Comprehensive genomic characterization of head and neck squamous cell carcinomas

Abstract

The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations. Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1. Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 mutations and CDKN2A inactivation with frequent copy number alterations including amplification of 3q26/28 and 11q13/22. A subgroup of oral cavity tumours with favourable clinical outcomes displayed infrequent copy number alterations in conjunction with activating mutations of HRAS or PIK3CA, coupled with inactivating mutations of CASP8, NOTCH1 and TP53. Other distinct subgroups contained loss-of-function alterations of the chromatin modifier NSD1, WNT pathway genes AJUBA and FAT1, and activation of oxidative stress factor NFE2L2, mainly in laryngeal tumours. Therapeutic candidate alterations were identified in most HNSCCs.

Figure 1. DNA copy number alterations.

a, Copy number alterations by anatomic site and HPV status for squamous cancers. Lung squamous cell carcinoma (LUSC, n = 358) and cervical squamous cell carcinoma (CESC, n = 114). b, Unsupervised analysis of copy number alteration of HNSCC (n = 279) with associated characteristics. The rectangle indicates chromosome 7 amplifications in the purple cluster. NA, not available. PowerPoint slide

Figure 2. Significantly mutated genes in HNSCC.

Genes (rows) with significantly mutated genes (identified using the MutSigCV algorithim; q < 0.1) ordered by q value; additional genes with trends towards significance are also shown. Samples (columns, n = 279) are arranged to emphasize mutual exclusivity among mutations. Left, mutation percentage in TCGA. Right, mutation percentage in COSMIC (‘upper aerodigestive tract’ tissue). Top, overall number of mutations per megabase. Colour coding indicates mutation type. PowerPoint slide

Figure 3. Candidate therapeutic targets and driver oncogenic events.

Alteration events for key genes are displayed by sample (n = 279). TSG, tumour suppressor gene. PowerPoint slide

Figure 4. Integrated analysis of genomic alterations.

a, b, Samples (n = 279) are displayed in columns and grouped by gene expression (a) or methylation (b) subtype (sub.). Unadjusted two-sided Fisher’s exact test P values assess the association of each genomic alteration. Methylation probe location of CpG islands, shores and shelves are shown on the left of b. Annotation shows HPV status and subtype (16, 33 and 35). CN, copy number. PowerPoint slide

Figure 5. Deregulation of signalling pathways and transcription factors.

Key affected pathways, components and inferred functions, are summarized in the main text and Supplementary Information section 7 for n = 279 samples. The frequency (%) of genetic alterations for HPV(−) and HPV(+) tumours are shown separately within sub-panels and highlighted. Also see Supplementary Fig. 7.15. Pathway alterations include homozygous deletions, focal amplifications and somatic mutations. Activated and inactivated pathways/genes, and activating or inhibitory symbols are based on predicted effects of genome alterations and/or pathway functions. PowerPoint slide