Microarray data analysis to identify miRNA biomarkers and construct the lncRNA-miRNA-mRNA network in lung adenocarcinoma

Abstract

MicroRNAs (miRNAs), regulatory noncoding RNAs, are involved in gene regulation and may play a role in cancer development. The aim of this study was to identify miRNAs involved in lung adenocarcinoma (LUAD) using bioinformatics analysis. MiRNA (GSE135918), mRNA (GSE136043) and lncRNA (GSE130779) microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed miRNAs (DEMis), mRNAs (DEMs), and lncRNA (DELs) in LUAD. We used DEMs for functional enrichment analysis. MiRNA expression quantification from The Cancer Genome Atlas (TCGA) was used to validate DEMis. LncBase Predicted v.2, Targetscan, and MiRBase were used to predict lncRNAs and mRNAs. The LUAD data in TCGA were used for overall survival (OS) analysis. We screened the downregulation of 8 DEMis and upregulation of 6 DEMis, and found that 70 signal pathways changed. We chose 3 relevant signaling pathways in lung cancer development, WNT, PI3K-Akt, and Notch, and scanned for mRNAs involved in them that are potential targets of these miRNAs. Then a lncRNA-miRNA-mRNA network was constructed. We also found 7 miRNAs that were associated with poor OS in LUAD. Low expression level of hsa-miR-30a was highly associated with poor OS in LUAD (P < .001) and the target genes of hsa-miR-30a-3p were abundant in the Wnt and AKT signaling pathways. In addition, our results reported for the first time that hsa-miR-3944 and hsa-miR-3652 were highly expressed in LUAD. And the high expression level of hsa-miR-3944 was associated with poor OS (P < .05). Hsa-miR-30a-3p may suppress the occurrence and progression of lung cancer through Wnt and AKT signaling pathways and become a good biomarker in LUAD. Hsa-miR-3944 and hsa-miR-3652 may serve as new biomarkers in LUAD. Abbreviations: ceRNA = competitive endogenous RNA, DELs = differentially expressed lncRNAs, DEMis = differentially expressed miRNAs, DEMs = differentially expressed mRNAs, GEO = Gene Expression Omnibus, GO = Gene ontology, KEGG = Kyoto Encyclopedia of Genes and Genomes, LUAD = lung adenocarcinoma, NSCLS = non-small cell lung cancer, OS = overall survival, PCA = principal component analysis, SCLC = small cell lung cancer (SCLC), TCGA = The Cancer Genome Atlas.

Screening Differential Expression Profiles of Urinary microRNAs in a Gentamycin-Induced Acute Kidney Injury Canine Model

“…However, in a clinical study, when compared to participants with AKI stage 3 renal non-recovery, hsa-miR-30a-3p was decreased in the serum of participants with AKI stage 3 renal recovery (0.74 vs. 0.89), but this finding was not statistically significant [28]. Interestingly, hsa-miR-30a-3p expression was down-regulated in lung adenocarcinoma, which was largely involved in the regulation of Wnt and AKT signaling pathways [29]. miR-30a-3p has been reported to be dysregulated in clear renal cell carcinomas, serving as an effective biomarker for the early diagnosis of lung cancer [30].…”