Comprehensive genomic profiling of penile squamous cell carcinoma and the impact of human papillomavirus status on immune‐checkpoint inhibitor‐related biomarkers

Background Advanced penile squamous cell carcinoma (pSCC) is a rare and aggressive malignancy with limited success of immune‐checkpoint inhibitors (ICIs). Approximately half of pSCC cases are associated with human papillomavirus (HPV) infection. Methods Evaluation was done retrospectively of the landscape of somatic alterations and ICI‐related biomarkers in pSCC by using the Caris Life Sciences data set with the aim to establish signatures for HPV‐dependent oncogenesis. The pSCC tumors were analyzed by using next‐generation sequencing (NGS) of DNA and RNA. Programmed death ligand 1 (PD‐L1) expression was evaluated by immunohistochemistry (IHC). Microsatellite instability (MSI) was tested by fragment analysis, IHC (SP142; ≥1%), and NGS. Tumor mutational burden (TMB)–high was defined as ≥10 mutations/Mb. HPV16/18 status was determined by using whole‐exome sequencing (WES) when available. Significance was adjusted for multiple comparisons (q value < .05). Results NGS of the overall cohort (N = 108) revealed TP53 (46%), CDKN2A (26%), and PIK3CA (25%) to be the most common mutations. Overall, 51% of tumors were PD‐L1+, 10.7% had high TMB, and 1.1% had mismatch repair–deficient (dMMR)/MSI‐high status. Twenty‐nine patients had their HPV status made available by WES (HPV16/18+, n = 13; HPV16/18−, n = 16). KMT2C mutations (33% vs. 0%) and FGF3 amplifications (30.8% vs. 0%) were specific to HPV16/18+ tumors, whereas CDKN2A mutations (0% vs. 37.5%) were exclusive to HPV16/18− tumors. TMB‐high was exclusively found in the HPV16/18+ group (30.8%). The two groups had comparable PD‐L1 and dMMR/MSI‐H status. Conclusions In a large and comprehensive NGS‐based evaluation of somatic alterations in pSCC, HPV16/18+ versus HPV16/18− pSCCs were molecularly distinct tumors. Our finding that TMB‐high is exclusive to HPV16/18+ tumors requires confirmation in larger data sets. Plain Language Summary Penile squamous cell carcinoma (pSCC) is a rare and aggressive malignancy in the advanced setting, with poor prognosis and little success with immune‐checkpoint inhibitors (ICIs) in an unselected patient approach. Human papillomavirus (HPV) infection is a known risk factor for pSCC; its impact on genomic tumor profiling is less defined. Using next‐generation sequencing, we explored the genetic landscape and ICI‐related biomarkers of pSCC and HPV‐driven oncogenic molecular signatures. Our results indicate that HPV‐positive and HPV‐negative pSCCs are molecularly distinct tumors. Increased