A melanoma mutation panel for individualized treatment of patient-derived melanoma cell cultures

Purpose: To identify new targets in melanoma for targeted treatment based on a mutational analysis of melanoma cell lines and subsequent individualized treatment combinations. Experimental Design: A series of 57 melanoma cell lines (mostly short-term cultures) are analyzed for their mutation pattern based on a mutation panel of 83 genes selected from the most abundant mutations (more than 5 % of samples). Of these, 28 cell lines are treated with small molecule inhibitors either as single-agent or combination therapy. Most effective therapies are estimated by Chou Talaley method, applied to multiple drug treatments, based on growth characteristics of melanoma cells during life-cell imaging. Results: In a number of cell lines, combination treatment showed better treatment response rates than monotherapy. BRAFi and an inhibitor of a further pathway is more efficient to induce an anti-proliferative effect than the standard therapy with a BRAFi-MEKi combination. Among these are PI3K/mTOR inhibitor apitolisib either together with a BRAFi or as triple combination with BRAFi/MEKi. A combination of BRAFi and CDK4/6 inhibitor palbociclib also showed significant synergy. The most promising drug combinations in NRASmut cell lines is a triple combination of MEKi, ERKi and and PI3K/mTOR apitolisib, or a combination of MEKi, apitolisib and aurora A kinase inhibitor alisertib. Transcriptomic analysis showed that BRAF and NRAS mutant cell lines could be differentiated by ARHGAP42 and DLD expression, both higher expressed in BRAFmut cell lines, and ARHGAP42 being a putative new target for BRAFmut melanoma cells. Conclusion: Combination treatment of melanoma cells with individual drug combinations based on mutational patterns are sometimes more effective than monotherapy or classical double-agent therapy and may thereby replace classical treatment approaches. A series of 57 melanoma cell lines (mostly short-term cultures) are analyzed for their mutation pattern based on a mutation panel of 83 genes selected from the most abundant mutations (more than 5 % of samples). Of these, 27 cell lines are treated with small molecule inhibitors either as single-agent or combination therapy. Most effective therapies are estimated by Chou Talaley method, applied to multiple drug treatments, based on growth characteristics of melanoma cells during life-cell imaging.研究目的：本研究旨在通过对黑色素瘤细胞系进行突变分析，并据此开发个体化治疗组合，筛选黑色素瘤靶向治疗的新靶点。实验设计：本研究对57株黑色素瘤细胞系（多为短期培养株）开展突变谱分析，所用的突变检测Panel包含83个从发生率≥5%的常见突变中筛选出的基因。其中28株细胞系接受小分子抑制剂单药或联合治疗。基于活细胞成像记录的黑色素瘤细胞生长特征，采用Chou-Talalay法评估多药联合治疗的最优方案。研究结果：在部分细胞系中，联合治疗的应答率优于单药治疗。BRAF抑制剂（BRAFi）联合另一通路抑制剂的抗增殖效果，优于经典的BRAFi-MEKi双靶联合疗法。此类有效组合包括：PI3K/mTOR抑制剂阿培利司（apitolisib）与BRAFi联用，或与BRAFi/MEKi组成三药联合方案；BRAFi联合CDK4/6抑制剂帕博西尼（palbociclib）也展现出显著协同效应。在NRAS突变型细胞系中，最具潜力的药物联合方案为MEKi、ERKi与PI3K/mTOR抑制剂阿培利司（apitolisib）组成的三药联合，或是MEKi、阿培利司联合极光A激酶抑制剂阿利塞利布（alisertib）的组合。转录组分析显示，BRAF与NRAS突变型细胞系可通过ARHGAP42和DLD的表达水平加以区分：二者在BRAF突变型细胞系中均高表达，其中ARHGAP42或可成为BRAF突变型黑色素瘤的潜在新型治疗靶点。研究结论：基于突变谱制定的个体化联合治疗方案，在部分场景下疗效优于单药治疗或经典双药联合疗法，有望替代传统黑色素瘤治疗方案。本研究对57株黑色素瘤细胞系（多为短期培养株）开展突变谱分析，所用的突变检测Panel包含83个从发生率≥5%的常见突变中筛选出的基因。其中27株细胞系接受小分子抑制剂单药或联合治疗。基于活细胞成像记录的黑色素瘤细胞生长特征，采用Chou-Talalay法评估多药联合治疗的最优方案。