diXa: a data infrastructure for chemical safety assessment.

MOTIVATION: The field of toxicogenomics (the application of '-omics' technologies to risk assessment of compound toxicities) has expanded in the last decade, partly driven by new legislation, aimed at reducing animal testing in chemical risk assessment but mainly as a result of a paradigm change in toxicology towards the use and integration of genome wide data. Many research groups worldwide have generated large amounts of such toxicogenomics data. However, there is no centralized repository for archiving and making these data and associated tools for their analysis easily available. RESULTS: The Data Infrastructure for Chemical Safety Assessment (diXa) is a robust and sustainable infrastructure storing toxicogenomics data. A central data warehouse is connected to a portal with links to chemical information and molecular and phenotype data. diXa is publicly available through a user-friendly web interface. New data can be readily deposited into diXa using guidelines and templates available online. Analysis descriptions and tools for interrogating the data are available via the diXa portal. AVAILABILITY AND IMPLEMENTATION: http://www.dixa-fp7.eu CONTACT: d.hendrickx@maastrichtuniversity.nl; info@dixa-fp7.eu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Gene expression profiling of flaxseed in mouse lung tissues-modulation of toxicologically relevant genes.

BACKGROUND: Flaxseed (FS), a nutritional supplement consisting mainly of omega-3 fatty acids and lignan phenolics has potent anti-inflammatory, anti-fibrotic and antioxidant properties. The usefulness of flaxseed as an alternative and complimentary treatment option has been known since ancient times. We have shown that dietary FS supplementation ameliorates oxidative stress and inflammation in experimental models of acute and chronic lung injury in mice resulting from diverse toxicants. The development of lung tissue damage in response to direct or indirect oxidant stress is a complex process, associated with changes in expression levels of a number of genes. We therefore postulated that flaxseed might modulate gene expression of vital signaling pathways, thus interfering with the development of tissue injury. METHODS: We evaluated gene expression in lungs of flaxseed-fed (10%FS) mice under unchallenged, control conditions. We reasoned that array technology would provide a powerful tool for studying the mechanisms behind this response and aid the evaluation of dietary flaxseed intervention with a focus on toxicologically relevant molecular gene targets. Gene expression levels in lung tissues were analyzed using a large-scale array whereby 28,800 genes were evaluated. RESULTS: 3,713 genes (12.8%) were significantly (p < 0.05) differentially expressed, of which 2,088 had a >1.5-fold change. Genes affected by FS include those in protective pathways such as Phase I and Phase II. CONCLUSIONS: The array studies have provided information on how FS modulates gene expression in lung and how they might be related to protective mechanisms. In addition, our study has confirmed that flaxseed is a nutritional supplement with potentially useful therapeutic applications in complementary and alternative (CAM) medicine especially in relation to treatment of lung disease.

SKDM human leukocyte antigen (HLA) tool: A comprehensive HLA and disease associations analysis software.

The immensely polymorphic and gene-rich landscape of the major histocompatibility complex on chromosome 6 necessitates a thorough and consistent investigation of its constituting elements. The human leukocyte antigens (HLAs) are an example of such polymorphic elements, implicated in many immune-based diseases. So far, analyses of HLA molecules in the context of diseases have been ad hoc, frequently incomplete, and extremely cumbersome. SKDM provides a comprehensive and automated workflow for detecting and dissecting HLA associations in diseases. We created a Java application to consistently perform our proposed method of analysis of HLAs in case-control datasets. The SKDM HLA tool can test for HLA allele differences between two populations and, by retrieving amino acid sequences, evaluates each polymorphic amino acid residue or a pocket of amino acids as an independent variant. Once primary associations are identified, the program examines zygosity and tests for strongest association, interaction, and linkage disequilibrium among amino acid epitopes of the same HLA molecule or between HLA isotypes. A summary of the analysis is output in plain language. The software and a user's manual are freely available at http://sourceforge.net/projects/skdm.

Association of variants of the interleukin-23 receptor gene with susceptibility to pediatric Crohn's disease.

BACKGROUND & AIMS: Recently an association was shown between the single nucleotide polymorphism (SNP), rs11209026, within the interleukin-23 receptor (IL23R) locus and Crohn's disease (CD) as a consequence of a genome-wide association study of this disease in adults. We examined the effects of this and other previously reported SNPs at this locus with respect to CD in children. METHODS: By using data from our ongoing genome-wide association study in our cohort of 142 pediatric CD patients and 281 matched controls, we investigated the association of the previously reported SNPs at the IL23R locus with the childhood form of this disease. RESULTS: By using the Fisher exact test, the minor allele frequency of rs11209026 in the patients was 1.75%, whereas it was 6.61% in the controls, yielding a protective odds ratio (OR) of 0.25 (95% confidence interval, 0.10-0.65; 1-sided P = 9.2 x 10(-4)). Furthermore, of all the SNPs previously reported, rs11209026 was associated the most strongly. A subsequent family based association test (which is more resistant to population stratification) with 65 sets of trios derived from our initial patient cohort yielded significant association with rs11209026 in a transmission disequilibrium test (1-sided P = .0017). In contrast, no association was detected to the caspase-recruitment domain 15 gene for the inflammatory bowel disease phenotype. CONCLUSIONS: The OR of the IL23R variant in our pediatric study is highly comparable with that reported previously in a non-Jewish adult inflammatory bowel disease case-control cohort (OR, 0.26). As such, variants in the IL23R gene confer a similar magnitude of risk of CD to children as for their adult counterparts.

HLA-A and HLA-DRB1 amino acid polymorphisms are associated with susceptibility and protection to pulmonary tuberculosis in a Greek population.

BACKGROUND: Pulmonary tuberculosis remains the single deadliest infectious disease causing high mortality in humans leading to 1.4 million deaths annually. Inherited genetic factors may explain why some people resist infection more successfully than others. METHODS: The polymorphisms of HLA-class I (-A, -B) and class II (-DRB1, -DQB1) genes have been evaluated using DNA-based typing in a population of 86 non-immunosuppressed, unrelated Greek patients with PTb and 46 healthy unrelated people without a history of PTb, who were all tested purified protein derivative positive (>14 mm). RESULTS: The HLA-A R(114) and HLA-DRßN(37) residues are associated with susceptibility. They operate independently from each other and their effect is detected when the population is evaluated for their concurrent presence (A R(114) positive or DRßN(37) positive or A R(114) and DRßN(37) positive). Furthermore the HLA-A S(77) appears to have a protective role, however in the presence of the DRßN(37), the A-S(77) does not exert its protective effect. CONCLUSION: The HLA residues A-S(77), A-R(114) and DRßN(37) in combination with PTb antigenic elements possibly modulate T-cell responses against MTb that lead to either protection or susceptibility. The HLA-A and -DRB1-dependent T-cell networks may interact among themselves and influence each other resulting in different PTb phenotypes.

DTI based diagnostic prediction of a disease via pattern classification.

The paper presents a method of creating abnormality classifiers learned from Diffusion Tensor Imaging (DTI) data of a population of patients and controls. The score produced by the classifier can be used to aid in diagnosis as it quantifies the degree of pathology. Using anatomically meaningful features computed from the DTI data we train a non-linear support vector machine (SVM) pattern classifier. The method begins with high dimensional elastic registration of DT images followed by a feature extraction step that involves creating a feature by concatenating average anisotropy and diffusivity values in anatomically meaningful regions. Feature selection is performed via a mutual information based technique followed by sequential elimination of the features. A non-linear SVM classifier is then constructed by training on the selected features. The classifier assigns each test subject with a probabilistic abnormality score that indicates the extent of pathology. In this study, abnormality classifiers were created for two populations; one consisting of schizophrenia patients (SCZ) and the other with individuals with autism spectrum disorder (ASD). A clear distinction between the SCZ patients and controls was achieved with 90.62% accuracy while for individuals with ASD, 89.58% classification accuracy was obtained. The abnormality scores clearly separate the groups and the high classification accuracy indicates the prospect of using the scores as a diagnostic and prognostic marker.

Dietary curcumin increases antioxidant defenses in lung, ameliorates radiation-induced pulmonary fibrosis, and improves survival in mice.

The effectiveness of lung radiotherapy is limited by radiation tolerance of normal tissues and by the intrinsic radiosensitivity of lung cancer cells. The chemopreventive agent curcumin has known antioxidant and tumor cell radiosensitizing properties. Its usefulness in preventing radiation-induced pneumonopathy has not been tested previously. We evaluated dietary curcumin in radiation-induced pneumonopathy and lung tumor regression in a murine model. Mice were given 1% or 5% (w/w) dietary curcumin or control diet prior to irradiation and for the duration of the experiment. Lungs were evaluated at 3 weeks after irradiation for acute lung injury and inflammation by evaluating bronchoalveolar lavage (BAL) fluid content for proteins, neutrophils and at 4 months for pulmonary fibrosis. In a separate series of experiments, an orthotopic model of lung cancer using intravenously injected Lewis lung carcinoma (LLC) cells was used to exclude possible tumor radioprotection by dietary curcumin. In vitro, curcumin boosted antioxidant defenses by increasing heme oxygenase 1 (HO-1) levels in primary lung endothelial and fibroblast cells and blocked radiation-induced generation of reactive oxygen species (ROS). Dietary curcumin significantly increased HO-1 in lungs as early as after 1 week of feeding, coinciding with a steady-state level of curcumin in plasma. Although both 1% and 5% w/w dietary curcumin exerted physiological changes in lung tissues by significantly decreasing LPS-induced TNF-alpha production in lungs, only 5% dietary curcumin significantly improved survival of mice after irradiation and decreased radiation-induced lung fibrosis. Importantly, dietary curcumin did not protect LLC pulmonary metastases from radiation killing. Thus dietary curcumin ameliorates radiation-induced pulmonary fibrosis and increases mouse survival while not impairing tumor cell killing by radiation.

Dietary flaxseed prevents radiation-induced oxidative lung damage, inflammation and fibrosis in a mouse model of thoracic radiation injury.

Flaxseed (FS) has high contents of omega-3 fatty acids and lignans with antioxidant properties. Its use in preventing thoracic X-ray radiation therapy (XRT)-induced pneumonopathy has never been evaluated. We evaluated FS supplementation given to mice given before and post-XRT. FS-derived lignans, known for their direct antioxidant properties, were evaluated in abrogating ROS generation in cultured endothelial cells following gamma radiation exposure. Mice were fed 10% FS or isocaloric control diet for three weeks and given 13.5 Gy thoracic XRT. Lungs were evaluated at 24 hours for markers of radiation-induced injury, three weeks for acute lung damage (lipid peroxidation, lung edema and inflammation), and at four months for late lung damage (inflammation and fibrosis). FS-Lignans blunted ROS generation in vitro, resulting from radiation in a dose-dependent manner. FS-fed mice had reduced expression of lung injury biomarkers (Bax, p21 and TGF-beta1) at 24 hours following XRT and reduced oxidative lung damage as measured by malondialdehyde (MDA) levels at 3 weeks following XRT. In addition, FS-fed mice had decreased lung fibrosis as determined by hydroxyproline content and decreased inflammatory cell influx into lungs at 4 months post XRT. Importantly, when Lewis lung carcinoma cells were injected systemically in mice, FS dietary supplementation did not appear to protect lung tumors from responding to thoracic XRT. Dietary FS is protective against pulmonary fibrosis, inflammation and oxidative lung damage in a murine model. Moreover, in this model, tumor radioprotection was not observed. FS lignans exhibited potent radiation-induced ROS scavenging action. Taken together, these data suggest that dietary flaxseed may be clinically useful as an agent to increase the therapeutic index of thoracic XRT by increasing the radiation tolerance of lung tissues.

Measuring brain lesion progression with a supervised tissue classification system.

Brain lesions, especially White Matter Lesions (WMLs), are associated with cardiac and vascular disease, but also with normal aging. Quantitative analysis of WML in large clinical trials is becoming more and more important. In this paper, we present a computer-assisted WML segmentation method, based on local features extracted from conventional multi-parametric Magnetic Resonance Imaging (MRI) sequences. A framework for preprocessing the temporal data by jointly equalizing histograms reduces the spatial and temporal variance of data, thereby improving the longitudinal stability of such measurements and hence the estimate of lesion progression. A Support Vector Machine (SVM) classifier trained on expert-defined WML's is applied for lesion segmentation on each scan using the AdaBoost algorithm. Validation on a population of 23 patients from 3 different imaging sites with follow-up studies and WMLs of varying sizes, shapes and locations tests the robustness and accuracy of the proposed segmentation method, compared to the manual segmentation results from an experienced neuroradiologist. The results show that our CAD-system achieves consistent lesion segmentation in the 4D data facilitating the disease monitoring.

Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier.

MOTIVATION: Most computational methodologies for microRNA gene prediction utilize techniques based on sequence conservation and/or structural similarity. In this study we describe a new technique, which is applicable across several species, for predicting miRNA genes. This technique is based on machine learning, using the Naive Bayes classifier. It automatically generates a model from the training data, which consists of sequence and structure information of known miRNAs from a variety of species. RESULTS: Our study shows that the application of machine learning techniques, along with the integration of data from multiple species is a useful and general approach for miRNA gene prediction. Based on our experiments, we believe that this new technique is applicable to an extensive range of eukaryotes' genomes. Specific structure and sequence features are first used to identify miRNAs followed by a comparative analysis to decrease the number of false positives (FPs). The resulting algorithm exhibits higher specificity and similar sensitivity compared to currently used algorithms that rely on conserved genomic regions to decrease the rate of FPs.