Addressing systematic inconsistencies between in vitro and in vivo transcriptomic mode of action signatures

Because of their broad biological coverage and increasing affordability transcriptomic technologies have increased our ability to evaluate cellular response to chemical stressors, providing a potential means of evaluating chemical response while decreasing dependence on apical endpoints derived from traditional long-term animal studies. It has recently been suggested that dose-response modeling of transcriptomic data may be incorporated into risk assessment frameworks as a means of approximating chemical hazard. However, identification of mode of action from transcriptomics lacks a similar systematic framework. To this end, we developed a web-based interactive browser-MoAviz-that allows visualization of perturbed pathways. We populated this browser with expression data from a large public toxicogenomic database (TG-GATEs). We evaluated the extent to which gene expression changes from in-life exposures could be associated with mode of action by developing a novel similarity index-the Modified Jaccard Index (MJI)-that provides a quantitative description of genomic pathway similarity (rather than gene level comparison). While typical compound-compound similarity is low (median MJI = 0.026), clustering of the TG-GATES compounds identifies groups of similar chemistries. Some clusters aggregated compounds with known similar modes of action, including PPARa agonists (median MJI = 0.315) and NSAIDs (median MJI = 0.322). Analysis of paired in vitro (hepatocyte)-in vivo (liver) experiments revealed systematic patterns in the responses of model systems to chemical stress. Accounting for these model-specific, but chemical-independent, differences improved pathway concordance by 36% between in vivo and in vitro models.