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Synergistic Targeting of Vemurafenib-Resistant Melanoma via Network-Guided Drug Combination and Biophysical Validation

ABSTRACT: Vemurafenib, a selective inhibitor targeting the BRAF V600E mutation, has improved outcomes in advanced melanoma. However, resistance frequently emerges, limiting its long-term effectiveness and highlighting the need for combination therapies. This study aimed to identify synergistic drug combinations to overcome vemurafenib resistance in BRAF-mutant melanoma using an integrative computational approach. We applied a modified version of SynGeNet, which combines gene expression data with protein–protein interaction networks, to predict effective drug combinations in the vemurafenib-resistant A375 melanoma cell line. The analysis identified sorafenib and pioglitazone as the most promising candidates. Sorafenib is a multi-kinase inhibitor targeting signaling pathways involved in proliferation and angiogenesis, while pioglitazone activates PPARγ and modulates stress responses. Transcriptomic profiling of resistant cells revealed enrichment in nucleotide metabolism, protein trafficking, and corticosteroid response pathways, alongside suppression of mitotic and cell cycle processes. In vitro validation confirmed that the sorafenib/pioglitazone combination reduces cell viability with a strong synergistic effect. We further applied a novel biophysical platform integrating QCM-D and lectin–glycan interaction analysis to assess glycosylation dynamics. The combination treatment reduced the glycan viscoelastic index, suggesting a shift toward a less metastatic phenotype.

ORGANISM(S): Homo sapiens

PROVIDER: GSE298236 | GEO | 2025/05/28

REPOSITORIES: GEO

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Project description:Recent data demonstrate that extracellular signals are transmitted through a network of proteins rather than hierarchical signaling pathways. This network model suggests why inhibition of a single component of a canonical pathway, even when targeting a mutationally activated driver of cancer, has insufficiently dramatic effects on the treatment of cancer. The biological outcome of signals propagated through a network is inherently more robust and resistant to inhibition of a single network component due to compensatory and redundant signaling events. In this study, we performed a functional chemical genetic screen analogous to synthetic lethal screening in yeast genetics to identify novel interactions between signaling inhibitors that would not be predicted based on our current understanding of signaling networks. We screened over 300 drug combinations in nine melanoma cell lines and have identified pairs of compounds that show synergistic cytotoxicity. Among the most robust and surprising results was synergy between sorafenib, a multi-kinase inhibitor with activity against Raf, and diclofenac, a non-steroidal anti-inflammatory drug (NSAID). This synergy did not correlate with the known RAS and BRAF mutational status of the melanoma cell lines. The NSAIDs celecoxib and ibuprofen could qualitatively substitute for diclofenac. Similarly, the MEK inhibitor PD325901 and the Raf inhibitor RAF265 could qualitatively substitute for sorafenib. These drug substitution experiments suggest that inhibition of cyclo-oxygenase and MAP kinase signaling are components of the observed synergistic cytotoxicity. Genome-wide expression profiling demonstrates synergy-specific down-regulation of survival-related genes. This study provides proof of principle that synthetic lethal screening can uncover novel functional drug combinations and suggests that the underlying signaling networks that control responses to targeted agents can vary substantially depending on unexplored components of the cell genotype. RNA from VMM39, DM331, and SLM2 cells with/without mutations in Ras and/or Braf, treated with Sorafenib and/or Diclofenac.

Project description:The first clinical trial testing the combination of targeted therapy with a BRAF inhibitor vemurafenib and immunotherapy with a CTLA-4 antibody ipilimumab was terminated early due to significant liver toxicities, possibly due to paradoxical activation of the MAPK pathway by BRAF inhibitors in tumors with wild type BRAF. MEK inhibitors can potentiate the MAPK inhibition in tumor, while potentially alleviating the unwanted paradoxical MAPK activation. With a mouse model of syngeneic BRAFV600E driven melanoma (SM1), we tested whether the addition of the MEK inhibitor trametinib would enhance the immunosensitization effects of the BRAF inhibitor dabrafenib. Combination of dabrafenib and trametinib with pmel-1 adoptive cell transfer (ACT) showed complete tumor regression. Bioluminescent imaging and tumor infiltrating lymphocyte (TIL) phenotyping showed increased effector infiltration to tumors with dabrafenib, trametinib or dabrafenib plus trametinib with pmel-1 ACT combination. Intracellular IFN gamma staining of the TILs and in vivo cytotoxicity studies showed trametinib was not detrimental to the effector functions in vivo. Dabrafenib increased tumor associated macrophages and T regulatory cells (Tregs) in the tumors, which can be overcome by addition of trametinib. Microarray analysis revealed increased melanoma antigen, MHC expression, and global immune-related gene upregulation with the triple combination therapy. Given the up-regulation of PD-L1 seen with dabrafenib and/or trametinib combined with antigen specific ACT, we tested the triple combination of dabrafenib, trametinib with anti-PD1 therapy, and observed superior anti-tumor effect to SM1 tumors. Our findings support the testing of these combinations in patients with BRAFV600E mutant metastatic melanoma. SM1 tumors were implanted into C57BL/6 mice. Mice were treated by ACT of pmel-1 splenocytes or C57BL/6 splenocytes as control. Pmel-1 treated mice were additionally treated with either vehicle, dabrafenib, trametinib, or combination of both drugs and control mice were treated with vehicle or combination of both drugs.

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Synergistic Targeting of Vemurafenib-Resistant Melanoma via Network-Guided Drug Combination and Biophysical Validation

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