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• Research Paper Volume 13, Issue 19 pp 23020-23035

  DCP1A is an unfavorable prognostic-related enhancer RNA in hepatocellular carcinoma

  Relevance score: 10.867436

  Hao Wu, Jinrui Zhang, Yi Bai, Sai Zhang, Zhixin Zhang, Wen Tong, Pinsheng Han, Bing Fu, Yamin Zhang, Zhongyang Shen

  Keywords: hepatocellular carcinoma, enhancer RNA, DCP1A, prognosis, bioinformatics

  Published in Aging on October 4, 2021

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  Long non-coding RNAs (lncRNAs) are associated with occurrence and development of tumors. Enhancer RNA (eRNA) is a special type of lncRNAs produced from transcription of enhancer elements. The function of eRNAs in tumors have elicited significant attention recently. However, the clinical significance and role of eRNAs in hepatocellular carcinoma (HCC) has not been fully explored. The current study sought to explore the expression level and prognostic value of key eRNAs in HCC. Bioinformatics analyses were used to explore expression levels of key prognostic eRNAs in HCC and their correlation with target genes. A total of 1580 enhancer RNAs (eRNAs) and 1791 target genes were initially retrieved from TCGA-LIHC gene expression database. Further analysis through survival and correlation analysis led to identification of 12 eRNAs and 13 target genes. The findings showed that DCP1A was the most prognosis-related eRNA. This eRNA showed the highest correlation with the target gene, PRKCD. Analysis showed that poor overall survival (OS) in HCC patients was correlated with high expression level of DCP1A (eRNA) and PRKCD (target gene). The up-regulation of DCP1A was associated with advanced tumor stage, larger tumor size and higher histological grade. The results of pan-cancer analysis showed that the expression of DCP1A was differentially expressed in 13 other types of tumor tissues and their corresponding normal tissues. This eRNA was highly expressed in digestive system tumors. Functional analysis showed that high expression level of DCP1A was implicated in multiple tumor-related signaling pathways. The findings of the current study indicated DCP1A is a novel biomarker that can be used as a potential therapeutic target for HCC patients.

• Research Paper pp undefined-undefined

  Identification of an immune-related eRNA prognostic signature for clear cell renal cell carcinoma

  Relevance score: 7.5393925

  Yang Lv, Lili Niu, Qiang Li, Wenchuan Shao, Xinghan Yan, Yang Li, Yulin Yue, Hongqi Chen

  Keywords: non-coding RNA, enhancer RNA, immune signature, tumor microenvironment, clear cell renal cell carcinoma

  Published in Aging on Invalid Date

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  Background: Immune-related enhancer RNAs (eRNAs) have garnered significant attention in cancer metabolism research, yet their specific roles in ccRCC have remained elusive.

  Methods: We retrieved eRNA expression profiles from TCGA database and identified immune-related eRNAs (IREs) by assessing their co-expression with immune genes. Utilizing consensus clustering, we organized these IREs into two distinct clusters. The construction of an IREs signature was accomplished through the LASSO and multivariate Cox analysis. Furthermore, we performed Cell Counting Kit-8 and clonogenic assays to assess changes in the proliferative capacity of Caki-1 and 769-P cells.

  Results: The existence of two clusters of immune-related eRNAs in ccRCC, each with distinctive prognostic and immunological attributes. Cluster B exhibited immunosuppressive properties and displayed a positive correlation with immunosuppressive cells. Functional enrichment analysis unveiled their involvement in several tumor-promoting pathways, metabolic pathways and immune pathways. The IREs signature demonstrated its potential to accurately predict patient immune and prognostic characteristics. AC003092.1, an eRNA strongly associated with patient survival, emerged as a potential oncogene significantly linked to adverse prognosis and the presence of immunosuppressive cells and checkpoints in ccRCC patients. Notably, AC003092.1 displayed marked upregulation in ccRCC tissues and cell lines, and its knockdown substantially inhibited the proliferation of Caki-1 and 769-P cells.

  Conclusion: We established a robust predictive model that played a vital role in determining the prognosis, clinicopathological characteristics and immune cell infiltration patterns of ccRCC patients. IRE, particularly AC003092.1, which was strongly associated with survival, hold promise as novel immunotherapeutic targets for ccRCC.