Mutational RNA signatures in environmentally-induced lung adenocarcinoma

Abstract

Introduction: Lung adenocarcinoma (LUAD) is the most frequent lung cancer in non-smokers. Although carcinogens other than smoking (i.e., radiation) likely cause LUAD, their molecular imprints are obscure. Objectives: To define the molecular imprints of smoking, its carcinogens, and radiation in LUAD RNA. Materials and Methods: FVB mice were exposed to tobacco smoke (500 mg/m3; 2 hrs/day; 5 months on/5 months off), its chemicals ethyl carbamate (1 g/Kg), diethylnitrosamine (20 mg/Kg), and methylnitrosourea (50 mg/Kg), or X-irradiation (15 Gy X-rays delivered to a 100 mm3 tissue voxel of the right upper lobe). Total lung tumor RNA was extracted using Trizol/RNAeasy, was analyzed on an Illumina HiSeq4000, and was interrogated employing STAR, DeSeqR, Pathvisio, GSEA, Samtools, SnpEff, and R*. Results: FVB mice developed LUAD in response to the carcinogens used. RNAseq of tumor tissues provided robust transcript abundance and sequence information, including single nucleotide variation at the mononucleotide, trinucleotide, gene, and chromosome levels, as well as insertions and deletions. The five different carcinogens produced markedly distinct mutational imprints on the exposed tissues. Interestingly, the signatures of smoking and its carcinogens were highly similar, contained KRAS and other point mutations, and were enriched in human KRAS-mutant LUAD, while the signatures of irradiated tissues displayed EGFR point mutations, a preponderance of transversions, and a distinct gene expression set. Conclusions: Bulk RNAseq of environmentally-induced mouse tumors can reveal carcinogenic exposures and causes. We are currently working to identify cellular origin-restricted signatures and to translate murine imprints to human LUAD.