Abstract 1340: Identification of epidermal growth factor receptor (EGFR) polymorphisms that modify risk for squamous cell carcinoma of the head and neck (HNSCC).
Authors: Fung Christopher , Trent Kerry , Joyce Sonali , Zhou Pei , Nukui Tomoko , Weeks Daniel E. , Diergaarde Brenda , Ye Yuanqing , Wu Xifeng , Yuan Jian-Min , Grandis Jennifer , Weissfeld Joel L. , Romkes Marjorie , Egloff Ann Marie 
Published: August 2014

Abstract
Background: EGFR is overexpressed in HNSCC and contributes to disease progression. HNSCC arising in individuals with and without tobacco use histories represent distinct disease etiologies. A thorough evaluation of EGFR polymorphisms for association with HNSCC risk has not been reported.
Methods: We determined the genotypes at 60 EGFR single nucleotide polymorphisms (SNPs) in 578 white HNSCC patients and 588 white cancer-free controls using the iPLEX gold mass spectrometry-based genotyping assay. EGFR SNPs were selected based on hypothesized function and/or tagging of EGFR with r2 ≥0.8 and minor allele frequencies of ≥5%. Associations with HNSCC risk were tested using the Fisher's exact test for genotype and for trend for number of alleles of each SNP. We also performed these analyses stratified by tobacco use. SNPs significantly associated with HNSCC (p&lt;0.05 for either test) were further tested using multivariable logistic regression (MLR) analysis. SNPs significant in MLR models were evaluated in an independent cohort of 408 white HNSCC patients and 408 white cancer-free subjects. Expression of non-coding RNA transcript EGFR-AS1 was detected by PCR amplification following reverse-transcription of RNA isolated from Fadu, CAL33 and LICR-LON-HN5 HNSCC cell lines.
Results: Of the 60 EGFR SNPs tested, 5 intronic SNPs (rs12535536, rs2075110, rs12538371, rs845561 and rs6970262) and 1 synonymous coding SNP (rs2072454) were found to be associated (p&lt;0.05) with HNSCC risk in the entire case-control cohort after adjustment for sex, age, and use of alcohol and tobacco. Among never tobacco users, rs12538371, rs845561, and rs6970262, residing within introns 15, 20 and 21, respectively, were significantly associated with HNSCC risk (p&lt;0.05) after adjustment for age and sex. Two of these SNPs (rs845561 and rs6970262) reside near histone H3 lysine27 acetylation-enriched regions in
ENCODE cell lines and sequences encoding the 2.8 kb spliced non-coding transcript EGFR AS1, which we detected in HNSCC cell lines. rs17586365 was significantly associated with HNSCC risk in MLR models restricted to tobacco users. However, SNPs rs6593206, rs2075110, rs12538371, rs845561 and rs6970262 were not associated with HNSCC risk in an independent cohort where all HNSCC cases had histories of tobacco use.
Conclusions: Common EGFR genetic variants may modify risk for HNSCC independent of known risk factors. The difference in tobacco use histories between two different cohorts may account for the discrepancy in the association between certain SNPs and HNSCC risk association. Three EGFR variants may specifically contribute to tobacco-independent HNSCC. The functional consequences of these SNPs or risk-conferring polymorphisms in linkage disequilibrium have yet to be defined.
Citation Format: Christopher Fung, Kerry Trent, Sonali Joyce, Pei Zhou, Tomoko Nukui, Daniel E. Weeks, Brenda Diergaarde, Yuanqing Ye, Xifeng Wu, Jian-Min Yuan, Jennifer Grandis, Joel L. Weissfeld, Marjorie Romkes, Ann Marie Egloff. Identification of epidermal growth factor receptor (EGFR) polymorphisms that modify risk for squamous cell carcinoma of the head and neck (HNSCC). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1340. doi:10.1158/1538-7445.AM2013-1340