Transcriptional signatures of regulatory and toxic responses to benzo-[a]-pyrene exposure

Abstract

BackgroundSmall molecule ligands often have multiple effects on the transcriptional program of a cell: they trigger a receptor specific response and additional, indirect responses ("side effects"). Distinguishing those responses is important for understanding side effects of drugs and for elucidating molecular mechanisms of toxic chemicals.ResultsWe explored this problem by exposing cells to the environmental contaminant benzo-[a]-pyrene (B[a]P). B[a]P exposure activates the aryl hydrocarbon receptor (Ahr) and causes toxic stress resulting in transcriptional changes that are not regulated through Ahr. We sought to distinguish these two types of responses based on a time course of expression changes measured after B[a]P exposure. Using Random Forest machine learning we classified 81 primary Ahr responders and 1,308 genes regulated as side effects. Subsequent weighted clustering gave further insight into the connection between expression pattern, mode of regulation, and biological function. Finally, the accuracy of the predictions was supported through extensive experimental validation.ConclusionUsing a combination of machine learning followed by extensive experimental validation, we have further expanded the known catalog of genes regulated by the environmentally sensitive transcription factor Ahr. More broadly, this study presents a strategy for distinguishing receptor-dependent responses and side effects based on expression time courses.

Prospects and challenges of multi-omics data integration in toxicology

“…The murine hepatocyte data set was derived from two separately published data sets that used exactly the same experimental conditions: Omics data were generated from murine hepatocyte cell lines after 2h, 4h, 12h, and 24h of exposure to Benzo[a]pyrene (B[a]P) at two different concentrations ( 50nM∕5 M ). Transcriptome data were measured with Affymetrix GeneChips by Michaelson et al (2011). SILAC-based proteomics and targeted metabolomics data were conducted by Kalkhof et al (2015).…”

Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water

“…The AHR is the principal transcription factor governing the activation of most phase I and some phase II enzymes and has been studied extensively (Michaelson et al, 2011). Upon binding of BaP to the AHR, the BaP–AHR complex translocates to the nucleus of the cell, where it dimerizes with the AHR nuclear translocator protein.…”

Neurotoxicity may be an overlooked consequence of benzo[a]pyrene exposure that is relevant to human health risk assessment

“…The aryl hydrocarbon receptor (AHR) is one of the most wellcharacterised transcription factors, and is involved in mediating cellular responses to xenobiotic compounds [31]. Under normal conditions, AHR is located in the cytoplasm in complex with heat shock protein 90 (Hsp90) and other proteins (Fig.…”