Hiding from heat: The transcriptomic response of two clam species is modulated by behaviour and habitat.

Rising occurrence of extreme warming events are profoundly impacting ecosystems, altering their functioning and services with significant socio-economic consequences. Particularly susceptible to heatwaves are intertidal shellfish beds, located in estuarine areas already stressed by factors such as rainfall events, red tides, eutrophication, and pollution. In Galicia, Northwestern Spain, these beds support vital shellfisheries, featuring the native clam Ruditapes decussatus and the non-indigenous R. philippinarum. Over recent decades, these populations have experienced notable abundance shifts due to various anthropogenic impacts, including climate change. In this habitat, patches of the seagrass Zostera noltei that coexist with bare sand can act as thermal refuges for benthic organisms such as clams. To assess the impact of heatwaves on these ecosystems, a mesocosm experiment was conducted. Juveniles of both clam species in two habitat types-bare sand and sand with Z. noltei-were exposed to simulated atmospheric heatwaves during diurnal low tide for four consecutive days. Subsequent transcriptomic analysis revealed that high temperatures had a more pronounced impact on the transcriptome of R. philippinarum compared to R. decussatus. The habitat type played a crucial role in mitigating heat stress in R. philippinarum, with the presence of Z. noltei notably ameliorating the transcriptomic response. These findings have direct applications in shellfishery management, emphasizing the importance of preserving undisturbed patches of Z. noltei as thermal refuges, contributing to the mitigation of heatwave effects on shellfish populations.

Selective Killing of BRCA2-Deficient Ovarian Cancer Cells via MRE11 Blockade.

The MRE11 nuclease is essential during DNA damage recognition, homologous recombination, and replication. BRCA2 plays important roles during homologous recombination and replication. Here, we show that effecting an MRE11 blockade using a prototypical inhibitor (Mirin) induces synthetic lethality (SL) in BRCA2-deficient ovarian cancer cells, HeLa cells, and 3D spheroids compared to BRCA2-proficient controls. Increased cytotoxicity was associated with double-strand break accumulation, S-phase cell cycle arrest, and increased apoptosis. An in silico analysis revealed Mirin docking onto the active site of MRE11. While Mirin sensitises DT40 MRE11+/- cells to the Top1 poison SN-38, it does not sensitise nuclease-dead MRE11 cells to this compound confirming that Mirin specifically inhibits Mre11 nuclease activity. MRE11 knockdown reduced cell viability in BRCA2-deficient PEO1 cells but not in BRCA2-proficient PEO4 cells. In a Mirin-resistant model, we show the downregulation of 53BP1 and DNA repair upregulation, leading to resistance, including in in vivo xenograft models. In a clinical cohort of human ovarian tumours, low levels of BRCA2 expression with high levels of MRE11 co-expression were linked with worse progression-free survival (PFS) (p = 0.005) and overall survival (OS) (p = 0.001). We conclude that MRE11 is an attractive SL target, and the pharmaceutical development of MRE11 inhibitors for precision oncology therapeutics may be of clinical benefit.

Designer matrices for intestinal stem cell and organoid culture.

Epithelial organoids recapitulate multiple aspects of real organs, making them promising models of organ development, function and disease. However, the full potential of organoids in research and therapy has remained unrealized, owing to the poorly defined animal-derived matrices in which they are grown. Here we used modular synthetic hydrogel networks to define the key extracellular matrix (ECM) parameters that govern intestinal stem cell (ISC) expansion and organoid formation, and show that separate stages of the process require different mechanical environments and ECM components. In particular, fibronectin-based adhesion was sufficient for ISC survival and proliferation. High matrix stiffness significantly enhanced ISC expansion through a yes-associated protein 1 (YAP)-dependent mechanism. ISC differentiation and organoid formation, on the other hand, required a soft matrix and laminin-based adhesion. We used these insights to build a fully defined culture system for the expansion of mouse and human ISCs. We also produced mechanically dynamic matrices that were initially optimal for ISC expansion and subsequently permissive to differentiation and intestinal organoid formation, thus creating well-defined alternatives to animal-derived matrices for the culture of mouse and human stem-cell-derived organoids. Our approach overcomes multiple limitations of current organoid cultures and greatly expands their applicability in basic and clinical research. The principles presented here can be extended to identify designer matrices that are optimal for long-term culture of other types of stem cells and organoids.

Dynamic changes in DNA methylation during seahorse (Hippocampus reidi) postnatal development and settlement.

INTRODUCTION: Most living marine organisms have a biphasic life cycle dependent on metamorphosis and settlement. These critical life-history events mean that a developmentally competent larva undergoes a range of coordinated morphological and physiological changes that are in synchrony with the ecological transition from a pelagic to a benthonic lifestyle. Therefore, transition from a pelagic to a benthonic habitat requires multiple adaptations, however, the underlying mechanisms regulating this process still remains unclear. Epigenetic regulation and specifically DNA methylation, has been suggested to be particularly important for organisms to adapt to new environments. Seahorses (Family Syngnathidae, Genus Hippocampus) are a fascinating group of fish, distinguished by their unique anatomical features, reproductive strategy and behavior. They are unique among vertebrate species due to their "male pregnancy", where males nourish developing embryos and larvae in a brood pouch until hatching and parturition occurs. After birth, free-swimming offspring are pelagic and subsequently they change into a demersal lifestyle. Therefore, to begin to address the question whether epigenetic processes could be involved in the transition from a planktonic to a benthonic lifestyle observed in seahorses, we studied global DNA methylation profiles in a tropical seahorse species (Hippocampus reidi) during postnatal development and settlement. RESULTS: We performed methylation-sensitive amplified polymorphism (MSAP) along with quantitative expression analysis for genes suggested to be involved in the methylation machinery at six age groups: 1, 5, 10, 20, 30 and 40 days after male's pouch release (DAR). Results revealed that the H. reidi genome has a significantly different DNA methylation profile during postnatal development and settlement on demersal habitats. Moreover, gene expression analysis showed up- and down-regulation of specific DNA methyltransferases (DNMTs) encoding genes. CONCLUSION: Our data show that the differences in the DNA methylation patterns seen among developmental stages and during the transition from a pelagic to a benthonic lifestyle suggest a potential for epigenetic regulation of gene expression (through DNA methylation) in this species. Therefore, epigenetic mechanisms could be necessary for seahorse settlement. Nevertheless, if these epigenetic mechanisms come from internal or if they are initiated via external environmental cues should be further investigated.

Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data.

BACKGROUND: A complete understanding of the genetic basis for sexual determination and differentiation is necessary in order to implement efficient breeding schemes at early stages of development. Atlantic salmon belongs to the family Salmonidae of fishes and represents a species of great commercial value. Although the species is assumed to be male heterogametic with XY sex determination, the precise genetic basis of sexual development remains unclear. The complexity is likely associated to the relatively recent salmonid specific whole genome duplication that may be responsible for certain genome instability. This instability together with the capacity of the sex-determining gene to move across the genome as reported by previous studies, may explain that sexual development genes are not circumscribed to the same chromosomes in all members of the species. In this study, we have used a 220 K SNP panel developed for Atlantic salmon to identify the chromosomes explaining the highest proportion of the genetic variance for sex as well as candidate regions and genes associated to sexual development in this species. RESULTS: Results from regional heritability analysis showed that the chromosomes explaining the highest proportion of variance in these populations were Ssa02 (heritability = 0.42, SE = 0.12) and Ssa21 (heritability = 0.26, SE = 0.11). After pruning by linkage disequilibrium, genome-wide association analyses revealed 114 SNPs that were significantly associated with sex, being Ssa02 the chromosome containing a greatest number of regions. Close examination of the candidate regions evidenced important genes related to sex in other species of Class Actinopterygii, including SDY, genes from family SOX, RSPO1, ESR1, U2AF2A, LMO7, GNRH-R, DND and FIGLA. CONCLUSIONS: The combined results from regional heritability analysis and genome-wide association have provided new advances in the knowledge of the genetic regulation of sex determination in Atlantic salmon, supporting that Ssa02 is the candidate chromosome for sex in this species and suggesting an alternative population lineage in Spanish wild populations according to the results from Ssa21.

Cross-Tissue Identification of Somatic Stem and Progenitor Cells Using a Single-Cell RNA-Sequencing Derived Gene Signature.

A long-standing question in biology is whether multipotent somatic stem and progenitor cells (SSPCs) feature molecular properties that could guide their system-independent identification. Population-based transcriptomic studies have so far not been able to provide a definite answer, given the rarity and heterogeneous nature of these cells. Here, we exploited the resolving power of single-cell RNA-sequencing to develop a computational model that is able to accurately distinguish SSPCs from differentiated cells across tissues. The resulting classifier is based on the combined expression of 23 genes including known players in multipotency, proliferation, and tumorigenesis, as well as novel ones, such as Lcp1 and Vgll4 that we functionally validate in intestinal organoids. We show how this approach enables the identification of stem-like cells in still ambiguous systems such as the pancreas and the epidermis as well as the exploration of lineage commitment hierarchies, thus facilitating the study of biological processes such as cellular differentiation, tissue regeneration, and cancer. Stem Cells 2017;35:2390-2402.

Pth4, an ancient parathyroid hormone lost in eutherian mammals, reveals a new brain-to-bone signaling pathway.

Regulation of bone development, growth, and remodeling traditionally has been thought to depend on endocrine and autocrine/paracrine modulators. Recently, however, brain-derived signals have emerged as key regulators of bone metabolism, although their mechanisms of action have been poorly understood. We reveal the existence of an ancient parathyroid hormone (Pth)4 in zebrafish that was secondarily lost in the eutherian mammals' lineage, including humans, and that is specifically expressed in neurons of the hypothalamus and appears to be a central neural regulator of bone development and mineral homeostasis. Transgenic fish lines enabled mapping of axonal projections leading from the hypothalamus to the brainstem and spinal cord. Targeted laser ablation demonstrated an essential role for of pth4-expressing neurons in larval bone mineralization. Moreover, we show that Runx2 is a direct regulator of pth4 expression and that Pth4 can activate cAMP signaling mediated by Pth receptors. Finally, gain-of-function experiments show that Pth4 can alter calcium/phosphorus levels and affect expression of genes involved in phosphate homeostasis. Based on our discovery and characterization of Pth4, we propose a model for evolution of bone homeostasis in the context of the vertebrate transition from an aquatic to a terrestrial lifestyle.-Suarez-Bregua, P., Torres-Nuñez, E., Saxena, A., Guerreiro, P., Braasch, I., Prober, D. A., Moran, P., Cerda-Reverter, J. M., Du, S. J., Adrio, F., Power, D. M., Canario, A. V. M., Postlethwait, J. H., Bronner, M E., Cañestro, C., Rotllant, J. Pth4, an ancient parathyroid hormone lost in eutherian mammals, reveals a new brain-to-bone signaling pathway.

Autolysosomal ß-catenin degradation regulates Wnt-autophagy-p62 crosstalk.

The Wnt/ß-catenin signalling and autophagy pathways each play important roles during development, adult tissue homeostasis and tumorigenesis. Here we identify the Wnt/ß-catenin signalling pathway as a negative regulator of both basal and stress-induced autophagy. Manipulation of ß-catenin expression levels in vitro and in vivo revealed that ß-catenin suppresses autophagosome formation and directly represses p62/SQSTM1 (encoding the autophagy adaptor p62) via TCF4. Furthermore, we show that during nutrient deprivation ß-catenin is selectively degraded via the formation of a ß-catenin-LC3 complex, attenuating ß-catenin/TCF-driven transcription and proliferation to favour adaptation during metabolic stress. Formation of the ß-catenin-LC3 complex is mediated by a W/YXXI/L motif and LC3-interacting region (LIR) in ß-catenin, which is required for interaction with LC3 and non-proteasomal degradation of ß-catenin. Thus, Wnt/ß-catenin represses autophagy and p62 expression, while ß-catenin is itself targeted for autophagic clearance in autolysosomes upon autophagy induction. These findings reveal a regulatory feedback mechanism that place ß-catenin at a key cellular integration point coordinating proliferation with autophagy, with implications for targeting these pathways for cancer therapy.

Matricellular protein SPARC/osteonectin expression is regulated by DNA methylation in its core promoter region.

BACKGROUND: SPARC/osteonectin is an evolutionarily conserved matricellular protein that modulates cell-matrix interaction and cell function. In all vertebrates, SPARC is dynamically expressed during embryogenesis. However, the precise function of SPARC and the regulatory elements required for its expression in particular during early embryogenesis are largely unknown. RESULTS: The present study was undertaken to explore the molecular mechanisms that regulate sparc gene expression by in vivo functional characterization of the sparc promoter and identification of possible putative regulatory elements that govern basal promoter activity. We report here transient expression analyses of eGFP expression from transgenic zebrafish containing a Sparc-iTol2-eGFP-BAC and/or 7.25 kb-sparc-Tol2-eGFP constructs. eGFP expression was specifically found in the notochord, otic vesicle, fin fold, intermediate cell mass, and olfactory placode of BAC and Tol2 transposon vectors injected embryos. Deletion analysis revealed that promoter activity resides in the unique 5'-untranslated intronic region. Computer-based analysis revealed a putative CpG island immediately proximal to the translation start site within the intron sequence. Global inhibition of methylation with 5-Aza-2-deoxycytidine promoted sparc expression in association with decreasing CpG methylation. CONCLUSIONS: Taken together, these data identify a contributory role for DNA methylation in regulating sparc expression in zebrafish embryogenesis.

Epigenetic regulation of sex ratios may explain natural variation in self-fertilization rates.

Self-fertilization (selfing) favours reproductive success when mate availability is low, but renders populations more vulnerable to environmental change by reducing genetic variability. A mixed-breeding strategy (alternating selfing and outcrossing) may allow species to balance these needs, but requires a system for regulating sexual identity. We explored the role of DNA methylation as a regulatory system for sex-ratio modulation in the mixed-mating fish Kryptolebias marmoratus. We found a significant interaction between sexual identity (male or hermaphrodite), temperature and methylation patterns when two selfing lines were exposed to different temperatures during development. We also identified several genes differentially methylated in males and hermaphrodites that represent candidates for the temperature-mediated sex regulation in K. marmoratus. We conclude that an epigenetic mechanism regulated by temperature modulates sexual identity in this selfing species, providing a potentially widespread mechanism by which environmental change may influence selfing rates. We also suggest that K. marmoratus, with naturally inbred populations, represents a good vertebrate model for epigenetic studies.

Heterozygosity-fitness correlations in a declining seabird population.

Loss of genetic diversity is thought to lead to increased risk of extinction in endangered populations due to decreasing fitness of homozygous individuals. Here, we evaluated the presence of inbreeding depression in a long-lived seabird, the European shag (Phalacrocorax aristotelis), after a severe decline in population size by nearly 70%. During three reproductive seasons, 85 breeders were captured and genotyped at seven microsatellite loci. Nest sites were monitored during the breeding season to estimate reproductive success as the number of chicks surviving to full-size-grown per nest. Captured birds were tagged with a ring with an individual code, and resighting data were collected during 7-year period. We found a strong effect of multilocus heterozygosity on female reproductive performance, and a significant, although weaker, effect on breeder survival. However, our matrix population model suggests that this relatively small effect of genetic diversity on breeder survival may have a profound effect on fitness. This highlights the importance of integrating life history consequences in HFC studies. Importantly, heterozygosity was correlated across loci, suggesting that genomewide effects, rather than single loci, are responsible for the observed HFCs. Overall, the HFCs are a worrying symptom of genetic erosion in this declining population. Many long-lived species are prone to extinction, and future studies should evaluate the magnitude of fitness impact of genetic deterioration on key population parameters, such as survival of breeders.

Cytogenetic evidences of genome rearrangement and differential epigenetic chromatin modification in the sea lamprey (Petromyzon marinus).

This work explores both the chromatin loss and the differential genome methylation in the sea lamprey (Petromyzon marinus) from a molecular cytogenetic point of view. Fluorescent in situ hybridization experiments on meiotic bivalents and mitotic chromosomes corroborate the chromatin loss previously observed during the development of the sea lamprey and demonstrate that the elimination affects not only to Germ1 sequences but also to the rpt200 satellite DNA and most part of the major ribosomal DNA present on the germinal line. 5-Methylcytosine immunolocation revealed that the GC-rich heterochromatin is highly methylated in the germ line but significantly less in somatic chromosomes. These findings not only support previous observations about genome rearrangements but also give new information about epigenetic changes in P. marinus. The key position of lampreys in the vertebrate phylogenetic tree makes them an interesting taxon to provide relevant information about genome evolution in vertebrates.

Karyotypic diversification in Mytilus mussels (Bivalvia: Mytilidae) inferred from chromosomal mapping of rRNA and histone gene clusters.

BACKGROUND: Mussels of the genus Mytilus present morphologically similar karyotypes that are presumably conserved. The absence of chromosome painting probes in bivalves makes difficult verifying this hypothesis. In this context, we comparatively mapped ribosomal RNA and histone gene families on the chromosomes of Mytilus edulis, M. galloprovincialis, M. trossulus and M. californianus by fluorescent in situ hybridization (FISH). RESULTS: Major rRNA, core and linker histone gene clusters mapped to different chromosome pairs in the four taxa. In contrast, minor rRNA gene clusters showed a different behavior. In all Mytilus two of the 5S rDNA clusters mapped to the same chromosome pair and one of them showed overlapping signals with those corresponding to one of the histone H1 gene clusters. The overlapping signals on mitotic chromosomes became a pattern of alternate 5S rRNA and linker histone gene signals on extended chromatin fibers. Additionally, M. trossulus showed minor and major rDNA clusters on the same chromosome pair. CONCLUSION: The results obtained suggest that at least some of the chromosomes bearing these sequences are orthologous and that chromosomal mapping of rRNA and histone gene clusters could be a good tool to help deciphering some of the many unsolved questions in the systematic classification of Mytilidae.

ß-catenin represses expression of the tumour suppressor 15-prostaglandin dehydrogenase in the normal intestinal epithelium and colorectal tumour cells.

BACKGROUND: Cyclooxygenase-2 (COX-2) overexpression in colorectal cancer increases levels of its pro-tumorigenic product prostaglandin E2 (PGE(2)). The recently identified colorectal tumour suppressor 15-prostaglandin dehydrogenase (15-PGDH) catalyses prostaglandin turnover and is downregulated at a very early stage in colorectal tumorigenesis; however, the mechanism responsible remains unclear. As Wnt/ß-catenin signalling is also deregulated early in colorectal neoplasia, a study was undertaken to determine whether ß-catenin represses 15-PGDH expression. METHODS: The effect of modulating Wnt/ß-catenin signalling (using ß-catenin siRNA, mutant TCF4, Wnt3A or GSK3 inhibition) on 15-PGDH mRNA, protein expression and promoter activity was determined in colorectal cell lines by immunoblotting, qRT-PCR and reporter assays. The effect of ß-catenin deletion in vivo was addressed by 15-PGDH immunostaining of ß-catenin(-/lox)-villin-creERT2 mouse tissue. 15-PGDH promoter occupancy was determined using chromatin immunoprecipitation and PGE(2) levels by ELISA. RESULTS: The study shows for the first time that ß-catenin knockdown upregulates 15-PGDH in colorectal adenoma and carcinoma cells without affecting COX-2 protein levels. A dominant negative mutant form of TCF4 (dnTCF4), unable to bind ß-catenin, also upregulated 15-PGDH; conversely, increasing ß-catenin activity using Wnt3A or GSK3 inhibition downregulated 15-PGDH. Importantly, inducible ß-catenin deletion in vivo also upregulated intestinal epithelial 15-PGDH. 15-PGDH regulation occurred at the protein, mRNA and promoter activity levels and chromatin immunoprecipitation indicated ß-catenin/TCF4 binding to the 15-PGDH promoter. ß-catenin knockdown decreased PGE(2) levels, and this was significantly rescued by 15-PGDH siRNA. CONCLUSION: These data suggest a novel role for ß-catenin in promoting colorectal tumorigenesis through very early 15-PGDH suppression leading to increased PGE(2) levels, possibly even before COX-2 upregulation.

What's my hamburger meat made of?

Outreach activities give high school students an opportunity to better understand the techniques and strategies used by researchers. Here is an experience with high school students designed to familiarize them with genetic methodologies. Students have been challenged to discover whether restaurant beef burgers are made with female or male beef. This represents a didactic way to introduce students to genetic traceability methodologies and also to demonstrate the usefulness of these methodologies in relation to food safety and, more importantly, in sustaining consumer confidence. The exercise is planned to be conducted in a one-day laboratory session.

Differentiated Epithelial Cells of the Gut.

The intestine is a prime example of self-renewal where stem cells give rise to progenitor cells called transit-amplifying cells which differentiate into more specialized cells. There are two intestinal lineages: the absorptive (enterocytes and microfold cells) and the secretory (Paneth cells, enteroendocrine, goblet cells, and tuft cells). Each of these differentiated cell types has a role in creating an "ecosystem" to maintain intestinal homeostasis. Here, we summarize the main roles of each cell type.

Intestinal Cell Differentiation and Phenotype in 2D and 3D Cell Culture Models.

Three-dimensional (3D) culture models are more physiologically relevant than two-dimensional (2D) cell culture models. 2D approaches cannot reproduce the complexity of the tumor microenvironment and are less able to translate biological insights; and drug response studies have many limitations to be extrapolated to the clinics. Here, we use the Caco-2 colon cancer cell line, which is an immortalized human epithelial cell line that under specific conditions can polarize and differentiate into a villus-like phenotype. We describe cell differentiation and cell growth in both 2D and 3D culture conditions, concluding that cell morphology, polarity, proliferation and differentiation are highly dependent on the type of cell culture system.

Novel Approach to Measure Transepithelial Electrical Resistance in Intestinal Cells.

The technique electric cell-substrate impedance sensing (ECIS) can be used to detect and monitor the behavior of intestinal cells. The methodology presented was designed to achieve results within a short time frame, and it was tailored to use a colonic cancer cell line. Differentiation of intestinal cancer cells has previously been reported to be regulated by retinoic acid (RA). Here, colonic cancer cells were cultured in the ECIS array before being treated with RA, and any changes in response to RA were monitored after treatment. The ECIS recorded changes in impedance in response to the treatment and vehicle. This methodology poses as a novel way to record the behavior of colonic cells and opens new avenues for in vitro research.

In Vitro and in Vivo Assays for Testing Retinoids Effect on Intestinal Progenitors' Lineage Commitments.

The intestine consists of epithelial cells surrounded by a complex environment as mesenchymal cells and the gut microbiota. With its impressive stem cell regeneration capability, the intestine is able to constantly replenish cells lost through apoptosis or abrasion by food passing through. Over the past decade, researchers have identified signaling pathways involved in stem cell homeostasis such as retinoids pathway. Retinoids are also involved in cell differentiation of healthy and cancer cells. In this study, we describe several approaches in vitro and in vivo to further investigate the effect of retinoids on stem cells, progenitors, and differentiated intestinal cells.

Design, synthesis, evaluation, and structure of vitamin D analogues with furan side chains.

Based on the crystal structures of human vitamin D receptor (hVDR) bound to 1α,25-dihydroxy-vitamin D(3) (1,25 D) and superagonist ligands, we previously designed new superagonist ligands with a tetrahydrofuran ring at the side chain that optimize the aliphatic side-chain conformation through an entropy benefit. Following a similar strategy, four novel vitamin D analogues with aromatic furan side chains (3a, 3b, 4a, 4b) have now been developed. The triene system has been constructed by an efficient stereoselective intramolecular cyclization of an enol triflate (A-ring precursor) followed by a Suzuki-Miyaura coupling of the resulting intermediate with an alkenyl boronic ester (CD-side chain, upper fragment). The furan side chains have been constructed by gold chemistry. These analogues exhibit significant pro-differentiation effects and transactivation potency. The crystal structure of 3a in a complex with the ligand-binding domain of hVDR revealed that the side-chain furanic ring adopts two conformations.