The epigenetic regulator TRIM24 controls melanoma cell dedifferentiation and resistance to treatment in melanoma

Abstract

Cancer cell plasticity plays a key role in tumor progression and treatment resistance in melanoma. While the transcriptional programs enabling adaptative switching between melanocytic and mesenchymal phenotypes are well characterized, unravelling druggable epigenetic regulators that sustain melanoma cell adaptation and resistance remains crucial. Herein, we identified TRIM24, a bromodomain protein frequently upregulated during melanoma metastatic progression, as a crucial regulator of melanoma cell plasticity towards invasive/resistant states. shRNA-mediated knock-down of TRIM24 or degradation using a TRIM24-specific PROTAC decrease the migratory capacities and increase the sensitivity to BRAF inhibitors of melanoma cells. Integration of transcriptomic (RNA-seq) and epigenomic (ATAC-seq, CUT&Tag) analyses reveals that TRIM24 reprograms the epigenome of melanoma cells, promoting mesenchymal and repressing melanocytic transcriptional programs. We further define a TRIM24-specific transcriptional signature, that is consistently enriched in treatment-resistant mesenchymal subpopulations in melanoma single-cell RNA-seq datasets. Accordingly, analysis of TRIM24 protein expression in melanoma patients highlights that high TRIM24 expression correlates with relapse to adjuvant immunotherapy. Finally, TRIM24 knock-down in immunocompetent mouse models synergises with immune checkpoint inhibitors. Overall, our findings spotlight TRIM24 as a major epigenetic regulator driving melanoma cell dedifferentiation and resistance to therapy, representing a promising druggable target to reverse phenotype switching and resensitize to treatment.