Identification of Genes Implicated in Methapyrilene-Induced Hepatotoxicity by Comparing Differential Gene Expression in Target and Nontarget Tissue

BACKGROUND: Toxicogenomics experiments often reveal thousands of transcript alterations that are related to multiple processes, making it difficult to identify key gene changes that are related to the toxicity of interest. OBJECTIVES: The objective of this study was to compare gene expression changes in a nontarget tissue to the target tissue for toxicity to help identify toxicity-related genes. METHODS: Male rats were given the hepatotoxicant methapyrilene at two dose levels, with livers and kidneys removed 24 hr after one, three, and seven doses for gene expression analysis. To identify gene changes likely to be related to toxicity, we analyzed genes on the basis of their temporal pattern of change using a program developed at the National Institute of Environmental Health Sciences, termed “EPIG” (extracting gene expression patterns and identifying co-expressed genes). RESULTS: High-dose methapyrilene elicited hepatic damage that increased in severity with the number of doses, whereas no treatment-related lesions were observed in the kidney. High-dose methapyrilene elicited thousands of gene changes in the liver at each time point, whereas many fewer gene changes were observed in the kidney. EPIG analysis identified patterns of gene expression correlated to the observed toxicity, including genes associated with endoplasmic reticulum stress and the unfolded protein response. CONCLUSIONS: By factoring in dose level, number of doses, and tissue into the analysis of gene expression elicited by methapyrilene, we were able to identify genes likely to not be implicated in toxicity, thereby allowing us to focus on a subset of genes to identify toxicity-related processes

Rule based classifier for the analysis of gene-gene and gene-environment interactions in genetic association studies

<p>Abstract</p> <p>Background</p> <p>Several methods have been presented for the analysis of complex interactions between genetic polymorphisms and/or environmental factors. Despite the available methods, there is still a need for alternative methods, because no single method will perform well in all scenarios. The aim of this work was to evaluate the performance of three selected rule based classifier algorithms, RIPPER, RIDOR and PART, for the analysis of genetic association studies.</p> <p>Methods</p> <p>Overall, 42 datasets were simulated with three different case-control models, a varying number of subjects (300, 600), SNPs (500, 1500, 3000) and noise (5%, 10%, 20%). The algorithms were applied to each of the datasets with a set of algorithm-specific settings. Results were further investigated with respect to a) the Model, b) the Rules, and c) the Attribute level. Data analysis was performed using WEKA, SAS and PERL.</p> <p>Results</p> <p>The RIPPER algorithm discovered the true case-control model at least once in >33% of the datasets. The RIDOR and PART algorithm performed poorly for model detection. The RIPPER, RIDOR and PART algorithm discovered the true case-control rules in more than 83%, 83% and 44% of the datasets, respectively. All three algorithms were able to detect the attributes utilized in the respective case-control models in most datasets.</p> <p>Conclusions</p> <p>The current analyses substantiate the utility of rule based classifiers such as RIPPER, RIDOR and PART for the detection of gene-gene/gene-environment interactions in genetic association studies. These classifiers could provide a valuable new method, complementing existing approaches, in the analysis of genetic association studies. The methods provide an advantage in being able to handle both categorical and continuous variable types. Further, because the outputs of the analyses are easy to interpret, the rule based classifier approach could quickly generate testable hypotheses for additional evaluation. Since the algorithms are computationally inexpensive, they may serve as valuable tools for preselection of attributes to be used in more complex, computationally intensive approaches. Whether used in isolation or in conjunction with other tools, rule based classifiers are an important addition to the armamentarium of tools available for analyses of complex genetic association studies.</p

Microscope-integrated optical coherence tomography: A new surgical tool in vitreoretinal surgery

Optical coherence tomography (OCT) has revolutionized imaging of ocular structures and various disease conditions. Though it has been used in the clinic for some decades, the OCT has only recently found its way into the operating theater. Early attempts at intraoperative OCT, hand-held and microscope mounted, have already improved our understanding of the surgical pathology and the role it might play in surgical decision-making. The microscope-integrated OCT now allows seamless, high-resolution, real-time imaging of surgical maneuvers from the incision to wound closure. Visualization of instruments and intraoperative tissue manipulation are possible with this in vivo modality and, therefore, help improve the outcome of surgery. In this article, we describe the advantages it offers during various vitreoretinal procedures

Phospholipase A 2 Is Necessary for Tumor Necrosis Factor a-induced Ceramide Generation in L929 Cells*

International audienceThe role of cytosolic phospholipase A 2 (cPLA 2 ) in the regulation of ceramide formation was examined in a cell line (L929) responsive to the cytotoxic action of tumor necrosis factor a (TNFa). In L929 cells, the addition of TNFa resulted in the release of arachidonate, which was followed by a prolonged accumulation of ceramide occurring over 5-12 h and reaching 250% over base line. The formation of ceramide was accompanied by the hydrolysis of sphingomyelin and the activation of three distinct sphingomyelinases (neutral Mg 21 -dependent, neutral Mg 21 -independent, and acidic enzymes). The variant cell line C12, which lacks cPLA 2 , is resistant to the cytotoxic action of TNFa. TNFa was able to activate nuclear factor kB in both the wild-type L929 cells and the C12 cells. However, TNFa was unable to cause the release of arachidonate or the accumulation of ceramide in C12 cells. C 6 -ceramide overcame the resistance to TNFa and caused cell death in C12 cells to a level similar to that in L929 cells. The introduction of the cPLA 2 gene into C12 cells resulted in partial restoration of TNFainduced arachidonate release, ceramide accumulation, and cytotoxicity. This study suggests that cPLA 2 is a necessary component in the pathways leading to ceramide accumulation and cell death.</div

Increases in Neutral, Mg2+-Dependent and Acidic, Mg2+-Independent Sphingomyelinase Activities Precede Commitment to Apoptosis and Are Not a Consequence of Caspase 3–Like Activity in Molt-4 Cells in Response to Thymidylate Synthase Inhibition by GW1843

Thymidylate synthase (TS) inhibition causes cell death, and this enzyme is the target for the important chemotherapy regime 5-fluorouracil/leucovorin. GW1843 (1843U89) is a potent and specific folate analog TS inhibitor in clinical development. Because of the importance of TS as a chemotherapy target, we are studying the mechanism of TS inhibition-induced cell death by GW1843. Ceramide is a regulatory lipid generated by the action of sphingomyelinase and is believed to signal apoptosis. The role of the ceramide in apoptotic signaling was studied in Molt-4 human T-cell leukemia cells undergoing cell death after treatment with GW1843. In response to GW1843, Molt-4 cells undergo apoptosis with both acidic pH, Mg2+-independent sphingomyelinase (ASMase) and neutral pH, Mg2+-dependent sphingomyelinase (NSMase) activities elevated as early steps in the initiation of apoptosis before Molt-4 commitment to death. These activities lead to ceramide production with kinetics consistent with a role as an effector molecule signaling the initiation of apoptosis in Molt-4 cells. These changes were found to be independent of caspase 3–like (CPP32/apopain) activity and DNA degradation, but were not separable from membrane blebbing or cell lysis in this cell line. In this report, kinetic evidence is provided for a role of ceramide in initiating GW1843-induced cell death of Molt-4 T-cell leukemia cells.</jats:p