A functional genomic approach to actionable gene fusions for precision oncology

Fusion genes represent a class of attractive therapeutic targets. Thousands of fusion genes have been identified in patients with cancer, but the functional consequences and therapeutic implications of most of these remain largely unknown. Here, we develop a functional genomic approach that consists of efficient fusion reconstruction and sensitive cell viability and drug response assays. Applying this approach, we characterize similar to 100 fusion genes detected in patient samples of The Cancer Genome Atlas, revealing a notable fraction of low-frequency fusions with activating effects on tumor growth. Focusing on those in the RTK-RAS pathway, we identify a number of activating fusions that can markedly affect sensitivity to relevant drugs. Last, we propose an integrated, level-of-evidence classification system to prioritize gene fusions systematically. Our study reiterates the urgent clinical need to incorporate similar functional genomic approaches to characterize gene fusions, thereby maximizing the utility of gene fusions for precision oncology

Effects of Anacetrapib in Patients with Atherosclerotic Vascular Disease

BACKGROUND: Patients with atherosclerotic vascular disease remain at high risk for cardiovascular events despite effective statin-based treatment of low-density lipoprotein (LDL) cholesterol levels. The inhibition of cholesteryl ester transfer protein (CETP) by anacetrapib reduces LDL cholesterol levels and increases high-density lipoprotein (HDL) cholesterol levels. However, trials of other CETP inhibitors have shown neutral or adverse effects on cardiovascular outcomes. METHODS: We conducted a randomized, double-blind, placebo-controlled trial involving 30,449 adults with atherosclerotic vascular disease who were receiving intensive atorvastatin therapy and who had a mean LDL cholesterol level of 61 mg per deciliter (1.58 mmol per liter), a mean non-HDL cholesterol level of 92 mg per deciliter (2.38 mmol per liter), and a mean HDL cholesterol level of 40 mg per deciliter (1.03 mmol per liter). The patients were assigned to receive either 100 mg of anacetrapib once daily (15,225 patients) or matching placebo (15,224 patients). The primary outcome was the first major coronary event, a composite of coronary death, myocardial infarction, or coronary revascularization. RESULTS: During the median follow-up period of 4.1 years, the primary outcome occurred in significantly fewer patients in the anacetrapib group than in the placebo group (1640 of 15,225 patients [10.8%] vs. 1803 of 15,224 patients [11.8%]; rate ratio, 0.91; 95% confidence interval, 0.85 to 0.97; P=0.004). The relative difference in risk was similar across multiple prespecified subgroups. At the trial midpoint, the mean level of HDL cholesterol was higher by 43 mg per deciliter (1.12 mmol per liter) in the anacetrapib group than in the placebo group (a relative difference of 104%), and the mean level of non-HDL cholesterol was lower by 17 mg per deciliter (0.44 mmol per liter), a relative difference of -18%. There were no significant between-group differences in the risk of death, cancer, or other serious adverse events. CONCLUSIONS: Among patients with atherosclerotic vascular disease who were receiving intensive statin therapy, the use of anacetrapib resulted in a lower incidence of major coronary events than the use of placebo. (Funded by Merck and others; Current Controlled Trials number, ISRCTN48678192 ; ClinicalTrials.gov number, NCT01252953 ; and EudraCT number, 2010-023467-18 .)

Shareholding operation of product remanufacturing – from a sustainable production perspective

We consider a supply chain in which an original equipment manufacturer (OEM) authorizes the remanufacturing business to a third-party remanufacturer (TPR). The OEM may make an investment to hold equity in TPR. This operation not only enables OEM to share the profit of the TPR as a forward shareholding supply chain, but also improve the production efficiency of the TPR and consequently benefits the whole supply chain. We characterize the equilibrium production decisions of all members by using Stackelberg game in such a supply chain. We find that shareholding operation by OEM helps increase the production quantity of remanufactured products and total market volume. From the economic perspective, our results show both sides in the forward shareholding supply chain prefer the shareholding operation if the equity holding cost and remanufactured cost is relatively small. Additionally, from an environmental perspective, our results show under certain relative pollution ratio of remanufactured products, shareholding operation can reduce environmental impact. Finally, we check the key results by stimulating numerical examples and obtain some useful management insights

Catalytic Transfer Hydrogenation and Ethanolysis of Furfural to Ethyl Levulinate Using Sulfonated Hf- or Ni-Catalysts Prepared with Mixed Solvents

Bifunctional Lewis (L) acid (Ni- or Hf-) site–Brønsted (B) acid catalysts designed to promote transfer hydrogenation reactions were prepared via hydrothermal and solvothermal methods using safe mixed solvents and sustainable precursors. By using N,N-dimethylformamide as a basis for the desired basicity, mixed solvents could be identified that allowed catalysts to be prepared with tunable ratios of Lewis to Brønsted acid sites (L/B). The as-prepared catalysts promoted transfer hydrogenation of furfural and ethanolysis to form ethyl levulinate (EL) using ethanol as a solvent and hydrogen donor source. Among the catalysts, sulfonated Hf-catalysts prepared with a cyclopentanone/formic acid mixed solvent (Hf-CPN/FA) with an L/B ratio of 6.4 gave 95% furfural conversion with 51.9% yield of EL, while the sulfonated Hf catalyst prepared with a cyclopentanone/γ-valerolactone mixed solvent (Hf-CPN/GVL) with a total Lewis and Brønsted acid site amount of 85.1 μmol/g gave 100% furfuryl alcohol (FAL) conversion with 72.5% yield of EL. Brønsted acid sites promoted reversible acetalization of furfural with ethanol into 2-furaldehyde diethyl acetal, while Lewis acid sites promoted furfural transfer hydrogenation into FAL and EL and further conversion into γ-valerolactone. The methods developed in this work eliminate dipolar aprotic solvents and harsh acids used in catalyst synthesis and allow sustainable production of EL from biomass-related chemicals

Coherence in Polycrystalline Thin Films of Twisted Molecular Crystals

Helicoidal crystallites in rhythmically banded spherulites manifest spectacular optical patterns in small molecules and polymers. It is shown that concentric optical bands indicating crystallographic orientations typically lose coherence (in-phase twisting) with growth from the center of nucleation. Here, coherence is shown to increase as the twist period decreases for seven molecular crystals grown from the melt. This dependence was correlated to crystallite fiber thickness and length, as well as crystallite branching frequency, a parameter that was extracted from scanning electron micrographs, and supported by numerical simulations. Hole mobilities for 2,5-didodecyl-3,6-di(thiophen-2-yl)pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione (DPP-C12) measured by using organic field-effect transistors demonstrated that more incoherent boundaries between optical bands in spherulites lead to higher charge transport for films with the same twist period. This was rationalized by combining our growth model with electrodynamic simulations. This work illustrates the emergence of complexity in crystallization processes (spherulite formation) that arises in the extra variable of helicoidal radial twisting. The details of the patterns analyzed here link the added complexity in crystal growth to the electronic and optical properties of the thin films.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Charge transport in twisted organic semiconductor crystals of modulated pitch

Many molecular crystals (approximately one third) grow as twisted, helicoidal ribbons from the melt, and this preponderance is even higher in restricted classes of materials, for instance, charge-transfer complexes. Previously, twisted crystallites of such complexes present an increase in carrier mobilities. Here, the effect of twisting on charge mobility is better analyzed for a monocomponent organic semiconductor, 2,5-bis(3-dodecyl-2-thienyl)-thiazolo[5,4-d]thiazole (BDT), that forms twisted crystals with varied helicoidal pitches and makes possible a correlation of twist strength with carrier mobility. Films are analyzed by X-ray scattering and Mueller matrix polarimetry to characterize the microscale organization of the polycrystalline ensembles. Carrier mobilities of organic field-effect transistors are five times higher when the crystals are grown with the smallest pitches (most twisted), compared to those with the largest pitches, along the fiber elongation direction. A tenfold increase is observed along the perpendicular direction. Simulation of electrical potential based on scanning electron microscopy images and density functional theory suggests that the twisting-enhanced mobility is mainly controlled by the fiber organization in the film. A greater number of tightly packed twisted fibers separated by numerous smaller gaps permit better charge transport over the film surface compared to fewer big crystallites separated by larger gaps

Targeting the entrance channel of NNIBP: discovery of diarylnicotinamide 1,4-disubstituted 1,2,3-triazoles as novel HIV-1 NNRTIs with high potency against wild-type and E138K mutant virus

Inspired by our previous efforts on the modifications of diarylpyrimidines as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTI) and reported crystallography study, novel diarylnicotinamide derivatives were designed with a "triazole tail" occupying the entrance channel in the NNRTI binding pocket of the reverse transcriptase to afford additional interactions. The newly designed compounds were then synthesized and evaluated for their anti-HIV activities in MT-4 cells. All the compounds showed excellent to good activity against wild-type HIV-1 strain with EC of 0.02-1.77 μM. Evaluations of selected compounds against more drug-resistant strains showed these compounds had advantage of inhibiting E138K mutant virus which is a key drug-resistant mutant to the new generation of NNRTIs. Among this series, propionitrile (3b2, EC = 0.020 μM, EC = 0.015 μM, CC = 40.15 μM), pyrrolidin-1-ylmethanone (3b8, EC = 0.020 μM, EC = 0.014 μM, CC = 58.09 μM) and morpholinomethanone (3b9, EC = 0.020 μM, EC = 0.027 μM, CC = 180.90 μM) derivatives are the three most promising compounds which are equally potent to the marketed drug Etravirine against E138K mutant strain but with much lower cytotoxicity. Furthermore, detailed SAR, inhibitory activity against RT and docking study of the representative compounds are also discussed.status: publishe

Self-Patterning Tetrathiafulvalene Crystalline Films

Tetrathiafulvalene (TTF) crystals grown from the melt are organized as spherulites in which helicoidal fibrils growing radially from the nucleation center twist in concert with one another. Alternating bright and dark concentric bands are apparent when films are viewed between crossed polarizers, indicating an alternating pattern of crystallographic faces exposed at the film surface. Band-dependent reorganization of the TTF crystals was observed during exposure to methanol vapor. Crystalline growth appears on bright bands at the expense of the dark bands. After a 24 h period of exposure to methanol vapor, the original spherulites were completely restructured, and the films comprise isolated, concentric circles of crystallites whose orientations are determined by the initial TTF crystal fibril orientation. While the surface of these outgrowths appears faceted and smooth, cross-sectional SEM images revealed a semiporous inner structure, suggesting solvent-vapor-induced recrystallization. Collectively, these results show that crystal twisting can be used to rhythmically redistribute material. Crystal twisting is a common and often controllable phenomenon independent of molecular or crystal structure and therefore offers a generalizable path to spontaneous pattern formation in a wide range of materials