Abstract 4804: High throughput whole exome DNA and transcriptome RNA sequencing to identify genetic drivers and alterations in HPV-negative and HPV-positive HNSCC cell lines
Authors: Cheng Hui , Yang Xinping , Si Han , Saleh Anthony , Coupar Jamie , Ferris Robert L. , Yarbrough Wendell G. , Prince Mark E. , Carey Thomas E. , Van Waes Carter , Chen Zhong 
Published: August 2015

Head and neck squamous cell carcinoma (HNSCC) is among the top cancer types with high frequencies of genetic alterations, including mutation and copy number variation (CNV). The Cancer Genome Atlas (TCGA) has profiled over 279 HNSCC tumors and generated a comprehensive genomic characterization of HNSCC. This has led to an urgent need for a panel of head and neck cell line models with genomic alterations representative of those found by TCGA. We performed whole exome DNA sequencing (exome DNA-seq) and transcriptome RNA sequencing (RNA-seq) on 15 HPV negative and 11 HPV positive HNSCC lines, which were compared with three normal human oral mucosa lines and 8 matched blood samples. Exome DNA- and RNA-seq were performed on the ABI SOLiD platform with an average depth of 87X and 44X respectively. Using an in-house analysis pipeline, we determined the CNVs and single nucleotide variants (SNV) obtained from DNA-seq to be able to compare with the genomic alterations found in TCGA, and also to cross-validate these with the SNVs identified in our RNA-seq. We identified chromosome losses in 3p, 5q, 8p, 9p and 18q and gains in 3q, 7p and 11q in a significant portion of cell lines with software CONTRA (COpy Number Targeted Resequencing Analysis), which are consistent with previous karyotype and TCGA CNV studies. Integrative analysis between CNV by exome-seq and gene expression by RNA-seq of these cell lines revealed a significant positive correlation in multiple oncogenes including PIK3CA, TP63, CCND1, FADD, BIRC2 and YAP1, which is in concordance with TCGA results. We established a workflow to determine deleterious mutations and somatic mutations using software ANNOVAR, in combination with functional prediction tool Mutation Assessor, and Sanger Institute's somatic mutation database, COSMIC, in order to characterize legacy and newer HNSCC lines without and with matched samples. We identified a median of 1588 potentially deleterious and/or somatic mutations for each cell line. The most recurrently mutated genes in TCGA with a functional impact are also frequently mutated in cell lines, including TP53, FAT1 and NOTCH1, etc. Many of the genomic alterations identified converge on the networks we previously defined in HNSCC, including the PI3K/AKT/mTOR, NFκB, and RAS/MAPK pathways. Our findings suggest that these cell lines can serve as HNSCC models for mechanistic and therapeutic studies, and thereby provide a valuable resource for the wider biomedical research community.

Supported by NIDCD intramural projects ZIA-DC-000016, 73 and 74.

Citation Format: Hui Cheng, Xinping Yang, Han Si, Anthony Saleh, Jamie Coupar, Robert L. Ferris, Wendell G. Yarbrough, Mark E. Prince, Thomas E. Carey, Carter Van Waes, Zhong Chen. High throughput whole exome DNA and transcriptome RNA sequencing to identify genetic drivers and alterations in HPV-negative and HPV-positive HNSCC cell lines. [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 4804. doi:10.1158/1538-7445.AM2015-4804