Causal RNA signatures in lung adenocarcinoma

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 and human/murine airway epithelial cells 16HBE14ο and MLE12 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/mouse; 6 Gy/100-mm Petri). Total lung tumor and cellular 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 and exposed cells 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 (indels). The five different carcinogens produced markedly distinct and reproducible imprints on the exposed cells and tissues. Interestingly, the signatures of smoking and its carcinogens were highly similar and contained KRAS and other point mutations, while the signatures of irradiated tissues displayed a preponderance of indels and a distinct gene expression set. Conclusions: Bulk RNAseq of mutated cells and environmental-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.