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. 2020 Jan 6;13(1):3.
doi: 10.1186/s12920-019-0648-7.

MiR-182-5p and its target HOXA9 in non-small cell lung cancer: a clinical and in-silico exploration with the combination of RT-qPCR, miRNA-seq and miRNA-chip

Li Gao  1 , Shi-Bai Yan  2 , Jie Yang  3 , Jin-Liang Kong  4 , Ke Shi  1 , Fu-Chao Ma  2 , Lin-Zhen Huang  1 , Jie Luo  5 , Shu-Ya Yin  1 , Rong-Quan He  2 , Xiao-Hua Hu  6 , Gang Chen  7
Affiliations

MiR-182-5p and its target HOXA9 in non-small cell lung cancer: a clinical and in-silico exploration with the combination of RT-qPCR, miRNA-seq and miRNA-chip

Li Gao et al. BMC Med Genomics. .

Abstract

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.

Keywords: HOXA9; Non-small cell lung cancer; RT-qPCR; miR-182-5p; miRNA-chips; miRNA-seq.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Meta-analysis of miRNA-chip data for LUAD. a. Forest plot for overall SMD; b. Subgroup analysis; c. Funnel plot of publication bias; d. Sensitivity analysis
Fig. 2
Fig. 2
Meta-analysis of miRNA-chip data for NSCLC. a. Forest plot for overall SMD; b. Subgroup analysis; c. Funnel plot of publication bias; d. Sensitivity analysis
Fig. 3
Fig. 3
The distinguishing ability of miR-182-5p in NSCLC tissues based on data from miRNA-chips. a. SROC curves; b. Forest plot for sensitivity and specificity; c. Summary of positive likelihood ratio and negative likelihood ratio
Fig. 4
Fig. 4
The distinguishing value of miR-182-5p in NSCLC serum based on data from miRNA-chips. a. SROC curves; b. Forest plot for sensitivity and specificity; c. Summary of positive likelihood ratio and negative likelihood ratio
Fig. 5
Fig. 5
The comprehensive meta-analysis for miR-182-5p expression in LUAD. a. Forest plot for overall SMD; b. Subgroup analysis; c. Funnel plot of publication bias; d. Sensitivity analysis
Fig. 6
Fig. 6
The comprehensive meta-analysis for miR-182-5p expression in NSCLC. a. Forest plot for overall SMD; b. Subgroup analysis; c. Funnel plot of publication bias; d. Sensitivity analysis
Fig. 7
Fig. 7
The distinguishing power of miR-182-5p in NSCLC tissues based on data from all studies. a. SROC curves; b. Forest plot for sensitivity; c. Forest plot for specificity; d. Summary of diagnostic scores
Fig. 8
Fig. 8
Functional enrichment analysis for candidate target genes of miR-182-5p. a. Bubble plot for gene ontology enrichment; b. Chord plot for Kyoto Encyclopedia of Genes and Genomes pathway analysis
Fig. 9
Fig. 9
PPI network for candidate target genes of miR-182-5p. Nodes and strings in the network represented target genes and interactions between target genes
Fig. 10
Fig. 10
Validation of the targeting regulatory relationship between HOXA9 and miR-182-5p. a. Differential expression of HOXA9 in LUAD and noncancer tissues from RT-qPCR data; b. Correlation analysis based on in-house RT-qPCR data for miR-182-5p and HOXA9 expression in LUAD; c. Differential expression of HOXA9 in NSCLC and noncancer tissues from RT-qPCR data; d. Correlation analysis based on in-house RT-qPCR data for miR-182-5p and HOXA9 expression in NSCLC; e. Dual-luciferase reporter assay
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