Huang Guirui, Huang Shuaiyang, Cui Hongsheng
Department of Respiratory, The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, China.
Front Pharmacol. 2022 Nov 28;13:993567. doi: 10.3389/fphar.2022.993567. eCollection 2022.
Molecular biology studies show that RNA N6-methyladenosine (m6A) modifications may take part in the incidence and development of idiopathic pulmonary fibrosis (IPF). Nonetheless, the roles of m6A regulators in IPF are not fully demonstrated. In this study, 12 significant m6A regulators were filtered out between healthy controls and IPF patients using GSE33566 dataset. Random forest algorithm was used to identify 11 candidate m6A regulators to predict the incidence of IPF. The 11 candidate m6A regulators included leucine-rich PPR motif-containing protein (LRPPRC), methyltransferase-like protein 3, FTO alpha-ketoglutarate dependent dioxygenase (FTO), methyltransferase-like 14/16, zinc finger CCCH domain-containing protein 13, protein virilizer homolog, Cbl proto-oncogene like 1, fragile X messenger ribonucleoprotein 1 and YTH domain containing 1/2. A nomogram model was constructed based on 11 candidate m6A regulators and considered beneficial to IPF patients using decision curve analysis. Consensus clustering method was used to distinctly divide IPF patients into two m6A patterns (clusterA and clusterB) based on 12 significant m6A regulators. M6A scores of all IPF patients were obtained using principal component analysis to quantify the m6A patterns. Patients in clusterB had higher m6A scores than those in clusterA. Furthermore, patients in clusterB were correlated with Th17 and Treg cell infiltration, innate immunity and Th1 immunity, while those in clusterA were correlated with adaptive immunity and Th2 immunity. Patients in clusterB also had higher expressions of mesenchymal markers and regulatory factors of fibrosis but lower expressions of epithelial markers. Lastly and interestingly, two m6A regulators, LRPPRC ( = 0.011) and FTO ( = 0.042), were identified as novel prognostic genes in IPF patients for the first time using an external GSE93606 dataset. Both of them had a positive correlation with a better prognosis and may serve as therapy targets. Thus, we conducted virtual screening to discover potential drugs targeting LRPPRC and FTO in the treatment of IPF. In conclusion, m6A regulators are crucial to the onset, development and prognosis of IPF. Our study on m6A patterns may provide clues for clinical diagnosis, prognosis and targeted therapeutic drugs development for IPF.
分子生物学研究表明，RNA N6-甲基腺苷（m6A）修饰可能参与特发性肺纤维化（IPF）的发生和发展。然而，m6A调节剂在IPF中的作用尚未完全阐明。在本研究中，利用GSE33566数据集在健康对照和IPF患者之间筛选出12个显著的m6A调节剂。采用随机森林算法识别出11个候选m6A调节剂以预测IPF的发病率。这11个候选m6A调节剂包括富含亮氨酸的PPR基序蛋白（LRPPRC）、甲基转移酶样蛋白3、FTOα-酮戊二酸依赖性双加氧酶（FTO）、甲基转移酶样14/16、含锌指CCCH结构域蛋白13、蛋白质雄性化同源物、Cbl原癌基因样1、脆性X信使核糖核蛋白1和含YTH结构域1/2。基于11个候选m6A调节剂构建了列线图模型，并通过决策曲线分析认为该模型对IPF患者有益。采用共识聚类方法，基于12个显著的m6A调节剂将IPF患者明显分为两种m6A模式（clusterA和clusterB）。利用主成分分析获得所有IPF患者的m6A评分以量化m6A模式。clusterB中的患者m6A评分高于clusterA中的患者。此外，clusterB中的患者与Th17和Treg细胞浸润、固有免疫和Th1免疫相关，而clusterA中的患者与适应性免疫和Th2免疫相关。clusterB中的患者还具有更高的间充质标志物表达和纤维化调节因子表达，但上皮标志物表达较低。最后且有趣的是，利用外部GSE93606数据集首次将两个m6A调节剂LRPPRC（P = 0.011）和FTO（P = 0.042）鉴定为IPF患者的新预后基因。它们均与较好的预后呈正相关，可作为治疗靶点。因此，我们进行了虚拟筛选以发现治疗IPF的靶向LRPPRC和FTO的潜在药物。总之，m6A调节剂对IPF的发病、发展和预后至关重要。我们对m6A模式的研究可能为IPF的临床诊断、预后及靶向治疗药物开发提供线索。
