Advancing chemical risk assessment decision-making with population variability data: challenges and opportunities.

Characterizing population variability, including identifying susceptible populations and quantifying their increased susceptibility, is an important aspect of chemical risk assessment, but one that is challenging with traditional experimental models and risk assessment methods. New models and methods to address population variability can be used to advance the human health assessments of chemicals in three key areas. First, with respect to hazard identification, evaluating toxicity using population-based in vitro and in vivo models can potentially reduce both false positive and false negative signals. Second, with respect to evaluating mechanisms of toxicity, enhanced ability to do genetic mapping using these models allows for the identification of key biological pathways and mechanisms that may be involved in toxicity and/or susceptibility. Third, with respect to dose-response assessment, population-based toxicity data can serve as a surrogate for human variability, and thus be used to quantitatively estimate the degree of human toxicokinetic/toxicodynamic variability and thereby increase confidence in setting health-protective exposure limits. A number of case studies have been published that demonstrate the potential opportunities for improving risk assessment and decision-making, and include studies using Collaborative Cross and Diversity Outbred mice, as well as populations of human cell lines from the 1000 Genomes project. Key challenges include the need to apply more sophisticated computational and statistical models analyzing population-based toxicity data, and the need to integrate these more complex analyses into risk assessments and decision-making.

Molecular and agro-morphological genetic diversity assessment of Chickpea mutants induced via ethyl methane sulfonate.

Iran, especially its western provinces, is one of the most chickpea producing countries of the world with the yield about 500 kg/ ha in average. Narrow genetic variability for chickpea is one of the most limitations in conventional breeding approaches. In this study, derived genetic variation among 94 chickpea (Bivanij cultivar) mutant lines produced by Ethyl Methane Sulfonate (EMS) were assessed based on ISSR, RAPD markers in M4 and morpho-agronomic traits in M3 generation. The induced variation via EMS in field experiment, showed significant differences among mutant lines based on almost measured traits. In overall, banding patterns of 6 ISSR primers and 8 RAPD primers revealed 21 (50%) and 24 (42.25%) polymorphic bands, respectively. The ranges of similarity coefficient in ISSR and RAPD markers were 0.62-1.00 and 0.72-1.00, respectively. Specific grouping was carried out by each cluster analysis including ISSR, RAPD, ISSR+RAPD and morpho-agronomic markers based on their similarity matrices. The results showed significant variation generated by EMS based on molecular markers and morpho-agronomic traits. Mantel tests between extracted similarity matrices from each marker system were statistically significant. It could be concluded that the generated variation with EMS as a chemical mutant can be used for chickpea breeding purposes.

Genetic variation of Lymnaea stagnalis tolerance to copper: A test of selection hypotheses and its relevance for ecological risk assessment.

The use of standardized monospecific testing to assess the ecological risk of chemicals implicitly relies on the strong assumption that intraspecific variation in sensitivity is negligible or irrelevant in this context. In this study, we investigated genetic variation in copper sensitivity of the freshwater snail Lymnaea stagnalis, using lineages stemming from eight natural populations or strains found to be genetically differentiated at neutral markers. Copper-induced mortality varied widely among populations, as did the estimated daily death rate and time to 50% mortality (LT50). Population genetic divergence in copper sensitivity was compared to neutral differentiation using the QST-FST approach. No evidence for homogenizing selection could be detected. This result demonstrates that species-level extrapolations from single population studies are highly unreliable. The study provides a simple example of how evolutionary principles could be incorporated into ecotoxicity testing in order to refine ecological risk assessment.

The impact of CYP2E1 genetic variability on risk assessment of VOC mixtures.

Humans are simultaneously exposed to multiple chemicals in the environment. Many of the chemicals use the same enzymes in their metabolic pathways. Competitive inhibition may occur as one of the possible interactions between the xenobiotics in human body. For example, many volatile organic compounds (VOCs) are metabolized using P450 enzymes, specifically CYP2E1. Inheritable gene alterations may result in changes of function of the enzymes in different human subpopulations. Variations in quantity and/or quality of particular isoenzymes may cause differences in the metabolism of VOCs. These variations may cause higher sensitivity in certain populations. Using examples of three different mixtures, this review paper outlines the variances in CYP2E1 isoenzymes, effect of exposure to such mixtures on sensitive populations, and approaches to mixtures risk assessment.

Compilation of a comprehensive gene panel for systematic assessment of genes that govern an individual's drug responses.

AIMS: Polymorphisms of genes involved in the pharmacokinetic and pharmacodynamic processes underlie the divergent drug responses among individuals. Despite some successes in identifying these polymorphisms, the candidate gene approach suffers from insufficient gene coverage whereas the genome-wide association approach is limited by less than ideal coverage of SNPs in some important genes. To expand the potential of the candidate approach, we aim to delineate a comprehensive network of drug-response genes for in-depth genetic studies. MATERIALS & METHODS: Pharmacologically important genes were extracted from various sources including literatures and web resources. These genes, along with their homologs and regulatory miRNAs, were organized based on their pharmacological functions and weighted by literature evidence and confidence levels. Their coverage was evaluated by analyzing three commercial SNP chips commonly used for genome-wide association studies: Affymetrix SNP array 6.0, Illumina HumanHap1M and Illumina Omni. RESULTS: A panel of drug-response genes was constructed, which contains 923 pharmacokinetic genes, 703 pharmacodynamic genes and 720 miRNAs. There are only 16.7% of these genes whose all known SNPs can be directly or indirectly (r(2) > 0.8) captured by the SNP chips with coverage of more than 80%. This is possibly because these SNPs chips have notably poor performance over rare SNPs and miRNA genes. CONCLUSION: We have compiled a panel of candidate genes that may be pharmacologically important. Using this knowledgebase, we are able to systematically evaluate genes and their variants that govern an individual's response to a given pharmaceutical therapy. This approach can serve as a necessary complement to genome-wide associations.

A multilevel approach to predict toxicity in copepod populations: assessment of growth, genetics, and population structure.

One of the goals of environmental risk assessment (ERA) is to understand effects of toxicant exposure on individual organisms and populations. We hypothesized that toxicant exposure can reduce genetic diversity and alter genotype composition, which may ultimately lead to a reduction in the average fitness of the exposed population. To test this hypothesis, we exposed a copepod, Nitocra psammophila, to a toxic reference compound and assayed resulting alterations in genetic structure, i.e. expected heterozygosity and percent polymorphic loci, as well as other population- and fitness-related measures, i.e. population abundance, demographic structure and juvenile growth. The copepods were exposed to 0.11-1.1 microg of the pentabromo-substituted diphenyl ether (BDE-47) mg(-1) freeze-dried algae for 24 days (i.e. >1 generation). There was no significant decline in total population abundance. However, there were significant alterations in population structure, manifested as diminished proportion of nauplii and increased proportion of copepodites. In addition, individual RNA content in copepodites decreased significantly in exposed individuals, indicating declined growth. Finally, in the exposed populations, heterozygosity was lower and genotype composition was altered compared to the controls. These results therefore confirm the hypothesized reduction in overall genetic variability resulting from toxicant exposure. Multilevel approaches, such as the one used in the present study, may help unravel subtle effects on the population level, thus increasing the predictive capacity of future ERA.

Physiological cost of tolerance to toxicants in the European flounder Platichthys flesus, along the French Atlantic Coast.

Physiological and genetic responses of flounder Platichthys flesus populations were investigated along the French Atlantic Coast in one moderately contaminated estuary (Ster) and three contaminated estuaries (Seine, Loire and Gironde). The focus of this study was to explore the relationship between stress resistance and energetic trade-offs, in order to detect possible differential physiological capacities or performances between individuals carrying particular alleles or genotypes (allozyme data) characterised as "tolerant" or "sensitive". A general reduction of the relative fecundity, the growth rate and the condition factor was highlighted in contaminated fish populations, suggesting that survival in such polluted systems implies energetic costs for fish thus reducing the energy available for particular functions. A lower observed heterozygosity was also detected in contaminated populations with respect to the Ster, suggesting a general decrease in genetic variability in response to chemical stress (with an exception for the Seine estuary). This study confirmed the previously detected relationship between PGM 85, AAT1 95 alleles and reduced DNA damage in contaminated fish [Marchand, J., Tanguy, A., Laroche, J., Quiniou, L., Moraga, D., 2003. Responses of European flounder Platichthys flesus populations to contamination in different estuaries along the Atlantic coast of France. Mar. Ecol. Prog. Ser. 260, 273-284] and furthermore suggested that, reduced fecundity and condition factor associated to the individuals carrying the previous alleles, were also reflecting the cost of resistance to stress in polluted populations. The cost of tolerance to stress as well as the high gene flow from neighbouring populations less exposed to contamination may explain the apparently moderate increase of the suspected "tolerant" alleles in contaminated flounder populations.

Genetic effects of contaminant exposure--towards an assessment of impacts on animal populations.

This review aims both to identify the potential risks to animal populations as a consequence of exposure to genotoxins and to identify the techniques most useful in assessing these risks. These evaluations are complicated by the fact that contaminant exposure acts both to restructure naturally occurring genetic diversity and, when contaminants have mutagenic activity, to enhance the rate of introduction of new variation. There is now evidence that contaminant exposure often leads to change in the genetic attributes of natural populations. Short-lived organisms often develop resistance to contaminants, with only modest impacts on diversity in the balance of the genome, although massive mortality occurs during the gene replacement. Resistance is, however, less likely to evolve in species with small population size, such as many wildlife species. Such species will experience population declines or extinction as the impact of contaminants on physiological systems is not counteracted by gene replacements. Even when adaptation to exposure occurs, populations may suffer diminished fitness as a consequence of the mutagenic effects of contaminants. The expression of these effects range from an increase in the incidence of developmental abnormalities to shifts in chromosomal and gene structure. The assessment of this broad range of impacts can only be accomplished with a spectrum of analytical approaches. However, recent advances in molecular and developmental genetics are now making possible the detailed assessment of these mutagenic impacts in natural populations.

Effect of dietary aflatoxin concentration on the assessment of genetic variability of response in a randombred population of chickens.

The effect of graded levels of dietary aflatoxin on the assessment of genetic variability of body weight and gain and plasma protein response was tested utilizing the Athens-Canadian randombred population of chickens. Dietary aflatoxin was administered at levels of either 0, 1.25, 2.50 or 5.0 microg/g of diet ad libitum from 7 to 21 days of age to progeny from 58 sire families. Twenty-one-day body weights, gain and plasma protein concentration were used to assess the variation in response.-The administration of increasing levels of aflatoxin resulted in a dose-related decrease of gains and plasma protein concentrations. Plasma protein concentrations were significantly higher among males than females within the control group; however, this difference was reversed as the severity of the aflatoxin challenge increased. Heritability estimates for all responses increased as the level of aflatoxin administered increased. This change was most notable for total plasma protein concentration. Phenotypic correlations for plasma protein concentration and growth measurements tended to diminish with increasing levels of aflatoxin. A similar trend was noted for the genetic correlations; however, a moderate correlation between growth responses and plasma protein response was detected in the 5.0-microg/g aflatoxin treatment group. Genetic correlations were calculated for the same characters between the different levels of aflatoxin. Regardless of which aflatoxin challenges were compared, a very high genetic correlation for 21-day body weight and 7- to 21-day gain was estimated. This variation in growth potential in the toxic environment paralleled that observed in the control environment but at a lower plane. Genetic correlations for plasma protein response across aflatoxin levels diminished as the difference between the levels of aflatoxin administered increased. Plasma protein concentration in the control environment was positively correlated with plasma protein response in groups fed a low level of aflatoxin, but negatively correlated when an aflatoxin challenge of 2.5 microg/g or more was given, suggesting that selection for aflatoxin resistance using plasma protein response as a selection criterion should be made under an aflatoxin stress environment.