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基于上皮-间质转化(EMT)相关长链非编码RNA(lncRNA)的肺腺癌预后分类器的鉴定及LINC01138在肿瘤进展中的作用

Identification of a prognostic classifier based on EMT-related lncRNAs and the function of LINC01138 in tumor progression for lung adenocarcinoma.

作者信息

Xiao Lingyan, Huang Yongbiao, Li Qian, Wang Sheng, Ma Li, Fan Zhijie, Tang Zhe, Yuan Xianglin, Liu Bo

机构信息

Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

出版信息

Front Mol Biosci. 2022 Aug 17;9:976878. doi: 10.3389/fmolb.2022.976878. eCollection 2022.

Abstract

This study aimed to develop a prognostic indicator based on epithelial-mesenchymal transition (EMT)-related long noncoding RNAs (lncRNAs) and explore the function of EMT-related lncRNAs in malignant progression in lung adenocarcinoma (LUAD). A LUAD dataset was acquired from The Cancer Genome Atlas (TCGA) to identify prognostic EMT-related lncRNAs via differential expression analysis and univariate Cox regression analysis. Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression analysis was utilized for variable selection and model construction. The EMT-related prognostic index (ERPI) was calculated according to the model and served as a classifier to divide LUAD individuals into high-ERPI and low-ERPI groups. A nomogram incorporating ERPI and clinicopathological variables was constructed. TCGA-LUAD, GSE50081, and GSE31210 were used to test the predictive capacity of the ERPI and nomogram. The characteristics of the tumor microenvironment (TME) were evaluated via the ESTIMATE, TIMER, and ssGSEA algorithms. Gene set variation analysis (GSVA) and ssGSEA were used to annotate the functions of the high-ERPI and low-ERPI groups. CCK8, transwell assay, wound-healing assay, and clone formation assay were conducted to clarify the biological functions of prognostic EMT-related lncRNAs. Ninety-seven differentially expressed EMT-related lncRNAs were identified, 15 of which were related to overall survival (OS). A prognostic signature was constructed based on 14 prognostic EMT-related lncRNAs to calculate the ERPI of each patient, and the predictive ability of ERPI was verified in TCGA, GSE50081, and GSE31210. The low-ERPI group survived longer and had a lower percentage of patients in advanced stage than the high-ERPI group. The nomogram had the highest predictive accuracy, followed by ERPI and stage. Patients with low ERPI had higher infiltration degree of immune cells and stronger immune responses than those with high ERPI. A series of experiments demonstrated that knockdown of dampened variability, proliferation, and motility of A549 and H460 cells. Our study developed a prognostic classifier with robust prognostic performance and clarified the biological functions of in LUAD, aiding in making individual treatments for patients with LUAD and dissecting the mechanism of oncogenesis.

摘要

本研究旨在基于上皮-间质转化(EMT)相关的长链非编码RNA(lncRNA)开发一种预后指标,并探讨EMT相关lncRNA在肺腺癌(LUAD)恶性进展中的作用。从癌症基因组图谱(TCGA)获取LUAD数据集,通过差异表达分析和单变量Cox回归分析来识别与预后相关的EMT相关lncRNA。采用最小绝对收缩和选择算子(LASSO)Cox回归分析进行变量选择和模型构建。根据该模型计算EMT相关预后指数(ERPI)并用作分类器,将LUAD个体分为高ERPI组和低ERPI组。构建了一个包含ERPI和临床病理变量的列线图。使用TCGA-LUAD、GSE50081和GSE31210来测试ERPI和列线图的预测能力。通过ESTIMATE、TIMER和ssGSEA算法评估肿瘤微环境(TME)的特征。使用基因集变异分析(GSVA)和ssGSEA对高ERPI组和低ERPI组的功能进行注释。进行CCK8、Transwell实验、伤口愈合实验和克隆形成实验,以阐明与预后相关的EMT相关lncRNA的生物学功能。共鉴定出97个差异表达的EMT相关lncRNA,其中15个与总生存期(OS)相关。基于14个与预后相关的EMT相关lncRNA构建了一个预后特征,以计算每位患者的ERPI,并在TCGA、GSE50081和GSE31210中验证了ERPI的预测能力。低ERPI组的生存期更长,晚期患者的比例低于高ERPI组。列线图的预测准确性最高,其次是ERPI和分期。低ERPI患者的免疫细胞浸润程度更高,免疫反应更强。一系列实验表明,敲低可降低A549和H460细胞的变异性、增殖和运动性。我们的研究开发了一种具有强大预后性能的预后分类器,并阐明了在LUAD中的生物学功能,有助于为LUAD患者制定个体化治疗方案并剖析肿瘤发生机制。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e1/9428519/e445a3ed0b5d/fmolb-09-976878-g001.jpg

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