Predicted STAT1-BRAF and IRF7-MET Regulatory Links Are Associated with MAPK Pathway Reactivation and Targeted Therapy Resistance in Melanoma

Resistance to BRAF inhibitors (BRAFi), alone or with MEK inhibitors (MEKi), limits durable responses in BRAF-mutant melanoma. To characterize resistance-associated cell-state evolution, we analyzed 674 melanoma cells from six mice bearing tumors from a single patient-derived BRAF V600E-mutant melanoma xenograft (PDX) lineage before treatment, during initial regression, at minimal residual disease, and at resistant regrowth. Unsupervised clustering based on a BRAF-centered network feature set comprising 2506 candidate genes identified six transcriptional states, which were characterized using transcriptomic analyses. Cluster 4 was detected exclusively at resistant regrowth, a phase marked by MAPK pathway reactivation, and exhibited enhanced JAK-STAT/interferon signaling and increased STAT1, STAT2, IRF7, IRF9, and RELB regulon activities. Network inference predicted STAT1-BRAF and IRF7-MET regulatory links, suggesting candidate routes to MAPK reactivation through BRAF overexpression and MET-mediated bypass signaling. External analyses partially recapitulated the resistance-associated transcriptional program in independent melanoma cell-line datasets and yielded limited, inconclusive evidence for the predicted STAT1-BRAF association in public perturbation datasets. Cluster 2 represented a pre-existing proliferative state whose signature was associated with shorter progression-free survival in pretreatment clinical cohorts. Together, these findings distinguish a therapy-associated acquired-resistance state from a pre-existing proliferative resistance-associated state and nominate the predicted STAT1-BRAF and IRF7-MET links for functional validation.