Deposition of onco-histone H3.3-G34W leads to DNA repair deficiency and activates cGAS/STING-mediated immune responses.

Mutations in histone H3.3-encoding genes causing mutant histone tails are associated with specific cancers such as pediatric glioblastomas (H3.3-G34R/V) and giant cell tumor of the bone (H3.3-G34W). The mechanisms by which these mutations promote malignancy are not completely understood. Here we show that cells expressing H3.3-G34W exhibit DNA double-strand breaks (DSBs) repair defects and increased cellular sensitivity to ionizing radiation (IR). Mechanistically, H3.3-G34W can be deposited to damaged chromatin, but in contrast to wild-type H3.3, does not interact with non-homologous end-joining (NHEJ) key effectors KU70/80 and XRCC4 leading to NHEJ deficiency. Together with defective cell cycle checkpoints reported previously, this DNA repair deficiency in H3.3-G34W cells led to accumulation of micronuclei and cytosolic DNA following IR, which subsequently led to activation of the cyclic GMP-AMP synthase/stimulator of interferon genes (cGAS/STING) pathway, thereby inducing release of immune-stimulatory cytokines. These findings suggest a potential for radiotherapy for tumors expressing H3.3-G34W, which can be further improved by combination with STING agonists to induce immune-mediated therapeutic efficacy.

Miniaturized enantioselective tubular devices for the electromechanical wireless separation of chiral analytes.

Chirality plays a crucial role in different research fields, ranging from fundamental physico-chemistry to applied aspects in materials science and medicine. In this context, enantioselective loading and pumping of chiral analytes for analysis, separation, and cargo delivery applications is an interesting scientific challenge. Herein, we introduce artificial chiral soft electromechanical pumps based on a bi-layer film built up by electrodepositing polypyrrole and an inherently chiral conducting oligomer at its internal surface. The enantioselective device can be driven by bipolar electrochemistry to act as a pump, allowing the selective loading and separation of different chiral analytes injected as pure enantiomers and in racemic form (i.e., doxorubicin, a chemotherapy drug, limonene, carvone, and a chiral ferrocene). The synergy between wireless electromechanical actuation and inherent enantiodiscrimination features makes these actuators excellent candidates for the controlled handling of chiral molecules in the frame of potential applications ranging from analysis to drug delivery.

Bipolar Electrochemical Measurement of Enantiomeric Excess with Inherently Chiral Polymer Actuators.

Straightforward enantioselective analytical methods are very important for drug safety, considering that in certain cases one of the two enantiomers of a chiral molecule might be harmful for humans. In this work, we propose a simple system for the direct and easy read-out of the enantiomeric excess of 3,4-dihydroxyphenylalanine (DOPA) as a model analyte. A conducting oligomer, i.e. oligo-(3,3'-dibenzothiophene), bearing inherently chiral features, is electrogenerated on a polypyrrole film. The resulting freestanding hybrid material is used as a wireless enantioselective actuator in a bipolar electrochemical cell. Combining in a single setup two individual actuators with opposite chiral features allows a direct visual read-out of enantiomeric excess, as the bending amplitude of each of the two actuators is directly correlated with the concentration of the corresponding stereoisomer of the analyte. Optimization of the experimental parameters results in efficient bending, giving access to the percentage values of the enantiomeric excess in mixtures containing different ratios of the antipodes, thus opening the way to potential applications for chiral in situ analysis.

Hybrid light-emitting devices for the straightforward readout of chiral information.

Bipolar electrochemistry has gained increasing attention in recent years as an attractive transduction concept in analytical chemistry in general and, more specifically, in the frame of chiral recognition. Herein, we use this concept of wireless electrochemistry, based on the combination of the enantioselective oxidation of a chiral probe with the emission of light from a light-emitting diode (LED), as an alternative for an easy and straightforward readout of the presence of chiral molecules in solution. A hybrid polymer-microelectronic device was designed, using an inherently chiral oligomer, that is, oligo-(3,3'-dibenzothiophene) and a polypyrrole strip as the anode and cathode of a miniaturized LED. The wireless induced redox reactions trigger light emission when the probe with the right chirality is present in solution, whereas no light emission is observed for the opposite enantiomer. The average light intensity shows a linear correlation with the analyte concentration, and the concept opens the possibility to quantify the enantiomeric excess in mixtures of the molecular antipodes.

Direct dynamic read-out of molecular chirality with autonomous enzyme-driven swimmers.

A key approach for designing bioinspired machines is to transfer concepts from nature to man-made structures by integrating biomolecules into artificial mechanical systems. This strategy allows the conversion of molecular information into macroscopic action. Here, we describe the design and dynamic behaviour of hybrid bioelectrochemical swimmers that move spontaneously at the air-water interface. Their motion is governed by the diastereomeric interactions between immobilized enantiopure oligomers and the enantiomers of a chiral probe molecule present in solution. These dynamic bipolar systems are able to convert chiral information present at the molecular level into enantiospecific macroscopic trajectories. Depending on the enantiomer in solution, the swimmers will move clockwise or anticlockwise; the concept can also be used for the direct visualization of the degree of enantiomeric excess by analysing the curvature of the trajectories. Deciphering in such a straightforward way the enantiomeric ratio could be useful for biomedical applications, for the read-out of food quality or as a more general analogue of polarimetric measurements.

Globally altered epigenetic landscape and delayed osteogenic differentiation in H3.3-G34W-mutant giant cell tumor of bone.

The neoplastic stromal cells of giant cell tumor of bone (GCTB) carry a mutation in H3F3A, leading to a mutant histone variant, H3.3-G34W, as a sole recurrent genetic alteration. We show that in patient-derived stromal cells H3.3-G34W is incorporated into the chromatin and associates with massive epigenetic alterations on the DNA methylation, chromatin accessibility and histone modification level, that can be partially recapitulated in an orthogonal cell line system by the introduction of H3.3-G34W. These epigenetic alterations affect mainly heterochromatic and bivalent regions and provide possible explanations for the genomic instability, as well as the osteolytic phenotype of GCTB. The mutation occurs in differentiating mesenchymal stem cells and associates with an impaired osteogenic differentiation. We propose that the observed epigenetic alterations reflect distinct differentiation stages of H3.3 WT and H3.3 MUT stromal cells and add to H3.3-G34W-associated changes.

Absolute Chiral Recognition with Hybrid Wireless Electrochemical Actuators.

Chiral discrimination is of crucial importance for many applications, including drug cross checking and electronic tongue-type devices. In a typical sensing scheme, an enantiomeric selector is combined with an appropriate transduction mechanism. We propose here a hybrid material composed of an electrically conducting oligomer i.e. oligo-(3,3'-dibenzothiophene) bearing inherently chiral features and polypyrrole as a support, which can undergo electrochemical actuation. The combination of both leads to a freestanding film that is addressable in a wireless way based on the principle of bipolar electrochemistry. The induced redox reactions lead to well-pronounced actuation when DOPA with the right chirality is present in solution as a model analyte, whereas absolutely no electromechanical response is measured for the wrong enantiomer. This constitutes a straightforward and absolute read out of chiral information where the amplitude of actuation is correlated with the concentration of the analyte. Optimization of the scheme results in highly efficient bending and thus opens up new directions in the field of chiral technologies.

Designing tubular conducting polymer actuators for wireless electropumping.

Rational design and shaping of soft smart materials offer potential applications that cannot be addressed with rigid systems. In particular, electroresponsive elastic materials are well-suited for developing original active devices, such as pumps and actuators. However, applying the electric stimulus requires usually a physical connection between the active part and a power supply. Here we report about the design of an electromechanical system based on conducting polymers, enabling the actuation of a wireless microfluidic pump. Using the electric field-induced asymmetric polarization of miniaturized polypyrrole tubes, it is possible to trigger simultaneously site-specific chemical reactions, leading to shrinking and swelling in aqueous solution without any physical connection to a power source. The complementary electrochemical reactions occurring at the opposite extremities of the tube result in a differential change of its diameter. In turn, this electromechanical deformation allows inducing highly controlled fluid dynamics. The performance of such a remotely triggered electrochemically active soft pump can be fine-tuned by optimizing the wall thickness, length and inner diameter of the material. The efficient and fast actuation of the polymer pump opens up new opportunities for actuators in the field of fluidic or microfluidic devices, such as controlled drug release, artificial organs and bioinspired actuators.

Chiral platinum-polypyrrole hybrid films as efficient enantioselective actuators.

We report the synthesis of a hybrid bilayer, being composed of a free-standing conducting polymer film and a layer of mesoporous metal, encoded with chiral features. The resulting structure constitutes an enantioselective actuator, which can be electrochemically addressed in a wireless way. The controlled discriminatory deformation of the film allows an easy readout of chiral information.

Wireless Coupling of Conducting Polymer Actuators with Light Emission.

Combining the actuation of conducting polymers with additional functionalities is an interesting fundamental scientific challenge and increases their application potential. Herein we demonstrate the possibility of direct integration of a miniaturized light emitting diode (LED) in a polypyrrole (PPy) matrix in order to achieve simultaneous wireless actuation and light emission. A light emitting diode is used as a part of an electroactive surface on which electrochemical polymerization allows direct incorporation of the electronic device into the polymer. The resulting free-standing polymer/LED hybrid can be addressed by bipolar electrochemistry to trigger simultaneously oxidation and reduction reactions at its opposite extremities, leading to a controlled deformation and an electron flow through the integrated LED. Such a dual response in the form of actuation and light emission opens up interesting perspectives in the field of microrobotics.

Facile Fabrication of Surface-Imprinted Macroporous Films for Chemosensing of Human Chorionic Gonadotropin Hormone.

We present an improved approach for the preparation of highly selective and homogeneous molecular cavities in molecularly imprinted polymers (MIPs) via the combination of surface imprinting and semi-covalent imprinting. Toward that, first, a colloidal crystal mold was prepared via the Langmuir-Blodgett (LB) technique. Then, human chorionic gonadotropin (hCG) template protein was immobilized on the colloidal crystal mold. Later, hCG derivatization with electroactive functional monomers via amide chemistry was performed. In a final step, optimized potentiostatic polymerization of 2,3'-bithiophene enabled depositing an MIP film as the macroporous structure. This synergistic strategy resulted in the formation of molecularly imprinted cavities exclusively on the internal surface of the macropores, which were accessible after dissolution of silica molds. The recognition of hCG by the macroporous MIP film was transduced with the help of electric transducers, namely, extended-gate field-effect transistors (EG-FET) and capacitive impedimetry (CI). These readout strategies offered the ability to create chemosensors for the label-free determination of the hCG hormone. Other than the simple confirmation of pregnancy, hCG assay is a common tool for the diagnosis and follow-up of ectopic pregnancy or trophoblast tumors. Concentration measurements with these EG-FET and CI-based devices allowed real-time measurements of hCG in the range of 0.8-50  and 0.17-2.0 fM, respectively, in 10 mM carbonate buffer (pH = 10). Moreover, the selectivity of chemosensors with respect to protein interferences was very high.

Wireless Electromechanical Readout of Chemical Information.

Collecting electrochemical information concerning the presence of molecules in a solution is usually achieved by measuring current, potential, resistance, or impedance via connection to a power supply. Here, we suggest wireless electromechanical actuation as a straightforward readout of chemical information. This can be achieved based on the concept of bipolar electrochemistry, which allows measuring the presence of different model species in a quantitative way. We validate the concept by using a free-standing polypyrrole film. Its positively polarized extremity participates in an oxidation of the analyte and delivers electrons to the opposite extremity for the reduction of the polymer. This reduction is accompanied by the insertion of counterions and thus leads to partial swelling of the film, inducing its bending. The resulting actuation is found to be a linear function of the analyte concentration, and also a Michaelis-Menten type correlation is obtained for biochemical analytes. This electromechanical transduction allows an easy optical readout and opens up very interesting perspectives not only in the field of sensing but also far beyond, such as for the elaboration of self-regulating biomimetic systems.

Electrically Controlled Nano and Micro Actuation in Memristive Switching Devices with On-Chip Gas Encapsulation.

Nanoactuators are a key component for developing nanomachinery. Here, an electrically driven device yielding actuation stresses exceeding 1 MPa withintegrated optical readout is demonstrated. 10 nm thick Al2 O3 electrolyte films are sandwiched between graphene and Au electrodes. These allow reversible room-temperature solid-state redox reactions, producing Al metal and O2 gas in a memristive-type switching device. The resulting high-pressure oxygen micro-fuel reservoirs are encapsulated under the graphene, swelling to heights of up to 1 µm, which can be dynamically tracked by plasmonic rulers. Unlike standard memristors where the memristive redox reaction occurs in single or few conductive filaments, the mechanical deformation forces the creation of new filaments over the whole area of the inflated film. The resulting on-off resistance ratios reach 108 in some cycles. The synchronization of nanoactuation and memristive switching in these devices is compatible with large-scale fabrication and has potential for precise and electrically monitored actuation technology.

Reactivation of endogenous retroviral elements via treatment with DNMT- and HDAC-inhibitors.

Inhibitors of DNA methyltransferases (DNMTis) or histone deacetylases (HDACis) are epigenetic drugs which are investigated since decades. Several have been approved and are applied in the treatment of hematopoietic and lymphatic malignancies, although their mode of action has not been fully understood. Two recent findings improved mechanistic insights: i) activation of human endogenous retroviral elements (HERVs) with concomitant synthesis of double-stranded RNAs (dsRNAs), and ii) massive activation of promoters from long terminal repeats (LTRs) which originated from past HERV invasions. These dsRNAs activate an antiviral response pathway followed by apoptosis. LTR promoter activation leads to synthesis of non-annotated transcripts potentially encoding novel or cryptic proteins. Here, we discuss the current knowledge of the molecular effects exerted by epigenetic drugs with a focus on DNMTis and HDACis. We highlight the role in LTR activation and provide novel data from both in vitro and in vivo epigenetic drug treatment.

Multiscale positive feedbacks contribute to unidirectional gastric disease progression induced by helicobacter pylori infection.

BACKGROUND: Helicobacter Pylori (HP) is the most common risk factor for gastric cancer. Nearly half the world's population is infected with HP, but only a small percentage of those develop significant pathology. The bacteria itself does not directly cause cancer; rather it promotes an environment that is conducive to tumor formation. Upon infection, HP induces transcriptional changes in the host, leading to enhanced proliferation and host immune response. In addition, HP causes direct damage to gastric epithelial cells. RESULTS: We present a multiscale mechanistic model of HP induced changes. The model includes four modules representing the host transcriptional changes in response to infection, gastric atrophy, the Hedgehog pathway response, and the restriction point that controls cell cycle. This model was able to recapture a number of literature reported observations and was used as an "in silico" representation of the biological system for further analysis. Dynamical analysis of the model revealed that HP might induce the activation of multiple interplayed positive feedbacks, which in turn might result in a "ratchet ladder" system that promotes a unidirectional progression of gastric disease. CONCLUSIONS: The current multiscale model is able to recapitulate the observed experimental features of HP host interactions and provides dynamic insights on the epidemiologically observed heterogeneity in disease progression. This model provides a solid framework that can be further expanded and validated to include additional experimental evidence, to understand the complex multi-pathway interactions characterizing HP infection, and to design novel treatment protocols for HP induced diseases.

Wireless Electrochemical Actuation of Conducting Polymers.

Electrochemical actuation of conducting polymers usually requires a direct connection to an electric power supply. In this contribution, we suggest to overcome this issue by using the concept of bipolar electrochemistry. This allows changing the oxidation state of the polymer in a gradual and wireless way. Free-standing polypyrrole films were synthesized with an intrinsic morphological asymmetry of their two faces in order to form a bilayer structure. Immersing such objects in an electrolyte solution and exposing them to a potential gradient leads to the asymmetric oxidation/reduction of the polymer, resulting in differential shrinking and swelling along the main axis. This additional asymmetry is responsible for a structural deformation. Optimization allowed highly efficient bending, which is expected to open up completely new directions in the field of actuation due to the wireless mode of action.

Generation of electrochemiluminescence at bipolar electrodes: concepts and applications.

Bipolar electrochemistry (BPE) is an unconventional technique where a conducting object is addressed electrochemically in an electrolyte without any wire connection with an external power supply. BPE has been known for decades but remained limited to only a couple of niche applications. However, it is now undergoing a true renewal of interest especially in the context of analytical chemistry. The bipolar electrode exhibits two distinct poles of opposite polarization with respect to the solution. This allows one to separate the localization of sensing elements versus reporting ones. Also, arrays of bipolar microelectrodes can be addressed simultaneously to perform parallel analyses. Among several reporting strategies, the combination of BPE with electro-chemiluminescence (ECL) is the most frequent choice owing to the very simple visual readout provided by ECL. This article reviews the field from the initial reports to the most recent ones, revealing numerous opportunities including novel analytical strategies for the detection of small molecular analytes and biorelevant molecules such as DNA, RNA, peptides, or other biomarkers. Graphical Abstract Principle of electrochemiluminescence generation at one extremity of a bipolar electrode.

Systematic evaluation of bundled SPC water for biomolecular simulations.

In bundled SPC water models, the relative motion of groups of four water molecules is restrained by distance-dependent potentials. Bundled SPC models have been used in hybrid all-atom/coarse-grained (AA/CG) multiscale simulations, since they enable to couple atomistic SPC water with supra-molecular CG water models that effectively represent more than a single water molecule. In the present work, we systematically validated and critically tested bundled SPC water models as solvent for biomolecular simulations. To that aim, we investigated both thermodynamic and structural properties of various biomolecular systems through molecular dynamics (MD) simulations. Potentials of mean force of dimerization of pairs of amino acid side chains as well as hydration free energies of single side chains obtained with bundled SPC and standard (unrestrained) SPC water agree closely with each other and with experimental data. Decomposition of the hydration free energies into enthalpic and entropic contributions reveals that in bundled SPC, this favorable agreement of the free energies is due to a larger degree of error compensation between hydration enthalpy and entropy. The Ramachandran maps of Ala3, Ala5, and Ala7 peptides are similar in bundled and unrestrained SPC, whereas for the (GS)2 peptide, bundled water leads to a slight overpopulation of extended conformations. Analysis of the end-to-end distance autocorrelation times of the Ala5 and (GS)2 peptides shows that sampling in more viscous bundled SPC water is about two times slower. Pronounced differences between the water models were found for the structure of a coiled-coil dimer, which is instable in bundled SPC but not in standard SPC. In addition, the hydration of the active site of the serine protease α-chymotrypsin depends on the water model. Bundled SPC leads to an increased hydration of the active site region, more hydrogen bonds between water and catalytic triad residues, and a significantly slower exchange of water molecules between the active site and the bulk. Our results form a basis for assessing the accuracy that can be expected from bundled SPC water models. At the same time, this study also highlights the importance of evaluating beforehand the effects of water bundling on the biomolecular system of interest for a particular multiscale simulation application.

Electropolymerization of polypyrrole by bipolar electrochemistry in an ionic liquid.

Bipolar electrochemistry has been recently explored for the modification of conducting micro- and nanoobjects with various surface layers. So far, it has been assumed that such processes should be carried out in low-conductivity electrolytes in order to be efficient. We report here the first bipolar electrochemistry experiment carried out in an ionic liquid, which by definition shows a relatively high conductivity. Pyrrole has been electropolymerized on a bipolar electrode, either in ionic liquid or in acetonitrile. The resulting polymer films were characterized by scanning electron microscopy and by contact profilometry. We demonstrate that the films obtained in an ionic liquid are thinner and smoother than the films synthesized in acetonitrile. Furthermore, a well-defined band of polypyrrole can be obtained in ionic liquid, in contrast to acetonitrile for which the polypyrrole film is present on the whole anodic part of the bipolar electrode.

High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications.

MiRNAs are discussed as diagnostic and therapeutic molecules. However, effective miRNA drug treatments with miRNAs are, so far, hampered by the complexity of the miRNA networks. To identify potential miRNA drugs in colorectal cancer, we profiled miRNA and mRNA expression in matching normal, tumor and metastasis tissues of eight patients by Illumina sequencing. We validated six miRNAs in a large tissue screen containing 16 additional tumor entities and identified miRNA-1, miRNA-129, miRNA-497 and miRNA-215 as constantly de-regulated within the majority of cancers. Of these, we investigated miRNA-1 as representative in a systems-biology simulation of cellular cancer models implemented in PyBioS and assessed the effects of depletion as well as overexpression in terms of miRNA-1 as a potential treatment option. In this system, miRNA-1 treatment reverted the disease phenotype with different effectiveness among the patients. Scoring the gene expression changes obtained through mRNA-Seq from the same patients we show that the combination of deep sequencing and systems biological modeling can help to identify patient-specific responses to miRNA treatments. We present this data as guideline for future pre-clinical assessments of new and personalized therapeutic options.