Dataset Information

Expression levels and co?targets of miRNA?126?3p and miRNA?126?5p in lung adenocarcinoma tissues: ?n exploration with RT?qPCR, microarray and bioinformatic analyses.

ABSTRACT: Lung adenocarcinoma (LUAD) is the most common histological subtype of lung cancer. Previous studies have found that many microRNAs (miRNAs), including miRNA?126?3p, may play a critical role in the development of LUAD. However, no study of LUAD has researched the synergistic effects and co?targets of both miRNA?126?3p and miRNA?126?5p. The present study used real?time quantitative polymerase chain reaction (RT?qPCR) to explore the expression values of miRNA?126?3p and miRNA?126?5p in 101 LUAD and 101 normal lung tissues. Ten relevant microarray datasets were screened to further validate the expression levels of miRNA?126?3p and ?5p in LUAD. Twelve prediction tools were employed to obtain potential targets of miRNA?126?3p and miRNA?126?5p. The results showed that both miRNA?126?3p and ?5p were expressed significantly lower in LUAD. A significant positive correlation was also present between miRNA?126?3p and ?5p expression in LUAD. In addition, lower expression of miRNA?126?3p and ?5p was indicative of vascular invasion, lymph node metastasis (LNM), and a later tumor/node/metastasis (TNM) stage of LUAD. The authors obtained 167 targets of miRNA?126?3p and 212 targets of miRNA?126?5p; 44 targets were co?targets of both. Eight co?target genes (IGF2BP1, TRPM8, DUSP4, SOX11, PLOD2, LIN28A, LIN28B and SLC7A11) were initially identified as key genes in LUAD. The results of the present study indicated that the co?regulation of miRNA?126?3p and miRNA?126?5p plays a key role in the development of LUAD, which also suggests a fail?proof mode between miRNA?3p and miRNA?126?5p.

SUBMITTER: Chen P

PROVIDER: S-EPMC6313014 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Expression levels and co‑targets of miRNA‑126‑3p and miRNA‑126‑5p in lung adenocarcinoma tissues: Αn exploration with RT‑qPCR, microarray and bioinformatic analyses.

Chen Peng P Gu Yong-Yao YY Ma Fu-Chao FC He Rong-Quan RQ Li Zu-Yun ZY Zhai Gao-Qiang GQ Lin Xia X Hu Xiao-Hua XH Pan Lin-Jiang LJ Chen Gang G

Oncology reports 20181204 2

Lung adenocarcinoma (LUAD) is the most common histological subtype of lung cancer. Previous studies have found that many microRNAs (miRNAs), including miRNA‑126‑3p, may play a critical role in the development of LUAD. However, no study of LUAD has researched the synergistic effects and co‑targets of both miRNA‑126‑3p and miRNA‑126‑5p. The present study used real‑time quantitative polymerase chain reaction (RT‑qPCR) to explore the expression values of miRNA‑126‑3p and miRNA‑126‑5p in 101 LUAD and ...[more]

PMID: 30535503

Similar Datasets

Project description:MicroRNAs (miRNAs/miRs) have been reported to be closely associated with numerous human diseases, including cholangiocarcinoma (CCA). However, the number of miRNAs known to be involved in CCA is limited, and the association between miR?132?3p and CCA remains unknown. In the present study, the clinical role of miR?132?3p and its potential signaling pathways were investigated by multiple approaches. Reverse transcription?quantitative PCR (RT?qPCR), CCA?associated Gene Expression Omnibus (GEO), ArrayExpress and Sequence Read Archive (SRA) miRNA?microarray or miRNA?sequencing data were screened, and meta?analyses were conducted, in order to calculate the receiver operating characteristic (ROC) curve and standardized mean difference (SMD). The predicted target genes of miR?132?3p were obtained from 12 online databases and were combined with the downregulated differentially expressed genes identified in the RNA?sequencing data of CCA. Gene Ontology annotation and pathway analysis were performed in WebGestalt. Protein?protein interaction analyses were conducted in STRING. The Cancer Genome Atlas (TCGA) mRNA expression profiles were used to validate the expression levels of hub genes at the mRNA level. The Human Protein Atlas was used to identify the protein expression levels of hub genes in CCA tissues and non?tumor biliary epithelium. The meta?analyses comprised 10 groups of RT?qPCR data, eight GEO microarray datasets and one TCGA miRNA?sequencing dataset. The SMD of miR?132?3p in CCA was 0.75 (95% CI: 0.25, 1.24), which indicated that miR?132?3p was overexpressed in CCA tissues. This finding was supported by a summary ROC value of 0.80 (95% CI: 0.76, 0.83). The pooled sensitivity and specificity were 0.81 (95% CI: 0.59, 0.93) and 0.71 (95% CI: 0.58, 0.81), respectively. The relative expression level of miR?132?3p in the early stage of CCA (stages I?II) was 6.8754±0.5279, which was markedly lower than that in the advanced stage (stages III?IVB), 7.3034±0.3267 (P=0.003). Consistently, the miR?132?3p level in low?grade CCA (grades G1?G2) was 6.7581±0.5297, whereas it was 7.1191±0.4651 in patients with high?grade CCA (grades G3?G4) (P=0.037). Furthermore, 555 potential target genes of miR?132?3p in CCA were mainly enriched in the 'Focal Adhesion?PI3K?Akt?mTOR?signaling pathway'. In conclusion, upregulation of miR?132?3p may serve a pivotal role in the tumorigenesis and progression of CCA by targeting different pathways. Further in vitro and in vivo studies are required to support the current findings.

Project description:BACKGROUND:MiR-182-5p, a cancer-related microRNA (miRNA), modulates tumorigenesis and patient outcomes in various human malignances. This study interroted the clinicopathological significance and molecular mechanisms of miR-182-5p in non-small cell lung cancer (NSCLC). METHODS:The clinical significance of miR-182-5p in NSCLC subtypes was determined based on an analysis of 124 samples (lung adenocarcinomas [LUADs], n =?101; lung squamous cell carcinomas [LUSCs], n =?23) obtained from NSCLC patients and paired noncancer tissues and an analysis of data obtained from public miRNA-seq database, miRNA-chip database, and the scientific literature. The NSCLC samples (n =?124) were analyzed using the real-time quantitative polymerase chain reaction (RT-qPCR). Potential targets of miR-182-5p were identified using lists generated by miRWalk v.2.0, a comprehensive atlas of predicted and validated targets of miRNA-target interactions. Molecular events of miR-182-5p in NSCLC were unveiled based on a functional analysis of candidate targets. The association of miR-182-5p with one of the candidate target genes, homeobox A9 (HOXA9), was validated using in-house RT-qPCR and dual-luciferase reporter assays. RESULTS:The results of the in-house RT-qPCR assays analysis of data obtained from public miRNA-seq databases, miRNA-chip databases, and the scientific literature all supported upregulation of the expression level of miR-182-5p level in NSCLC. Moreover, the in-house RT-qPCR data supported the influence of upregulated miR-182-5p on malignant progression of NSCLC. In total, 774 prospective targets of miR-182-5p were identified. These targets were mainly clustered in pathways associated with biological processes, such as axonogenesis, axonal development, and Ras protein signal transduction, as well as pathways involved in axonal guidance, melanogenesis, and longevity regulation, in multiple species. Correlation analysis of the in-house RT-qPCR data and dual-luciferase reporter assays confirmed that HOXA9 was a direct target of miR-182-5p in NSCLC. CONCLUSIONS:The miR-182-5p expression level was upregulated in NSCLC tissues. MiR-182-5p may exert oncogenic influence on NSCLC through regulating target genes such as HOXA9.

Project description:To examine the clinical value of miR-198-5p in lung squamous cell carcinoma (LUSC).Gene Expression Omnibus (GEO) microarray datasets were used to explore the miR-198-5p expression and its diagnostic value in LUSC. Real-time reverse transcription quantitative polymerase chain reaction was used to evaluate the expression of miR-198-5p in 23 formalin-fixed, paraffin-embedded (FFPE) LUSC tissues and corresponding non-cancerous tissues. The correlation between miR-198-5p expression and clinic pathological features was assessed. Meanwhile, putative target messenger RNAs of miR-198-5p were identified based on the analysis of differentially expressed genes in the Cancer Genome Atlas (TCGA) and 12 miRNA prediction tools. Subsequently, the putative target genes were sent to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses.MiR-198-5p was low expressed in LUSC tissues. The combined standard mean difference (SMD) values of miR-198-5p expression based on GEO datasets were -?0.30 (95% confidence interval (CI) -?0.54, -?0.06) and -?0.39 (95% CI -?0.83, 0.05) using fixed effect model and random effect model, respectively. The sensitivity and specificity were not sufficiently high, as the area under the curve (AUC) was 0.7749 (Q*?=?0.7143) based on summarized receiver operating characteristic (SROC) curves constructed using GEO datasets. Based on the in-house RT-qPCR, miR-198-5p expression was 4.3826?±?1.7660 in LUSC tissues and 4.4522?±?1.8263 in adjacent normal tissues (P?=?0.885). The expression of miR-198-5p was significantly higher in patients with early TNM stages (I-II) than that in cases with advanced TNM stages (III-IV) (5.4400?±?1.5277 vs 3.5690?±?1.5228, P?=?0.008). Continuous variable-based meta-analysis of GEO and PCR data displayed the SMD values of -?0.26 (95% CI -?0.48, -?0.04) and -?0.34 (95% CI -?0.71, 0.04) based on fixed and random effect models, respectively. As for the diagnostic value of miR-198-5p, the AUC based on the SROC curve using GEO and PCR data was 0.7351 (Q*?=?0.6812). In total, 542 genes were identified as the targets of miR-198-5p. The most enriched Gene Ontology terms were epidermis development among biological processes, cell junction among cellular components, and protein dimerization activity among molecule functions. The pathway of non-small cell lung cancer was the most significant pathway identified using Kyoto Encyclopedia of Genes and Genomes analysis.The expression of miR-198-5p is related to the TNM stage. Thus, miR-198-5p might play an important role via its target genes in LUSC.

Dataset Information

Expression levels and co?targets of miRNA?126?3p and miRNA?126?5p in lung adenocarcinoma tissues: ?n exploration with RT?qPCR, microarray and bioinformatic analyses.

Publications

Expression levels and co‑targets of miRNA‑126‑3p and miRNA‑126‑5p in lung adenocarcinoma tissues: Αn exploration with RT‑qPCR, microarray and bioinformatic analyses.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets