Construction and Analysis of a ceRNA Network Reveals Potential Prognostic Markers in Colorectal Cancer

• Main Authors: Li Guo, Guowei Yang, Yihao Kang, Sunjing Li, Rui Duan, Lulu Shen, Wenwen Jiang, Bowen Qian, Zibo Yin, Tingming Liang
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2020-05-01
• Series: Frontiers in Genetics
• Subjects: colorectal cancer; competing endogenous RNA; ceRNA network; prognostic marker; long noncoding RNA; miRNA
• Online Access: https://www.frontiersin.org/article/10.3389/fgene.2020.00418/full

Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide and is derived from an accumulation of genetic and epigenetic changes. This study explored potential prognostic markers in CRC via the construction and in-depth analysis of a competing endogenous RNA (ceRNA) network, which was generated through a three-step process. First, we screened candidate hub genes in CRC as the primary gene markers to survey their related regulatory non-coding RNAs, miRNAs. Second, the interacting miRNAs were used to search for associated lncRNAs. Thus, candidate RNAs were first constructed into ceRNA networks based on close associations with miRNAs. Further analysis at the isomiR level was also performed for each miRNA locus to understand the detailed expression patterns of the multiple variants. Finally, RNAs were performed an in-depth analysis of expression correlations, which contributed to further screening and validation of potential RNAs with close correlations to each other. Using this approach, nine hub genes, 13 related miRNAs, and 29 candidate lncRNAs were collected and used to construct the ceRNA network. Further in-depth analysis identified the MFAP5-miR-200b-3p-AC005154.6 axis as a potential prognostic marker in CRC. MFAP5 and miR-200b-3p have previously been reported to play important roles in tumorigenesis. These RNAs showed potential prognostic values, and the combination of them may have more sensitivity than using them alone. In conclusion, MFAP5, miR-200b-3p, and AC005154.6 may have potential prognostic value in CRC and may provide a prognostic reference for this patient population.