Improved methods for inference of genotype-specific response to environmental toxins

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PROJECT SUMMARY Why do some individuals appear to be more sensitive than others to environmental perturbation? The answer to this question has broad implications ranging from our ability to make predictions about disease risk from genotype, to our ability to identify the drivers of inter-individual variability. Here, we propose to study the broad question of how the interplay between genetic and environmental variation mediates disease risk following a toxic environmental exposure. Specifically, we will examine the consequences of environmental exposure to hexavalent chromium [Cr(VI)] a ubiquitous environmental pollutant. Cr(VI) is a potent carcinogen and its toxicity extends far beyond its genotoxic effects, including neurotoxicity, mitochondrial defects, immune aberrations, and reproductive defects, to list a few. Although Cr(VI) is a common environmental and major health hazard, we know little about how genetic variation drives differential susceptibility to its toxicity, or the molecular pathways involved. Exploring the contribution of genotype-by- environment interactions to individual variation has been very challenging in humans. To address this problem we created a new community resource to study the genetic basis of complex trait variation in Drosophila melanogaster made of large, synthetic outbred populations. With this new and versatile community resource, we can rear thousands of genetically unique flies drawn from a common genetic pool, expose them to a range of different environments [here, Cr(VI)], and contrast the ensuing genetic architectures. We have simultaneously developed a new high throughput protocols to sequence the DNA and assay the transcriptome of thousands of flies at very low cost allowing for advance systems genetics analysis. Using this platform, in aim 1, we will phenotype thousands of individual flies for a variety of traits know to be impacted by Cr(VI) exposure. This combination of design improvements and technological advances produces a large boost in both statistical power and genetic resolution. It allows us to ask if the shift in sensitivity some individuals experience under environmental stress can be explained by the release of genetic susceptibility through of GxE. In aims 2, we will use a systems genetic approach study variation in sensitivity from the perspective of the regulatory systems disruption. Individuals more sensitive to environmental stress appear to have decreased transcriptional robustness for many genes. This variation in robustness appears to be under genetic control and we have developed an analytical framework to identify such context-dependent transcriptional networks and their genetic regulators. Finally, in aim 3, we examine how environmentally sensitive alleles are background-dependent, and what genetic factors modulate their penetrance? We will use CRISPR/Cas9 to knock-out and knock-in alleles into targeted genes identified in aim 1 and will crossed these transgenic lines to the synthetic flies from aim 1 and the F1 progeny will be genotyped and phenotyped for Cr(VI) responses to identify modifiers.