Whole-exome sequencing reveals novel mutations and epigenetic regulation in hypopharyngeal carcinoma
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Ping Wu1, Honglong Wu2,3,4, Yaoyun Tang1, Shi Luo1, Xing Fang1, Chubo Xie1, Jian He1, Suping Zhao1, Xiaofeng Wang2,3, Jiajia Xu2,3, Xi Chen2,3, Dongfang Li2,3, Huanming Yang5,6 and Jian Wang5,6
1Department of Otorhinolaryngology Head & Neck Surgery, Province Key Laboratory of Otolaryngology Critical Diseases, Xiangya Hospital of Central South University, Changsha 410008, China
2Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
3Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
4Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
5BGI-Shenzhen, Shenzhen 518083, China
6James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
Yaoyun Tang, email: [email protected]
Keywords: hypopharyngeal cancer, whole-exome sequencing, mutations, epigenetic, therapeutic target
Received: April 12, 2017 Accepted: May 23, 2017 Published: July 28, 2017
Hypopharyngeal cancer (HPC) frequently presents at an advanced stage, resulting in poor prognosis. Although combined surgical therapy and chemoradiotherapy have improved the survival for patients with HPC over the past 3 decades, the mortality rate in late-stage diagnosis of HPC is unsatisfactory. In this study, we performed whole-exome sequencing (WES) of 23 hypopharyngeal tumor and paired adjacent normal tissue to identify novel candidate driver genes associated with hypopharyngeal carcinoma. We identified several copy number variants (CNVs) and 15 somatic mutation genes that were associated with hypopharyngeal carcinoma. Mutations in nine new genes (PRB4, NSD1, REC8, ZNF772, ZNF69, EI24, CYFIP2, NEFH, KRTAP4-5) were also indentified. PRB4 and NSD1 expression were significantly upregulated in hypopharyngeal carcinoma, which was confirmed in an independent cohort using IHC. There was a positive relationship between PRB4 and NSD1. Downregulation of PRB4 by siRNA could inhibit cell growth, colony formation and cell invasion. Notably, we here demonstrate that NSD1 could bind to the promoter regions of PRB4 and activate promoter activity by reducing the binding of H3K27me2 and increasing the binding of H3K36me2 on PRB4 promoter. In summary, we pinpoint the predominant mutations in hypopharyngeal carcinoma by WES, highlighting the substantial genetic alterations contributing to hypopharyngeal carcinoma tumorigenesis. We also indentify a novel epigenetically regulatory between PRB4 and NSD1 that contribute to hypopharyngeal carcinoma tumorigenesis. They may become potential prognostic biomarkers and therapeutic target for hypopharyngeal carcinoma treatment.
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