Understanding genetic toxicity through data mining: the process of building knowledge by integrating multiple genetic toxicity databases.

ABSTRACT Genetic toxicity data from various sources were integrated into a rigorously designed database using the ToxML schema. The public database sources include the U.S. Food and Drug Administration (FDA) submission data from approved new drug applications, food contact notifications, generally recognized as safe food ingredients, and chemicals from the NTP and CCRIS databases. The data from public sources were then combined with data from private industry according to ToxML criteria. The resulting "integrated" database, enriched in pharmaceuticals, was used for data mining analysis. Structural features describing the database were used to differentiate the chemical spaces of drugs/candidates, food ingredients, and industrial chemicals. In general, structures for drugs/candidates and food ingredients are associated with lower frequencies of mutagenicity and clastogenicity, whereas industrial chemicals as a group contain a much higher proportion of positives. Structural features were selected to analyze endpoint outcomes of the genetic toxicity studies. Although most of the well-known genotoxic carcinogenic alerts were identified, some discrepancies from the classic Ashby-Tennant alerts were observed. Using these influential features as the independent variables, the results of four types of genotoxicity studies were correlated. High Pearson correlations were found between the results of Salmonella mutagenicity and mouse lymphoma assay testing as well as those from in vitro chromosome aberration studies. This paper demonstrates the usefulness of representing a chemical by its structural features and the use of these features to profile a battery of tests rather than relying on a single toxicity test of a given chemical. This paper presents data mining/profiling methods applied in a weight-of-evidence approach to assess potential for genetic toxicity, and to guide the development of intelligent testing strategies.

Priority-based assessment of food additives database of the U.S. Food and Drug Administration Center for Food Safety and Applied Nutrition.

The priority-based assessment of food additives (PAFA) is a database maintained by the U.S. Food and Drug Administration (FDA) Center for Food Safety and Applied Nutrition. PAFA contains extensive administrative, chemical, and toxicological information on 1685 regulated direct food additives. The database also has limited administrative and chemical information on an additional 1236 direct additives. The total 2921 substances represent everything added to food in the United States. PAFA contains up to 150 different kinds of information about each chemical. Administrative and chemical information includes Chemical Abstracts Service Registry numbers, Code of Federal Regulations citations, the annual usage and estimated daily U.S. human consumption, the Joint Committee on Food Additives Allowable Daily Intakes, the FDA Redbook structure categories of the chemicals, and their technical effects. Toxicology information shows the type of studies done for each chemical, the species of animals tested, the toxicological effects observed and the sites where they were seen, the lowest doses that cause a toxicological effect in each study, a source citation, and other types of related information.

Cytogenetic analysis of mouse metaphase II oocytes following exposure to tritiated water.

Female mice were given different dosages (0, 3.0, 7.5, 15.0, or 30 muCi/ml) of tritium in their drinking water continuously from 3 to 7 weeks of age to assess the effects on germ cell chromosomes. At 8-9 weeks of age, mice were superovulated and metaphase II oocytes were processed and C-banded for cytogenetic analyses. Chromatid acentric fragments were the only type of structural aberration detected, and their incidence was higher in controls than in any of the tritiated water (HTO) groups. Analysis of numerical chromosomal aberrations revealed that the incidence of hypoploid (N = 19) oocytes was higher in oocytes from mice who drank HTO as compared with controls. However, the effects of HTO upon aneuploidy induction was not definitive due to the increase the incidence of aberrations in mouse oocytes can be related to the low dose rate resulting from chronic HTO exposure and possibly death of tritium-damaged cells.

Use of toxicological information in drug design.

This paper is an extension of the keynote address and another talk at the Symposium on the Use of Toxiciological Information in Drug Design. The symposium was organized by American Chemical Society's Chemical Information Division at the 220th National Meeting of the American Chemical Society in Washington, DC, August 20-24, 2000. We outline an approach for meeting the scientific information needs of the U.S. Food and Drug Administration (FDA). Ready access to scientific information is critical to support safety-related regulatory decisions and is especially valuable in situations where available experimental information from in vivo/in vitro studies are inadequate or unavailable. This approach also has applications for lead selection in drug discovery. A pilot electronic toxicology/safety knowledge base and computational toxicology initiative is underway in the FDA Center for Drug Evaluation and Research (CDER) that may be a prototype for an FDA knowledge base. The objectives of this effort are: (i) to strengthen and broaden the scientific basis of regulatory decisions, (ii) to provide the Agency with an electronic scientific institutional memory, (iii) to create a scientific resource for regulatory and applied research, and (iv) to establish an internal Web-based support service that can provide decision support information for regulators that will facilitate the review process and improve consistency and uniformity. An essential component of this scientific knowledge base is the creation of a comprehensive electronic inventory of CDER-regulated substances that permit identification of clusters of substances having similar chemical, pharmacological or toxicological activities, and molecular structure/substructures. Furthermore, the inventory acts as a pointer and link to other databases and critical non-clinical and clinical pharmacology/toxicology studies and reviews in FDA archives. Clusters of related substances are identified through the use of: (i) an extensive index of alternative names for each substance, (ii) a molecular structure key field consisting of a rudimentary or core structure represented as an ISIS.mol-file, (iii) global search terms (molecular group, chemical class, clinical indication, or pharmacologic activity), and (iv) molecular clustering using structure/sub-structure similarity indices. The information contained in a toxicology knowledge database has limited value unless means are available to extract information, identify relationships, and create and test hypotheses. One such means is computational toxicology, also called in silico toxicology, ComTox, or e-TOX. Computational toxicology is the application of computer technology and information processing (informatics) to analyze, model, and estimate chemical toxicity based upon structure activity relationships (SAR). A computational toxicology software package, MCASE, has been evaluated and successfully improved by CDER through the incorporation of data from FDA archives and concomitant alterations of the logic used in the interpretation of the results to reflect the data analysis and hazard identification practices and priorities of the Center. Our modifications and uses of the MCASE program are discussed in detail.

(Q)SAR modeling and safety assessment in regulatory review.

The ability to predict clinical safety based on chemical structures is becoming an increasingly important part of regulatory decision making. (Quantitative) structure-activity relationship ((Q)SAR) models are currently used to evaluate late-arising safety concerns and possible nonclinical effects of a drug and its related compounds when adequate safety data are absent or equivocal. Regulatory use will likely increase with the standardization of analytical approaches, more complete and reliable data collection methods, and a better understanding of toxicity mechanisms.

Sister chromatid exchanges induced in rabbit lymphocytes by ethylene oxide after inhalation exposure.

Ethylene oxide, which is the simplest epoxide and an extremely important commercial compound, has been used by many investigators as a model compound to study mutagenicity by alkylation of DNA. Knowledge of in vivo dose-effect relations under experimental conditions may provide further insight into the dynamics of the sister chromatid exchange (SCE) response. It may also provide information on temporal aspects of sampling design for human worker populations. Groups of four male New Zealand white rabbits were exposed in inhalation chambers to 0, 10, 50, and 250 parts per million (ppm) ethylene oxide for 6 hr a day, 5 days a week, for 12 weeks. Peripheral blood samples were taken before the start of exposure, at intervals during exposure, and up to 15 weeks after the end of exposure to measure SCE rates in peripheral lymphocytes as well as standard hematological endpoints. Additionally, the level of reduced glutathione (GSH) in liver and blood was measured in a set of concurrently exposed animals at the end of the 12-week exposure. Results show that exposure to 10 ppm does not cause a detectable increase in SCE rates. However, exposure to 50 and 250 ppm does cause an increase in SCEs that decreases after exposure ends, but still remains above baseline levels 15 weeks after exposure. Hematological and GSH measurements did not differ between control and exposed groups. These results indicate that inhalation exposure to the mutagenic alkylating agent ethylene oxide results in a dose-related SCE effect, and that SCE is a more sensitive indicator of exposure than either standard hematological end points or GSH levels.

Sister chromatid exchanges in bone marrow cells of mice maintained on tritiated water.

The ability of tritium to induce sister chromatid exchanges (SCEs) has been investigated in male mice of the Hale-Stoner-Brookhaven strain maintained on drinking water containing 3.0 microCi/ml tritiated water (HTO). At selected intervals after 28-261 days of consuming HTO, the frequency of SCEs and the kinetics of cellular proliferation were measured in bone marrow cells of animals maintained on HTO, and in age-matched control groups, by 5-bromo-2'-deoxyuridine labelling methods. A statistically significant (1 percent level) elevation of SCEs was observed after 81, 163, 192, 247 and 261 days of HTO ingestion. The frequency of induced SCEs increased linearly with the ingestion time. These results are of particular interest since ionizing radiation is generally not considered to be an efficient inducer of SCEs.

A system for simultaneous exposure of small animals to 60-Hz electric and magnetic fields.

Equipment designed for simultaneous exposure of rodents to 60-Hz electric and magnetic fields is described. Three identical systems were constructed, each capable of continuous exposure of 256 rats or 640 mice to a nominal electric field at less than 50 kV/m, and to horizontal and vertical magnetic fields at less than 1 mT. Design features, construction details, and results of various tests of the systems are described. Tests were made: of phase relations between electric and magnetic fields; of uniformity of electric and magnetic fields; of changes across time in electric-field intensity as a result of animals' soiling of cages and various washing routines; of resistance of bedding material during humid and dry conditions; and of acoustic noise due to background, to field-generation equipment, and to air conditioning equipment. The results demonstrated that fields were effectively generated but that significant and troublesome changes in electric-field intensity occurred because of cage-soiling. However, when cages were frequently cleaned, field intensities were consistent from one exposure to another.