Gan Ying, Li Aolin, Liu Jun, Wang Xiaofei, Zhang Zhenan, Li Qinhan, Ye Xiongjun, Yao Lin, Zhang Qian
Department of Urology, Peking University First Hospital, Beijing, China.
Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China.
Front Genet. 2022 Jan 21;12:795611. doi: 10.3389/fgene.2021.795611. eCollection 2021.
N-methyladenosine (mA) is the most extensive messenger RNA modification. Despite recent advances in the biological roles of mA, its role in the development and progression of renal cell carcinoma (RCC) remains unclear. In this study, we gained the transcriptome-wide mA profile and gene expression pattern in RCC and paired adjacent peritumoral tissues by meRIP-seq and RNA-seq. mA modifications of mRNAs were validated by meRIP-qPCR in tissues, and targeted methylation or demethylation was validated by using a CRISPR-Cas13b-based tool in RCC cell lines. Our findings showed that there were 13,805 mA peaks among 5,568 coding gene transcripts (mRNAs) in adjacent tissues and 24,730 mA peaks among 6,866 mRNAs in tumor tissues. Furthermore, mA modification sites were usually located in the coding sequences (CDS), and some near the start and stop codons. Gene Ontology analysis revealed that coding genes had differential N-methyladenosine sites and were enriched in kidney development and cancer-related signaling pathways. We also found that different levels of mA modifications could regulate gene expression. In summary, our results provided evidence for studying the potential function of RNA mA modification and mA-mediated gene expression regulation in human RCC.
N-甲基腺苷（mA）是最广泛存在的信使核糖核酸修饰。尽管近年来在mA的生物学作用方面取得了进展，但其在肾细胞癌（RCC）发生发展中的作用仍不清楚。在本研究中，我们通过甲基化RNA免疫沉淀测序（meRIP-seq）和RNA测序（RNA-seq）获得了RCC及其配对的相邻肿瘤旁组织的全转录组mA图谱和基因表达模式。通过组织中的甲基化RNA免疫沉淀定量PCR（meRIP-qPCR）验证了mRNA的mA修饰，并在RCC细胞系中使用基于CRISPR-Cas13b的工具验证了靶向甲基化或去甲基化。我们的研究结果表明，相邻组织中5568个编码基因转录本（mRNA）中有13805个mA峰，肿瘤组织中6866个mRNA中有24730个mA峰。此外，mA修饰位点通常位于编码序列（CDS）中，有些靠近起始密码子和终止密码子。基因本体分析显示，编码基因具有不同的N-甲基腺苷位点，并且在肾脏发育和癌症相关信号通路中富集。我们还发现不同水平的mA修饰可以调节基因表达。总之，我们的结果为研究RNA mA修饰的潜在功能以及mA介导的基因表达调控在人类RCC中的作用提供了证据。
