The mutational landscape of head and neck squamous cell carcinoma

Abstract

Head and neck squamous cell carcinoma (HNSCC) is a common, morbid, and frequently lethal malignancy. To uncover its mutational spectrum, we analyzed whole-exome sequencing data from 74 tumor-normal pairs. The majority exhibited a mutational profile consistent with tobacco exposure; human papillomavirus was detectable by sequencing DNA from infected tumors. In addition to identifying previously known HNSCC genes (TP53, CDKN2A, PTEN, PIK3CA, and HRAS), our analysis revealed many genes not previously implicated in this malignancy. At least 30% of cases harbored mutations in genes that regulate squamous differentiation (for example, NOTCH1, IRF6, and TP63), implicating its dysregulation as a major driver of HNSCC carcinogenesis. More generally, the results indicate the ability of large-scale sequencing to reveal fundamental tumorigenic mechanisms.

Fig. 1

Mutation rates, base substitution frequencies, and rearrangements in head and neck cancers. (A) Rate of synonymous and non-synonymous mutations, expressed in mutations per megabase of covered target sequence. Non-synonymous mutation rates range from 0.43 to 17.1 mutations/megabase (mean = 3.3). (B) Breakdown of individual base substitution rates used for mutation significance, for the same samples as panel (A). The samples were ordered by the rate of G→T transversions, which are indicative of smoking-induced mutations. (C) Key clinical parameters for the samples described in panels (A) and (B) (table S10). The first row indicates HPV detection by sequencing, the second row indicates HPV detection by real-time PCR.

Fig. 2

NOTCH gene mutations identified in head and neck cancer. A. schematic diagram of the domain structure of NOTCH1. (domain structures of NOTCH2 and NOTCH3 are similar). All nonsense mutations occur upstream of the TAD domain, which is required for transactivation of target genes. Each arrowhead represents a single point mutation in an individual tumor, of the class indicated to the left.

Fig. 3

Genetic disruption of a squamous differentiation program in head and neck cancers. (A) Heatmap representation of individual mutations present in a series of 74 tumors, represented in columns. (Top) HPV status by tumor. (Middle) Matrix of mutations in individual genes by type of mutation and tumor. (Left) Number of mutations in each gene. Percentages represent the fraction of tumors harboring at least one mutation in the specified gene. (Right) Delected recurrently mutated genes ranked by q-value. Genes that define the core differentiation cluster are listed in red. (B) Proposed partial wiring diagram of the molecular circuitry of HNSCC. Blue, loss of function; red, gain of function. Numbers listed beneath each protein represent the fraction of tumors harboring mutations, amplifications, or deletions in the corresponding genes.