Abstract 3435: Genome-wide RNA and DNA high throughput sequencing reveals proinflammatory and death gene signatures in head and neck squamous cell carcinoma lines with different HPV status
Authors: Yang Xinping , Cheng Hui , Si Han , Saleh Anthony , Maiorov Emine Guven , Coupar Jamie , Keskin Ozlem , Gursoy Attila , Nussinov Ruth , Ferris Robert L. , Yarbrough Wendell G. , Prince Mark E. , Carey Thomas E. , Waes Carter Van , Chen Zhong 
Published: May 2015

Abstract
Our laboratory previously discovered that aberrant NF-κB signaling and activation plays a critical role in promoting the oncogenic progression of head and neck squamous cell carcinoma (HNSCC). The Cancer Genome Atlas (TCGA) project, which investigated 279 HNSCC tissue specimens, uncovered significant genomic alterations of key molecules involved in NF-κB and death signaling, including amplification of FADD and BIRC2/3, mutation of caspase-8, and altered RIPKs in HPV(-), or deletion of TRAF3 in HPV(+) HNSCC tissues. Using PRISM (Protein Interactions by Structural Matching), we modeled protein-protein interaction complexes three dimensionally and identified ∼30 proteins that potentially interact with these genetically altered molecules involved in NF-κB and death pathways. Among more than 20 major cancer types that TCGA project has investigated, we found that HNSCC ranks among the top cancers harboring alterations of these genes, which are present in more than 70% of HNSCC tumors. To further investigate and identify models for functional studies of these genetic and phenotypic alterations, we performed whole transcriptome (RNA-seq) and genome-wide exome DNA sequencing (exome DNA-seq) in 16 HPV(-) and 8 HPV(+) HNSCC lines, and compared them with three normal human oral mucosa lines and 8 matched blood samples. RNA-seq or exome DNA-seq was performed using total RNA depleted of rRNA, or exome captured genomic DNA. The samples were multiplexed, amplified, and sequenced with ABI SOLiD sequencer. Quality control of the output data was performed using FastQC, and the reads were mapped to the human reference genome (Hg19). The data were further analyzed with LifeScope2.5 and an in-house developed computation program of publicly available software and R package. RNA-seq had an average of 168 million mapped reads per sample with an estimate mean read depth of ∼44X coverage, and exome DNA-seq had an average of ∼87X coverage in each cell line sequenced. We identified amplifications, overexpression and mutations among the molecules involved in the NF-κB and death pathways in HPV positive or negative cell lines, which mimic the genetic and phenotypic defects identified in the HNSCC TCGA project. Our data are consistent with the finding from the TCGA project, and support the conclusion that genetic and expression alterations of the molecules involved in NF-κB and the death pathways are the important events leading HNSCC oncogenesis. Molecular mechanisms and targeted therapies can be further investigated in these HNSCC lines having the defined genetic and phenotypic defects associated with different HPV status.
Supported by NIDCD intramural projects ZIA-DC-000016, 73 and 74.
Citation Format: Xinping Yang, Hui Cheng, Han Si, Anthony Saleh, Emine Guven Maiorov, Jamie Coupar, Ozlem Keskin, Attila Gursoy, Ruth Nussinov, Robert L. Ferris, Wendell G. Yarbrough, Mark E. Prince, Thomas E. Carey, Carter Van Waes, Zhong Chen. Genome-wide RNA and DNA high throughput sequencing reveals proinflammatory and death gene signatures in head and neck squamous cell carcinoma lines with different HPV status. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3435. doi:10.1158/1538-7445.AM2014-3435