Centre for Functional Genomics and Bio-Chips, Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, 1000 Ljubljana, Slovenia.
Department of Animal Science, Biotechnical Faculty, University of Ljubljana, 1230 Domžale, Slovenia.
Int J Mol Sci. 2021 Jul 12;22(14):7477. doi: 10.3390/ijms22147477.
Circular RNAs (circRNAs) are increasingly recognized as having a role in cancer development. Their expression is modified in numerous cancers, including hepatocellular carcinoma (HCC); however, little is known about the mechanisms of their regulation. The aim of this study was to identify regulators of circRNAome expression in HCC. Using publicly available datasets, we identified RNA binding proteins (RBPs) with enriched motifs around the splice sites of differentially expressed circRNAs in HCC. We confirmed the binding of some of the candidate RBPs using ChIP-seq and eCLIP datasets in the ENCODE database. Several of the identified RBPs were found to be differentially expressed in HCC and/or correlated with the overall survival of HCC patients. According to our bioinformatics analyses and published evidence, we propose that NONO, PCPB2, PCPB1, ESRP2, and HNRNPK are candidate regulators of circRNA expression in HCC. We confirmed that the knocking down the epithelial splicing regulatory protein 2 (ESRP2), known to be involved in the maintenance of the adult liver phenotype, significantly changed the expression of candidate circRNAs in a model HCC cell line. By understanding the systemic changes in transcriptome splicing, we can identify new proteins involved in the molecular pathways leading to HCC development and progression.
环状 RNA（circRNAs）在癌症发展中的作用正逐渐被认识。它们在许多癌症中的表达发生改变，包括肝细胞癌（HCC）；然而，关于它们的调控机制知之甚少。本研究旨在鉴定 HCC 中 circRNA 组表达的调控因子。我们使用公开可用的数据集，鉴定了在 HCC 中差异表达的 circRNAs 剪接位点周围富集基序的 RNA 结合蛋白（RBPs）。我们使用 ENCODE 数据库中的 ChIP-seq 和 eCLIP 数据集验证了一些候选 RBPs 的结合。一些鉴定出的 RBPs 在 HCC 中表达差异，和/或与 HCC 患者的总生存期相关。根据我们的生物信息学分析和已发表的证据，我们提出 NONO、PCPB2、PCPB1、ESRP2 和 HNRNPK 是 HCC 中 circRNA 表达的候选调控因子。我们证实，已知参与维持成人肝表型的上皮剪接调节蛋白 2（ESRP2）的敲低，显著改变了 HCC 细胞系中候选 circRNAs 的表达。通过了解转录组剪接的系统变化，我们可以鉴定出参与导致 HCC 发生和发展的分子途径的新蛋白。
