Cluster analysis in predicting the carcinogenicity of chemicals using short-term assays

Cluster analysis can be a useful tool for exploratory data analysis to uncover natural groupings in data, and initiate new ideas and hypotheses about such groupings. When applied to short-term assay results, it provides and improves estimates for the sensitivity and specificity of assays, provides indications of association between assays and, in turn, which assays can be substituted for one another in a battery, and allows a data base containing test results on chemicals of unknown carcinogenicity to be linked to a data base for which animal carcinogenicity data are available. Cluster analysis was applied to the Gene-Tox data base (which contains short-term test results on chemicals of both known and unknown carcinogenicity). The results on chemicals of known carcinogenicity were different from those obtained when the entire data base was analyzed. This suggests that the associations (and possibly the sensitivities and specificities) which are based on chemicals of known carcinogenicity may not be representative of the true measures. Cluster analysis applied to the total data base should be useful in improving these estimates. Many of the associations between the assays which were found through the use of cluster analysis could be 'validated' based on previous knowledge of the mechanistic basis of the various tests, but some of the associations were unsuspected. These associations may be a reflection of a non-ideal data base. As additional data becomes available and new clustering techniques for handling non-ideal data bases are developed, results from such analyses could play an increasing role in strengthening prediction schemes which utilize short-term tests results to screen chemicals for carcinogenicity, such as the carcinogenicity and battery selection (CPBS) method (Chankong et al., 1985).     

Statistical analysis of Salmonella test data and comparison to results of animal cancer tests

A quantitative framework for the analysis of results of the Salmonella (Ames) test is presented, and the relationship between mutagenesis and carcinogenesis is examined. Color graphics are used for the Salmonella data to describe variability, and trends across multiple chemicals and test conditions. Positivity in the Salmonella test, using statistical criteria to classify results, is compared to positivity in carcinogenesis bioassays for 48 chemicals tested in NCI/NTP-sponsored programs. Sensitivity of the Salmonella test across 5 tester strains was 91% (21/23), while specificity was only 36% (9/25). Results were most concordant for TA100 Aroclor-induced rat S9: sensitivity was 87%, specificity 64%. The correlation of mutagenic potency and carcinogenic potency was 0.41 (p less than 0.001) for 80 chemicals, using results from both the general published literature and the NCI/NTP-sponsored programs. After removal of 3 extreme values, the correlation was 0.24 (p = 0.04).     

The carcinogenicity prediction and battery selection (CPBS) method: a Bayesian approach

Recently, a large number of relatively inexpensive in vitro short-term tests have been developed to help predict the carcinogenicity of chemicals. The carcinogenicity prediction and battery selection (CPBS) method utilizes the results of such short-term tests to screen for chemicals that are most likely to cause cancer. The method is an integrated approach for analyzing large, often sparsely filled, data bases containing short-term test results, which often have only marginal representation of known non-carcinogens. The CPBS method is developed for the purpose of (i) determining the reliability and predictive capability of individual and batteries of short-term tests, and (ii) developing a strategy for formulating and selecting optimally preferred batteries of short-term tests for screening chemicals for further testing. The term 'optimally preferred' connotes the best acceptable combination of tests in terms of trade-offs among the multiple attributes of each test and resulting battery (e.g., cost, sensitivity, specificity, etc). The CPBS method consists of 5 major tasks: (1) data consolidation, (2) parameter estimation, (3) predictivity calculation, (4) battery selection and (5) risk assessment. Although there is a great need for more research and improvement, the CPBS method at its present stage should add an important method to the maze of the thousands of new chemicals that are introduced into drugs, foods, consumer goods and to the environment every year. This method should also provide an enhanced identification procedure for classifying chemicals more accurately as suspected carcinogens or non-carcinogens.     

Comparison of the olfactory sensitivity of two sympatric steppe grasshopper species (Orthoptera: Acrididae) to plant volatile compounds

Two Oedipodinae grasshopper species Oedaleus decorus asiaticus B.-Bienko and Angaracris baraben-sis Pall. (Orthoptera: Acrididae) are important pests on the natural grasslands in Inner Mongolia and often require insecticide treatment during outbreaks[1]. They both prefer overgrazed steppes and xerophytous habi-tats, and have thus been suggested as indicator species for steppe deterioration in typical steppe zones of In-ner Mongolia[2]. The two species have a sympatric distribution and sync…     

A new classification system for the actions of IRS chemicals traditionally used for malaria control

Knowledge of how mosquitoes respond to insecticides is of paramount importance in understanding how an insecticide functions to prevent disease transmission. A suite of laboratory assays was used to quantitatively characterize mosquito responses to toxic, contact irritant, and non-contact spatial repellent actions of standard insecticides. Highly replicated tests of these compounds over a range of concentrations proved that all were toxic, some were contact irritants, and even fewer were non-contact repellents. Of many chemicals tested, three were selected for testing in experimental huts to confirm that chemical actions documented in laboratory tests are also expressed in the field. The laboratory tests showed the primary action of DDT is repellent, alphacypermethrin is irritant, and dieldrin is only toxic. These tests were followed with hut studies in Thailand against marked-released populations. DDT exhibited a highly protective level of repellency that kept mosquitoes outside of huts. Alphacypermethrin did not keep mosquitoes out, but its strong irritant action caused them to prematurely exit the treated house. Dieldrin was highly toxic but showed no irritant or repellent action. Based on the combination of laboratory and confirmatory field data, we propose a new paradigm for classifying chemicals used for vector control according to how the chemicals actually function to prevent disease transmission inside houses. The new classification scheme will characterize chemicals on the basis of spatial repellent, contact irritant and toxic actions.     

Predictive assay for rodent carcinogenicity using in vivo biochemical parameters: operational characteristics and complementarity.

111 chemicals of known rodent carcinogenicity (49 carcinogens, 62 noncarcinogens), including many promoters of carcinogenesis, nongenotoxic carcinogens, hepatocarcinogens, and halogenated hydrocarbons, were selected for study. The chemicals were administered by gavage in two dose levels to female Sprague-Dawley rats. The effects of these 111 chemicals on 4 biochemical assays (hepatic DNA damage by alkaline elution (DD), hepatic ornithine decarboxylase activity (ODC), serum alanine aminotransferase activity (ALT), and hepatic cytochrome P-450 content (P450)) were determined. Composite parameters are defined as follows: CP = [ODC and P450), CT = [ALT and ODC), and TS = [DD or CP or CT]. The operational characteristics of TS for predicting rodent cancer were sensitivity 55%, specificity 87%, positive predictivity 77%, negative predictivity 71%, and concordance 73%. For these chemicals, the 73% concordance of this study was superior to the concordance obtained from published data from other laboratories on the Ames test (53%), structural alerts (SA) (46%), chromosome aberrations in Chinese hamster ovary cells (ABS) (48%), cell mutation in mouse lymphoma 15178Y cells (MOLY) (52%), and sister-chromatid exchange in Chinese hamster ovary cells (SCE) (60%). The 4 in vivo biochemical assays were complementary to each other. The composite parameter TS also shows complementarity to all 5 other predictors of rodent cancer examined in this paper. For example, the Ames test alone has a concordance of only 53%. In combination with TS, the concordance is increased to 62% (Ames or TS) or to 63% (Ames and TS). For the 67 chemicals with data available for SA, the concordance for predicting rodent carcinogenicity was 47% (for SA alone), 54% (for SA or TS), and 66% (for SA and TS). These biochemical assays will be useful: (1) to predict rodent carcinogenicity per se, (2) to 'confirm' the results of short-term mutagenicity tests by the high specificity mode of the biochemical assays (the specificity and positive predictivity are both 100%), and (3) to be a component of future complementary batteries of tests for predicting rodent carcinogenicity.     

Behavioural and electrophysiological studies of taste discrimination by the maxillary palps of larvae of Locusta migratoria (L.).

1. Behavioural studies show that larvae of Locusta migratoria (L.) can discriminate between certain simple chemicals and between chemicals obtained from plant sources. 2. Electrophysiological tests show that within each sensillum the same neurones respond to different chemicals. 3. The frequency of occurrence of sensilla with enhanced specificity to certain chemicals is investigated. 4. Statistical tests confirm that, despite the variability of response, across-fibre analysis could allow discrimination between chemicals provided an adequate number of senilla are used. 5. The conclusions are discussed in relation to current theories of chemoreceptor functioning.     

Comparison of the olfactory sensitivity of two sympatric steppe grasshopper species (Orthoptera: Acrididae) to plant volatile compounds

Electroantennogram (EAG) responses of male and female Oedipodinae grasshoppers, Oedaleus decorus asiaticus B.-Bienko and Angaracris barabensis Pall to 37 plant volatile compounds were recorded. The two species have sympatric distribution and synchronous seasonal activity in Inner Mongolia Grasslands. They have different host plant preference with Oedaleus decorus asiaticus graminivorous and A. barabensis forbivorous. The EAG response profiles to 37 compounds of the two species and their both sexes were similar. Most of the green leaf volatiles elicited higher EAG responses in both species and sexes than terpenic compounds and some aromatic compounds. Strong EAG responses were elicited by 6-carbon alcohols (1-hexanol, Z-hexen-2-ol-1, E-2-hexen-1-ol, E-hexen-3-ol-1), aldehyde (E-2-hexen-1-al), ester (Z-hexen-3-yl acetate), and 7-carbon alcohols (1-heptanol) in both species and sexes. Monoterpenes with functional groups of alcohols and aldehydes were more stimulating than other monoterpenes tested. The sesquiterpenes tested elicited relatively low responses. Benzaldehyde elicited the highest responses for both species among aromatic components. Oedaleus decorus asiaticus showed higher EAG responses than A. barabensis to the green leaf volatiles, 1-decanol, 1-nonanol, 1-pentanol, hexanal, Z-hexen-3-yl acetate and to the sesquiterpenes (-)-trans-caryophyllene. Males have higher responses than females in Oedaleus decorus asiaticus. No sexual difference was observed in A. barabensis. Dose-dependent responses to six selected chemicals were observed from females. In both species, all the chemicals tested elicit EAG responses at concentration between 10^-3 mol/L and 10^-2 mol/L, except that the responses of A. barabensis to terpineol had a threshold concentration of 10-2 mol/L benzaldehyde and 1-hexanol had the highest slopes in dose curves, while 1-octen-3-ol showed the smallest slope in responses to the six chemicals tested. Comparative studies on the responses of two antennal sections and the whole antenna to six selected chemicals were carried out using females of both species. A significant EAG response was only recorded from the distal part of the antenna and not from the proximal seven segments.     

Spiked Sediment Toxicity Testing of Hydrophobic Organic Chemicals: Bioavailability,Technical Considerations,and Applications

Many evaluations estimating safe levels of hydrophobic organic chemicals in sediments do not account for confounding factors such as physical habitat quality or covariance among chemicals. Controlled experiments demonstrating cause and effect can be conducted with spiked sediment toxicity tests, but application of this methodology has been limited in part by concerns about chemical bioavailability and challenges in achieving target concentrations. Relevant literature was reviewed to assess the utility of standardizing sediment equilibration times; hydrophobicity, complex sediment characteristics, and temperature were identified as potentially equally important factors. Disequilibrium appears likely following limited equilibration time but should yield conservative toxicity test results relative to aged field sediments. Nominal and measured concentrations in over 20 published studies were compared to assess spiked chemical recovery (i.e., measured concentration/nominal concentration). Recovery varied substantially among studies and was not readily predictable based on spiking or extraction method, chemical properties, or measured sediment characteristics, although unmeasured differences between sediments appeared to be important. Factors affecting specific studies included chemical adsorption to glassware, biodegradation, and volatilization. Pre- and post-toxicity test analyses are recommended to confirm exposure concentrations. Studies with 2,3,7,8-tetrachloro-dibenzo-p-dioxin (2,3,7,8-TCDD) and hexachlorobenzene (HCB) exemplify the utility of verifying results of field studies using spiked sediment tests. Sediments spiked with these chemicals at concentrations greatly exceeding those in associated field studies caused no adverse effects in test organisms, demonstrating that other chemicals co-occurring in test sediment samples caused toxicity initially attributed to 2,3,7,8-TCDD and HCB in the field studies. Another key application of spiked sediment tests has been the investigation of TOC as the primary factor affecting bioavailability of hydrophobic organic chemicals. A review of LC50s for nine chemicals reported in 12 studies shows that comparable LC50s derived in different sediments generally agree within a factor of five when concentrations are normalized to a constant TOC. Additionally, use of spiked sediment toxicity testing to investigate toxicological interactions among chemicals provides a promising approach to improving the ability to predict sediment toxicity in the field.     

The zebra mussel (Dreissena polymorpha), a new pest in North America: reproductive mechanisms as possible targets of control strategies

Summary

The zebra mussel (Dreissena polymorpha) has spread rapidly in temperate fresh waters of North America since its introduction into the Great Lakes in 1985 or 1986. It attaches to hard substrates, forming layers, occluding water intakes, encrusting and killing native mussels, filtering algae in competition with other planktivores, and possibly interfering with fish spawning. It reproduces prolifically, suggesting that an approach to its control may be by controlling its reproduction. Previous literature suggests that spawning in bivalves is regulated by both environmental and internal chemical cues. A suggested sequence is that phytoplankton chemicals initially trigger spawning; chemicals associated with gametes provide a species-specific pheromonal positive feedback for spawning; and the response to environmental chemicals is mediated internally by serotonin (5-HT). The role of 5-HT in zebra mussels is under investigation. Both males and females can be induced to spawn by either injection or external application of 5-HT. The response can also be activated by 8-hydroxy-2-(di-n-propylamino)-tetralin, an agonist at 5-HT_1A receptors. HPLC analysis has detected 5-HT as the major biogenic amine in both male and female gonads. 5-HT immunocytochemistry demonstrates nerves containing serotonergic fibers innervating gonads of both males and females, with prominent varicosities surrounding the follicles in both sexes. A role of 5-HT in mediating spawning responses in zebra mussels is thus strongly supported. These studies have shown that reproductive behavior of zebra mussels can be modified by outside chemicals, a property that may be exploited for purposes of control.     

Re-evaluation of the relationship between rodent populations and acorn masting: a review from the aspect of nutrients and defensive chemicals in acorns

The responses of rodent populations to acorn masting were examined by reviewing 17 studies from the aspect of acorn nutrients and defensive chemicals. Oak species were grouped into three types based on their acorn nutritional characteristics by cluster analysis: Type 1 acorns (two North American red oaks, subgenus Erythrobalanus) were high in tannins and high in fat and proteins (and consequently rich in metabolizable energy); Type 2 acorns (two Japanese evergreen oaks, Cyclobalanopsis; three Japanese deciduous oaks, Lepidobalanus; one North American white oak, Lepidobalanus) were high in tannins but low in fat and proteins; and Type 3 acorns (one Cyclobalanopsis species; seven Lepidobalanus species) were low in tannins and had intermediate levels of fat and proteins. These three acorn groups were nutritionally, and thereby ecologically, not equivalent. Rodents, in general, responded differently to acorn masting depending on their feeding habits and the nutritional characteristics of acorns. Granivorous rodents showed positive responses to masting of Type 1 and 3 acorns, whereas rodents with feeding habits intermediate between granivory and herbivory showed positive responses to masting of Type 3 acorns. In addition, for herbivorous rodents, the responses to masting of any types of acorns have not been reported. The present findings emphasize that the relationship between rodents and acorn masting should not easily be generalized, because there are large variations in characteristics of both acorns and rodents. The viewpoint presented in this review could offer more convincing interpretations to the contradictory observations, found in the studies reviewed, on the response of rodent populations to acorn masting.     

Application of a cellular test battery in the decision point approach to carcinogen identification

The assessment of the potential carcinogenicity of a chemical requires a systematic approach taking into account various types of data. Important information on the DNA reactivity and other genetic effects of chemicals can be obtained from a battery of cellular tests. A battery is described which includes DNA repair in hepatocytes, mutagenesis in Salmonella typhimurium, mutagenesis, chromosome alterations, and transformation in mammalian cells. The interpretation of findings in this battery for the identification of potential carcinogenicity of chemicals is discussed.     

Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification

Fourier transform-all reaction monitoring (FT-ARM) is a novel approach for the identification and quantification of peptides that relies upon the selectivity of high mass accuracy data and the specificity of peptide fragmentation patterns. An FT-ARM experiment involves continuous, data-independent, high mass accuracy MS/MS acquisition spanning a defined m/z range. Custom software was developed to search peptides against the multiplexed fragmentation spectra by comparing theoretical or empirical fragment ions against every fragmentation spectrum across the entire acquisition. A dot product score is calculated against each spectrum to generate a score chromatogram used for both identification and quantification. Chromatographic elution profile characteristics are not used to cluster precursor peptide signals to their respective fragment ions. FT-ARM identifications are demonstrated to be complementary to conventional data-dependent shotgun analysis, especially in cases where the data-dependent method fails because of fragmenting multiple overlapping precursors. The sensitivity, robustness, and specificity of FT-ARM quantification are shown to be analogous to selected reaction monitoring-based peptide quantification with the added benefit of minimal assay development. Thus, FT-ARM is demonstrated to be a novel and complementary data acquisition, identification, and quantification method for the large scale analysis of peptides.     

A comparison of ecotoxicological tests

A simple, inexpensive and rapid method of determining toxicity by using a bacterium as the indicator organism was developed and compared with 23 other tests. The average correlation coefficient when comparing these 23 tests with the present test was 0.800, ranging from 0.580 to 0.950. Eleven of the tests were compared in detail by using 35 of the chemicals on the Multicentre Evaluation of In Vitro Cytotoxicity list of test chemicals. Comparing results from the present test with test results for these 35 chemicals with Microtox, Biotox, Daphnia magna, rat hepatocytes and ascites tumour cell resulted in correlation coefficients ranging from 0.871 to 0.933. Comparisons of the test data with rodent LD50 values, human lethal dose estimates from autopsies and human lethal doses obtained from the literature provided correlation coefficients ranging from 0.580 to 0.770, indicating that the test compares less favourably with these methods. This test provides data comparable to data from other ecotoxicological tests.     

Phage T7-inactivation test. A possibility of quantitative mutagenicity screening

A new method is described for the quantitative characterization of the genotoxic effect of chemicals. The method is based on the determination of the inactivation of bacteriophage T7 and on the application of a simple mathematical model valid for the processes during, or at least in the initial stage of the interaction of chemicals and phages. A value characteristic for the chemical is defined and it is determined from the inactivation kinetics. Typical inactivation kinetic curves and some problems of the application of the model as well as the mutagenicity index values determined for about 30 substances are presented. The substances examined have mutagenicity index values covering a range of six orders of magnitude. The obtained values are compared with the results of different mutagenicity/carcinogenicity tests and discussed on the basis of data in the literature. The presented method is proposed to be applied for quantitative mutagenicity screening of chemicals.     

Turning all the lights on: quantum dots in cellular assays

Quantum dot materials are increasingly used in cellular assays, and offer a powerful and enabling complement to existing methods of labeling proteins, such as green fluorescent protein. These materials give researchers the ability to study specificity and functional responses in cellular systems, in a highly multiplexed manner, at either a molecular or cellular level. The recent literature bears witness to the increasing use of quantum dots for the investigation of chemicals on biological systems, and paves the way to the use of these assays for high-throughput analysis of functional responses in relevant models at scales including molecular, cellular and whole animal.     

Genetic variations and haplotype diversity of the UGT1 gene cluster in the Chinese population

Vertebrates require tremendous molecular diversity to defend against numerous small hydrophobic chemicals. UDP-glucuronosyltransferases (UGTs) are a large family of detoxification enzymes that glucuronidate xenobiotics and endobiotics, facilitating their excretion from the body. The UGT1 gene cluster contains a tandem array of variable first exons, each preceded by a specific promoter, and a common set of downstream constant exons, similar to the genomic organization of the protocadherin (Pcdh), immunoglobulin, and T-cell receptor gene clusters. To assist pharmacogenomics studies in Chinese, we sequenced nine first exons, promoter and intronic regions, and five common exons of the UGT1 gene cluster in a population sample of 253 unrelated Chinese individuals. We identified 101 polymorphisms and found 15 novel SNPs. We then computed allele frequencies for each polymorphism and reconstructed their linkage disequilibrium (LD) map. The UGT1 cluster can be divided into five linkage blocks: Block 9 (UGT1A9), Block 9/7/6 (UGT1A9, UGT1A7, and UGT1A6), Block 5 (UGT1A5), Block 4/3 (UGT1A4 and UGT1A3), and Block 3' UTR. Furthermore, we inferred haplotypes and selected their tagSNPs. Finally, comparing our data with those of three other populations of the HapMap project revealed ethnic specificity of the UGT1 genetic diversity in Chinese. These findings have important implications for future molecular genetic studies of the UGT1 gene cluster as well as for personalized medical therapies in Chinese.     

A Response-Additive Model for Analyzing Mixtures of Two Chemicals in the Salmonella Reversion Assay

A statistical model is proposed for analyzing the mutagenic responses produced by mixtures of two chemicals in the Salmonella reversion assay. This model is based on the simplex-lattice design for mixtures with the total concentration fixed. The dose-response relationship is expressed as a function of both the proportions of the two chemicals and the total concentration of the chemicals in the mixture. If the joint action of two chemicals can be predicted by response-additivity, then the response of the mixture at the total concentration T can be represented by the weighted average of the responses produced by the individual chemicals at the same concentration T with the weights for individual responses being equal to the proportions of the chemicals in the mixture. Two non-additive models, synergism and antagonism, are discussed. An example is illustrated by analyzing the joint mutagenic effects of 1-nitrobenzo(a)pyrene (1-NBP), and 3-NBP in the Salmonella reversion assay.     

True versus apparent malaria infection prevalence: the contribution of a Bayesian approach

Aims

To present a new approach for estimating the “true prevalence” of malaria and apply it to datasets from Peru, Vietnam, and Cambodia.

Methods

Bayesian models were developed for estimating both the malaria prevalence using different diagnostic tests (microscopy, PCR & ELISA), without the need of a gold standard, and the tests'' characteristics. Several sources of information, i.e. data, expert opinions and other sources of knowledge can be integrated into the model. This approach resulting in an optimal and harmonized estimate of malaria infection prevalence, with no conflict between the different sources of information, was tested on data from Peru, Vietnam and Cambodia.

Results

Malaria sero-prevalence was relatively low in all sites, with ELISA showing the highest estimates. The sensitivity of microscopy and ELISA were statistically lower in Vietnam than in the other sites. Similarly, the specificities of microscopy, ELISA and PCR were significantly lower in Vietnam than in the other sites. In Vietnam and Peru, microscopy was closer to the “true” estimate than the other 2 tests while as expected ELISA, with its lower specificity, usually overestimated the prevalence.

Conclusions

Bayesian methods are useful for analyzing prevalence results when no gold standard diagnostic test is available. Though some results are expected, e.g. PCR more sensitive than microscopy, a standardized and context-independent quantification of the diagnostic tests'' characteristics (sensitivity and specificity) and the underlying malaria prevalence may be useful for comparing different sites. Indeed, the use of a single diagnostic technique could strongly bias the prevalence estimation. This limitation can be circumvented by using a Bayesian framework taking into account the imperfect characteristics of the currently available diagnostic tests. As discussed in the paper, this approach may further support global malaria burden estimation initiatives.