Genetic Changes Associated with Distant Metastasis in HPV-Positive Oropharyngeal Squamous Cell Carcinoma
Angela Earhart, Eric Duncavage, Jim Lewis. Washington University School of Medicine, St. Louis, MO
Background: The incidence of oropharyngeal squamous cell carcinoma (OPSCC) has been on the rise in the past few decades. While the role of HPV in tumor biology has been extensively studied and is well established, the genetic changes underlying disease progression, which is mostly in the form of distant metastasis, are largely unknown. We sought to determine if DNA sequence mutations could differentiate patients with HPV positive OPSCC who develop distant metastasis (DM) with those who do not (NDM).
Design: Nine cases were selected from an existing large database, all of which were positive for p16 immunohistochemistry and HPV type 16 E6/E7 by RNA in situ hybridization. Five of these had documented DM, and 4 had no disease recurrence (minimum clinical follow up of 4 years). DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue. Exon enrichment was performed using Agilent v3 capture reagents, and DNA was sequenced on a HiSeq 2000 using 2 x 101 bp reads. The resulting data was aligned to the human hg19 reference and variants called using the Genome Analysis Toolkit. Variants preset in dbSNP (version 132) were removed from the analysis.
Results: On average, 55M reads were generated in each case, resulting in >50x average exome coverage. Non-SNP single nucleotide variants (SNVs) were identified in 1260 genes across all cases. There were 220 genes mutated solely in the DM cases and 60 in just the NDM cases. The most likely biologically significant genes within the DM group that were not present in the NDM group were MST1 (4/5; 80%), EPHB2 (2/5; 40%), ASPM (2/5; 40%), FGFR2 (2/5; 40%) and CTDSPL (2/5; 40%). Many of these are tumor suppressor proteins. Non-synonymous mutations in genes previously identified in OPSCC were present in both the DM and NDM cases and included TP53 (3/9; 30%) and PIK3CA (1/9; 11%).
Conclusions: Using whole exome sequencing on formalin fixed tissue, we found several potential novel genes mutated in OSCC patients with DM that were wild type in NDM patients. The function and significance for many of these are not well characterized, particularly for head and neck cancer, but some are established tumor suppressor proteins, and some may be useful as prognostic biomarkers or for future targeted therapies.
Category: Head & Neck
Monday, March 4, 2013 9:30 AM
Poster Session I Stowell-Orbison/Surgical Pathology/Autopsy Awards Poster Session # 190, Monday Morning