Table 9_Methylation and gene expression patterns in adamantinomatous craniopharyngioma highlight a panel of genes associated with disease progression-free survival.xlsx

IntroductionOver the past decade, advancements in next-generation sequencing have significantly enhanced our understanding of the molecular pathogenesis of adamantinomatous craniopharyngiomas (ACP).
ObjectiveThis study integrated methylome and transcriptome analyses in ACP samples to explore the potential interplay between DNA methylation and RNA expression signatures for diagnostic and prognostic applications in ACP patients.
MethodsThis cross-sectional study evaluated clinicopathological features, DNA methylation, and gene expression profiles in 15 patients with ACP (33% women, age range: 3–55 years, 53% diagnosed before 18 years) treated at Ribeirao Preto Medical School, University of São Paulo.
ResultsMultidimensional scaling and principal component analysis identified two distinct clusters (ACP-A: n=9, ACP-B: n=6) with consistent composition across DNA methylation and gene expression profiles. While most clinical and histopathological characteristics were similar between clusters, ACP-A exhibited a longer median progression-free survival. ACP-B showed a higher prevalence of hypomethylated probes in CGI sites, and 63% of differentially methylated positions (DMPs) located in gene body regions. Differential methylation patterns were categorized into Methyl-Set1 (hypomethylated in ACP-A and hypermethylated in ACP-B) and Methyl-Set2 (hypermethylated in ACP-A and hypomethylated in ACP-B). Clustering analyses based on the methylation levels of probes and expression levels of the stringently filtered 212- and 37-gene sets further confirmed these two distinct ACP subgroups. Functional enrichment analysis highlighted key roles in synaptic modulation, nervous system development, cell adhesion, as well as pathways linked to RAS signaling, GTPase activity, and membrane potential regulation.
ConclusionAlthough clinical characteristics were largely comparable between the clusters, ACP-B patients exhibited shorter median progression-free survival, suggesting a more aggressive phenotype. The higher prevalence of hypomethylation in ACP-B indicates increased transcriptional activation, potentially driving tumor aggressiveness. The strong concordance between methylation and transcriptomic data in the 212- and 37-gene sets underscores their potential as a clinically relevant molecular biomarker panel. These gene sets demonstrate robustness in distinguishing ACP clusters, making it a promising tool for clinical sample classification.

引言：近十年来，下一代测序（next-generation sequencing）技术的进步极大地提升了我们对造釉细胞瘤型颅咽管瘤（adamantinomatous craniopharyngiomas, ACP）分子发病机制的认知。
研究目的：本研究对ACP样本开展甲基化组（methylome）与转录组（transcriptome）联合分析，旨在探讨DNA甲基化与RNA表达特征之间的潜在相互作用，以期为ACP患者的诊断及预后评估提供依据。
研究方法：本横断面研究纳入了圣保罗大学里贝朗普雷图医学院收治的15例ACP患者（其中女性占33%，年龄范围3~55岁，53%的患者在18岁前确诊），对其临床病理特征、DNA甲基化及基因表达谱进行了评估。
研究结果：多维标度分析与主成分分析（principal component analysis）鉴定出两个独立的ACP亚型簇（ACP-A：n=9，ACP-B：n=6），其DNA甲基化与基因表达谱的构成具有高度一致性。尽管两个亚型簇的多数临床及组织病理特征无显著差异，但ACP-A组的中位无进展生存期（median progression-free survival）更长。ACP-B组的CpG岛（CGI）位点中低甲基化探针占比更高，且63%的差异甲基化位点（differentially methylated positions, DMPs）位于基因体区域。我们将差异甲基化模式分为甲基化集1（Methyl-Set1，在ACP-A中呈低甲基化、ACP-B中呈高甲基化）与甲基化集2（Methyl-Set2，在ACP-A中呈高甲基化、ACP-B中呈低甲基化）。基于探针甲基化水平以及经严格筛选的212个基因和37个基因集的表达水平进行的聚类分析，进一步验证了这两个独立的ACP亚型。功能富集分析（functional enrichment analysis）显示，这些基因集主要参与突触调节、神经系统发育、细胞黏附等生物学过程，以及RAS信号通路、GTP酶活性、膜电位调控等信号通路。
结论：尽管两个亚型簇的临床特征总体相似，但ACP-B组患者的中位无进展生存期更短，提示其具有更具侵袭性的表型。ACP-B组中低甲基化的高发生率提示转录激活水平升高，可能是肿瘤侵袭性增强的驱动因素。212个基因和37个基因集的甲基化数据与转录组数据具有高度一致性，表明其可作为具有临床应用价值的分子生物标志物组合。这些基因集在区分ACP亚型簇时表现出良好的稳定性，有望成为临床样本分类的有效工具。