Proteome integral solubility alteration assay combined with multi-criteria decision-making analysis for developing adverse outcome pathways

Abstract

Understanding the biological impact of chemicals is hindered by the high number and diversity of compounds in the market. To simplify the chemical risk assessment, the adverse outcome pathway (AOP) method has arisen as a framework to predict the impact of chemical exposure on human and environmental health. The development of this predictive tool requires knowledge of the molecular interaction between chemicals and protein targets. Those molecular initiating events connect alterations of cellular function with physiological impairment. This strategy aims to focus on the complex biological interaction to predict the impact on health. The high-throughput identification of all chemical targets can be obtained by a proteomics-based thermal shift assay, however, selecting the priority target candidate is a biased process strongly dependent on expert knowledge and literature. Here, we unravel new molecular initiating event from a tested chemical combining the target deconvolution by the proteome integral solubility alteration (PISA) assay, and the target selection by an analytical hierarchy process (AHP) approach. In the proof-of-concept study, we identified by PISA assay 8 protein targets for 2,3,7,8 tetrachlorodibenzo-p-dioxin (TCDD) from the soluble proteome from hepatic cells containing 2824 proteins. The definition of the AHP approach facilitates the selection of heat shock protein beta-1 (Hspb1) as the most suitable protein for developing AOPs. Our results demonstrated that the process of target identification is independent from a chemical characterization, and that the process of data curation and target selection is less sensitive to lack of toxicological information. We anticipate that this innovative integration of methods could decipher the chemical-protein interactions from new chemicals including the new alternative chemicals designed for chemical replacement and that would discover new molecular initiating events to support more sustainable methodologies to gain time and resources in chemicals assessment. SYNOPSISOur combined methodologies can determine the most suitable target to develop adverse outcome pathways from the proteome-wide protein target identification.