Abstract 3411: Biological subtypes of nasopharyngeal carcinoma by genomic profiling
Authors: Kai Xun Joshua Tay, Chunfang Zhu, Sujay Vennam, Sushama Varma, Quynh-Thu Le, John Sunwoo, Robert West
Journal: Cancer Research (2018)

Abstract Objective: Nasopharyngeal carcinoma (NPC) is a common Epstein-barr virus-associated epithelial malignancy in several parts of the world including Southeast Asia. While the majority of patients are treated uniformly with a combination of chemo and radiation therapy, 20% of patients experience recurrence, most commonly in the form of distant metastasis. NPC subtypes based on underlying differences in biology are unexplored and are likely responsible for the heterogeneous clinical response. As NPC biopsies are small and have significant stromal infiltrate, obtaining pure epithelial cells for genomic profiling is a challenge. We aim to overcome these limitations to identify biological subtypes and dysregulated molecular pathways in NPC. Methods: We first evaluated 217 whole exomes sequences, including 102 microdissected tumors, from three previous studies for single nucleotide variants and copy number changes, following GATK standards and using next generation sequencing copy number callers. We then applied a novel method for gene expression profiling developed in our lab to a new cohort of EBV-positive primary NPC cases from our institution. We performed laser capture microdissection, separately dissecting tumor, normal and microenvironment for each case. We applied Smart-3SEQ, a novel 3' end RNA-Seq technique which allows for the accurate quantification of transcript abundance in dissected FFPE samples comprising only a few hundred cells. Results: We achieved a per-base concordance of 80.4% between copy number profiles by SNP array and whole exome sequencing. Unsupervised clustering identified three distinct copy-number groups of NPC tumors, with a low copy-number group demonstrating an 18.7% better 5-year disease-specific survival, not attributable to stage. Apart from broad cytogenetic changes, narrow regions of amplifications (e.g. 1q21, 11q13) and deletions (e.g. 9p21, 11q22) were important for defining copy-number subtypes. Preliminary differential gene expression analysis showed that genes involved in cell cycle and cellular differentiation were significantly dysregulated in tumor cells (p &amp;lt; 0.001 and p = 0.03 respectively), while genes involved in cilia assembly and flagella transport were upregulated in normal cells (p &amp;lt; 0.001 for both). Our further analysis includes defining tumor subtypes based on gene expression, identifying key driver pathways, and correlating with EBV-latent gene expression, the immune environment, as well as clinical outcome. Conclusion: NPC tumors are biologically heterogeneous and can be classified based on their mutational and gene expression profiles. This provides an important basis for the consideration of escalation and de-escalation of therapy in selected patient groups. Citation Format: Kai Xun Joshua Tay, Chunfang Zhu, Sujay Vennam, Sushama Varma, Quynh-Thu Le, John Sunwoo, Robert West. Biological subtypes of nasopharyngeal carcinoma by genomic profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3411.