Ramelyte, E. | bioRxiv Science

bioRxiv2026

p63 and PITX1 sustain a pre-invasive malignant keratinocyte population in squamous cell carcinoma precursors

BackgroundCutaneous squamous cell carcinoma (cSCC) is among the most common human cancers, yet the cellular identity and molecular programs of its preinvasive precursor, actinic keratosis (AK), remains poorly defined. MethodsWe applied CITE-seq to patient-matched AK, UV-exposed normal skin, and non-UV-exposed normal skin (n=5 patients, 12 biopsies) and performed spatial whole-transcriptome profiling in an independent cohort (n=4) to map pre-invasive keratinocyte states at single-cell resolution. ResultsWe identify AK-specific keratinocytes (ASK), a discrete population localized to the dysplastic basal epidermis and characterized by UV-associated mutational signatures (SBS7b), high mutational burden, and recurrent copy number alterations including 9p loss and 8q gain. ASK occupies a basal-like undifferentiated state sustained by a {Delta}Np63/PITX1 regulatory module that attenuates Notch/HES1-driven differentiation and activates glycolytic metabolism. Comparison with published cSCC data reveals that ASK share core tumor-propagating gene networks with tumor-specific keratinocytes (TSK), including IGFBP6, IGFBP2, and ITGA6, but lack invasion effectors MMP1, MMP10, and PTHLH. Functional experiments identify IGFBP6 as a pro-proliferative factor in AK-derived keratinocytes. The AK microenvironment shows expansion of inflammatory basal keratinocytes, barrier disruption, and early immunosuppressive T cell remodeling. ConclusionsThese findings define the molecular identity of a pre-invasive malignant keratinocyte population governed by p63/PITX1 and distinguish early oncogenic programs shared with invasive cSCC from later-acquired invasion effectors, identifying candidate targets for prevention or treatment of squamous cell carcinoma.

cancer biology↗

bioRxiv2023

The genetic evolution of acral melanoma

Acral melanoma is an aggressive type of melanoma with unknown origins, arising on the sole, palm, or nail apparatus. It is the most common type of melanoma in individuals with dark skin and is notoriously challenging to treat. Our study examined exome sequencing data from 139 tissue samples, spanning different progression stages, collected from 37 patients. We found that 78.4% of the melanomas displayed one or more clustered copy number transitions with focal amplifications, recurring predominantly on chromosomes 5, 11, 12, and 22. These genomic "hailstorms" were typically shared across all progression stages within individual patients. Genetic alterations known to activate TERT also arose early. By contrast, mutations in the MAP- kinase pathway appeared later during progression, often leading to different tumor areas harboring non-overlapping driver mutations. We conclude that the evolutionary trajectories of acral melanomas substantially diverge from those of melanomas on sun-exposed skin, where MAP-kinase pathway activation initiates the neoplastic cascade followed by immortalization later. The punctuated formation of hailstorms, paired with early TERT activation, suggests a unique mutational mechanism underlying the origins of acral melanoma. Our findings highlight an essential role for telomerase, likely in re-stabilizing tumor genomes after hailstorms have initiated the tumors. The marked genetic heterogeneity, in particular of MAP-kinase pathway drivers, may partly explain the limited success of targeted and other therapies in treating this melanoma subtype.

cancer biology↗