Table4_Transcriptome-wide 1-methyladenosine functional profiling of messenger RNA and long non-coding RNA in bladder cancer.XLSX

Introduction: Post-transcriptional RNA modifications are crucial regulators of tumor development and progression. In many biological processes, N1-methyladenosine (m1A) plays a key role. However, little is known about the links between chemical modifications of messenger RNAs (mRNAs) and long noncoding RNAs (lncRNAs) and their function in bladder cancer (BLCA).
Methods: Methylated RNA immunoprecipitation sequencing and RNA sequencing were performed to profile mRNA and lncRNA m1A methylation and expression in BLCA cells, with or without stable knockdown of the m1A methyltransferase tRNA methyltransferase 61A (TRMT61A).
Results: The analysis of differentially methylated gene sites identified 16,941 peaks, 6,698 mRNAs, and 10,243 lncRNAs in the two groups. Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the differentially methylated and expressed transcripts showed that m1A-regulated transcripts were mainly related to protein binding and signaling pathways in cancer. In addition, the differentially genes were identified that were also differentially m1A-modified and identified 14 mRNAs and 19 lncRNAs. Next, these mRNAs and lncRNAs were used to construct a lncRNA-microRNA-mRNA competing endogenous RNA network, which included 118 miRNAs, 15 lncRNAs, and 8 mRNAs. Finally, the m1A-modified transcripts, SCN2B and ENST00000536140, which are highly expressed in BLCA tissues, were associated with decreased overall patient survival.
Discussion: This study revealed substantially different amounts and distributions of m1A in BLCA after TRMT61A knockdown and predicted cellular functions in which m1A may be involved, providing evidence that implicates m1A mRNA and lncRNA epitranscriptomic regulation in BLCA tumorigenesis and progression.

引言：转录后RNA修饰是肿瘤发生与进展的关键调控因子。在诸多生物学过程中，N1-甲基腺苷（N1-methyladenosine，m1A）发挥着关键作用。然而，目前对于信使RNA（messenger RNAs，mRNAs）与长链非编码RNA（long noncoding RNAs，lncRNAs）的化学修饰及其在膀胱癌（bladder cancer，BLCA）中的功能关联，我们所知甚少。
方法：本研究采用甲基化RNA免疫沉淀测序与RNA测序技术，对稳定敲低或未敲低m1A甲基转移酶tRNA甲基转移酶61A（tRNA methyltransferase 61A，TRMT61A）的膀胱癌细胞系，开展mRNA与lncRNA的m1A甲基化及表达谱分析。
结果：对差异甲基化基因位点的分析显示，两组样本中共鉴定出16941个峰、6698个mRNA及10243个lncRNA。对差异甲基化与差异表达转录本进行基因本体（Gene Ontology，GO）富集分析及京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，KEGG）通路分析，结果表明m1A调控的转录本主要与蛋白质结合及癌症信号通路相关。此外，本研究还鉴定出同时存在差异m1A修饰与差异表达的基因，其中包含14个mRNA与19个lncRNA。随后，我们利用这些mRNA与lncRNA构建了lncRNA-微小RNA（microRNA，miRNA）-mRNA内源竞争RNA（competing endogenous RNA，ceRNA）调控网络，该网络包含118个miRNA、15个lncRNA及8个mRNA。最后，我们发现于膀胱癌组织中高表达的m1A修饰转录本SCN2B与ENST00000536140，与患者总体生存率降低显著相关。
讨论：本研究揭示了TRMT61A敲低后膀胱癌中m1A的修饰水平与分布存在显著差异，并预测了m1A可能参与的细胞生物学过程，为m1A介导的mRNA与lncRNA表观转录组调控在膀胱癌发生与进展中的作用提供了实验依据。