Multi-scale genomic, transcriptomic and proteomic analysis of colorectal cancer cell lines to identify novel biomarkers

This work was partially funded by the Strategic Educational Pathways Scholarship (Malta). The scholarship is part-financed by the European Union – European Social Fund (ESF) under Operational Programme II – Cohesion Policy 2007-2013, “Empowering People for More Jobs and a Better Quality of Life”. This project was additionally funded by Medical Research Scotland.Selecting colorectal cancer (CRC) patients likely to respond to therapy remains a clinical challenge. The objectives of this study were to establish which genes were differentially expressed with respect to treatment sensitivity and relate this to copy number in a panel of 15 CRC cell lines. Copy number variations of the identified genes were assessed in a cohort of CRCs. IC50’s were measured for 5-fluorouracil, oxaliplatin, and BEZ-235, a PI3K/mTOR inhibitor. Cell lines were profiled using array comparative genomic hybridisation, Illumina gene expression analysis, reverse phase protein arrays, and targeted sequencing of KRAS hotspot mutations. Frequent gains were observed at 2p, 3q, 5p, 7p, 7q, 8q, 12p, 13q, 14q, and 17q and losses at 2q, 3p, 5q, 8p, 9p, 9q, 14q, 18q, and 20p. Frequently gained regions contained EGFR, PIK3CA, MYC, SMO, TRIB1, FZD1, and BRCA2, while frequently lost regions contained FHIT and MACROD2. TRIB1 was selected for further study. Gene enrichment analysis showed that differentially expressed genes with respect to treatment response were involved in Wnt signalling, EGF receptor signalling, apoptosis, cell cycle, and angiogenesis. Stepwise integration of copy number and gene expression data yielded 47 candidate genes that were significantly correlated. PDCD6 was differentially expressed in all three treatment responses. Tissue microarrays were constructed for a cohort of 118 CRC patients and TRIB1 and MYC amplifications were measured using fluorescence in situ hybridisation. TRIB1 and MYC were amplified in 14.5% and 7.4% of the cohort, respectively, and these amplifications were significantly correlated (p≤0.0001). TRIB1 protein expression in the patient cohort was significantly correlated with pERK, Akt, and Caspase 3 expression. In conclusion, a set of candidate predictive biomarkers for 5-fluorouracil, oxaliplatin, and BEZ235 are described that warrant further study. Amplification of the putative oncogene TRIB1 has been described for the first time in a cohort of CRC patients.Publisher PDFPeer reviewe

Colors of graphene and graphene-oxide multilayers on various substrates

We investigated the colors of graphene and graphene-oxide multilayers that were deposited on various dielectric layers. In particular, the effects of the material thickness, the types of dielectric layers, and the existence of a back silicon substrate were analyzed. The colors of graphene-oxide layers on a SiO(2)/Si substrate were found to periodically change as the material thickness increased. However, the colors of graphene layers on the same substrate became saturated without a similar periodic change. The calculated colors corresponding to the material thicknesses were verified by optical microscopy and profilometry. We believe that these results demonstrate the possibility of utilizing color as a simple tool for detecting and estimating the thicknesses of graphene and graphene-oxide multilayers

Colors of graphene and graphene-oxide multilayers on various substrates Colors of graphene and graphene-oxide multilayers on various substrates

Abstract We investigated the colors of graphene and graphene-oxide multilayers that were deposited on various dielectric layers. In particular, the effects of the material thickness, the types of dielectric layers, and the existence of a back silicon substrate were analyzed. The colors of graphene-oxide layers on a SiO 2 /Si substrate were found to periodically change as the material thickness increased. However, the colors of graphene layers on the same substrate became saturated without a similar periodic change. The calculated colors corresponding to the material thicknesses were verified by optical microscopy and profilometry. We believe that these results demonstrate the possibility of utilizing color as a simple tool for detecting and estimating the thicknesses of graphene and graphene-oxide multilayers

In vitro protocol for validating interface pressure sensors for therapeutic compression garments: Importance of sphygmomanometer placement and initial cuff diameter

An optimal protocol is needed to validate the performance of future interface pressure sensors for compression garments when using a sphygmomanometer. PicoPress® was used on a rigid plastic cylinder (r=4 cm). An FDA-cleared aneroid sphygmomanometer was used to apply pressures from 10-60 mmHg with a diameter of 8 cm or 12 cm placed either beneath the sphygmomanometer’s airbag or fabric cuff. A two-tail t-test was performed (P<0.05 for significance) for all applied pressures. PicoPress® outputs vary with sensor placement (airbag vs fabric cuff) and the initial cuff diameter. Sensor placement overlying the sphygmomanometer’s fabric cuff compared to the airbag led to significantly higher pressures (37%-135%) depending on the cuff diameter size. These differences were nearly all statistically significant (P<0.05). Validation of new interface pressure sensors deploying a sphygmomanometer for calibration should specify the location of sensor placement location and initial diameter with a preference for placement under the airbag

Cooptimization of Adhesion and Power Conversion Efficiency of Organic Solar Cells by Controlling Surface Energy of Buffer Layers

Here, we demonstrate the cooptimization of the interfacial fracture energy and power conversion efficiency (PCE) of poly­[<i>N</i>-9′-heptadecanyl-2,7-carbazole-<i>alt</i>-5,5-(4′,7′-di-2-thienyl-2′,1′,3′-benzothiadiazole)] (PCDTBT)-based organic solar cells (OSCs) by surface treatments of the buffer layer. The investigated surface treatments of the buffer layer simultaneously changed the crack path and interfacial fracture energy of OSCs under mechanical stress and the work function of the buffer layer. To investigate the effects of surface treatments, the work of adhesion values were calculated and matched with the experimental results based on the Owens–Wendt model. Subsequently, we fabricated OSCs on surface-treated buffer layers. In particular, ZnO layers treated with poly­[(9,9-bis­(3′-(<i>N</i>,<i>N</i>-dimethyl­amino)­propyl)-2,7-fluorene)-<i>alt</i>-2,7-(9,9-dioctylfluorene)] (PFN) simultaneously satisfied the high mechanical reliability and PCE of OSCs by achieving high work of adhesion and optimized work function

FABRICATION AND MEASUREMENT OF SUSPENDED SILICON CARBIDE NANOWIRE DEVICES AND DEFLECTION

In this paper, we report the measurement of the deflection of beta-SiC nanowires supported at both ends. Such wires hold promise as active elements in NEMS/MEMS devices. To ensure the stable mechanical clamping and electrical contacts between electrodes and nanowires, we have developed a method of metal deposition to improve the contacts. This method consists of multiple depositions at different angles in order to avoid the shadow effect and reduce the compressive residual stress. The improvement of the contacts was verified via SEM observation and electrical transport measurements. To suspend the nanowire, a dielectric layer underneath was removed, followed by critical point drying. The change of electrical resistance was measured when the suspended nanowires were deflected by either capillary forces arising from the surface tension or electrostatic forces

Accelerated Degradation Due to Weakened Adhesion from Li-TFSI Additives in Perovskite Solar Cells

Reliable integration of organometallic halide perovskite in photovoltaic devices is critically limited by its low stability in humid environments. Furthermore, additives to increase the mobility in the hole transport material (HTM) have deliquescence and hygroscopic properties, which attract water molecules and result in accelerated degradation of the perovskite devices. In this study, a double cantilever beam (DCB) test is used to investigate the effects of additives in the HTM layer on the perovskite layer through neatly delaminating the interface between the perovskite and HTM layers. Using the DCB test, the bottom surface of the HTM layers is directly observed, and it is found that the additives are accumulated at the bottom along the thickness (i.e., through-plane direction) of the films. It is also found that the additives significantly decrease the adhesion at the interface between the perovskite and HTM layers by more than 60% through hardening the HTM films. Finally, the adhesion-based degradation mechanism of perovskite devices according to the existence of additives is proposed for humid environments

Precise Filtration of Chronic Myeloid Leukemia Cells by an Ultrathin Microporous Membrane with Backflushing to Minimize Fouling

A cell filtration platform that affords accurate size separation and minimizes fouling was developed. The platform features an ultra-thin porous membrane (UTM) filter, a pumping head filtration with backflush (PHF), and cell size measurement (CSM) software. The UTM chip is an ultrathin free-standing membrane with a large window area of 0.68 mm2, a pore diameter of 5 to 9 μm, and a thickness of less than 0.9 μm. The PHF prevents filter fouling. The CSM software analyzes the size distributions of the supernatants and subnatants of isolated cells and presents the data visually. The D99 particle size of cells of the chronic myeloid leukemia (CML) line K562 decreased from 22.2 to 17.5 μm after passage through a 5-μm filter. K562 cells could be separated by careful selection of the pore size; the recovery rate attained 91.3%. The method was compared to conventional blocking models by evaluating the mean square errors (MSEs) between the measured and calculated filtering volumes. The filtering rate was fitted by a linear regression model with a significance that exceeded 0.99 based on the R2 value. The platform can be used to separate various soft biomaterials and afford excellent stability during filtration

Simple approach for high-contrast optical imaging and characterization of graphene-based sheets

A simple optical method is presented for identifying and measuring the effective optical properties of nanometer-thick, graphene-based materials, based on the use of substrates consisting of a thin dielectric layer on silicon. High contrast between the graphene-based materials and the substrate is obtained by choosing appropriate optical properties and thickness of the dielectric layer. The effective refractive index and optical absorption coefficient of graphene oxide, thermally reduced graphene oxide, and graphene are obtained by comparing the predicted and measured contrasts