ABSTRACT
Genetic predisposition is one of the major risk factors for pediatric cancer, with ~10% of children being carriers of a predisposing germline alteration. It is likely that this is the tip of the iceberg and many children are underdiagnosed, as most of the analysis focuses on single or short nucleotide variants, not considering the full spectrum of DNA alterations. Hence, we applied optical genome mapping (OGM) to our cohort of 34 pediatric cancer patients to perform an unbiased germline screening and analyze the frequency of structural variants (SVs) and their impact on cancer predisposition. All children were clinically highly suspicious for germline alterations (concomitant conditions or congenital anomalies, positive family cancer history, particular cancer type, synchronous or metachronous tumors), but whole exome sequencing (WES) had failed to detect pathogenic variants in cancer predisposing genes. OGM detected a median of 49 rare SVs (range 27-149) per patient. By analysis of 18 patient-parent trios, we identified three de novo SVs. Moreover, we discovered a likely pathogenic deletion of exon 3 in the known cancer predisposition gene BRCA2, and identified a duplication in RPA1, which might represent a new cancer predisposition gene. We conclude that optical genome mapping is a suitable tool for detecting potentially predisposing SVs in addition to WES in pediatric cancer patients.
Subject(s)
Germ-Line Mutation , Neoplasms , Child , Humans , Genetic Predisposition to Disease , Mutation , Neoplasms/genetics , Chromosome MappingABSTRACT
Bromodomain protein 4 (BRD4) is a member of the bromodomain and extra-terminal domain (BET) protein family. It binds to acetylated histone tails via its tandem bromodomains BD1 and BD2 and forms a complex with the positive transcription elongation factor b, which controls phosphorylation of RNA polymerase II, ultimately leading to stimulation of transcription elongation. An essential role of BRD4 in cell proliferation and cancer growth has been reported in several recent studies. We analyzed the binding of BRD4 BD1 and BD2 to different partners and showed that the strongest interactions took place with di- and tetra-acetylated peptides derived from the histone 4 N-terminal tail. We also found that several histone 4 residues neighboring the acetylated lysines significantly influenced binding. We generated 10 different BRD4 BD1 mutants and analyzed their affinities to acetylated histone tails and to the BET inhibitor JQ1 using several complementary biochemical and biophysical methods. The impact of these mutations was confirmed in a cellular environment. Altogether, the results show that Trp-81, Tyr-97, Asn-140, and Met-149 play similarly important roles in the recognition of acetylated histones and JQ1. Pro-82, Leu-94, Asp-145, and Ile-146 have a more differentiated role, suggesting that different kinds of interactions take place and that resistance mutations compatible with BRD4 function are possible. Our study extends the knowledge on the contribution of individual BRD4 amino acids to histone and JQ1 binding and may help in the design of new BET antagonists with improved pharmacological properties.
Subject(s)
Azepines/metabolism , Histones/metabolism , Nuclear Proteins/antagonists & inhibitors , Nuclear Proteins/metabolism , Transcription Factors/antagonists & inhibitors , Transcription Factors/metabolism , Triazoles/metabolism , Acetylation , Amino Acid Sequence , Animals , Azepines/pharmacology , Cell Cycle Proteins , Chromatin/metabolism , HEK293 Cells , Histones/chemistry , Humans , Ligands , Models, Molecular , Molecular Sequence Data , Mutagenesis, Site-Directed , Mutation , Nuclear Proteins/chemistry , Nuclear Proteins/genetics , Peptide Fragments/chemistry , Peptide Fragments/metabolism , Protein Binding , Protein Stability , Protein Structure, Tertiary , Transcription Factors/chemistry , Transcription Factors/genetics , Triazoles/pharmacologyABSTRACT
Axonal surface proteins encompass a group of heterogeneous molecules, which exert a variety of different functions in the highly interdependent relationship between axons and Schwann cells. We recently revealed that the tumour suppressor protein merlin, mutated in the hereditary tumour syndrome neurofibromatosis type 2, impacts significantly on axon structure maintenance in the peripheral nervous system. We now report on a role of neuronal merlin in the regulation of the axonal surface protein neuregulin 1 important for modulating Schwann cell differentiation and myelination. Specifically, neuregulin 1 type III expression is reduced in sciatic nerve tissue of neuron-specific knockout animals as well as in biopsies from seven patients with neurofibromatosis type 2. In vitro experiments performed on both the P19 neuronal cell line and primary dorsal root ganglion cells demonstrate the influence of merlin on neuregulin 1 type III expression. Moreover, expression of ERBB2, a Schwann cell receptor for neuregulin 1 ligands is increased in nerve tissue of both neuron-specific merlin knockout animals and patients with neurofibromatosis type 2, demonstrating for the first time that axonal merlin indirectly regulates Schwann cell behaviour. Collectively, we have identified that neuronally expressed merlin can influence Schwann cell activity in a cell-extrinsic manner.
Subject(s)
Neuregulin-1/physiology , Neurofibromin 2/physiology , Neurons/physiology , Receptor, ErbB-2/biosynthesis , Schwann Cells/metabolism , Signal Transduction/physiology , Adult , Aged , Animals , Cell Line , Cells, Cultured , Female , Humans , Male , Mice, Inbred C57BL , Mice, Knockout , Mice, Transgenic , Middle Aged , Neurofibromatosis 2/metabolism , Neurofibromatosis 2/pathology , Neurons/pathology , Schwann Cells/pathologyABSTRACT
PURPOSE: To assess the metformin effect on endometrial stromal cell decidualization, proliferation, gene and protein expression of IGFBPs, IGFs and their receptors. METHODS: Human endometrial stromal cells (hESCs) were cultured from endometrial biopsies of 11 women undergoing surgery for benign reasons. hESCs were decidualized with and without metformin in increasing doses. Supernatant and cells were harvested after decidualization for 12-14 days, followed by real-time PCR of IGFBP 1-6, IGF I, IGF II and their receptors. Prolactin, and IGFBP-1, -3, and -6 were additionally analyzed in supernatant by ELISA. Proliferation of hESCs and decidualization of hESCs were assessed under the influence of metformin. Data were analyzed using the paired t test with p < 0.05 considered significant. RESULTS: While lower concentrations of metformin (10(-4), 10(-5 )M) did not influence the decidualization and proliferation capacity of hESCs, higher concentrations (10(-3), 10(-2 )M metformin) significantly (p < 0.05) diminished decidualization, as well as stromal cell proliferation in a dose-dependent manner. Higher concentrations of metformin lead to a significant (p < 0.05) dose-dependent attenuation of the progesterone effect with regard to IGFBP-1, -3, -5, -6, as well as IGF I receptor, while it did not change the expression of IGFBP-2 and -4, IGF I and II and the IGF II receptor. This was confirmed on the protein level for IGFBP-1, -3, and -6. CONCLUSION: We were able to demonstrate for the first time a dose-dependent local effect of metformin within hESCs. Metformin might therefore influence locally the endometrial proliferation and maturation, and could open up new treatment options for gynecological diseases by vaginal application of metformin.
Subject(s)
Embryo Implantation/drug effects , Endometrium/metabolism , Hypoglycemic Agents/pharmacology , Metformin/pharmacology , Stromal Cells/metabolism , Cells, Cultured , Dose-Response Relationship, Drug , Endometrium/drug effects , Epithelial Cells/metabolism , Female , Humans , Hypoglycemic Agents/administration & dosage , Insulin-Like Growth Factor Binding Protein 1/genetics , Insulin-Like Growth Factor Binding Protein 1/metabolism , Insulin-Like Growth Factor I/genetics , Insulin-Like Growth Factor I/metabolism , Insulin-Like Growth Factor II/genetics , Insulin-Like Growth Factor II/metabolism , Metformin/administration & dosage , Progesterone/pharmacology , Prolactin/genetics , Prolactin/metabolism , Receptor, IGF Type 1/genetics , Receptor, IGF Type 1/metabolism , Stromal Cells/drug effectsABSTRACT
We have developed a surface plasmon resonance (SPR)-based inhibition in solution assay (ISA) to search for inhibitors of the medium affinity (KD = 0.8 µM) interaction between an E6-derived peptide (E6peptide) immobilized on the sensor and a PDZ domain (MAGI-1 PDZ1) in the mobile phase. DZ domains are widespread protein-protein interaction modules that recognize the C-terminus of various partners. Simulations indicated that relatively low compound concentrations (10 µM) and limited peptide densities (Rmax < 200 resonance units) should allow the detection of inhibitors with a target affinity close to 100 µM, which was then demonstrated experimentally. ISA screening, carried out on the Prestwick Chemical Library® (1120 compounds), identified 36 compounds that inhibited the interaction by more than 5%. Concentration-dependent ISA, carried out on a subset of 19 potential inhibitors, indicated that 13 of these indeed affected the interaction between MAGI-1 PDZ1 and the E6peptide. No effect was observed for 84 compounds randomly chosen among noninhibitors. One of the four best inhibitors was a peptide binder, and three were PDZ binders with KD in the 10-50 µM range. We propose that a medium (µM) affinity between the target and surface-bound partner is optimal for SPR-based ISA screening.
Subject(s)
Cell Adhesion Molecules, Neuronal/genetics , Cell Adhesion Molecules, Neuronal/metabolism , Computer Simulation , Small Molecule Libraries/metabolism , Surface Plasmon Resonance/methods , Adaptor Proteins, Signal Transducing , Amino Acid Sequence , Cell Adhesion Molecules , Guanylate Kinases , Humans , Molecular Sequence Data , Protein Binding/physiology , Random Allocation , Small Molecule Libraries/analysis , SolutionsABSTRACT
The combination of electrophysiology and neuroimaging methods allows the simultaneous measurement of electrical activity signals with calcium dynamics from single neurons to neuronal networks across distinct brain regions in vivo. While traditional electrophysiological techniques are limited by photo-induced artefacts and optical occlusion for neuroimaging, different types of transparent neural implants have been proposed to resolve these issues. However, reproducing proposed solutions is often challenging and it remains unclear which approach offers the best properties for long-term chronic multimodal recordings. We therefore created a streamlined fabrication process to produce, and directly compare, two types of transparent surface micro-electrocorticography (µECoG) implants: nano-mesh gold structures (m-µECoGs) versus a combination of solid gold interconnects and PEDOT:PSS-based electrodes (pp-µECoGs). Both implants allowed simultaneous multimodal recordings but pp-µECoGs offered the best overall electrical, electrochemical, and optical properties with negligible photo-induced artefacts to light wavelengths of interest. Showing functional chronic stability for up to four months, pp-µECoGs also allowed the simultaneous functional mapping of electrical and calcium neural signals upon visual and tactile stimuli during widefield imaging. Moreover, recordings during two-photon imaging showed no visible signal attenuation and enabled the correlation of network dynamics across brain regions to individual neurons located directly below the transparent electrical contacts.
Subject(s)
Calcium , Optogenetics , Electrodes, Implanted , Optogenetics/methods , Electrophysiology/methods , GoldABSTRACT
We investigated the suitability of surface plasmon resonance (SPR) for providing quantitative binding information from direct screening of a chemical library on protein tyrosine phosphatase 1b (PTP1B). The experimental design was established from simulations to detect binding with K(D) < 10â»4 M. The 1120 compounds (cpds) were injected sequentially at concentrations [C(cpd)] of 0.5 or 10 µM over various target surfaces. An optimized evaluation procedure was applied. More than 90% of cpds showed no detectable signal in four screens. The 30 highest responders at C(cpd)=10 µM, of which 25 were selected in at least one of three screens at C(cpd)=0.5 µM, contained 22 promiscuous binders and 8 potential PTP1B-specific binders with K(D) ~10â»5 M. Inhibition of PTP1B activity was assayed and confirmed for 6 of these, including sanguinarine, a known PTP1B inhibitor. C(cpd) dependence studies fully confirmed screening conclusions. The quantitative consistency of SPR data led us to propose a structure-activity relationship (SAR) model for developing selective PTP1B inhibitors based on the ranking of 10 arylbutylpiperidine analogs.
Subject(s)
Drug Discovery/methods , Enzyme Inhibitors/isolation & purification , Protein Tyrosine Phosphatase, Non-Receptor Type 1/metabolism , Small Molecule Libraries , Surface Plasmon Resonance/methods , Amino Acid Sequence , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Inhibitory Concentration 50 , Open Reading Frames , Protein Tyrosine Phosphatase, Non-Receptor Type 1/antagonists & inhibitorsABSTRACT
The isolation and culture of single floating myofibers with their adjacent muscle stem cells allow the analysis and comparison of muscle stem cells from aged and young mice. This method has the advantage that muscle stem cells are cultured on the myofiber, thereby culturing them in conditions as close to their endogenous niche as possible. Here we describe the isolation, culture, transfection with siRNA, and subsequent immunostaining for muscle stem cells on their adjacent myofibers from aged and young mice.
Subject(s)
Adult Stem Cells/cytology , Cell Culture Techniques/methods , Muscle Fibers, Skeletal/cytology , Muscle, Skeletal/cytology , Adult Stem Cells/metabolism , Aging , Animals , Antibodies , Cell Differentiation , Collagenases , Immunophenotyping , Mice , Muscle Fibers, Skeletal/metabolism , Muscle, Skeletal/metabolism , MyoD Protein/immunology , MyoD Protein/metabolism , PAX7 Transcription Factor/immunology , PAX7 Transcription Factor/metabolism , RNA, Small Interfering , Satellite Cells, Skeletal Muscle/cytology , Satellite Cells, Skeletal Muscle/metabolism , Transfection , WorkflowABSTRACT
Alphaviruses such as the Venezuelan equine encephalitis virus (VEEV) are important human emerging pathogens transmitted by mosquitoes. They possess a unique viral mRNA capping mechanism catalyzed by the viral non-structural protein nsP1, which is essential for virus replication. The alphaviruses capping starts by the methylation of a GTP molecule by the N7-guanine methyltransferase (MTase) activity; nsP1 then forms a covalent link with m7GMP releasing pyrophosphate (GT reaction) and the m7GMP is next transferred onto the 5'-diphosphate end of the viral mRNA to form a cap-0 structure. The cap-0 structure decreases the detection of foreign viral RNAs, prevents RNA degradation by cellular exonucleases, and promotes viral RNA translation into proteins. Additionally, reverse-genetic studies have demonstrated that viruses mutated in nsP1 catalytic residues are both impaired towards replication and attenuated. The nsP1 protein is thus considered an attractive antiviral target for drug discovery. We have previously demonstrated that the guanylylation of VEEV nsP1 can be monitored by Western blot analysis using an antibody recognizing the cap structure. In this study, we developed a high throughput ELISA screening assay to monitor the GT reaction through m7GMP-nsP1 adduct quantitation. This assay was validated using known nsP1 inhibitors before screening 1220 approved compounds. 18 compounds inhibiting the nsP1 guanylylation were identified, and their IC50 determined. Compounds from two series were further characterized and shown to inhibit the nsP1 MTase activity. Conversely, these compounds barely inhibited a cellular MTase demonstrating their specificity towards nsP1. Analogues search and SAR were also initiated to identify the active pharmacophore features. Altogether the results show that this HT enzyme-based assay is a convenient way to select potent and specific hit compounds targeting the viral mRNA capping of Alphaviruses.
Subject(s)
Antiviral Agents/pharmacology , Encephalitis Virus, Venezuelan Equine/drug effects , Encephalitis Virus, Venezuelan Equine/enzymology , Viral Nonstructural Proteins/antagonists & inhibitors , Animals , Chlorocebus aethiops , Drug Approval , Enzyme-Linked Immunosorbent Assay , High-Throughput Screening Assays , Humans , Inhibitory Concentration 50 , RNA Caps , Vero Cells , Virus Replication/drug effectsABSTRACT
Two highly pathogenic human coronaviruses associated with severe respiratory syndromes emerged since the beginning of the century. The severe acute respiratory syndrome SARS-coronavirus (CoV) spread first in southern China in 2003 with about 8000 infected cases in few months. Then in 2012, the Middle East respiratory syndrome (MERS-CoV) emerged from the Arabian Peninsula giving a still on-going epidemic associated to a high fatality rate. CoVs are thus considered a major health threat. This is especially true as no vaccine nor specific therapeutic are available against either SARS- or MERS-CoV. Therefore, new drugs need to be identified in order to develop antiviral treatments limiting CoV replication. In this study, we focus on the nsp14 protein, which plays a key role in virus replication as it methylates the RNA cap structure at the N7 position of the guanine. We developed a high-throughput N7-MTase assay based on Homogenous Time Resolved Fluorescence (HTRF®) and screened chemical libraries (2000 compounds) on the SARS-CoV nsp14. 20 compounds inhibiting the SARS-CoV nsp14 were further evaluated by IC50 determination and their specificity was assessed toward flavivirus- and human cap N7-MTases. Our results reveal three classes of compounds: 1) molecules inhibiting several MTases as well as the dengue virus polymerase activity unspecifically, 2) pan MTases inhibitors targeting both viral and cellular MTases, and 3) inhibitors targeting one viral MTase more specifically showing however activity against the human cap N7-MTase. These compounds provide a first basis towards the development of more specific inhibitors of viral methyltransferases.
Subject(s)
Antiviral Agents/isolation & purification , Drug Evaluation, Preclinical/methods , Exoribonucleases/antagonists & inhibitors , Methyltransferases/antagonists & inhibitors , Severe acute respiratory syndrome-related coronavirus/enzymology , Viral Nonstructural Proteins/antagonists & inhibitors , Fluorometry , Humans , Inhibitory Concentration 50 , Microbial Sensitivity TestsABSTRACT
The bromodomain and extraterminal (BET) subfamily of bromodomain-containing proteins has emerged in the last few years as an exciting, novel target group. BRD4, the best studied BET protein, is implicated in a number of hematological and solid tumors. This is linked to its role in modulating transcription elongation of essential genes involved in cell cycle and apoptosis such as c-Myc and BCL2. Potent BET inhibitors with promising antitumor efficacy in a number of preclinical cancer models have been identified in recent years. This led to clinical studies focusing mostly on the treatment of leukemia and lymphoma, and first encouraging signs of efficacy have already been reported. Here we discuss the biology of BRD4, its known interaction partners and implication in different tumor types. Further, we summarize the current knowledge on BET bromodomain inhibitors.
Subject(s)
Antineoplastic Agents/therapeutic use , Nuclear Proteins/antagonists & inhibitors , Transcription Factors/antagonists & inhibitors , Animals , Cell Cycle Proteins , Hematologic Neoplasms/drug therapy , Humans , Mice , Nuclear Proteins/chemistry , Nuclear Proteins/metabolism , Nuclear Proteins/physiology , Protein Structure, Tertiary , Transcription Factors/chemistry , Transcription Factors/metabolism , Transcription Factors/physiologyABSTRACT
Bromodomain protein 4 (BRD4), a member of the bromodomain and extra-terminal (BET) protein family, acts as a central element in transcriptional elongation and plays essential roles in cell proliferation. Inhibition of BRD4 binding to acetylated histone tails via its two bromodomains, BD1 and BD2, with small-molecule inhibitors has been shown to be a valid strategy to prevent cancer growth. We have evaluated and established two novel assays that quantify the interaction of transfected BRD4 BD1 with chemical inhibitors inside cultured cells. Both methods are based on the principle of ligand-induced protein stabilization by which the binding of a small-molecule inhibitor stabilizes intracellular BRD4 BD1 and protects it from proteolytic degradation. We demonstrate the universal character of this principle by using two orthogonal, highly sensitive detection technologies for the quantification of BRD4 BD1 levels in cellular lysates: enzyme fragment complementation and time-resolved fluorescence resonance energy transfer (TR-FRET). Upon optimization of both assays to a miniaturized high-throughput format, the methods were validated by testing a set of small-molecule BET inhibitors and comparing the results with those from a cell-free binding assay and a biophysical thermal shift assay. In addition, point mutations were introduced into BRD4 BD1, and the corresponding mutants were characterized in the TR-FRET stabilization assay.
Subject(s)
Drug Discovery , High-Throughput Screening Assays , Ligands , Nuclear Proteins/antagonists & inhibitors , Transcription Factors/antagonists & inhibitors , Cell Cycle Proteins , Cell Line , Fluoroimmunoassay , High-Throughput Screening Assays/methods , High-Throughput Screening Assays/standards , Humans , Mutation , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Protein Stability/drug effects , Reproducibility of Results , Small Molecule Libraries , Transcription Factors/genetics , Transcription Factors/metabolismABSTRACT
The autosomal dominant disorder neurofibromatosis type 2 (NF2) is a hereditary tumor syndrome caused by inactivation of the NF2 tumor suppressor gene, encoding merlin. Apart from tumors affecting the peripheral and central nervous systems, most NF2 patients develop peripheral neuropathies. This peripheral nerve disease can occur in the absence of nerve-damaging tumors, suggesting an etiology that is independent of gross tumor burden. We discovered that merlin isoform 2 (merlin-iso2) has a specific function in maintaining axonal integrity and propose that reduced axonal NF2 gene dosage leads to NF2-associated polyneuropathy. We identified a merlin-iso2-dependent complex that promotes activation of the GTPase RhoA, enabling downstream Rho-associated kinase to promote neurofilament heavy chain phosphorylation. Merlin-iso2-deficient mice exhibited impaired locomotor capacities, delayed sensory reactions and electrophysiological signs of axonal neuropathy. Sciatic nerves from these mice and sural nerve biopsies from NF2 patients revealed reduced phosphorylation of the neurofilament H subunit, decreased interfilament spacings and irregularly shaped axons.