Whole exome sequencing of longitudinal samples from a melanoma patient receiving MEK plus CDK4/6 inhibitor therapy.

Combined MEK and CDK4/6 inhibition (MEKi+CDK4i) has shown promising clinical outcomes in NRAS mutant melanoma patients. Here, we interrogated longitudinal biopsies from a patient who initially responded to MEKi+CDK4i therapy but subsequently developed resistance. Whole exome sequencing and functional validation identified an acquired PIK3CAE545K mutation as conferring drug resistance. We demonstrate that PIK3CAE545K pre-existed in a rare subpopulation that was missed by both clinical and research testing, but was revealed upon multi-region sampling due to PIK3CAE545K being non-uniformly distributed. This resistant population rapidly expanded after the initiation of MEKi+CDK4i therapy and persisted in all successive samples even after immune checkpoint therapy and distant metastasis. Functional studies identified activated S6K1 as both a key marker and specific therapeutic vulnerability downstream of PIK3CAE545K-induced resistance. These results demonstrate that comprehensive analysis of pre-treatment samples can reveal rare pre-existing resistant subpopulations and also posit S6K1 as a common downstream therapeutic nexus for the MAPK, CDK4/6, and PI3K pathways.EGA study EGAS00001002846

MEK抑制剂（MEK inhibitor, MEKi）联合CDK4/6抑制剂（CDK4/6 inhibitor, CDK4/6i）在NRAS突变型黑色素瘤患者中已展现出颇具前景的临床疗效。本研究对一名初始对MEKi+CDK4/6i治疗产生应答，但后续出现耐药的患者的纵向活检样本进行了分析。通过全外显子组测序与功能验证，我们证实获得性PIK3CAE545K突变可介导药物耐药。研究发现，PIK3CAE545K突变预先存在于一个罕见的细胞亚群中，该亚群被临床检测与科研检测均漏检，但由于该突变的分布并不均一，通过多区域取样得以被发现。该耐药细胞亚群在MEKi+CDK4/6i治疗启动后迅速扩增，并在后续所有样本中持续存在，即使在接受免疫检查点治疗并发生远处转移后亦是如此。功能研究证实，活化的S6K1是PIK3CAE545K突变介导的耐药通路下游的关键标志物，同时也是特异性的治疗易感靶点。本研究结果表明，对治疗前样本进行全面分析可揭示罕见的预先存在的耐药细胞亚群，同时证实S6K1可作为MAPK、CDK4/6及PI3K通路下游的共同治疗枢纽靶点。EGA研究 EGAS00001002846