非小细胞肺癌的微阵列数据的综合生物信息学分析。
Integrated bioinformatics analysis of microarray data from non-small cell lung cancer.
发表日期:2023 Jul 31
作者:
Lulu Feng, Wenping Cai, Shan Jin, Caipu Chun, Chengyan Wang, Luping Ma, Hao Peng, Xingxing Dong, Jinfang Jiang, Xianling Lu, Lijuan Pang
来源:
GENES & DEVELOPMENT
摘要:
非小细胞肺癌(NSCLC)由于其高死亡率、缺乏早期诊断标志物以及远处转移的预防问题,治疗面临着主要挑战。为了识别NSCLC中的潜在miRNAs和关键基因,寻找新的生物标志物和靶向基因治疗。从基因表达数据库(GEO)中获取了GSE102286、GSE56036、GSE25508、GSE53882、GSE29248和GSE101929数据集,并使用GEO2R和R软件包筛选差异共表达miRNAs(DE-miRNAs)和长非编码RNAs(DElncRs)。通过String和Funrich数据库对DE-miRNAs-靶基因进行通路富集分析,构建蛋白质相互作用(PPI)网络和竞争性内源性RNA(ceRNA)网络,并使用Cytoscape软件可视化。从五个数据集中筛选出19个共表达DE-miRNAs。预测的7683个上调和下调的DE-miRNAs-靶基因在癌症相关通路中显著集中。PPI网络中的前10个中枢节点被鉴定为中枢基因,例如MYC、EGFR、HSP90AA1和TP53、MYC和ACTB。通过构建miRNA-中枢基因网络,发现hsa-miR-21、hsa-miR-141、hsa-miR-200b和hsa-miR-30a、hsa-miR-30d、hsa-miR-145可能调节大部分中枢基因,而hsa-miR-141、hsa-miR-200和hsa-miR-145在miRNA和ceRNA调控网络中表达水平较高。总之,识别到的hsa-miR-21、hsa-miR-141、hsa-miR-200b、hsa-miR-30a、hsa-miR-30d和hsa-miR-145为理解NSCLC发展提供了新的理论依据。
Non-small cell lung cancer (NSCLC), with its high mortality rate, lack of early diagnostic markers and prevention of distant metastases are the main challenges in treatment. To identify potential miRNAs and key genes in NSCLC to find new biomarkers and target gene therapies. The GSE102286, GSE56036, GSE25508, GSE53882, GSE29248 and GSE101929 datasets were obtained from the Gene Expression Omnibus (GEO) database and screened for differentially co-expressed miRNAs (DE-miRNAs) and lncRNAs (DElncRs) by GEO2R and R software package. Pathway enrichment analysis of DE-miRNAs-target genes was performed by String and Funrich database to construct protein-protein interaction (PPI) and competing endogenous RNA (ceRNA) network and visualized with Cytoscape software. Nineteen co-expressed DE-miRNAs were screened from five datasets. The 7683 predicted up- and down-regulated DE-miRNAs-target genes were significantly concentrated in cancer-related pathways. The top 10 hub nodes in the PPI were identified as hub genes, such as MYC, EGFR, HSP90AA1 and TP53, MYC, and ACTB. By constructing miRNA-hub gene networks, hsa-miR-21, hsa-miR-141, hsa-miR-200b and hsa-miR-30a, hsa-miR-30d, hsa-miR-145 may regulate most hub genes and hsa-miR-141, hsa-miR-200, hsa-miR-145 had higher levels in the miRNA and ceRNA regulatory networks, respectively. In conclusion, the identification of hsa-miR-21, hsa-miR-141, hsa-miR-200b hsa-miR-30a, hsa-miR-30d and hsa-miR-145 provides a new theoretical basis for understanding the development of NSCLC.