Supplemental methods Supplementary Figure 1. Total and phospho-PTK2/FAK is overexpressed in selected radioresistant HNSCC cells compared to radiosensitive cell lines via immunoblot. Supplementary Figure 2. A.) Inhibition of PTK2/FAK expression via stable expression of shRNA to PTK2/FAK in HN31 HNSCC cells. B.) Stable inhibition of PTK2/FAK leads to radiosensitization in vitro. C & D.) The combination of PF562271 and radiation leads to C.) increased γ-H2AX expression and D.) higher levels of G2/M arrest and sub-G1 staining in Fadu HNSCC cells. Supplementary Figure 3. A & B.) PTK2/FAK is highly expressed in a large public database of HNSCC cell lines (www.oncomine.com) (A.) and tumor specimens (TCGA) (B.) compared to other tumor types. Supplementary Table 1. HNSCC cell lines included in RPPA. Supplementary Table 2. Tumor characteristics of the institutional cohorts. Supplementary Table 3. Univariate and multivariate analysis of PTK2/FAK copy number and disease free survival (DFS) in the two institutional cohorts and the Head and Neck Cancer TCGA cohort. NA - not included in the model. HR - Hazard ratio. 95% CI- 95% Confidence Interval. Supplementary Table 4. Tumor characteristics of the HNSCC TCGA cohort.
ARTICLE ABSTRACT
Purpose: Head and neck squamous cell carcinoma (HNSCC) is commonly treated with radiotherapy, and local failure after treatment remains the major cause of disease-related mortality. To date, human papillomavirus (HPV) is the only known clinically validated, targetable biomarkers of response to radiation in HNSCC.Experimental Design: We performed proteomic and transcriptomic analysis of targetable biomarkers of radioresistance in HPV-negative HNSCC cell lines in vitro, and tested whether pharmacologic blockade of candidate biomarkers sensitized cells to radiotherapy. Candidate biomarkers were then investigated in several independent cohorts of patients with HNSCC.Results: Increased expression of several targets was associated with radioresistance, including FGFR, ERK1, EGFR, and focal adhesion kinase (FAK), also known as PTK2. Chemical inhibition of PTK2/FAK, but not FGFR, led to significant radiosensitization with increased G2–M arrest and potentiated DNA damage. PTK2/FAK overexpression was associated with gene amplification in HPV-negative HNSCC cell lines and clinical tumors. In two independent cohorts of patients with locally advanced HPV-negative HNSCC, PTK2/FAK amplification was highly associated with poorer disease-free survival (DFS; P = 0.012 and 0.034). PTK2/FAK mRNA expression was also associated with worse DFS (P = 0.03). Moreover, both PTK2/FAK mRNA (P = 0.021) and copy number (P = 0.063) were associated with DFS in the Head and Neck Cancer subgroup of The Cancer Genome Atlas.Conclusions: Proteomic analysis identified PTK2/FAK overexpression is a biomarker of radioresistance in locally advanced HNSCC, and PTK2/FAK inhibition radiosensitized HNSCC cells. Combinations of PTK2/FAK inhibition with radiotherapy merit further evaluation as a therapeutic strategy for improving local control in HPV-negative HNSCC. Clin Cancer Res; 22(18); 4643–50. ©2016 AACR.
