Comprehensive Analysis of DNA Methylation and Gene Expression Datasets Identified MMP9 and TWIST1 as Important Pathogenic Genes of Lung Adenocarcinoma

Identification of a Potentially Functional microRNA-mRNA Regulatory Network in Lung Adenocarcinoma Using a Bioinformatics Analysis

BACKGROUND

Lung adenocarcinoma (LUAD) is a common lung cancer with a high mortality, for which microRNAs (miRNAs) play a vital role in its regulation. Multiple messenger RNAs (mRNAs) may be regulated by miRNAs, involved in LUAD tumorigenesis and progression. However, the miRNA-mRNA regulatory network involved in LUAD has not been fully elucidated.

METHODS

Differentially expressed miRNAs and mRNA were derived from the Cancer Genome Atlas (TCGA) dataset in tissue samples and from our microarray data in plasma (GSE151963). Then, common differentially expressed (Co-DE) miRNAs were obtained through intersected analyses between the above two datasets. An overlap was applied to confirm the Co-DEmRNAs identified both in targeted mRNAs and DEmRNAs in TCGA. A miRNA-mRNA regulatory network was constructed using Cytoscape. The top five miRNA were identified as hub miRNA by degrees in the network. The functions and signaling pathways associated with the hub miRNA-targeted genes were revealed through Gene Ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The key mRNAs in the protein-protein interaction (PPI) network were identified using the STRING database and CytoHubba. Survival analyses were performed using Gene Expression Profiling Interactive Analysis (GEPIA).

RESULTS

The miRNA-mRNA regulatory network consists of 19 Co-DEmiRNAs and 760 Co-DEmRNAs. The five miRNAs (miR-539-5p, miR-656-3p, miR-2110, let-7b-5p, and miR-92b-3p) in the network were identified as hub miRNAs by degrees (>100). The 677 Co-DEmRNAs were targeted mRNAs from the five hub miRNAs, showing the roles in the functional analyses of the GO analysis and KEGG pathways (inclusion criteria: 836 and 48, respectively). The PPI network and Cytoscape analyses revealed that the top ten key mRNAs were NOTCH1, MMP2, IGF1, KDR, SPP1, FLT1, HGF, TEK, ANGPT1, and PDGFB. SPP1 and HGF emerged as hub genes through survival analysis. A high SPP1 expression indicated a poor survival, whereas HGF positively associated with survival outcomes in LUAD.

CONCLUSION

This study investigated a miRNA-mRNA regulatory network associated with LUAD, exploring the hub miRNAs and potential functions of mRNA in the network. These findings contribute to identify new prognostic markers and therapeutic targets for LUAD patients in clinical settings.

miR-19a-3p Facilitates Lung Adenocarcinoma Cell Phenotypes by Inhibiting TEK

Background: Both TEK and miR-19a-3p have been reported to regulate lung adenocarcinoma (LUAD) progression. However, the association between TEK and miR-19a-3p in LUAD remained unknown. This research aimed to investigate a novel miR-19a-3p/TEK interactome in LUAD cells. Methods: The mRNA expression and protein expression in the cell lines were determined using qPCR and Western blot assay, respectively. CCK-8 assay, EDU assay, flow cytometry cell apoptosis assay, scratch assay, and cell-to-extracellular matrix adhesion assay were performed to detect the proliferation, apoptosis, migration, and adhesion ability of A549 and H1975 cell lines. Results: Findings revealed that both mRNA and protein levels of TEK were downregulated in the LUAD tumor tissues and cell lines. It was also found that compared with the control group, the transfection of TEK overexpression plasmids into H1975 and A549 cell lines significantly inhibited cancerous phenotypes. However, experimental results indicated that by downregulating TEK, miR-19a-3p promoted LUAD cell phenotypes. Conclusion: This research demonstrated that an interactome existed between miR-19a-3p and TEK and that miR-19a-3p could suppress LUAD tumors by inhibiting TEK. This novel interactome could be used as a novel therapy target for LUAD.

Methylation biomarkers with discriminating ability are potential therapeutic targets in lung adenocarcinoma

Aims: Given the reversibility of methylation, biomarkers with discriminating ability are of great interest for targeted therapeutic sites. Materials & methods: Methylation array data of 461 lung adenocarcinoma (LUAD) patients comprising of 458 tumor and 32 LUAD paracancerous samples were compared using partial least squares discrimination analysis and receiver operating characteristics analysis. Results: A six-DNA methylation signature (corresponding to five genes) was found to significantly discriminate normal and LUAD samples. Kyoto Encyclopedia of Genes and Genomes analysis indicated enrichment of methylation sites in the Wnt pathway in LUAD compared with controls. Conclusion: This six-DNA methylation signature demonstrated potential as a novel biomarker for diagnosis and therapeutic targets. Further, inhibition of Wnt signaling pathway may be an important step in LUAD progression.

Twist1 promotes astrocytoma development by stimulating vasculogenic mimicry

Astrocytomas are one of the most vascularized types tumor in human cancers. Micro-vascular proliferation is an important factor for the classification of astrocytoma. Vasculogenic mimicry (VM) is a novel tumor vascular model that develops independently of endothelial cells, and serves an important role in astrocytoma. Twist family bHLH transcription factor 1 (Twist1) is able to regulate the formation of VM; thus in the present study, the expression and importance of Twist1 was studied in astrocytoma tissues. The present study confirmed that the expression of Twist1 was associated with the grade of astrocytoma. Twist1 promotes the formation of VM and the development of astrocytomas, and may also regulate the formation of VM via vascular endothelial-cadherin and matrix metalloproteinase-9.

Polymorphism of MMP-9 gene is not associated with the risk of urinary cancers: Evidence from an updated meta-analysis

OBJECTIVE

Matrix metalloproteinases 9 (MMP-9) is a zinc-dependent gelatinase, which could decrease the expression of extracellular matrix proteins and influence the metastatic behavior of tumors. In order to draw a comprehensive and precise result about the relationship of MMP-9 and urinary cancers, we presented the current meta-analysis.

METHODS

We searched the PubMed, EMbase, Web of Science, CBM, CNKI and Wanfang databases, the cited references were also manually searched again, covering all the papers published until August 2018. Quality assessment was conducted using the Newcastle-Ottawa Scale. All the meta-analysis was conducted with Stata version 12.0 software to assess the strength of the association. Linkage disequilibrium (LD) analyses of gene polymorphisms and in-silico analysis of MMP-9 expression were also conducted to illustrate the relationship.

RESULTS

17 case-control studies comprise of more than 6154 cases and 6330 controls were enrolled and analyzed. After analyzed, we found that there is no significant association between rs3918241, rs2250889, rs17576 and rs17577 of MMP-9 and urinary cancers. LD analysis uncovered a significant LD between rs3918241 and rs17577 in CEU, CHB&CHS, ESN, and JPT populations (CEU: r² = 1.0; CHB&CHS: r² = 1.0; ESN: r² = 0.74; JPT: r² = 0.77), as well as a remarkable LD between rs17576 and rs2250889 in CHB&CHS and JPT populations (CHB&CHS: r² = 0.81; JPT: r² = 0.82). Furthermore, in-silico results indicated that the expression of MMP-9 in cancer tissue was higher than that in normal tissue in prostate cancer (Transcripts Per Kilobase Million (TPM) = 7.14 vs. 1.36, P < 0.001), bladder cancer (TPM = 14.2 vs. 2.47, P < 0.001), kidney renal clear cell carcinoma (TPM = 7.43 vs. 1.61, P < 0.001), kidney renal papillary cell carcinoma (TPM = 5.52 vs. 1.74, P = 0.002).

CONCLUSIONS

rs3918241, rs2250889, rs17576 and rs17577 polymorphisms of MMP-9 are not associated with altered risk of urinary cancer. More studies with large sample size focused on the combined effect of two or more polymorphisms of MMP-9 are necessary in the future.