Multi-omics approaches confirm metal ions mediate the main toxicological pathways of metal-bearing nanoparticles in lung epithelial A549 cellsElectronic supplementary information (ESI) available: ESI 1: cytotoxicity of tested particles to A549 cells. ESI 2: dissolution of NPs and MPs in cell culture medium using ICP-OES. ESI 3: methods. ESI 4: univariate analyses of omics data. ESI 5: PCA scores plots of omics data. ESI 6: IMPaLA pathway analysis of omics data. ESI 7: candidate nano-specific mol

The toxicity of silver (Ag) and zinc oxide (ZnO) nanoparticles (NPs) has been associated with their dissolution or ability to release metal ions while the toxicity of cerium dioxide (CeO 2 ) NPs has been related to their ability to induce or reduce oxidative stress dependent on their surface redox state. To examine the underlying biochemical mechanisms, multiple omics technologies were applied to characterise the responses at the molecular level in cells exposed to various metal-based particles and their corresponding metal ions. Human lung epithelial carcinoma cells (A549) were exposed to various Ag, ZnO, and CeO 2 NPs, Ag and ZnO micro-sized particles (MPs), Ag ions (Ag + ) and zinc ions (Zn 2+ ) over a 24 h time course. Molecular responses at exposure levels that caused ∼20% cytotoxicity were characterised by direct infusion mass spectrometry lipidomics and polar metabolomics and by RNAseq transcriptomics. All Ag, Zn and ZnO exposures resulted in significant metabolic and transcriptional responses and the great majority of these molecular changes were common to both ionic and NP exposures and characteristic of metal ion exposure. The low toxicity CeO 2 NPs elicited few molecular changes, showing slight evidence of oxidative stress for only one of the four CeO 2 NPs tested. The multiple omics analyses highlight the main pathways implicated in metal ion-mediated effects. These results can be used to establish adverse outcome pathways as well as strategies to group nanomaterials for risk assessment. Our analyses confirm that the dissolution of metal ions mediates the main toxicological pathways of silver and zinc oxide nanoparticles.