Abstract 2523: Targeted exome sequencing profiles genetic alterations in oral squamous cell carcinoma from Japanese patients

Abstract

Abstract Somatic mutation analysis is a standard practice in the study of human cancers to identify mutations that cause therapeutic sensitization and resistance. We performed comprehensive genomic analyses that used PCR target enrichment and next-generation sequencing on Ion Torrent semiconductor sequencers. Forty-seven oral squamous cell cancer (OSCC) samples and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverage of the entire coding regions of 409 cancer-related genes (covered regions: 95.4% of total, 1.69 megabases of target sequence). The number of somatic mutations in 47 patients with OSCC ranged from 1 to 20 with a mean of 7.60. The most frequent mutations were in TP53 (61.7%), NOTCH1 (25.5%), CDKN2A (19.1%), SYNE1 (14.9%), PIK3CA (10.6%), ROS1 (10.6%), and TAF1L (10.6%). The majority of TP53 mutations (83.9%) are localized in the DNA binding domain of the protein (residues 100-300). Importantly, TP53 mutations tended to be more frequent in HPV-negative OSCCs compared to HPV-positive cases (p = 0.00026). We also detected copy number variations (CNVs) in the segments of the genome that could be duplicated or deleted from deep sequencing data. The genes most frequently affected were EGFR (gain in 38.3%) and CCND1 (gain in 34.0%), followed by PIK3CA (gain in 31.9%), RB1 (loss in 27.7%), ERBB2 (gain in 23.4%), MYC (gain in 23.4%), CCND2 (gain in 17.0%), MYCN (gain in 14.9%), ATM (loss in 14.9%), MDM2 (gain in 14.9%), CDKN2A (loss in 14.9%), NRAS (gain in 12.8%), HRAS (gain in 12.8%), BCL2L1 (gain in 12.8%), and KRAS (gain in 8.5%). We validated 100%, 100%, 83.3%, 83.3% and 100% of the OSCC tissues that showed CNV gain for CCND1, CCND2, HRAS, NRAS and KRAS respectively in quantitative PCR copy number analysis. Pathway assessment showed that the somatic aberrations within OSCC genomes are mainly involved in several important pathways, including cell cycle regulation and RTK-MAPK-PI3K. Univariate survival analysis revealed that mutations in NOTCH1 and PIK3CA were found to be associated with worse overall survival in OSCC patients (P = 0.0054 and P = 0.0162, respectively). Interestingly, RTK-MAPK-PI3K pathway alteration correlated to poor survival, suggesting that RTK-MAPK-PI3K pathway is potentially a therapeutic target in this disease. We detected the tumor-specific TP53 mutation in the plasma cell-free DNA from two OSCC patients, and after surgery, the test for these mutations became negative. This study may enable better selection of therapies and deliver improved outcomes for OSCC patients when combined with clinical diagnostics. Citation Format: Yasushi Sasaki, Takafumi Nakagaki, Kazuhiro Ogi, Masashi Idogawa, Takashi Tokino. Targeted exome sequencing profiles genetic alterations in oral squamous cell carcinoma from Japanese patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2523.