Prediction of potent shRNAs with a sequential classification algorithm

We present SplashRNA, a sequential classifier to predict potent microRNA-based short hairpin RNAs (shRNAs). Trained on published and novel datasets, SplashRNA outperforms previous algorithms and reliably predicts the most efficient shRNAs for a given gene. Combined with an optimized miR-E backbone, >90% of high-scoring SplashRNA predictions trigger >85% protein knockdown when expressed from a single genomic integration. SplashRNA can significantly improve the accuracy of loss-of-function genetics studies and facilitates the generation of compact shRNA libraries.

Simultaneous detection of multiple mRNA markers CK19, CEA, c-Met, Her2/neu and hMAM with membrane array, an innovative technique with a great potential for breast cancer diagnosis

The objective of this study was mainly to develop and evaluate a membrane array-based method simultaneously detecting the expression levels of a multiple mRNA marker panel in the peripheral blood for used in complementary breast cancer diagnosis. The mRNA markers employed included cytokeratin 19 (CK-19), carcinoembryonic antigen (CEA), c-Met, Her2/neu, and mammaglobin (hMAM). The specimens of peripheral blood were collected from 80 healthy women and 102 female patients with breast cancer. The expression levels of molecular markers were evaluated by real-time Q-PCR and membrane array. Data obtained from real-time Q-PCR and membrane array were subjected to linear regression analysis, revealing that there was a high degree of correlation between the results of these two methods (r=0.979, P<0.0001). The result of membrane array assay with a combined panel of five mRNA markers was demonstrated to achieve sensitivity of 80.6%, and specificity of 83.8% for breast cancer detection, much higher than those of analysis of single marker. In addition, we demonstrated that the membrane array method could detect circulating cancer cells at a density as low as five cancer cells per 1 ml of blood. The analysis of correlation between the outcome of membrane array and clinicopathological characteristics indicated that overexpression of the multiple marker panel was significantly correlated with tumor size (P=0.030) and TNM stage (0.009). In conclusion, the detection of circulating cancer cells by means of membrane array simultaneously monitoring five mRNA markers could significantly enhance the sensitivity and specificity for cancer cell detection.

Approaches to characterizing human health risks of exposure to fibers

Naturally occurring and man-made (synthetic) fibers of respirable sizes are substances that have been identified by the U.S. Environmental Protection Agency (U.S. EPA) as priority substances for risk reduction and pollution prevention under the Toxic Substances Control Act (TSCA). The health concern for respirable fibers is based on the link of occupational asbestos exposure and environmental erionite fiber exposure to the development of chronic respiratory diseases, including interstitial lung fibrosis, lung cancer, and mesothelioma in humans. There is also considerable laboratory evidence indicating that a variety of fibers of varying physical and chemical characteristics can elicit fibrogenic and carcinogenic effects in animals under certain exposure conditions. This paper discusses key scientific issues and major default assumptions and uncertainties pertaining to the risk assessment of inhaled fibers. This is followed by a description of the types of assessment performed by the U.S. EPA to support risk management actions of new fibers and existing fibers under TSCA. The scope and depth of these risk assessments, however, vary greatly depending on whether the substance under review is an existing or a new fiber, the purpose of the assessment, the availability of data, time, and resources, and the intended nature of regulatory action. In general, these risk assessments are of considerable uncertainty because health hazard and human exposure information is often incomplete for most fibers. Furthermore, how fibers cause diseases and what specific determinants are critical to fiber-induced toxicity and carcinogenicity are still not completely understood. Further research to improve our knowledge base in fiber toxicology and additional toxicity and exposure data gathering are needed to more accurately characterize the health risks of inhaled fibers.

Development of structure-activity relationship rules for predicting carcinogenic potential of chemicals

Since the inception of Section 5 (Premanufacturing/Premarketing Notification, PMN) of the Toxic Substances Control Act (TSCA), structure-activity relationship (SAR) analysis has been effectively used by U.S. Environmental Protection Agency's (EPA) Structure Activity Team (SAT) in the assessment of potential carcinogenic hazard of new chemicals for which test data are not available. To capture, systematize and codify the Agency's predictive expertise in order to make it more widely available to assessors outside the TSCA program, a cooperative project was initiated to develop a knowledge rule-based expert system to mimic the thinking and reasoning of the SAT. In this communication, we describe the overall structure of this expert system, discuss the scientific bases and principles of SAR analysis of chemical carcinogens used in the development of SAR knowledge rules, and delineate the major factors/rules useful for assessing the carcinogenic potential of fibers, polymers, metals/metalloids and several major classes of organic chemicals. An integrative approach using available short-term predictive tests and non-cancer toxicological data to supplement SAR analysis has also been described.

Evaluation of reduced protocols for carcinogenicity testing of chemicals: report of a joint EPA/NIEHS workshop

The current U.S. Environmental Protection Agency (EPA) and other national/international guidelines specify the use of two species and two sexes rodents (usually the rat and the mouse) for carcinogenicity testing of chemicals. In view of the enormous number of chemicals to be tested, the high cost of testing, and the large number of animals used in the present protocol, many academic, industrial, and government authorities are examining the possibility of using a reduced protocol (less than two species and two sexes of rodents) for carcinogenicity testing of chemicals. The use of a reduced protocol offers many advantages as well as some disadvantages. To pursue further the potential implications and impacts of using a reduced protocol for carcinogenicity testing on the processes of hazard identification and risk assessment, a workshop entitled "Evaluation of Reduced Protocols for Carcinogenicity Testing of Chemicals" was held at the Embassy Suites Hotel in Alexandria, Virginia on September 22 and 23, 1992. It was cosponsored by EPA's Office of Prevention, Pesticides and Toxic Substances (OPPTS) and the National Toxicology Program of the National Institutes of Environmental Health Sciences (NTP/NIEHS) and attended by more than 60 participants from government, industry, academia, and the general public. The Expert Consensus Panel and most of the participants supported the use of reduced protocols in carcinogenicity testing. However, it was recognized that reduced protocols may not be appropriate for the testing of all chemicals and that additional analyses/data may be needed for selection of the most appropriate reduced protocol for certain chemicals/chemical classes.

Papillary carcinoma of rete testis

A case of a rare papillary adenocarcinoma of the rete testis (epididymis) with a solitary metastasis to a periaortic lymph node is reported. The favorable outcome over a three and one-third-year period after radical orchiectomy and retroperitoneal lymphadenectomy has been observed. We believe this is the first report of such a tumor being treated with lymphadenectomy.

Phosphorylation of chromosomal proteins from mammary cell lines

Phosphorylation of histone and none-histone chromosomal proteins in two clonal mouse mammary cell lines having low (V-14) and high (T-19) tumorigenicity was investigated. Logarithmic phase cells were incubated in medium containing 125 muCi/ml[32P]-orthophosphate. Cell nuclei were isolated, chromosomal proteins (histones and non-histones) extracted and their amino acid composition, protein/DNA mass ratios, 32P-uptake and gel electrophoretic patterns examined. Significant differences in the histone and NHC-protein phosphorylation of these two cell lines were found. Comparison of radioactivity profiles of electrophoretically separated T-19 and V-14 NHC-proteins showed that 60% of the T-19 bands in the mol. wt range of 160,000 to 15,000 daltons had increased [32P]-orthophosphate uptake. Differences in histone radiolabelling between V-14 and T-19 were confined to the H1, H3 and H4 classes. [32P]-ATP-pool measurements of V-14 and T-19 at 30, 60 and 120 min of incubation were similar, hence the difference in 32P-uptake was not due to ATP-pool fluctuations. Results of studies on growth rate, growth potential and the possibility that comparisons were made between cells at different stages of the growth cycle indicated that these variables did not account for the higher phosphorylation of T-19 chromosomal proteins. The increased [32P]-phosphate uptake into T-19 cell protein was correlated with an elevated content of NHC and histone proteins and pointed towards a correlation between the degree of phosphorylation and the high tumorigenicity of this cell line.

Interaction of the tobacco-specific nitrosamines, methylethylnitrosamine and N-nitrosonornicotine, with DNA and guanosine

In vitro binding of the tobacco-specific nitrosamines, methylethylnitrosamine (MEN) and nitrosonornicotine (NNN), to exogenous DNA and guanosine was studies in a rat liver microsome-catalyzed system. MEN (N-[ethyl-1-14C]) binds covalently to calf thymus DNA whereas NNN (N'-[pyrrolidine-2-14C]) binds only to guanosine but not to DNA. Pretreatment of the rats with either phenobarbital (PB) or 3-methylcholanthrene (MC) greatly diminishes the binding of 14C-MEN to DNA. Both MEN-demethylase and -deethylase activities are stimulated by PB pretreatment and inhibited by MC pretreatment, but the degree of stimulation and inhibition of the two dealkylases are not the same. Addition of cytosol to the incubation system does not enhance but suppresses the binding of 14C-MEN to DNA. Inclusion of mitochondria in the system has no effect on the binding. Addition of benzylamine (250 microM), which is a potent inhibitor of dimethylnitrosamine-demethylase, however totally abolishes the binding of 14C-MEN catalyzed by microsomes. The data suggest that ethylcarbonium ion may be the metabolically activated intermediate of MEN that binds to DNA.

Role of dimethylnitrosamine-demethylase in the metabolic activation of dimethylinitrosamine

In vivo administration to rats of the mixed-function oxidase modifiers 3-methylcholanthrene (MC), pregnenolone-16 alpha-carbonitrile (PCN) or beta-naphthoflavnoe (beta-f) inhibits the hepatic microsome-catalyzed in vitro binding of dimethylnitrosamine (DMN) to DNA. This parallels their effect on DMN-demethylase I, regarded to be the sole activating step in DMN carcinogenesis and fails to account for the previously observed anomaly that MC and PCN inhibit, while beta-NF enhances, the hepatocarcinogenic activity of DMN. The in vitro binding of DMN is clearly dependent on microsomes and NADPH, and is strongly enhanced by soluble cytoplasmic proteins; the presence of the latter has no effect. however, on the relative response to pretreatment by the modifiers. In mice beta-NF enhances and PCN inhibits DMN-demethylase I; beta-NF has no effect on either the cytochrome P-450 level or on the LD50, while PCN strongly increases the cytochrome P-450 level but without influencing the LD50. Neither of the two modifiers has any effect in mice on the host-mediated mutagenicity of DMN in a dose-response study, except for the highest dose of DMN (200 mg/kg) where PCN pretreatment significantly enhanced mutagenicity. To account for the anomalous observations, other potential pathways of DMN metabolism have been explored. Whole rat liver nuclei or isolated nuclear membrane fractions contain no DMN-demethylase or diethylnitrosamine-deethylase activity. In a microsomal mixed-function amine-oxidase assay system neither purified enzyme preparations nor whole microsomes catalyze NADPH oxidation in the presence of DMN as substrate. In addition, the purified enzyme does not catalyze formaldehyde production in the DMN-demethylase assay system. Benzylamine, a typical inhibitor of mitochondrial monoamine oxidase (MAO), is a potent inhibitor of DMN-demethylase activity, but microsomes are devoid of MAO activity. Furthermore, purified MAO has no DMN-demethylase activity. The differential effect of modifiers on the carcinogenicity of DMN probably involves pathways other than DMN metabolism.

Effect of calcitonin on the phosphorylation of non-histones from cultured bone cells

32P-uptake into non-histones from bone cell cultures was selectively stimulated in the presence of calcitonin. Comparison of the control and experimental radioactivity profiles of non-histones fractionated by SDS gel electrophoresis showed that, in response to calcitonin stimulation, there was a 2- to 3-fold increase in the specific activity associated with non-histone proteins in the molecular weight range of 10,000 to 45,000 daltons while that of bands between 50,000 to 200,000 decreased.