A novel EMT-related risk score model for Uveal melanoma based on ZNF667-AS1 and AP005121.1

Abstract

Uveal melanoma (UM) has emerged as one of the most common primary intraocular malignant tumors worldwide. Long non-coding RNAs (lncRNAs) are increasingly recognized as decisive factors in the progression and metastasis of UM, involving in epithelial-mesenchymal transition (EMT) of UM. We conducted a comprehensive analysis of lncRNAs closely associated with EMT-related genes in the TCGA UM cohort, identifying 961 EMT-related lncRNAs. Through univariate COX analysis, we identified 9 survival-related EMT-related lncRNAs (sER-lncRNAs), further establishing an EMT-related risk scoring model (ER-RSM) with two sER-lncRNAs (ZNF667-AS1 and AP005121.1) identified by multivariate COX analysis. Through this ER-RSM, low-risk UM patients achieved better overall survival than high-risk UM patients. AP005121.1 was positively correlated with higher stage and M staging in UM patients, while ZNF667-AS1 was positively correlated with earlier stage, T, and M staging in UM patients. In vitro, AP005121.1 expression was higher in UM tumor tissues and cell lines than in adjacent normal tissues and human retinal pigment epithelial cells, whereas ZNF667-AS1 expression showed the opposite pattern. siR-AP005121.1 significantly inhibited migration and invasion ability of UM cells and suppressed the EMT pathway, while siR-ZNF667-AS1 promoted migration and invasion of UM cells and activated the EMT pathway. In this study, we screened sER-lncRNAs and constructed an ER-RSM to investigate the relationship between sER-lncRNAs and prognosis and clinical staging of UM. Additionally, we validated the expression of sER-lncRNAs in UM clinical samples and cell lines. The ER-RSM may provide potential key insights for the diagnosis and therapeutic intervention of UM patients.

Keywords: EMT; lncRNA; prognosis; risk score model; uveal melanoma.

Figure 1

Survival-related ER-lncRNAs. The forest plot illustrates the UM prognostic significance of sER-lncRNAs (ZNF667-AS1, AC104129.1, L3MBTL4-AS1, AP005121.1, AC005840.2, AC008555.4, AC136475.3, AC124798.1, and AP003390.1).

Figure 2

EMT-related risk score model (ER-RSM) is constructed by ZNF667-AS1 and AP005121.1. (A) The distribution of risk scores in the high-risk and low-risk groups of UM patients. (B) The survival status comparison between the high-risk group and low-risk group of UM patients. (C) The heatmap demonstrates the expression levels of the included sER-lncRNAs.

Figure 3

The UM survival curve of ER-RSM. (A) Kaplan-Meier survival curve of survival probability in the high-risk and low-risk groups of UM patients. The survival probability of ZNF667-AS1 (B) and AP005121.1 (C).

Figure 4

Receiver operating characteristic (ROC) curve of ER-RSM and clinical characteristics. ROC curves demonstrate the prognostic accuracy of risk scores, gender, stage, T-stage and M-stage in 1- (A), 3- (B) and 5- (C) year.

Figure 5

The correlations between the ER-RSM and clinical characteristics. Relationships between ER-RSM and stage (A), T-stage (B) and M-stage (C).

Figure 6

The independent risk factor of UM patients. Univariate (A) and multivariate (B) analysis of ER-RSM and clinical characteristics.

Figure 7

Nomogram of ER-RSM. (A) A nomogram is constructed to predict the 1-, 3-, and 5-year survival probability of UM patients by detecting the expression of sER-lncRNAs. (B) The calibration curve of nomogram.

Figure 8

Relationship between the ER-RSM and infiltration abundances of immune cells. The relationships between ER-RSM and infiltration abundances of B cells (A); CD4+T cells (B); CD8+T cells (C); neutrophils (D); macrophages (E); dendritic cells (F) are detected by Pearson correlation analysis.

Figure 9

The expression and function of ZNF667-AS1 and AP005121.1 in UM. The qPCR results display the expression levels of ZNF667-AS1 (A) and AP005121.1 (B) in UM cell lines and ARPE-19. The expression of ZNF667-AS1 (C) and AP005121.1 (D) in UM tissues and adjacent normal tissues. The knockdown efficiency of ZNF667-AS1 (E) and AP005121.1 (F) is detected by qPCR in MUM-2B cells. (G-I) siR-ZNF667-AS1 promotes the migration and invasion of MUM-2B cells, while siR-AP005121.1 inhibits the migration and invasion of MUM-2B cells. (J) siR-ZNF667-AS1 promotes the expression of Vimentin and N-cadherin, while decreases the expression of E-cadherin; siR-AP005121.1 inhibits the expression of Vimentin and N-cadherin, while promotes the expression of E-cadherin.