Heads Up! Predictive Gene Signatures in Head and Neck Cancer May Be Coming Soon

Transcriptomics and Epigenomics in head and neck cancer: available repositories and molecular signatures

For many years, head and neck squamous cell carcinoma (HNSCC) has been considered as a single entity. However, in the last decades HNSCC complexity and heterogeneity have been recognized. In parallel, high-throughput omics techniques had allowed picturing a larger spectrum of the behavior and characteristics of molecules in cancer and a large set of omics web-based tools and informative repository databases have been developed. The objective of the present review is to provide an overview on biological, prognostic and predictive molecular signatures in HNSCC. To contextualize the selected data, our literature survey includes a short summary of the main characteristics of omics data repositories and web-tools for data analyses. The timeframe of our analysis was fixed, encompassing papers published between January 2015 and January 2019. From more than 1000 papers evaluated, 61 omics studies were selected: 33 investigating mRNA signatures, 11 and 13 related to miRNA and other non-coding-RNA signatures and 4 analyzing DNA methylation signatures. More than half of identified signatures (36) had a prognostic value but only in 10 studies selection of a specific anatomical sub-site (8 oral cavity, 1 oropharynx and 1 both oral cavity and oropharynx) was performed. Noteworthy, although the sample size included in many studies was limited, about one-half of the retrieved studies reported an external validation on independent dataset(s), strengthening the relevance of the obtained data. Finally, we highlighted the development and exploitation of three gene-expression signatures, whose clinical impact on prognosis/prediction of treatment response could be high. Based on this overview on omics-related literature in HNSCC, we identified some limits and strengths. The major limits are represented by the low number of signatures associated to DNA methylation and to non-coding RNA (miRNA, lncRNA and piRNAs) and the availability of a single dataset with multiple omics on more than 500 HNSCC (i.e. TCGA). The major strengths rely on the integration of multiple datasets through meta-analysis approaches and on the growing integration among omics data obtained on the same cohort of patients. Moreover, new approaches based on artificial intelligence and informatic analyses are expected to be available in the next future.

Epidermal growth factor receptor variant III in head and neck squamous cell carcinoma is not relevant for targeted therapy and irradiation

BACKGROUND

The epidermal growth factor receptor (EGFR) is an important regulator of cell growth and survival, and is highly variable in tumor cells. The most prevalent variation of the EGFR extracellular domain is the EGFR variant III (EGFRvIII). Some studies imply that EGFRvIII may be responsible for the poor response to the monoclonal EGFR-antibody Cetuximab, used therapeutically in head and neck squamous cell carcinoma (HNSCC). Due to inconsistent data in the literature regarding EGFRvIII prevalence and clinical relevance in HNSCC, especially its predictive value, we examined EGFRvIII-transfected cell lines and patient tissue samples.

RESULTS

In contrast to other recent publications, we were able to demonstrate EGFRvIII expression in HNSCC. However, we noted that the different detection methods yielded inconsistent results. Furthermore, our EGFRvIII transfected and EGFR wild type cell lines exhibited similar characteristics and response rates in the performed in vitro experiments.

MATERIALS AND METHODS

We conducted various inhibition and combined irradiation experiments using three EGFRvIII-transfected cell lines. Moreover, a patient cohort of 149 cases consisting of formalin fixed and paraffin embedded (FFPE) and fresh-frozen specimens was assayed via reverse transcriptase PCR (rtPCR) with gel electrophoresis and sequencing for EGFRvIII prevalence. In the rtPCR assays, we used five previously published EGFRvIII primers and EGFRvIII-positive glioblastoma tissue as a positive control. In addition, immunohistochemical staining was conducted.

CONCLUSIONS

EGFRvIII can be detected in HNSCC patient samples. Nevertheless, the low prevalence and similar response rates to targeted drugs and irradiation in vitro cast doubt regarding the clinical relevance of EGFRvIII in HNSCC.