Inorganic UV filter-based sunscreens labelled as eco-friendly threaten sea urchin populations

Although the negative effects of inorganic UV filters have been documented on several marine organisms, sunscreen products containing such filters are available in the market and proposed as eco-friendly substitutes for harmful, and already banned, organic UV filters (e.g. octinoxate and oxybenzone). In the present study, we investigated the effects of four sunscreen products, labelled by cosmetic companies as "eco-friendly", on the early developmental stages of the sea urchin Paracentrotus lividus, a keystone species occurring in vulnerable coastal habitats. Among sunscreens tested, those containing ZnO and TiO2 or their mix caused severe impacts on sea urchin embryos. We show that inorganic UV filters were incorporated by larvae during their development and, despite the activation of defence strategies (e.g. phagocytosis by coelomocytes), generated anomalies such as skeletal malformations and tissue necrosis. Conversely, the sunscreen product containing only new-generation organic UV filters (e.g. methylene bis-benzotriazolyl tetramethyl, ethylhexyl triazone, butylphenol diethylamino hydroxybenzoyl hexyl benzoate) did not affect sea urchins, thus resulting actually eco-compatible. Our findings expand information on the impact of inorganic UV filters on marine life, corroborate the need to improve the eco-friendliness assessment of sunscreen products and warn of the risk of bioaccumulation and potential biomagnification of inorganic UV filters along the marine food chain.

Abstract A12: Pervasive hypermutation of super-enhancer regions dysregulates oncogene expression in diffuse large B-cell lymphoma

Coding-genome sequencing efforts have identified several genes/pathways altered in Diffuse Large B-cell Lymphoma (DLBCL), including new potential therapeutic targets. However, the mutational contribution of the non-coding genome of DLBCL remains largely unexplored. To identify functionally relevant non-coding mutations targeting regulatory domains, we integrated enhancer (E)/super-enhancer (SE) identification, by ChIP-seq analysis of the hallmark H3K27 histone mark, with whole genome sequencing (WGS) and RNA-seq analysis in 29 DLBCL cell lines representative of the major DLBCL subtypes, along with germinal center (GC) B cells representing the normal counterpart of DLBCL. Following validation in 93 normal/tumor DLBCL biopsies, we found that active SEs are specifically hypermutated (≥3 somatic mutations/Kb) in 99% of DLBCLs, as compared to the same loci when not active as SE (in total, 159 hypermutated SEs, with at least 2/case). As evidence of oncogenic relevance, we have shown that the hypermutated SEs linked to the BCL6 and BCL2 proto-oncogenes prevent the binding and transcriptional downregulation by transcriptional repressors. Genetic correction of selected mutations using the CRISPR/Cas9 technology restored repressor DNA-binding, downregulated target gene expression, and led to the counter-selection of cells harboring corrected alleles, indicating oncogenic dependency from the SE mutations. A third recurrently hypermutated SE was the CXCR4-SE, affected in 19% of cases. CXCR4 encodes for a G-protein coupled chemokine receptor involved in cell migration within the GC, and is mutationally activated in 40% of Waldenström macrobulinemia (WM), a post-GC lymphoproliferative disease. We identified a mutational hotspot preventing the binding of the NR3C1 glucocorticoid receptor in 7.5% of DLBCL cases. Correction of the mutations in cell lines led to counter selection and reduced expression of CXCR4. Conversely, the introduction of a mutation disrupting NR3C1 binding in WT DLBCL cells increased CXCR4 expression. Together, these results are consistent with dependency of the mutant cells on the CXCR4-SE mutation, and confirm a direct link between SE mutations in this region and deregulated gene expression through escape from NR3C1-mediated suppression. In primary cases, mutations in the NR3C1 binding site of the CXCR4-SE were observed in the absence of NR3C1 coding mutations and correlated with increased CXCR4 transcript levels, as documented by RNA-seq. Together with the oncogenic role of CXCR4 in WM, these findings reveal this chemokine receptor as a potential oncogenic target in DLBCL. Collectively, these findings reveal a new layer of genetic alterations, which identifies novel mechanisms of dysregulation for known oncogenes, as well as new dysregulated genes and pathways, with implications for precision classification and therapeutic targeting of DLBCL. * Co-senior authors.

Citation Format: Elodie Bal, Rahul Kumar, Mohammad Hadigol, Antony B. Holmes, Laura K. Hilton, Jui Wan Loh, Kostiantyn Dreval, Jasper Wong, Sofija Vlasevska, Clarissa Corinaldesi, Rajesh Kumar Soni Soni, Katia Basso, Ryan D. Morin, Hossein Khiabanian, Laura Pasqualucci, Riccardo Dalla-Favera. Pervasive hypermutation of super-enhancer regions dysregulates oncogene expression in diffuse large B-cell lymphoma [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A12.

The Prostacyclin Analogue Iloprost Modulates CXCL10 in Systemic Sclerosis

The prostacyclin analogue iloprost is used to treat vascular alterations and digital ulcers, the early derangements manifesting in systemic sclerosis (SSc), an autoimmune disease leading to skin and organ fibrosis. Bioindicator(s) of SSc onset and progress are still lacking and the therapeutic approach remains a challenge. The T helper 1 (Th1) chemokine interferon (IFN)γ-induced protein 10 (IP-10/CXCL10) associates with disease progression and worse prognosis. Endothelial cells and fibroblasts, under Th1-dominance, release CXCL10, further enhancing SSc’s detrimental status. We analyzed the effect of iloprost on CXCL10 in endothelial cells, dermal fibroblasts, and in the serum of SSc patients. Human endothelial cells and dermal fibroblasts activated with IFNγ/Tumor Necrosis Factor (TNF)α, with/without iloprost, were investigated for CXCL10 secretion/expression and for intracellular signaling cascade underlying chemokine release (Signal Transducer and Activator of Transcription 1, STAT1; Nuclear Factor kappa-light-chain-enhancer of activated B cells, NF-kB; c-Jun NH₂-terminal kinase, JNK: Phosphatidyl-Inositol 3-kinase (PI3K)/protein kinase B, AKT; Extracellular signal-Regulated Kinase 1/2, ERK1/2). CXCL10 was quantified in sera from 25 patients taking iloprost, satisfying the American College of Rheumatology (ACR)/European Alliance of Associations for Rheumatology (EULAR) 2013 classification criteria for SSc, and in sera from 20 SSc sex/age-matched subjects without therapy, previously collected. In human endothelial cells and fibroblasts, iloprost targeted CXCL10, almost preventing IFNγ/TNFα-dependent cascade activation in endothelial cells. In SSc subjects taking iloprost, serum CXCL10 was lower. These in vitro and in vivo data suggest a potential role of iloprost to limit CXCL10 at local vascular/dermal and systemic levels in SSc and warrant further translational research aimed to ameliorate SSc understanding/management.

Super-enhancer hypermutation alters oncogene expression in B cell lymphoma

Diffuse large B cell lymphoma (DLBCL) is the most common B cell non-Hodgkin lymphoma and remains incurable in around 40% of patients. Efforts to sequence the coding genome identified several genes and pathways that are altered in this disease, including potential therapeutic targets1-5. However, the non-coding genome of DLBCL remains largely unexplored. Here we show that active super-enhancers are highly and specifically hypermutated in 92% of samples from individuals with DLBCL, display signatures of activation-induced cytidine deaminase activity, and are linked to genes that encode B cell developmental regulators and oncogenes. As evidence of oncogenic relevance, we show that the hypermutated super-enhancers linked to the BCL6, BCL2 and CXCR4 proto-oncogenes prevent the binding and transcriptional downregulation of the corresponding target gene by transcriptional repressors, including BLIMP1 (targeting BCL6) and the steroid receptor NR3C1 (targeting BCL2 and CXCR4). Genetic correction of selected mutations restored repressor DNA binding, downregulated target gene expression and led to the counter-selection of cells containing corrected alleles, indicating an oncogenic dependency on the super-enhancer mutations. This pervasive super-enhancer mutational mechanism reveals a major set of genetic lesions deregulating gene expression, which expands the involvement of known oncogenes in DLBCL pathogenesis and identifies new deregulated gene targets of therapeutic relevance.

Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.

Tracking Immunoglobulin Repertoire and Transcriptomic Changes in Germinal Center B Cells by Single-Cell Analysis

In response to T-cell-dependent antigens, mature B cells in the secondary lymphoid organs are stimulated to form germinal centers (GCs), which are histological structures deputed to antibody affinity maturation, a process associated with immunoglobulin gene editing by somatic hypermutation (SHM) and class switch recombination (CSR). GC B cells are heterogeneous and transition across multiple stages before being eliminated by apoptosis or committing to post-GC differentiation as memory B cells or plasma cells. In order to explore the dynamics of SHM and CSR during the GC reaction, we identified GC subpopulations by single-cell (sc) transcriptomics and analyzed the load of immunoglobulin variable (V) region mutations as well as the isotype class distribution in each subpopulation. The results showed that the large majority of GC B cells display a quantitatively similar mutational load in the V regions and analogous IGH isotype class distribution, except for the precursors of memory B cells (PreM) and plasma cells (PBL). PreM showed a bimodal pattern with about half of the cells displaying high V region germline identity and enrichment for unswitched IGH, while the rest of the cells carried a mutational load similar to the bulk of GC B cells and showed a switched isotype. PBL displayed a bias toward expression of IGHG and higher V region germline identity compared to the bulk of GC B cells. Genes implicated in SHM and CSR were significantly induced in specific GC subpopulations, consistent with the occurrence of SHM in dark zone cells and suggesting that CSR can occur within the GC.

Targeting human plasmacytoid dendritic cells through BDCA2 prevents skin inflammation and fibrosis in a novel xenotransplant mouse model of scleroderma

OBJECTIVES

Plasmacytoid dendritic cells (pDC) have been implicated in the pathogenesis of autoimmune diseases, such as scleroderma (SSc). However, this has been derived from indirect evidence using ex vivo human samples or mouse pDC in vivo. We have developed human-specific pDC models to directly identify their role in inflammation and fibrosis, as well as attenuation of pDC function with BDCA2-targeting to determine its therapeutic application.

METHODS

RNAseq of human pDC with TLR9 agonist ODN2216 and humanised monoclonal BDCA2 antibody, CBS004. Organotypic skin rafts consisting of fibroblasts and keratinocytes were stimulated with supernatant from TLR9-stimulated pDC and with CBS004. Human pDC were xenotransplanted into Nonobese diabetic/severe combined immunodeficiency (NOD SCID) mice treated with Aldara (inflammatory model), or bleomycin (fibrotic model) with CBS004 or human IgG control. Skin punch biopsies were used to assess gene and protein expression.

RESULTS

RNAseq shows TLR9-induced activation of human pDC goes beyond type I interferon (IFN) secretion, which is functionally inactivated by BDCA2-targeting. Consistent with these findings, we show that BDCA2-targeting of pDC can completely suppress in vitro skin IFN-induced response. Most importantly, xenotransplantation of human pDC significantly increased in vivo skin IFN-induced response to TLR agonist and strongly enhanced fibrotic and immune response to bleomycin compared with controls. In these contexts, BDCA2-targeting suppressed human pDC-specific pathological responses.

CONCLUSIONS

Our data indicate that human pDC play a key role in inflammation and immune-driven skin fibrosis, which can be effectively blocked by BDCA2-targeting, providing direct evidence supporting the development of attenuation of pDC function as a therapeutic application for SSc.

Muscle Damage in Systemic Sclerosis and CXCL10: The Potential Therapeutic Role of PDE5 Inhibition

Skeletal muscle damage is a common clinical manifestation of systemic sclerosis (SSc). C-X-C chemokine ligand 10 (CXCL10) is involved in myopathy and cardiomyopathy development and is associated with a more severe SSc prognosis. Interestingly, the phosphodiesterase type 5 inhibitor (PDE5i) sildenafil reduces CXCL10 sera levels of patients with diabetic cardiomyopathy and in cardiomyocytes. Here, we analyzed the levels of CXCL10 in the sera of 116 SSc vs. 35 healthy subjects and explored differences in 17 SSc patients on stable treatment with sildenafil. CXCL10 sera levels were three-fold higher in SSc vs. healthy controls, independent of subset and antibody positivity. Sildenafil treatment was associated with lower CXCL10 sera levels. Serum CXCL10 strongly correlated with the clinical severity of muscle involvement and with creatine kinase (CK) serum concentration, suggesting a potential involvement in muscle damage in SSc. In vitro, sildenafil dose-dependently reduced CXCL10 release by activated myocytes and impaired cytokine-induced Signal transducer and activator of transcription 1 (STAT1), Nuclear factor-κB (NFκB) and c-Jun N-terminal kinase (JNK) phosphorylation. This was also seen in cardiomyocytes. Sildenafil-induced CXCL10 inhibition at the systemic and human muscle cell level supports the hypothesis that PDE5i could be a potential therapeutic therapy to prevent and treat muscle damage in SSc.

Single-cell analysis of germinal-center B cells informs on lymphoma cell of origin and outcome

In response to T cell-dependent antigens, mature B cells are stimulated to form germinal centers (GCs), the sites of B cell affinity maturation and the cell of origin (COO) of most B cell lymphomas. To explore the dynamics of GC B cell development beyond the known dark zone and light zone compartments, we performed single-cell (sc) transcriptomic analysis on human GC B cells and identified multiple functionally linked subpopulations, including the distinct precursors of memory B cells and plasma cells. The gene expression signatures associated with these GC subpopulations were effective in providing a sc-COO for ∼80% of diffuse large B cell lymphomas (DLBCLs) and identified novel prognostic subgroups of DLBCL.

Long non-coding RNA HOTAIR induces GLI2 expression through Notch signalling in systemic sclerosis dermal fibroblasts

OBJECTIVES

Systemic sclerosis (SSc) is characterised by tissue fibrosis of the major organs of the body including the skin, lungs and heart. We have previously reported that the lncRNA HOTAIR plays a central role in the activation of SSc myofibroblasts, the key cellular elements of fibrosis. HOTAIR induces fibroblast activation through H3K27me3-mediated activation of the Notch signalling pathway. Here we aimed to identify the signalling events downstream of Notch that drive SSc myofibroblast activation.

METHODS

Patient fibroblasts were obtained from full-thickness forearm skin biopsies of 3 adult patients with SSc of recent onset. The lncRNA HOTAIR was expressed in healthy dermal fibroblasts by lentiviral transduction. Hedgehog signalling pathway was inhibited with GANT61 and GLI2 siRNA. Gamma secretase inhibitors RO4929097 and DAPT were used to block Notch signalling. GSK126 was used to inhibit Enhancer of Zeste 2 (EZH2).

RESULTS

Overexpression of HOTAIR in dermal fibroblasts induced the expression of the Hedgehog pathway transcription factor GLI2. This is mediated by activation of Notch signalling following epigenetic downregulation of miRNA-34a expression. Inhibition of H3K27 methylation and Notch signalling reduced expression of GLI2 in HOTAIR-expressing fibroblasts as well as in SSc dermal fibroblasts. Importantly, the inhibition of GLI2 function using GANT61 or siRNA mitigates the pro-fibrotic phenotype induced by HOTAIR.

CONCLUSIONS

Our data indicates that GLI2 expression is stably upregulated in SSc myofibroblasts through HOTAIR and that GLI2 mediates the expression of pro-fibrotic markers downstream of Notch.

Assessing the efficiency and eco-sustainability of bioremediation strategies for the reclamation of highly contaminated marine sediments

Coastal sediments subjected to high anthropogenic impacts can accumulate large amounts of polycyclic aromatic hydrocarbons (PAHs) and metals, demanding effective and eco-sustainable remediation solutions. In this study, we carried out bioremediation experiments on marine sediments highly contaminated with PAHs and metals. In particular, we investigated the effects of biostimulation (by the addition of inorganic nutrients), bioaugmentation (by the addition of fungi belonging to Aspergillus sp.) and microbial fuel cell-based strategies on PAH degradation and on changes in metal partitioning. Results reported here indicate that all biotreatments determined a significant decrease of PAH concentrations (at least 60%) in a relatively short time interval (few weeks) and that biostimulation was the most effective approach (>90%). Biostimulation determined a faster degradation rate of high than low molecular weight PAHs, indicating a preferential biodegradation of specific PAH congeners. At the same time, the biotreatments changed the partitioning of metals, including their solubilization, suggesting the need of parallel environmental risk assessment. Our findings also suggest that ex situ biotreatments can have a lower carbon footprint than current management options of contaminated sediments (i.e., landfill disposal and/or disposal in confined aquatic facilities), but integration with other strategies for metal removal (e.g. through bioleaching) from sediments is needed for their safe re-use. Overall, results presented here provide new insights into the development of effective and eco-sustainable bioremediation strategies for the reclamation of highly contaminated marine sediments.

Chemical contamination can promote turnover diversity of benthic prokaryotic assemblages: The case study of the Bagnoli-Coroglio bay (southern Tyrrhenian Sea)

Chemical contamination of marine ecosystems represents a major concern for the detrimental consequences at different levels of biological organization. However, the impact of chronic contamination on the diversity and assemblage composition of benthic prokaryotes is still largely unknown, and this limits our understanding of the potential implications on ecosystem functioning. The Bagnoli-Coroglio bay (Gulf of Naples, Tyrrhenian Sea) is a typical example of coastal area heavily contaminated by metals and hydrocarbons, released for decades by industrial activities, which ceased at the beginning of nineties. In the present study we analyzed the abundance, diversity and assemblage composition of benthic prokaryotic assemblages at increasing distance from the historical source of contamination in relation to the heavy hydrocarbons (C > 12), polycyclic aromatic hydrocarbons (PAHs) and heavy metal concentrations in the sediments. Prokaryotic abundance in the sediments differed among sites, and was mostly driven by environmental factors rather than by contamination levels. Conversely, the richness of prokaryotic taxa was relatively high in all samples, was driven by contamination levels and decreased significantly with increasing contamination (15-38%). Moreover, our results indicate large variations in the composition of the benthic prokaryotic assemblages among sites, mostly explained by the different levels and types of chemical contaminants found in the sediments. Overall, our findings suggest that chemical contaminants, even after decades from the end of their release, can profoundly influence the richness and turnover diversity of the benthic prokaryotic assemblages, in turn promoting a high diversification of the benthic bacterial and archaeal assemblages by selecting those lineages more adapted to specific mixtures of different contaminants. Our results open new perspectives for understanding of the long-term effects of chemical contamination on the benthic prokaryotic assemblages and the ecological processes they mediate.

Anthropogenic noise and biological sounds in a heavily industrialized coastal area (Gulf of Naples, Mediterranean Sea)

Underwater noise is one of the most widespread threats to the world oceans. Its negative impact on fauna is nowadays well established, but baseline data to be used in management and monitoring programs are still largely lacking. In particular, the acoustic assessment of human-impacted marine coastal areas provides complementary information on the health status of marine ecosystems. The objective of our study was to provide a baseline of underwater noise levels and biological sounds at two sites within the Gulf of Naples (Italy), one of which is located in Bagnoli-Coroglio, a Site of National Interest (SIN) for its high contamination levels. Within the SIN, sounds were recorded both before and during sediment coring activities (vibrocorer sampling), in order to investigate the potential acoustic impact due to such operations. Acoustic recordings were analyzed following the European Marine Strategy Framework Directive indications as defined in the frame of the Descriptor 11. Results reported here show that the investigated area is characterized by a high anthropogenic noise pressure. Ambient noise levels were principally driven by shipping noise and biological sounds of invertebrates (e.g., snapping shrimps). Sounds referable to other biological activity were difficult to detect because heavily masked by shipping noise. Coring activity determined a substantial introduction of additional noise at a local spatial scale. This study expands underwater noise baseline data to be further implemented in future monitoring programs of coastal areas affected by anthropogenic impacts. In addition, it proposes new cues for using underwater acoustic monitoring tools to complement traditional methodologies for evaluating health status of ecosystems and for investigating recovery rates after restoration/reclamation programs.

Impact of historical contamination on meiofaunal assemblages: The case study of the Bagnoli-Coroglio Bay (southern Tyrrhenian Sea)

The effects of contaminants on marine organisms have been documented since decades, but the long-term responses and recovery rates of benthic communities to mixtures of contaminants, several years after the cessation of industrial activities, need to be further investigated. Bagnoli-Coroglio Bay (Gulf of Naples, Tyrrhenian Sea) is a typical example of historically contaminated coastal area due to industrial activities stopped at the beginning of nineties. In the present study we carried out a fine spatial scale analysis of the distribution of meiofaunal (and nematodes) assemblages along five bathymetric transects located at increasing distance from the historical source of contamination in relation with the polycyclic aromatic hydrocarbon and heavy metal concentrations present in the sediment. Meiofaunal abundance and biomass changed widely along transects but independent from the distance from the source of contamination. Even when the contamination levels were expected to induce significant detrimental biological consequences, meiofaunal abundance and biomass were similar to those reported in unpolluted benthic coastal areas worldwide. Conversely, biodiversity in terms of meiofaunal taxa richness was generally low (range: 5-8 taxa in 12 of the overall 15 stations investigated). This was explained by the lack of sensitive groups such as ostracods, gastrotrichs and tardigrades commonly encountered in benthic coastal ecosystems, thus reflecting an overall poor/moderate environmental quality of the investigated area. Nematode (structural and functional) diversity was also low, particularly at stations characterized by higher contamination levels. At the same time, nematode species composition did not change significantly among stations suggesting a widespread effect of contaminants able to reduce the variability (i.e., turnover diversity) within the assemblages of the whole study area. Overall, our results indicate that even decades after the cessation of contaminant emissions, benthic biodiversity was affected in terms of both meiofaunal taxa and nematode species. These findings strongly reinforce the call for reducing sources of chronic pollution in marine ecosystems and provide new insights for a better understanding of the ecological recovery of historically contaminated marine environments.

The phosphodiesterase 5 inhibitor sildenafil decreases the proinflammatory chemokine IL-8 in diabetic cardiomyopathy: in vivo and in vitro evidence

PURPOSE

Interleukin (IL)-8 is a proinflammatory C-X-C chemokine involved in inflammation underling cardiac diseases, primary or in comorbid condition, such diabetic cardiomyopathy (DCM). The phosphodiesterase type 5 inhibitor sildenafil can ameliorate cardiac conditions by counteracting inflammation. The study aim is to evaluate the effect of sildenafil on serum IL-8 in DCM subjects vs. placebo, and on IL-8 release in human endothelial cells (Hfaec) and peripheral blood mononuclear cells (PBMC) under inflammatory stimuli.

METHODS

IL-8 was quantified: in sera of (30) DCM subjects before (baseline) and after sildenafil (100 mg/day, 3-months) vs. (16) placebo and (15) healthy subjects, by multiplatform array; in supernatants from inflammation-challenged cells after sildenafil (1 µM), by ELISA.

RESULTS

Baseline IL-8 was higher in DCM vs. healthy subjects (149.14 ± 46.89 vs. 16.17 ± 5.38 pg/ml, p < 0.01). Sildenafil, not placebo, significantly reduced serum IL-8 (23.7 ± 5.9 pg/ml, p < 0.05 vs. baseline). Receiver operating characteristic (ROC) curve for IL-8 was 0.945 (95% confidence interval of 0.772 to 1.0, p < 0.01), showing good capacity of discriminating the response in terms of drug-induced IL-8 decrease (sensitivity of 0.93, specificity of 0.90). Sildenafil significantly decreased IL-8 protein release by inflammation-induced Hfaec and PBMC and downregulated IL-8 mRNA in PBMC, without affecting cell number or PDE5 expression.

CONCLUSION

Sildenafil might be suggested as potential novel pharmacological tool to control DCM progression through IL-8 targeting at systemic and cellular level.

GLOSSary: the GLobal Ocean 16S subunit web accessible resource

BACKGROUND

Environmental metagenomics is a challenging approach that is exponentially spreading in the scientific community to investigate taxonomic diversity and possible functions of the biological components. The massive amount of sequence data produced, often endowed with rich environmental metadata, needs suitable computational tools to fully explore the embedded information. Bioinformatics plays a key role in providing methodologies to manage, process and mine molecular data, integrated with environmental metagenomics collections. One such relevant example is represented by the Tara Ocean Project.

RESULTS

We considered the Tara 16S miTAGs released by the consortium, representing raw sequences from a shotgun metagenomics approach with similarities to 16S rRNA genes. We generated assembled 16S rDNA sequences, which were classified according to their lengths, the possible presence of chimeric reads, the putative taxonomic affiliation. The dataset was included in GLOSSary (the GLobal Ocean 16S Subunit web accessible resource), a bioinformatics platform to organize environmental metagenomics data. The aims of this work were: i) to present alternative computational approaches to manage challenging metagenomics data; ii) to set up user friendly web-based platforms to allow the integration of environmental metagenomics sequences and of the associated metadata; iii) to implement an appropriate bioinformatics platform supporting the analysis of 16S rDNA sequences exploiting reference datasets, such as the SILVA database. We organized the data in a next-generation NoSQL "schema-less" database, allowing flexible organization of large amounts of data and supporting native geospatial queries. A web interface was developed to permit an interactive exploration and a visual geographical localization of the data, either raw miTAG reads or 16S contigs, from our processing pipeline. Information on unassembled sequences is also available. The taxonomic affiliations of contigs and miTAGs, and the spatial distribution of the sampling sites and their associated sequence libraries, as they are contained in the Tara metadata, can be explored by a query interface, which allows both textual and visual investigations. In addition, all the sequence data were made available for a dedicated BLAST-based web application alongside the SILVA collection.

CONCLUSIONS

GLOSSary provides an expandable bioinformatics environment, able to support the scientific community in current and forthcoming environmental metagenomics analyses.

Transforming Growth Factor β Activation Primes Canonical Wnt Signaling Through Down-Regulation of Axin-2

OBJECTIVE

Aberrant activation of Wnt signaling has been observed in tissues from patients with systemic sclerosis (SSc). This study aimed to determine the role of transforming growth factor β (TGFβ) in driving the increased Wnt signaling, through modulation of axis inhibition protein 2 (Axin-2), a critical regulator of the Wnt canonical pathway.

METHODS

Canonical Wnt signaling activation was analyzed by TOPflash T cell factor/lymphoid enhancer factor promoter assays. Axin-2 was evaluated in vitro by analysis of Axin-2 primary/mature transcript expression and decay, TGFβ receptor type I (TGFβRI) blockade, small interfering RNA-mediated depletion of tristetraprolin 1, and XAV-939-mediated Axin-2 stabilization. In vivo, Axin-2 messenger RNA (mRNA) and protein expression was determined in skin and lung biopsy samples from mice that express a kinase-deficient TGFβRII specifically on fibroblasts (TβRIIΔk-fib-transgenic mice) and from littermate controls.

RESULTS

SSc fibroblasts displayed an increased response to canonical Wnt ligands despite basal levels of Wnt signaling that were comparable to those in healthy control fibroblasts in vitro. Notably, we showed that SSc fibroblasts had reduced basal expression of Axin-2, which was caused by an endogenous TGFβ-dependent increase in Axin-2 mRNA decay. Accordingly, we observed that TGFβ decreased Axin-2 expression both in vitro in healthy control fibroblasts and in vivo in TβRIIΔk-fib-transgenic mice. Additionally, using Axin-2 gain- and loss-of-function experiments, we demonstrated that the TGFβ-induced increased response to Wnt activation characteristic of SSc fibroblasts depended on reduced bioavailability of Axin-2.

CONCLUSION

This study highlights the importance of reduced bioavailability of Axin-2 in mediating the increased canonical Wnt response observed in SSc fibroblasts. This novel mechanism extends our understanding of the processes involved in Wnt/β-catenin-driven pathology and supports the rationale for targeting the TGFβ pathway to regulate the aberrant Wnt signaling observed during fibrosis.

The phosphodiesterase 5 inhibitor tadalafil regulates lipidic homeostasis in human skeletal muscle cell metabolism

PURPOSE

Tadalafil seems to ameliorate insulin resistance and glucose homeostasis in humans. We have previously reported that tadalafil targets human skeletal muscle cells with an insulin (I)-like effect. We aim to evaluate in human fetal skeletal muscle cells after tadalafil or I: (i) expression profile of I-regulated genes dedicated to cellular energy control, glycolitic activity or microtubule formation/vesicle transport, as GLUT4, PPARγ, HK2, IRS-1, KIF1C, and KIFAP3; (ii) GLUT4, Flotillin-1, and Caveolin-1 localization, all proteins involved in energy-dependent cell trafficking; (iii) activation of I-targeted paths, as IRS-1, PKB/AKT, mTOR, P70/S6K. Free fatty acids intracellular level was measured. Sildenafil or a cGMP synthetic analog were used for comparison; PDE5 and PDE11 gene expression was evaluated in human fetal skeletal muscle cells.

METHODS

RTq-PCR, PCR, western blot, free fatty acid assay commercial kit, and lipid stain non-fluorescent assay were used.

RESULTS

Tadalafil upregulated I-targeted investigated genes with the same temporal pattern as I (GLUT4, PPARγ, and IRS-1 at 3 h; HK2, KIF1C, KIFAP3 at 12 h), re-localized GLUT4 in cell sites positively immune-decorated for Caveolin-1 and Flotillin-1, suggesting the involvement of lipid rafts, induced specific residue phosphorylation of IRS-1/AKT/mTOR complex in association with free fatty acid de novo synthesis. Sildenafil or GMP analog did not affect GLUT4 trafficking or free fatty acid levels.

CONCLUSION

In human fetal skeletal muscle cells tadalafil likely favors energy storage by modulating lipid homeostasis via IRS-1-mediated mechanisms, involving activation of I-targeted genes and intracellular cascade related to metabolic control. Those data provide some biomolecular evidences explaining, in part, tadalafil-induced favorable control of human metabolism shown by clinical studies.

Testosterone insulin-like effects: an in vitro study on the short-term metabolic effects of testosterone in human skeletal muscle cells

PURPOSE

Testosterone by promoting different metabolic pathways contributes to short-term homeostasis of skeletal muscle, the largest insulin-sensitive tissue and the primary site for insulin-stimulated glucose utilization. Despite evidences indicate a close relationship between testosterone and glucose metabolism, the molecular mechanisms responsible for a possible testosterone-mediated insulin-like effects on skeletal muscle are still unknown.

METHODS

Here we used undifferentiated proliferating or differentiated human fetal skeletal muscle cells (Hfsmc) to investigate the short-term effects of testosterone on the insulin-mediated biomolecular metabolic machinery. GLUT4 cell expression, localization and the phosphorylation/activation of AKT, ERK, mTOR and GSK3β insulin-related pathways at different time points after treatment with testosterone were analyzed.

RESULTS

Independently from cells differentiation status, testosterone, with an insulin-like effect, induced Glut4-mRNA expression, GLUT4 protein translocation to the cytoplasmic membrane, while no effect was observed on GLUT4 protein expression levels. Furthermore, testosterone treatment modulated the insulin-dependent signal transduction pathways inducing a rapid and persistent activation of AKT, ERK and mTOR, and a transient inhibition of GSK3β. T-related effects were shown to be androgen receptor dependent.

CONCLUSION

All together our data indicate that testosterone through the activation of non-genomic pathways, participates in skeletal muscle glucose metabolism by inducing insulin-related effects.

Phosphodiesterase Type 5 Inhibitor Sildenafil Decreases the Proinflammatory Chemokine CXCL10 in Human Cardiomyocytes and in Subjects with Diabetic Cardiomyopathy

T helper 1 (Th1) type cytokines and chemokines are bioactive mediators in inflammation underling several diseases and co-morbid conditions, such as cardiovascular and metabolic disorders. Th1 chemokine CXCL10 participates in heart damage initiation/progression; cardioprotection has been recently associated with sildenafil, a type 5 phosphodiesterase inhibitor. We aimed to evaluate the effect of sildenafil on CXCL10 in inflammatory conditions associated with diabetic cardiomyopathy. We analyzed: CXCL10 gene and protein in human cardiac, endothelial, and immune cells challenged by pro-inflammatory stimuli with and without sildenafil; serum CXCL10 in diabetic subjects at cardiomyopathy onset, before and after 3 months of treatment with sildenafil vs. placebo. Sildenafil significantly decreased CXCL10 protein secretion (IC₅₀ = 2.6 × 10⁻⁷) and gene expression in human cardiomyocytes and significantly decreased circulating CXCL10 in subjects with chemokine basal level ≥ 930 pg/ml, the cut-off value as assessed by ROC analysis. In conclusion, sildenafil could be a pharmacologic tool to control CXCL10-associated inflammation in diabetic cardiomyopathy.

Potential role for the VDR agonist elocalcitol in metabolic control: Evidences in human skeletal muscle cells

Vitamin D plays a pivotal role to maintain skeletal muscle integrity and health. Vitamin D deficiency characterizes inflammatory myopathy (IM) and diabetes, often overlapping diseases involving skeletal muscle damage. Vitamin D receptor (VDR) agonists likely exert beneficial effects in both IM and metabolic disturbances. We aim to evaluate in vitro the effect of elocalcitol, a non-hypercalcemic VDR agonist, on the biomolecular metabolic machinery of human skeletal muscle cells (Hfsmc), vs. insulin (I). We analyzed GLUT4, Flotillin-1, Caveolin-3 and Caveolin-1 cell expression/localization; mTOR, AKT, ERK and 4E-BP1 phosphorylation; IL-6 myokine release; VDR expression. We investigated in vivo vitamin D status in IM subjects, evaluating VDR muscular expression and serum vitamin D with metabolism-related parameters, as glycemia, triglycerides, cholesterol, resistin and adiponectin. In Hfsmc, elocalcitol exerted an I-like effect, promoting GLUT4 re-localization in Flotillin-1, Caveolin-3 and Caveolin-1 positive sites and mTOR, AKT, ERK, 4E-BP1 activation; it enhanced IL-6 myokine release. IM subjects, all normoglycemic, showed VDR/vitamin D deficiency that, together with high lipidemic and resistin profile, possibly increases the risk to develop metabolic diseases. VDR agonists as elocalcitol may be therapeutic tools for skeletal muscle integrity/function maintenance, an indispensable condition for health homeostasis.

Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses

In benthic deep-sea ecosystems, which represent the largest biome on Earth, viruses have a recognised key ecological role, but their diversity is still largely unknown. Identifying the taxonomic composition of viruses is crucial for understanding virus-host interactions, their role in food web functioning and evolutionary processes. Here, we compared the performance of various bioinformatic tools (BLAST, MG-RAST, NBC, VMGAP, MetaVir, VIROME) for analysing the viral taxonomic composition in simulated viromes and viral metagenomes from different benthic deep-sea ecosystems. The analyses of simulated viromes indicate that all the BLAST tools, followed by MetaVir and VMGAP, are more reliable in the affiliation of viral sequences and strains. When analysing the environmental viromes, tBLASTx, MetaVir, VMGAP and VIROME showed a similar efficiency of sequence annotation; however, MetaVir and tBLASTx identified a higher number of viral strains. These latter tools also identified a wider range of viral families than the others, providing a wider view of viral taxonomic diversity in benthic deep-sea ecosystems. Our findings highlight strengths and weaknesses of available bioinformatic tools for investigating the taxonomic diversity of viruses in benthic ecosystems in order to improve our comprehension of viral diversity in the oceans and its relationships with host diversity and ecosystem functioning.

Phosphodiesterase type 5 inhibitors: back and forward from cardiac indications

PDE5 inhibitors (PDE5i) are widely known as treatment for erectile dysfunction (ED). This favorable action has emerged as a "side effect" from pioneering studies when PDE5i have been originally proposed as treatment for coronary artery disease (CAD). PDE5i showed marginal benefits for CAD treatment; although disappointing for that indication, they improved systemic and pulmonary vasodilation and ameliorated general endothelial function. Therefore, PDE5i have been approved and licensed also for pulmonary artery hypertension (PAH), besides ED. Nowadays, fine-tuned biomolecular mechanisms of PDE5i are well recognized to be beneficial onto myocardial contractility and geometry, to reduce tissue fibrosis, hypertrophy and apoptosis. PDE5i consistently exert benefits on heart failure, infarct, cardiomyopathy. The concept that PDE5i likely blunt Th1-driven inflammatory processes, which shift the homeostatic balance from health to disease, has emerged; PDE5i seem to decrease the release of active biomolecules from cells to tissues interested by inflammation. In this view, following clinical and basic research progresses, PDE5i can be undoubtedly "re-allocated" for cardiac indications and, hopefully, they could be approved as therapeutic tools to treat and prevent heart disease. This review aims to summarize PDE5i different clinical applications, from past to present and future, focusing on their potential power as treatment for cardiac diseases.

Extracellular DNA can preserve the genetic signatures of present and past viral infection events in deep hypersaline anoxic basins

Deep hypersaline anoxic basins (DHABs) of the Mediterranean Sea are among the most extreme ecosystems on Earth and host abundant, active and diversified prokaryotic assemblages. However, factors influencing biodiversity and ecosystem functioning are still largely unknown. We investigated, for the first time, the impact of viruses on the prokaryotic assemblages and dynamics of extracellular DNA pool in the sediments of La Medee, the largest DHAB found on Earth. We also compared, in La Medee and L'Atalante sediments, the diversity of prokaryotic 16S rDNA sequences contained in the extracellular DNA released by virus-induced prokaryotic mortality. We found that DHAB sediments are hot-spots of viral infections, which largely contribute to the release of high amounts of extracellular DNA. DNase activities in DHAB sediments were much higher than other extracellular enzymatic activities, suggesting that extracellular DNA released from killed prokaryotes can be the most suitable trophic resource for benthic prokaryotes. Preserved extracellular DNA pools, which contained novel and diversified gene sequences, were very similar between the DHABs but dissimilar from the respective microbial DNA pools. We conclude that the strong viral impact in DHAB sediments influences the genetic composition of extracellular DNA, which can preserve the signatures of present and past infections.

Impact of aquaculture on benthic virus-prokaryote interactions in the Mediterranean Sea

We investigated the effects of organic enrichment due to the biodeposition from fish farms on benthic prokaryotic and viral abundance and production, viral-induced prokaryotic mortality, enzymatic activities and bacterial diversity. We compared four areas across the Mediterranean Sea, from Cyprus to Spain, and two different habitats: sediments covered by the seagrass Posidonia oceanica and soft-bottom unvegetated sediments. In several cases, the sediments beneath the cages showed higher prokaryotic and viral abundance and production, and higher rates of organic matter decomposition. However, the differences between impact and control sediments were not consistent at all regions and habitats. Benthic bacterial diversity was always lower below the cages, where high viral-induced bacterial mortality rates were also observed. The δ- and γ-Proteobacteria dominated in both impacted and control sediments, but the relative importance of sulphate-reducing δ-Proteobacteria increased beneath the cages. We conclude that aquaculture can have a significant impact on benthic prokaryotes and viruses, by stimulating prokaryotic metabolism and viral infections, reducing bacterial diversity and altering assemblage composition. However, these impacts vary depending upon the sediment type and the habitat characteristics.

Damage and degradation rates of extracellular DNA in marine sediments: implications for the preservation of gene sequences

The extracellular DNA pool in marine sediments is the largest reservoir of DNA of the world oceans and it potentially represents an archive of genetic information and gene sequences involved in natural transformation processes. However, no information is at present available for the gene sequences contained in the extracellular DNA and for the factors that influence their preservation. In the present study, we investigated the depurination and degradation rates of extracellular DNA in a variety of marine sediment samples characterized by different ages (up to 10,000 years) and environmental conditions according to the presence, abundance and diversity of prokaryotic gene sequences. We provide evidence that depurination of extracellular DNA in these sediments depends upon the different environmental factors that act synergistically and proceeds at much slower rates than those theoretically predicted or estimated for terrestrial ecosystems. These findings suggest that depurination in marine sediments is not the main process that limits extracellular DNA survival. Conversely, DNase activities were high suggesting a more relevant role of biologically driven processes. Amplifiable prokaryotic 16S rDNA sequences were present in most benthic systems analysed, independent of depurination and degradation rates and of the ages of the sediment samples. Additional molecular analyses revealed that the extracellular DNA pool is characterized by relatively low-copy numbers of prokaryotic 16S rDNA sequences that are highly diversified. Overall, our results suggest that the extracellular DNA pool in marine sediments represents a repository of genetic information, which can be used for improving our understanding of the biodiversity, functioning and evolution of ecosystems over different timescales.

Prokaryote diversity and virus abundance in shallow hydrothermal vents of the Mediterranean Sea (Panarea Island) and the Pacific Ocean (north Sulawesi-Indonesia)

Despite their ubiquitous distribution in tectonically active coastal zones, shallow water hydrothermal vents have been less investigated than deep-sea vents. In the present study, we investigated the role of viral control and fluid emissions on prokaryote abundance, diversity, and community structure (total Archaea, total Bacteria, and sulphate-reducing bacteria) in waters and sediments surrounding the caldera of four different shallow-water hydrothermal vents (three located in the Mediterranean Sea and one in the Pacific Ocean). All vents, independent of their location, generally displayed a significant decrease of benthic prokaryote abundance, as well as its viable fraction, with increasing distance from the vent. Prokaryote assemblages were always dominated by Bacteria. Benthic Archaea accounted for 23-33% of total prokaryote abundance in the Mediterranean Sea and from 13 to 29% in the Pacific Ocean, whereas in the water column they accounted for 25-38%. The highest benthic bacterial ribotype richness was observed in close proximity of the vents (i.e., at 10-cm distance from the emissions), indicating that vent fluids might influence bacterial diversity in surrounding sediments. Virioplankton and viriobenthos abundances were low compared to other marine systems, suggesting that temperature and physical-chemical conditions might influence viral survival in these vent systems. We thus hypothesize that the high bacterial diversity observed in close proximity of the vents is related with the highly variable vent emissions, which could favor the coexistence of several prokaryotic species.

Exo-enzymatic activities and dissolved organic pools in relation with mucilage development in the Northern Adriatic Sea

We tested the hypothesis that the appearance of mucilage in the Northern Adriatic Sea was related with the accumulation of dissolved organic compounds released by intensive enzymatic activities and not utilized as direct substrate for microbial growth. To do this enzymatic activities and dissolved organic and inorganic pools in periods characterized by the presence of mucilage and in the same seasons but in absence of mucilage were compared. Extracellular enzymatic activities (aminopeptidase, beta-glucosidase and alkaline phosphatase), nutrient pool concentrations (total dissolved nitrogen, dissolved organic nitrogen, total dissolved phosphorus, dissolved organic phosphorus) and the biochemical composition of particulate and dissolved organic matter (in terms of proteins and carbohydrates) were determined on a monthly basis over a period of 3 years. Aminopeptidase and alkaline phosphatase activities displayed higher values in springs preceding the appearance of mucilage than in spring when no mucilage was observed. Beta-Glucosidase activity showed significantly higher values in summer periods characterized by the massive production of mucilage than in summers without mucilage events. The months preceding mucilage events were also characterized by an increase of the alkaline phosphatase to aminopeptidase activity ratio and by a significant accumulation of dissolved proteins. These findings, together with the significant increase of the DON/DOP ratio, suggest that mucilage formation is favoured by the deficiency of organic P. The present study provides compelling evidences that mucilage formation is favoured by the unbalance between organic matter mobilization by enzymatic activities and the accumulation of labile dissolved organic-N compounds.

Viruses, prokaryotes and DNA in the sediments of a deep-hypersaline anoxic basin (DHAB) of the Mediterranean Sea

Viral and prokaryote abundance were investigated in a deep-hypersaline anoxic basin of the Eastern Mediterranean Sea (DHAB Atalante basin at c. 3000 m depth). This system was compared with two nearby deep-sea sites characterized by oxic conditions. Viral abundance and virus to prokaryote abundance ratio in hypersaline anoxic sediments displayed values close to those reported in oxic sites. The analysis of vertical profiles of viral abundance in the Atalante basin revealed the lack of significant changes with depth in the sediment, suggesting that benthic viruses in these anoxic and hypersaline conditions are preserved or resistant to decay. The anoxic basin displayed also very high concentrations of labile organic components (proteins and lipids) and extracellular DNA. These findings suggest that the DHAB sediments represent a reservoir for long-term preservation of benthic viruses and nucleic acids.

Large-scale spatial distribution of virioplankton in the Adriatic Sea: testing the trophic state control hypothesis

Little is known concerning environmental factors that may control the distribution of virioplankton on large spatial scales. In previous studies workers reported high viral levels in eutrophic systems and suggested that the trophic state is a possible driving force controlling the spatial distribution of viruses. In order to test this hypothesis, we determined the distribution of viral abundance and bacterial abundance and the virus-to-bacterium ratio in a wide area covering the entire Adriatic basin (Mediterranean Sea). To gather additional information on factors controlling viral distribution on a large scale, functional microbial parameters (exoenzymatic activities, bacterial production and turnover) were related to trophic gradients. At large spatial scales, viral distribution was independent of autotrophic biomass and all other environmental parameters. We concluded that in contrast to what was previously hypothesized, changing trophic conditions do not directly affect virioplankton distribution. Since virus distribution was coupled with bacterial turnover times, our results suggest that viral abundance depends on bacterial activity and on host cell abundance.

Viruses and marine pollution

This short review summarises the present knowledge on pollutant impacts on marine viruses, virus-host systems and their potential ecological implications. Excess nutrients from sewage and river effluents are a primary cause of marine eutrophication and mucilage formation, often related to the development of large viral assemblages. At the same time, hydrocarbons, polychlorinated biphenyl and pesticides alter ecosystem functioning and can determinate changes in the virus-host interactions, thus increasing the potential of viral infection. All these pollutants might have synergistic effects on the virus-host system and are able to induce prophage, thus increasing the impact of viruses on marine ecosystems.

Sunscreen products increase virus production through prophage induction in marine bacterioplankton

Classical pollutants (e.g., hydrocarbon, pesticides) have been recently recognized to induce lytic cycle in lysogenic bacteria, but information on micro-pollutants is almost completely lacking. We investigated the effects of cosmetic sun products (sunscreen and solar oil) on viral abundance and bacterial activity. We found that both sunscreen and solar oil acted as pollutants, inducing viral development and controlling bacterial abundance and production, thus leading to an increase of the virus to bacterium ratio. Short-term experiments revealed that sunscreen supplementation induced the lytic cycle in a large fraction of total bacterial abundance (13-24% of bacteria, at low and high concentrations, respectively), whereas solar oil had a lower impact (6-9%). A synchronized development of the phage-host system was observed only after sunscreen addition. The addition of sunscreen, even at low concentrations, had a significant impact on all enzymatic activities (aminopeptidase, glucosidase, and phosphatase), which increased significantly. However, when enzymatic activities were normalized per cell, a selective enhancement was observed for certain enzymes (e.g., aminopeptidase) and inhibition for others (e.g., glucosidase). These results indicate that sunscreen products can modify C, N, and P biogeochemical cycling in seawater and increase virus abundance through prophage induction in marine bacterioplankton.