Abstract 4060: SOX2 is a master regulator of classical squamous cell carcinoma

Abstract Classical squamous cell carcinoma is defined by recurrent 3q amplification and overexpression of the lineage-specific transcription factor SOX2. However, the extent to which SOX2 contributes this molecular subtype remains incompletely understood. Here, we identify SOX2 as a master regulator of the classical SCC subtype through integrated analysis of chromatin accessibility, transcription factor binding, 3D chromatin interactions, and gene expression. Across TCGA and cell line datasets, classical SCCs exhibit SOX2 copy number gain, focal amplification, and elevated expression. Dependency analyses reveal that classical SCC cell lines are uniquely sensitive to SOX2 loss, which we functionally validate using SOX2 CRISPRi, resulting in impaired proliferation and reduced SOX2 protein levels. ATAC-seq following SOX2 depletion demonstrates that SOX2 is required to maintain chromatin accessibility at thousands of regulatory elements. Regions that lose accessibility upon knockdown show the strongest SOX2 ChIP-seq binding and are enriched for SOX2 motifs. Conversely, SOX2 overexpression in SOX2-low non-classical SCC lines is sufficient to induce chromatin opening at newly bound enhancers, supporting a direct pioneer factor role for SOX2. HiChIP profiling reveals that SOX2 loss disrupts enhancer-promoter chromatin loops, whereas SOX2 overexpression creates new interactions at target genes. SOX2-dependent looping events overlap strongly with SOX2-driven accessibility changes. Finally, transcriptomic analyses show that SOX2-regulated enhancer-promoter interactions activate pathways enriched in classical SCC. Genes associated with SOX2-driven loops and accessibility changes exhibit the strongest expression alterations.Together, these data demonstrate that SOX2 is both necessary and sufficient to activate classical SCC epigenomic and transcriptional programs. By functioning as a pioneer factor that controls chromatin accessibility, chromatin looping, and downstream oncogenic expression, SOX2 emerges as a central regulator of classical SCC. Citation Format: Reilly Falter, Yueqiang Song, Xiaoyang Zhang. SOX2 is a master regulator of classical squamous cell carcinoma abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 4060.