Identification of an atypical etiological head and neck squamous carcinoma subtype featuring the CpG island methylator phenotype

Abstract

Head and neck squamous cell carcinoma (HNSCC) is broadly classified into HNSCC associated with human papilloma virus (HPV) infection, and HPV negative HNSCC, which is typically smoking-related. A subset of HPV negative HNSCCs occur in patients without smoking history, however, and these etiologically ‘atypical’ HNSCCs disproportionately occur in the oral cavity, and in female patients, suggesting a distinct etiology.

To investigate the determinants of clinical and molecular heterogeneity, we performed unsupervised clustering to classify 528 HNSCC patients from The Cancer Genome Atlas (TCGA) into putative intrinsic subtypes based on their profiles of epigenetically (DNA methylation) deregulated genes.

HNSCCs clustered into five subtypes, including one HPV positive subtype, two smoking-related subtypes, and two atypical subtypes. One atypical subtype was particularly genomically stable, but featured widespread gene silencing associated with the ‘CpG island methylator phenotype’ (CIMP).

Further distinguishing features of this ‘CIMP-Atypical’ subtype include an antiviral gene expression profile associated with pro-inflammatory M1 macrophages and CD8+ T cell infiltration, CASP8 mutations, and a well-differentiated state corresponding to normal SOX2 copy number and SOX2OT hypermethylation. We developed a gene expression classifier for the CIMP-Atypical subtype that could classify atypical disease features in two independent patient cohorts, demonstrating the reproducibility of this subtype. Taken together, these findings provide unprecedented evidence that atypical HNSCC is molecularly distinct, and postulates the CIMP-Atypical subtype as a distinct clinical entity that may be caused by chronic inflammation.

Highlights

• •

  We identified five etiologically distinct DNA methylation subtypes of head and neck squamous cell carcinoma.

• •

  One subtype appears not to be associated with smoking or HPV, and may represent a distinct etiological entity.

• •

  Distinctive molecularly features of this subtype include CIMP, CASP8 mutations, and antiviral immune response.

To identify factors that define clinical and biological variability in head and neck squamous cell carcinoma (HNSCC), we clustered patients into subtypes based on their epigenetic profiles, revealing five subtypes, including previously identified subtypes. We focus on discovery of a subtype that matches the clinical characteristics previously ascribed to ‘atypical’ HNSCC, i.e., HNSCC that is not caused by the classic HNSCC risk factors of smoking or HPV. This subtype is biologically distinct across multiple molecular data types, and was reproducible in independent patient populations. We postulate that this ‘CIMP-Atypical’ subtype represents a clinically distinct HNSCC subtype of unknown cause.