The m6A-enriched lncRNA LINC00839 promotes tumor progression by binding TAF15 and activate AOC1 transcription in nasopharyngeal carcinoma [ChIP-Seq]. The m6A-enriched lncRNA LINC00839 promotes tumor progression by binding TAF15 and activate AOC1 transcription in nasopharyngeal carcinoma [ChIP-Seq]

Dysregulations of long non-coding RNAs (lncRNA) contribute to tumorigenesis by modulating specific cancer-related pathways, but the roles of m6A-enriched lncRNAs and underlying mechanisms remain elusive in nasopharyngeal carcinoma (NPC). Here, we reanalyzed the previous genome-wide analysis of lncRNA profile, and discerned that an oncogenic m6A-enriched lncRNA, LINC00839, which was substantially upregulated in NPC and correlated with poor clinical prognosis, promoted NPC growth and metastasis in vitro and in vivo. Mechanistically, LINC00839 interacted directly with transcription factor, TATA-box binding protein associated factor (TAF15), and coordinated its recruitment to promoter region of amine oxidase copper-containing 1 (AOC1), thereby activating AOC1 transcription in trans. Ectopic expression of AOC1 partially rescued the inhibitory effect of downregulation of LINC00839 in NPC. Furthermore, silencing vir like m6A methyltransferase associated (VIRMA) and insulin-like growth factor 2 mRNA-binding proteins 1 (IGF2BP1) were found to attenuate the expression level and RNA stability of LINC00839 in an m6A-dependent manner. This study unveils a novel oncogenic VIRMA/IGF2BP1–LINC00839–TAF15–AOC1 axis, and highlights significance and prognostic value of LINC00839 in NPC carcinogenesis. Overall design: We reanalyzed the previous genome-wide analysis of lncRNA profile. The in vitro and in vivo functions of LINC00839 were confirmed by CCK8, colony formation, transwell migration and invasion assays, and animal experiments. RNA pulldown, mass spectrometry, RNA immunoprecipitation (RIP) and chromatin immunoprecipitation (CHIP) were conducted to investigate the downstream gene modulated by LINC00839. Methylated RIP (MeRIP) and RNA stability assays were performed to clarify the N6-methyladenosine (m6A)-modified status and attenuated rates of LINC00839.

长链非编码RNA（long non-coding RNAs，lncRNA）的表达失调可通过调控特定癌症相关通路参与肿瘤发生，但在鼻咽癌（nasopharyngeal carcinoma，NPC）中，富含N6-甲基腺嘌呤（N6-methyladenosine，m6A）的lncRNA的作用及其潜在机制仍不明晰。本研究重新分析了既往的全基因组lncRNA表达谱研究，鉴定出一种致癌性富含m6A的lncRNA——LINC00839，该分子在鼻咽癌中显著上调，且与不良临床预后密切相关，可在体内外促进鼻咽癌的增殖与转移。机制上，LINC00839可直接与转录因子TATA盒结合蛋白相关因子（TATA-box binding protein associated factor，TAF15）相互作用，并协助其募集至含铜胺氧化酶1（amine oxidase copper-containing 1，AOC1）的启动子区域，从而反式激活AOC1的转录。外源过表达AOC1可部分逆转LINC00839下调对鼻咽癌产生的抑制作用。此外，研究发现敲低VIR样m6A甲基转移酶相关蛋白（vir like m6A methyltransferase associated，VIRMA）及胰岛素样生长因子2 mRNA结合蛋白1（insulin-like growth factor 2 mRNA-binding proteins 1，IGF2BP1）可通过m6A依赖的方式降低LINC00839的表达水平并削弱其RNA稳定性。本研究揭示了一条全新的致癌性VIRMA/IGF2BP1–LINC00839–TAF15–AOC1信号轴，并阐明了LINC00839在鼻咽癌发生发展中的重要意义与预后价值。实验设计概述：本研究重新分析了既往的全基因组lncRNA表达谱研究。通过CCK8实验、集落形成实验、Transwell迁移与侵袭实验以及动物实验，验证了LINC00839的体内外生物学功能。采用RNA下拉实验、质谱分析、RNA免疫沉淀（RNA immunoprecipitation，RIP）及染色质免疫沉淀（chromatin immunoprecipitation，CHIP）探究LINC00839调控的下游靶基因。通过甲基化RNA免疫沉淀（methylated RIP，MeRIP）及RNA稳定性实验，明确了LINC00839的m6A修饰状态及其RNA降解速率。