ZNF197-AS1/miR-425/GABARAPL1 axis: a novel regulatory mechanism in uveal melanoma

Abstract

This study investigates the role of the long noncoding RNA (lncRNA) ZNF197-AS1 in uveal melanoma (UM), focusing on its function within a competing endogenous RNA (ceRNA) network. Using the UM-related TCGA (The Cancer Genome Atlas) dataset, we analyzed the expression levels of ZNF197-AS1 and its correlation with miR-425 and GABARAPL1, an essential autophagy-related gene. Our analysis revealed that ZNF197-AS1 acts as a ceRNA by competitively binding to miR-425, resulting in the upregulation of GABARAPL1. This interaction plays a crucial role in the growth and metastasis of UM. The expression of GABARAPL1 showed a strong correlation with the clinical outcomes of patients with UM. Furthermore, in vitro assays confirmed that ZNF197-AS1 impedes UM cell proliferation, migration, and invasion by modulating the miR-425/GABARAPL1 axis. These findings suggest that ZNF197-AS1 can effectively inhibit UM progression through this ceRNA regulatory network. This study provides valuable insights into the molecular mechanisms underlying UM and highlights the potential of targeting the ZNF197-AS1/miR-425/GABARAPL1 axis as a therapeutic strategy for UM.NEW & NOTEWORTHY This study identifies the ZNF197-AS1/miR-425/GABARAPL1 axis as a novel regulatory mechanism in uveal melanoma. ZNF197-AS1 upregulates GABARAPL1 by sponging miR-425, inhibiting UM cell proliferation, migration, and invasion. This discovery highlights a potential therapeutic target, providing new insights into UM progression and patient outcomes.

Keywords: GABARAPL1; ZNF197-AS1; ceRNA regulatory network; miR-425; uveal melanoma.

Graphical abstract

Figure 1.

Screening of differentially expressed genes in the UM-associated lncRNA, miRNA, and mRNA expression datasets in the TCGA database. A: Venn diagram of mRNAs and ARGs. Green and blue represent mRNAs and ARGs, respectively, and the overlap represents ARGs in mRNAs. B: Pie charts represent the distribution of lncRNAs, miRNAs, and ARGs related to the prognosis of patients with UM. Green represents a correlation with the prognosis of patients with UM, and red represents no correlation with the prognosis of patients with UM. TCGA, The Cancer Genome Atlas; UM, uveal melanoma.

Figure 2.

Construction of the ceRNA regulatory network of ZNF197-AS1/miR-425/GABARAPL1 related to the prognosis of patients with UM. A: visualization results of the ceRNA regulatory network by the Cytoscape software. Yellow represents lncRNAs, green represents miRNAs, and blue represents mRNAs. The red font represents a positive correlation between the gene and the patient’s prognosis, and the black font represents a negative correlation between the gene and the patient’s prognosis. B: GABARAPL1 expression in the miR-425 and ZNF197-AS1 high- and low-expression groups was based on their median expression values. C: the correlation analysis between GABARAPL1 expression and ZNF197-AS1 expression. D: survival analysis of patients with UM in the ZNF197-AS1, GABARAPL1, and miR-425 high- and low-expression groups was based on their median expression values. The abscissa indicates the survival time, and the ordinate indicates the survival rate. Red lines indicate the high-expression group, and blue lines indicate the low-expression group. ceRNA, competing endogenous RNA; UM, uveal melanoma.

Figure 3.

Correlation analysis of the ARG GABARAPL1 with the clinicopathological characteristics of patients with UM. A: a heat map of the correlation of GABARAPL1 with the clinicopathological characteristics of patients with UM. Below indicate the genes and clinical groups represented by each color block, among which *P < 0.05 corresponds to clinicopathological characteristics. B: GABARAPL1 expression in different ages and T stages of patients with UM. There are 42 cases younger than 65, 32 cases over 65, 38 cases at T3, and 36 cases at T4. UM, uveal melanoma.

Figure 4.

Independent prognostic analysis of the ARG GABARAPL1 and the prognosis of patients with UM. A forest map of the multivariate Cox regression analysis. The left represents clinicopathological characteristics and gene name, N represents the case of patients with UM (74 cases), and the hazard ratio represents the risk rate, where a risk rate >1 indicates high risk and <1 indicates low risk. The right indicates the risk rate distribution of genes and P values, in which the left distribution indicates low risk and the right distribution represents high risk. UM, uveal melanoma.

Figure 5.

Correlation of the ceRNA regulatory network ZNF197-AS1/miR-425/GABARAPL1 with immune cells in the peripheral blood samples of patients with UM in the TCGA dataset. A: neutrophil content in the ZNF197-AS1, GABARAPL1, and miR-425 high- and low-expression groups was based on their median expression values. B: correlation between ZNF197-AS1, miR-425, and GABARAPL1 expression and immune cells analyzed by the COR test. ceRNA, competing endogenous RNA; TCGA, The Cancer Genome Atlas; UM, uveal melanoma.

Figure 6.

Correlation analysis between the ceRNA regulatory network and prognostic markers. A: independent survival analysis of prognostic genes, where red dots correspond to high-risk genes and blue dots correspond to low-risk genes. B: survival analysis of 80 patients with UM stratified into high- and low-expression groups based on the median expression of each gene. The x-axis represents survival time, and the y-axis represents the survival rate. The red line represents the high-expression group, whereas the blue line represents the low-expression group. C: ROC curve analysis of SPHK1 for predicting the prognosis of patients with UM. The green, blue, and red curves represent the ROC curve analysis for 1, 3, and 5 years, respectively. D: correlation analysis of ZNF197-AS1/miR-425/GABARAPL1 with the prognostic marker SPHK1. ceRNA, competing endogenous RNA; ROC curve, receiver operating characteristic curve; UM, uveal melanoma.

Figure 7.

Inhibitory effects of the ceRNA regulatory network ZNF197-AS1/miR-425/GABARAPL1 on the proliferation, migration, and invasion of UM MP46 cells. A: the expression of ZNF197-AS1, GABARAPL1, and miR-425 in ARPE-19, MP46, and 92-1 cells was measured by RT-qPCR. B: the expression of ZNF197-AS1, GABARAPL1, and miR-425 in MP46 cells was determined by RT-qPCR. MP46 cells were transfected with one-ZNF197-AS1 or combined with miR-425 mimic. C: the proliferation of MP46 cells was measured by CCK-8. D: the migration and invasion of MP46 cells were determined by Transwell assay (scale bar = 50 µm). E: MMP-2 and MMP-9 levels in the supernatant of MP46 cells were analyzed by ELISA. *P <0.05. Cell experiments were repeated three times. ceRNA, competing endogenous RNA; MMP, matrix metalloproteinase; UM, uveal melanoma.

Figure 8.

The impact of ceRNA regulatory network ZNF197-AS1/miR-425/GABARAPL1 on the proliferation, migration, and invasion capabilities of 92-1 cells. A: detection of ZNF197-AS1/miR-425/GABARAPL1 expression levels in 92-1 cells of each group by RT-qPCR. B: detection of proliferation capability of 92-1 cells in each group by CCK-8 assay. C: detection of migration and invasion capabilities of 92-1 cells in each group by Transwell assay (scale bar: 50 µm). D: detection of MMP-2 and MMP-9 levels in the supernatant of MP46 cells in each group by ELISA. *P < 0.05 compared between the two groups, and all cell experiments were repeated three times. ceRNA, competing endogenous RNA; MMP, matrix metalloproteinase.