Using Semantic Web Technologies to Enable Cancer Genomics Discovery at Petabyte Scale.

Increased efforts in cancer genomics research and bioinformatics are producing tremendous amounts of data. These data are diverse in origin, format, and content. As the amount of available sequencing data increase, technologies that make them discoverable and usable are critically needed. In response, we have developed a Semantic Web-based Data Browser, a tool allowing users to visually build and execute ontology-driven queries. This approach simplifies access to available data and improves the process of using them in analyses on the Seven Bridges Cancer Genomics Cloud (CGC; www.cancergenomicscloud.org). The Data Browser makes large data sets easily explorable and simplifies the retrieval of specific data of interest. Although initially implemented on top of The Cancer Genome Atlas (TCGA) data set, the Data Browser's architecture allows for seamless integration of other data sets. By deploying it on the CGC, we have enabled remote researchers to access data and perform collaborative investigations.

The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized-A New Paradigm in Large-Scale Computational Research.

The Seven Bridges Cancer Genomics Cloud (CGC; www.cancergenomicscloud.org) enables researchers to rapidly access and collaborate on massive public cancer genomic datasets, including The Cancer Genome Atlas. It provides secure on-demand access to data, analysis tools, and computing resources. Researchers from diverse backgrounds can easily visualize, query, and explore cancer genomic datasets visually or programmatically. Data of interest can be immediately analyzed in the cloud using more than 200 preinstalled, curated bioinformatics tools and workflows. Researchers can also extend the functionality of the platform by adding their own data and tools via an intuitive software development kit. By colocalizing these resources in the cloud, the CGC enables scalable, reproducible analyses. Researchers worldwide can use the CGC to investigate key questions in cancer genomics. Cancer Res; 77(21); e3-6. ©2017 AACR.

Augmented oxidative stress in infertile women with persistent chlamydial infection.

There is established association between oxidative stress, infections of genital tract and fertility. Genital tract infections may provoke increased production of free radicals and generate oxidative stress that can be involved in pathophysiology of a number of reproductive diseases and complications during pregnancy. The aim of this study was to determine connection between oxidative stress and infertility associated with persistent chlamydial infection. Serum samples of infertile women with tubal factor infertility (TFI), women with multiple spontaneous abortions (MSA) and fertile women was screened for C. trachomatis MOMP specific IgG and IgA antibodies and cHSP60 specific igG antibodies using ELISA. The levels of superoxide anion radical, nitric oxide and reduced glutathione were determined spectrophotometricaly. Serum levels of testosterone, luteinizing hormone and follicle stimulating hormone were determined by enzyme-linked fluorescent immunoassay method. Our results showed that persistent infection was more prevalent in TFI than in MSA group, whereas seropositivity was higher in MSA than in TFI group of patients. We also found that superoxide anion was significantly lower, while LH was markedly higher in TFI and MSA group of patients. However, when our results were analyzed according to the serological status of chlamydial infection, we found that parameters of oxidative stress, superoxide anion and index of oxidative stress, defined as relative ratio between superoxide anion and nitrites sum and glutathione ((O2-+NO2-)/GSH) were significantly elevated in infertile patients with persistent chlamydial infection compared to seropositive and seronegative patients. Our findings point to the possible impact of Chlamydia trachomatis infection on prooxidative-antioxidative balance that can influence fertility potential in women with persistent chlamydial infection.

Cell surface antigen profiling using a novel type of antibody array immobilised to plasma ion-implanted polycarbonate.

To identify and sort out subpopulations of cells from more complex and heterogeneous assemblies of cells is important for many biomedical applications, and the development of cost- and labour-efficient techniques to accomplish this is warranted. In this report, we have developed a novel array-based platform to discriminate cellular populations based on differences in cell surface antigen expressions. These cell capture microarrays were produced through covalent immobilisation of CD antibodies to plasma ion immersion implantation-treated polycarbonate (PIII-PC), which offers the advantage of a transparent matrix, allowing direct light microscopy visualisation of captured cells. The functionality of the PIII-PC array was validated using several cell types, resulting in unique surface antigen expression profiles. PIII-PC results were compatible with flow cytometry, nitrocellulose cell capture arrays and immunofluorescent staining, indicating that the technique is robust. We report on the use of this PIII-PC cluster of differentiation (CD) antibody array to gain new insights into neural differentiation of mouse embryonic stem (ES) cells and into the consequences of genetic targeting of the Notch signalling pathway, a key signalling mechanism for most cellular differentiation processes. Specifically, we identify CD98 as a novel marker for neural precursors and polarised expression of CD9 in the apical domain of ES cell-derived neural rosettes. We further identify expression of CD9 in hitherto uncharacterised non-neural cells and enrichment of CD49e- and CD117-positive cells in Notch signalling-deficient ES cell differentiations. In conclusion, this work demonstrates that covalent immobilisation of antibody arrays to the PIII-PC surface provides faithful cell surface antigen data in a cost- and labour-efficient manner. This may be used to facilitate high throughput identification and standardisation of more precise marker profiles during stem cell differentiation and in various genetic and disease contexts.

Notch signaling maintains neural rosette polarity.

Formation of the metazoan body plan requires a complex interplay of morphological changes and patterning, and central to these processes is the establishment of apical/basal cell polarity. In the developing nervous system, apical/basal cell polarity is essential for neural tube closure and maintenance of the neural stem cell population. In this report we explore how a signaling pathway important for nervous system development, Notch signaling, impacts on apical/basal cell polarity in neural differentiation. CSL(-/-) mouse embryos, which are devoid of canonical Notch signaling, demonstrated a neural tube phenotype consistent with cell polarity and convergent extension defects, including deficiencies in the restricted expression of apical polarity markers in the neuroepithelium. CSL(-/-) mouse embryonic stem (ES) cells, cultured at low density, behaved as wild-type in the establishment of neural progenitors and apical specification, though progression through rosette formation, an in vitro correlate of neurulation, required CSL for correct maintenance of rosette structure and regulation of neuronal differentiation. Similarly, acute pharmacological inhibition of Notch signaling led to the breakdown of neural rosettes and accelerated neuronal differentiation. In addition to functional Notch signaling, rosette integrity was found to require actin polymerization and Rho kinase (ROCK) activity. Disruption of rosettes through inhibition of actin polymerization or ROCK activity, however, had no effect on neuronal differentiation, indicating that rosette maintenance is not a prerequisite for normal neuronal differentiation. In conclusion, our data indicate that Notch signaling plays a role not only in differentiation, but also in organization and maintenance of polarity during development of the early nervous system.