Abstract 4806: Characterizing the genomic landscape of premalignant colorectal polyps using next-generation sequencing

Abstract

Abstract Adenomatous polyps are the premalignant lesions that precede the development of colorectal cancers (CRC). The normal mucosa-adenoma-carcinoma sequence was originally described more than 2 decades ago; however, no comprehensive annotation of the genomic landscape of polyps has been reported to date. Familial Adenomatous Polyposis (FAP) is a mendelian disorder caused by germline mutations in the APC gene, has an autosomal dominant pattern of inheritance and is characterized by the development of adenomas in the entire intestine, thus conferring patients with a life-time risk for CRC development of 100%. Patients diagnosed with hereditary polyposis syndromes such as FAP represents the perfect model to acquire tissue samples from polyps, at-risk normal mucosa and germline allowing this type of high-throughput studies. We have performed whole exome sequencing in paired polyps and germline blood samples of 12 individuals with FAP (25 polyps and 12 blood samples) using the Illumina HiSeq 2000 platform. Using standard bioinformatics pipelines, we have identified a total of 1064 functional mutations (somatic mutations and indels) that we have classified using a 5-tier system based on functional predictions generated by several in silico tools. We have used hapLOH to ascertain for genomic imbalances from exome data and identified 26 events. Validation was performed using Sanger sequencing in a set of the identified events confirming 90% of the somatic mutations and 50% of the indels. Allelic imbalances in 5q were partially confirmed using microsatellite analysis. APC, KRAS, FBXW7, TCFL2 and ARID1A were among the 16 genes found to be recurrently mutated. Pathway enrichment analysis of the mutated gene list revealed deregulation of the Wnt, MAPK kinase and ERBB pathways, thus indicating potential avenues for chemoprevention drug development. Moreover, we assessed and compared the genomic characteristics such as the rate of transitions/transversion, mutational rate [mutations/Megabase (Mb)] and genomic imbalances with stage I CRC from the The Cancer Genome Atlas in order to understand better the carcinogenic process in the colonic epithelium at the genomic level. The signature profile of transition/transversions displayed by polyps showed abundance of C>T (followed by T>C changes) and was very similar to stage I non-hypermutator CRCs. In contrast, the mutational rate was lower in polyps (1.75 vs 3.95 mutations/Mb) and the pattern of genomic imbalances shared some events with stage I CRCs (loss of 5q and events in chromosome 7) but there were notable events seen only in the stage I CRCs most likely involved with further steps in the carcinogenesis process (loss of 18q and 17p). In conclusion, genomic assessment of premalignant colonic polyps revealed mutational patterns that are similar to stage I CRC and pointed to deregulated pathways that are potential candidates for biomarker and chemoprevention drug development. Citation Format: Ester Borras, Anthony San Lucas, Kyle Chang, Gita Bhatia, Hong Wu, Jerry Fowler, Y. Nancy You, Patrick M. Lynch, Melissa W. Taggart, Ernest T. Hawk, Gabriel Capella, Paul Scheet, Eduardo Vilar. Characterizing the genomic landscape of premalignant colorectal polyps using next-generation sequencing. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4806. doi:10.1158/1538-7445.AM2015-4806