Toward an integrated map of genetic interactions in cancer cells

Cancer genomes often harbor hundreds of molecular aberrations. Such genetic variants can be drivers or passengers of tumorigenesis and create vulnerabilities for potential therapeutic exploitation. To identify genotype‐dependent vulnerabilities, forward genetic screens in different genetic backgrounds have been conducted. We devised MINGLE, a computational framework to integrate CRISPR/Cas9 screens originating from different libraries building on approaches pioneered for genetic network discovery in model organisms. We applied this method to integrate and analyze data from 85 CRISPR/Cas9 screens in human cancer cells combining functional data with information on genetic variants to explore more than 2.1 million gene‐background relationships. In addition to known dependencies, we identified new genotype‐specific vulnerabilities of cancer cells. Experimental validation of predicted vulnerabilities identified GANAB and PRKCSH as new positive regulators of Wnt/β‐catenin signaling. By clustering genes with similar genetic interaction profiles, we drew the largest genetic network in cancer cells to date. Our scalable approach highlights how diverse genetic screens can be integrated to systematically build informative maps of genetic interactions in cancer, which can grow dynamically as more data are included.     

The butyrylcholinesterase knockout mouse is obese on a high-fat diet

Butyrylcholinesterase (BChE) inactivates the appetite stimulating hormone octanoyl-ghrelin. The hypothesis was tested that BChE−/− mice would have abnormally high body weight and high levels of octanoyl-ghrelin. It was found that BChE−/− mice fed a standard 5% fat diet had normal body weight. However, BChE−/− mice fed a diet containing 11% fat became obese. Their obesity was not explained by increased levels of octanoyl-ghrelin, or by increased caloric intake, or by decreased exercise. Instead, a role for BChE in fat utilization was suggested.     

CoA Synthase is in complex with p85αPI3K and affects PI3K signaling pathway

The complex interplay between cellular signaling and metabolism in eukaryotic cells just start to emerge. Coenzyme A (CoA) and its derivatives play a key role in cell metabolism and also participate in regulatory processes. CoA Synthase (CoASy) is a mitochondria-associated enzyme which mediates two final stages of de novo CoA biosynthesis. Here, we report that CoASy is involved in signaling events in the cell and forms a functional complex with p85αPI3K in vivo. Importantly, observed interaction of endogenous CoASy and p85αPI3K is regulated in a growth factor dependent manner. Surprisingly, both catalytic p110α and regulatory p85α subunits of PI3K were detected in mitochondrial fraction where mitochondria-localized p85αPI3K was found in complex with CoASy. Unexpectedly, significant changes of PI3K signaling pathway activity were observed in experiments with siRNA-mediated CoASy knockdown pointing on the role of CoA biosynthetic pathway in signal transduction.     

Heavy metal-induced oxidative damage, defense reactions, and detoxification mechanisms in plants

Heavy metal (HMs) contamination is widespread globally due to anthropogenic, technogenic, and geogenic activities. The HMs exposure could lead to multiple toxic effects in plants by inducing reactive oxygen species (ROS), which inhibit most cellular processes at various levels of metabolism. ROS being highly unstable could play dual role (1) damaging cellular components and (2) act as an important secondary messenger for inducing plant defense system. Cells are equipped with enzymatic and non-enzymatic defense mechanisms to counteract this damage. Some are constitutive and others that are activated only when a stress-specific signal is perceived. Enzymatic scavengers of ROS include superoxide dismutase, catalase, glutathione reductase, and peroxidase, while non-enzymatic antioxidants are glutathione, ascorbic acid, α-tocopherol, flavonoids, anthocyanins, carotenoids, and organic acids. The intracellular and extracellular chelation mechanisms of HMs are associated with organic acids such as citric, malic and oxalic acid, etc. The important mechanism of detoxification includes metal complexation with glutathione, amino acids, synthesis of phytochelatins and sequestration into the vacuoles. Excessive stresses induce a cascade, MAPK (mitogen-activated protein kinase) pathway and synthesis of metal-detoxifying ligands. Metal detoxification through MAPK cascade and synthesis of metal-detoxifying ligands will be of considerable interest in the field of plant biotechnology. Further, the photoprotective roles of pigments of xanthophylls cycle under HMs stress were also discussed.     

Surface films of Escherichia coli colonies

Abstract Escherichia coli colony surfaces were examined using SEM and TEM. The results indicated that bacterial colonies in the course of their development produce surface films which become thicker with increased growth duration. Membrane vesicles contribute to the formation of the surface film. The complex organization of the film suggests that it may perform specific functions.     

Extracellular vesicle RNAs reflect placenta dysfunction and are a biomarker source for preterm labour

Preterm birth (PTB) can lead to lifelong complications and challenges. Identifying and monitoring molecular signals in easily accessible biological samples that can diagnose or predict the risk of preterm labour (PTL) in pregnant women will reduce or prevent PTBs. A number of studies identified putative biomarkers for PTL including protein, miRNA and hormones from various body fluids. However, biomarkers identified from these studies usually lack consistency and reproducibility. Extracellular vesicles (EVs) in circulation have gained significant interest in recent years as these vesicles may be involved in cell‐cell communication. We have used an improved small RNA library construction protocol and a newly developed size exclusion chromatography (SEC)‐based EV purification method to gain a comprehensive view of circulating RNA in plasma and its distribution by analysing RNAs in whole plasma and EV‐associated and EV‐depleted plasma. We identified a number of miRNAs in EVs that can be used as biomarkers for PTL, and these miRNAs may reflect the pathological changes of the placenta during the development of PTL. To our knowledge, this is the first study to report a comprehensive picture of circulating RNA, including RNA in whole plasma, EV and EV‐depleted plasma, in PTL and reveal the usefulness of EV‐associated RNAs in disease diagnosis.     

Benchmark of different charges for prediction of the partitioning coefficient through the hydrophilic/lipophilic index

A few different theoretical methods for assigning the partial atomic charges were benchmarked for calculation of the hydrophilic/lipophilic index (HLI). The coefficients were selected to produce the best correlation of the HLI values with the experimental octanol-water partition. Different parameters were checked in calculations of partial charges to get the best performance of the HLI values obtained. Thus, four partitioning schemes (Coulson, Mulliken, Merz-Kollman, Ford-Wang) were benchmarked for calculations of atomic charges with six semiempirical methods (AM1, PM3, RM1, PM6, PM6-D3H4, PM7). Moreover, five distinct types of partial atomic charges (Mulliken, Hirshfeld, Löwdin, CHELPG, NPA), obtained at the Hartree–Fock and DFT levels of theory with three basis sets, were tested for their ability to produce the HLI values with the best correlation to experimental logP coefficients of 50 mono-charged organic anions. In the case of the semiempirical methods, the best correlation between the HLI and logP values (the correlation coefficient r?=?0.9216) was obtained with the AM1 Ford–Wang parametric electrostatic potential charges. The Mulliken and Coulson charges calculated with the PM7 method can be used as an alternative to AM1, with the r values of 0.9107 and 0.8984, respectively. In the case of the DFT, the PBE/def2-TZVP natural population analysis charges produce the best correlation (r?=?0.9220). Nevertheless, in spite of a marginally lower performance (r?=?0.9159), the NPA charges computed at the PBE/def2-SVP level are more robust and can be regarded as the optimum choice for calculating the HLI values.

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Graphical abstract The hydrophilic/lipophilic index (HLI)

     

New belemnites (Megateuthididae,Cylindroteuthididae) from the Bajocian and Bathonian of the Yuryung-Tumus Peninsula,northern Siberia,Russia and their palaeobiogeographic implications

New species of Paramegateuthis (Megateuthididae) and Cylindroteuthis (Cylindroteuthididae) are described from the Bajocian–Bathonian boundary interval of the Yuryung-Tumus Peninsula, northern Siberia, Russia. Additionally, Paramegateuthis subishmensis Stoyanova-Vergilova, 1983, first documented from the Sub-Mediterranean region, is described herein from the Arctic. We propose the presence of a temporary passage between the Boreal and Tethyan seas in the European part of Russia during the Early Bajocian Humphriesianum Chronozone as an explanation of the migration of P. subishmensis. New belemnite records from the Yuryung-Tumus section contribute to the palaeontological characteristics of the Arctic domain.     

Effects of 5-azacytidine on the development of parthenogenetic mouse embryos

This study describes the effects of 5-azacytidine (5-azaC) on the development of diploid parthenogenetic embryos (PE) of CBA, C57BL/6 and (CBA × C57BL/6)F₁ mice in vitro at the 1-cell or the blastocyst stage or in vivo after implantation. Our findings indicate that genomic imprinting is modulated by genetic background. Non-fertilized C57BL/6 eggs form diploid parthenogenetic blastocysts at a much higher frequency than CBA eggs. Eggs from F₁ hybrid females form parthenogenetic blastocysts at an approximately intermediate level between these inbred strains of mice. C57BL/6 PE do not develop to the somite stages. In contrast, CBA PE and F₁ PE develop to various somite stages. Following administration of 5–azaC at 1.0 μmol/L in vitro at the 1- -cell stage, the number of implantations of C57BL/6 PE transferred to pseudopregnant females increased. In contrast, the number of implantations and somite F₁ PE did not significantly change following exposure to 5–azaC. However, administration of 5-azaC at the 1-cell stage stimulates development of somite F₁ PE. Administration of 5-azaC at 0.2 and 1.0 μmol/L in vitro at the blastocyst stage did not change the number of implantations of C57BL/6 PE. However, the number of implantations and somite CBA PE decreased. After injection of 5azaC at 0.24mg/kg in vivo at day 8 of gestation, some F₁ PE developed to 26–35 somites compared with a maximum of 25 somites in controls. The different effects of 5-azaC on the development of PE depend upon the mouse strain used and the stage of development.