Grandis, J. R. | bioRxiv Science

bioRxiv2025

Human Papilloma Virus does not fully inactivate p53 in HNSCC

Head and neck squamous cell carcinoma (HNSCC) is a major global health challenge. Inactivation of the tumor suppressor p53 is the most frequent molecular event in this malignancy. p53 inactivation occurs either through TP53 mutations in human papilloma virus (HPV)-negative cases or via HPV-mediated p53 degradation in HPV-positive (HPV+) cases, where most tumors retain a wild-type (WT) TP53 allele. This underscores the critical role of p53-regulated processes in HNSCC pathogenesis. Clinically, HPV+ HNSCC is associated with significantly better outcomes than HPV-negative cases. However, despite HPV E6-mediated degradation of p53, approximately 10% of HPV+ HNSCC tumors harbor TP53 mutations, suggesting an additional selective pressure to suppress p53 signaling. In this study, we demonstrate that HPV+ TP53-WT HNSCC cells have residual, tumor suppressive p53 activity. Specifically, analysis of human tumor data reveals that among HPV+ HNSCC cases, those with WT TP53 have significantly better survival outcomes than both HPV+ cases with TP53 mutations and HPV-negative cases. Experimentally, genetic ablation of WT p53 in HPV+ HNSCC cells increased proliferation, migration, and invasion. Transcriptomic analysis revealed that p53 continues to regulate gene expression despite the presence of HPV. Further, human tumors with HPV+ TP53-WT status exhibit tumor-suppressive methylation patterns, fewer chromosomal alterations, and suppression of PI3K-AKT signaling compared to HPV+ TP53-mutant tumors. Importantly, loss of WT p53 in HPV+ HNSCC cells increased the levels of PI3K catalytic subunit p110, reduced expression of the molecular PI3K-AKT inhibitor INPP5D and enhanced sensitivity to pharmacologic PI3K inhibition. Together, our findings challenge the prevailing view that p53 is completely inactivated in HPV+ HNSCC and reveal tumor suppressive, p53-driven mechanisms that persist in these tumors. These insights highlight a potential role for TP53-based stratification in guiding treatment decisions and suggest new therapeutic vulnerabilities in HPV+ HNSCC.

cancer biology↗

bioRxiv2025

Loss of Fanconi anemia proteins causes a reliance on lysosomal exocytosis

Mutations in the FA pathway lead to a rare genetic disease that increases risk of bone marrow failure, acute myeloid leukemia, and solid tumors. FA patients have a 500 to 800-fold increase in head and neck squamous cell carcinoma compared to the general population and the treatment for these malignancies are ineffective and limited due to the deficiency in DNA damage repair. Using unbiased CRISPR-interference screening, we found the loss of FA function renders cells dependent on key exocytosis genes such as SNAP23. Further investigation revealed that loss of FA pathway function induced deficiencies in lysosomal health, dysregulation of autophagy and increased lysosomal exocytosis. The compromised cellular state caused by the loss of FA genes is accompanied with decreased lysosome abundance and increased lysosomal membrane permeabilization in cells. We found these signatures in vitro across multiple cell types and cell lines and in clinically relevant FA patient cancers. Our findings are the first to connect the FA pathway to lysosomal exocytosis and thus expands our understanding of FA as a disease and of induced dependencies in FA mutant cancers.

cell biology↗