Clinical significance of miR-1180-3p in hepatocellular carcinoma: a study based on bioinformatics analysis and RT-qPCR validation

Abstract

miRNAs play an indispensable role in human carcinogenesis. Dysregulated miR-1180-3p has been observed in several types of cancer, including hepatocellular carcinoma (HCC). This study intends to correlate the expression level of miR-1180-3p with clinical features and overall survival in HCC patients. The expression and clinical significance of miR-1180-3p, selected from GEO and TCGA databases, were verified using an RT-qPCR method. The target genes of miR-1180-3p were obtained using 3 miRNA target gene prediction databases, and their functions were analyzed using the online tool WebGestalt. miR-1180-3p expression was significantly upregulated in 88 HCC tissues compared with non-tumor liver tissues (0.004 ± 0.009 vs. 0.002 ± 0.002, t = - 2.099, P = 0.038). Additionally, we found that the expression levels of miR-1180-3p were significantly correlated with tumor number (χ² = 9.157, P = 0.006) and MVI (χ² = 11.354, P = 0.003). Based on Kaplan-Meier analysis, patients with high miR-1180 expression had a shorter overall survival than those with low miR-1180-3p expression (P = 0.002). Furthermore, multivariate Cox analyses indicated that miR-1180-3p expression was an independent prognostic factor for overall survival (HR = 13.36, 95% CI 1.16, 153.69, P = 0.038). In addition, a total of 733 target genes of miR-1180-3p were found from three prediction databases. The GO analyses demonstrated that the target genes were closely related to the proliferation and malignancy of tumors. The KEGG analysis showed that target genes were enriched in several key cancer-related signaling pathways, including the Pathways in cancer, the Ras signaling pathway, and the MAPK signaling pathway. In conclusion, we demonstrate that miR-1180-3p is upregulated in HCC and is associated with a poor prognosis. Thus, miR-1180-3p might be useful as a prognostic marker for HCC.

Figure 1

The different expression of miRNAs (GSE36915). The “limma” package in R (version 3.5.2) was used to define the abnormally expressed miRNAs and the volcano plot was created by “ggplot2” package. Red spots represent up-regulated genes, and green spots represent down-regulated genes.

Figure 2

The correlation of miR-452-5p expression with overall survival of HCC patients in TCGA (Kaplan–Meier analysis). The survival curve was visualized by GraphPad Prism 8.0.2 (www.graphpad.com ).The cutoff values of miR-452-5p (cutoff = 13.45) was used to classify patients with HCC into high (n = 98) or low (n = 245) expression groups.

Figure 3

The correlation of miR-183-5p expression with overall survival of HCC patients in TCGA (Kaplan–Meier analysis). The survival curve was visualized by GraphPad Prism 8.0.2 (www.graphpad.com). The cutoff values of miR-183-5p (cutoff = 5.20) was used to classify patients with HCC into high (n = 41) or low (n = 302) expression groups.

Figure 4

The correlation of miR-1180-3p expression with overall survival of HCC patients in TCGA (Kaplan–Meier analysis). The survival curve was visualized by GraphPad Prism 8.0.2 (www.graphpad.com). The cutoff values of miR-1180-3p (cutoff = 6.63) was used to classify patients with HCC into high (n = 91) or low (n = 252) expression groups.

Figure 5

The expression of miR-1180-3p in HCC samples. The scatter diagram was created by GraphPad Prism 8.0.2 (www.graphpad.com). miR-1180-3p expression is significantly higher in HCC tumor tissues compared to matched Non-tumor liver tissues (0.004 ± 0.009 vs 0.002 ± 0.002, t = − 2.099, P = 0.038).

Figure 6

The prognostic significance of miR-1180-3p in HCC samples. The survival curve was visualized by GraphPad Prism 8.0.2 (www.graphpad.com). The log-rank test shows that HCC patients with high miR-1180-3p expression have higher overall survival than those with low expression of miR-1180-3p. The cutoff values of miR-1180-3p (cutoff = 0.01) was used to classify patients with HCC into high (n = 11) or low (n = 77) expression groups.

Figure 7

The GO analysis of miR-1180-3p target genes. WebGestalt (https://www.webgestalt.org) was used to perform Gene GO enrichment analysis and GraphPad Prism 8.0.2 was used to visualize results by created a histogram. The top 5 GO enrichment terms of target genes in biological process ontology, cellular component ontology, molecular function ontology.

Figure 8

The KEGG analysis of miR-1180-3p target genes. WebGestalt (https://www.webgestalt.org) was used to perform KEGG analysis and Bubble chart was created by ggplot2 package in R 3.5.2. The top 10 signaling pathways of the miR-1180-3p target genes by KEGG analysis.