Abstract 2148: Combined comparative genome hybridization (CGH) and pathway analysis of oral squamous cell carcinomas with respect to nodal status and extracapsular spread (ECS)
Authors: Bryony H. Lloyd, Julia A. Woolgar, Janet M. Risk, Richard Shaw, David R. Sibson
Journal: Cancer Research (2010)

Abstract Background: Over half of the new 560,000 head and neck squamous cell carcinomas annually worldwide occur in the oral cavity (OSCC). We recently and others have reported that ECS in the cervical lymph nodes represents the most significant adverse prognostic indicator in OSCC, proving rapidly fatal in &amp;gt;75% of cases despite radical surgery and adjuvant chemoradiotherapy (Shaw et al., Head Neck, 2009). Increased interest in neo-adjuvant chemotherapy and targeted therapies contrasts to the neglected clinical biology of OSCC and the best strategies are unclear. Purpose: We aimed to use CGH analysis in an initial exploratory study hypothesising significant enrichment of molecular pathways according to the presence of ECS. Methods: Macromolecules were purified from fresh frozen samples representing T2 and T4 stage OSCC cases (n=43) having no nodal involvement, positive nodes or positive nodes plus ECS from a larger single centre series (n&amp;gt;200). CGH analysis was performed using 720,000 human genomic probes per array. Genomic segmentation was used to identify regional copy number changes. Genes within the segments were mapped to canonical pathways to assess significance according to metadata defining the samples. Results: Principal component analysis grouped the samples according to gender, stage, recurrence and nodal status, listed in order of decreasing separation. Node positive status was clearly distinguished by copy number changes significantly affecting multiple pathways including cytoskeletal remodelling: TGF and WNT pathway (p = 7.78 ×10−8), keratin filaments (p = 1.377 ×10−7), transcription: receptor mediated HIF regulation (p = 4.055 × 10−7), immune response: IL9 signalling pathway (p = 1.1 × 10−6) and chemotaxis (p = 3.8 × 10−6). Other significantly altered pathways included Notch signalling and TNFs/NF-kB/IAP apoptosis for both T4 and T2 tumours (p = 9.7 ×10−5 and p = 9.95 ×10−4, respectively). Significantly affected networks included angiogenesis, protein folding and proteasome proteolysis between disease free versus recurrence (p = 6.98 × 10−3; p = 0.022; p= 0.0218, respectively). Significant associations for ECS were not found. Discussion: This is the highest density CGH array study on specific aspects of OSCC of which we are aware. Its high resolution uniquely allowed candidate pathways associated with features of the samples to be determined. Samples with ECS could not be distinguished. This may be a result of their smaller numbers (n=11). Potentially, reduced host immune response underlying the ECS cases may be crucial, offering an alternative explanation. Future work expanding the number of samples especially with regard to ECS cases and also including expression array studies is underway. These are planned to further test the significance and examine the possibility of expression changes associated with ECS. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2148.