High-resolution mutational landscape of the primed colon in early onset colorectal cancer

This application is being submitted in response to the Notice of Special Interest (NOSI) identified as NOT-CA23-045. This administrative supplement expands the research proposed in the parent U54 grant, which is dedicated to investigating how a ‘primed’ colon (histologically normal but molecularly altered) drives adenoma progression and what features of the primed colon could serve as colorectal cancer (CRC) risk biomarkers. Here we extend this goal to the study of the primed colon in patients with early onset CRC (eoCRC), which is defined as CRC that develops in individuals younger than age 50. The incidence of eoCRC has nearly doubled in the last 3 decades for unknown reasons. Consistent with the hypotheses of the parent R01, in this project we hypothesize that eoCRC is associated with a ‘primed’ colon that carries 1) expanded clones with mutations in cancer driver genes, and 2) mutational signatures that reflect underlying mutagenic processes that predispose to cancer development and progression. This hypothesis is based on strong preliminary results generated by our lab and published last year, which showed oncogenic mutations in TP53 and occasionally KRAS in the normal colon of patients with CRC. These mutations were present at a very low frequency but could be identified thanks to high resolution of duplex sequencing, an ultra-accurate sequencing method that enables ultra-deep (>1,000x) sequencing. In this project we will expand our capture panel to include the 7 most common CRC driver genes as well as a mutagenesis panel that includes 48Kb of non-coding genomic areas, which are ideal for mutational signature assessment. Mutational signatures capture the mutational footprint of DNA mutagens and have emerged as a valuable tool to determine the contribution of lifestyle, environmental, and genetic factors to the mutation burden of a given sample. We propose a case-control study including 40 individuals with CRC (20 with eoCRC and 20 with late onset CRC) and 40 age-matched controls. We will analyze normal colon at least 10cm away from CRC and will use ultra-deep duplex sequencing (~5000x) and novel computational tools for mutational assessment to achieve two Specific Aims. Aim 1: To determine the burden of cancer driver mutations in the normal colon of individuals with eoCRC. Aim 2: To determine normal colon mutational signatures associated with eoCRC. This research will pioneer the creation of the first high-resolution mutational landscape of primed colon in early onset colorectal cancer and provide insight into the etiology of eoCRC. In addition, our efforts will produce much needed data to understand colorectal carcinogenesis in young adults and to develop CRC risk biomarkers based on the analysis of normal colon biopsies.