Yang Chen, Yu Tian, Li Qingwen, Xie Fang, Lin Qin
Department of Radiation Oncology, Xiamen Cancer Center, Xiamen Key Laboratory of Radiation Oncology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University Xiamen 361003, Fujian, China.
Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College Beijing 100005, China.
Am J Transl Res. 2022 Jul 15;14(7):4931-4947. eCollection 2022.
RNA N6-methyladenosine (m6A) has been found to have a critical impact on clear cell renal cell carcinoma (ccRCC) by affecting the tumor microenvironment (TME) and immune cell (IC) infiltration and is related to the treatment and survival rate of patients with ccRCC. However, the mechanism of m6A in TME and IC infiltration remained unclear.
Nonnegative Matrix Factorization (NMF) clustering was performed on 650 ccRCC cases from the Cancer Genome Atlas (TCGA) and the Gene-Expression Omnibus (GEO) datasets. The immune infiltration was generated by the single-sample gene-set enrichment analysis (ssGSEA) algorithm. Survival analyses were performed using the Kaplan-Meier method, and the significance of the differences was determined using the log-rank test. The m6A score was constructed based on the expression of m6A regulators to quantify m6A modification. The package "survminer R" was employed to layer patients' low and high scores groups and predict the immunotherapy response.
Three different patterns of m6A modification were established, and significant differences in TME and IC infiltration features were found in these three patterns. Survival analysis demonstrated that m6A cluster A and m6A gene cluster A experienced a longer survival time. Evaluation of m6A modification patterns in individual tumors was initiated by the m6A score. The low m6A score subtype was characterized by increased tumor mutation burden (TMB) and immune infiltration, whereas a high m6A score with a lack of immune cell infiltration showed significantly better overall survival. m6A score was also associated with the expression of programmed cell death protein 1 (PD-L1) and cytotoxic T lymphocyte antigen 4 (CTLA-4). Patients in the high m6A score group had high PD-L1 expression and low CTLA-4 expression. Significant differences in prognosis were identified among types of different TMB and m6A scores, where low TMB and high m6A score had longer survival time.
This research indicated that m6A modification greatly affected TME and IC infiltration. Physicians can develop practical immunotherapy strategies for patients with ccRCC by evaluating m6A-associated genes.
已发现RNA N6-甲基腺嘌呤（m6A）通过影响肿瘤微环境（TME）和免疫细胞（IC）浸润对透明细胞肾细胞癌（ccRCC）产生关键影响，且与ccRCC患者的治疗及生存率相关。然而，m6A在TME和IC浸润中的机制仍不清楚。
对来自癌症基因组图谱（TCGA）和基因表达综合数据库（GEO）数据集的650例ccRCC病例进行非负矩阵分解（NMF）聚类。免疫浸润通过单样本基因集富集分析（ssGSEA）算法生成。使用Kaplan-Meier方法进行生存分析，并使用对数秩检验确定差异的显著性。基于m6A调节因子的表达构建m6A评分以量化m6A修饰。使用“survminer R”软件包对患者的低分和高分群体进行分层并预测免疫治疗反应。
建立了三种不同的m6A修饰模式，在这三种模式中发现TME和IC浸润特征存在显著差异。生存分析表明，m6A簇A和m6A基因簇A的生存时间更长。通过m6A评分开始对个体肿瘤中的m6A修饰模式进行评估。低m6A评分亚型的特征是肿瘤突变负担（TMB）增加和免疫浸润，而高m6A评分且缺乏免疫细胞浸润的患者总体生存率显著更好。m6A评分还与程序性细胞死亡蛋白1（PD-L1）和细胞毒性T淋巴细胞抗原4（CTLA-4）的表达相关。高m6A评分组患者的PD-L1表达高而CTLA-4表达低。在不同TMB和m6A评分类型之间确定了预后的显著差异，其中低TMB和高m6A评分的患者生存时间更长。
本研究表明m6A修饰极大地影响了TME和IC浸润。医生可以通过评估与m6A相关的基因，为ccRCC患者制定切实可行的免疫治疗策略。
