TP53 loss-of-function mutations (TP53LOF) might be a driver of poor prognosis and chemoresistance in both human papillomavirus-independent (HPV-) and HPV-associated (HPV+) penile squamous cell carcinoma (PSCC), but the specific impact of TP53 and HPV status on disease biology and prognosis is unclear. Using single-cell RNA and TCR sequencing, we established a first transcriptomic atlas of the PSCC microenvironment stratified by TP53LOF and HPV-status. Six HPV+TP53wild type (WT), 6 HPV-TP53WT and 4 TP53LOF PSCC samples and 6 controls were included. This PSCC atlas revealed 65 cell subtypes within 83,682 cells. TP53LOF tumors exhibit a partial epithelial-to-mesenchymal transition, immune-excluded, angiogenic and morphologically invasive environment, underlying their aggressive phenotype. HPV-TP53WT tumors show stemness and immune-exhaustion. HPV+TP53WT tumors mirror normal epithelial maturation with upregulation of antibody-drug-conjugate targets and activation of innate immunity. These findings offer unprecedented in-depth insights in PSCC biology underlying prognostic differences based on TP53 and HPV-status. These prognostic differences between patient groups were validated in 541 PSCC patients using Kaplan-Meier survival estimates which confirmed that patients with aberrant p53 staining fare much worse than patients with either HPV- or HPV+ tumors and WT p53 expression. Hence, our findings might facilitate patient selection for clinical trials and provide clues for testing novel biomarker-driven therapies in PSCC based on TP53 gene mutations and HPV-status.

Single-cell Atlas of Penile Cancer Reveals TP53 Mutations as a Driver of an Aggressive Phenotype, Irrespective of Human Papillomavirus Status, and Provides Clues for Treatment Personalization. Elst et al. – 2024 – European Urology

Data Availability

Raw sequencing reads of the scRNA-seq experiments generated for this study are deposited in the EGA European Genome-Phenome Archive database under EGAS50000000217 and will be released under controlled access upon publication. Data requests will be reviewed by the UZLeuven-VIB data access committee and data can be released upon the signing of a Data Transfer Agreement that will include the necessary conditions to guarantee the protection of personal data (according to European GDPR law). Alternatively, the filtered count matrix and basic metadata required to replicate the analysis described in the paper are available on this website. Please note that sample and patient identifiers have been anonymized and shuffled in these data releases and may not match those described in the paper or the supplement.