Multi-omics systems toxicology study of mouse lung assessing the effects of aerosols from two heat-not-burn tobacco products and cigarette smoke.

•Multi-omics systems toxicology study, comprising five omics data modalities.•Multi-Omics Factor Analysis and multi-modality functional network interpretation.•Cigarettes smoke (CS) induced complex immunoregulatory interactions across molecular layers.•Aerosols from two heat-not-burn tobacco products had less impact on lungs than CS.