Identification of novel enhancer RNA biomarkers and corresponding prognostic signatures of hepatocellular carcinoma

Abstract

Abstract Background Researchers now pique an interest on enhancer RNAs (eRNAs). Their roles in hepatocellular carcinoma (HCC) remain to be elucidated. Further investigation on eRNAs may shed light on putative prognosis biomarkers and therapeutic targets, which may benefit for early diagnosis of HCC. Methods RNA-Seq data and clinical information were obtained from TCGA cohort. Data were analyzed using R software. Prognosis-related eRNAs were identified, and their target genes of eRNAs were predicted based on the correlation level. We performed enrichment and pan-cancer analyses, constructed prognostic model using selected eRNAs and target genes. QPCR was performed for validation. Results 125 prognosis-related eRNAs were identified. 15 eRNA and target gene pairs were selected for the association with HCC tumorigenesis-related biological behaviors. We chose AL137803.1 for further investigation. We revealed target genes, C5orf58, NDC1, LINC00501 and G6PD could be prognostic signatures of HCC. The prediction value was confirmed and pan-cancer analyses also demonstrated multiple function of the key eRNA and its target genes. Our hypothesis was validated eventually. Conclusion A novel eRNA AL137803.1 may be a potential biomarker of HCC, besides its putative target genes may serve as prognostic signatures.