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

• DOI: 10.1016/j.eururo.2024.03.038
• Publication Date: 2024-04-26T06:47:35Z
• Authors: Laura Elst; Gino Philips; Kaat Vandermaesen; Ayse Bassez; Francesca Lodi; Manon T.A. Vreeburg; Oscar R. Brouwer; Rogier Schepers; Thomas Van Brussel; Sambit K. Mohanty; Anil V. Parwani; Lien Spans; Isabelle Vanden B...; Gerd Jacomen; Marcella Baldewijns; Diether Lambrechts; Maarten Albersen
• Keywords: Male; Human papillomavirus; Budding; T-cell receptor sequencing; Trajectory analysis; Papillomavirus Infections; Human Papillomavirus Viruses; Middle Aged; Prognosis; Penile squamous cell carcinoma; Single-cell RNA sequencing; Phenotype; Epithelial-to-mesenchymal transition; Mutation; Carcinoma, Squamous Cell; Tumor Microenvironment; Humans; TP53; Tumor Suppressor Protein p53; Single-Cell Analysis; Precision Medicine; Penile Neoplasms; Papillomaviridae; Aged

TP53 loss-of-function (TP53LOF) mutations might be a driver of poor prognosis and chemoresistance in both human papillomavirus (HPV)-independent (HPV-) and HPV-associated (HPV+) penile squamous cell carcinoma (PSCC). Here, we aim to describe transcriptomic differences in the PSCC microenvironment stratified by TP53LOF and HPV status.We used single-cell RNA sequencing (scRNA-seq) and T-cell receptor sequencing to obtain a comprehensive atlas of the cellular architecture of PSCC. TP53LOF and HPV status were determined by targeted next-generation sequencing and sequencing HPV-DNA reads. Six HPV+ TP53 wild type (WT), six HPV- TP53WT, and four TP53LOF PSCC samples and six controls were included. Immunohistochemistry and hematoxylin-eosin confirmed the morphological context of the observed signatures. Prognostic differences between patient groups were validated in 541 PSCC patients using Kaplan-Meier survival estimates.Patients with aberrant p53 staining fare much worse than patients with either HPV- or HPV+ tumors and WT p53 expression. Using scRNA-seq, we 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. Inherent to the scRNA-seq analysis, low sample size is a limitation and validation of signatures in large PSCC cohorts is needed.This first scRNA-seq atlas offers unprecedented in-depth insights into PSCC biology underlying prognostic differences based on TP53 and HPV status. Our findings provide clues for testing novel biomarker-driven therapies in PSCC.Here, we analyzed tissues of penile cancer at the level of individual cells, which helps us understand why patients who harbor a deactivating mutation in the TP53 gene do much worse than patients lacking such a mutation. Such an analysis may help us tailor future therapies based on TP53 gene mutations and human papillomavirus status of these tumors.