Biology subjects

Eeckhaut, I.

Publications and source records attributed to Eeckhaut, I..

6 recordsLinked to original sources

bioRxiv2026

Single-cell transcriptomics reveals transcriptional diversity of sea cucumber perivisceral fluid coelomocytes

Echinoderms possess a complex immune system, primarily relying on coelomocytes - immune cells circulating in coelomic fluids. Over the last few decades, various coelomocytes have been described based on morphological features, with holothuroids exhibiting the highest diversity of cell morphotypes among the different echinoderm classes. However, while the overall immune function of these cells is broadly accepted, their respective functions remain unclear, and molecular data specific to the different cell types are still limited in the literature. In this study, we address this gap in functional information and molecular data by using single-cell RNA sequencing (scRNA-seq) on coelomocytes from the perivisceral fluid of Holothuria forskali. We identified 10 distinct clusters, each assumed to correspond to a distinct transcriptional coelomocyte population. Among these, cluster 0 occupies a central position relative to the others, suggesting it may represent "progenitor cells", whereas cluster 6 is markedly divergent from all other clusters. Functional enrichment analyses revealed that some clusters ensure key immune functions, including pathogen recognition, phagocytosis, complement activation and redox balance regulation. In addition, examination of the processed samples under a microscope confirms the presence of a small proportion of recently discovered carotenocytes (7.0%) in the perivisceral fluid, a cell type rich in carotenoids. By using transcriptomics data previously obtained for this cell type by bulk RNA sequencing (bRNA-seq), it was possible to confidently identify cluster 6 as carotenocytes and provide further insights into their gene expression. While further analyses are needed to link other clusters to the different morphotypes previously described in the literature, this pioneer study presents preliminary data on the functional diversity of holothuroid coelomocytes, which could be of broad interest for a better understanding of holothuroid immunity as well as for the study of immune cell lineage evolution across deuterostomes.

evolutionary biology↗

bioRxiv2025

Carotenoid-based immune response in sea cucumbers relies on newly identified coelomocytes -- the carotenocytes

Sea cucumbers (Holothuroidea, Echinodermata) are marine deuterostomes possessing a complex innate immune system composed of a wide diversity of immune cells--coelomocytes, making them compelling models for exploring the evolution of immunity. This study investigates the functional specialisation of coelomocytes within the two main echinoderm body fluids, namely the perivisceral fluid (PF) from the perivisceral cavity and the hydrovascular fluid (HF) from the hydrovascular-- ambulacral system. Given their specific distribution restricted to the HF, hemocyte-like cells (HELs) are particularly investigated. In echinoderms, hemocytes have been described as reddish cells containing haemoglobin and thus presenting a function in oxygen transport. Using an integrative approach combining cell morphological analyses, pigment profiling and multi-omics technologies, we demonstrate, in the sea cucumber Holothuria forskali, that HELs harbour exceptionally high concentrations of carotenoids, primarily canthaxanthin and astaxanthin--potent antioxidant molecules responsible for their pigmentation. Transcriptomics and proteomics analyses reveal that HELs express candidate genes involved in the carotenoid metabolism pathway as well as catalase, an antioxidant enzyme. Additionally, spectral flow cytometry assays reveal that HELs do not produce reactive oxygen species in contrast to most coelomocyte types, reinforcing the hypothesis of their antioxidant function. HELs also contribute to the formation of large red bodies (i.e., coelomocyte aggregates) and increase in concentration following lipopolysaccharide injections, indicating an active role in immune defence. Given these results, we hypothesise that these cells act after the culmination of the immune response, forming an antioxidant shell around the cellular aggregates to mitigate oxidative stress from reactive oxygen species (ROS) produced within the aggregate while encapsulating pathogens, thus protecting the host tissues. The discovery of carotenoid-carrying coelomocytes constitutes the first report of pigmented coelomocytes in sea cucumbers (except respiratory pigments), challenging the long-standing assumption that these cells contain haemoglobin. Therefore, we propose renaming hemocytes into carotenocytes, at least in this species. However, we think that this newly described coelomocyte type has been wrongly identified as haemoglobin-containing cells in many previous studies and could be present in many other holothuroid species. Our findings thus establish a new paradigm in the study of coelomocytes in echinoderms as well as the function of the hydrovascular system, unique to this phylum.

evolutionary biology↗

bioRxiv2024

Opsin-based photoreception in Crinoids

Opsins are essential photoreceptor proteins that enable both visual and nonvisual light perception in metazoans. Although extensively studied in eyed invertebrates, their role in eyeless organisms such as echinoderms remains underexplored. Within the echinoderm phylum, studies have primarily focused on sea stars, sea urchins, and brittle stars, leaving crinoids, the most basal echinoderm lineage, entirely unexplored. Currently, only a limited number of behavioural observations have suggested that crinoids may possess light sensitivity. This study investigated the behavioural, morphofunctional, and molecular foundations of opsin-based photoreception in Antedon bifida, a European crinoid species from the comatulid order. In this context, the behavioural response to different light wavelengths, characterisation of opsin genes in the recent chromosome-scale genome of this species, opsin immunolocalisation within the crinoid tissues, and in vitro functional characterisation of opsins have been investigated. In vivo tests indicated significant negative phototactic behaviour induced by a wide range of light wavelengths (463-630 nm) with maximum sensitivity to blue light ({lambda}max = 463 nm). In silico genome analyses revealed the presence of only three rhabdomeric opsin genes, located on chromosomes 4 (Abif-opsin 4.1) and 6 (Abif-opsin 4.2 and 4.3). All crinoid opsins were phylogenetically clustered as a sister group to all other echinoderm rhabdomeric opsins, supporting their evolution via duplication of an ancestral gene in the crinoid lineage. The low opsin diversity contrasts with that of other echinoderms, which are generally characterised by up to eight bilaterian opsin types. Interestingly, A. bifida opsin sequences present typical amino acid residues of rhabdomeric opsins of other bilaterians, including two conserved cysteines (C110 and C187), the probable ancestral E181 counterion, the typical G-protein signalling NPxxY(x)6F pattern, a highly conserved lysine potentially covalently bound to a chromophore, and the (D)RY motif, all of which support a photoreceptive function. Heterologous in vitro expression in HEK293T cell cultures subsequently confirmed the photoreceptive function of all three A. bifida opsins. Indeed, these three crinoid opsins formed active complexes with 11, cis-retinal association, and once purified, showed different absorbance peaks in the short wavelengths of the visible light spectrum ranging from 425 to 520 nm. Finally, immunoreactivity to newly generated antibodies against sea star opsins highlighted two potential crinoid opsins in several tissues associated with the ambulacral grooves of the calyx and pinnules. Within these tissues, one Abif-opsin is potentially expressed both in the ectoneural basiepithelial nerve plexus and in the hyponeural nerve plexus. However, a different opsin is also expressed in the sensory papillae of tube feet. Localisation of at least two opsins in different sensory structures suggests the presence of a complex extraocular photoreception system based exclusively on rhabdomeric opsins in this crinoid species.

zoology↗

bioRxiv2021

Integument transcriptome profile of the European sea cucumber Holothuria forskali (Holothuroidea, Echinodermata)

In non-model organisms, Next Generation Sequencing (NGS) technology improve our ability to analyze gene expression and identify new genes or transcripts of interest. In this research, paired-end Illumina HiSeq sequencing has been used to describe a composite transcriptome based on two libraries generated from dorsal and ventral integuments of the European sea cucumber Holothuria forskali (Holothuroidea, Echinodermata). A total of 43,044,977 million HQ reads were initially generated. After de novo assembly, a total of 111,194 unigenes were predicted. On all predicted unigenes, 32,569 show significant matches with genes/proteins present in the reference databases. Around 50% of annotated unigenes were significantly similar to sequences from the purple sea urchin Strongylocentrotus purpuratus genome. Annotation analyses were performed on predicted unigenes using public reference databases. These RNA-seq data provide an interesting resource for researchers with a broad interest in sea cucumber biology.

zoology↗

bioRxiv2021

Investigating densities of Symbiodiniaceae in two species of Antipatharians (black corals) from Madagascar

Here, we report the first methodological approach to investigate the presence and estimate the density of Symbiodiniaceae cells in corals of the order Antipatharia subclass Hexacorallia, known as black corals. Antipatharians are understudied ecosystem engineers of shallow (<30 m depth), mesophotic (30-150 m) and deep-sea (>200 m) reefs. They provide habitat to a vast number of marine fauna, enhancing and supporting coral reefs biodiversity globally. Nonetheless, little biological and ecological information exists on antipatharians, including the extent at which global change disturbances are threatening these corals. The assumption that they were exempted from threats related to climate change was challenged by findings of high density of dinoflagellates within three antipatharian colonies. Further methodical studies were necessary to investigate the regularity of these findings. An integrated design combining microscopy and molecular techniques was used to investigate the presence and estimate density of Symbiodiniaceae cells within two antipatharians species -Cupressopathes abies and Stichopathes maldivensis -from shallow and mesophotic reefs of SW Madagascar. Symbiodiniaceae-like cells were found within the two species from both shallow and mesophotic reefs, although the overall cell density was very low (0-4 cell mm-3). These findings suggest that high abundance of Symbiodiniaceae is not characteristic of antipatharians, which has relevant implications considering disruptions associated to climate change affecting other corals. However, the high densities of dinoflagellates found in antipatharian colonies exposed to higher light irradiance in other studies should be further examined.

molecular biology↗

bioRxiv2018

Thioredoxins induce oocyte maturation in holothuroids (Echinodermata)

Chromatographic fractions of a rough extract of echinoid spawn (REES) has been demonstrated to efficiently induce oocyte maturation in aspidochirote holothuroids. The method is so efficient that it is now used in holothuriculture to get fertilised eggs even outside the reproductive period of the aquacultured species. We here isolate and identify from echinoid spawns the molecule responsible for the induction of the oocyte maturation in the Mediterranean holothuroid Holothuria tubulosa and the Indo-Pacific Holothuria scabra. The use of proteinase K and dialysing membranes indicates that the active molecule is a protein with a molecular weight superior to 12,000 kDa. The active molecule has been isolated on G-100 Sephadex chromatography column. Active chromatographic fractions include seven proteins identified with nanoLC-MS/MS technique. One of them, identify as a thioredoxin-2 and to which the name Trx-REES has been given, leads up to levels of maturation similar to those obtained with the REES and with a commercial thioredoxin extracted from Escherichia coli. Occurrence of thioredoxin in REES was confirmed by immunoblot analysis, and the maturation-inducing properties of thioredoxin were positively checked in using anti-thioredoxin antibodies. A peptide of 6 AAs corresponding to the active site of Trx-REES, composed of WCNPCK, was synthesised and its efficiency in holothuroid oocyte maturation tested. At some concentrations, the peptide was 1.2 times more active than the REES.

zoology↗