甲状腺髓样癌（MTC）由于其特定的细胞起源，呈现出与其他甲状腺癌不同的生物学背景。这种异质且罕见的肿瘤具有很高的晚期疾病患病率，因此解决有限的治疗选择和加强复杂的临床管理至关重要。鉴于甲基化信息的临床可获取性较高，我们构建了迄今为止最大的 MTC 甲基化队列。78 个新鲜冷冻 MTC 样本构成了我们的甲基化队列。综合研究过程结合了机器学习、统计分析和体外实验。我们的研究开创性地识别了用于风险分层的三类聚类系统，表现出明显的表观基因组异质性。 MTC-B 中总体甲基化状态升高，加上 MTC-A 和 MTC-C 表现出的低甲基化位点的“相互排斥性”，共同表征了 MTC 特异性甲基化模式。结合转录组，我们进一步描述了这三个簇的特征，以仔细研究其生物学特性。我们的研究强调了几个 MTC 特异性的异常 DNA 甲基化事件。研究发现，在预后不良的 MTC-C 中，NNAT 表达显着降低，其启动子区域与上调的差异甲基化区域重叠。体外实验进一步证实了NNAT的治疗潜力。此外，我们建立了包含68个探针的AUC相对较高的弹性网络逻辑回归模型，旨在用于未来的验证和系统的临床应用。对低发病率疾病进行研究提出了重大挑战，我们提供了强大的资源和全面的研究框架协助正在进行的 MTC 病例纳入，并促进对其分子生物学特征的深入剖析。

Medullary thyroid carcinoma (MTC) presents a distinct biological context from other thyroid cancers due to its specific cellular origin. This heterogeneous and rare tumor has a high prevalence of advanced diseases, making it crucial to address the limited therapeutic options and enhance complex clinical management. Given the high clinical accessibility of methylation information, we construct the largest MTC methylation cohort to date.78 fresh-frozen MTC samples constituted our methylation cohort. The comprehensive study process incorporated machine learning, statistical analysis, and in vitro experiments.Our study pioneered the identification of a 3-class clustering system for risk stratification, exhibiting pronounced epigenomic heterogeneity. The elevated overall methylation status in MTC-B, combined with the "mutual exclusivity" of hypomethylated sites displayed by MTC-A and MTC-C, distinctively characterized the MTC-specific methylation pattern. Integrating with the transcriptome, we further depicted the features of these three clusters to scrutinize biological properties. Several MTC-specific aberrant DNA methylation events were emphasized in our study. NNAT expression was found to be notably reduced in poor-prognostic MTC-C, with its promoter region overlapping with an upregulated differentially methylated region. In vitro experiments further affirmed NNAT's therapeutic potential. Moreover, we built an elastic-net logistic regression model with a relatively high AUC encompassing 68 probes, intended for future validation and systematic clinical application.Conducting research on diseases with low incidence poses significant challenges, and we provide a robust resource and comprehensive research framework to assist in ongoing MTC case inclusion and facilitate in-depth dissection of its molecular biological features.