Comparison of Breast Cancer to Healthy Control Tissue Discovers Novel Markers with Potential for Prognosis and Early Detection

This study was initiated to identify biomarkers with potential value for the early detection of poor-outcome breast cancer. Two sets of well-characterized tissues were utilized: one from breast cancer patients with favorable vs. poor outcome and the other from healthy women undergoing reduction mammaplasty. Over 46 differentially expressed genes were identified from a large list of potential targets by a) mining publicly available expression data (identifying 134 genes for quantitative PCR) and b) utilizing a commercial PCR array. Three genes show elevated expression in cancers with poor outcome and low expression in all other tissues, warranting further investigation as potential blood markers for early detection of cancers with poor outcome. Twelve genes showed lower expression in cancers with poor outcome than in cancers with favorable outcome but no differential expression between aggressive cancers and most healthy controls. These genes are more likely to be useful as prognostic tissue markers than as serum markers for early detection of aggressive disease. As a secondary finding was that, when histologically normal breast tissue was removed from a distant site in a breast with cancer, 7 of 38 specimens displayed a cancer-like expression profile, while the remaining 31 were genetically similar to the reduction mammaplasty control group. This finding suggests that some regions of ipsilateral histologically ‘normal’ breast tissue are predisposed to becoming malignant and that normal-appearing tissue with malignant signature might warrant treatment to prevent new primary tumors

Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information

BACKGROUND: Expression microarrays are increasingly used to characterize environmental responses and host-parasite interactions for many different organisms. Probe selection for cDNA microarrays using expressed sequence tags (ESTs) is challenging due to high sequence redundancy and potential cross-hybridization between paralogous genes. In organisms with limited genomic information, like marine organisms, this challenge is even greater due to annotation uncertainty. No general tool is available for cDNA microarray probe selection for these organisms. Therefore, the goal of the design procedure described here is to select a subset of ESTs that will minimize sequence redundancy and characterize potential cross-hybridization while providing functionally representative probes. RESULTS: Sequence similarity between ESTs, quantified by the E-value of pair-wise alignment, was used as a surrogate for expected hybridization between corresponding sequences. Using this value as a measure of dissimilarity, sequence redundancy reduction was performed by hierarchical cluster analyses. The choice of how many microarray probes to retain was made based on an index developed for this research: a sequence diversity index (SDI) within a sequence diversity plot (SDP). This index tracked the decreasing within-cluster sequence diversity as the number of clusters increased. For a given stage in the agglomeration procedure, the EST having the highest similarity to all the other sequences within each cluster, the centroid EST, was selected as a microarray probe. A small dataset of ESTs from Atlantic white shrimp (Litopenaeus setiferus) was used to test this algorithm so that the detailed results could be examined. The functional representative level of the selected probes was quantified using Gene Ontology (GO) annotations. CONCLUSIONS: For organisms with limited genomic information, combining hierarchical clustering methods to analyze ESTs can yield an optimal cDNA microarray design. If biomarker discovery is the goal of the microarray experiments, the average linkage method is more effective, while single linkage is more suitable if identification of physiological mechanisms is more of interest. This general design procedure is not limited to designing single-species cDNA microarrays for marine organisms, and it can equally be applied to multiple-species microarrays of any organisms with limited genomic information

Dew-worms in white nights: High-latitude light constrains earthworm (Lumbricus terrestris) behaviour at the soil surface

Soil is an effective barrier to light penetration that limits the direct influence of light on belowground organisms. Variation in aboveground light conditions, however, is important to soil-dwelling animals that are periodically active on the soil surface. A prime example is the earthworm Lumbricus terrestris L. (the dew-worm), an ecosystem engineer that emerges nocturnally on the soil surface. In the summer, the northernmost populations of L. terrestris are exposed to a time interval with no daily dark period. During a two-week period preceding the summer solstice, we studied the constraints that boreal night illumination imposes on L. terrestris surface activity by comparing their behaviour under ambient light with artificially-induced darkness. Looking for evidence of geographical divergence in light response, we compared the behaviour of native L. terrestris (Jokioinen, S–W Finland; 60°48′N) with two markedly more southern populations, from Preston (Lancashire, UK; 53°47′N) and Coshocton (Ohio, USA; 40°22′N) where the nights have a period of darkness throughout the year (total latitudinal range ca. 2300 km). Under ambient light conditions, L. terrestris emergence on the soil surface was diminished by half compared with the darkened treatment and it peaked at the darkest period of the night. Also mating rate decreased considerably under ambient light. The native dew-worms were generally the most active under ambient light. They emerged earlier in the evening and ceased their activity later in the morning than dew-worms from the two more southerly populations. The differences in behaviour were, however, significant mainly between native and UK dew-worms. In the darkened treatment, the behaviour of the three earthworm origins did not differ. Under the experimental conditions light condition was the dominant environmental factor controlling surface activity, but elevated night-time air temperature and humidity also encouraged dew-worm emergence without discernible differences among geographical origins. Our results show, that in boreal summer, the high level of night illumination strongly limits soil-surface activity of dew-worms. Considering the important regulatory role of L. terrestris in many ecosystem processes, this can have significant corollaries in dew-worm impacts on the environment. Although evidence for geographical differentiation in behaviour was obtained, the results point to phenotypic flexibility in L. terrestris light response

Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms

BACKGROUND: The Marine Genomics project is a functional genomics initiative developed to provide a pipeline for the curation of Expressed Sequence Tags (ESTs) and gene expression microarray data for marine organisms. It provides a unique clearing-house for marine specific EST and microarray data and is currently available at . DESCRIPTION: The Marine Genomics pipeline automates the processing, maintenance, storage and analysis of EST and microarray data for an increasing number of marine species. It currently contains 19 species databases (over 46,000 EST sequences) that are maintained by registered users from local and remote locations in Europe and South America in addition to the USA. A collection of analysis tools are implemented. These include a pipeline upload tool for EST FASTA file, sequence trace file and microarray data, an annotative text search, automated sequence trimming, sequence quality control (QA/QC) editing, sequence BLAST capabilities and a tool for interactive submission to GenBank. Another feature of this resource is the integration with a scientific computing analysis environment implemented by MATLAB. CONCLUSION: The conglomeration of multiple marine organisms with integrated analysis tools enables users to focus on the comprehensive descriptions of transcriptomic responses to typical marine stresses. This cross species data comparison and integration enables users to contain their research within a marine-oriented data management and analysis environment

Inhibition of iNOS as a Novel Effective Targeted Therapy Against Triple-Negative Breast Cancer

INTRODUCTION: Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer with no effective targeted therapy. Inducible nitric oxide synthase (iNOS) is associated with poor survival in patients with breast cancer by increasing tumor aggressiveness. This work aimed to investigate the potential of iNOS inhibitors as a targeted therapy for TNBC. We hypothesized that inhibition of endogenous iNOS would decrease TNBC aggressiveness by reducing tumor initiation and metastasis through modulation of epithelial-mesenchymal transition (EMT)-inducing factors. METHODS: iNOS protein levels were determined in 83 human TNBC tissues and correlated with clinical outcome. Proliferation, mammosphere-forming efficiency, migration, and EMT transcription factors were assessed in vitro after iNOS inhibition. Endogenous iNOS targeting was evaluated as a potential therapy in TNBC mouse models. RESULTS: High endogenous iNOS expression was associated with worse prognosis in patients with TNBC by gene expression as well as immunohistochemical analysis. Selective iNOS (1400 W) and pan-NOS (L-NMMA and L-NAME) inhibitors diminished cell proliferation, cancer stem cell self-renewal, and cell migration in vitro, together with inhibition of EMT transcription factors (Snail, Slug, Twist1, and Zeb1). Impairment of hypoxia-inducible factor 1α, endoplasmic reticulum stress (IRE1α/XBP1), and the crosstalk between activating transcription factor 3/activating transcription factor 4 and transforming growth factor β was observed. iNOS inhibition significantly reduced tumor growth, the number of lung metastases, tumor initiation, and self-renewal. CONCLUSIONS: Considering the effectiveness of L-NMMA in decreasing tumor growth and enhancing survival rate in TNBC, we propose a targeted therapeutic clinical trial by re-purposing the pan-NOS inhibitor L-NMMA, which has been extensively investigated for cardiogenic shock as an anti-cancer therapeutic

Patterns of Mobile Device Use by Caregivers and Children During Meals in Fast Food Restaurants

En: Pediatrics, Vol. 133, No. 4, pp. e844-e849Background and Objectives: Mobile devices are a ubiquitous part of American life, yet how families use this technology has not been studied. We aimed to describe naturalistic patterns of mobile device use by caregivers and children to generate hypotheses about its effects on caregiver–child interaction. Methods: Using nonparticipant observational methods, we observed 55 caregivers eating with 1 or more young children in fast food restaurants in a single metropolitan area. Observers wrote detailed field notes, continuously describing all aspects of mobile device use and child and caregiver behavior during the meal. Field notes were then subjected to qualitative analysis using grounded theory methods to identify common themes of device use. Results: Forty caregivers used devices during their meal. The dominant theme salient to mobile device use and caregiver–child interaction was the degree of absorption in devices caregivers exhibited. Absorption was conceptualized as the extent to which primary engagement was with the device, rather than the child, and was determined by frequency, duration, and modality of device use; child response to caregiver use, which ranged from entertaining themselves to escalating bids for attention, and how caregivers managed this behavior; and separate versus shared use of devices. Highly absorbed caregivers often responded harshly to child misbehavior. Conclusions: We documented a range of patterns of mobile device use, characterized by varying degrees of absorption. These themes may be used as a foundation for coding schemes in quantitative studies exploring device use and child outcomes

Role of RPL39 in Metaplastic Breast Cancer

Background: Metaplastic breast cancer is one of the most therapeutically challenging forms of breast cancer because of its highly heterogeneous and chemoresistant nature. We have previously demonstrated that ribosomal protein L39 (RPL39) and its gain-of-function mutation A14V have oncogenic activity in triple-negative breast cancer and this activity may be mediated through inducible nitric oxide synthase (iNOS). The function of RPL39 and A14V in other breast cancer subtypes is currently unknown. The objective of this study was to determine the role and mechanism of action of RPL39 in metaplastic breast cancer. Methods: Both competitive allele-specific and droplet digital polymerase chain reaction were used to determine the RPL39 A14V mutation rate in metaplastic breast cancer patient samples. The impact of RPL39 and iNOS expression on patient overall survival was estimated using the Kaplan-Meier method. Co-immunoprecipitation and immunoblot analyses were used for mechanistic evaluation of RPL39. Results: The RPL39 A14V mutation rate was 97.5% (39/40 tumor samples). High RPL39 (hazard ratio = 0.71, 95% confidence interval = 0.55 to 0.91, P = .006) and iNOS expression (P = .003) were associated with reduced patient overall survival. iNOS inhibition with the pan-NOS inhibitor NG-methyl-L-arginine acetate decreased in vitro proliferation and migration, in vivo tumor growth in both BCM-4664 and BCM-3807 patient-derived xenograft models (P = .04 and P = .02, respectively), and in vitro and in vivo chemoresistance. Mechanistically, RPL39 mediated its cancer-promoting actions through iNOS signaling, which was driven by the RNA editing enzyme adenosine deaminase acting on RNA 1. Conclusion: NOS inhibitors and RNA editing modulators may offer novel treatment options for metaplastic breast cancer

Conducting polymer 3D microelectrodes

Conducting polymer 3D microelectrodes have been fabricated for possible future neurological applications. A combination of micro-fabrication techniques and chemical polymerization methods has been used to create pillar electrodes in polyaniline and polypyrrole. The thin polymer films obtained showed uniformity and good adhesion to both horizontal and vertical surfaces. Electrodes in combination with metal/conducting polymer materials have been characterized by cyclic voltammetry and the presence of the conducting polymer film has shown to increase the electrochemical activity when compared with electrodes coated with only metal. An electrochemical characterization of gold/polypyrrole electrodes showed exceptional electrochemical behavior and activity. PC12 cells were finally cultured on the investigated materials as a preliminary biocompatibility assessment. These results show that the described electrodes are possibly suitable for future in-vitro neurological measurements

Symmetry Energy II: Isobaric Analog States

Using excitation energies to isobaric analog states (IAS) and charge invariance, we extract nuclear symmetry coefficients, from a mass formula, on a nucleus-by-nucleus basis. Consistently with charge invariance, the coefficients vary weakly across an isobaric chain. However, they change strongly with nuclear mass and range from a_a~10 MeV at mass A~10 to a_a~22 MeV at A~240. Following the considerations of a Hohenberg-Kohn functional for nuclear systems, we determine how to find in practice the symmetry coefficient using neutron and proton densities, even when those densities are simultaneously affected by significant symmetry-energy and Coulomb effects. These results facilitate extracting the symmetry coefficients from Skyrme-Hartree-Fock (SHF) calculations, that we carry out using a variety of Skyrme parametrizations in the literature. For the parametrizations, we catalog novel short-wavelength instabilities. In comparing the SHF and IAS results for the symmetry coefficients, we arrive at narrow (+-2.4 MeV) constraints on the symmetry energy values S(rho) at 0.04<rho<0.13 fm^-3. Towards normal density the constraints significantly widen, but the normal value of energy a_a^V and the slope parameter L are found to be strongly correlated. To narrow the constraints, we reach for the measurements of asymmetry skins and arrive at a_a^V=(30.2-33.7) MeV and L=(35-70) MeV, with those values being again strongly positively correlated along the diagonal of their combined region. Inclusion of the skin constraints allows to narrow the constraints on S(rho), at 0.04<rho<0.13 fm^-3, down to +-1.1 MeV. Several microscopic calculations, including variational, Bruckner-Hartree-Fock and Dirac-Bruckner-Hartree-Fock, are consistent with our constraint region on S(rho).Comment: 101 pages, 27 figures, 2 tables; submitted to Nuclear Physics

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