Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics

To expand the antisense oligonucleotide (ASO) fluorescence labeling toolbox beyond covalent conjugation of external dyes (e.g. ATTO-, Alexa Fluor-, or cyanine dyes), we herein explore fluorescent base analogues (FBAs) as a novel approach to endow fluorescent properties to ASOs. Both cytosine and adenine analogues (tC, tCO, 2CNqA, and pA) were incorporated into a 16mer\ua0ASO sequence with a 3-10-3 cEt-DNA-cEt (cEt = constrained ethyl) gapmer design. In addition to a comprehensive photophysical characterization, we assess the label-induced effects on the gapmers’ RNA affinities, RNA-hybridized secondary structures, and knockdown efficiencies. Importantly, we find practically no perturbing effects for gapmers with single FBA incorporations in the biologically critical gap region and, except for pA, the FBAs do not affect the knockdown efficiencies. Incorporating two cytosine FBAs in the gap is equally well tolerated, while two adenine analogues give rise to slightly reduced knockdown efficiencies and what could be perturbed secondary structures. We furthermore show that the FBAs can be used to visualize gapmers inside live cells using fluorescence microscopy and flow cytometry, enabling comparative assessment of their uptake. This altogether shows that FBAs are functional ASO probes that provide a minimally perturbing in-sequence labeling option for this highly relevant drug modality

A high-throughput Galectin-9 imaging assay for quantifying nanoparticle uptake, endosomal escape and functional RNA delivery

RNA-based therapies have great potential to treat many undruggable human diseases. However, their efficacy, in particular for mRNA, remains hampered by poor cellular delivery and limited endosomal escape. Development and optimisation of delivery vectors, such as lipid nanoparticles (LNPs), are impeded by limited screening methods to probe the intracellular processing of LNPs in sufficient detail. We have developed a high-throughput imaging-based endosomal escape assay utilising a Galectin-9 reporter and fluorescently labelled mRNA to probe correlations between nanoparticle-mediated uptake, endosomal escape frequency, and mRNA translation. Furthermore, this assay has been integrated within a screening platform for optimisation of lipid nanoparticle formulations. We show that Galectin-9 recruitment is a robust, quantitative reporter of endosomal escape events induced by different mRNA delivery nanoparticles and small molecules. We identify nanoparticles with superior escape properties and demonstrate cell line variances in endosomal escape response, highlighting the need for fine-tuning of delivery formulations for specific applications

Interaction Kinetics of Individual mRNA-Containing Lipid Nanoparticles with an Endosomal Membrane Mimic: Dependence on pH, Protein Corona Formation, and Lipoprotein Depletion

Lipid nanoparticles (LNPs) have emerged as potent carriers for mRNA delivery, but several challenges remain before this approach can offer broad clinical translation of mRNA therapeutics. To improve their efficacy, a better understanding is required regarding how LNPs are trapped and processed at the anionic endosomal membrane prior to mRNA release. We used surface-sensitive fluorescence microscopy with single LNP resolution to investigate the pH dependency of the binding kinetics of ionizable lipid-containing LNPs to a supported endosomal model membrane. A sharp increase of LNP binding was observed when the pH was lowered from 6 to 5, accompanied by stepwise large-scale LNP disintegration. For LNPs preincubated in serum, protein corona formation shifted the onset of LNP binding and subsequent disintegration to lower pH, an effect that was less pronounced for lipoprotein-depleted serum. The LNP binding to the endosomal membrane mimic was observed to eventually become severely limited by suppression of the driving force for the formation of multivalent bonds during LNP attachment or, more specifically, by charge neutralization of anionic lipids in the model membrane due to their association with cationic lipids from earlier attached LNPs upon their disintegration. Cell uptake experiments demonstrated marginal differences in LNP uptake in untreated and lipoprotein-depleted serum, whereas lipoprotein-depleted serum increased mRNA-controlled protein (eGFP) production substantially. This complies with model membrane data and suggests that protein corona formation on the surface of the LNPs influences the nature of the interaction between LNPs and endosomal membranes

Novel endosomolytic compounds enable highly potent delivery of antisense oligonucleotides

The therapeutic and research potentials of oligonucleotides (ONs) have been hampered in part by their inability to effectively escape endosomal compartments to reach their cytosolic and nuclear targets. Splice-switching ONs (SSOs) can be used with endosomolytic small molecule compounds to increase functional delivery. So far, development of these compounds has been hindered by a lack of high-resolution methods that can correlate SSO trafficking with SSO activity. Here we present in-depth characterization of two novel endosomolytic compounds by using a combination of microscopic and functional assays with high spatiotemporal resolution. This system allows the visualization of SSO trafficking, evaluation of endosomal membrane rupture, and quantitates SSO functional activity on a protein level in the presence of endosomolytic compounds. We confirm that the leakage of SSO into the cytosol occurs in parallel with the physical engorgement of LAMP1-positive late endosomes and lysosomes. We conclude that the new compounds interfere with SSO trafficking to the LAMP1-positive endosomal compartments while inducing endosomal membrane rupture and concurrent ON escape into the cytosol. The efficacy of these compounds advocates their use as novel, potent, and quick-acting transfection reagents for antisense ONs

Biomarkers of nanomaterials hazard from multi-layer data

Nanomaterials have a range of potential applications, however, toxicity remains a concern, limiting application and requiring extensive testing. Here, the authors report on a predictive framework made using a range of tests linking materials properties with toxicity, allowing the prediction of toxicity from physiochemical and biological properties.There is an urgent need to apply effective, data-driven approaches to reliably predict engineered nanomaterial (ENM) toxicity. Here we introduce a predictive computational framework based on the molecular and phenotypic effects of a large panel of ENMs across multiple in vitro and in vivo models. Our methodology allows for the grouping of ENMs based on multi-omics approaches combined with robust toxicity tests. Importantly, we identify mRNA-based toxicity markers and extensively replicate them in multiple independent datasets. We find that models based on combinations of omics-derived features and material intrinsic properties display significantly improved predictive accuracy as compared to physicochemical properties alone.Peer reviewe

Nanoparticles for imaging and photodynamic therapy of cancers : toward a specific therapeutic targeting of retinoblastoma

L'avancée technologique dans les nanosciences a permis le développement d'une large gamme de matériaux nanostructurés aux applications biomédicales. Ces outils, constitués de matériaux différents, ont été développés à des fins de diagnostic et de thérapie pour réaliser notamment le ciblage, le marquage cellulaire, l'imagerie médicale et pour concevoir des systèmes de délivrance de médicaments pour le traitement de cancers ou de maladies infectieuses. La création de nano-objets regroupant l'ensemble de ces propriétés de type théranostique constitue une étape essentielle vers un traitement personnalisé et non invasif des cancers solides de petite taille. Dans cette thèse, une première partie est consacrée à la mise au point et à l'utilisation de nanoparticules de silice mésoporeuse pour le traitement des rétinoblastomes. Ce travail visait à améliorer la thérapie photodynamique en augmentant la biodisponibilité de molécules actives dans les cellules cancéreuses par deux stratégies : leur vectorisation par un nano-objet et le ciblage spécifique des cellules cancéreuses. Pour cela, les profils d'expression des récepteurs du mannose ont été analysés et les récepteurs MRC2 et CD209 se sont révélés être de bons candidats pour une thérapie ciblée du rétinoblastome. La deuxième partie des recherches réalisées s'oriente vers l'élaboration de différents nanosystèmes pour le traitement des cancers et l'imagerie médicale. Premièrement, des nanotransporteurs de principe actif à relargage pH-sensible, structurés à partir de nanoparticule de silice mésoporeuse, ont été étudiés. Ces systèmes de délivrance, sous l'effet de stimuli internes, se sont révélés être très efficaces in vitro et ex vivo pour le traitement du cancer du côlon. Deuxièmement, le potentiel de délivrance contrôlée de molécules anticancéreuses renfermées dans des nanomachines soumises à une activation externe biphotonique, a été démontré sur des cellules de cancer du sein. Enfin, les propriétés de nanoparticules magnétiques de polymères de coordination cyano-pontés se sont révélées très prometteuses pour une utilisation en tant que nouvel agent de contraste intravasculaire pour l'imagerie par résonance magnétique in vivo.The technological advance in nanoscience has allowed the development of a wide range of nanostructured materials for biomedical applications. These tools, composed of different materials, have been developed for diagnosis and therapy, in particular to achieve targeting, cellular labeling, medical imaging and to design drug delivery systems for the treatment of cancer or infectious diseases. The elaboration of nano-tools possessing these theranostic properties would be a major step towards personalized and non-invasive treatments of small solid cancers.In this thesis, the first part is devoted to the development and the application of mesoporous silica nanoparticles for the treatment of retinoblastoma. The aim of this work was to improve photodynamic therapy by increasing the bioavailability of active molecules in cancer cells following two strategies: their vectorization through nanodevice and the specific targeting of cancer cells. For this, expression profiles of mannose receptors were analyzed and both MRC2 and CD209 receptors were found to be interesting candidates for targeted therapy of retinoblastoma.The second part corresponds to a multidisciplinary approach focused on the research of different nanosystems designed for cancer treatment and medical imaging. We first studied pH-operated hybrid silica nanocarriers designed for drug release. Under internal stimuli, these delivery systems have shown to be very efficient in vitro and ex vivo against colon cancer. Then, we demonstrated the potential of nanoimpellers designed for anticancer drug delivery mediated by external two-photon activation on breast cancer cells. Finally, we report the promising use in vivo of new magnetic cyano-bridged coordination polymer nanoparticles as an efficient intravascular magnetic resonance imaging contrast agent

Combination treatment with proteasome inhibitors and antiestrogens has a synergistic effect mediated by p21WAF1 in estrogen receptor-positive breast cancer

International audienc

Profiling of Sub-Lethal in Vitro Effects of Multi-Walled Carbon Nanotubes Reveals Changes in Chemokines and Chemokine Receptors

Engineered nanomaterials are potentially very useful for a variety of applications, but studies are needed to ascertain whether these materials pose a risk to human health. Here, we studied three benchmark nanomaterials (Ag nanoparticles, TiO2 nanoparticles, and multi-walled carbon nanotubes, MWCNTs) procured from the nanomaterial repository at the Joint Research Centre of the European Commission. Having established a sub-lethal concentration of these materials using two human cell lines representative of the immune system and the lungs, respectively, we performed RNA sequencing of the macrophage-like cell line after exposure for 6, 12, and 24 h. Downstream analysis of the transcriptomics data revealed significant effects on chemokine signaling pathways. CCR2 was identified as the most significantly upregulated gene in MWCNT-exposed cells. Using multiplex assays to evaluate cytokine and chemokine secretion, we could show significant effects of MWCNTs on several chemokines, including CCL2, a ligand of CCR2. The results demonstrate the importance of evaluating sub-lethal concentrations of nanomaterials in relevant target cells