Data Sheet 4_m6A methylation profiling as a prognostic marker in nasopharyngeal carcinoma: insights from MeRIP-Seq and RNA-Seq.xlsx

BackgroundNasopharyngeal carcinoma (NPC) is a type of malignant tumors commonly found in Southeast Asia and China, with insidious onset and clinical symptoms. N6-methyladenosine (m6A) modification significantly contributes to tumorigenesis and progression by altering RNA secondary structure and influencing RNA-protein binding at the transcriptome level. However, the mechanism and role of abnormal m6A modification in nasopharyngeal carcinoma remain unclear.
MethodsNasopharyngeal Carcinoma tissues from 3 patients and non-cancerous nasopharyngeal tissues from 3 individuals, all from Fujian Cancer Hospital, were sequenced for m6A methylation. These were combined with transcriptome sequencing data from 192 nasopharyngeal cancer tissues. Genes linked to prognosis were discovered using differential analysis and univariate Cox regression. Subsequently, a prognostic model associated with m6A was developed through the application of LASSO regression analysis. The model’s accuracy was verified using both internal transcriptome databases and external databases. An extensive evaluation of the tumor’s immune microenvironment and signaling pathways was performed, analyzing both transcriptomic and single-cell data.
ResultsThe m6A methylation sequencing analysis revealed 194 genes with varying expression levels, many of which are predominantly associated with immune pathways. By integrating transcriptome sequencing data, 19 m6A-modified genes were found to be upregulated in tumor tissues, leading to the development of a three-gene (EME1, WNT4, SHISA2) risk prognosis model. The group with lower risk exhibited notable enrichment in pathways related to immunity, displaying traits like enhanced survival rates, stronger immune profiles, and increased responsiveness to immunotherapy when compared to the higher-risk group. Single-cell analysis revealed that malignant cells exhibited the highest risk score levels compared to immune cells, with a high-risk score indicating worse biological behavior. The three hub genes demonstrated significant correlation with m6A modification regulators, and MeRIP-RT-PCR confirmed the occurrence of m6A methylation in these genes within nasopharyngeal carcinoma cells.
ConclusionsA prognostic model for nasopharyngeal carcinoma risk based on m6A modification genes was developed, and its prognostic value was confirmed through self-assessment data. The study highlighted the crucial impact of m6A modification on the immune landscape of nasopharyngeal cancer.

背景：鼻咽癌（Nasopharyngeal carcinoma, NPC）是东南亚及中国高发的恶性肿瘤，起病隐匿且临床症状多不典型。N6-甲基腺苷酸（N6-methyladenosine, m6A）修饰可通过改变RNA二级结构、在转录组层面调控RNA与蛋白质结合，在肿瘤发生与进展中发挥关键作用。然而，异常m6A修饰在鼻咽癌中的作用机制尚未明确。
方法：本研究采集福建省肿瘤医院3例鼻咽癌患者的癌组织与3例非癌性鼻咽组织，开展m6A甲基化测序；并整合192例鼻咽癌组织的转录组测序数据。通过差异分析与单变量Cox回归分析筛选预后相关基因，随后采用LASSO回归分析构建m6A相关预后模型。通过内部转录组数据库与外部数据库验证模型预测准确性，并结合转录组与单细胞数据，对肿瘤免疫微环境及信号通路展开全面评估。
结果：m6A甲基化测序分析共鉴定出194个差异表达基因，其中多数与免疫通路密切相关。结合转录组测序数据，本研究发现19个m6A修饰基因在癌组织中呈上调表达，据此构建了由EME1、WNT4、SHISA2三个基因组成的风险预后模型。与高风险组相比，低风险组显著富集免疫相关通路，表现为生存率更高、免疫特征更显著、对免疫治疗响应性更强。单细胞分析结果显示，恶性细胞的风险评分高于免疫细胞，高风险评分提示肿瘤生物学行为更差。三个核心基因与m6A修饰调控因子存在显著相关性，MeRIP-RT-PCR实验证实了鼻咽癌细胞中这些基因存在m6A甲基化修饰。
结论：本研究构建了基于m6A修饰基因的鼻咽癌风险预后模型，并通过自建数据集验证了该模型的预后价值；同时揭示了m6A修饰对鼻咽癌免疫微环境的关键调控作用。