FGFR3-driven gene regulatory network analysis reveals a pro-tumoral role for p63 in luminal bladder tumors.

However, the underlying gene regulatory network (GRN) remains poorly characterized. Here, we inferred an FGFR3-mutated GRN using a bottom-up bioinformatics approach, integrating transcriptomic data from bladder cancer cell lines, FGFR3-mutated tumors, and FGFR3-perturbation experiments in human and mouse models.

Using CRISPR-Cas9 screen public data, we identified transcription factors (TFs) from this GRN that regulate the viability of FGFR3-mutated cells, with a focus on p63 (TP63). We showed that FGFR3 activation upregulates p63 in patient-derived xenografts and cell lines, while single-cell RNA sequencing revealed heterogeneous p63 activation associated with basal differentiation. Functional studies, including TP63 knock-down in FGFR3-dependent in vitro and in vivo models and RNA-seq along with p63 ChIP-seq, demonstrated that p63 directly promotes cell proliferation and migration, and uncovered a positive feedback loop between FGFR3 and p63.