Data from: Epigenomic study identifies a novel mesenchyme homeobox2-GLI1 transcription axis involved in cancer drug resistance, overall survival and therapy prognosis in lung cancer patients

Several homeobox-related gene (HOX) transcription factors such as mesenchyme HOX-2 (MEOX2) have previously been associated with cancer drug resistance, malignant progression and/or clinical prognostic responses in lung cancer patients; however, the mechanisms involved in these responses have yet to be elucidated. Here, an epigenomic strategy was implemented to identify novel MEOX2 gene promoter transcription targets and propose a new molecular mechanism underlying lung cancer drug resistance and poor clinical prognosis. Chromatin immunoprecipitation (ChIP) assays derived from non-small cell lung carcinomas (NSCLC) hybridized on gene promoter tiling arrays and bioinformatics analyses were performed, and quantitative, functional and clinical validation were also carried out. We statistically identified a common profile consisting of 78 gene promoter targets, including Hedgehog-GLI1 gene promoter sequences (FDR≤0.1 and FDR≤0.2). The GLI-1 gene promoter region from -2,192 to -109 was occupied by MEOX2, accompanied by transcriptionally active RNA Pol II and was epigenetically linked to the active histones H3K27Ac and H3K4me3; these associations were quantitatively validated. Moreover, siRNA genetic silencing assays identified a MEOX2-GLI1 axis involved in cellular cytotoxic resistance to cisplatinum in a dose-dependent manner, as well as cellular migration and proliferation. Finally, Kaplan-Maier survival analyses identified significant MEOX2-dependent GLI-1 protein expression associated with clinical progression and poorer overall survival using an independent cohort of NSCLC patients undergoing platinum-based oncological therapy with both epidermal growth factor receptor (EGFR)-non-mutated and EGFR-mutated status. In conclusion, this is the first study to investigate epigenome-wide MEOX2-transcription factor occupation identifying a novel overexpressed MEOX2-GLI1 axis and its clinical association with platinum-based cancer drug resistance and EGFR-tyrosine kinase inhibitor (TKI)-based therapy responses in NSCLC patients.

此前已有研究证实，多种同源盒（homeobox）相关转录因子（HOX家族）——如间质同源盒-2（MEOX2）——与肺癌患者的癌症耐药、恶性进展及临床预后应答存在关联；然而，介导此类应答的分子机制仍有待阐明。本研究采用表观基因组学（epigenomic）研究策略，旨在鉴定MEOX2基因启动子的新型转录靶标，并揭示肺癌耐药与不良临床预后背后的全新分子机制。本研究对非小细胞肺癌（NSCLC）样本开展染色质免疫沉淀（ChIP）实验，将所得产物与基因启动子平铺芯片（gene promoter tiling arrays）进行杂交，同时开展生物信息学（bioinformatics）分析，并完成了定量、功能及临床验证实验。通过统计学分析，本研究鉴定出包含78个基因启动子靶标的共性特征谱，其中涵盖刺猬-GLI1（Hedgehog-GLI1）基因启动子序列（错误发现率FDR分别≤0.1与≤0.2）。MEOX2可结合GLI-1基因启动子的-2192至-109区域，该区域同时存在具有转录活性的RNA聚合酶II（RNA Pol II），且在表观遗传学层面与活性组蛋白H3K27乙酰化（H3K27Ac）及H3K4三甲基化（H3K4me3）存在关联；上述关联均得到定量验证。此外，通过小干扰RNA（siRNA）基因沉默实验，本研究证实MEOX2-GLI1信号轴可介导细胞对顺铂（cisplatinum）的细胞毒性耐药，且该效应呈剂量依赖性，同时可调控细胞迁移与增殖。最后，本研究利用接受铂类抗肿瘤治疗的独立非小细胞肺癌（NSCLC）患者队列（涵盖表皮生长因子受体（EGFR）野生型与突变型两类人群），通过卡普兰-迈耶（Kaplan-Maier）生存分析发现，MEOX2依赖性GLI-1蛋白表达与临床进展及更差的总生存期显著相关。综上，本研究是首个针对全表观基因组水平的MEOX2转录因子结合位点开展分析的研究，鉴定出过表达的MEOX2-GLI1信号轴，并明确其与非小细胞肺癌患者的铂类癌症耐药及表皮生长因子受体酪氨酸激酶抑制剂（EGFR-tyrosine kinase inhibitor, TKI）治疗应答存在临床关联。