Department of Respiratory and Critical Care Medicine, Changhai Hospital, Shanghai, China.
Sci Rep. 2023 Apr 12;13(1):5941. doi: 10.1038/s41598-023-32452-4.
5-methyladenosine (m5C) modification regulates gene expression and biological functions in oncologic areas. However, the effect of m5C modification in chronic hypersensitivity pneumonitis (CHP) and idiopathic pulmonary fibrosis (IPF) remains unknown. Expression data for 12 significant m5C regulators were obtained from the interstitial lung disease dataset. Five candidate m5C regulators, namely tet methylcytosine dioxygenase 2, NOP2/Sun RNA methyltransferase 5, Y-box binding protein 1, tRNA aspartic acid methyltransferase 1, and NOP2/Sun RNA methyltransferase 3 were screened using random forest and nomogram models to predict risks of pulmonary fibrosis. Next, we applied the consensus clustering method to stratify the samples with different m5C patterns into two groups (cluster A and B). Finally, we calculated immune cell infiltration scores via single-sample gene set enrichment analysis, then compared immune cell infiltration, related functions as well as the expression of programmed cell death 1 (PD-1, PDCD1) and programmed death protein ligand-1 (PD-L1, CD274) between the two clusters. Principal component analysis of m5C-related scores across the 288 samples revealed that cluster A had higher immune-related expression than B. Notably, T helper cell (Th) 2 type cytokines and Th1 signatures were more abundant in clusters A and B, respectively. Our results suggest that m5C is associated with and plays a crucial role in development of pulmonary fibrosis. These m5C patterns could be potential biomarkers for identification of CHP and IPF, and guide future development of immunotherapy or other new drugs strategies for pulmonary fibrosis.
5- 甲基腺苷(m5C)修饰调节肿瘤学领域的基因表达和生物学功能。然而,m5C 修饰在慢性过敏性肺炎(CHP)和特发性肺纤维化(IPF)中的作用尚不清楚。从间质性肺病数据集获得了 12 个显著的 m5C 调节剂的表达数据。使用随机森林和列线图模型筛选了 5 个候选 m5C 调节剂,即四甲基胞嘧啶双加氧酶 2、NOP2/Sun RNA 甲基转移酶 5、Y 框结合蛋白 1、天冬氨酸 tRNA 甲基转移酶 1 和 NOP2/Sun RNA 甲基转移酶 3,以预测肺纤维化的风险。接下来,我们应用共识聚类方法将具有不同 m5C 模式的样本分为两组(A 组和 B 组)。最后,我们通过单样本基因集富集分析计算免疫细胞浸润评分,然后比较两组之间的免疫细胞浸润、相关功能以及程序性细胞死亡 1(PD-1、PDCD1)和程序性死亡蛋白配体 1(PD-L1、CD274)的表达。288 个样本中 m5C 相关评分的主成分分析表明,A 组的免疫相关表达高于 B 组。值得注意的是,A 组和 B 组分别富含辅助性 T 细胞(Th)2 型细胞因子和 Th1 特征。我们的研究结果表明,m5C 与肺纤维化的发生发展有关,并发挥关键作用。这些 m5C 模式可能是鉴定 CHP 和 IPF 的潜在生物标志物,并为肺纤维化的免疫治疗或其他新药策略的未来发展提供指导。