Establishing RAS mutation tropism

The overall goal of the project is to decipher mechanisms shaping mutational bias of Kras gene in a chemical carcinogenesis mouse model. The method is to examine the type of Kras mutations recovered in urethane-induced lung tumors from mice of different genetic backgrounds. Specifically, two groups of mice are used. The first group of mice was used to study the role of tumor suppressor p53 in shaping mutational bias by selecting against excessive oncogenic signaling and was composed of B6/129 mixed strain SftpcCreER/CreER, Trp53flox/flox mice that are either native, Krasex3op (a codon optimized Kras allele) heterozygous or Krasex3op homozygous. The second group of mice are pure 129 strain and are either native and Krasex3op homozygous. Three types of sequencing data were obtained. The first type is from Kras cDNA sequencing of urethane-induced lung tumors derived from the first group of mice. This data was used to determine Kras mutations in lung tumors from mice of different genetic backgrounds. The second type is from Maximum Depth Sequencing, an error-corrected next generation sequencing assay, of Kras exon 1 and exon 2 in the genomic DNA extracted from normal mouse lung tissues from some of the first group, as well as the second group of mice, treated with either urethane or PBS vehicle. This data was used to determine Kras mutational spectrum shortly after carcinogen exposure and evaluate the specificity of the mutagenesis process prior to clonal expansion. The third type is from whole exome sequencing of urethane-induced lung tumors from a subset of the first group of mice. This data was used to determine mutations in other cancer genes as well as the overall mutation spectrum of the tumor.