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Role of Oatp2b1 in Drug Absorption and Drug-Drug Interactions [Articles]

The organic anion transporting polypeptide (OATP)2B1 is localized on the basolateral membrane of hepatocytes and is expressed in enterocytes. Based on its distribution pattern and functional similarity to OATP1B-type transporters, OATP2B1 might have a role in the absorption and disposition of a range of xenobiotics. Although several prescription drugs, including hydroxymethylglutaryl-coenzyme A-CoA reductase inhibitors (statins) such as fluvastatin, are OATP2B1 substrates in vitro, evidence supporting the in vivo relevance of this transporter remains limited, and most has relied on substrate-inhibitor interactions resulting in altered pharmacokinetic properties of the victim drugs. To address this knowledge deficit, we developed and characterized an Oatp2b1-deficient mouse model and evaluated the impact of this transporter on the absorption and disposition of fluvastatin. Consistent with the intestinal localization of Oatp2b1, we found that the genetic deletion or pharmacological inhibition of Oatp2b1 was associated with decreased absorption of fluvastatin by 2- to 3-fold. The availability of a viable Oatp2b1-deficient mouse model provides an opportunity to unequivocally determine the contribution of this transporter to the absorption and drug-drug interaction potential of drugs.

SIGNIFICANCE STATEMENT

The current investigation suggests that mice deficient in Oatp2b1 provide a valuable tool to study the in vivo importance of this transporter. In addition, our studies have identified novel potent inhibitors of OATP2B1 among the class of tyrosine kinase inhibitors, a rapidly expanding class of drugs used in various therapeutic areas that may cause drug-drug interactions with OATP2B1 substrates.




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Interaction of the Brain-Selective Sulfotransferase SULT4A1 with Other Cytosolic Sulfotransferases: Effects on Protein Expression and Function [Articles]

Sulfotransferase (SULT) 4A1 is a brain-selective sulfotransferase-like protein that has recently been shown to be essential for normal neuronal development in mice. In the present study, SULT4A1 was found to colocalize with SULT1A1/3 in human brain neurons. Using immunoprecipitation, SULT4A1 was shown to interact with both SULT1A1 and SULT1A3 when expressed in human cells. Mutation of the conserved dimerization motif located in the C terminus of the sulfotransferases prevented this interaction. Both ectopically expressed and endogenous SULT4A1 decreased SULT1A1/3 protein levels in neuronal cells, and this was also prevented by mutation of the dimerization motif. During differentiation of neuronal SH-SY5Y cells, there was a loss in SULT1A1/3 protein but an increase in SULT4A1 protein. This resulted in an increase in the toxicity of dopamine, a substrate for SULT1A3. Inhibition of SULT4A1 using small interference RNA abrogated the loss in SULT1A1/3 and reversed dopamine toxicity. These results show a reciprocal relationship between SULT4A1 and the other sulfotransferases, suggesting that it may act as a chaperone to control the expression of SULT1A1/3 in neuronal cells.

SIGNIFICANCE STATEMENT

The catalytically inactive sulfotransferase (SULT) 4A1 may regulate the function of other SULTs by interacting with them via a conserved dimerization motif. In neuron-like cells, SULT4A1 is able to modulate dopamine toxicity by interacting with SULT1A3, potentially decreasing the metabolism of dopamine.




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Reply to Cosgrove: Non-enzymatic action of expansins [Letters to the Editor]

In our computational study, we use molecular simulations to substantiate a hypothetical mechanism for glycosidic bond cleavage in the presence of a single catalytic acid at the active site of the mutant D10N HiCel45A. In addition to discussing this plausible mechanism from the context of structurally related MltA lytic transglycosylase and subfamily C GH45s, we also suggest the implications of the plausible mechanism for our current understanding of the action of expansins and lytic transglycosylases. As correctly pointed out by Professor Cosgrove (1), there is large body of evidence, a significant portion of which was regrettably not discussed in our paper, that suggests that expansins are incapable of lytic action on polysaccharide substrates. Whereas these insights do not change the results or the conclusions of our article, we would like to thank Professor Cosgrove for these additional insights. In particular, our main point with respect to expansins is that our results suggest the possibility that expansins are capable of nonhydrolytic lytic activity. Our intention was not to suggest this was the mechanism of expansins, but that it should be considered based on our results and the similarity of the active sites.The molecular mechanisms of how expansins enable cell wall expansion remains to be fully understood. Whereas our proposed mechanism resulting in the formation of the 1,6-anhdro product might be found in expansins and might contribute to the mode of action of expansins, we would like to emphasize that the intent of this study was only to suggest this as a...




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Non-enzymatic action of expansins [Letters to the Editor]

From their simulations of endoglucanase Cel45A, Bharadwaj et al. (1) propose that structurally related expansins and MltA may cut glycan backbones without generating reducing ends. This is tenable for MltA, a peptidoglycan lytic transglycosylase whose action produces nonreducing 1,6-anhydro products, but is untenable for expansins.Expansins loosen plant cell walls and induce wall expansion. Contrary to the assertion by Bharadwaj et al., the conclusion that expansins are not lytic is not merely based on lack of new reducing ends but is supported by multiple (negative) tests for polysaccharide cleavage that do not rely on detection of reducing ends. At least eight studies with three divergent groups of expansins document this point. For instance, α-expansin did not reduce the viscosity of various wall polysaccharide solutions, an endolytic assay that does not rely on measuring reducing ends (e.g. see Ref. 2 and other studies).Walls treated with α-expansin did not release saccharide fragments, measured by pulsed amperometric detection, which can detect nonreducing saccharides (3).In the case of β-expansins, protein treatments did not cleave the backbones of a wide range of dye-coupled cross-linked wall polysaccharides; nor did they cleave backbones of polysaccharides extracted from plant cell walls, measured by gel permeation chromatography (4).For five microbial expansins, tests with a range of dye-coupled cross-linked polysaccharides likewise did not detect lytic activity (e.g. see Ref. 5). Thus, extensive published evidence argues against lytic action by expansins, as proposed by Bharadwaj (1), and attempts to identify 1,6-anhydro products seem unlikely to succeed.




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Roles of active-site residues in catalysis, substrate binding, cooperativity, and the reaction mechanism of the quinoprotein glycine oxidase [Enzymology]

The quinoprotein glycine oxidase from the marine bacterium Pseudoalteromonas luteoviolacea (PlGoxA) uses a protein-derived cysteine tryptophylquinone (CTQ) cofactor to catalyze conversion of glycine to glyoxylate and ammonia. This homotetrameric enzyme exhibits strong cooperativity toward glycine binding. It is a good model for studying enzyme kinetics and cooperativity, specifically for being able to separate those aspects of protein function through directed mutagenesis. Variant proteins were generated with mutations in four active-site residues, Phe-316, His-583, Tyr-766, and His-767. Structures for glycine-soaked crystals were obtained for each. Different mutations had differential effects on kcat and K0.5 for catalysis, K0.5 for substrate binding, and the Hill coefficients describing the steady-state kinetics or substrate binding. Phe-316 and Tyr-766 variants retained catalytic activity, albeit with altered kinetics and cooperativity. Substitutions of His-583 revealed that it is essential for glycine binding, and the structure of H583C PlGoxA had no active-site glycine present in glycine-soaked crystals. The structure of H767A PlGoxA revealed a previously undetected reaction intermediate, a carbinolamine product-reduced CTQ adduct, and exhibited only negligible activity. The results of these experiments, as well as those with the native enzyme and previous variants, enabled construction of a detailed mechanism for the reductive half-reaction of glycine oxidation. This proposed mechanism includes three discrete reaction intermediates that are covalently bound to CTQ during the reaction, two of which have now been structurally characterized by X-ray crystallography.




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Prediction of tunnelling impact on flow rates of adjacent extraction water wells

The decline or drying up of groundwater sources near a tunnel route is damaging to groundwater users. Therefore, forecasting the impact of a tunnel on nearby groundwater sources is a challenging task in tunnel design. In this study, numerical and analytical approaches were applied to the Qomroud water conveyance tunnel (located in Lorestan province, Iran) to assess the impact of tunnelling on the nearby extraction water wells. Using simulation of groundwater-level fluctuation owing to tunnelling, the drawdown at the well locations was determined. From the drawdowns and using Dupuit's equation, the depletion of well flow rates after tunnelling was estimated. To evaluate the results, observed well flow rates before and after tunnelling were compared with the predicted flow rates. The observed and estimated water well flows (before and after tunnelling) showed a regression factor of 0.64, pointing to satisfactory results




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Cordycepin Inhibits Cancer Cell Proliferation and Angiogenesis through a DEK Interaction via ERK Signaling in Cholangiocarcinoma [Gastrointestinal, Hepatic, Pulmonary, and Renal]

Cholangiocarcinoma (CCA) is a malignant tumor that arises from the epithelial cells of the bile duct and is notorious for its poor prognosis. The clinical outcome remains disappointing, and thus more effective therapeutic options are urgently required. Cordycepin, a traditional Chinese medicine, provides multiple pharmacological strategies in antitumors, but its mechanisms have not been fully elucidated. In this study, we reported that cordycepin inhibited the viability and proliferation capacity of CCA cells in a time- and dose-dependent manner determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) and colony formation assay. Flow cytometry and Hoechst dye showed that cordycepin induced cancer cell apoptosis via extracellular signal-regulated kinase (ERK) 1/2 deactivation. Moreover, cordycepin significantly reduced the angiogenetic capabilities of CCA in vitro as examined by tube formation assay. We also discovered that cordycepin inhibited DEK expression by using Western blot assay. DEK serves as an oncogenic protein that is overexpressed in various gastrointestinal tumors. DEK silencing inhibited CCA cell viability and angiogenesis but not apoptosis induction determined by Western blot and flow cytometry. Furthermore, cordycepin significantly inhibited tumor growth and angiogenic capacities in a xenograft model by downregulating the expression of DEK, phosphorylated ERK1/2 CD31 and von Willebrand factor (vWF). Taken together, we demonstrated that cordycepin inhibited CCA cell proliferation and angiogenesis with a DEK interaction via downregulation in ERK signaling. These data indicate that cordycepin may serve as a novel agent for CCA clinical treatment and prognosis improvement.

SIGNIFICANCE STATEMENT

Cordycepin provides multiple strategies in antitumors, but its mechanisms are not fully elucidated, especially on cholangiocarcinoma (CCA). We reported that cordycepin inhibited the viability of CCA cells, induced apoptosis via extracellular signal-regulated kinase 1/2 deactivation and DEK inhibition, and reduced the angiogenetic capabilities of CCA both in vivo and in vitro.




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Hepatic Transporter Alterations by Nuclear Receptor Agonist T0901317 in Sandwich-Cultured Human Hepatocytes: Proteomic Analysis and PBPK Modeling to Evaluate Drug-Drug Interaction Risk [Metabolism, Transport, and Pharmacogenomics]

In vitro approaches for predicting drug-drug interactions (DDIs) caused by alterations in transporter protein regulation are not well established. However, reports of transporter regulation via nuclear receptor (NR) modulation by drugs are increasing. This study examined alterations in transporter protein levels in sandwich-cultured human hepatocytes (SCHH; n = 3 donors) measured by liquid chromatography–tandem mass spectrometry–based proteomic analysis after treatment with N-[4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl]-N-(2,2,2-trifluoroethyl)benzenesulfonamide (T0901317), the first described synthetic liver X receptor agonist. T0901317 treatment (10 μM, 48 hours) decreased the levels of organic cation transporter (OCT) 1 (0.22-, 0.43-, and 0.71-fold of control) and organic anion transporter (OAT) 2 (0.38-, 0.38-, and 0.53-fold of control) and increased multidrug resistance protein (MDR) 1 (1.37-, 1.48-, and 1.59-fold of control). The induction of NR downstream gene expression supports the hypothesis that T0901317 off-target effects on farnesoid X receptor and pregnane X receptor activation are responsible for the unexpected changes in OCT1, OAT2, and MDR1. Uptake of the OCT1 substrate metformin in SCHH was decreased by T0901317 treatment. Effects of decreased OCT1 levels on metformin were simulated using a physiologically-based pharmacokinetic (PBPK) model. Simulations showed a clear decrease in metformin hepatic exposure resulting in a decreased pharmacodynamic effect. This DDI would not be predicted by the modest changes in simulated metformin plasma concentrations. Altogether, the current study demonstrated that an approach combining SCHH, proteomic analysis, and PBPK modeling is useful for revealing tissue concentration–based DDIs caused by unexpected regulation of hepatic transporters by NR modulators.

SIGNIFICANCE STATEMENT

This study utilized an approach combining sandwich-cultured human hepatocytes, proteomic analysis, and physiologically based pharmacokinetic modeling to evaluate alterations in pharmacokinetics (PK) and pharmacodynamics (PD) caused by transporter regulation by nuclear receptor modulators. The importance of this approach from a mechanistic and clinically relevant perspective is that it can reveal drug-drug interactions (DDIs) caused by unexpected regulation of hepatic transporters and enable prediction of altered PK and PD changes, especially for tissue concentration–based DDIs.




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Direct interaction between CEP85 and STIL mediates PLK4-driven directed cell migration [SHORT REPORT]

Yi Liu, Jaeyoun Kim, Reuben Philip, Vaishali Sridhar, Megha Chandrashekhar, Jason Moffat, Mark van Breugel, and Laurence Pelletier

PLK4 has emerged as a prime target for cancer therapeutics, and its overexpression is frequently observed in various types of human cancer. Recent studies have further revealed an unexpected oncogenic activity of PLK4 in regulating cancer cell migration and invasion. However, the molecular basis behind the role of PLK4 in these processes still remains only partly understood. Our previous work has demonstrated that an intact CEP85–STIL binding interface is necessary for robust PLK4 activation and centriole duplication. Here, we show that CEP85 and STIL are also required for directional cancer cell migration. Mutational and functional analyses reveal that the interactions between CEP85, STIL and PLK4 are essential for effective directional cell motility. Mechanistically, we show that PLK4 can drive the recruitment of CEP85 and STIL to the leading edge of cells to promote protrusive activity, and that downregulation of CEP85 and STIL leads to a reduction in ARP2 (also known as ACTR2) phosphorylation and reorganization of the actin cytoskeleton, which in turn impairs cell migration. Collectively, our studies provide molecular insight into the important role of the CEP85–STIL complex in modulating PLK4-driven cancer cell migration.

This article has an associated First Person interview with the first author of the paper.




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The Bewildering Antitubercular Action of Pyrazinamide [Review]

Pyrazinamide (PZA) is a cornerstone antimicrobial drug used exclusively for the treatment of tuberculosis (TB). Due to its ability to shorten drug therapy by 3 months and reduce disease relapse rates, PZA is considered an irreplaceable component of standard first-line short-course therapy for drug-susceptible TB and second-line treatment regimens for multidrug-resistant TB. Despite over 60 years of research on PZA and its crucial role in current and future TB treatment regimens, the mode of action of this unique drug remains unclear. Defining the mode of action for PZA will open new avenues for rational design of novel therapeutic approaches for the treatment of TB. In this review, we discuss the four prevailing models for PZA action, recent developments in modulation of PZA susceptibility and resistance, and outlooks for future research and drug development.




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Posttranscriptional Regulation of tnaA by Protein-RNA Interaction Mediated by Ribosomal Protein L4 in Escherichia coli [Article]

Escherichia coli ribosomal protein (r-protein) L4 has extraribosomal biological functions. Previously, we described L4 as inhibiting RNase E activity through protein-protein interactions. Here, we report that from stabilized transcripts regulated by L4-RNase E, mRNA levels of tnaA (encoding tryptophanase from the tnaCAB operon) increased upon ectopic L4 expression, whereas TnaA protein levels decreased. However, at nonpermissive temperatures (to inactivate RNase E), tnaA mRNA and protein levels both increased in an rne temperature-sensitive [rne(Ts)] mutant strain. Thus, L4 protein fine-tunes TnaA protein levels independently of its inhibition of RNase E. We demonstrate that ectopically expressed L4 binds with transcribed spacer RNA between tnaC and tnaA and downregulates TnaA translation. We found that deletion of the 5' or 3' half of the spacer compared to the wild type resulted in a similar reduction in TnaA translation in the presence of L4. In vitro binding of L4 to the tnaC-tnaA transcribed spacer RNA results in changes to its secondary structure. We reveal that during early stationary-phase bacterial growth, steady-state levels of tnaA mRNA increased but TnaA protein levels decreased. We further confirm that endogenous L4 binds to tnaC-tnaA transcribed spacer RNA in cells at early stationary phase. Our results reveal the novel function of L4 in fine-tuning TnaA protein levels during cell growth and demonstrate that r-protein L4 acts as a translation regulator outside the ribosome and its own operon.

IMPORTANCE Some ribosomal proteins have extraribosomal functions in addition to ribosome translation function. The extraribosomal functions of several r-proteins control operon expression by binding to own-operon transcripts. Previously, we discovered a posttranscriptional, RNase E-dependent regulatory role for r-protein L4 in the stabilization of stress-responsive transcripts. Here, we found an additional extraribosomal function for L4 in regulating the tna operon by L4-intergenic spacer mRNA interactions. L4 binds to the transcribed spacer RNA between tnaC and tnaA and alters the structural conformation of the spacer RNA, thereby reducing the translation of TnaA. Our study establishes a previously unknown L4-mediated mechanism for regulating gene expression, suggesting that bacterial cells have multiple strategies for controlling levels of tryptophanase in response to varied cell growth conditions.




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Synergistic Interactions of Indole-2-Carboxamides and {beta}-Lactam Antibiotics against Mycobacterium abscessus [Mechanisms of Action]

New drugs or therapeutic combinations are urgently needed against Mycobacterium abscessus. Previously, we demonstrated the potent activity of indole-2-carboxamides 6 and 12 against M. abscessus. We show here that these compounds act synergistically with imipenem and cefoxitin in vitro and increase the bactericidal activity of the β-lactams against M. abscessus. In addition, compound 12 also displays synergism with imipenem and cefoxitin within infected macrophages. The clinical potential of these new drug combinations requires further evaluation.




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Antiviral Properties and Mechanism of Action Studies of the Hepatitis B Virus Capsid Assembly Modulator JNJ-56136379 [Antiviral Agents]

Capsid assembly is a critical step in the hepatitis B virus (HBV) life cycle, mediated by the core protein. Core is a potential target for new antiviral therapies, the capsid assembly modulators (CAMs). JNJ-56136379 (JNJ-6379) is a novel and potent CAM currently in phase II trials. We evaluated the mechanisms of action (MOAs) and antiviral properties of JNJ-6379 in vitro. Size exclusion chromatography and electron microscopy studies demonstrated that JNJ-6379 induced the formation of morphologically intact viral capsids devoid of genomic material (primary MOA). JNJ-6379 accelerated the rate and extent of HBV capsid assembly in vitro. JNJ-6379 specifically and potently inhibited HBV replication; its median 50% effective concentration (EC50) was 54 nM (HepG2.117 cells). In HBV-infected primary human hepatocytes (PHHs), JNJ-6379, when added with the viral inoculum, dose-dependently reduced extracellular HBV DNA levels (median EC50 of 93 nM) and prevented covalently closed circular DNA (cccDNA) formation, leading to a dose-dependent reduction of intracellular HBV RNA levels (median EC50 of 876 nM) and reduced antigen levels (secondary MOA). Adding JNJ-6379 to PHHs 4 or 5 days postinfection reduced extracellular HBV DNA and did not prevent cccDNA formation. Time-of-addition PHH studies revealed that JNJ-6379 most likely interfered with postentry processes. Collectively, these data demonstrate that JNJ-6379 has dual MOAs in the early and late steps of the HBV life cycle, which is different from the MOA of nucleos(t)ide analogues. JNJ-6379 is in development for chronic hepatitis B treatment and may translate into higher HBV functional cure rates.




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An Individual Participant Data Population Pharmacokinetic Meta-analysis of Drug-Drug Interactions between Lumefantrine and Commonly Used Antiretroviral Treatment [Clinical Therapeutics]

Treating malaria in HIV-coinfected individuals should consider potential drug-drug interactions. Artemether-lumefantrine is the most widely recommended treatment for uncomplicated malaria globally. Lumefantrine is metabolized by CYP3A4, an enzyme that commonly used antiretrovirals often induce or inhibit. A population pharmacokinetic meta-analysis was conducted using individual participant data from 10 studies with 6,100 lumefantrine concentrations from 793 nonpregnant adult participants (41% HIV-malaria-coinfected, 36% malaria-infected, 20% HIV-infected, and 3% healthy volunteers). Lumefantrine exposure increased 3.4-fold with coadministration of lopinavir-ritonavir-based antiretroviral therapy (ART), while it decreased by 47% with efavirenz-based ART and by 59% in the patients with rifampin-based antituberculosis treatment. Nevirapine- or dolutegravir-based ART and malaria or HIV infection were not associated with significant effects. Monte Carlo simulations showed that those on concomitant efavirenz or rifampin have 49% and 80% probability of day 7 concentrations <200 ng/ml, respectively, a threshold associated with an increased risk of treatment failure. The risk of achieving subtherapeutic concentrations increases with larger body weight. An extended 5-day and 6-day artemether-lumefantrine regimen is predicted to overcome these drug-drug interactions with efavirenz and rifampin, respectively.




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Evaluation of Dose-Fractionated Polymyxin B on Acute Kidney Injury Using a Translational In Vivo Rat Model [Pharmacology]

We investigated dose-fractionated polymyxin B (PB) on acute kidney injury (AKI). PB at 12 mg of drug/kg of body weight per day (once, twice, and thrice daily) was administered in rats over 72 h. The thrice-daily group demonstrated the highest KIM-1 increase (P = 0.018) versus that of the controls (P = 0.99) and histopathological damage (P = 0.013). A three-compartment model best described the data (bias, 0.129 mg/liter; imprecision, 0.729 mg2/liter2; R2, 0.652,). Area under the concentration-time curve at 24 h (AUC24) values were similar (P = 0.87). The thrice-daily dosing scheme resulted in the most PB-associated AKI in a rat model.




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Adduct Formation of Delamanid with NAD in Mycobacteria [Mechanisms of Action]

Delamanid (DLM), a nitro-dihydroimidazooxazole derivative currently approved for pulmonary multidrug-resistant tuberculosis (TB) therapy, is a prodrug activated by mycobacterial 7,8-didemethyl-8-hydroxy 5-deazaflavin electron transfer coenzyme (F420)-dependent nitroreductase (Ddn). Despite inhibiting the biosynthesis of a subclass of mycolic acids, the active DLM metabolite remained unknown. Comparative liquid chromatography-mass spectrometry (LC-MS) analysis of DLM metabolites revealed covalent binding of reduced DLM with a nicotinamide ring of NAD derivatives (oxidized form) in DLM-treated Mycobacterium tuberculosis var. Bacille de Calmette et Guérin. Isoniazid-resistant mutations in the type II NADH dehydrogenase gene (ndh) showed a higher intracellular NADH/NAD ratio and cross-resistance to DLM, which were restored by complementation of the mutants with wild-type ndh. Our data demonstrated for the first time the adduct formation of reduced DLM with NAD in mycobacterial cells and its importance in the action of DLM.




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Method Enables Nanoscale Mapping of Protein Interactions on Live Cells [Techniques]

A new method called MicroMapping can identify nanoscale protein–protein interactions on live cells.




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Sensitive Determination of Infectious Titer of Recombinant Adeno-Associated Viruses (rAAVs) Using TCID50 End-Point Dilution and Quantitative Polymerase Chain Reaction (qPCR)

Adeno-associated virus (AAV) recombinants are currently the vector of choice for many gene therapy applications. As experimental therapies progress to clinical trials, the need to characterize recombinant adeno-associated viruses (rAAVs) accurately and reproducibly increases. Accurate determination of rAAV infectious titer is important for determining the activity of each vector lot and for ensuring lot-to-lot consistency. The following protocol developed in our laboratory uses a 96-well TCID50 format and quantitative polymerase chain reaction (qPCR) detection for the determination of rAAV infectious titer.




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Titration of Recombinant Adeno-Associated Virus (rAAV) Genome Copy Number Using Real-Time Quantitative Polymerase Chain Reaction (qPCR)

This protocol is used to determine the concentration of DNase-resistant vector genomes (i.e., packaged in the capsid) in purified recombinant adeno-associated virus (rAAV) preparations. The protocol begins with treatment of the vector stock with DNase I to eliminate unencapsidated AAV DNA or contaminating plasmid DNA. This is followed by a heat treatment to heat-inactivate DNase I, to disrupt the viral capsid, and to release the packaged vector genomes for quantification by real-time polymerase chain reaction (PCR) using a set of standards (linearized plasmid used for vector production) containing known copy numbers. To accomplish high-throughput titration, the primer and probe sets used in real-time PCR are usually designed to target common elements present in most rAAV genomes, such as promoters and poly(A) signals. This strategy significantly reduces the number of PCRs, controls, and turnaround time. Several important controls should be included in the assay as follows: The first two controls should have a known copy number of the rAAV genome plasmid treated or not treated with DNase I. This control tests the effectiveness of DNase treatment. To control for potential cross-contamination between samples during the preparation process, a blank control containing nuclease-free water only should be processed and tested in parallel. A validation vector sample with a known titer should be included in every assay to monitor interassay variability. Finally, for the PCR run, a no-template control (NTC) is included to indicate cross-contamination during PCR setup.




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Retraction: Insulin-Like Growth Factor I Suppresses Bone Morphogenetic Protein Signaling in Prostate Cancer Cells by Activating mTOR Signaling




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Risk SNP-Mediated Enhancer-Promoter Interaction Drives Colorectal Cancer through Both FADS2 and AP002754.2

Although genome-wide association studies (GWAS) have identified more than 100 colorectal cancer risk loci, most of the biological mechanisms associated with these loci remain unclear. Here we first performed a comprehensive expression quantitative trait loci analysis in colorectal cancer tissues adjusted for multiple confounders to test the determinants of germline variants in established GWAS susceptibility loci on mRNA and long noncoding RNA (lncRNA) expression. Combining integrative functional genomic/epigenomic analyses and a large-scale population study consisting of 6,024 cases and 10,022 controls, we then prioritized rs174575 with a C>G change as a potential causal candidate for colorectal cancer at 11q12.2, as its G allele was associated with an increased risk of colorectal cancer (OR = 1.26; 95% confidence interval = 1.17–1.36; P = 2.57 × 10–9). rs174575 acted as an allele-specific enhancer to distally facilitate expression of both FADS2 and lncRNA AP002754.2 via long-range enhancer–promoter interaction loops, which were mediated by E2F1. AP002754.2 further activated a transcriptional activator that upregulated FADS2 expression. FADS2, in turn, was overexpressed in colorectal cancer tumor tissues and functioned as a potential oncogene that facilitated colorectal cancer cell proliferation and xenograft growth in vitro and in vivo by increasing the metabolism of PGE2, an oncogenic molecule involved in colorectal cancer tumorigenesis. Our findings represent a novel mechanism by which a noncoding variant can facilitate long-range genome interactions to modulate the expression of multiple genes including not only mRNA, but also lncRNA, which provides new insights into the understanding of colorectal cancer etiology.Significance:This study provides an oncogenic regulatory circuit among several oncogenes including E2F1, FADS2, and AP002754.2 underlying the association of rs174575 with colorectal cancer risk, which is driven by long-range enhancer–promoter interaction loops.Graphical Abstract:http://cancerres.aacrjournals.org/content/canres/80/9/1804/F1.large.jpg.




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Assessment of Apparent Internal Carotid Tandem Occlusion on High-Resolution Vessel Wall Imaging: Comparison with Digital Subtraction Angiography [EXTRACRANIAL VASCULAR]

BACKGROUND AND PURPOSE:

Not all tandem occlusions diagnosed on traditional vascular imaging modalities, such as MRA, represent actual complete ICA occlusion. This study aimed to explore the utility of high-resolution vessel wall imaging in identifying true ICA tandem occlusions and screening patients for their suitability for endovascular recanalization.

MATERIALS AND METHODS:

Patients with no signal in the ICA on MRA were retrospectively reviewed. Two neuroradiologists independently reviewed their high-resolution vessel wall images to assess whether there were true tandem occlusions and categorized all cases into intracranial ICA occlusion, extracranial ICA occlusion, tandem occlusion, or near-occlusion. DSA classified patient images into the same 4 categories, which were used as the comparison with high-resolution vessel wall imaging. The suitability for recanalization of occluded vessels was evaluated on high-resolution vessel wall imaging compared with DSA.

RESULTS:

Forty-five patients with no ICA signal on MRA who had available high-resolution vessel wall imaging and DSA images were included. Among the 34 patients (34/45, 75.6%) with tandem occlusions on DSA, 18 cases also showed tandem occlusions on high-resolution vessel wall imaging. The remaining 16 patients, intracranial ICA, extracranial ICA occlusions and near-occlusions were found in 2, 6, and 8 patients, respectively, on the basis of high-resolution vessel wall imaging. A total of 20 cases (20/45, 44.4%) were considered suitable for recanalization on the basis of both DSA and high-resolution vessel wall imaging. Among the 25 patients deemed unsuitable for recanalization by DSA, 11 were deemed suitable for recanalization by high-resolution vessel wall imaging.

CONCLUSIONS:

High-resolution vessel wall imaging could allow identification of true ICA tandem occlusion in patients with an absence of signal on MRA. Findings on high-resolution vessel wall imaging can be used to screen more suitable candidates for recanalization therapy.




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Risks from tax avoidance in real estate transaction

As home sellers commonly propose to state a lower price in the sale contract than the actual transaction value, home buyers have to bear additional risks from such real estate transactions.




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After the COVID-19 pandemic, older generations should reflect on the need for climate action

The COVID-19 pandemic has prompted a cornucopia of reflections about what is to be learned from it. One of the issues around which this has been the case is climate change.

There are a few ways in which climate change is linked to reflections on the pandemic. One of these links is seeing the pandemic and where there has been relative success in dealing with it as a good case study in the value of scientific advice over politics. The wish is that as a result science might regain a more secure foothold in the debate around climate change. This is generally coupled with a reflection on the extent to which the pandemic might have been even better prepared for and dealt with had early generic warnings about the likelihood of a pandemic been heeded, and also if warnings about the actual pandemic had been acted on earlier than they were at the beginning of 2020. The hope is that this lesson in the consequences of not heeding warnings will rub off on the climate change debate, if not on the most committed climate change deniers.

Another link between the pandemic and climate change is one less reflected on, although I did see at least one article on it, and that is the whole issue of inter-generational ethics that arises. The lock downs associated with COVID-19 tended to be justified on two grounds: One was containing the spread in such a way as to prevent health-care systems from being overwhelmed, and the other had to do with containing the spread of the virus for the sake of the those who were most likely to die from it, namely the elderly, an argument certainly borne out by the statistics even if it is the case that some younger people seem, for reasons yet to be determined, very vulnerable.

And so it was that multitudes of young people have had to put their lives and dreams on hold in order to safeguard the lives of many who are much older than them.  Young people have mostly willingly and without complaint acceded to the moral imperative and practical wisdom of sacrificing things like their personal, educational, athletic, travel, financial and/or employment hopes for the greater good, specifically for the older generation in their society. 

Other groups, like frontline health-care workers, and those newly classified as working in essential jobs, like grocery store workers, have also been asked to make a disproportionate sacrifice. But that is for another article on how their real value has been revealed -- and how that value should be recognized in the post-pandemic world (better wages for one thing). 

Unfortunately, the link between the demands on the young in the pandemic containment strategy and the debate on climate change manifests itself in observing, so far, the unwillingness of populations, and their governments, to demand a reverse moral imperative from older citizens when it comes to sacrifices they might make for the sake of younger and future generations. What are older citizens prepared to sacrifice to safeguard the quality of the lives younger citizens will lead in the coming decades, by substantially reducing our carbon footprint, and seriously dealing with other environmental challenges?

One could argue that, in the case of Canadians, the population has done its part by electing a majority of MPs committed to action on climate change, only to be let down by a government that wants to have its cake and eat it too on climate change by imposing a carbon tax and buying a pipeline. Nevertheless, as we emerge on the other side of the pandemic, hopefully sooner rather than later, it seems to me that there will be a new opportunity for moral reflection on what the generations owe each other. Of course right-wing politicians are always claiming to be worried about passing on fiscal debt to the next generation. But passing on an environmental deficit is a much more real and  serious issue. Part of the moral logic of pandemic containment has been asking one generation to sacrifice for another. It seems only fair then that the political debate about climate change should at some point soon become much more focused on what the older generation can do for the younger generation. Demanding real action from their political leaders, even if it means locking down or at the very least winding down lifestyles that have become ingrained would be a good start. And for those who can afford it, showing a willingness to pay higher taxes to build the infrastructure of a sustainable and livable future would also be in order.     

Bill Blaikie, former MP and MLA, writes on Canadian politics, political parties and Parliament.

Image: John Englart/Flickr

May 8, 2020




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Sci-Fi Action Platformer Dark Light Launches May 8 for Steam Early Access, Later for Switch

Developer Mirari & Co. announced the science-fiction action platformer Dark Light for Windows PC via Steam Early Access on May 8 and later for the Nintendo Switch when the game leaves Steam Early Access. 

Mirari & Co. is looking to release the game within one year of the Steam Early Access release, however, it depends "on how we are taking players suggestions and advice to shaping the game."

View the latest trailer of the game below:

Here is an overview of the game:

Dark Light is a science-fiction action-platformer with unique gameplay. Explore an apocalyptic cyberpunk world full of supernatural beings. Encounter and defeat creatures of darkness invisible to the naked eye, detected only with the light source from your drone. Experience the horror and feel their presence as they surround you.

As a Dark Hunter you were dropped into a wreaked world. To survive, you need to equip yourself, fight your way through, and collect ‘shards’ from killing supernatural creatures to reinforce your energy. Through survival, you will explore the mysterious dark zones of the apocalypse world.

Key Features:

  • Cinematic quality graphic, detailed characters and environment design, and vivid animation with lush visual effect.
  • A variety of range, melee, and throwable weapons; unique items; and multiple ways to upgrade weapons, special equipment, and the player to shape your own character skills.
  • Non-linear map structure for you to choose your own path to explore the dark zones. Encounter horrifying supernatural enemies, fearsome bosses, and friendly NPCs, and fight with invisible creatures that can only be seen in a special light source.
  • Detect invisible enemies and reveal hidden paths with the special light source from your drone.

A life-long and avid gamer, William D'Angelo was first introduced to VGChartz in 2007. After years of supporting the site, he was brought on in 2010 as a junior analyst, working his way up to lead analyst in 2012. He has expanded his involvement in the gaming community by producing content on his own YouTube channel and Twitch channel dedicated to gaming Let's Plays and tutorials. You can contact the author at wdangelo@vgchartz.com or on Twitter @TrunksWD.

Full Article - https://www.vgchartz.com/article/443411/sci-fi-action-platformer-dark-light-launches-may-8-for-steam-early-access-later-for-switch/




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The Ascent is a Cyberpunk Action RPG, Announced for Xbox Series X and Xbox One

The Ascent is a new solo and co-op action RPG set in a cyberpunk world from developer Neon Giant and publisher Curve Digital. It was announced today during Microsoft's Inside Xbox showcase for the Xbox Series X and Xbox One. It will feature Smart Delivery. The Ascent will launch in Holiday 2020.

View the reveal trailer below:

Here is an overview of the game:

The Ascent is a solo and co-op action RPG set in a cyberpunk world. The mega corporation that owns you and everyone, The Ascent Group, has just collapsed. Confusion and chaos ensue, security and order are in disarray, and without protection, everyone is left to fend for themselves. Stop gangs and hostile corporations from taking over and discover what really happened.

Explore the Ascent Group arcology

Make allies as well as enemies as you explore the brimming arcology and its wide range of districts, from the deep slums to the higher luxury spheres.

Shoot and Loot

Consider enemies' height and weaknesses into account when fighting, making the most out of every opportunity. Take down even the worst opponents to find the rarest loot.

Customization and Augmentations

Modify your body with cyberware and gear up with weapons and equipment that suit your playstyle. Take a slick and precise approach or arm yourself to the teeth and go full chrome.

Solo or Co-op

Play the entire game alone or work together with up to three friends in local or online co-op.

A life-long and avid gamer, William D'Angelo was first introduced to VGChartz in 2007. After years of supporting the site, he was brought on in 2010 as a junior analyst, working his way up to lead analyst in 2012. He has expanded his involvement in the gaming community by producing content on his own YouTube channel and Twitch channel dedicated to gaming Let's Plays and tutorials. You can contact the author at wdangelo@vgchartz.com or on Twitter @TrunksWD.

Full Article - https://www.vgchartz.com/article/443427/the-ascent-is-a-cyberpunk-action-rpg-announced-for-xbox-series-x-and-xbox-one/




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Monster-fighting action game Scarlet Nexus is coming to PC

This anime-style action game about fighting off the creatively-named “others” was one of the many trailers we peeped during Xbox’s big reveal real yesterday. Bandai Namco have announced that Scarlet Nexus is actually coming to PC as well, so we’ll get to do a bit of monster butt-kickin’ too. Is that an evil bouquet of […]



  • PC Game News
  • Bandai Namco
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  • Bandai Namco Studios

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Doom Eternal review: A welcome adrenaline-inducing distraction

Doom Eternal does contain gratuitous violence, but the evidence suggests violence in video games doesn't affect people's behaviour in the real world, says Jacob Aron




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Legal action could be used to stop Starlink affecting telescope images

A group of astronomers has called for legal action to stop the launch of thousands of satellites designed by companies like SpaceX and OneWeb to beam high-speed internet around the world




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Extraction review – hokey, high-octane action thriller

Chris Hemsworth plays a super-tough mercenary on an all-guns-blazing mission to rescue a crime lord’s kidnapped son

Sadly, this has nothing to do with dentistry. Extraction is a made-for-Netflix action thriller from veterans of the Marvel Comic Universe – screenwriter Joe Russo, stunt-specialist-turned-director Sam Hargrave and star Chris Hemsworth. It’s based on the graphic novel Ciudad (which Russo co-authored), transferring the action from the Paraguayan city of Ciudad Del Este to Dhaka in Bangladesh.

Extraction is a little bit hokey and absurd, and the very end has an exasperating cop-out – but it has to be admitted that, in terms of pure action octane, Russo and Hargrave bring the noise, and there are quite a few long-distance “sniper” scenes in which people get taken out from miles away as the bullet travels through their skulls with a resonant thoonk.

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Tennis, golf swing into action

It’s only the beginning of May, but for local golfers and tennis players, Monday felt like Christmas. Golf courses and tennis courts were officially allowed to open Monday as a part ...




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&#39;Bois Locker Room&#39;: Experts Say Youngsters Need Rehabilitative Measures, Not Just Punitive Action

A dialogue on sex, consent, ownership over bodies must be introduced from a young age so that it becomes part of a dominant narrative, say experts.






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Never-Trump group's 'mourning' ad gets presidential reaction

President Donald Trump took to Twitter overnight to attack the Lincoln Project for their latest ad criticizing the president’s coronavirus response.




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Light, sound, action: Extending the life of acoustic waves on microchips

Data centres and digital information processors are reaching their capacity limits and producing heat. Foundational work here on optical-acoustic microchips opens door to low-heat, low-energy, fast internet.




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Health Secretary Matt Hancock promises testing of all key NHS and social care workers as he sets out PPE action plan

Read our live coronavirus updates HERE Coronavirus: The symptoms




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Top professor demands action from minsters with coronavirus lockdown set to be extended

Scientist tells ministers to get act together over virus tests and planning 'Brexit-style level of control needed' Follow our live coronavirus updates HERE Coronavirus: the symptoms




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Sir Philip Rutnam formally begins legal action against Home Secretary Priti Patel over constructive dismissal claims

Former Home Office Permanent Secretary Sir Philip Rutnam has formally begun legal action against Home Secretary Priti Patel, claiming "constructive dismissal".




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Met Police faces legal action over PC Keith Palmer&apos;s murder in Westminster terror attack

The Met Police is facing legal action in regards to the murder of PC Keith Palmer in the Westminster terror attack.




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Questions raised over coronavirus pandemic response with Boris Johnson&apos;s initial actions criticised

Questions have been raised over the Government's response to the coronavirus pandemic with Boris Johnson's early actions amid the crisis criticised.




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Greta Thunberg posts House on Fire video to call for more climate action on World Earth Day

Greta Thunberg has released a video showing a family calmly getting ready for the day while their house burns down around them as a symbol of the threat of climate change.




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Deaf campaigners launch legal action against Government over lack of sign language at coronavirus briefings

Deaf campaigners have begun legal proceedings against the Government over the lack of sign language interpreters during the daily coronavirus briefings.




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Meghan Markle loses first stage of High Court privacy action against Mail on Sunday

The publisher of the Mail on Sunday has won the first High Court skirmish in the Duchess of Sussex's privacy claim against it over publication of a letter to her estranged father.




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The imaginary American town that became a tourist attraction

Map-makers insert fake towns or trap-streets to catch out plagiarists, but Agloe, in New York state, took on a strange life of its own

In 2008, Argleton village in west Lancashire appeared on Google, complete with weather reports, a job site and an estate agent advertising houses for sale. Argleton vanished two years later. While its site was – and still is – a damp field in the middle of nowhere, it’s worth noting that Argleton is an anagram of G Not Real. Although Google never admitted to having created it, Argleton was a phantom settlement, planted as a trap.

In the world of digital mapping and cartography, snares to catch unwary plagiarists take the form of fake roads or places, known as “trap streets” or “paper towns”. For some, such as Lye Close or Noereal Road, the clue is in the name. (A real alleyway in Cardiff that served as a trap street in the 2014 Dr Who episode Face the Raven may, conversely, be the world’s only fictional fictional street.)

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Widower seeks class-action lawsuit against N.S. gunman's estate

A man whose wife was killed in the April mass shooting in Nova Scotia is the plaintiff named in a proposed class-action lawsuit against the estate of the deceased gunman, denturist Gabriel Wortman.



  • News/Canada/Nova Scotia

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Sony vetoed live-action 'Spider-Man' cameos in 'Into the Spider-Verse'

Tom Holland, Andrew Garfield and Tobey Maguire were conspicuous by their absence from 'Spider-Man: Into the Spider-Verse'.




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'Hercules' live-action remake won't be shot-for-shot as Russos want to 'bring something new'

The new 'Hercules' may not even be a musical, according to the Russo Brothers.




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Hastings United besieged by swarm of bees; Messi back in action

With almost all football off because of the coronavirus, star players have found themselves at a loose end. How are they filling their time?




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Proposed class-action lawsuit filed against N.S. mass shooter's estate on behalf of families

A proposed class-action lawsuit has been filed against the estate of the perpetrator of Canada’s worst mass shooting, which left 22 people dead in several Nova Scotia communities last month.




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Home Secretary Priti Patel facing legal action from Sir Philip Rutnam after bullying allegations

Legal action has been formally launched against Priti Patel following allegations of bullying from a top civil servant.