PO.MCB06.02 · 分子与细胞生物学
在两个独立队列中鉴定出与早发性结直肠癌肿瘤位置相关的DNA甲基化特征
DNA methylation signatures associated with tumor location in early-onset colorectal cancer identified across two independent cohorts
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
背景：早发性结直肠癌(EOCRC;18-49岁)的发病率在全球范围内持续上升，其中直肠癌的增长速度快于近端或远端结肠癌。种系变异不能完全解释这些趋势或直肠肿瘤的不成比例增长，提示表观遗传机制可能发挥作用。然而，DNA甲基化(DNAm)与EOCRC肿瘤位置的关联仍知之甚少。
方法：我们使用癌症基因组图谱(TCGA)作为发现队列，以鉴定EOCRC中肿瘤位置特异性的DNAm标志物。首先，我们开展了一项全表观基因组关联研究，以FDR<0.2筛选胞嘧啶-磷酸-鸟嘌呤位点(CpGs),随后进行校正年龄、性别、分期和治疗的多变量logistic回归。CpG位点作为自变量建模,肿瘤位置(直肠[定义为直肠和直肠乙状结肠]与结肠)作为结局;显著的CpGs定义为FDR<0.05。为验证这些发现,我们采用相同的分析框架,在来自UT西南医学中心(UTSW)的独立EOCRC患者肿瘤组织队列中检测TCGA所鉴定的CpGs。对于重复验证的CpGs,我们评估了DNAm模式,映射到注释基因,并进行了通路富集分析。TCGA作为发现数据集,UTSW数据集作为验证队列。
结果：在TCGA队列的67例患者中(31.3%为直肠,平均年龄44岁,55.2%为女性,73%为白人,41.8%为III期),766个CpG位点在直肠与结肠肿瘤之间存在显著差异(FDR<0.05);其中27.7%在直肠肿瘤中高甲基化,72.3%低甲基化。UTSW验证队列包括72例患者(31.9%为直肠,45.8%为女性,56.9%为白人,37.5%为III期)。在可用于验证检测的504个CpGs中,266个显示出相同的关联方向,其中14.3%在直肠/直肠乙状结肠肿瘤中相对于结肠肿瘤高甲基化,85.7%低甲基化。对重复验证的CpGs进行主成分分析显示,直肠和结肠肿瘤形成各自独立的聚类。重复验证的CpGs映射到202个基因,包括SRC、IGF1R、EPHB3和MAP4K4。通路富集分析突出显示了与上皮细胞迁移、细胞间黏附和免疫激活相关的过程。
结论：肿瘤位置特异性的DNAm特征可区分EOCRC中的直肠肿瘤与结肠肿瘤,且近半数TCGA所鉴定的CpGs在独立患者肿瘤组织样本中显示出方向一致的重复验证。这些发现支持DNAm在EOCRC解剖异质性中发挥生物学作用,并确定了一组重点CpGs和通路,可供未来的机制研究以揭示表观遗传驱动因素。
查看英文原文 English abstract
Background: Incidence of early-onset colorectal cancer (EOCRC; ages 18-49) continues to rise globally, with rectal cancers increasing more rapidly than proximal or distal colon cancers. Germline variation does not fully explain these trends or the disproportionate rise in rectal tumors, suggesting a role for epigenetic mechanisms. However, the association of DNA methylation (DNAm) to EOCRC tumor location remains poorly understood.
Methods: We used The Cancer Genome Atlas (TCGA) as the discovery cohort to identify tumor location-specific DNAm markers in EOCRC. First, we conducted an epigenome-wide association study, screening Cytosine-Phosphate-Guanine site, (CpGs) at FDR< 0.2, followed by multivariable logistic regression adjusting for age, sex, stage, and treatment. CpG sites were modeled as independent variables and tumor location (rectum [defined as rectum and rectosigmoid] vs. colon) as the outcome; significant CpGs were defined at <fdr 0.05.="" to="" validate="" these="" findings,="" we="" tested="" the="" tcga-identified="" cpgs="" in="" an="" independent="" eocrc="" cohort="" of="" patient="" tumor="" tissue="" from="" ut="" southwestern="" medical="" center="" (utsw)="" using="" same="" analytic="" framework.="" for="" replicated="" cpgs,="" evaluated="" dnam="" patterns,="" mapped="" annotated="" genes,="" and="" conducted="" pathway="" enrichment="" analysis.="" tcga="" served="" as="" discovery="" dataset,="" utsw="" dataset="" replication="" cohort.
Results: Among the TCGA cohort of 67 patients, (31.3% rectum, mean age 44 years, 55.2% women, 73% White, 41.8% stage III), 766 CpG sites differed significantly between rectal and colonic tumors (FDR < 0.05); 27.7% were hypermethylated and 72.3% were hypomethylated in rectum tumors. The UTSW replication cohort included 72 patients (31.9% rectum, 45.8% women, 56.9% White, 37.5% stage III). Of the 504 CpGs available for replication testing, 266 showed the same direction of association, with 14.3% hypermethylated and 85.7% hypomethylated in rectal/rectosigmoid versus colonic tumors. Principal component analysis on replicated CpGs demonstrated separate clusters of rectum and colonic tumors. Replicated CpGs mapped to 202 genes, including SRC, IGF1R, EPHB3, and MAP4K4. Pathway enrichment analysis highlighted processes related to epithelial cell migration, cell-cell adhesion, and immune activation.
Conclusion: Tumor location-specific DNAm signatures differentiate rectal from colonic tumors in EOCRC, and nearly half of TCGA-identified CpGs showed directional replication in independent patient tumor tissue samples. These findings support a biological role for DNAm in anatomic heterogeneity of EOCRC and identify a focused set of CpGs and pathways for future mechanistic investigation to uncover epigenetic drivers.
利益披露 Disclosure
A. B. Rathod, None..
A. G. Singal, None..
C. C. Murphy, None.