Comprehensive genomic characterization of head and neck squamous cell carcinomas (pdf 4292; PubMed Link)
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.
Five Figures in the Main Text:
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.
Figure 2 | Significantly mutated genes in HNSCC. Genes (rows) with significantly mutated genes (identified using the MutSigCV algorithm; 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.
Figure 3 | Candidate therapeutic targets and driver oncogenic events. Alteration events for key genes are displayed by sample (n = 279). TSG, tumour suppressor gene.
Figure 4 | Integrated analysis of genomic alterations. a,b,Samples (n=279) ared isplayed 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.
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.
Ten Parts of Supplementary Information:
S1: Biospecimen collection and clinical data
S1.1. Biospecimen collection and clinical data
S1.2. HPV detection methods
S1.3. Survival analysis **
Figure S1.1. HPV status as a function of clinical and molecular characteristics
Figure S1.2. Receiver operating characteristic (ROC) curves in HPV-associated miRNAs in oropharyngeal HNSCC
Figure S1.3. DNA methylation signatures of HPV
Figure S1.4. Survival analysis for select clinical and genomic variables
Figure S1.5. Survival analysis for platform-specific subtypes
Table S1.1. Summary of clinical data
Data file S1.1. Data freeze clinical dataset (This file contains clinical and demographic information for all patients)
Data file S1.2. Summary of HPV detection results (This file contains the results of molecular analyses used to determine the HPV status of all patients. These include data from in situ hybridization, p16 staining, RNA and DNA sequencing, and the MassArray assay.)
Data file S1.3 Mutation signatures by HPV status (This file contains counts of base changes seen in APOBEC and smoking mutation signatures for HPV(+) and HPV(-) subjects. Fisher’s exact test p-values are also shown.)
S2: Copy number analysis
S2.1. SSNP array-based copy number analysis
S2.2. Structural alterations
Figure S2.1. GISTIC 2.0 analysis of significantly reoccurring focal alteration in 279 HNSCC tumors
Figure S2.2. GISTIC amplification and deletion peaks in lung squamous cell and cervical squamous cell carcinoma
Figure S2.3. Comparison of GISTIC 2.0 analyses of 243 HPV(–) and 36 HPV(+) head and neck tumors
Figure S2.4. Number of copy number segments in HPV(+) and HPV(–) samples
Data file S2.1. GISTIC amplification and deletion peak annotation in head and neck squamous cell (all samples, by HPV
status, and by site), lung squamous cell carcinoma, cervical squamous cell carcinoma (results from GISTIC analyses for head and neck (HNSC), lung, and cervical squamous cell carcinoma. Additional analyses for HNSC were conducted by HPV status and tumor site.)
Data file S2.2. Fisher’s exact test p-values for frequency comparisons of significantly reoccurring alterations by HPV
status and site (results of analyses of frequency comparisons of significantly reoccurring DNA copy number alterations by HPV status and tumor site. Fisher’s exact test p-values are also shown.)
S3: RNA sequencing
S3.1. RNA sequencing and expression quantification
S3.2. RNA-Seq for confirmation of somatic alterations reported in whole exome sequencing
S3.3. Gene fusion detection
S3.4. RNA-Seq for gene splicing and viral integration
Figure S3.1. RNA-Seq for confirmation of somatic alterations reported in whole exome sequencing
Figure S3.2. FGFR3-TACC3 fusion event
Figure S3.3. EGFR vIII mutant sample
Figure S3.4. Exon 14 skipping in MET+
Figure S3.5. Alterations of CDKN2A gene structure, copy number, and expression of its protein coding transcripts p16INK4A and p14ARF
Figure S3.6. Integration of DNA mutation type, copy number, and gene expression for CDKN2A+
Figure S3.7. Alterations of FAT1 gene structure, copy number, and expression
Figure S3.8. Integration of DNA mutation type, copy number, and gene expression for FAT1+
Figure S3.9. Integration of DNA mutation type, copy number, and gene expression for predicted driver genes relevant to HNSCC
Figure S3.10. Distribution of HPV integration breakpoints across the host genome
Figure S3.11. The KLK12 gene documents recurrent alternate transcription in HNSCC Figure S3.12. Heterogeneous TP63 isoform usage in HNSCC+
Data file S3.1. RNA-Seq predicted fusions ( contains the results of fusion detection analyses performed with MapSplice. )
Data file S3.2. Viral integration sites (information about HPV viral integration sites based on the analysis of RNA and DNA sequencing
data.)
Data file S3.3. SigFuge clustering results for alternatively spliced genes (the results of SigFuge analyses to detect differential expression of multiple gene isoforms. Uncorrected p-values are shown.)
