Gene Expression Profiles Identify Epithelial-to-Mesenchymal Transition and Activation of Nuclear Factor-κB Signaling as Characteristics of a High-risk Head and Neck Squamous Cell Carcinoma

TLDR

Gene expression signatures from DNA microarray analyses show promise as predictive biomarkers of clinical outcome. The study aimed to identify a high‑risk recurrence signature in HNSCC using formalin‑fixed tumors and validate it against an independent fresh‑frozen dataset. The authors profiled 40 FFPE and 6 matched frozen HNSCC samples from 29 patients, trained a 75‑gene recurrence‑predictive signature on FFPE data, validated it on an independent 60‑patient frozen cohort, and performed Gene Set Enrichment Analysis to explore biological pathways. High‑risk tumors exhibited significantly poorer recurrence‑free survival (P = 0.002 and 0.03), and Gene Set Enrichment Analysis revealed EMT, NF‑κB activation, and cell‑adhesion pathways as key drivers, supporting the 75‑gene list as a prognostic biomarker and highlighting EMT/NF‑κB as potential therapeutic targets. Cancer Res 2006; 66(16): 8210‑8.

Abstract

Abstract Gene expression signatures generated from DNA microarray analyses have shown promise as predictive biomarkers of clinical outcome. In this study, we determined a high-risk signature for disease recurrence using formalin-fixed head and neck squamous cell carcinoma (HNSCC) tumors and compared the results with an independent data set obtained from fresh frozen tumors. We also showed that genes involved in epithelial-to-mesenchymal transition (EMT) and nuclear factor-κB (NF-κB) signaling deregulation are the most prominent molecular characteristics of the high-risk tumors. Gene expression was determined in 40 samples, including 34 formalin-fixed tissues and 6 matched frozen tissues, from 29 HNSCC patients. A 75-gene list predictive of disease recurrence was determined by training on the formalin-fixed tumor data set and tested on data from the independent frozen tumor set from 60 HNSCC patients. The difference in recurrence-free survival (RFS) between the high-risk versus low-risk groups in the training and test sets was statistically significant (P = 0.002 and 0.03, respectively, log-rank test). In addition, the gene expression data was interrogated using Gene Set Enrichment Analysis to determine biological significance. The most significant sets of genes enriched in the high-risk tumors were genes involving EMT, NF-κB activation, and cell adhesion. In conclusion, global gene expression analysis is feasible using formalin-fixed tissue. The 75-gene list can be used as a prognostic biomarker of recurrence, and our data suggest that the molecular determinants of EMT and NF-κB activation can be targeted as the novel therapy in the identified high-risk patients. (Cancer Res 2006; 66(16): 8210-8)