In vitro to in vivo extrapolation modeling to facilitate the integration of transcriptomics data into genotoxicity assessment

Abstract

In vitro transcriptomics holds promise for high-throughput, human-relevant data but is not yet integrated into regulatory decision-making due to the lack of standardized approaches. For genotoxicity assessment, transcriptomic biomarkers such as GENOMARK and TGx-DDI facilitate qualitative and quantitative analysis of complex in vitro transcriptomic datasets. However, advancing their use in quantitative testing requires standardized methods for deriving transcriptomic Points of Departure (tPoDs) and linking them to in vivo responses. Herein, we investigated different approaches to calculate tPoDs and applied in vitro to in vivo extrapolation to obtain administered equivalent doses (AEDs). Human HepaRG cells were exposed for 72 h to 10 known in vivo genotoxicants (glycidol, methyl methanesulfonate, nitrosodimethylamine, 4-nitroquinoline-N-oxide, aflatoxin B1, colchicine, cyclophosphamide, mitomycin C, ethyl methanesulfonate, and N-Nitroso-N-ethylurea) from the highest concentration that induces up to 50 % cytotoxicity through a range of lower concentrations. Gene expression data was generated using a customized version of the TempO-Seq® human S1500 + gene panel. The GENOMARK and TGx-DDI biomarkers produced genotoxic calls for all of these reference genotoxicants. Next, we performed benchmark concentration (BMC) modeling to generate both genotoxicity-specific biomarker (tPoD_biomarkers) and generic tPoDs (tPoD _S1500+). High-throughput toxicokinetic models estimated the human AEDs for these tPoDs, which were compared with (a) previously reported genotoxicity-specific AEDs from other New Approach Methodologies, and (b) in vivo PoDs from animal studies. We found that the generic AEDs were more conservative than genotoxicity-specific biomarker AEDs. For six of the nine genotoxicants, transcriptomic AEDs were lower than the in vivo PoDs; refined kinetic models may improve predictions. Overall, in vitro transcriptomic data in HepaRG cells provide protective estimates of in vivo genotoxic concentrations, consistent with other in vitro genotoxicity testing systems.