Bromodomain inhibition overcomes treatment resistance in distinct molecular subtypes of melanoma

Therapy of BRAF-mutant melanoma with selective inhibitors of BRAF (BRAFi) and MEK (MEKi) represents a major clinical advance but acquired resistance to therapy has emerged as a key obstacle. To date, no clinical approaches successfully resensitize to BRAF/MEK inhibition. Here, we develop a therapeutic strategy for melanoma using bromosporine, a bromodomain inhibitor. Bromosporine (bromo) monotherapy produced significant anti-tumor effects against established melanoma cell lines and patient-derived xenografts (PDXs). Combinatorial therapy involving bromosporine and cobimetinib (bromo/cobi) showed synergistic anti-tumor effects in multiple BRAFi-resistant PDX models. The bromo/cobi combination was superior in vivo to standard BRAFi/MEKi therapy in the treatment-naive BRAF-mutant setting and to MEKi alone in the setting of immunotherapy-resistant NRAS- and NF1-mutant melanoma. RNA sequencing of xenografts treated with bromo/cobi revealed profound down-regulation of genes critical to cell division and mitotic progression. Bromo/cobi treatment resulted in marked DNA damage and cell-cycle arrest, resulting in induction of apoptosis. These studies introduce bromodomain inhibition, alone or combined with agents targeting the mitogen activated protein kinase pathway, as a rational therapeutic approach for melanoma refractory to standard targeted or immunotherapeutic approaches.

Melanoma is the fifth most common malignancy in the Unites States, with an estimated 106,110 new cases in 2021 (1). The death toll attributed to melanoma has decreased sharply, owing in part to the revolution that has taken place in the therapy of advanced disease, with significant advances both in immunotherapeutic and targeted interventions. In the realm of targeted therapy, the efficacy of small molecule inhibitors targeting mutant BRAF in metastatic melanoma (2, 3) represented a landmark in the targeted therapy of cancer. Subsequently, the combination of BRAF and MEK inhibition resulted in increased response rates and prolonged survival (4–6). More recently, durable responses have been reported with BRAF/MEK-targeted therapy (7). However, despite these clear improvements in patient outcome, many patients eventually progress. As a result, the development of acquired resistance to targeted agents constitutes a significant clinical obstacle. While numerous mechanisms of resistance to targeted therapy have been described (8), many of these mechanisms result in reactivation of the mitogen activated protein kinase (MAPK) pathway in which BRAF operates (9, 10). Therefore, new therapeutic approaches will be required to increase the proportion of responding patients, the durability of the responses observed, and to resensitize melanoma cells to BRAF inhibitors upon the development of acquired resistance. To date, few effective targets for combinatorial therapy with BRAF inhibitors (beyond MEK) have been identified, and none that have proved superior to the BRAFi/MEKi combination.Previously, we identified an important role for the BPTF gene in melanoma progression, and as a potential therapeutic target (11). BPTF promotes melanoma progression by activating a cascade of gene expression including ERK, BCL2, and BCL-XL, resulting in promotion of cell-cycle progression and suppression of apoptosis. BPTF gene silencing resulted in abrogation of the proliferative and metastatic potential of melanoma cells and in sensitization to BRAF inhibition (11).Recently, bromodomain inhibition has emerged as a novel approach to cancer therapy. Bromodomains are protein motifs that bind to acetylated lysine residues on histones, with a critical role in chromatin remodeling (12, 13). The development of ligands targeting the BET (bromodomain and extracellular-terminal) family member BRD4 (14) demonstrated the potential of small molecule inhibition of the bromodomain-acetyl-lysine interaction and is being pursued actively in the clinical arena. However, BET family bromodomains do not share significant sequence homology with that of BPTF (15), indicating that distinct inhibitors will be required to effectively target BPTF. Collectively, these observations suggest the potential utility of a bromodomain inhibitor, alone or in combination with MAPK pathway inhibition, as a rational therapeutic strategy for melanoma, which represents the focus of the current analysis.