Integrative assessment of apical and molecular respiratory exposure effects in an 18-month systems toxicology study with A/J mice Smoking cessation is the most effective measure for reducing the risk of smoking-related diseases. However, switching to less harmful products (modified risk tobacco products [MRTP]) can be an alternative to help reduce such risk for adult smokers who would otherwise continue to smoke. Standard toxicology endpoints for toxicological assessment of aerosols from less harmful products and cigarette smoke (CS) can lack sensitivity, and systems toxicology can yield deeper insights into toxicological mechanisms. In an 18-month chronic carcinogenicity/toxicity study in A/J mice (OECD Test Guideline 453), we assessed the aerosol of Tobacco Heating System 2.2 (THS 2.2), a candidate MRTP based on the heat-not-burn principle, in comparison with 3R4F CS. To capture toxicity- and disease-relevant mechanisms, we complemented standard toxicology endpoints with multiomics systems toxicology analyses, including proteomics and mRNA/miRNA transcriptomics analyses. Here, we report the integrative assessment of the apical and molecular exposure effects on the respiratory tract (nose, larynx, and lungs). Compared with 3R4F CS, THS 2.2 aerosol exerted far fewer effects on respiratory tract histology, including adaptive tissue changes in nasal and laryngeal epithelia and inflammation and emphysematous changes in the lungs. Omics analyses revealed inflammatory responses following 3R4F CS exposure (e.g., antimicrobial peptide response in the nose) and both shared and distinct oxidative and xenobiotic responses upon 3R4F CS exposure across the respiratory tract. Integrative computational analyses confirmed the substantially lower impact of THS 2.2 aerosol than 3R4F CS on toxicologically and disease-relevant molecular processes such as inflammation, oxidative stress responses, and xenobiotic metabolism. Overall, this work exemplifies how apical and molecular endpoints, including proteomics endpoints, can be combined effectively for toxicological assessment and further supports the findings on the reduced respiratory risks of THS 2.2 aerosol. Reference: Titz et al. Respiratory effects of exposure to aerosol from the candidate modified-risk tobacco product THS 2.2 in an 18-month systems toxicology study with A/J mice. Toxicological Sciences. accepted.