Signatures of somatic mutations and gene expression from p16INK4A positive head and neck squamous cell carcinomas (HNSCC).

Human papilloma virus (HPV) causes a subset of head and neck squamous cell carcinomas (HNSCC) of the oropharynx. We combined targeted DNA- and genome-wide RNA-sequencing to identify genetic variants and gene expression signatures respectively from patients with HNSCC including oropharyngeal squamous cell carcinomas (OPSCC). DNA and RNA were purified from 35- formalin fixed and paraffin embedded (FFPE) HNSCC tumor samples. Immuno-histochemical evaluation of tumors was performed to determine the expression levels of p16INK4A and classified tumor samples either p16+ or p16-. Using ClearSeq Comprehensive Cancer panel, we examined the distribution of somatic mutations. Somatic single-nucleotide variants (SNV) were called using GATK-Mutect2 ("tumor-only" mode) approach. Using RNA-seq, we identified a catalog of 1,044 and 8 genes as significantly expressed between p16+ and p16-, respectively at FDR 0.05 (5%) and 0.1 (10%). The clinicopathological characteristics of the patients including anatomical site, smoking and survival were analyzed when comparing p16+ and p16- tumors. The majority of tumors (65%) were p16+. Population sequence variant databases, including gnomAD, ExAC, COSMIC and dbSNP, were used to identify the mutational landscape of somatic sequence variants within sequenced genes. Hierarchical clustering of The Cancer Genome Atlas (TCGA) samples based on HPV-status was observed using differentially expressed genes. Using RNA-seq in parallel with targeted DNA-seq, we identified mutational and gene expression signatures characteristic of p16+ and p16- HNSCC. Our gene signatures are consistent with previously published data including TCGA and support the need to further explore the biologic relevance of these alterations in HNSCC.

Demographic and Socioeconomic Factors Associated With Metastases at Presentation in HPV-Related Squamous Cell Carcinoma of the Head and Neck: An NCDB Analysis.

PURPOSE: Human papillomavirus (HPV)-related squamous cell carcinomas of the head and neck (SCCHNs) tend to have a distinct prognosis. Socioeconomic and demographic factors associated with metastatic disease at presentation and diagnosis in patients with HPV-related SCCHN tumors were examined. METHODS: The National Cancer Database (NCDB) was queried to assess patients with HPV-related oropharyngeal carcinomas (HPVOPCAs) and HPV-related nonoropharyngeal carcinomas (HPVNOPCAs) diagnosed between 2010 and 2014. Rate of metastases at presentation was analyzed using clinical M stage. Multivariable analysis was performed evaluating race, ethnicity, sex, age, facility location, facility type, insurance status, income, education, and tumor and nodal stage using logistic regression. RESULTS: A total of 12,857 patients with HPVOPCA and 952 patients with HPVNOPCA were included. Private insurance was carried by 64% and 47% of patients with HPVOPCA and HPVNOPCA, respectively. HPVOPCA was located in the tonsil in 56% of patients. For both HPVOPCA and HPVNOPCA, there was no meaningful difference in distant metastasis at presentation based on facility type or location, sex, race, Hispanic ethnicity, or urban or rural location. For HPVOPCA, there were significantly lower odds of metastasis in privately insured patients compared with uninsured patients (odds ratio [OR], 0.37; 95% CI, 0.21 to 0.64; P < .001) and higher odds of metastasis for patients living in census tracts with the lowest rates of high school graduates compared with the highest rates (OR, 1.81; 95% CI, 1.02 to 3.19; P = .041) and for patients with higher tumor stage (OR, 3.67, 95% CI, 2.25 to 5.99; P < .001) and nodal stage (OR, 3.34; 95% CI, 2.11 to 5.29; P < .001). For HPVNOPCA, neither higher T or N stage nor any demographic features were found to be associated with metastasis at presentation. CONCLUSION: This large retrospective analysis identifies likely modifiable risk factors for metastatic presentation in HPVOPCA. Educational interventions may result in modifications of these patterns.

Small Cell and Squamous Cell Carcinomas of the Head and Neck: Comparing Incidence and Survival Trends Based on Surveillance, Epidemiology, and End Results (SEER) Data.

BACKGROUND: Small cell carcinomas of the head and neck (SmCCHNs) are rare neoplasms with an unfavorable prognosis. Population-based data describing survival and prognostic factors for SmCCHN are limited. METHODS: Data were obtained from the U.S. National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER) database for 1973-2013. Patient and tumor-related characteristics for SmCCHN were compared with those for squamous cell carcinoma of the head and neck (SCCHN). Survival was compared by constructing Kaplan-Meier curves and Cox proportional hazard models with and without propensity score matching. RESULTS: The data set included 609 SmCCHN and 227,943 SCCHN cases. Both histological subtypes were more common in men than women and more common in white patients. SmCCHN was most likely to originate in the larynx, glottis and hypopharynx, or salivary glands and to present with more advanced stage and grade. SCCHN was most likely to originate in the oral cavity and was found infrequently in the salivary glands. Overall 5- and 10-year survival estimates were 27% and 18% for SmCCHN and 46% and 31% for SCCHN, respectively. In multivariable survival analyses adjusting for age, sex, race, marital status, year of diagnosis, stage, grade, and receipt of radiation, the hazard ratio (HR) comparing SmCCHN with SCCHN was 1.53 with a 95% confidence interval (CI) from 1.39 to 1.68. Average 5-year survival varied widely between the histologic types when comparing tumor sites: 14.5% for SmCCHN versus 48.9% for SCCHN in the oropharynx. In propensity score matched analyses, the corresponding HR was 1.27 (95% CI, 1.15-1.40). CONCLUSION: Compared with SCCHN, SmCCHN carries a worse survival and is more likely to present with more advanced stage. IMPLICATIONS FOR PRACTICE: Small cell carcinoma of the head and neck (SmCCHN) is a rare subtype of head and neck cancer. In this Surveillance, Epidemiology, and End Results (SEER) data analysis, the characteristics and survival of SmCCHN are compared with those of the common squamous cell carcinoma of the head and neck. Results show that SmCCHN carries a worse prognosis and tends to present at a more advanced stage; SmCCHN also is ten times more likely to originate from the salivary glands. These findings may have implications for clinical practice, as location of the tumor may strongly associate with the pathologic diagnosis. If a SmCCHN is diagnosed, a disseminated disease is likely; hence vigilance in staging procedures is indicated.