RNA methylation-related genes of m6A, m5C, and m1A predict prognosis and immunotherapy response in cervical cancer

To investigate the prognostic value of N6-methyladenosine (m6A)-, 5-methylcytosine (m5C)-, and N1-methyladenosine (m1A)-related genes in cervical cancer (CESC) and predicting immunotherapy response.
We downloaded cervical cancer mRNA expression profiles, clinical data, and m6A, m5C, m1A-related genes from public databases, and subjected them to serial bioinformatics analysis and clinical sample validation.
Differential analysis revealed 106 methylation-related differential genes (MEDs), including 44 differentially downregulated and 62 upregulated genes. We then obtained methylation models containing 10 genes by univariate and multifactorial COX analysis. High risk genes with HR > 1 include IQGAP3, PTBP1, STAC3, CUX1, SLC2A1, and CA2, and low risk genes with HR < 1 include IGBP1, DUOX1, CHAF1A, and STAC3. We verified the accuracy of the model from inside TCGA and outside GSE39001 (AUC = 0.729). K-M analysis showed shorter survival times in the High-risk group, and Immunocytic infiltration analysis showed model genes closely associated with six immune cells. The high-risk group may benefit more effectively from immunosuppressive therapy, especially anti-CTLA-4 therapy (p < .05). We also screened nine drugs for potential treatment and verified the expression of three key genes SLC2A1, CUX1, and CA2 using immunohistochemistry and RT-qPCR experiments with clinical samples.
We identified a prognostic model using m6A/m5C/m1A-related genes in cervical cancer, which can predict survival time and correlate with immune cell infiltration. Additionally, anti-CTLA-4 may be used as an immunotherapeutic agent for cervical cancer.KEY MESSAGES
Cervical cancer still has a high mortality rate, we aim to establish a strong prognostic index and new treatment goals for improving patient survival.
The role of three types of RNA methylation modifications, m6A, m5C, and m1A, in cervical cancer, remains unknown. Therefore, it is essential to explore the potential molecular mechanisms of m6A, m5C, and m1A methylation regulation in cervical cancer.
We also screened nine drugs for potential treatment and anti-CTLA-4 may be used as an immunotherapeutic agent for cervical cancer. We verified the expression of three key genes SLC2A1, CUX1, and CA2

Cervical cancer still has a high mortality rate, we aim to establish a strong prognostic index and new treatment goals for improving patient survival.
The role of three types of RNA methylation modifications, m6A, m5C, and m1A, in cervical cancer, remains unknown. Therefore, it is essential to explore the potential molecular mechanisms of m6A, m5C, and m1A methylation regulation in cervical cancer.
We also screened nine drugs for potential treatment and anti-CTLA-4 may be used as an immunotherapeutic agent for cervical cancer. We verified the expression of three key genes SLC2A1, CUX1, and CA2

本研究旨在探讨N6-甲基腺苷（N6-methyladenosine, m6A）、5-甲基胞嘧啶（5-methylcytosine, m5C）及N1-甲基腺苷（N1-methyladenosine, m1A）相关基因在宫颈癌（CESC）中的预后价值，并预测其免疫治疗应答效果。
我们从公共数据库下载了宫颈癌mRNA表达谱、临床数据以及与m6A、m5C、m1A相关的基因，对其进行了系列生物信息学分析与临床样本验证。
差异分析共筛选得到106个甲基化相关差异基因（methylation-related differential genes, MEDs），其中44个为表达下调基因，62个为表达上调基因。通过单因素与多因素Cox比例风险回归分析，我们构建了包含10个基因的甲基化预后模型。风险比（hazard ratio, HR）>1的高危基因包括IQGAP3、PTBP1、STAC3、CUX1、SLC2A1及CA2；HR<1的低危基因包括IGBP1、DUOX1、CHAF1A及STAC3。
我们分别在TCGA队列内部与GSE39001外部队列中验证了该模型的准确性，其受试者工作特征曲线下面积（Area Under the Curve, AUC）为0.729。Kaplan-Meier（K-M）生存分析显示，高危组患者的生存时间更短；免疫细胞浸润分析显示，该模型基因与6种免疫细胞密切相关。高危组患者或可从免疫抑制治疗中获益更多，尤其是抗CTLA-4治疗（p<0.05）。
本研究同时筛选出9种潜在治疗药物，并利用临床样本通过免疫组化与实时定量聚合酶链反应（real-time quantitative polymerase chain reaction, RT-qPCR）实验验证了3个关键基因SLC2A1、CUX1及CA2的表达水平。
本研究基于宫颈癌中m6A、m5C、m1A相关基因构建了预后模型，该模型可预测患者生存时间并与免疫细胞浸润状态相关；此外，抗CTLA-4治疗可作为宫颈癌的免疫治疗方案。
核心要点：
宫颈癌目前仍存在较高的死亡率，本研究旨在构建可靠的预后指标与全新的治疗靶点，以改善患者的生存结局。
目前m6A、m5C、m1A这三类RNA甲基化修饰在宫颈癌中的作用尚不明确，因此探索宫颈癌中m6A、m5C及m1A甲基化调控的潜在分子机制具有重要意义。
本研究同时筛选出9种潜在治疗药物，且抗CTLA-4可作为宫颈癌的免疫治疗方案；我们验证了3个关键基因SLC2A1、CUX1及CA2的表达水平。
宫颈癌目前仍存在较高的死亡率，本研究旨在构建可靠的预后指标与全新的治疗靶点，以改善患者的生存结局。
目前m6A、m5C、m1A这三类RNA甲基化修饰在宫颈癌中的作用尚不明确，因此探索宫颈癌中m6A、m5C及m1A甲基化调控的潜在分子机制具有重要意义。
本研究同时筛选出9种潜在治疗药物，且抗CTLA-4可作为宫颈癌的免疫治疗方案；我们验证了3个关键基因SLC2A1、CUX1及CA2的表达水平。