The Genomic Landscape of Vulvar Squamous Cell Carcinoma

Abstract

Vulvar squamous cell cancer (VSC) accounts for 90% of vulvar cancers. Next-generation sequencing studies of VSC imply human papillomavirus (HPV) and p53 status play separate roles in carcinogenesis and prognosis. We sought to describe the genomic landscape and analyze the immunologic profiles of VSC with respect to HPV and p53 status. A total of 443 VSC tumors underwent tumor profiling. Next-generation sequencing was performed on genomic DNA isolated from formalin-fixed paraffin-embedded tumor samples. PD-L1, microsatellite instability were tested by fragment analysis, IHC, and next-generation sequencing. Tumor mutational burden—high was defined as >10 mutations per MB. HPV 16/18 positive (HPV+) status was determined using whole exome sequencing on 105 samples. Three cohorts were identified from 105 samples with known HPV: HPV+, HPV−/p53wt, and HPV−/p53mt. Where HPV and p53 status were examined, TP53 mutations were exclusive of HPV+ tumors. In all, 37% of samples were HPV+. Among the 66 HPV− tumors, 52 (78.8%) were HPV−/p53mt and 14 (21.2%) were HPV−/p53wt. The HPV−/p53wt cohort had a higher rate of mutations in the PI3KCA gene (42.9% HPV−/p53wt vs 26.3% HPV+ vs. 5.8% HPV−/p53mt, q=0.028) and alterations in the PI3K/AkT/mTOR pathway (57.1% HPV−/p53wt vs. 34.2% HPV+ vs. 7.7% HPV−/p53mt, q=0.0386) than the other 2 cohorts. Ninety-eight VSC tumors with HPV16/18 information underwent transcriptomic analysis and immune deconvolution method. No differences were observed in immune profiles. The HPV−/p53wt VSC tumors had significantly higher rates of mutations in the PI3KCA gene and alterations in the PI3K/AkT/mTOR pathway, a potential target that merits further investigation in this subgroup.