans.