Targeting KRAS4A splicing through the RBM39/DCAF15 pathway inhibits cancer stem cells.

The commonly mutated human KRAS oncogene encodes two distinct KRAS4A and KRAS4B proteins generated by differential splicing. We demonstrate here that coordinated regulation of both isoforms through control of splicing is essential for development of Kras mutant tumors. The minor KRAS4A isoform is enriched in cancer stem-like cells, where it responds to hypoxia, while the major KRAS4B is induced by ER stress. KRAS4A splicing is controlled by the DCAF15/RBM39 pathway, and deletion of KRAS4A or pharmacological inhibition of RBM39 using Indisulam leads to inhibition of cancer stem cells. Our data identify existing clinical drugs that target KRAS4A splicing, and suggest that levels of the minor KRAS4A isoform in human tumors can be a biomarker of sensitivity to some existing cancer therapeutics.

Effects of Molecular Weight of Functionalized Liquid Butadiene Rubber as a Processing Aid on the Properties of SSBR/Silica Compounds.

Liquid butadiene rubber (LqBR) which used as a processing aid play a vital role in the manufacturing of high-performance tire tread compounds. However, the studies on the effect of molecular weight, microstructure, and functionalization of LqBR on the properties of compounds are still insufficient. In this study, non-functionalized and center-functionalized liquid butadiene rubbers (N-LqBR and C-LqBR modified with ethoxysilyl group, respectively) were synthesized with low vinyl content and different molecular weights using anionic polymerization. In addition, LqBR was added to the silica-filled SSBR compounds as an alternative to treated distillate aromatic extract (TDAE) oil, and the effect of molecular weight and functionalization on the properties of the silica-filled SSBR compound was examined. C-LqBR showed a low Payne effect and Mooney viscosity because of improved silica dispersion due to the ethoxysilyl functional group. Furthermore, C-LqBR showed an increased crosslink density, improved mechanical properties, and reduced organic matter extraction compared to the N-LqBR compound. LqBR reduced the glass transition temperature (Tg) of the compound significantly, thereby improving snow traction and abrasion resistance compared to TDAE oil. Furthermore, the energy loss characteristics revealed that the hysteresis loss attributable to the free chain ends of LqBR was dominant.

Development of High Dielectric Electrostrictive PVDF Terpolymer Blends for Enhanced Electromechanical Properties.

Electroactive polymers with high dielectric constants and low moduli can offer fast responses and large electromechanical strain under a relatively low electric field with regard to theoretical driving forces of electrostriction and electrostatic force. However, the conventional electroactive polymers, including silicone rubbers and acrylic polymers, have shown low dielectric constants (ca. < 4) because of their intrinsic limitation, although they have lower moduli (ca. < 1 MPa) than inorganics. To this end, we proposed the high dielectric PVDF terpolymer blends (PVTC-PTM) including poly(vinylidene fluoride-trifluoroethylene-chlorofluoro-ethylene) (P(VDF-TrFE-CFE), PVTC) as a matrix and micelle structured poly(3-hexylthiophene)-b-poly(methyl methacrylate) (P3HT-b-PMMA, PTM) as a conducting filler. The dielectric constant of PVTC-PTM dramatically increased up to 116.8 at 100 Hz despite adding only 2 wt% of the polymer-type filler (PTM). The compatibility and crystalline properties of the PVTC-PTM blends were examined by microscopic, thermal, and X-ray studies. The PVTC-PTM showed more compatible blends than those of the P3HT homopolymer filler (PT) and led to higher crystallinity and smaller crystal grain size relative to those of neat PVTC and PVTC with the PT filler (PVTC-PT). Those by the PVTC-PTM blends can beneficially affect the high-performance electromechanical properties compared to those by the neat PVTC and the PVTC-PT blend. The electromechanical strain of the PVTC-PTM with 2 wt% PTM (PVTC-PTM2) showed ca. 2-fold enhancement (0.44% transverse strain at 30 Vpp µm-1) relative to that of PVTC. We found that the more significant electromechanical performance of the PVTC-PTM blend than the PVTC was predominantly due to the electrostrictive force rather than electrostatic force. We believe that the acquired PVTC-PTM blends are great candidates to achieve the high-performance electromechanical strain and take all benefits derived from the all-organic system, including high electrical breakdown strength, processibility, dielectrics, and large strain, which are largely different from the organic-inorganic hybrid nanocomposite systems.

Thermal and Flame Retardant Properties of Phosphate-Functionalized Silica/Epoxy Nanocomposites.

We report a flame retardant epoxy nanocomposite reinforced with 9,10-dihydro-9-oxa-10-phosphaphenantrene-10-oxide (DOPO)-tethered SiO2 (DOPO-t-SiO2) hybrid nanoparticles (NPs). The DOPO-t-SiO2 NPs were successfully synthesized through surface treatment of SiO2 NPs with (3-glycidyloxypropyl)trimethoxysilane (GPTMS), followed by a click reaction between GPTMS on SiO2 and DOPO. The epoxy nanocomposites with DOPO-t-SiO2 NPs as multifunctional additive exhibited not only high flexural strength and fracture toughness but also excellent flame retardant properties and thermal stability, compared to those of pristine epoxy and epoxy nanocomposites with a single additive of SiO2 or DOPO, respectively. Our approach allows a facile, yet effective strategy to synthesize a functional hybrid additive for developing flame retardant nanocomposites.

Vulcanizate Structures of SBR Compounds with Silica and Carbon Black Binary Filler Systems at Different Curing Temperatures.

The tire industry has shown an increasing demand for the reduction in rolling resistance. Efforts have been made to improve the viscoelastic properties of tire compounds and reduce the weight of tires through optimization of the vulcanizate structure, which has become extremely complex. In this study, vulcanizates using carbon black and silica as binary fillers were prepared at various curing temperatures. Vulcanizate structures with respect to curing temperature were classified according to the chemical crosslink density by sulfur, carbon black bound rubber (i.e., physical crosslink due to carbon black), and silica-silane-rubber network. All properties exhibited a decreasing trend under the application of high curing temperatures, and the decrease in the crosslink density per unit content of filler with an increase in curing temperature was shown to be greater in carbon black than in silica. Mechanical and viscoelastic properties were also measured to evaluate the impact that the compound variates have on tire tread performance. These results serve as a guideline for determining the content and filler type and for setting the cure condition during the design of actual compound formulations to increase the crosslink density of rubber while retaining the necessary mechanical and viscoelastic properties for practical application.

Alkaline Hydrolysis and Dyeing Characteristics of Sea-Island-Type Ultramicrofibers of PET Tricot Fabrics with Black Disperse Dye.

In this study, we investigated conditions for the alkaline hydrolysis and black-disperse dyeing of sea-island-type polyethylene terephthalate (PET) ultramicrofiber tricot fabric. We examined the weight loss ratios and tensile strengths according to the NaOH content (10%-30% on mass of fabric (omf)) during treatment; the optimal conditions used 25% omf NaOH for 30 min at 100 °C for an average weight loss ratio of 23.47%. By scanning electron microscope (SEM) analysis, the 'sea' components are extracted with increasing NaOH concentration until 25% omf NaOH, and damage of the 'island' components above 25% omf NaOH leads to a reduction in tensile strength. The dyeing conditions, including temperature (95-135 °C), time (20-60 min), pH buffer solution concentration (1-9 g/L), and contents of dispersant (1-9 g/L) and UV-absorbent (5%-25% omf) were also explored. The optimal dyeing conditions were established as a dye concentration of 8% omf with 1 g/L dispersant, 1 g/L pH buffer solution concentration, and 10% omf UV-absorbent at 135 °C for 40 min at a 1:10 goods-to-liquor ratio. The rubbing colorfastness values for the fabrics dyed with the black disperse dye spanned four grades under dry and wet conditions. The light colorfastness values of the dyed fabrics were good to excellent in the range of 4-5 grades.

Incorporation of a Molecular Prognostic Classifier Improves Conventional Non-Small Cell Lung Cancer Staging.

INTRODUCTION: Despite adoption of molecular biomarkers in the management of NSCLC, the recently adopted eighth edition of the TNM staging system utilized only clinicopathologic characteristics and validated improvement in risk stratification of early-stage disease has remained elusive. We therefore evaluated the integration of a clinically validated molecular prognostic classifier into conventional staging. METHODS: A novel staging system, the TNMB (with the B denoting biology) system, which integrates a 14-gene molecular prognostic classifier into the eighth edition of the TNM staging system, was developed by using data from 321 patients with NSCLC at the University of California, San Francisco. The TNMB staging system was subsequently validated in an independent, multicenter cohort of 1373 patients, and its implementation was compared with adoption of the seventh and eighth edition staging systems utilizing metrics of reclassification. RESULTS: Compared with staging according to the eighth edition of the TNM system, the TNMB staging system enhanced the identification of high-risk patients, with a net reclassification improvement of 0.33 (95% confidence interval [CI]: 0.24-0.41). It better predicted differences in survival, with a relative integrated discrimination improvement of 22.1% (95% CI: 8.8%-35.3%), and it improved agreement between observed and predicted survival, with a decrease in the reclassification calibration statistic of from 39 to 21. The seventh and eighth editions failed to change the net reclassification improvement (0.01 [95% CI: -0.04 to 0.03] and 0.03 [95% CI: 0.00 to 0.06], respectively) or relative integrated discrimination improvement (2.1% [95% CI: -5.8 to 9.9] and -2.5% [95% CI: -17.6 to 12.4], respectively); in addition, the eighth edition worsened calibration, with an increase in the reclassification calibration statistic from 23 to 25. CONCLUSIONS: Incorporation of a molecular prognostic classifier significantly improved identification of high-risk patients and survival predictions compared with when conventional staging is used. The TNMB staging system may lead to improved survival of early-stage disease through more effective application of adjuvant therapy.

Membrane-bound full-length Sonic Hedgehog identifies cancer stem cells in human non-small cell lung cancer.

The mechanism of Sonic Hedgehog (Shh) pathway activation in non-small cell lung cancer (NSCLC) is poorly described. Using an antibody against the Shh C-terminal domain, we found a small population of Shh-positive (Shh+) cells in NSCLC cells. The objective of this study was to characterize these Shh+ cells. Shh+ and Shh- cells were sorted by using Fluorescence Activated Cell Sorting (FACS) on 12 commercial NSCLC cell lines. Functional analyses on sorted cells were performed with gene expression assays (qRT-PCR and microarray) and cells were treated with cytotoxic chemotherapy and a targeted inhibitor of Shh signaling (GDC0449). We used in vivo models of nude mice inoculated with Shh+ and Shh- sorted cells and drug-treated cells. Finally, we confirmed our results in fresh human NSCLC samples (n=48) paired with normal lung tissue. We found that Shh+ cells produced an uncleaved, full-length Shh protein detected on the membranes of these cells. Shh+ cells exerted a paracrine effect on Shh- cells, inducing their proliferation and migration. Shh+ cells were chemo-resistant and showed features of cancer stem cells (CSCs) in vitro and in vivo. Pharmacological inhibition of the Shh pathway suppressed their CSC features. A high percentage of Shh+ cells was associated with poor prognosis in early-stage NSCLC patients. In conclusion, we describe for the first time the presence of an abnormal membrane-bound full-length Shh protein in human cancer cells that allows the identification of CSCs in vitro and in vivo.

Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues.

Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS). We therefore tested the two most commonly used WGA methods, multiple displacement amplification (MDA-Qiagen REPLI-g kit) and the hybrid or modified PCR-based method (Sigma/Rubicon Genomics Inc. GenomePlex kit) in FFPE normal and tumor tissue specimens. For the normalized copy number analysis, the FFPE process caused none or very minimal bias. Variations in copy number were minimal in samples amplified using the GenomePlex kit, but they were statistically significantly higher in samples amplified using the REPLI-g kit. The pattern was similar for variant allele frequencies across the samples, which was minimal for the GenomePlex kit but highly variable for the REPLI-g kit. These findings suggest that each WGA method should be tested thoroughly before using it for clinical cancer samples.

Mobile Genome Express (MGE): A comprehensive automatic genetic analyses pipeline with a mobile device.

The development of next-generation sequencing (NGS) technology allows to sequence whole exomes or genome. However, data analysis is still the biggest bottleneck for its wide implementation. Most laboratories still depend on manual procedures for data handling and analyses, which translates into a delay and decreased efficiency in the delivery of NGS results to doctors and patients. Thus, there is high demand for developing an automatic and an easy-to-use NGS data analyses system. We developed comprehensive, automatic genetic analyses controller named Mobile Genome Express (MGE) that works in smartphones or other mobile devices. MGE can handle all the steps for genetic analyses, such as: sample information submission, sequencing run quality check from the sequencer, secured data transfer and results review. We sequenced an Actrometrix control DNA containing multiple proven human mutations using a targeted sequencing panel, and the whole analysis was managed by MGE, and its data reviewing program called ELECTRO. All steps were processed automatically except for the final sequencing review procedure with ELECTRO to confirm mutations. The data analysis process was completed within several hours. We confirmed the mutations that we have identified were consistent with our previous results obtained by using multi-step, manual pipelines.

FAIM2, as a novel diagnostic maker and a potential therapeutic target for small-cell lung cancer and atypical carcinoid.

Lung neuroendocrine (NE) tumors are a heterogeneous group of tumors arising from neuroendocrine cells that includes typical carcinoid, atypical carcinoid, small cell lung cancer (SCLC), and large cell NE cancer. The subtyping of NE tumors is based on the number of mitoses per high powered field and the presences of necrosis. However, the best diagnostic criteria to differentiate various subtypes of lung NE tumors remains controversial and few diagnostic markers distinguish typical and atypical carcinoid. In this study, we show that FAIM2, an inhibitory molecule in the Fas-apoptosis pathway, is significantly overexpressed in SCLC compared to non-small cell lung cancer. In addition, FAIM2 expression is significantly higher in atypical carcinoid than typical carcinoid. As atypical carcinoid has been shown to have worse clinical outcomes than typical carcinoid, our data suggests that FAIM2 may be a useful diagnostic marker for atypical carcinoid. Knockdown of FAIM2 expression increases Fas-induced apoptotic cell death in SCLC cells. Etoposide treatment combined with FAIM2 inhibition also shows modest but significant reduction of viable SCLC cells. Taken together, our results suggest that FAIM2 is a potential NE tumor marker with higher expression in atypical carcinoid and SCLC, and could be a new therapeutic target for SCLC.

Development of a robust DNA quality and quantity assessment qPCR assay for targeted next-generation sequencing library preparation.

Next-generation sequencing (NGS) is becoming a standard for genetic analyses of clinical samples. DNAs retrieved from formalin-fixed, paraffin-embedded (FFPE) tissue specimens are commonly degraded, and specimens such as core biopsies are sometimes too small to obtain enough DNA for NGS applications. Thus, it is important to measure both the DNA quantity and quality accurately from clinical samples. However, there is no standard method for DNA quantity and quality analyses for NGS library preparation. We tested four different methods (PicoGreen, Qubit® fluorometry, TaqMan and SYBR-Green-based qPCR assay) and compared each to RNase P TaqMan as a reference control. We found that SYBR-Green-based qPCR assay provides a consistent and accurate DNA quantification while keeping its cost relatively low and the throughput high. We designed a dual-probe SYBR-Green qPCR assay for DNA quantity and quality assessment for targeted NGS library preparation. This assay provides a Dscore (degradation score) of the interrogated DNA by analyzing two different sizes of amplicons. We show an example of a clinical sample with a very high Dscore (high degradation). With a regular DNA quantification, without considering the degradation status, no correct NGS libraries were obtained. However, after optimizing the library condition by considering its poor DNA quality, a reasonably good library and sequencing results were obtained. In summary, we developed and presented a new DNA quantity and quality analysis qPCR assay for the targeted NGS library preparation. This assay may be mostly efficient for the clinical samples with high degradation and poor DNA quality.

Comprehensive evaluation and validation of targeted next-generation sequencing performance in two clinical laboratories.

Next-generation sequencing (NGS) has led to breakthroughs for genetic and genomic analyses and personalized medicine approaches for many diseases. More and more clinical laboratories are using NGS as a genetic screening tool for providing mutation information that is used to select the best treatment regimens for cancer patients. However, several obstacles prevent the routine implementation of NGS technology into the clinical molecular diagnosis setting: the sophisticated sample preparation process, high cost, time-consuming data analyses, as well as the reproducibility and accuracy of interpretation. To systematically evaluate the performance and quality of targeted NGS cancer panel analyses in clinical laboratories, we performed three different tests: i) laboratory-to-laboratory accuracy test, ii) intra-laboratory precision validation, and iii) limit of detection test, using formalin-fixed, paraffin-embedded cancer tissue specimens, cell lines and mutation positive DNA. A laboratory-to-laboratory accuracy test performed using 51 samples showed 100% sensitivity and 99.97% specificity. For the intra-laboratory precision test, 100% reproducibility was observed. For the limit of detection test, KRAS mutations from samples diluted from 70 to 2% of mutant allele frequencies were detected correctly. We believe that the present study demonstrated the feasibility of clinical implementation of a targeted NGS cancer panel analysis for personalized medicine.

Whole exome and targeted deep sequencing identify genome-wide allelic loss and frequent SETDB1 mutations in malignant pleural mesotheliomas.

Malignant pleural mesothelioma (MPM), a rare malignancy with a poor prognosis, is mainly caused by exposure to asbestos or other organic fibers, but the underlying genetic mechanism is not fully understood. Genetic alterations and causes for multiple primary cancer development including MPM are unknown. We used whole exome sequencing to identify somatic mutations in a patient with MPM and two additional primary cancers who had no evidence of venous, arterial, lymphovascular, or perineural invasion indicating dissemination of a primary lung cancer to the pleura. We found that the MPM had R282W, a key TP53 mutation, and genome-wide allelic loss or loss of heterozygosity, a distinct genomic alteration not previously described in MPM. We identified frequent inactivating SETDB1 mutations in this patient and in 68 additional MPM patients (mutation frequency: 10%, 7/69) by targeted deep sequencing. Our observations suggest the possibility of a new genetic mechanism in the development of either MPM or multiple primary cancers. The frequent SETDB1 inactivating mutations suggest there could be new diagnostic or therapeutic options for MPM.

An integrative approach for the identification of prognostic and predictive biomarkers in rectal cancer.

INTRODUCTION: Colorectal cancer is the third most common cancer in the world, a small fraction of which is represented by locally advanced rectal cancer (LARC). If not medically contraindicated, preoperative chemoradiotherapy, represent the standard of care for LARC patients. Unfortunately, patients shows a wide range of response rates in which approximately 20% has a complete pathological response, whereas in 20 to 40% the response is poor or absent. RESULTS: The following specific gene signature, able to discriminate responders' patients from non-responders, were founded: AKR1C3, CXCL11, CXCL10, IDO1, CXCL9, MMP12 and HLA-DRA. These genes are mainly involved in immune system pathways and interact with drugs traditionally used in the adjuvant treatment of rectal cancer. DISCUSSION: The present study suggests that new ideas for therapy could be found not only limited to studying genes differentially expressed between the two groups of patients but deepening the mechanisms, associated to response, in which they are involved. METHODS: Gene expression studies performed by: Agostini et al., Rimkus et al. and Kim et al. have been merged through a meta-analysis of the raw data. Gene expression data-sets have been processed using A-MADMAN. Common differentially expressed gene (DEG) were identified through SAM analysis. To further characterize the identified DEG we deeply investigated its biological role using an integrative computational biology approach.

Genetic variation in the functional ENG allele inherited from the non-affected parent associates with presence of pulmonary arteriovenous malformation in hereditary hemorrhagic telangiectasia 1 (HHT1) and may influence expression of PTPN14.

HHT shows clinical variability within and between families. Organ site and prevalence of arteriovenous malformations (AVMs) depend on the HHT causative gene and on environmental and genetic modifiers. We tested whether variation in the functional ENG allele, inherited from the unaffected parent, alters risk for pulmonary AVM in HHT1 mutation carriers who are ENG haploinsufficient. Genetic association was found between rs10987746 of the wild type ENG allele and presence of pulmonary AVM [relative risk = 1.3 (1.0018-1.7424)]. The rs10987746-C at-risk allele associated with lower expression of ENG RNA in a panel of human lymphoblastoid cell lines (P = 0.004). Moreover, in angiogenically active human lung adenocarcinoma tissue, but not in uninvolved quiescent lung, rs10987746-C was correlated with expression of PTPN14 (P = 0.004), another modifier of HHT. Quantitative TAQMAN expression analysis in a panel of normal lung tissues from 69 genetically heterogeneous inter-specific backcross mice, demonstrated strong correlation between expression levels of Eng, Acvrl1, and Ptpn14 (r2 = 0.75-0.9, P < 1 × 10(-12)), further suggesting a direct or indirect interaction between these three genes in lung in vivo. Our data indicate that genetic variation within the single functional ENG gene influences quantitative and/or qualitative differences in ENG expression that contribute to risk of pulmonary AVM in HHT1, and provide correlative support for PTPN14 involvement in endoglin/ALK1 lung biology in vivo. PTPN14 has been shown to be a negative regulator of Yap/Taz signaling, which is implicated in mechanotransduction, providing a possible molecular link between endoglin/ALK1 signaling and mechanical stress. EMILIN2, which showed suggestive genetic association with pulmonary AVM, is also reported to interact with Taz in angiogenesis. Elucidation of the molecular mechanisms regulating these interactions in endothelial cells may ultimately provide more rational choices for HHT therapy.

CK2α, over-expressed in human malignant pleural mesothelioma, regulates the Hedgehog signaling pathway in mesothelioma cells.

BACKGROUND: The Hedgehog (Hh) signaling pathway has been implicated in stem cell maintenance and its activation is aberrant in several types of cancer including mesothelioma. Protein kinase CK2 affects several cell signaling pathways through the mechanism of phosphorylation. METHODS: Protein and mRNA levels of CK2α and Gli1 were tested by quantitative RT-PCR and immunohistochemistry staining in mesothelioma samples and cell lines. Down-regulated Gli1 expression and transcriptional activity were demonstrated by RT-PCR, Western blot and luciferase reporter assay. RESULTS: In this study, we show that CK2α is over-expressed and a positive regulator of Hegdehog/Gli1 signaling in human malignant pleural mesothelioma. First of all, we found that the mRNA levels of CK2α and Gli1 were broadly elevated and correlated (n = 52, r = 0.401, P < 0.05), compared with LP9 (a normal mesothelial cell line). We then investigated their expression at the protein level, and found that all the 7 mesothelioma cell lines tested showed positive staining in CK2α and Gli1 immunohistochemistry. Correlation analysis by Pearson test for CK2α and Gli1 expression in the 75 mesothelioma tumors and the 7 mesothelioma cell lines showed that the two protein expression was significantly correlated (n = 82, r = 0.554, P < 0.01). Furthermore, we demonstrated that Gli1 expression and transcriptional activity were down-regulated after CK2α was silenced in two mesothelioma cell lines (H28 and H2052). CK2α siRNA also down-regulated the expression of Hh target genes in these cell lines. Moreover, treatment with a small-molecule CK2α inhibitor CX-4945 led to dose-dependent inhibition of Gli1 expression and transcriptional activity. Conversely, forced over-expression of CK2α resulted in an increase in Gli1 transcriptional activity in H28 cells. CONCLUSIONS: Thus, we report for the first time that over-expressed CK2α positively regulate Hh/Gli1 signaling in human mesothelioma.

Comprehensive genomic analyses of a metastatic colon cancer to the lung by whole exome sequencing and gene expression analysis.

We performed whole exome sequencing and gene expression analysis on a metastatic colon cancer to the lung, along with the adjacent normal tissue of the lung. Whole exome sequencing uncovered 71 high-confidence non­synonymous mutations. We selected 16 mutation candidates, and 13 out of 16 mutations were validated by targeted deep sequencing using the Ion Torrent PGM customized AmpliSeq panel. By integrating mutation, copy number and gene expression microarray data, we identified a JAZF1 mutation with a gain-of-copy, suggesting its oncogenic potential for the lung metastasis from colon cancer. Our pathway analyses showed that the identified mutations closely reflected characteristics of the metastatic site (lung) while mRNA gene expression patterns kept genetic information of its primary tumor (colon). The most significant gene expression network was the 'Colorectal Cancer Metastasis Signaling', containing 6 (ADCY2, ADCY9, APC, GNB5, K-ras and LRP6) out of the 71 mutated genes. Some of these mutated genes (ADCY9, ADCY2, GNB5, K-ras, HDAC6 and ARHGEF17) also belong to the 'Phospholipase C Signaling' network, which suggests that this pathway and its mutated genes may contribute to a lung metastasis from colon cancer.

Reduction in oxidative stress during cellular responses to chemically functionalised graphene.

The two-dimensional nanocarbon material graphene (Gr) has been extensively studied due to its many potential biomedical applications including regenerative medicine, drug delivery, bioimaging, and biosensing. The effects of nitrogen-functionalisation on chemically driven Gr (CDG) cellular responses were studied by investigating the generation of reactive oxygen species (ROS) and mitochondrial morphology as well as focal adhesion, shape, proliferation and viability of HeLa cells grown on functionalised CDG (f-CDG) films. The drop casting of CDG nanosheets formed thin CDG films and the formation of nitrogen groups on the f-CDG thin films was mediated by N2 plasma treatment without the formation of observable surface defects. N-containing functional groups on the CDG thin films contributed to an increase in hydrophilicity. The proliferation and viability of HeLa cells grown on the f-CDG thin films were enhanced compared to those grown on CDG films alone and control samples. N-functionalisation of CDG thin films effectively reduced the ROS generated from cells on the f-CDG films. These results indicate that N2 plasma treatment of CDG is very useful in improving biocompatibility for the bio-application of graphene materials.

Rewiring of human lung cell lineage and mitotic networks in lung adenocarcinomas.

Analysis of gene expression patterns in normal tissues and their perturbations in tumours can help to identify the functional roles of oncogenes or tumour suppressors and identify potential new therapeutic targets. Here, gene expression correlation networks were derived from 92 normal human lung samples and patient-matched adenocarcinomas. The networks from normal lung show that NKX2-1 is linked to the alveolar type 2 lineage, and identify PEBP4 as a novel marker expressed in alveolar type 2 cells. Differential correlation analysis shows that the NKX2-1 network in tumours includes pathways associated with glutamate metabolism, and identifies Vaccinia-related kinase (VRK1) as a potential drug target in a tumour-specific mitotic network. We show that VRK1 inhibition cooperates with inhibition of poly (ADP-ribose) polymerase signalling to inhibit growth of lung tumour cells. Targeting of genes that are recruited into tumour mitotic networks may provide a wider therapeutic window than that seen by inhibition of known mitotic genes.