Department of BioScience and Biotechnology, Banasthali Vidyapith, Banasthali, 304022 Tonk, Rajasthan, India.
Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, 741235, India.
Gene. 2020 Dec 15;762:145035. doi: 10.1016/j.gene.2020.145035. Epub 2020 Aug 8.
Circular RNAs belong to the class of endogenous long non-coding RNAs that play important roles in many physiological processes including tumorigenesis. One such process is the onset of colorectal cancers (CRC) which is one of the most prevalent cancers in the world. However, the involvement of the circRNAs in CRC progression is still obscure. In this study, we screened the differentially expressed circRNAs in CRC by taking 10 pairs of tumor and non-tumor transcriptomic data. Datasets were downloaded from EBI ENA database and differential expression analysis was performed. For functional characterization and pathway enrichment of differentially expressed circRNAs, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were employed. Interactions with miRNAs and RNA binding proteins (RBPs) were predicted using miRanda, miRTarBase and starBase tools respectively. Our results identified total of 122 differentially expressed circRNAs in CRC onset, including 85 upregulated and 37 downregulated. GO and KEGG analyses revealed these circRNAs to be involved in many tumorigenic pathways. In addition, we predicted many miRNA and RBP targets of significantly expressed circRNAs that could exhibit the functional role in CRC progression. Combined analyses of miRanda, miRTarBase and KEGG pathway suggested that the possibly affected genes by circRNA-miRNA sponge to be associated with many cancer related pathways. From our findings we concluded 16 novel differentially expressed circRNAs that could play important roles in carcinogenesis of CRC. Our findings provide new insights in circRNA research and could therefore be useful in the development of potential biomarker and therapeutic approaches for CRC.
环状 RNA 属于内源性长非编码 RNA 类,在包括肿瘤发生在内的许多生理过程中发挥重要作用。其中一个过程是结直肠癌 (CRC) 的发生,它是世界上最常见的癌症之一。然而,circRNA 参与 CRC 进展的机制尚不清楚。在这项研究中,我们通过对 10 对肿瘤和非肿瘤转录组数据进行筛选,发现了 CRC 中差异表达的 circRNA。数据集从 EBI ENA 数据库下载,并进行差异表达分析。为了对差异表达的 circRNA 进行功能特征分析和通路富集分析,我们使用了基因本体论(GO)和京都基因与基因组百科全书(KEGG)。使用 miRanda、miRTarBase 和 starBase 工具分别预测了差异表达 circRNA 与 miRNA 和 RNA 结合蛋白(RBP)的相互作用。我们的研究结果共鉴定出 CRC 发病中 122 个差异表达的 circRNA,包括 85 个上调和 37 个下调。GO 和 KEGG 分析表明,这些 circRNA 参与了许多肿瘤发生途径。此外,我们预测了许多显著表达的 circRNA 的 miRNA 和 RBP 靶标,这些靶标可能在 CRC 进展中发挥功能作用。miRanda、miRTarBase 和 KEGG 通路的综合分析表明,circRNA-miRNA 海绵可能影响的基因与许多癌症相关通路有关。从我们的发现中,我们得出了 16 个新的差异表达 circRNA,它们可能在 CRC 的致癌作用中发挥重要作用。我们的研究结果为 circRNA 研究提供了新的见解,因此可能对 CRC 潜在的生物标志物和治疗方法的开发有用。