Department of Clinical Laboratory, Sir Run Run Shaw Hospital of Zhejiang University School of Medicine, Qingchun East Road, Jianggan District, Hangzhou, 310016, Zhejiang, China.
Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, 310013, Zhejiang, China.
J Transl Med. 2022 May 4;20(1):197. doi: 10.1186/s12967-022-03395-7.
N6-methyladenosine (mA) RNA methylation plays a critical role in key genetic events for various cancers; yet, how mA functions within the tumor microenvironment (TME) remains to be elucidated.
A total of 65,362 single cells from single-cell RNA-seq data derived from 33 CRC tumor samples were analyzed by nonnegative matrix factorization (NMF) for 23 mA RNA methylation regulators. CRC and Immunotherapy cohorts from public repository were used to determine the prognosis and immune response of TME clusters.
The fibroblasts, macrophages, T and B cells were respectively grouped into 4 to 5 subclusters and then classified according to various biological processes and different marker genes. Furthermore, it revealed that the mA RNA methylation regulators might be significantly related to the clinical and biological features of CRC, as well as the pseudotime trajectories of main TME cell types. Bulk-seq analysis suggested that these mA-mediated TME cell subclusters had significant prognostic value for CRC patients and distinguished immune response for patients who underwent ICB therapy, especially for the CAFs and macrophages. Notably, CellChat analysis revealed that RNA mA methylation-associated cell subtypes of TME cells manifested diverse and extensive interaction with tumor epithelial cells. Further analysis showed that ligand-receptor pairs, including MIF - (CD74 + CXCR4), MIF - (CD74 + CD44), MDK-NCL and LGALS9 - CD45, etc. mediated the communication between mA associated subtypes of TME cells and tumor epithelial cells.
Taken together, our study firstly revealed the mA methylation mediated intercellular communication of the tumor microenvironment in the regulation of tumor growth and antitumor immunomodulatory processes.
N6-甲基腺苷（mA）RNA 甲基化在各种癌症的关键遗传事件中起着至关重要的作用；然而，mA 在肿瘤微环境（TME）中的功能仍有待阐明。
通过非负矩阵分解（NMF）对 33 个 CRC 肿瘤样本的单细胞 RNA-seq 数据中 65362 个单细胞进行分析，共鉴定出 23 个 mA RNA 甲基化调控因子。从公共数据库中选取 CRC 和免疫治疗队列，确定 TME 聚类的预后和免疫反应。
成纤维细胞、巨噬细胞、T 细胞和 B 细胞分别被分为 4 到 5 个子簇，然后根据不同的生物学过程和不同的标记基因进行分类。此外，结果表明 mA RNA 甲基化调控因子可能与 CRC 的临床和生物学特征以及主要 TME 细胞类型的伪时间轨迹显著相关。bulk-seq 分析表明，这些 mA 介导的 TME 细胞亚群对 CRC 患者具有显著的预后价值，并区分了接受 ICB 治疗的患者的免疫反应，特别是对 CAFs 和巨噬细胞。值得注意的是，CellChat 分析表明，TME 细胞中与 RNA mA 甲基化相关的细胞亚型与肿瘤上皮细胞表现出多样化和广泛的相互作用。进一步分析表明，配体-受体对，包括 MIF-（CD74+CXCR4）、MIF-（CD74+CD44）、MDK-NCL 和 LGALS9-CD45 等，介导了 mA 相关 TME 细胞亚群与肿瘤上皮细胞之间的通讯。
综上所述，本研究首次揭示了 mA 甲基化介导的肿瘤微环境细胞间通讯在肿瘤生长和抗肿瘤免疫调节过程中的调控作用。
