Ghanei Mahmoud, Poursheikhani Arash, Aarabi Azadeh, Taghechian Negin, Abbaszadegan Mohammad Reza
Medical Genetics and Molecular Medicine Department, Medical School, Mashhad University of Medical Sciences, Mashhad, Iran.
Medical Genetics Research Center, Medical School, Mashhad University of Medical Sciences, Mashhad, Iran.
Iran J Basic Med Sci. 2022 Jun;25(6):704-714. doi: 10.22038/IJBMS.2022.62181.13762.
Due to diagnosis of gastric cancer in advanced stages as well as its poor prognosis, finding biomarkers is essential. In this study, using the TCGA RNAseq data of gastric cancer patients, we evaluated the diagnostic value of lncRNAs that had differential expression.
We evaluated -value, FDR, and log fold change for whole transcripts. Next, by comparison of the RNAseq gene names with the total known lncRNA names, we identified differential expressed lncRNAs. Following this, specificity and sensitivity for lncRNAs coming from the previous step were calculated. For more confirmation, we predicted target genes and performed GO and KEGG signaling pathway analysis. In the end, we examined reliability and consistency of expression of this signature in three gastric cancer cell lines and one of them in twenty tumors and tumor-adjacent normal tissue samples using qRT-PCR.
Five lncRNAs had proper sensitivity and specificity and had target genes involved in cancer-related signaling pathways; however, they showed different expression patterns in TCGA data and .
The results of our study demonstrated that the five-lncRNAs , and require more investigation to be confirmed as diagnostic biomarkers in gastric cancer.
由于胃癌多在晚期被诊断出来且预后较差，因此寻找生物标志物至关重要。在本研究中，我们利用胃癌患者的TCGA RNA测序数据，评估了差异表达的长链非编码RNA（lncRNA）的诊断价值。
我们评估了整个转录本的P值、错误发现率（FDR）和对数倍变化。接下来，通过将RNA测序基因名称与已知的lncRNA总名称进行比较，我们鉴定出差异表达的lncRNA。在此之后，计算了上一步中lncRNA的特异性和敏感性。为了进一步确认，我们预测了靶基因并进行了基因本体（GO）和京都基因与基因组百科全书（KEGG）信号通路分析。最后，我们使用定量逆转录聚合酶链反应（qRT-PCR）检测了该特征在三种胃癌细胞系中的表达可靠性和一致性，以及在其中一种细胞系的20个肿瘤和肿瘤旁正常组织样本中的表达情况。
5种lncRNA具有合适的敏感性和特异性，且其靶基因参与癌症相关信号通路；然而，它们在TCGA数据和……中表现出不同的表达模式。
我们的研究结果表明，这5种lncRNA……需要更多研究来确认其作为胃癌诊断生物标志物的地位。
