The landscape of therapeutic vulnerabilities in EGFR inhibitor osimertinib drug tolerant persister cells [ChIP-seq]

Third-generation EGFR tyrosine kinase inhibitors (EGFR-TKIs), including osimertinib, an irreversible EGFR-TKI, are important treatments for non-small cell lung cancer with EGFR-TKI sensitizing or EGFR T790M resistance mutations. Whilst patients treated with osimertinib show clinical benefit, disease progression and drug resistance are common. Emergence of de novo acquired resistance from a drug tolerant persister (DTP) cell population is one mechanism proposed to explain progression on osimertinib and other targeted cancer therapies. Here we profiled osimertinib DTPs using RNA-seq, ChIP-seq, and ATAC-seq to characterize the features of these cells and performed drug screens to identify therapeutic opportunities. H1975 EGFR mutant NSCLC cells were treated with 500 nM of osimertinib for 24 days (osimertinib DTPs) or treated with 500 nM of osimertinib for 21 days followed by 150 nM of AZD5153 for 3 days (osimertinib DTP AZD5153 sequential combination). In parallel, H1975 cells were grown in drug-free media for 21 days then treated with DMSO control for 3 days (DMSO control). The experiment was done using biological triplicates. Including the Input control there were 10 ChIP-seq samples.

第三代EGFR酪氨酸激酶抑制剂（EGFR-TKIs）包括不可逆EGFR-TKI奥希替尼（osimertinib），是治疗携带EGFR-TKI敏感突变或EGFR T790M耐药突变的非小细胞肺癌的重要临床手段。尽管接受奥希替尼治疗的患者可获得临床获益，但疾病进展与耐药仍较为常见。由药物耐受性持久细胞（drug tolerant persister, DTP）群体介导的从头获得性耐药，是阐释奥希替尼及其他靶向癌症疗法治疗后疾病进展的潜在机制之一。本研究通过RNA测序（RNA-seq）、染色质免疫共沉淀测序（ChIP-seq）及转座酶可及性测序（ATAC-seq）对奥希替尼诱导的DTP细胞进行特征分析，并开展药物筛选实验以识别潜在治疗靶点。实验设计如下：将携带EGFR突变的非小细胞肺癌H1975细胞分为三组，分别为：1. 奥希替尼DTP组：以500 nM奥希替尼处理24天；2. 奥希替尼DTP联合AZD5153序贯处理组：先用500 nM奥希替尼处理21天，再以150 nM AZD5153处理3天；3. DMSO对照组：将H1975细胞在无药培养基中培养21天后，用二甲基亚砜（DMSO）处理3天。所有实验均设置三次生物学重复。本实验包含Input对照，共计10个ChIP-seq样本。