Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides.

BACKGROUND: In proteomics, the interpretation of mass spectra representing peptides carrying multiple complex modifications remains challenging, as it is difficult to strike a balance between reasonable execution time, a limited number of false positives, and a huge search space allowing any number of modifications without a priori. The scientific community needs new developments in this area to aid in the discovery of novel post-translational modifications that may play important roles in disease. RESULTS: To make progress on this issue, we implemented SpecGlobX (SpecGlob eXTended to eXperimental spectra), a standalone Java application that quickly determines the best spectral alignments of a (possibly very large) list of Peptide-to-Spectrum Matches (PSMs) provided by any open modification search method, or generated by the user. As input, SpecGlobX reads a file containing spectra in MGF or mzML format and a semicolon-delimited spreadsheet describing the PSMs. SpecGlobX returns the best alignment for each PSM as output, splitting the mass difference between the spectrum and the peptide into one or more shifts while considering the possibility of non-aligned masses (a phenomenon resulting from many situations including neutral losses). SpecGlobX is fast, able to align one million PSMs in about 1.5 min on a standard desktop. Firstly, we remind the foundations of the algorithm and detail how we adapted SpecGlob (the method we previously developed following the same aim, but limited to the interpretation of perfect simulated spectra) to the interpretation of imperfect experimental spectra. Then, we highlight the interest of SpecGlobX as a complementary tool downstream to three open modification search methods on a large simulated spectra dataset. Finally, we ran SpecGlobX on a proteome-wide dataset downloaded from PRIDE to demonstrate that SpecGlobX functions just as well on simulated and experimental spectra. We then carefully analyzed a limited set of interpretations. CONCLUSIONS: SpecGlobX is helpful as a decision support tool, providing keys to interpret peptides carrying complex modifications still poorly considered by current open modification search software. Better alignment of PSMs enhances confidence in the identification of spectra provided by open modification search methods and should improve the interpretation rate of spectra.

Bis-nor-diterpene from Cnidoscolus quercifolius (Euphorbiaceae) induces tubulin depolymerization-mediated apoptosis in BRAF-mutated melanoma cells.

A phytochemical investigation of cytotoxic extract and fractions of Cnidoscolus quercifolius Pohl led to isolation of five terpenoids, including three lupane-type triterpenes (1-3) and two bis-nor-diterpenes (4-5). Compounds 4 (phyllacanthone) and 5 (favelanone) are commonly found in this species and have unique chemical structure. Although their cytotoxic activity against cancer cells has been previously reported, the anticancer potential of these molecules remains poorly explored. In this paper, the antimelanoma potential of phyllacanthone (PHY) was described for the first time. Cell viability assay showed a promising cytotoxic activity (IC50 = 40.9 µM) against chemoresistant human melanoma cells expressing the BRAF oncogenic mutation (A2058 cell line). After 72 h of treatment, PHY inhibited cell migration and induced apoptosis and cell cycle arrest (p < 0.05). Immunofluorescence assay showed that the pro-apoptotic effect of PHY is probably associated with tubulin depolymerization, resulting in cytoskeleton disruption of melanoma cells. Molecular docking investigation confirmed this hypothesis given that satisfactory interaction between PHY and tubulin was observed, particularly at the colchicine binding site. These results suggest PHY from C. quercifolius could be potential leader for the design of new antimelanoma drugs.

Intergenerational effects of environmentally-aged microplastics on the Crassostrea gigas.

This study focused on the impacts of aged aquaculture microplastics (MPs) on oysters (Crassostrea gigas). Adult oysters were exposed for two months to a cocktail of MPs representative of the contamination of the Pertuis Charentais area (Bay of Biscay, France) and issuing from oyster framing material. The MPs mixture included 28% of polyethylene, 40% of polypropylene and 32% of PVC (polyvinyl chloride). During the exposure, tissues were sampled for various analyzes (MP quantification, toxicity biomarkers). Although no effect on the growth of adult oysters was noted, the mortality rate of bivalves exposed to MPs (0.1 and 10 mg. L-1 MP) increased significantly (respectively 13.3 and 23.3% of mortalities cumulative). On the one hand, the responses of biomarkers revealed impacts on oxidative stress, lipid peroxidation and environmental stress. At 56 days of exposure, significant increases were noted for Glutathione S-Transferase (GST, 10 mg. L-1 MP), Malondialdehyde (MDA, 10 mg. L-1 MP) and Laccase (LAC, 0.1 and 10 mg. L-1 MP). No variations were observed for Superoxyde Dismutase (SOD). Besides, ingestion of MPs in oyster tissues and the presence in biodeposits was highlighted. In addition, in vitro fertilisations were performed to characterize MPs effects on the offspring. Swimming behavior, development and growth of D-larvae were analysed at 24-, 48- and 72-h after fertilisation. D-larvae, from exposed parents, demonstrated reduced locomotor activity. Developmental abnormalities and arrest as well as growth retardation were also noted. This study highlighted direct and intergenerational effects of MPs from aged plastic materials on Pacific oysters.

A Marine λ-Oligocarrageenan Inhibits Migratory and Invasive Ability of MDA-MB-231 Human Breast Cancer Cells through Actions on Heparanase Metabolism and MMP-14/MMP-2 Axis.

Sugar-based molecules such as heparins or natural heparan sulfate polysaccharides have been developed and widely studied for controlling heparanase (HPSE) enzymatic activity, a key player in extracellular matrix remodelling during cancer pathogenesis. However, non-enzymatic functions of HPSE have also been described in tumour mechanisms. Given their versatile properties, we hypothesized that sugar-based inhibitors may interfere with enzymatic but also non-enzymatic HPSE activities. In this work, we assessed the effects of an original marine λ-carrageenan derived oligosaccharide (λ-CO) we previously described, along with those of its native counterpart and heparins, on cell viability, proliferation, migration, and invasion of MDA-MB-231 breast cancer cells but also of sh-MDA-MB-231 cells, in which the expression of HPSE was selectively downregulated. We observed no cytotoxic and no anti-proliferative effects of our compounds but surprisingly λ-CO was the most efficient to reduce cell migration and invasion compared with heparins, and in a HPSE-dependent manner. We provided evidence that λ-CO tightly controlled a HPSE/MMP-14/MMP-2 axis, leading to reduced MMP-2 activity. Altogether, this study highlights λ-CO as a potent HPSE "modulator" capable of reducing not only the enzymatic activity of HPSE but also the functions controlled by the HPSE levels.

Toxicity and risk assessment of six widely used pesticides on embryo-larval development of the Pacific oyster, Crassostrea gigas.

This study aims to assess the toxic effects and the potential risk of widely used agricultural pesticides on the development (malformations and developmental arrest), growth and swimming activity of oyster D-larvae (Crassostrea gigas). Freshly fertilized oyster embryos were exposed for 24 h at 24 °C to different concentrations (0, 0.01, 0.1, 1 and 10 µg.L-1) of six different pesticides: Glyphosate and its commercial solution (Roundup), Isoproturon, Nicosulfuron, Chlortoluron and Boscalid. The six pesticides tested induced a significant increase in larval malformations and developmental arrests. All pesticides except Glyphosate and Isoproturon affected larval growth. Roundup, Nicosulfuron, Chlortoluron and Boscalid also affected the swimming behaviour of the D-larvae, with a significant decrease recorded in their maximum swimming speed. Comparison of the LOEC (Lowest-Observed-Effect Concentration) of each compound led to the following toxicity classification: Boscalid > Chlortoluron = Nicosulfuron > Glyphosate > Roundup > Isoproturon, with respectively LOEC of 0.0028; 0.015; 0.017; 0.11; 0.3 and 0.78 µg.L-1. By comparison of the maximum concentrations in the Pertuis Charentais (South West, France) and LOEC of each pesticide, the following risk scale was obtained: Chlortoluron > Boscalid > Glyphosate > Roundup > Nicosulfuron > Isoproturon. Our results revealed that Chlortoluron, Boscalid and to a lesser extent Glyphosate represent a potential threat to early life stages of oyster living in the Pertuis Charentais marine area.

Polymethoxyflavones from Gardenia oudiepe (Rubiaceae) induce cytoskeleton disruption-mediated apoptosis and sensitize BRAF-mutated melanoma cells to chemotherapy.

A series of 10 natural and semisynthetic flavonoids (1 to 10) were obtained from Gardenia oudiepe (Rubiaceae), an endemic plant from New Caledonia. Most of them were polymethoxylated flavones (PMFs) of rare occurrence. After a cell viability screening test, PMFs 2 and 3 showed significant cytotoxic activity against A2058 human melanoma cells (IC50 = 3.92 and 8.18 µM, respectively) and were selected for in-depth pharmacological assays. Both compounds inhibited cell migration and induced apoptosis and cell cycle arrest after 72h of treatment. Immunofluorescence assays indicated that these outcomes were possibly related to the induction of cytoskeleton disruption associated to actin and tubulin depolymerization. These data were confirmed by molecular docking studies, which showed a good interaction between PMFs 2 and 3 and tubulin, particularly at the colchicine binding site. As A2058 are considered as chemoresistant to conventional chemotherapy, compounds 2 and 3 (½IC50) were associated to clinically-used antimelanoma drugs (vemurafenib and dacarbazine) and combined therapies efficacy was assessed by the MTT assay. PMFs 2 restored the sensitivity of A2058 cells to dacarbazine treatment (IC50 = 49.38 µM vs. >100 µM). Taken together, these data suggest that PMFs from G. oudiepe could be potential leaders for the design of new antimelanoma drugs.

Experimental ingestion of fluorescent microplastics by pacific oysters, Crassostrea gigas, and their effects on the behaviour and development at early stages.

Plastics are persistent synthetic polymers that accumulate as waste in the marine environment. Microplastics (MPs, <5 mm) can be found either as microbeads in body care and some industrial products or as plastic debris through degradation. Plastic microbeads (1-5 µm, fluorescent, Cospheric) were used to characterise the MP ingestion and determine their potential harmful effects on both the swimming behaviour and development of oyster D-larvae (Crassostrea gigas). For 24 h, embryos were first exposed to MPs at a temperature of 24 °C. In addition, 3 day-old D-larvae were exposed to the same temperature for 1, 3 and 5 h. Three concentrations of MPs were used: 0.1, 1 and 10 mg MP. L-1. After a 24-h period of embryonic exposure, we noted that MP agglomerates were stuck to the D-larvae coat and locomotor eyelashes. We also observed a significant increase in severe malformations and developmental arrests for larvae exposed to MPs ranging from 1 mg MP. L-1. In terms of swimming behaviour, the maximum speed recorded was lower for larvae exposed at 0.1 and 1 mg MP. L-1. After an acute exposure to MPs, particles were found in the digestive tract of 3 dpf (days post fertilisation) D-larvae. After 1-h exposure, the concentrations tested (0.1, 1 and 10 mg MP. L-1) resulted in respectively 38%, 86% and 98%. The larvae swimming behaviour was recorded and analysed. Unlike the results observed at the embryo-larval stage, 3-dpf larvae showed significant impacts with no dose-response effect.

High density polyethylene (HDPE) microplastics impair development and swimming activity of Pacific oyster D-larvae, Crassostrea gigas, depending on particle size.

Understanding the effects of plastic debris on marine ecosystems is essential in encouraging decision-makers to take action. The present study investigates the effect of a 24 h experimental exposure to high density polyethylene (HDPE) microplastics (MPs) of different sizes (4-6, 11-13 and 20-25 µm) and at three concentrations (0.1, 1 and 10 mg MP.L-1) on the development and locomotor activity of early stages of Pacific oyster, Crassostrea gigas. The bivalve embryo-larval assay (NF ISO 17244, 2015) was used in this study but with additional toxicity criteria: developmental arrests, abnormal D-larvae, maximum speed and swimming trajectory. Copper (Cu), was used as a positive control. Our results show that smaller MPs (4-6 and 11-13 µm) induced higher rates of malformations and developmental arrests than the larger ones (20-25 µm). In addition, a dose-dependent decrease of maximum swimming speed was observed for larvae exposed to MPs of 4-6 and 11-13 µm. On the other hand, there was no significant difference in swimming speed with the largest MPs size tested (20-25 µm). For all three sizes of MPs, there was a decrease in straight-line swimming trajectories, and an increase in circular trajectories. This abnormal swimming behaviour could affect larvae survival as well as colonization of new habitats.

Bixin, an apocarotenoid isolated from Bixa orellana L., sensitizes human melanoma cells to dacarbazine-induced apoptosis through ROS-mediated cytotoxicity.

Cutaneous melanoma has a high capacity to metastasize and significant resistance to conventional therapeutic protocols, which makes its treatment difficult. The combination of conventional drugs with cytostatic molecules of low toxicity has been shown to be an interesting alternative for sensitization of tumor cells to chemotherapy. In this study, we evaluated the effect of bixin, an abundant apocarotenoid present in Bixa orellana, on the sensitization of human melanoma cells (A2058) to dacarbazine treatment, an anticancer agent clinically used for the therapy of metastatic melanoma. UPLC-DAD-MS/MS analyses of bioactive extracts from B. orellana seeds led to the identification of two new apocarotenoids: 6,8'-diapocarotene-6,8'-dioic acid and 6,7'-diapocarotene-6,7'-dioic acid. After being identified as its major compound, bixin (Z-bixin) was evaluated on A2058 cells expressing the oncogenic BRAF VE600 mutation and resistant to dacarbazine treatment. Bixin promoted growth inhibition, reduced cell migration, induced apoptosis and cell cycle arrest in the G2/M phase. When associated with dacarbazine, bixin restored the sensitivity of A2058 cells to chemotherapy, enhancing its antiproliferative, anti-migratory and pro-apoptotic effects. Combined treatment also induced higher ROS (reactive oxygen species) and MDA (malondialdehyde, a lipid peroxidation marker) generation than monotreatment, suggesting that the oxidative stress caused by bixin contributes significantly to its sensitizing effect. Taken together, these data suggest that bixin exerts intrinsic antimelanoma activity by mechanisms complementary to those of dacarbazine, encouraging its use in combined therapy for cutaneous melanoma treatment.

Zeaxanthin from Porphyridium purpureum induces apoptosis in human melanoma cells expressing the oncogenic BRAF V600E mutation and sensitizes them to the BRAF inhibitor vemurafenib

Abstract Zeaxanthin, an abundant carotenoid present in fruits, vegetables and algae was reported to exert antiproliferative activity and induce apoptosis in human uveal melanoma cells. It also inhibited uveal melanoma tumor growth and cell migration in nude mice xenograft models. Here we report that zeaxanthin purified from the rhodophyte Porphyridium purpureum (Bory) K.M.Drew & R.Ross, Porphyridiaceae, promotes apoptosis in the A2058 human melanoma cell line expressing the oncogenic BRAF V600E mutation. Zeaxanthin 40 µM (IC50) induced chromatin condensation, nuclear blebbing, hypodiploidy, accumulation of cells in sub-G1 phase, DNA internucleosomal fragmentation and activation of caspase-3. Western blot analysis revealed that zeaxanthin induced up-regulation of the pro-apoptotic factors Bim and Bid and inhibition of NF-κB transactivation. Additionally, zeaxanthin sensitized A2058 melanoma cells in vitro to the cytotoxic activity of vemurafenib, a BRAF inhibitor widely used for the clinical management of melanoma, suggesting its potential interest as dietary adjuvant increasing melanoma cells sensitivity to chemotherapy.