Impact of germline and somatic missense variations on drug binding sites.

Advancements in next-generation sequencing (NGS) technologies are generating a vast amount of data. This exacerbates the current challenge of translating NGS data into actionable clinical interpretations. We have comprehensively combined germline and somatic nonsynonymous single-nucleotide variations (nsSNVs) that affect drug binding sites in order to investigate their prevalence. The integrated data thus generated in conjunction with exome or whole-genome sequencing can be used to identify patients who may not respond to a specific drug because of alterations in drug binding efficacy due to nsSNVs in the target protein\u27s gene. To identify the nsSNVs that may affect drug binding, protein-drug complex structures were retrieved from Protein Data Bank (PDB) followed by identification of amino acids in the protein-drug binding sites using an occluded surface method. Then, the germline and somatic mutations were mapped to these amino acids to identify which of these alter protein-drug binding sites. Using this method we identified 12 993 amino acid-drug binding sites across 253 unique proteins bound to 235 unique drugs. The integration of amino acid-drug binding sites data with both germline and somatic nsSNVs data sets revealed 3133 nsSNVs affecting amino acid-drug binding sites. In addition, a comprehensive drug target discovery was conducted based on protein structure similarity and conservation of amino acid-drug binding sites. Using this method, 81 paralogs were identified that could serve as alternative drug targets. In addition, non-human mammalian proteins bound to drugs were used to identify 142 homologs in humans that can potentially bind to drugs. In the current protein-drug pairs that contain somatic mutations within their binding site, we identified 85 proteins with significant differential gene expression changes associated with specific cancer types. Information on protein-drug binding predicted drug target proteins and prevalence of both somatic and germline nsSNVs that disrupt these binding sites can provide valuable knowledge for personalized medicine treatment. A web portal is available where nsSNVs from individual patient can be checked by scanning against DrugVar to determine whether any of the SNVs affect the binding of any drug in the database.The Pharmacogenomics Journal advance online publication, 26 January 2016; doi:10.1038/tpj.2015.97

Lifetime measurements of Triaxial Strongly Deformed bands in 163^{163}Tm

With the Doppler Shift Attenuation Method, quadrupole transition moments, $Q_t$, were determined for the two recently proposed Triaxial Strongly Deformed (TSD) bands in $^{163}$Tm. The measured $Q_t$ moments indicate that the deformation of these bands is larger than that of the yrast, signature partners. However, the measured values are smaller than those predicted by theory. This observation appears to be valid for TSD bands in several nuclei of the regionComment: 8 pages, 5 figures. Submitted to Physical Review

Activation of PKA leads to mesenchymal-to-epithelial transition and loss of tumor-initiating ability

The epithelial-to-mesenchymal transition enables carcinoma cells to acquire malignancy-associated traits and the properties of tumor-initiating cells (TICs). TICs have emerged in recent years as important targets for cancer therapy, owing to their ability to drive clinical relapse and enable metastasis. Here, we propose a strategy to eliminate mesenchymal TICs by inducing their conversion to more epithelial counterparts that have lost tumor-initiating ability. We report that increases in intracellular levels of the second messenger, adenosine 3',5'-monophosphate, and the subsequent activation of protein kinase A (PKA) induce a mesenchymal-to-epithelial transition (MET) in mesenchymal human mammary epithelial cells. PKA activation triggers epigenetic reprogramming of TICs by the histone demethylase PHF2, which promotes their differentiation and loss of tumor-initiating ability. This study provides proof-of-principle for inducing an MET as differentiation therapy for TICs and uncovers a role for PKA in enforcing and maintaining the epithelial state

An Intrinsically Disordered Region of the Acetyltransferase p300 with Similarity to Prion-Like Domains Plays a Role in Aggregation

Several human diseases including neurodegenerative disorders and cancer are associated with abnormal accumulation and aggregation of misfolded proteins. Proteins with high tendency to aggregate include the p53 gene product, TAU and alpha synuclein. The potential toxicity of aberrantly folded proteins is limited via their transport into intracellular sub-compartments, the aggresomes, where misfolded proteins are stored or cleared via autophagy. We have identified a region of the acetyltransferase p300 that is highly disordered and displays similarities with prion-like domains. We show that this region is encoded as an alternative spliced variant independently of the acetyltransferase domain, and provides an interaction interface for various misfolded proteins, promoting their aggregation. p300 enhances aggregation of TAU and of p53 and is a component of cellular aggregates in both tissue culture cells and in alpha-synuclein positive Lewy bodies of patients affected by Parkinson disease. Down-regulation of p300 impairs aggresome formation and enhances cytotoxicity induced by misfolded protein stress. These data unravel a novel activity of p300, offer new insights into the function of disordered domains and implicate p300 in pathological aggregation that occurs in neurodegeneration and cancer

Cast CF8C-Plus Stainless Steel for Turbocharger Applications

The purpose of this Cooperative Research and Development Agreement (CRADA) project is to provide the critical test data needed to qualify CF8C-Plus cast stainless steel for commercial production and use for turbocharger housings with upgraded performance and durability relative to standard commercial cast irons or stainless steels. The turbocharger technologies include, but are not limited to, heavy-duty highway diesel engines, and passenger vehicle diesel and gasoline engines. This CRADA provides additional critical high-temperature mechanical properties testing and data analysis needed to quality the new CF8C-Plus steels for turbocharger housing applications

Complex ferromagnetic state and magnetocaloric effect in single crystalline Nd_{0.7}Sr_{0.3}MnO_{3}

The magnetocaloric effect in single crystalline Nd_{0.7}Sr_{0.3}MnO_{3} is investigated by measuring the field-induced adiabatic change in temperature which reveals a single negative peak around 130 K well below the Curie temperature (T_C=203 K). In order to understand this unusual magnetocaloric effect, we invoke the reported {55}^Mn spin-echo nuclear magnetic resonance, electron magnetic resonance and polarized Raman scattering measurements on Nd_{0.7}Sr_{0.3}MnO_{3}. We show that this effect is a manifestation of a competition between the double exchange mechanism and correlations arising from coupled spin and lattice degrees of freedom which results in a complex ferromagnetic state. The critical behavior of Nd_{0.7}Sr_{0.3}MnO_{3} near Curie temperature is investigated to study the influence of the coupled degrees of freedom. We find a complicated behavior at low fields in which the order of the transition could not be fixed and a second-order-like behavior at high fields.Comment: Accepted for publication in Phys. Rev.

Outflow Facility Effects of 3 Schlemm’s Canal Microinvasive Glaucoma Surgery Devices

Purpose To study the effect of 3 Schlemm’s canal (SC) microinvasive glaucoma surgery (MIGS) devices on outflow facility. Design Paired comparisons, randomized design, baseline-controlled study. Participants Thirty-six pairs of dissected anterior segments from donated human eye bank eyes without glaucoma were studied. A baseline measurement was collected from each eye to serve as its control. Methods Using a constant pressure perfusion method, outflow facility was measured in paired eyes from human donors. Measurements were made at perfusion pressures of 10 mmHg, 20 mmHg, 30 mmHg, and 40 mmHg. Outflow facility was measured before (baseline control) and after the implantation of an SC glaucoma drainage device or sham procedure. Three sets of experiments were carried out comparing 1 and 2 iStent Trabecular Micro-Bypass Stents and 2 iStent Inject implants with the Hydrus Microstent. Main Outcome Measures Change in outflow facility from baseline or contralateral eye. Results After Hydrus placement, the outflow facility increased from 0.23±0.03 μl/minute per millimeter of mercury at baseline to 0.38±0.03 μl/minute per millimeter of mercury (P < 0.001). The percent increase in outflow facility was 79±21% for the Hydrus and 11±16% for the 2 iStent Inject devices, a difference that was significant (P = 0.018). Outflow facility with 1 iStent (0.38±0.07 μl/minute per millimeter of mercury) was greater than baseline (0.28±0.03 μl/minute per millimeter of mercury; P = 0.031). The 1 iStent showed a greater increase in outflow facility from baseline (0.10±0.04 μl/minute per millimeter of mercury) compared with the sham procedure (–0.08±0.05 μl/minute per millimeter of mercury; P = 0.042). No other significant differences were found. Conclusions The longer the MIGS device, and thus the more SC that it dilates, the greater the outflow facility

Level Structure of 103Ag at high spins

High spin states in $^{103}$Ag were investigated with the Gammasphere array, using the $^{72}$Ge($^{35}$Cl,$2p2n$)$^{103}$Ag reaction at an incident beam energy of 135 MeV. A $\Delta J$=1 sequence with predominantly magnetic transitions and two nearly-degenerate $\Delta J=1$ doublet bands have been observed. The dipole band shows a decreasing trend in the $B(M1)$ strength as function of spin, a well established feature of magnetic bands. The nearly-degenerate band structures satisfy the three experimental signatures of chirality in the nuclei; however microscopic calculations are indicative of a magnetic phenomeno

Evaluation of alternative solvents in common amide coupling reactions : replacement of dichloromethane and N,N-dimethylformamide

A range of alternative solvents have been evaluated within amidation reactions employing common coupling reagents with a view to identifying suitable replacements for dichloromethane and N,N-dimethylformamid

Therapeutic potential of TLR8 agonist GS-9688 (selgantolimod) in chronic hepatitis B: re-modelling of antiviral and regulatory mediators

Background & Aims: GS‐9688 (selgantolimod) is a toll‐like receptor 8 (TLR8) agonist in clinical development for the treatment of chronic hepatitis B (CHB). Antiviral activity of GS‐9688 has previously been evaluated in vitro in hepatitis B virus (HBV)‐infected hepatocytes and in vivo in the woodchuck model of CHB. Here we evaluated the potential of GS‐9688 to boost responses contributing to viral control and to modulate regulatory mediators. Approach & Results: We characterised the effect of GS‐9688 on immune cell subsets in vitro in PBMC of healthy controls and CHB patients. GS‐9688 activated dendritic cells and mononuclear phagocytes to produce IL‐12 and other immunomodulatory mediators, inducing a comparable cytokine profile in healthy controls and CHB patients. GS‐9688 increased the frequency of activated natural killer (NK) cells, mucosal‐associated invariant T‐cells (MAITs), CD4+ follicular helper T‐cells (TFH) and, in ~50% of patients, HBV‐specific CD8+T‐cells expressing interferon‐γ (IFNγ). Moreover, in vitro stimulation with GS‐9688 induced NK cell expression of IFNγ and TNFα and promoted hepatocyte lysis. We also assessed whether GS‐9688 inhibited immunosuppressive cell subsets that might enhance antiviral efficacy. Stimulation with GS‐9688 reduced the frequency of CD4+ regulatory T‐cells and monocytic myeloid‐derived suppressor cells (MDSC). Residual MDSC expressed higher levels of negative immune regulators, galectin‐9 and PD‐L1. Conversely, GS‐9688 induced an expansion of immunoregulatory TNF‐related apoptosis‐inducing ligand+ (TRAIL) regulatory NK cells and degranulation of arginase‐I+ polymorphonuclear‐MDSC (PMN‐MDSC). Conclusions: GS‐9688 induces cytokines in human PBMC that are able to activate antiviral effector function by multiple immune mediators (HBV‐specific CD8+T‐cells, TFH, NK cells and MAITs). Whilst reducing the frequency of some immunoregulatory subsets, it enhances the immunosuppressive potential of others, highlighting potential biomarkers and immunotherapeutic targets to optimise the antiviral efficacy of GS‐9688