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一种计算机模拟方法用于探索六个基因作为肺腺癌的分子特征。

An in-silico approach leads to explore six genes as a molecular signatures of lung adenocarcinoma.

作者信息

Abdel-Maksoud Mostafa A, Hassan Fatima, Mubarik Uzma, Mubarak Ayman, Farrag Mohamed A, Alghamdi Sumaiah, Atuahene Sampson Agyapong, Almekhlafi Sally, Aufy Mohammed

机构信息

Department of Botany and Microbiology, College of Science, King Saud University Riyadh 11451, Saudi Arabia.

Fatima Jinnah Medical University Lahore Pakistan.

出版信息

Am J Cancer Res. 2023 Mar 15;13(3):727-757. eCollection 2023.

Abstract

Due to heterogenetic-specific nature of the available biomarkers, the incidence of lung adenocarcinoma (LUAD) is on the rise worldwide. Previously reported LUAD-related hub genes were searched from the medical literature via literature mining and were processed to identify few top genes via degree method. Later, a comprehensive in silico methodology was applied on the selected real hub genes to identify their tumor driving, diagnostic, and prognostic roles in LUAD patients with divers clinicopathological variables. Out of total 145 extracted hub genes, six genes including CDC6, PBK, AURKA, KIF2C, OIP5, and PRC1 were identified as real hub genes. The expression analysis showed that all these genes were significantly up-regulated across LUAD samples of different clinicopathological variables. In addition, a variety of unique correlations among the expression and of real hub genes and some other parameters including promoter methylation status, overall survival (OS), genetic changes, tumor purity, and immune cell infiltration have also been explored in the present study. Moreover, via TFS-miRNA-mRNA regulatory network, one important TF (E2F1) and one important miRNAs (hsa-mir-34a-5p) that targeted all the real hub genes were also identified. Finally, a variety of drugs also predicted to be very useful in treating LUAD. The discovery of the real hub genes, TFS-miRNA-mRNA network, and chemotherapeutic drugs associated with LUAD provides new insights into underlying mechanisms and treatment of LUAD overcoming heterogeneity barriers.

摘要

由于现有生物标志物具有异质性特异性,肺腺癌(LUAD)在全球的发病率呈上升趋势。通过文献挖掘从医学文献中搜索先前报道的与LUAD相关的枢纽基因,并通过度方法进行处理以识别少数顶级基因。随后,对选定的真正枢纽基因应用了一种全面的计算机模拟方法,以确定它们在具有不同临床病理变量的LUAD患者中的肿瘤驱动、诊断和预后作用。在总共提取的145个枢纽基因中,包括CDC6、PBK、AURKA、KIF2C、OIP5和PRC1在内的6个基因被确定为真正的枢纽基因。表达分析表明,所有这些基因在不同临床病理变量的LUAD样本中均显著上调。此外,本研究还探讨了真正枢纽基因的表达与其他一些参数(包括启动子甲基化状态、总生存期(OS)、基因变化、肿瘤纯度和免疫细胞浸润)之间的各种独特相关性。此外,通过TFS-miRNA-mRNA调控网络,还确定了一个靶向所有真正枢纽基因的重要转录因子(E2F1)和一个重要的微小RNA(hsa-mir-34a-5p)。最后,还预测了多种药物对治疗LUAD非常有用。与LUAD相关的真正枢纽基因、TFS-miRNA-mRNA网络和化疗药物的发现为LUAD的潜在机制和克服异质性障碍的治疗提供了新的见解。

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