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. 2020 Jan-Dec:19:1533033820956998.
doi: 10.1177/1533033820956998.

An Integrated Analysis of mRNAs and miRNAs Microarray Profiles to Screen miRNA Signatures Involved in Nasopharyngeal Carcinoma

Lei Liu  1   2   3   4 , Hailing Wang  5   6   7 , Chaohui Yan  1   2   3   4 , Shudong Tao  1   2   3   4
Affiliations

An Integrated Analysis of mRNAs and miRNAs Microarray Profiles to Screen miRNA Signatures Involved in Nasopharyngeal Carcinoma

Lei Liu et al. Technol Cancer Res Treat. 2020 Jan-Dec.

Abstract

Objective: We aim to identify several microRNAs (miRNAs/miRs)-messenger RNAs (mRNAs) biomarkers correlated to nasopharyngeal carcinoma (NPC) based on an integrated analysis of miRNA and mRNAs microarray expression profiles.

Methods: The available mRNA and miRNA microarray datasets were retrieved from Gene Expression Omnibus (GEO) database according to pre-determined screening criteria. Differentially expressed miRNA and mRNAs (DEmiRNAs and DEmRNAs) were extracted between NPC and noncancerous nasopharyngeal tissues. The target genes of DEmiRNAs were predicted with miRTarBase followed by the construction of DEmiRNAs-target DEmRNAs network, and functional analyses were performed. The DEmiRNAs expressions were validated and the performance of these DEmiRNAs was assessed by the area under the curve (AUC) values. Finally, the correlations between DEmiRNAs and specific clinical factors were analyzed.

Results: There were 1140 interaction pairs (including let-7d/f-MYC/HMGA2 and miR-452-ITGA9) in DEmiRNAs-target DEmRNAs network. The GO annotation analysis showed that several genes such as MYC, HMGA2 and ITGA9 primarily participated in cellular process. KEGG analysis showed that these targets were associated with cell cycle and cancer-related pathways. Down-regulated let-7(-d and -f) and up-regulated miR-452 were verified in datasets. The AUC values of these 3 DEmiRNAs (let-7d, let-7-f and miR-452) was 0.803, 0.835 and 0.735, respectively. Besides, miR-452 was significantly related to survival rate of NPC patients.

Conclusion: The findings implied let-7d/f-MYC/HMGA2 and miR-452-ITGA9 might be promising targets for the detection and treatment of NPC.

Keywords: biomarker; mRNA; microRNA; nasopharyngeal carcinoma.

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Conflict of interest statement

Declaration of Conflicting Interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Figures

Figure 1.
Figure 1.
The DEmiRNAs-target DEmRNAs network. The orange ovals show the up-regulated target genes for DEmiRNAs and blue ovals indicates the down-regulated target genes for DEmiRNAs in nasopharyngeal carcinoma tissues. The red triangles indicate up-regulated miRNAs while green triangles denote down-regulated miRNAs in nasopharyngeal carcinoma tissues. DEmiRNAs: differentially expressed microRNAs.
Figure 2.
Figure 2.
Pathway in cancer from the Kyoto Encyclopedia of Genes and Genomes enrichment analysis. The red color shows the up-regulated genes while blue color represents the down-regulated genes in nasopharyngeal carcinoma tissues. The green color indicates genes which had no significant difference between nasopharyngeal carcinoma tissues and control tissues.
Figure 3.
Figure 3.
MicroRNAs in cancer from the Kyoto Encyclopedia of Genes and Genomes enrichment analysis. The red color shows the up-regulated genes while blue color represents the down-regulated genes in nasopharyngeal carcinoma tissues. The green color indicates genes which had no significant difference between nasopharyngeal carcinoma tissues and control tissues.
Figure 4.
Figure 4.
The ROC curves of key miRNAs in GSE43329 and GSE48442 datasets. The X-axis indicated 1-specificity and Y-axis represented sensitivity. (A) ROC curve of let-7f in GSE43329 dataset; (B) ROC curve of let-7 g in GSE43329 dataset; (C)ROC curve of miR-29a in GSE43329 dataset; (D) ROC curve of miR-452 in GSE48442 dataset. ROC: receiver operating characteristic.
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