Xiao Xiao, Xu Ren, Lu Jun, Xin Beibei, Wang Chenyang, Zhu Kexin, Zhang Hao, Chen Xinyu
School of Physics, Changchun University of Science and Technology, Changchun, China.
Research & Development Department, Shanghai Rightongene Biotechnology Co., Ltd., Shanghai, China.
Front Oncol. 2024 Oct 21;14:1470827. doi: 10.3389/fonc.2024.1470827. eCollection 2024.
Osimertinib, one of the third-generation -tyrosine kinase inhibitors (TKIs) designed to target T790M mutation, significantly improves the prognosis of lung cancer. However, drug resistance still happens and amplification is responsible for one of the main causes. Fluorescence hybridization (FISH) is the gold standard for amplification detection, but fundamentally limited by observer subjectivity. Herein, we assessed the value of next-generation sequencing (NGS) method in amplification detection in non-small cell lung cancer (NSCLC), as well as revealed the mutation profiling of NSCLC patients with osimertinib resistance to provide some valuable clues to the mechanisms of resistance.
A total of 317 cancer tissue samples from 317 NSCLC patients at time of progression following osimertinib were submitted to NGS and only 96 tissues were tested by FISH simultaneously. With FISH results as gold standard, enumeration algorithm was applied to establish the optimal model for identifying amplification using gene copy number (GCN) data.
The optimal model for identifying amplification was constructed based on the GCN of , , and , which achieved a 74.0% overall agreement with FISH and performed well in identifying amplification except polysomy with a sensitivity of 85.7% and a specificity of 93.9%. The inconsistency between NGS and FISH occurred mainly in polysomy subtype, while GCN ≥ 5 could be reliably recognized by NGS. Moreover, the most frequently mutated genes in NSCLC patients with osimertinib resistance were (59.94%), followed by (43.85%), (9.46%), (6.31%), and ATM (5.36%). The known resistance mechanisms, including amplification, (C797S, L718Q/R), , , , , , , and mutations were also disclosed in our cohort.
NGS assay can achieve a high concordance with FISH in amplification detection and has advantages in portraying various genetic alterations, which is of worthy in clinical promotion.
奥希替尼是一种旨在靶向T790M突变的第三代酪氨酸激酶抑制剂（TKIs），可显著改善肺癌的预后。然而，耐药性仍然会发生，基因扩增是主要原因之一。荧光原位杂交（FISH）是基因扩增检测的金标准，但从根本上受到观察者主观性的限制。在此，我们评估了二代测序（NGS）方法在非小细胞肺癌（NSCLC）基因扩增检测中的价值，并揭示了对奥希替尼耐药的NSCLC患者的突变谱，为耐药机制提供一些有价值的线索。
收集317例NSCLC患者在奥希替尼治疗进展时的癌组织样本进行NGS检测，同时仅对96例组织进行FISH检测。以FISH结果作为金标准，应用枚举算法建立基于基因拷贝数（GCN）数据识别基因扩增的最优模型。
基于、、和的GCN构建了识别基因扩增的最优模型，其与FISH的总体一致性达到74.0%，在识别基因扩增方面表现良好，除多倍体外，敏感性为85.7%，特异性为93.9%。NGS与FISH之间的不一致主要发生在多倍体亚型中，而NGS可以可靠地识别GCN≥5的情况。此外，对奥希替尼耐药的NSCLC患者中最常发生突变的基因是（59.94%），其次是（43.85%）、（9.46%）、（6.31%）和ATM（5.36%）。我们的队列中还发现了已知的耐药机制，包括基因扩增、（C797S、L718Q/R）、、、、、、和突变。
NGS检测在基因扩增检测中与FISH具有高度一致性，在描绘各种基因改变方面具有优势，值得临床推广。
