Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
J Thorac Oncol. 2021 Mar;16(3):404-418. doi: 10.1016/j.jtho.2020.10.156. Epub 2020 Nov 26.
Variable genomic breakpoints have been identified through the application of target-capture DNA next-generation sequencing (NGS) for ALK, ROS1, and RET fusion detection in NSCLC. We investigated whether ALK, ROS1, and RET genomic breakpoint location can predict matched targeted therapy efficacy.
NSCLCs were analyzed by DNA NGS, target-specific RNA NGS, whole-transcriptome sequencing, and immunohistochemistry.
In total, 3787 NSCLC samples were analyzed. DNA NGS detected ALK, ROS1, and RET fusions in 241, 59, and 76 cases, respectively. These fusions were divided into canonical (single EML4-ALK, CD74/EZR/TPM3/SDC4-ROS1, and KIF5B/CCDC6-RET fusions), noncanonical (single non-EML4-ALK, non-CD74/EZR/TPM3/SDC4-ROS1, and non-KIF5B/CCDC6-RET fusions), and primary/reciprocal (both primary and reciprocal rearrangements were detected) subtypes on the basis of genomic breakpoint position, and noncanonical and primary/reciprocal subtypes were defined as uncommon fusions. Further RNA sequencing and immunohistochemistry revealed that six of 47 (12.8%) uncommon fusions were actually nonproductive rearrangements that generated no aberrant transcripts or proteins. Moreover, genomic breakpoints of canonical ALK and RET, but not ROS1, fusions always predicted breakpoints at the transcript level, whereas 85.4% (35 of 41) of uncommon fusions actually produced canonical fusion transcripts. Patients with uncommon ALK fusion (n = 31) who received first-line crizotinib exhibited shorter median progression-free survival than those with canonical ALK fusion (n = 53, 8.4 mo versus 12.0 mo, p = 0.004). However, no difference in progression-free survival was observed when only ALK RNA or protein-positive cases were analyzed (p = 0.185).
Uncommon ALK, ROS1, and RET genomic breakpoint is an unreliable predictor of matched targeted therapy efficacy. Functional validation by RNA or protein assay may add value for the accurate detection and interpretation of rare fusions.
通过应用靶向捕获 DNA 下一代测序（NGS）检测 NSCLC 中的 ALK、ROS1 和 RET 融合，已经确定了可变的基因组断点。我们研究了 ALK、ROS1 和 RET 基因组断点位置是否可以预测匹配的靶向治疗疗效。
通过 DNA NGS、靶向特异性 RNA NGS、全转录组测序和免疫组织化学分析 NSCLC。
共分析了 3787 例 NSCLC 样本。DNA NGS 在 241、59 和 76 例中分别检测到 ALK、ROS1 和 RET 融合。这些融合根据基因组断点位置分为经典（单个 EML4-ALK、CD74/EZR/TPM3/SDC4-ROS1 和 KIF5B/CCDC6-RET 融合）、非经典（单个非-EML4-ALK、非-CD74/EZR/TPM3/SDC4-ROS1 和非-KIF5B/CCDC6-RET 融合）和原发性/相互（均检测到原发性和相互重排）亚型，非经典和原发性/相互亚型定义为不常见的融合。进一步的 RNA 测序和免疫组织化学显示，47 个不常见融合中的 6 个（12.8%）实际上是无功能重排，没有产生异常转录本或蛋白。此外，经典 ALK 和 RET 融合的基因组断点，但不是 ROS1 融合的基因组断点，总是预测转录水平的断点，而 85.4%（35/41）的不常见融合实际上产生了经典融合转录本。接受一线克唑替尼治疗的不常见 ALK 融合患者（n=31）的中位无进展生存期短于经典 ALK 融合患者（n=53，8.4 个月与 12.0 个月，p=0.004）。然而，当仅分析 ALK RNA 或蛋白阳性病例时，无进展生存期无差异（p=0.185）。
不常见的 ALK、ROS1 和 RET 基因组断点是匹配靶向治疗疗效的不可靠预测因子。通过 RNA 或蛋白检测进行功能验证可能为准确检测和解释罕见融合增加价值。
