Bioinformatics Analysis of Microarray Datasets to Identify Prognostic Factors in Lung Adenocarcinoma.
- 作者列表："Jin X","Xu L","Guan Y","Zhang Z","Li H
:Most patients with lung adenocarcinoma (LUAD) present high recurrence rate and poor prognosis after therapy. Therefore, the purpose of this study was to identify prognostic factors involved in LUAD. Five microarray datasets (including GSE75037, GSE63459, GSE43458, GSE32863, and GSE10072) were downloaded. After data preprocessing and quality control, meta-analysis was performed to screen differentially expressed genes (DEGs) using the MetaDE.ES method in MetaDE package. Subsequently, network construction and module identification were conducted by the Weighted Gene Co-expression Network Analysis method. Moreover, survival-associated genes were identified using the univariate and multivariate Cox regression method in survival package. The risk score model was constructed by prognosis associated genes, followed by the Kaplan-Meier survival analysis. Oncomine expressions analysis of several prognosis associated genes was conducted. The expression levels of key genes were detected using quantitative real-time PCR experiments. A total of 1434 DEGs between LUAD and normal samples were identified. Nine disease-associated modules were identified, in which M8 module was most correlated with LAUD phenotype. A total of 89 indicators (including T stage, M stage, and ADIPOR2) were significantly associated with LAUD prognosis, while only T stage and 9 DEGs (e.g., ARHGEF3, GTSE1, RBM15 and CD52) were retained as the potential prognostic factors following multivariate COX regression analysis. The upregulated adiponectin receptor 2 (ADIPOR2), rho guanine nucleotide exchange factor 3 (ARHGEF3), and CD52 molecule (CD52), and downregulated GTSE1 were validated in LAUD samples of Oncomine database. Importantly, ADIPOR2 and ARHGEF3 were confirmed to be down-regulated in LUAD tissues. ADIPOR2, ARHGEF3, G2 and S-phase expressed 1 (GTSE1) and CD52 might be promising prognostic factors in LUAD.
: 大多数肺腺癌 (LUAD) 患者治疗后复发率高，预后差。因此，本研究的目的是确定LUAD的预后因素。下载了五个微阵列数据集 (包括GSE75037 、GSE63459 、GSE43458 、GSE32863 和GSE10072)。在数据预处理和质量控制后，使用MetaDE包中的MetaDE.ES方法进行meta分析以筛选差异表达基因 (DEGs)。随后，通过加权基因共表达网络分析方法进行网络构建和模块鉴定。此外，使用生存包中的单变量和多变量Cox回归方法鉴定生存相关基因。通过预后相关基因构建风险评分模型，随后进行Kaplan-Meier生存分析。对几种预后相关基因进行Oncomine表达分析。利用实时定量PCR实验检测关键基因的表达水平。在LUAD和正常样品之间总共鉴定了 1434 个DEGs。鉴定了 9 个疾病相关模块，其中M8 模块与LAUD表型最相关。共有 89 项指标 (包括T分期、M分期和ADIPOR2) 与LAUD预后显著相关，而只有T分期和 9 项DEGs (e.g.，ARHGEF3，GTSE1，RBM15 和CD52) 保留作为多因素COX回归分析后的潜在预后因素。在Oncomine数据库的LAUD样本中验证了上调的脂联素受体 2 (ADIPOR2) 、rho鸟嘌呤核苷酸交换因子 3 (ARHGEF3) 和CD52 分子 (CD52) 以及下调的GTSE1。重要的是，ADIPOR2 和ARHGEF3 被证实在LUAD组织中被下调。ADIPOR2 、ARHGEF3 、G2 和S期表达 1 (GTSE1) 和CD52 可能是LUAD有前景的预后因素。
METHODS::Pulmonary artery sling is a rare congenital anomaly of the origin and course of the left pulmonary artery. Patients with this condition typically present with respiratory failure in young infancy, and asymptomatic cases are uncommon. We describe the case of an adult patient with a lung adenocarcinoma of the right upper lobe, extending into the hilum and superior mediastinum, and with a previously unknown pulmonary artery sling anomaly. The local invasiveness of the tumor and the peculiar vascular anatomy contributed to a unique surgical scenario, wherein multiple reconstructive procedures were required.
METHODS::Patients with idiopathic pulmonary fibrosis (IPF) have higher risk of developing lung cancer, for example, squamous cell carcinoma (SCC), and show poor prognosis, while the molecular basis has not been fully investigated. Here we conducted DNA methylome analysis of lung SCC using 20 SCC samples with/without IPF, and noncancerous lung tissue samples from smokers/nonsmokers, using Infinium HumanMethylation 450K array. SCC was clustered into low- and high-methylation epigenotypes by hierarchical clustering analysis. Genes hypermethylated in SCC significantly included genes targeted by polycomb repressive complex in embryonic stem cells, and genes associated with Gene Ontology terms, for example, "transcription" and "cell adhesion," while genes hypermethylated specifically in high-methylation subgroup significantly included genes associated with "negative regulation of growth." Low-methylation subgroup significantly correlated with IPF (78%, vs. 17% in high-methylation subgroup, p = 0.04), and the correlation was validated by additional Infinium analysis of SCC samples (n = 44 in total), and data from The Cancer Genome Atlas (n = 390). The correlation between low-methylation subgroup and IPF was further validated by quantitative methylation analysis of marker genes commonly hypermethylated in SCC (HOXA2, HOXA9 and PCDHGB6), and markers specifically hypermethylated in high-methylation subgroup (DLEC1, CFTR, MT1M, CRIP3 and ALDH7A1) in 77 SCC cases using pyrosequencing (p = 0.003). Furthermore, low-methylation epigenotype significantly correlated with poorer prognosis among all SCC patients, or among patients without IPF. Multivariate analysis showed that low-methylation epigenotype is an independent predictor of poor prognosis. These may suggest that lung SCC could be stratified into molecular subtypes with distinct prognosis, and low-methylation lung SCC that significantly correlates with IPF shows unfavorable outcome.
METHODS::The role of Fyn-related kinase (FRK) in malignant tumors remains controversial. Our study investigated the function of FRK in lung cancer. Immunohistochemistry staining and generating a knockout of FRK by CRISPR/Cas9 in H1299 (FRK-KO-H1299) cells were strategies used to explore the role of FRK. Immunohistochemistry staining indicated that FRK expression was elevated in 223 lung cancer tissues compared to 26 distant normal lung tissues. FRK contributed to poor survival status in lung cancer patients and acted as a predictor for poor prognosis of lung cancer. Knockout of FRK by CRISPR/Cas9 markedly inhibited proliferation, invasion, colony formation and epithelial-mesenchymal transition (EMT) process in the lung cancer cell line H1299. Further exploration indicated that FRK-KO damaged the stemness phenotype of H1299 by inhibiting CD44 and CD133 expression. Seahorse detection and a U-13 C flux assay revealed that FRK-KO induced metabolism reprogramming by inhibiting the Warburg effect and changing the energy type in H1299 cells. Epidermal growth factor stimulation recovered the expression of FRK and biological functions, metabolic reprogramming and stemness phenotype of H1299 cells. FRK plays an oncogenic role in lung cancer cells via a novel regulation mechanism of enhancing the stemness of H1299 cells by inducing metabolism reprogramming, which finally promotes EMT and metastasis. Our study also indicates that FRK could be used as a potential therapeutic target for drug development.