Abstract A02: Integrative analysis identifies differential miRNA expression in HPV-positive head and neck squamous cell carcinoma including mir-9 overexpression and corresponding downregulation of the target YAP1
Authors: Heymach Claudia Isabel , Diao Lixia , Tong Pan , Ng Patrick Kwok Shing , Mills Gordon B. , Wang Jing , Byers Lauren 
Published: October 2015

Abstract
Background: HPV-positive (HPV+) head and neck squamous cell cancer (HNSCC) differs significantly from HPV-negative (HPV-) in terms of biology, response to treatment, and clinical outcome. The molecular mechanisms underlying these differences and the potential contribution of microRNA (miRNA) in regulating the behavior of HPV- disease are not well understood.
Methods: We conducted an integrated analysis of miRNA expression as well as protein and mRNA expression from HPV+ and HPV - HNSCC to identify candidate genes and proteins that might be regulated by miRs. We first compared miRs in HPV+ (n=36) versus HPV- (n=243) cancers from The Cancer Genome Atlas (TCGA) to identify miRs that were differentially expressed between these groups (by t-test, p≤0.05, fold change≥2.8). Using TargetScan and the mirWalk systems, we then predicted potential targets for these miRs. Next, differences in the expression of predicted targets were evaluated by comparing levels of proteins (assessed using reverse phase proteomic arrays (RPPA)) and mRNA levels (by RNASeq) between HPV+ and HPV- tumors.
Results: We identified eight miRs that differed significantly between HPV+ versus HPV- HNSCC tumors. Among these miRs, mir-9, mir-20b, mir-363, and mir-106a were higher in HPV+ tumors, while mir-767, mir-105, mir-1269, and mir-206 were present at lower levels. Predicted target genes of these miRs that were confirmed to be differentially expressed at the mRNA or protein level include YAP1, a known effector of the Hippo pathway and predicted target gene for mir-9. Specifically, HPV+ tumors demonstrated lower YAP1 mRNA expression (p=3.48E-05, fold change=-1.6) as well as lower levels of phosphorylated YAP 1 protein (p=.0015. fold change=-1.7). Other potential candidates identified include EEF2 (mir-106a target) and phosophorylated PDK1 (mir-363 target), which both exhibited lower protein levels in HPV+ cancer.
Conclusions: Our analysis identified eight miRs that differed significantly between HPV + and HPV- cancers. Through an integrative analysis, we identified the YAP1 pathway as a potential target for mir-9 , a miR that has previously been found to be elevated in other cancers, including non-small cell lung cancer. These data suggest that miRs may contribute to differences between HPV+ and HPV- HNSCCs. Further investigations on the role of miRs in the pathogenesis of HPV+ and HPV- OSCCs are ongoing.
Citation Format: Claudia Isabel Heymach, Lixia Diao, Pan Tong, Patrick Kwok Shing Ng, Gordon B. Mills, Jing Wang, Lauren Byers. Integrative analysis identifies differential miRNA expression in HPV-positive head and neck squamous cell carcinoma including mir-9 overexpression and corresponding downregulation of the target YAP1. [abstract]. In: Proceedings of the Thirteenth Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2014 Sep 27-Oct 1; New Orleans, LA. Philadelphia (PA): AACR; Can Prev Res 2015;8(10 Suppl): Abstract nr A02.