Abstract 1137: Deep targeted and whole exome sequencing identifies driver mutations in the airway epithelium of individuals at high risk for lung cancer
Authors: Rahman SM Jamshedur , Chu Shih-kai , Zhao Shilin , Zou Yong , Hui Angela , Stricker Thomas , Diehn Maximilian , Massion Pierre P. 
Published: September 2020

Abstract
Insights into tumor mutational burden of the airway epithelium may play important role in stratifying individuals at different levels of risk for lung cancer. Comparison of the genetic profiles of normal airway epithelial cells to tumor mutations can yield valuable information regarding shared mutations as well as presence of neoantigens. We hypothesized that cytologically normal bronchial epithelium of patients with lung cancer and those at high risk for lung cancer harbor driver mutations that can be identified by deep targeted sequencing of selected genes implicated in cancer and whole exome sequencing. We performed next generation sequence-based CAPP-Seq (CAncer Personalized Profiling by deep Sequencing) and whole exome sequencing (WES) of DNA from the bronchial epithelial cells from the bronchial brushings of individuals at-risk (low and high) for lung cancer and patients with lung cancer. Bronchial brushings were collected from consented individuals at the time of bronchoscopy at Vanderbilt University Medical Center and the Nashville Veterans Affairs Medical Center. We used Tammemagi risk model to calculate the risk of developing lung cancer. Lung tumor tissues from matched individuals were also sequenced. Using CAPPSeq, a total of 129 mutations were identified in bronchial brushings. Among individuals without cancer, driver mutations included TP53, PIK3CA, NOTCH1, KRAS, MET, CUL3, NF1, KEAP1 and EGFR mutations in 5 out of 13 high risk and 2 out of 7 low risk individuals. Among individuals with cancer, 13 out of 22 brushings harbored driver mutations in TP53, PIK3CA, ARID1A, PTEN, NOTCH1, KRAS, MET, NFE2L2, CUL3, NF1, and KEAP1 of which mutations in TP53 and PTEN were identified in both tumor and bronchial brushings. At least one mutation was called in 18 brushings of individuals with lung cancer. Mutations detected in both individuals with and without cancer were TP53, PIK3CA, NOTCH1, KRAS, MET, CUL3, and NF1. Using WES on the DNA from the same bronchial brushings (low risk-9; high risk-8 and lung cancer-17), we identified 90 mutations that were also identified by CAPPSeq. Most of the mutations identified by CAPPSeq with &gt;5% variant allelic frequencies (VAF) were also identified by WES. However, WES was not sensitive enough to identify mutations with less than 0.5% VAF. Out of 9 mutations in TP53 identified in the brushings by CAPPSeq, 4 were identified by WES. Mutation in KMTD2, a histone methylation enzyme and believed to be a tumor suppressor, was identified by WES in the brushings and the tumor tissues of patients with lung cancer as well as in one high risk brushings. We identified mutations in cancer driver genes in the bronchial brushings of individuals with and without lung cancer. This field of cancerization effect may provide a tool for risk assessment for lung cancer. This research was funded by U01CA196405 to PPM.
Citation Format: SM Jamshedur Rahman, Shih-kai Chu, Shilin Zhao, Yong Zou, Angela Hui, Thomas Stricker, Maximilian Diehn, Pierre P. Massion. Deep targeted and whole exome sequencing identifies driver mutations in the airway epithelium of individuals at high risk for lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1137.