Inconsistency in Expression Pattern of a Five-lncRNA Signature As a Potential Diagnostic Biomarker for Gastric Cancer Patients in Bioinformatics and in Vitro

BACKGROUND: Due to the diagnosis of gastric cancer in advance stages as well as its poor prognosis, finding biomarkers is essential. OBJECTIVE: In this study, using the TCGA RNAseq data of gastric cancer patients, we evaluated the diagnostic value of lncRNAs which had differential expression . METHODS: we evaluated P value, FDR, log fold change for whole transcripts. Next, by comparison of the RNAseq gene names with total known lncRNA names, we identified differntial expressed lncRNAs. Folowing, we calculated specificity and sensitivity for lncRNAs came from previous step. For more confirmation, we predict target genes and performed GO and KEGG signalling pathway analysis. At the end, we examined the reliability and consistency of expression of this signature in three gastric cancer cell lines and one of them in twenty tumoric and tumor adjacent normal tissue samples using qRT-PCR. RESULTS: Five lncRNAs had proper sensitivity and specificity and had target genes involved in cancer-related signaling pathways; however, they showed different expression pattern in TCGA data and in vitro. CONCLUSIONS: The results of our study demonstrated that the five-lncRNAs PART1 , UCA1 , DIRC3 , HOTAIR , and HOXA11AS require more investigation to be confirmed as a diagnostic biomarker in gastric cancer.