Molecular Profiling of HNSCC Cells and Tumors Reveals a Rational Approach to Preclinical Model Selection

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common type of cancer worldwide. The increasing amount of genomic information on human tumors and cell lines provides more biological data to design preclinical studies. We and others previously reported whole exome sequencing data of 106 HNSCC primary tumors. In 2012, high throughput genomic data and pharmacological profiling of anticancer drugs of hundreds of cancer cell lines were reported. Here we compared the genomic data of 39 HNSCC cell lines with the genomic findings in 106 HNSCC tumors. Amplification of eight genes (PIK3CA, EGFR, CCND2, KDM5A, ERBB2, PMS1, FGFR1 and WHSCIL1) and deletion of five genes (CDKN2A, SMAD4, NOTCH2, NRAS and TRIM33) were found in both HNSCC cell lines and tumors. Seventeen genes were only mutated in HNSCC cell lines (>10%) suggesting that these mutations may arise through immortalization in tissue culture. Conversely, 11 genes were only mutated in >10% of human HNSCC tumors. Several mutant genes in the EGFR pathway are shared both in cell lines and in tumors. Pharmacological profiling of eight anticancer agents in six HNSCC cell lines suggested that PIK3CA mutation may serve as a predictive biomarker for the drugs targeting the EGFR/PI3K pathway. These findings suggest that a correlation of gene mutations between HNSCC cell lines and human tumors may be used to guide the selection of preclinical models for translational research. Implications: Findings provide novel insight on preclinical model selection for mutation-driven head and neck cancer studies.