Rivas Solange, Sepúlveda Romina V, Tapia Ignacio, Estay Catalina, Soto Vicente, Blanco Alejandro, González Evelin, Armisen Ricardo
Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago 7550000, Chile.
Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República 330, Santiago 8370146, Chile.
Int J Mol Sci. 2024 Dec 22;25(24):13715. doi: 10.3390/ijms252413715.
Targeted therapy indications for actionable variants in non-small-cell lung cancer (NSCLC) have primarily been studied in Caucasian populations, with limited data on Latin American patients. This study utilized a 52-genes next-generation sequencing (NGS) panel to analyze 1560 tumor biopsies from NSCLC patients in Chile, Brazil, and Peru. The RNA sequencing reads and DNA coverage were correlated to improve the detection of the actionable exon 14 skipping variant (METex14). The pathogenicity of variants of uncertain significance (VUSs) was assessed using bioinformatic methods, based on their predicted driver potential. The effects of the predicted drivers VUS T992I and H1094Y on c-MET signaling activation, proliferation, and migration were evaluated in HEK293T, BEAS-2B, and H1993 cell lines. Subsequently, c-Met inhibitors were tested in 2D and 3D cell cultures, and drug affinity was determined using 3D structure simulations. The prevalence of variants in the South American cohort was 8%, and RNA-based diagnosis detected 27% more cases of than DNA-based methods. Notably, 20% of cases with RNA reads below the detection threshold were confirmed using DNA analysis. The novel actionable T992I and H1094Y variants induced proliferation and migration through c-Met/Akt signaling. Both variants showed sensitivity to crizotinib and savolitinib, but the H1094Y variant exhibited reduced sensitivity to capmatinib. These findings highlight the importance of RNA-based diagnosis and reveal the drug sensitivity profiles of novel actionable variants from an understudied patient population.
非小细胞肺癌（NSCLC）中可操作变异的靶向治疗适应症主要在白种人群中进行了研究，而关于拉丁美洲患者的数据有限。本研究使用了一个包含52个基因的下一代测序（NGS）面板，对来自智利、巴西和秘鲁的1560例NSCLC患者的肿瘤活检样本进行分析。将RNA测序读数与DNA覆盖度相关联，以提高对可操作的外显子14跳跃变异（METex14）的检测。基于其预测的驱动潜力，使用生物信息学方法评估意义未明变异（VUS）的致病性。在HEK293T、BEAS-2B和H1993细胞系中评估了预测驱动因子VUS T992I和H1094Y对c-MET信号激活、增殖和迁移的影响。随后，在二维和三维细胞培养中测试了c-Met抑制剂，并使用三维结构模拟确定药物亲和力。南美队列中变异的患病率为8%，基于RNA的诊断比基于DNA的方法多检测出27%的病例。值得注意的是，20% RNA读数低于检测阈值的病例通过DNA分析得到了确诊。新发现的可操作变异T992I和H1094Y通过c-Met/Akt信号诱导增殖和迁移。这两种变异对克唑替尼和赛沃替尼均表现出敏感性，但H1094Y变异对卡马替尼的敏感性降低。这些发现突出了基于RNA诊断的重要性，并揭示了来自研究较少患者群体的新的可操作变异的药物敏感性概况。
