O1-18-3 - Exome Sequencing and Snp Array Reveal Epigenome Modifier Defects in Nasopharyngeal Carcinoma

Abstract

Background: Nasopharyngeal carcinoma (NPC) is a type of head and neck carcinoma that develops from the lateral wall of the nasopharynx. It has a specific high incidence in south china, Hong Kong and Singapore with a poorly understood molecular basis.Methods: Whole exome sequencing(WES) and genome-wide SCNV was performed on 56 matched tumor and germline DNA to identify somatic mutations and copy number variations in NPC patients.Functional experiments were performed including knocking down and overexpression of candidate gene in NPC cells, western blots, Soft Agar colony assay, mice tumor exnograft and short time drug treatment proliferation assay.Results: A total of 1,577 nonsilent somatic mutations were discovered by WES and validated by Sanger sequencing. SCNV analysis identified recurrent copy number changes affecting P16, ARID1A and other known cancer genes. Epigenome modification proteins were observed to be frequently mutated in NPC (75%). Patients with epigenome defect showed an increase in mutation burden as well as poor overall survival.Among these mutated epigenome modifiers, ARID1A showed the most frequent alterations (19.6%). Depletion of ARID1A in NPC cells with shRNA led to a significant increase in migration, colony formation and in vivo tumor exnograft growth. On the other hand, overexpression of ARID1A showed opposite biological effect.The observations that epigenome modifiers frequently mutated in NPC suggested that HDAC inhibitors might be a novel therapeutic solution for NPC. Three inhibitors (SAHA panobinostat and belinostat) all showed potent anti-tumor effects on NPC cell lines as determined by MTT assays.Conclusions: By next generation sequencing and SNP arrays, we identified common alterations affecting epigenome modifiers in NPC and that the chromatin remodeling protein ARID1A as a novel tumor suppressor in NPC. In addition, our pre-clinical results suggested that HDAC inhibitors might be a candidate therapeutic agent for NPC treatment.