Publications de l’unité
Année de publication : 2019
Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye librariesBeilstein Journal of Organic Chemistry : 15 : 1872–1889 : DOI : 10.3762/bjoc.15.183 En savoir plus
A library of 52 distyryl and 9 mono-styryl cationic dyes was synthesized and investigated with respect to their optical properties, propensity to aggregation in aqueous medium, and capacity to serve as fluorescence “light-up” probes for G-quadruplex (G4) DNA and RNA structures. Among the 61 compounds, 57 dyes showed preferential enhancement of fluorescence intensity in the presence of one or another G4-DNA or RNA structure, while no dye displayed preferential response to double-stranded DNA or single-stranded RNA analytes employed at equivalent nucleotide concentration. Thus, preferential fluorimetric response towards G4 structures appears to be a common feature of mono- and distyryl dyes, including long-known mono-styryl dyes used as mitochondrial probes or protein stains. However, the magnitude of the G4-induced “light-up” effect varies drastically, as a function of both the molecular structure of the dyes and the nature or topology of G4 analytes. Although our results do not allow to formulate comprehensive structure–properties relationships, we identified several structural motifs, such as indole- or pyrrole-substituted distyryl dyes, as well as simple mono-stryryl dyes such as DASPMI [2-(4-(dimethylamino)styryl)-1-methylpyridinium iodide] or its 4-isomer, as optimal fluorescent light-up probes characterized by high fluorimetric response (I/I0 of up to 550-fold), excellent selectivity with respect to double-stranded DNA or single-stranded RNA controls, high quantum yield in the presence of G4 analytes (up to 0.32), large Stokes shift (up to 150 nm) and, in certain cases, structural selectivity with respect to one or another G4 folding topology. These dyes can be considered as promising G4-responsive sensors for in vitro or imaging applications. As a possible application, we implemented a simple two-dye fluorimetric assay allowing rapid topological classification of G4-DNA structures.Replier
Oxidation-Sensitive Polymersomes Based on Amphiphilic Diblock Copolypeptoids.Biomacromolecules : XXXX : XXXX-XXXX : DOI : 10.1021/acs.biomac.9b00713 En savoir plus
Stimuli-responsive polymersomes formed by amphiphilic block copolymers have attracted substantial attention as smart and robust containers for drug delivery and nano/microreactors. Biosourced amphiphilic diblock copolypeptoids were developed that can self-assemble into oxidation-responsive unilamellar vesicles. These vesicles can burst under the action of reactive oxygen species which can be the hydrogen peroxide or the singlet oxygen produced by light-activation of a photosensitizer with spatiotemporal control. Polysarcosine (PSar, also called poly(-methyl glycine)) was selected as the hydrophilic block because of its resistance to protein adsorption and low toxicity, similar to poly(ethylene glycol) (PEG). We designed and synthesized poly(-3-(methylthio)propyl glycine) as the hydrophobic block. Its polyglycine backbone is the same as that of PSar, and especially, its hydrophobic N-substituents, thioether side chains, can be oxidized to hydrophilic sulfoxides. These oxidation-responsive polymersomes entirely based on N-substituted poly(amino acid)s were biocompatible as confirmed by cell viability tests and may find applications in drug delivery, biosensing, biodetection, and nano/microreactors.Replier
Involvement of G-quadruplex regions in mammalian replication origin activity.Nature communications : 3274 : DOI : 10.1038/s41467-019-11104-0 En savoir plus
Genome-wide studies of DNA replication origins revealed that origins preferentially associate with an Origin G-rich Repeated Element (OGRE), potentially forming G-quadruplexes (G4). Here, we functionally address their requirements for DNA replication initiation in a series of independent approaches. Deletion of the OGRE/G4 sequence strongly decreased the corresponding origin activity. Conversely, the insertion of an OGRE/G4 element created a new replication origin. This element also promoted replication of episomal EBV vectors lacking the viral origin, but not if the OGRE/G4 sequence was deleted. A potent G4 ligand, PhenDC3, stabilized G4s but did not alter the global origin activity. However, a set of new, G4-associated origins was created, whereas suppressed origins were largely G4-free. In vitro Xenopus laevis replication systems showed that OGRE/G4 sequences are involved in the activation of DNA replication, but not in the pre-replication complex formation. Altogether, these results converge to the functional importance of OGRE/G4 elements in DNA replication initiation.Replier
Disrupted Iron Storage in Dental Fluorosis.Journal of dental research : 98 : 994-1001 : DOI : 10.1177/0022034519855650 En savoir plus
Enamel formation and quality are dependent on environmental conditions, including exposure to fluoride, which is a widespread natural element. Fluoride is routinely used to prevent caries. However, when absorbed in excess, fluoride may also lead to altered enamel structural properties associated with enamel gene expression modulations. As iron plays a determinant role in enamel quality, the aim of our study was to evaluate the iron metabolism in dental epithelial cells and forming enamel of mice exposed to fluoride, as well as its putative relation with enamel mechanical properties. Iron storage was investigated in dental epithelial cells with Perl’s blue staining and secondary ion mass spectrometry imaging. Iron was mainly stored by maturation-stage ameloblasts involved in terminal enamel mineralization. Iron storage was drastically reduced by fluoride. Among the proteins involved in iron metabolism, ferritin heavy chain (Fth), in charge of iron storage, appeared as the preferential target of fluoride according to quantitative real-time polymerase chain reaction, Western blotting, and immunohistochemistry analyses. Fluorotic enamel presented a decreased quantity of iron oxides attested by electron spin resonance technique, altered mechanical properties measured by nanoindentation, and ultrastructural defects analyzed by scanning electron microscopy and energy dispersive x-ray spectroscopy. The in vivo functional role of Fth was illustrated with mice, which incorporated less iron into their dental epithelium and exhibited poor enamel quality. These data demonstrate that exposure to excessive fluoride decreases ameloblast iron storage, which contributes to the defective structural and mechanical properties in rodent fluorotic enamel. They raise the question of fluoride’s effects on iron storage in other cells and organs that may contribute to its effects on population health.Replier
CO2-activated reversible transition between polymersomes and micelles with AIE fluorescence.Angewandte Chemie (International ed. in English) : 58 : 10260-10265 : DOI : 10.1002/anie.201905089 En savoir plus
Fluorescent polymersomes with both aggregation-induced emission (AIE) and CO2-responsive properties were developed from amphiphilic block copolymer PEG-b-P(DEAEMA-co-TPEMA) in which the hydrophobic block was a copolymer made of tetraphenylethene functionalized methacrylate (TPEMA) and 2-(diethylamino)ethyl methacrylate (DEAEMA) with unspecified sequence arrangement. Four block copolymers with different DEAEMA/TPEMA and hydrophilic/hydrophobic ratios were synthesized and bright AIE polymersomes were prepared by nanoprecipitation in THF/water and dioxane/water systems. Polymersomes of PEG45-b-P(DEAEMA36-co-TPEMA6) were chosen to study the CO2-responsive property. Upon CO2 bubbling vesicles transformed to small spherical micelles, and upon Ar bubbling micelles returned to vesicles with the presence of a few intermediate morphologies. These polymersomes might have promising applications as sensors, nanoreactors or controlled release systems.Replier
Tomographic Collection of Block-Based Sparse STEM Images: Practical Implementation and Impact on the Quality of the 3D Reconstructed VolumeMaterials : 12 : 2281 : DOI : 10.3390/ma12142281 En savoir plus
The reduction of the electron dose in electron tomography of biological samples is of high significance to diminish radiation damages. Simulations have shown that sparse data collection can perform efficient electron dose reduction. Frameworks based on compressive-sensing or inpainting algorithms have been proposed to accurately reconstruct missing information in sparse data. The present work proposes a practical implementation to perform tomographic collection of block-based sparse images in scanning transmission electron microscopy. The method has been applied on sections of chemically-fixed and resin-embedded Trypanosoma brucei cells. There are 3D reconstructions obtained from various amounts of downsampling, which are compared and eventually the limits of electron dose reduction using this method are explored.Replier
Thermodynamically stable and genetically unstable G-quadruplexes are depleted in genomes across species.Nucleic acids research : 47 : 6098-6113 : DOI : 10.1093/nar/gkz463 En savoir plus
G-quadruplexes play various roles in multiple biological processes, which can be positive when a G4 is involved in the regulation of gene expression or detrimental when the folding of a stable G4 impairs DNA replication promoting genome instability. This duality interrogates the significance of their presence within genomes. To address the potential biased evolution of G4 motifs, we analyzed their occurrence, features and polymorphisms in a large spectrum of species. We found extreme bias of the short-looped G4 motifs, which are the most thermodynamically stable in vitro and thus carry the highest folding potential in vivo. In the human genome, there is an over-representation of single-nucleotide-loop G4 motifs (G4-L1), which are highly conserved among humans and show a striking excess of the thermodynamically least stable G4-L1A (G3AG3AG3AG3) sequences. Functional assays in yeast showed that G4-L1A caused the lowest levels of both spontaneous and G4-ligand-induced instability. Analyses across 600 species revealed the depletion of the most stable G4-L1C/T quadruplexes in most genomes in favor of G4-L1A in vertebrates or G4-L1G in other eukaryotes. We discuss how these trends might be the result of species-specific mutagenic processes associated to a negative selection against the most stable motifs, thus neutralizing their detrimental effects on genome stability while preserving positive G4-associated biological roles.Replier
Hydrogen isotopic anomalies in extraterrestrial organic matter: Role of cosmic ray irradiation and implications for UCAMMsAstronomy & Astrophysics : 627 : A122 : DOI : 10.1051/0004-6361/201935143 En savoir plus
Context. Micrometeorites represent, at timescales shorter than a few million years, the dominant source of extraterrestrial matter at the surface of the Earth. Analyses of ultracarbonaceous micrometeorites recovered from Antarctica, known as UCAMMs reveal an exceptionally N-rich organic matter associated with spatially extended high D enrichments. Experiments show that this specific organic matter might have been formed in the outer solar system by energetic irradiation of N-rich icy surfaces.
Aims. We experimentally investigate the hydrogen isotopic fractionation resulting from irradiation of normal and D-rich N2-CH4 ices by high energy ions, simulating the exposition to Galactic cosmic rays of icy bodies surfaces orbiting at large heliocentric distances.
Methods. Films of N2-CH4 ices and a N2-CH4/CD4/N2-CH4 « sandwich » ice were exposed to 129Xe13+ ion beams at 92 and 88 MeV. The chemical evolution of the samples was monitored using in situ Fourier transform infrared spectroscopy. After irradiation, targets were annealed to room temperature. The solid residues of the whole process left after ice sublimation were characterized in situ by infrared spectroscopy, and the hydrogen isotopic composition measured ex situ by imaging secondary ion mass spectrometry at the sub-micron scale (NanoSIMS).
Results. Irradiation leads to the formation of new molecules and radicals. After annealing, the resulting poly-HCN-like macro-molecular residue exhibits an infrared spectrum close to that of UCAMMs. The residue resulting from irradiation of N2-CH4 ices does not exhibit a significant deuterium enrichment comparable to that found in extraterrestrial organic matter. The residue formed by irradiation of D-rich ices shows the formation of isotopic heterogeneities with localised hotspots and an extended contribution likely due to the diffusion of the radiolytic products from the D-rich layer.
Conclusions. These results show that high-energy cosmic ray irradiation does not induce the large hydrogen isotopic fractionation observed at small spatial scale in interplanetary organics. By contrast, large D/H ratio heterogeneities at the sub-micron spatial scale in extraterrestrial organic matter can result from isotopically heterogeneous ices mixtures (i.e. condensed with different D/H ratios), which were transformed into refractory organic matter upon irradiation.Replier
A hypercaloric diet induces hepatic oxidative stress, infiltration of lymphocytes, and mitochondrial reshuffle in Psammomys obesus, a murine model of insulin resistance.Comptes rendus biologies : DOI : 10.1016/j.crvi.2019.04.003 En savoir plus
The aim of this study was to show, for the first time, the effect of a hypercaloric diet on the mitochondrial reshuffle of hepatocytes during the progression from steatosis to steatohepatitis to cirrhosis in Psammomys obesus, a typical animal model of the metabolic syndrome. Metabolic and oxidative stresses were induced by feeding the animal through a standard laboratory diet (SD) for nine months. Metabolic parameters, liver malondialdehyde (MDA) and glutathione (GSH), were evaluated. The pathological evolution was examined by histopathology and immunohistochemistry, using CD3 and CD20 antibodies. The dynamics of the mitochondrial structure was followed by transmission electron microscopy. SD induced a steatosis in this animal that evolved under the effect of oxidative and metabolic stress by the appearance of adaptive inflammation and fibrosis leading the animal to the cirrhosis stage with serious hepatocyte damage by the triggering, at first the mitochondrial fusion-fission cycles, which attempted to maintain the mitochondria intact and functional, but the hepatocellular oxidative damage was increased inducing a vicious circle of mitochondrial alteration and dysfunction and their elimination by mitophagy. P. obesus is an excellent animal model of therapeutic research that targets mitochondrial dysfunction in the progression of steatosis.Replier
Novel cationic bis(acylhydrazones) as modulators of Epstein–Barr virus immune evasion acting through disruption of interaction between nucleolin and G-quadruplexes of EBNA1 mRNAEuropean Journal of Medicinal Chemistry : 178 : 13-29 : DOI : 10.1016/j.ejmech.2019.05.042 En savoir plus
The oncogenic Epstein-Barr virus (EBV) evades the immune system through limiting the expression of its highly antigenic and essential genome maintenance protein, EBNA1, to the minimal level to ensure viral genome replication, thereby also minimizing the production of EBNA1-derived antigenic peptides. This regulation is based on inhibition of translation of the virally-encoded EBNA1 mRNA, and involves the interaction of host protein nucleolin (NCL) with G-quadruplex (G4) structures that form in the glycine–alanine repeat (GAr)-encoding sequence of the EBNA1 mRNA. Ligands that bind to these G4-RNA can prevent their interaction with NCL, leading to disinhibition of EBNA1 expression and antigen presentation, thereby interfering with the immune evasion of EBNA1 and therefore of EBV (M.J. Lista et al., Nature Commun., 2017, 8, 16043). In this work, we synthesized and studied a series of 20 cationic bis(acylhydrazone) derivatives designed as G4 ligands. The in vitro evaluation showed that most derivatives based on central pyridine (Py), naphthyridine (Naph) or phenanthroline (Phen) units were efficient G4 binders, in contrast to their pyrimidine (Pym) counterparts, which were poor G4 binders due to a significantly different molecular geometry. The influence of lateral heterocyclic units (N-substituted pyridinium or quinolinium residues) on G4-binding properties was also investigated. Two novel compounds, namely PyDH2 and PhenDH2, used at a 5 μM concentration, were able to significantly enhance EBNA1 expression in H1299 cells in a GAr-dependent manner, while being significantly less toxic than the prototype drug PhenDC3 (GI50 > 50 μM). Antigen presentation, RNA pull-down and proximity ligation assays confirmed that the effect of both drugs was related to the disruption of NCL–EBNA1 mRNA interaction and the subsequent promotion of GAr-restricted antigen presentation. Our work provides a novel modular scaffold for the development of G-quadruplex-targeting drugs acting through interference with G4–protein interaction.Replier
Identification of New Potent Acetylcholinesterase Inhibitors Using Virtual Screening and In Vitro Approaches.Molecular informatics : 38 : 1800118 : DOI : 10.1002/minf.201800118 En savoir plus
Acetylcholinesterase (AChE) is currently the most favorable target for the symptomatic treatment and reduction of Alzheimer’s disease (AD). In order to identify new potent inhibitors of this enzyme, we describe herein a new structure‐based virtual screening (SBVS) using the Institut Curie‐CNRS chemical library (ICCL), which contained at the screening date 14307 compounds. The strategy undertaken in this work consisted of the use of several docking programs in SBVS calculations followed by the application of a consensus method (vSDC) and a scrupulous visual analysis. It allowed us to obtain a high degree of success, with a yield of almost 86 %, since 12 hits were identified among only 14 molecules tested in vitro. Still more remarkably, 6 of these hits were more active than galantamine, the reference inhibitor. These hits were predicted to have good ADMET properties. The two most promising compounds can serve as leads for AD treatment.
Identification of three-way DNA junction ligands through screening of chemical libraries and validation by complementary in vitro assays.Journal of Medicinal Chemistry : 62 : 4456-4466 : DOI : 10.1021/acs.jmedchem.8b01978 En savoir plus
The human genome is replete with repetitive DNA sequences that can fold into thermodynamically stable secondary structures such as hairpins and quadruplexes. Cellular enzymes exist to cope with these structures whose stable accumulation would result in DNA damage through interference with DNA transactions such as transcription and replication. Therefore, chemical stabilization of secondary DNA structures offers an attractive way to foster DNA transaction-associated damages to trigger cell death in proliferating cancer cells. While much emphasis has been recently given to DNA quadruplexes, we focused here on three-way DNA junctions (TWJ) and report on a strategy to identify TWJ-targeting agents through a combination of in vitro techniques (TWJ-Screen, PAGE, FRET-melting, ESI-MS, dialysis equilibrium and SRB assays). We designed a complete workflow and screened 1200 compounds to identify promising three-way DNA junction ligands selected on stringent criteria in terms of TWJ folding ability, affinity and selectivity.Replier
Correlative infrared nanospectroscopy and transmission electron microscopy to investigate nanometric amyloid fibrils: prospects and challenges.Journal of microscopy : 274 : 23-31 : DOI : 10.1111/jmi.12779 En savoir plus
Propagation of structural information through conformational changes in host-encoded amyloid proteins is at the root of many neurodegenerative disorders. Although important breakthroughs have been made in the field, fundamental issues like the 3D-structures of the fibrils involved in some of those disorders are still to be elucidated. To better characterise those nanometric fibrils, a broad range of techniques is currently available. Nevertheless none of them is able to perform direct chemical characterisation of single protein fibrils. In this work, we propose to investigate the structure of the C-terminal region of a bacterial protein called Hfq as a model amyloidogenic protein, using a correlative approach. The complementary techniques used are transmission electron microscopy and a newly developed infrared nanospectroscopy technique called AFM-IR. We introduce and discuss the strategy that we have implemented as well as the protocol, challenges and difficulties encountered during this study to characterise amyloid assemblies at the nearly single-molecule level. LAY DESCRIPTION: Propagation of structural information through conformational changes in amyloid proteins is at the root of many neurodegenerative disorders. Amyloids are nanostructures originating from the aggregation of multiple copies of peptide or protein monomers that eventually form fibrils. Often described as being the cause for the development of various diseases, amyloid fibrils are of major significance in the public health domain. While important breakthroughs have been made in the field, fundamental issues like the 3D-structures of the fibrils implied in some of those disorders are still to be elucidated. To better characterise these fibrils, a broad range of techniques is currently available for the detection and visualisation of amyloid nanostructures. Nevertheless none of them is able to perform direct chemical characterisation of single protein fibrils. In this work, we propose to investigate the structure of model amyloidogenic fibrils using a correlative approach. The complementary techniques used are transmission electron microscopy and a newly developed infrared nanospectroscopy technique called AFM-IR that allows chemical characterisation at the nanometric scale. The strategy, protocol, challenges and difficulties encountered in this approach are introduced and discussed herein.Replier
Probing Ligand and Cation Binding Sites in G-Quadruplex Nucleic Acids by Mass Spectrometry and Electron Photodetachment Dissociation SequencingAnalyst : 144 : 3518-3524 : DOI : 10.1039/C9AN00398C En savoir plus
Mass spectrometry provides exquisite detail on ligand and cation binding stoichiometries with a DNA target. The next important step is to develop reliable methods to determine the cation and ligand binding sites in each complex separated by the mass spectrometer. To circumvent the caveat of ligand derivatization for cross-linking, which may alter the ligand binding mode, we explored a tandem mass spectrometry (MS/MS) method that does not require ligand derivatization, and is therefore also applicable to localize metal cations. By obtaining more negative charge states for the complexes using supercharging agents, and by creating radical ions by electron photodetachment, oligonucleotide bonds become weaker than the DNA-cation or DNA-ligand noncovalent bonds upon collision-induced dissociation of the radicals. This electron photodetachment (EPD) method allows to locate the binding regions of cations and ligands by top-down sequencing of the oligonucleotide target. The very potent G-quadruplex ligands 360A and PhenDC3 were found to replace a potassium cation and bind close to the central loop of 4-repeat human telomeric sequences.Replier
Mannose distribution in glycoconjugated tetraphenylporphyrins governs their uptake mechanism and phototoxicityJournal of Porphyrins and Phthalocyanines : 23 : 175-184 : DOI : 10.1142/S1088424619500184 En savoir plus
Tetraphenylporphyrins (TPPs) have been proposed for the treatment of retinoblastoma by photodynamic therapy. Glycoconjugated compounds were synthesized for improving TPP solubility and amphipathy, and to specifically target mannose receptors overexpressed at the surface of cells. The efficiency of four TPP derivatives with different chemical structures was compared by phototoxicity tests and flow cytometry experiments. Interestingly, the absence/presence and distribution of saccharide moieties in the various compounds affected differently their mechanism of interaction with cancer cells and their phototoxic efficiency. For glycodendrimeric TPP-1 and TPP-2 incubated with retinoblastoma cells, a fast two-step uptake-equilibrium process was observed, whereas for a dendrimeric TPP without saccharide moieties (TPP-1c) and a glycoconjugated compound with no dendrimeric structure (TPP(DegMan)3) uptake was very slow. The difference in uptake profiles and kinetics between TPP-1c on the one hand and TPP-1 and TPP-2 on the other hand would account for the interaction of the two glycodendrimeric compounds with a mannose receptor. These TPPs encapsulated in endosomes would induce less damage to cells upon illumination. TPP(DegMan)3 showed the highest phototoxicity, but its efficiency was unaffected by pretreatment of cells by mannan. The penetration of this glycoconjugated compound in cells and its phototoxic effect appeared independent of its interaction with a mannose receptor. Thus, if glycoconjugation influenced TPPs behavior in solution and interaction with serum proteins, phototoxicity was not necessarily related to upfront molecular recognition.Replier