DataSheet1_Integrative analysis of DNA methylomes reveals novel cell-free biomarkers in lung adenocarcinoma.PDF

Lung cancer is a leading cause of cancer-related deaths worldwide, with a low 5-year survival rate due in part to a lack of clinically useful biomarkers. Recent studies have identified DNA methylation changes as potential cancer biomarkers. The present study identified cancer-specific CpG methylation changes by comparing genome-wide methylation data of cfDNA from lung adenocarcinomas (LUAD) patients and healthy donors in the discovery cohort. A total of 725 cell-free CpGs associated with LUAD risk were identified. Then XGBoost algorithm was performed to identify seven CpGs associated with LUAD risk. In the training phase, the 7-CpGs methylation panel was established to classify two different prognostic subgroups and showed a significant association with overall survival (OS) in LUAD patients. We found that the methylation of cg02261780 was negatively correlated with the expression of its representing gene GNA11. The methylation and expression of GNA11 were significantly associated with LAUD prognosis. Based on bisulfite PCR, the methylation levels of five CpGs (cg02261780, cg09595050, cg20193802, cg15309457, and cg05726109) were further validated in tumor tissues and matched non-malignant tissues from 20 LUAD patients. Finally, validation of the seven CpGs with RRBS data of cfDNA methylation was conducted and further proved the reliability of the 7-CpGs methylation panel. In conclusion, our study identified seven novel methylation markers from cfDNA methylation data which may contribute to better prognosis for LUAD patients.

肺癌是全球范围内与癌症相关死亡的首要病因，其5年生存率偏低，部分原因在于临床可用生物标志物的匮乏。近期已有研究将DNA甲基化改变鉴定为潜在的癌症生物标志物。本研究通过在发现队列中对比肺腺癌（LUAD）患者与健康供者的循环游离DNA（cell-free DNA, cfDNA）全基因组甲基化数据，鉴定出了癌症特异性的CpG甲基化改变，共得到725个与LUAD风险相关的循环游离CpG位点。随后采用XGBoost（极限梯度提升算法）筛选出7个与LUAD风险相关的CpG位点。在训练阶段，本研究构建了7-CpG甲基化标志物组合，用于区分两类不同的预后亚组，且该组合与LUAD患者的总生存期（overall survival, OS）存在显著关联。我们发现cg02261780位点的甲基化水平与其对应基因GNA11的表达呈负相关关系，GNA11的甲基化水平与表达量均与LUAD患者的预后显著相关。基于亚硫酸氢盐PCR（bisulfite PCR）技术，本研究在20名LUAD患者的肿瘤组织及其配对的非恶性组织中，对5个CpG位点（cg02261780、cg09595050、cg20193802、cg15309457及cg05726109）的甲基化水平进行了验证。最后，本研究利用循环游离DNA甲基化的简化代表性亚硫酸氢盐测序（Reduced Representation Bisulfite Sequencing, RRBS）数据对7个CpG位点进行了验证，进一步证实了7-CpG甲基化标志物组合的可靠性。综上，本研究从循环游离DNA甲基化数据中筛选出7个全新的甲基化标志物，有望为LUAD患者的预后改善提供助力。