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Paul M. Weinberger, MD; Mark Merkley, BS; Jeffrey R. Lee, MD; Bao-Ling Adam, PhD; Christine G. Gourin, MD; Robert H. Podolsky, PhD; Bruce G. Haffty, MD; Evangelia Papadavid, MD; Clarence Sasaki, MD; Amanda Psyrri, MD; William S. Dynan, PhD

Arch Otolaryngol Head Neck Surg. 2009;135(7):694-703.

Objective  To evaluate head and neck squamous cell carcinomas (HNSCCs) for differences in protein expression between oral cavity, oropharynx, larynx, and hypopharynx subsites.

Design  Retrospective proteomic analysis using tissue microarray (TMA) and 2-dimensional difference gel electrophoresis (2D-DIGE). For the TMA, automated quantitative protein expression analysis was used to interrogate levels of 4 cell-cycle regulatory proteins chosen for their known roles in cancer (cyclin D1, p53, Rb, and p14). For the 2D-DIGE, lesional and normal adjacent tissues were enriched by laser capture microdissection. Total protein was extracted, analyzed by 2D-DIGE with saturation dye labeling, and evaluated for relative abundance levels of individual protein spots.

Setting  Two tertiary-care academic medical centers.

Patients  Seventy-one patients with HNSCC for TMA, and 14 patients with HNSCC with frozen tumor and normal tissue for 2D-DIGE.

Results  The automated quantitative analysis of protein expression analysis revealed no difference between subsite for cyclin D1, p53, Rb, or p14 expression. The 2D-DIGE study was based on 28 gels (14 cancer gels and 14 adjacent normal gels), and 732 spots were identified as matching across more than 90% of gels. Significance was evaluated based on false discovery rate (FDR) estimated from permuted data sets. There were no significant differences in protein expression between subsites (FDR greater than or equal to 30% in all instances).

Conclusions  Observed differences in outcomes between HNSCCs from different subsites may not reflect differences in tumor biologic characteristics between subsites. Rather, it is possible that observed clinical heterogeneity among HNSCCs may be based on other factors, such as viral vs chemical carcinogenesis.

Author Affiliations: Departments of Otolaryngology (Drs Weinberger and Gourin) and Pathology (Dr Lee), Institute for Molecular Medicine and Genetics (Mr Merkley and Drs Lee and Dynan), and Center for Biotechnology and Genomic Medicine (Drs Adam and Podolsky), Medical College of Georgia, Augusta; Charlie Norwood VA Medical Center, Augusta (Dr Lee); Department of Radiation Oncology, University of Medicine and Dentistry of New Jersey–Robert Wood Johnson Medical School, Newark (Dr Haffty); and Departments of Medical Oncology (Drs Papadavid and Psyrri) and Surgery (Dr Sasaki), Yale University, New Haven, Connecticut.

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