Squamous cell carcinoma of the head and neck (SCCHN) is the seventh most common form of cancer worldwide and accounts for more than 90% of head and neck cancer cases. DNA methylation has recently been recognized as a useful marker for diagnosing and monitoring the progression of many types of cancer. The CpG island sites frequently become hypermethylated during tumorigenesis, and often exhibit distinctive tumor type and stage related patterns. Distinct gene expression profiles are observed between tumors from nonsmokers and smokers suggestive of independent gene regulation pathways within the two groups. Here, we have established the feasibility of identifying a panel of methylation loci specific to SCCHN that are dependent on smoking history status. We have conducted a preliminary DNA methylation screening analysis using the Illumina GoldenGate Methylation Cancer Panel I with DNA isolated from snap frozen primary SCCHN tumor tissues (n=97) for which smoking history data was available. We observed that SCCHN tumor samples tend to be hypermethylated across the 1505 loci in comparison to matched blood genomic DNA samples and to blood DNA samples from healthy controls. A total of 300 loci were hypermethylated (β score >0.8) among the tumor samples. Despite variability among the SCCHN cases in age and sex, methylation profiles belonging to the same tumor sites clustered together. Using a graph-theoretic approach to identify patterns of methylation, the methylation profile was distinctive between nonsmokers and smokers, but not different between active and former smokers regardless of the amount smoked defined by number of packyears. A subset of genes showed a common methylation profile regardless of smoking status, however, in general, the prevalence of methylation was higher among smokers. Interestingly, two cases who self-reported no smoking history by questionnaire, had tumors which appeared to share the smoker methylation profile. Upon further investigation, one subject had reported significant environmental tobacco smoke exposure and the second had a smoking history documented in their medical chart. This preliminary data suggests that methylation status may not only represent a useful biomarker for monitoring and early detection of SCCHN, but may also aid in the identification of genes differentially regulated in smokers and nonsmokers, which in turn could lead to novel strategies for molecular targeted therapies. In addition, graph theory based evaluation of the coherence in overall methylation pattern or profile for subjects may provide further insight into critical carcinogenesis pathways or processes differentially affected by smoking. Supported in part by NIH 1P50 CA097190.

99th AACR Annual Meeting-- Apr 12-16, 2008; San Diego, CA