Application of Benchmark Dose Analysis to in vitro Genotoxicity Data for Compound Risk Characterisation

Abstract

Genotoxic risk from exposure to pharmaceutical compounds has historically been focussed on dichotomous hazard characterisation, with little regulatory acceptance of risk assessment paradigms. The regulations focus on testing novel compounds with outdated genotoxicity test systems. Recent overwhelming support of the Benchmark Dose (BMD) methodology provides the baseline for advanced exposure risk assessments. Novel flow cytometric in vitro DNA damage response assays (MultiFlow and ToxTracker) have been developed that provide quantitative dose-response information that can be used in a high-throughput screening environment. In the following work, BMD modelling is applied to the MultiFlow and ToxTracker biomarker dose-response datasets. This work demonstrates that the MultiFlow dose-response biomarker datasets are amenable to BMD analysis for a set of clastogens and aneugens, and that the biomarker dose-responses correlate with dose-responses from the gold-standard in vitro micronucleus assay. A detailed appraisal of BMD confidence intervals (CIs) is provided for a selection of 10 clastogens requiring metabolic activation (with S9), demonstrating the criticality of using BMD uncertainty measures in comparative potency analysis. A comparative potency algorithm is developed and utilised in machine learning to distinguish four S9-dependent groupings: high and low-level potentiation, no effect, and diminution. A deep dive case study is presented for MultiFlow and ToxTracker analysis of Topoisomerase II Poisons, where BMD CI potency ranks are shown to correlate broadly with compound structural information. The Adverse Outcome Pathway (AOP) for Topoisomerase-II Poisoning is developed upon, and the Lhasa Derek Nexus alerts are mapped to the AOP. A Quantitative Structural Activity Relationship model is developed using Topoisomerase-II Poison molecular descriptors and BMD measurements from MultiFlow and ToxTracker biomarkers that correspond to Key Events relative to the Topoisomerase-II Poison AOP. This thesis provides an all-encompassing report of in vitro DNA damage response biomarker BMD analysis for compound potency ranking and read across.