Towards Analytics Aware Ontology Based Access to Static and Streaming Data (Extended Version)

Real-time analytics that requires integration and aggregation of heterogeneous and distributed streaming and static data is a typical task in many industrial scenarios such as diagnostics of turbines in Siemens. OBDA approach has a great potential to facilitate such tasks; however, it has a number of limitations in dealing with analytics that restrict its use in important industrial applications. Based on our experience with Siemens, we argue that in order to overcome those limitations OBDA should be extended and become analytics, source, and cost aware. In this work we propose such an extension. In particular, we propose an ontology, mapping, and query language for OBDA, where aggregate and other analytical functions are first class citizens. Moreover, we develop query optimisation techniques that allow to efficiently process analytical tasks over static and streaming data. We implement our approach in a system and evaluate our system with Siemens turbine data

RORγ is a targetable master regulator of cholesterol biosynthesis in a cancer subtype.

Tumor subtype-specific metabolic reprogrammers could serve as targets of therapeutic intervention. Here we show that triple-negative breast cancer (TNBC) exhibits a hyper-activated cholesterol-biosynthesis program that is strongly linked to nuclear receptor RORγ, compared to estrogen receptor-positive breast cancer. Genetic and pharmacological inhibition of RORγ reduces tumor cholesterol content and synthesis rate while preserving host cholesterol homeostasis. We demonstrate that RORγ functions as an essential activator of the entire cholesterol-biosynthesis program, dominating SREBP2 via its binding to cholesterol-biosynthesis genes and its facilitation of the recruitment of SREBP2. RORγ inhibition disrupts its association with SREBP2 and reduces chromatin acetylation at cholesterol-biosynthesis gene loci. RORγ antagonists cause tumor regression in patient-derived xenografts and immune-intact models. Their combination with cholesterol-lowering statins elicits superior anti-tumor synergy selectively in TNBC. Together, our study uncovers a master regulator of the cholesterol-biosynthesis program and an attractive target for TNBC

MiR-205-driven downregulation of cholesterol biosynthesis through SQLE-inhibition identifies therapeutic vulnerability in aggressive prostate cancer

Prostate cancer (PCa) shows strong dependence on the androgen receptor (AR) pathway. Here, we show that squalene epoxidase (SQLE), an enzyme of the cholesterol biosynthesis pathway, is overexpressed in advanced PCa and its expression correlates with poor survival. SQLE expression is controlled by micro-RNA 205 (miR-205), which is significantly downregulated in advanced PCa. Restoration of miR-205 expression or competitive inhibition of SQLE led to inhibition of de novo cholesterol biosynthesis. Furthermore, SQLE was essential for proliferation of AR-positive PCa cell lines, including abiraterone or enzalutamide resistant derivatives, and blocked transactivation of the AR pathway. Inhibition of SQLE with the FDA approved antifungal drug terbinafine also efficiently blocked orthotopic tumour growth in mice. Finally, terbinafine reduced levels of prostate specific antigen (PSA) in three out of four late-stage PCa patients. These results highlight SQLE as a therapeutic target for the treatment of advanced PCa

Terbinafine Resistance of Trichophyton Clinical Isolates Caused by Specific Point Mutations in the Squalene Epoxidase Gene.

Terbinafine is one of the allylamine antifungal agents whose target is squalene epoxidase (SQLE). This agent has been extensively used in the therapy of dermatophyte infections. The incidence of patients with tinea pedis or unguium tolerant to terbinafine treatment prompted us to screen the terbinafine resistance of all javax.xml.bind.JAXBElement@dc06fb4 clinical isolates from the laboratory of the Centre Hospitalier Universitaire Vaudois collected over a 3-year period and to identify their mechanism of resistance. Among 2,056 tested isolates, 17 (≈1%) showed reduced terbinafine susceptibility, and all of these were found to harbor javax.xml.bind.JAXBElement@374d721c gene alleles with different single point mutations, leading to single amino acid substitutions at one of four positions (Leu javax.xml.bind.JAXBElement@4655f570 , Phe javax.xml.bind.JAXBElement@112b804a , Phe javax.xml.bind.JAXBElement@1f18e014 , and His javax.xml.bind.JAXBElement@4319ac79 ) of the SQLE protein. Point mutations leading to the corresponding amino acid substitutions were introduced into the endogenous javax.xml.bind.JAXBElement@2a0e3f1f gene of a terbinafine-sensitive javax.xml.bind.JAXBElement@67eac3c4 (formerly javax.xml.bind.JAXBElement@3f2a876d ) strain. All of the generated javax.xml.bind.JAXBElement@315e9e95 transformants expressing mutated SQLE proteins exhibited obvious terbinafine-resistant phenotypes compared to the phenotypes of the parent strain and of transformants expressing wild-type SQLE proteins. Nearly identical phenotypes were also observed in javax.xml.bind.JAXBElement@6af3a966 transformants expressing mutant forms of javax.xml.bind.JAXBElement@5bb6b31f SQLE proteins. Considering that the genome size of dermatophytes is about 22 Mb, the frequency of terbinafine-resistant clinical isolates was strikingly high. Increased exposure to antifungal drugs could favor the generation of resistant strains

Changes to cholesterol trafficking in macrophages by Leishmania parasites infection

Leishmania spp. are protozoan parasites that are transmitted by sandfly vectors during blood sucking to vertebrate hosts and cause a spectrum of diseases called leishmaniases. It has been demonstrated that host cholesterol plays an important role during Leishmania infection. Nevertheless, little is known about the intracellular distribution of this lipid early after internalization of the parasite. Here, pulse‐chase experiments with radiolabeled cholesteryl esterified to fatty acids bound to low‐density lipoproteins indicated that retention of this source of cholesterol is increased in parasite‐containing subcellular fractions, while uptake is unaffected. This is correlated with a reduction or absence of detectable NPC1 (Niemann–Pick disease, type C1), a protein responsible for cholesterol efflux from endocytic compartments, in the Leishmania mexicana habitat and infected cells. Filipin staining revealed a halo around parasites within parasitophorous vacuoles (PV) likely representing free cholesterol accumulation. Labeling of host cell membranous cholesterol by fluorescent cholesterol species before infection revealed that this pool is also trafficked to the PV but becomes incorporated into the parasites’ membranes and seems not to contribute to the halo detected by filipin. This cholesterol sequestration happened early after infection and was functionally significant as it correlated with the upregulation of mRNA‐encoding proteins required for cholesterol biosynthesis. Thus, sequestration of cholesterol by Leishmania amastigotes early after infection provides a basis to understand perturbation of cholesterol‐dependent processes in macrophages that were shown previously by others to be necessary for their proper function in innate and adaptive immune responses

GeneFishing to reconstruct context specific portraits of biological processes.

Rapid advances in genomic technologies have led to a wealth of diverse data, from which novel discoveries can be gleaned through the application of robust statistical and computational methods. Here, we describe GeneFishing, a semisupervised computational approach to reconstruct context-specific portraits of biological processes by leveraging gene-gene coexpression information. GeneFishing incorporates multiple high-dimensional statistical ideas, including dimensionality reduction, clustering, subsampling, and results aggregation, to produce robust results. To illustrate the power of our method, we applied it using 21 genes involved in cholesterol metabolism as "bait" to "fish out" (or identify) genes not previously identified as being connected to cholesterol metabolism. Using simulation and real datasets, we found that the results obtained through GeneFishing were more interesting for our study than those provided by related gene prioritization methods. In particular, application of GeneFishing to the GTEx liver RNA sequencing (RNAseq) data not only reidentified many known cholesterol-related genes, but also pointed to glyoxalase I (GLO1) as a gene implicated in cholesterol metabolism. In a follow-up experiment, we found that GLO1 knockdown in human hepatoma cell lines increased levels of cellular cholesterol ester, validating a role for GLO1 in cholesterol metabolism. In addition, we performed pantissue analysis by applying GeneFishing on various tissues and identified many potential tissue-specific cholesterol metabolism-related genes. GeneFishing appears to be a powerful tool for identifying related components of complex biological systems and may be used across a wide range of applications

Differential epigenetic reprogramming in response to specific endocrine therapies promotes cholesterol biosynthesis and cellular invasion

Endocrine therapies target the activation of the oestrogen receptor alpha (ERα) via distinct mechanisms, but it is not clear whether breast cancer cells can adapt to treatment using drug-specific mechanisms. Here we demonstrate that resistance emerges via drug-specific epigenetic reprogramming. Resistant cells display a spectrum of phenotypical changes with invasive phenotypes evolving in lines resistant to the aromatase inhibitor (AI). Orthogonal genomics analysis of reprogrammed regulatory regions identifies individual drug-induced epigenetic states involving large topologically associating domains (TADs) and the activation of super-enhancers. AI-resistant cells activate endogenous cholesterol biosynthesis (CB) through stable epigenetic activation in vitro and in vivo. Mechanistically, CB sparks the constitutive activation of oestrogen receptors alpha (ERα) in AI-resistant cells, partly via the biosynthesis of 27-hydroxycholesterol. By targeting CB using statins, ERα binding is reduced and cell invasion is prevented. Epigenomic-led stratification can predict resistance to AI in a subset of ERα-positive patients

Effect of obesity on blood-brain barrier integrity in ischemic brain using mouse model

One of the consequences of obesity is the brain ischemia which is leading to the loss of blood-brain barrier to its integrity and subsequently to the accumulation of Beta-amyloid peptide which leads to the early onset of the Alzheimer's disease. The interest of this study was investigating the various factors which may impact the degradation or the clearance of the peptide. To achieve this goal, in-vivo and in-vitro studies were conducted concerning the enzymatic activity that involved in the degradation process of the peptide and the impact of natural compounds that influencing the accumulation and/or clearance of the peptide, respectively. Furthermore, a study of the hypothesized role of the peptide as an anti-microbial agent was considered too. Impact of cholesterol on the Insulin-degrading enzyme (IDE) was considered. On the cell surface, many enzymes could be implicated in the degrading process including IDE. However, it was found that IDE is the predominant enzyme which degrades the peptide between cells. The aforementioned investigation was performed by employing several cell lines and experiments and using fluorescence and absorbance plate reader, WB, and qRT-PCR techniques. While, investigating the impact of chemical compounds was performed by using circular dichroism spectrometry (CD). AlamarBlue assay was employed in investigating the role of the peptide as AMP.Die Ischämie des Gehirns und der daraus entstehende Verlust der Integrität der Blut-Hirn-Schranke ist eine Folge von Adipositas. Daraufhin kommt es zur Akkumulation vom Beta-Amyloid Peptiden und daraus folgend zu einer frühen Manifestation von Alzheimer Demenz. Das Ziel dieser Studie war es, die verschiedenen Einflussfaktoren der Degradation und Clearance des Beta-Amyloids zu untersuchen. Zu diesem Zweck wurden in-vivo und in-vitro Modelle benutzt, um die Enzymaktivität in der Peptid-Degradation sowie den Einfluss von natürlichen Verbindungen auf die Akkumulation bzw. Clearance zu beobachten. Die vermutete Rolle des Beta-Amyloids als antimikrobielles Peptid wurde außerdem untersucht. Viele Enzyme an der Zelloberfläche, unter anderem auch das Insulin-degrading Enzyme (IDE), können an der Degradation des Beta-Amyloids beteiligt sein. Jedoch konnte IDE als das vorherrschende Enzym der Degradation zwischen den Zellen ausgemacht werden. Auch die Cholesterol-Wirkung auf das Insulin-degrading Enzyme (IDE) wurde angesehen. Die beschriebenen Untersuchungen konnten mittels verschiedener Zelllinien, Fluoreszenz- und Extinktionsmessungen, Western Blot und qRT-PCR durchgeführt werden. Dagegen wurde der Einfluss chemischer Verbindungen mit der Circulardichroismus-Spektroskopie untersucht. Die Rolle des Beta-Amyloids als antimikrobielles Peptid konnte mittels AlamarBlue-Assay untersucht werden

Doa10/MARCH6 architecture interconnects E3 ligase activity with lipid-binding transmembrane channel to regulate SQLE

Transmembrane E3 ligases play crucial roles in homeostasis. Much protein and organelle quality control, and metabolic regulation, are determined by ER-resident MARCH6 E3 ligases, including Doa10 in yeast. Here, we present Doa10/MARCH6 structural analysis by cryo-EM and AlphaFold predictions, and a structure-based mutagenesis campaign. The majority of Doa10/MARCH6 adopts a unique circular structure within the membrane. This channel is established by a lipid-binding scaffold, and gated by a flexible helical bundle. The ubiquitylation active site is positioned over the channel by connections between the cytosolic E3 ligase RING domain and the membrane-spanning scaffold and gate. Here, by assaying 95 MARCH6 variants for effects on stability of the well-characterized substrate SQLE, which regulates cholesterol levels, we reveal crucial roles of the gated channel and RING domain consistent with AlphaFold-models of substrate-engaged and ubiquitylation complexes. SQLE degradation further depends on connections between the channel and RING domain, and lipid binding sites, revealing how interconnected Doa10/MARCH6 elements could orchestrate metabolic signals, substrate binding, and E3 ligase activity

Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia

Altered metabolism is a hallmark of cancer. However, the role of genomic changes in metabolic genes driving the tumour metabolic shift remains to be elucidated. Here, we have investigated the genomic and transcriptomic changes underlying this shift across ten different cancer types.A systematic pan-cancer analysis of 6538 tumour/normal samples covering ten major cancer types identified a core metabolic signature of 44 genes that exhibit high frequency somatic copy number gains/amplifications (>20 % cases) associated with increased mRNA expression (ρ > 0.3, q < 10(-3)). Prognostic classifiers using these genes were confirmed in independent datasets for breast and kidney cancers. Interestingly, this signature is strongly associated with hypoxia, with nine out of ten cancer types showing increased expression and five out of ten cancer types showing increased gain/amplification of these genes in hypoxic tumours (P ≤ 0.01). Further validation in breast and colorectal cancer cell lines highlighted squalene epoxidase, an oxygen-requiring enzyme in cholesterol biosynthesis, as a driver of dysregulated metabolism and a key player in maintaining cell survival under hypoxia.This study reveals somatic genomic alterations underlying a pan-cancer metabolic shift and suggests genomic adaptation of these genes as a survival mechanism in hypoxic tumours