Abstract
Enhancer RNAs (eRNAs) have emerged as key players in the pathology of several tumors, including uveal melanoma. Here, we aimed to explore the prognostic values of eRNAs in uveal melanoma (UVM) patients. The expressing data and survival data of UVM patients were downloaded from TCGA and GSE22138 datasets. The Kaplan-Meier methods with the log-rank test were applied to screen survival-related eRNAs in UVM. GEPIA was applied to analyze the associations between expressions of eRNA and disease-free survival. KEGG assays were applied to explore the potential signaling pathways of the key eRNA. The prognostic values of eRNAs were further explored by multivariate assays by the R package survival. The eRNAs were validated in pan-cancer. In this study, we identified 89 survival-related eRNAs in UVM based on TCGA datasets. Based on GSE22138 datasets, we found 27 survival-related eRNAs in UVM. Only two eRNAs (LINC00689 and ELFN1-AS1) were overlapped in both two datasets. The results of multivariate analysis revealed that both LINC00689 and ELFN1-AS1 were independent prognostic factors in UVM patients. The pan-cancer validation results further confirmed the prognostic values of LINC00689 and ELFN1-AS1 in eight tumors. Overall, we identified two novel UVM-related eRNAs, LINC00689 and ELFN1-AS1 which may serve as prognostic and diagnostic biomarkers of UVM patients for clinical decision-making.
Highlights
Uveal melanoma (UVM) is a malignant tumor that originates in melanocytes of the choroid plexus, ciliary body, and iris of the eye [1]
The deficiency of the protein-coding ability of Enhancer RNAs (eRNAs) limits their biological function in cellular progression, more and more evidences suggest that many eRNAs display a potential effect in genetic and epigenetic regulation
Based on GSE22138 datasets, we found 27 survival-related eRNAs in UVM
Summary
Uveal melanoma (UVM) is a malignant tumor that originates in melanocytes of the choroid plexus, ciliary body, and iris of the eye [1]. No effective treatments are available for metastatic cases due to the limited knowledge of the mechanisms involved in UVM metastasis and progression [3, 4]. More and more advancements in the managements of UVM patients have occurred, the long-term survivals remain poor [5, 6]. Many nonprotein-coding genes, accounting for about 75% of the genome, have been identified due to the tremendous progress of genome and transcriptome sequencing [7, 8]. Long noncoding RNAs (lncRNAs) are RNAs > 200 nucleotides which are transcribed from nonprotein-coding genes [9]. Enhancer RNAs (eRNAs) are a subclass of lncRNAs transcribed within gene enhancers [10, 11]. The deficiency of the protein-coding ability of eRNAs limits their biological function in cellular progression, more and more evidences suggest that many eRNAs display a potential effect in genetic and epigenetic regulation [12, 13]. A large number of eRNAs remained to be clinically identified
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