Meso-scale spatial analysis of papilloma formation and clonal expansion in cancerized skin

Somatic driver mutations pervade phenotypically normal epithelia, yet only a minority of clones progress to tumors. To understand how tissue context modulates clonal selection, we apply the classical two-stage DMBA/TPA model of carcinogenesis to mouse back skin. We collect coordinate-registered, meso-scale grids spanning multiple centimeters with 1-mm punches and profile genotype and transcriptome from the same positions (WES, n = 473; bulk RNA-seq, n = 690), complemented by matched single-cell RNA-seq. This paired, spatially resolved design enables direct coupling of clonal selection metrics to local transcriptional programs. All sequenced papillomas ( n = 6) harbor Hras ^Q61L mutation events, but expected frequency versus observed papillomas indicate that Hras ^Q61L is necessary but insufficient to drive tumorigenesis within the observation period. To quantify how field-level signaling constrains driver potency, we compute pathway activities and introduce a Laplacian-based "ruggedness" score to capture meso-scale heterogeneity. We find that field-level signaling is rewired before visible tumorigenesis: TNF-associated epithelial necroptosis rises broadly across promoted skin, while TGFB activity becomes spatially "rugged"with papillomas at local TGFB signaling minima. Selection mapping reveals a context shift: in untreated skin, positive selection corresponds with cell cycle deregulation; in the cancerized field, it correlates with impaired differentiation. Moreover, the coupling between WNT signaling and selection evident in untreated tissue is abrogated for DMBA-initiated mutations. These data show that programs such as differentiation regulation, necroptosis, and TGFB topology reshape the selective landscape, constraining the effective potency of driver mutations and explaining why clones differ in their capacity to expand and progress to tumors.