Multi-Omics Analysis Revealed Increased De Novo Synthesis of Serine and Lower Activity of the Methionine Cycle in Breast Cancer Cell Lines.

A pipeline for metabolomics, based on UPLC-ESI-MS, was tested on two malignant breast cancer cell lines of the sub-types ER(+), PR(+), and HER2(3+) (MCF-7 and BCC), and one non-malignant epithelial cancer cell line (MCF-10A). This allowed us to quantify 33 internal metabolites, 10 of which showed a concentration profile associated with malignancy. Whole-transcriptome RNA-seq was also carried out for the three mentioned cell lines. An integrated analysis of metabolomics and transcriptomics was carried out using a genome-scale metabolic model. Metabolomics revealed the depletion of several metabolites that have homocysteine as a precursor, which was consistent with the lower activity of the methionine cycle caused by lower expression of the AHCY gene in cancer cell lines. Increased intracellular serine pools in cancer cell lines appeared to result from the over-expression of PHGDH and PSPH, which are involved in intracellular serine biosynthesis. An increased concentration of pyroglutamic acid in malignant cells was linked to the overexpression of the gene CHAC1.

Contribution of branched chain amino acids to energy production and mevalonate synthesis in cancer cells.

Leucine, isoleucine and valine, known as branched chain amino acids (BCAAs), have been reported to be degraded by different cancer cells, and their biodegradation pathways have been suggested as anticancer targets. However, the mechanisms by which the degradation of BCAAs could support the growth of cancer cells remains unclear. In this work, 13C experiments have been carried out in order to elucidate the metabolic role of BCAA degradation in two breast cancer cell lines (MCF-7 and BCC). The results revealed that up to 36% of the energy production via respiration by MCF-7 cells was supported by the degradation of BCAAs. Also, 67% of the mevalonate (the precursor of cholesterol) synthesized by the cells was coming from the degradation of leucine. The results were lower for BCC cells (14 and 30%, respectively). The non-tumorigenic epythelial cell line MCF-10A was used as a control, showing that 10% of the mitochondrial acetyl-CoA comes from the degradation of BCAAs and no mevalonate production. Metabolic flux analysis around the mevalonate node, also revealed that significant amounts of acetoacetate are being produced from BCAA derived carbon, which could be at the source of lipid synthesis. From these results we can conclude that the degradation of BCAAs is an important energy and carbon source for the proliferation of some cancer cells and its therapeutic targeting could be an interesting option.

Ethidium Binding to Salmonella enterica ser. Typhimurium Cells and Salmon Sperm DNA.

Bacterial resistance to antibiotics due to increased efficiency of the efflux is a serious problem in clinics of infectious diseases. Knowledge of the factors affecting the activity of efflux pumps would help to find the solution. For this, fast and trustful methods for efflux analysis are needed. Here, we analyzed how the assay conditions affect the accumulation of efflux indicators ethidium (Et+) and tetraphenylphosphonium in Salmonella enterica ser. Typhimurium cells. An inhibitor phenylalanyl-arginyl-ß-naphtylamide was applied to evaluate the input of RND family pumps into the total efflux. In parallel to spectrofluorimetric analysis, we used an electrochemical assessment of Et+ concentration. The results of our experiments indicated that Et+ fluorescence increases immediately after the penetration of this indicator into the cells. However, when cells bind a high amount of Et+, the intensity of the fluorescence reaches the saturation level and stops reacting to the accumulated amount of this indicator. For this reason, electrochemical measurements provide more trustful information about the efficiency of efflux when cells accumulate high amounts of Et+. Measurements of Et+ interaction with the purified DNA demonstrated that the affinity of this lipophilic cation to DNA depends on the medium composition. The capacity of DNA to bind Et+ considerably decreases in the presence of Mg2+, Polymyxin B or when DNA is incubated in high ionic strength media.

Fatty Acid Synthesis and Degradation Interplay to Regulate the Oxidative Stress in Cancer Cells.

Both cytosolic fatty acid synthesis (FAS) and mitochondrial fatty acid oxidation (FAO) have been shown to play a role in the survival and proliferation of cancer cells. This study aimed to confirm experimentally whether FAS and FAO coexist in breast cancer cells (BCC). By feeding cells with 13C-labeled glutamine and measuring labeling patterns of TCA intermediates, it was possible to show that part of the cytosolic acetyl-CoA used in lipid synthesis is also fed back into the mitochondrion via fatty acid degradation. This results in the transfer of reductive potential from the cytosol (in the form of NADPH) to the mitochondrion (in the form of NADH and FADH2). The hypothesized mechanism was further confirmed by blocking FAS and FAO with siRNAs. Exposure to staurosporine (which induces ROS production) resulted in the disruption of simultaneous FAS and FAO, which could be explained by NADPH depletion.

Interaction of ethidium and tetraphenylphosphonium cations with Salmonella enterica cells.

BACKGROUND AND OBJECTIVE: One of the main causes of bacterial resistance to antimicrobials is multidrug resistance induced by the increased efficiency of the efflux pumps. In this study we analyzed how the conditions of assay affect the efflux of indicator substrates ethidium (Et+) and tetraphenylphosphonium (TPP+) in Salmonella enterica ser. Typhimurium cells. Impact of the outer membrane permeability barrier, composition and temperature of the medium on accumulation of the indicator compounds also was analyzed. MATERIALS AND METHODS: The fluorescence of Et+ and Nile Red was measured using 96-well plates and a plate reader. In parallel to traditional studies of fluorescence we applied a constructed selective electrode to follow the accumulation of Et+ in S. enterica cells. Simultaneously with monitoring of Et+ concentration in the cell incubation medium, electrochemical measurements of TPP+ accumulation were performed. Furthermore, Et+ and TPP+ were used within the same sample as agents competing for the interaction with the efflux pumps. An inhibitor phenylalanyl-arginyl-ß-naphtylamide (PAßN) was applied to evaluate the input of RND-family pumps in the total efflux of these indicator compounds. RESULTS: S. enterica cells with the intact outer membrane (OM) bound very low amounts of Et+ or TPP+. Cells with the permeabilized OM accumulate considerably higher amounts of the indicator compounds at pH 8.0, but only Et+ was considerably accumulated at pH 6.5. At conditions of electrochemical monitoring accumulation of Et+ by the permeabilized cells at 37°C was considerably faster than at 23°C, but at the higher temperature most of the cell-accumulated Et+ was extruded back to the medium. The fluorescence of Et+ in suspension of cells incubated in 400mmol/L Tris buffer was about twice higher compared to 100mmol/L one. The inhibitory action of TPP+ on Et+ efflux was evident only in 400mmol/L Tris although PAßN effectively increased Et+ fluorescence at both buffer concentrations. CONCLUSIONS: Results of our experiments indicate that ionic strength of the incubation medium influence the selectivity, the medium temperature and the assay conditions impact the kinetics of efflux. The lower accumulated amount and the weaker fluorescence of Et+ registered in slightly acidic medium indicate that ΔΨ plays a role in the accumulation of this indicator cation. The bound amount of Et+ to the de-energized or permeabilized cells considerably varies depending on the conditions and methods of de-energization or permeabilization of cells. Tris/EDTA permeabilization of the cells does not inhibit the efflux.

Scaffold design for artificial tissue with bone marrow stem cells.

OBJECTIVE: The aim of this study was to test polymeric materials (collagen, fibrin, polyimide film, and polylactic acid) for single- and multi-layer scaffold formation. MATERIALS AND METHODS: In our study, we used rabbit bone marrow stem cells (rBMSCs) and human mesenchymal stem cells (hMSCs) with materials of a different origin for the formation of an artificial scaffold, such as a collagen scaffold, fibrin scaffold produced from clotted rabbit plasma, electrospun poly(lactic acid) (PLA) mats, polyimide film (PI), and the combination of the latter two. Cell imaging was performed 3-14 days after cell cultivation in the scaffolds. Time-lapse imaging was used to determine hMSC mobility on the PI film. RESULTS: Cell incorporation in collagen and clotted fibrin scaffolds was evaluated after 2-week cultivation in vitro. Histological analysis showed that cells penetrated only external layers of the collagen scaffold, while the fibrin clot was populated with rBMSCs through the entire scaffold thickness. As well, cell behavior on the laser micro-structured PI film was analyzed. The mobility of hMSCs on the smooth PI film and the micro-machined surface was 20±2µm/h and 18±4µm/h, respectively. After 3-day cultivation, hMSCs were capable of spreading through the whole 100±10µm-thick layer of the electrospun PLA scaffold and demonstrated that the multilayer scaffold composed of PI and PLA materials ensured a suitable environment for cell growth. CONCLUSIONS: The obtained results suggest that electrospinning technology and femtosecond laser micro-structuring could be employed for the development of multi-layer scaffolds. Different biopolymers, such as PLA, fibrin, and collagen, could be used as appropriate environments for cell inhabitation and as an inner layer of the multi-layer scaffold. PI could be suitable as a barrier blocking cell migration from the scaffold. However, additional studies are needed to determine optimal parameters of inner and outer scaffold layers.

Mode of the Interaction of Efflux Inhibitor Phenylalanyl-arginyl-ß-naphtylamide with Bacterial Cells.

An increased efflux activity is one of the major reasons for bacterial antibiotic resistance. The usage of efflux pump inhibitors could be a promising approach to restoring the activity of inefficient antibiotics. The interaction of the RND family efflux pump inhibitor phenylalanyl-arginyl-ß-naphthylamide (PAßN) with Salmonella enterica ser. Typhimurium cells was assayed using traditional microbiological techniques and a novel PAßN-selective electrode. Monitoring the PAßN concentration in the medium using the electrode enabled the real-time measurements of this compound's interaction with bacterial cells. We showed that S. Typhimurium cells accumulate a high amount of PAßN because of its high affinity to lipopolysaccharides (LPSs), the major constituent of the outer layer of the outer membrane, and does not affect the functioning of the plasma membrane. EDTA enhanced the binding of PAßN to S. Typhimurium cells and the purified E. coli LPSs, but the energization of the cells by glucose does not affect the cell-bound amount of this inhibitor. Polycationic antibiotic Polymyxin B released both the cells accumulated and the suspended LPS-bound PAßN.

Phosphorylation-dependent allosteric regulation of Cx43 gap junction inhibitor potency.

Physiological and pathological processes such as homeostasis, embryogenesis, development, tumorigenesis, and cell movement depend on the intercellular communication through gap junctions (GJIC). Connexin (Cx)-based GJ channels are formed of two apposing hemichannels in the contiguous cells and provide a direct pathway for electrical and metabolic intercellular communication. The main modulators of GJ conductance are transjunctional voltage, intracellular pH, Ca2+, Mg2+, and phosphorylation. Chemical modulators of GJIC are being used in cases of various intercellular communication-dependent diseases. In this study, we used molecular docking, dual whole-cell patch-clamp, and Western blotting to investigate the impact of connexin phosphorylation on GJ chemical gating by α-pinene and other GJ inhibitors (octanol, carbenoxolone, mefloquine, intracellular pH, glycyrrhetinic acid, and sevoflurane) in HeLa cells expressing exogenous Cx43 (full length and truncated at amino acid 258) and other connexins typical of heart and/or nervous system (Cx36, Cx40, Cx45, and Cx47), and in cells expressing endogenous Cx43 (Novikoff and U-87). We found that Ca2+-regulated kinases, such as Ca2+/calmodulin-dependent kinase II, atypical protein kinase C, cyclin-dependent kinase, and Pyk2 kinase may allosterically modulate the potency of α-pinene through phosphorylation of Cx43 C-terminus. The identified new phenomenon was Cx isoform-, inhibitor-, and cell type-dependent. Overall, these results suggest that compounds, the potency of which depends on receptor phosphorylation, might be of particular interest in developing targeted therapies for diseases accompanied by high kinase activity, such as cardiac arrhythmias, epilepsy, stroke, essential tremor, inflammation, and cancer.

Rab40c regulates focal adhesions and PP6 activity by controlling ANKRD28 ubiquitylation.

Rab40c is a SOCS box-containing protein which binds Cullin5 to form a ubiquitin E3 ligase complex (Rab40c/CRL5) to regulate protein ubiquitylation. However, the exact functions of Rab40c remain to be determined, and what proteins are the targets of Rab40c-Cullin5-mediated ubiquitylation in mammalian cells are unknown. Here we showed that in migrating MDA-MB-231 cells Rab40c regulates focal adhesion's number, size, and distribution. Mechanistically, we found that Rab40c binds the protein phosphatase 6 (PP6) complex and ubiquitylates one of its subunits, ankyrin repeat domain 28 (ANKRD28), thus leading to its lysosomal degradation. Furthermore, we identified that phosphorylation of FAK and MOB1 is decreased in Rab40c knock-out cells, which may contribute to focal adhesion site regulation by Rab40c. Thus, we propose a model where Rab40c/CRL5 regulates ANKRD28 ubiquitylation and degradation, leading to a decrease in PP6 activity, which ultimately affects FAK and Hippo pathway signaling to alter focal adhesion dynamics.

The effect of nutmeg essential oil constituents on Novikoff hepatoma cell viability and communication through Cx43 gap junctions.

Essential oils from plants are a potential source of molecules having anti-inflammatory, anticancer, cardiotropic, and other activities. However, most of these effects lack mechanistic explanations and structure-activity relationship testing. In the present study, we: 1) identified the nutmeg essential oil (NEO) composition; 2) using molecular docking, we determined the putative regulatory binding sites on the connexin 43 (Cx43) that is responsible for gap junction-dependent intercellular communication (GJIC) in the majority of tissues; 3) examined the effect of NEO and its three constituents - sabinene, α-pinene, and α-copaene - on GJ conductance and gating in Novikoff cells expressing endogenous Cx43; and 4) verified whether NEO effects on GJIC correlated with its action on Novikoff cell viability, proliferation, and colony formation capability. Our results revealed NEO and its constituents as potent and efficient Cx43 GJ inhibitors acting by slow gating mechanism. In addition, NEO reduced Novikoff hepatoma cell viability, proliferation, and colony formation capability; however, this was achieved at higher doses and was unrelated to its effects on GJIC.

Genome scale metabolic models as tools for drug design and personalized medicine.

In this work we aim to show how Genome Scale Metabolic Models (GSMMs) can be used as tools for drug design. By comparing the chemical structures of human metabolites (obtained using their KEGG indexes) and the compounds contained in the DrugBank database, we have observed that compounds showing Tanimoto scores higher than 0.9 with a metabolite, are 29.5 times more likely to bind the enzymes metabolizing the considered metabolite, than ligands chosen randomly. By using RNA-seq data to constrain a human GSMM it is possible to obtain an estimation of its distribution of metabolic fluxes and to quantify the effects of restraining the rate of chosen metabolic reactions (for example using a drug that inhibits the enzymes catalyzing the mentioned reactions). This method allowed us to predict the differential effects of lipoamide analogs on the proliferation of MCF7 (a breast cancer cell line) and ASM (airway smooth muscle) cells respectively. These differential effects were confirmed experimentally, which provides a proof of concept of how human GSMMs could be used to find therapeutic windows against cancer. By using RNA-seq data of 34 different cancer cell lines and 26 healthy tissues, we assessed the putative anticancer effects of the compounds in DrugBank which are structurally similar to human metabolites. Among other results it was predicted that the mevalonate pathway might constitute a good therapeutic window against cancer proliferation, due to the fact that most cancer cell lines do not express the cholesterol transporter NPC1L1 and the lipoprotein lipase LPL, which makes them rely on the mevalonate pathway to obtain cholesterol.

Femtosecond laser micro-machined polyimide films for cell scaffold applications.

Engineering of sophisticated synthetic 3D scaffolds that allow controlling behaviour and location of the cells requires advanced micro/nano-fabrication techniques. Ultrafast laser micro-machining employing a 1030-nm wavelength Yb:KGW femtosecond laser and a micro-fabrication workstation for micro-machining of commercially available 12.7 and 25.4 µm thickness polyimide (PI) film was applied. Mechanical properties of the fabricated scaffolds, i.e. arrays of differently spaced holes, were examined via custom-built uniaxial micro-tensile testing and finite element method simulations. We demonstrate that experimental micro-tensile testing results could be numerically simulated and explained by two-material model, assuming that 2-6 µm width rings around the holes possessed up to five times higher Young's modulus and yield stress compared with the rest of the laser intacted PI film areas of 'dog-bone'-shaped specimens. That was attributed to material modification around the micro-machined holes in the vicinity of the position of the focused laser beam track during trepanning drilling. We demonstrate that virgin PI films provide a suitable environment for the mobility, proliferation and intercellular communication of human bone marrow mesenchymal stem cells, and discuss how cell behaviour varies on the micro-machined PI films with holes of different diameters (3.1, 8.4 and 16.7 µm) and hole spacing (30, 35, 40 and 45 µm). We conclude that the holes of 3.1 µm diameter were sufficient for metabolic and genetic communication through membranous tunneling tubes between cells residing on the opposite sides of PI film, but prevented the trans-migration of cells through the holes. Copyright © 2016 John Wiley & Sons, Ltd.

Transcriptional hallmarks of cancer cell lines reveal an emerging role of branched chain amino acid catabolism.

A comparative analysis between cancer cell lines and healthy dividing cells was performed using data (289 microarrays and 50 RNA-seq samples) from 100 different cancer cell lines and 6 types of healthy stem cells. The analysis revealed two large-scale transcriptional events that characterize cancer cell lines. The first event was a large-scale up-regulation pattern associated to epithelial-mesenchymal transition, putatively driven by the interplay of the SP1 transcription factor and the canonical Wnt signaling pathway; the second event was the failure to overexpress a diverse set of genes coding membrane and extracellular proteins. This failure is putatively caused by a lack of activity of the AP-1 complex. It was also shown that the epithelial-mesenchymal transition was associated with the up-regulation of 5 enzymes involved in the degradation of branched chain amino acids. The suitability of silencing one of this enzymes (branched chain amino acid transaminase 2; BCAT2) with therapeutic effects was tested experimentally on the breast cancer cell line MCF-7 and primary cell culture of breast tumor (BCC), leading to lower cell proliferation. The silencing of BCAT2 did not have any significant effect on ASM and MCF10A cells, which were used as models of healthy dividing cells.

Evaluation of the efficiency of synthesized efflux pump inhibitors on Salmonella enterica ser. typhimurium cells.

Multidrug efflux pump inhibitors have a great potential as pharmacological agents that increase the drug susceptibility of bacterial pathogens. Our study was focused on the synthesis and evaluation of the efficiency of resistance-nodulation-division (RND) family efflux pump inhibitors. The efficiency of these inhibitors was investigated on Salmonella enterica ser. typhimurium cells using tetraphenylphosphonium (TPP(+) ) and ethidium cations as the efflux pump substrates. Results of our study indicated that efficiency of the inhibitors depends on the cell outer membrane permeability and method of the assay used. Temperature of the incubation medium and a solvent of the inhibitor used have only minor effect on results of the assay.