He Feng, Guo Qin, Jiang Guo-Xiu, Zhou Yan
The First Affiliated Hospital of Chengdu Medical College, School of Clinical Medicine, Chengdu Medical College, Chengdu, China.
National Health Commission (NHC), Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China.
Front Oncol. 2022 Aug 22;12:927810. doi: 10.3389/fonc.2022.927810. eCollection 2022.
To characterize the entire profile of mA modifications and differential expression patterns for circRNAs in colorectal cancer (CRC).
First, High-throughput MeRIP-sequencing and RNA-sequencing was used to determine the difference in mA methylome and expression of circRNA between CRC tissues and tumor-adjacent normal control (NC) tissues. Then, GO and KEGG analysis detected pathways involved in differentially methylated and differentially expressed circRNAs (DEGs). The correlations between mA status and expression level were calculated using a Pearson correlation analysis. Next, the networks of circRNA-miRNA-mRNA were visualized using the Target Scan and miRanda software. Finally, We describe the relationship of distance between the mA peak and internal ribosome entry site (IRES) and protein coding potential of circRNAs.
A total of 4340 mA peaks of circRNAs in CRC tissue and 3216 mA peaks of circRNAs in NC tissues were detected. A total of 2561 mA circRNAs in CRC tissues and 2129 mA circRNAs in NC tissues were detected. Pathway analysis detected that differentially methylated and expressed circRNAs were closely related to cancer. The conjoint analysis of MeRIP-seq and RNA-seq data discovered 30 circRNAs with differentially mA methylated and synchronously differential expression. RT-qPCR showned circRNAs (has_circ_0032821, has_circ_0019079, has_circ_0093688) were upregulated and circRNAs (hsa_circ_0026782, hsa_circ_0108457) were downregulated in CRC. In the ceRNA network, the 10 hyper-up circRNAs were shown to be associated with 19 miRNAs and regulate 16 mRNAs, 14 hypo-down circRNAs were associated with 30 miRNAs and regulated 27 mRNAs. There was no significant correlation between the level of mA and the expression of circRNAs. The distance between the mA peak and IRES was not significantly related to the protein coding potential of circRNAs.
Our study found that there were significant differences in the mA methylation patterns of circRNAs between CRC and NC tissues. MA methylation may affect circRNA-miRNA-mRNA co-expression in CRC and further affect the regulation of cancer-related target genes.
表征结直肠癌（CRC）中环RNA的mA修饰及差异表达模式的全貌。
首先，采用高通量MeRIP测序和RNA测序来确定CRC组织与肿瘤邻近正常对照（NC）组织之间mA甲基化组和circRNA表达的差异。然后，通过GO和KEGG分析检测参与差异甲基化和差异表达的circRNA（DEG）的通路。使用Pearson相关分析计算mA状态与表达水平之间的相关性。接下来，使用Target Scan和miRanda软件可视化circRNA-miRNA-mRNA网络。最后，我们描述了mA峰与内部核糖体进入位点（IRES）之间的距离与circRNA的蛋白质编码潜力的关系。
在CRC组织中检测到共4340个circRNA的mA峰，在NC组织中检测到3216个circRNA的mA峰。在CRC组织中检测到共2561个mA circRNA，在NC组织中检测到2129个mA circRNA。通路分析检测到差异甲基化和表达的circRNA与癌症密切相关。MeRIP-seq和RNA-seq数据的联合分析发现30个具有差异mA甲基化和同步差异表达的circRNA。RT-qPCR显示circRNA（has_circ_0032821、has_circ_0019079、has_circ_0093688）在CRC中上调，circRNA（hsa_circ_0026782、hsa_circ_0108457）在CRC中下调。在ceRNA网络中，10个高上调的circRNA显示与19个miRNA相关并调节16个mRNA，14个低下调的circRNA与30个miRNA相关并调节27个mRNA。mA水平与circRNA的表达之间无显著相关性。mA峰与IRES之间的距离与circRNA的蛋白质编码潜力无显著相关性。
我们的研究发现CRC与NC组织之间circRNA的mA甲基化模式存在显著差异。mA甲基化可能影响CRC中circRNA-miRNA-mRNA的共表达，并进一步影响癌症相关靶基因的调控。
