Head and neck cancer arises in the epithelium of the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx. By using a systems level approach to analyze the head and neck cancer proteome based on clinical metadata and genome-wide transcriptomics data, 792 genes were found to be associated with prognostic outcome.

Head and neck cancer arises in the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx, and this type of cancer is common in several regions of the world where tobacco usage and alcohol consumption is high. Head and neck cancers comprise approximately 10% of all newly diagnosed cancers in the western world, and as much as one-third in India. The 5-year survival rate is approximately 60%, and is dependent on grade and location(s) of primary tumor. There is increasing evidence that viruses might contribute to this type of cancer, and both human papilloma virus (HPV) and Epstein-Barr virus have been associated with development of head and neck cancer and nasopharyngeal cancer. Surprisingly, patients with advanced forms of cancer in the upper region of the throat have better outcome if the tumor is HPV-positive. Existence of head and neck cancer in young adults and non-users of tobacco and alcohol also suggests that a genetic predisposition may be a possible etiological factor. Most head and neck cancers arise from squamous epithelium and consists of squamous cell carcinomas of different histologic grades. The tumor cells in well-differentiated cancers closely resemble normal squamous epithelium, whereas poorly differentiated cancers are difficult to classify as being of squamous epithelial origin. Salivary gland tumors (mainly adenocarcinomas) comprise a minority of head and neck cancers.

The analysis of prognostic genes in head and neck cancer was based on publicly available gene expression data and clinical metadata from the Cancer Genome Atlas (TCGA), consisting of 499 patients. According to the analysis, 792 genes were associated with prognostic outcome, out of which 341 genes were associated with unfavourable prognosis and 451 genes with favourable prognosis.

The LIMA1 gene encodes a cytoskeleton-associated protein that binds to actin monomers and filaments, and LIMA1 is associated with unfavourable prognosis in head and neck cancer. Immunohistochemical staining of LIMA1 shows varying cytoplasmic and membranous expression in head and neck cancer (Figure 1).

CALML5, a calcium-binding protein that may be implicated in differentiation of keratinocytes, is shown to be associated with favourable prognosis in patients with head and neck cancer. Immunohistochemical staining of CALML5 shows a differential nuclear and cytosolic expression pattern in head and neck cancer samples (Figure 2).

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References and links

Uhlén M et al, 2017. A pathology atlas of the human cancer transcriptome. Science.
PubMed: 28818916 DOI: 10.1126/science.aan2507

Histology dictionary - Head and Neck Cancer