Abstract 977: RNA-sequencing analysis implicates novel non-coding RNAs in human papillomavirus-associated head and neck squamous cell carcinoma

Abstract

Abstract Head and neck squamous cell carcinoma (HNSCC) is an aggressive disease marked by frequent recurrence and metastasis and stagnant survival rates. Given the recent emergence of human papillomavirus (HPV) as a major etiological factor in head and neck cancers, there exists a pressing need to better resolve the molecular heterogeneity of HNSCCs, define more precise diagnostic and prognostic tools, and develop a wider repertoire of targeted therapies. Non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), have been increasingly viewed as promising sources of insight into cancer onset and progression, with their diverse regulatory roles, tissue specificity, and aberrant expression in various human diseases now established by a multitude of studies. Using RNA-sequencing data from 466 HNSCC patients in The Cancer Genome Atlas (TCGA), we sought to investigate the transcriptome-wide dysregulation of both classes of ncRNAs in HPV-associated HNSCCs. Differential expression analyses controlled for patient smoking status revealed 5 lncRNAs and 9 miRNAs exhibiting significantly altered regulation between HPV-negative and HPV-positive HNSCC tumors (FDR < 1 × 10-10). Among these, 8 ncRNAs were additionally correlated with HNSCC tumor stage, invasion, and anatomic site, among other clinical characteristics (Kruskal-Wallis, p < 0.05). We subsequently validated the dysregulation of several candidate HPV-associated ncRNAs in vitro after ectopically expressing HPV16 E6/E7 in a panel of normal oral epithelial and HPV-negative HNSCC cell lines. To explore the functional consequences of our identified HPV-associated ncRNAs, we further investigated lnc-SP9-1:1, an lncRNA upregulated by 73.89 fold in HPV-positive compared to HPV-negative HNSCCs (FDR < 1 × 10-10). Cell proliferation, migration, and matrigel invasion assays were performed to evaluate the effects of siRNA-mediated lnc-SP9-1:1 knockdown in E6/E7 overexpressing cell lines. While the specific roles of the vast majority of non-coding transcripts remain unknown, their consistent dysregulation in HPV-positive HNSCCs, coupled with their ongoing functional characterization, promises to unravel new layers of understanding of the molecular underpinnings of HPV-associated HNSCCs and nominate new biomarkers and therapeutic candidates for this specific disease. Citation Format: Angela E. Zou, Aswini R. Krishnan, Yinan Xuan, Maarouf A. Saad, Avinaash Korrapati, Sunil J. Advani, Jessica Wang-Rodriguez, Weg Ongkeko. RNA-sequencing analysis implicates novel non-coding RNAs in human papillomavirus-associated head and neck squamous cell carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 977.