Lineage master regulator and cancer-selective partner transcription factors rewire 3D genome topology for tumor-specific gene control

Lineage-determining transcription factors (TFs), such as p63 in epithelial tissues, establish normal tissue identity but can also drive carcinogenesis. The epigenetic basis for these divergent effects, however, is unclear. Here, we show that p63 reorganizes three-dimensional (3D) chromatin topology in squamous cell carcinoma (SCC) through cooperation with the tumor-selective partner TF, FOXK1. Multi-omic profiling across normal and malignant states reveals that p63 enhances connectivity between cis-regulatory elements near oncogenes and promotes a secondary enhancer looping architecture, in which p63 and FOXK1-enriched enhancers indirectly contact target promoters via FOXK1-associated intermediate anchors lacking p63 binding. FOXK1 mediates p63-dependent chromatin looping, as FOXK1 loss selectively weakens p63-dependent loops and reduces transcription of associated target genes. The p63–FOXK1 interaction is observed in human tumor samples but not in normal tissues. Together, our findings define an epigenetic mechanism by which a lineage master TF and tumor-restricted partner TF reshape 3D chromatin structure to drive oncogenic transcription, with implications for tumor cell identity and therapy.