Disentangling tumorigenesis-associated DNA methylation changes in colorectal tissues from those associated with ageing

Physiological ageing and tumorigenesis are both associated with epigenomic alterations in human tissue cells, the most extensively investigated of which entails de novo cytosine methylation (i.e., hypermethylation) within the CpG dinucleotides of CpG islands. Genomic regions that become hypermethylated during tumorigenesis are generally believed to overlap regions that acquire methylation in normal tissues as an effect of ageing. To define the extension of this overlap, we analysed the DNA methylomes of 48 large-bowel tissue samples taken from women of different ages during screening colonoscopy: 18 paired samples of normal and lesional tissues from donors harbouring a precancerous lesion and 12 samples of normal mucosa from tumour-free donors. Each sample was subjected to targeted, genome-wide bisulphite sequencing of ~2.5% of the genome, including all CpG islands. In terms of both its magnitude and extension along the chromatin, tumour-associated DNA hypermethylation in these regions was much more conspicuous than that observed in the normal mucosal samples from older (vs. younger) tumour-free donors. 83% of the ageing-associated hypermethylated regions (n = 2501) coincided with hypermethylated regions observed in tumour samples. However, 86% of the regions displaying hypermethylation in precancerous lesions (n = 16,772) showed no methylation changes in the ageing normal mucosa. The tumour-specificity of this latter hypermethylation was validated using published sets of data on DNA methylation in normal and neoplastic colon tissues. This extensive set of genomic regions displaying tumour-specific hypermethylation represents a rich vein of putative biomarkers for the early, non-invasive detection of colorectal tumours in women of all ages.

人体组织细胞的生理衰老与肿瘤发生均与表观基因组改变相关，其中研究最为广泛的一类改变为CpG岛（CpG island）内CpG二核苷酸位点的胞嘧啶从头甲基化（de novo cytosine methylation，即高甲基化）。学界普遍认为，肿瘤发生过程中发生高甲基化的基因组区域，与正常组织因衰老效应而获得甲基化的区域存在重叠。为明确该重叠的范围，我们对48份取自不同年龄女性筛查性结肠镜检查的大肠组织样本的DNA甲基化组（DNA methylome）进行了分析：其中18份为携带癌前病变（precancerous lesion）供体的正常组织与病变组织配对样本，另有12份来自无肿瘤供体的正常黏膜样本。所有样本均接受了靶向覆盖约2.5%基因组的全基因组亚硫酸氢盐测序（bisulphite sequencing），涵盖所有CpG岛。从甲基化幅度与沿染色质的分布范围来看，该类区域中肿瘤相关DNA高甲基化的程度，远高于老年（相较于年轻）无肿瘤供体正常黏膜样本中观察到的高甲基化。我们发现，2501个衰老相关高甲基化区域（n=2501）中有83%与肿瘤样本中的高甲基化区域重合。然而，在16772个癌前病变相关高甲基化区域中，有86%在衰老的正常黏膜组织中未发生甲基化改变。我们利用已发表的正常与肿瘤性结肠组织DNA甲基化数据集，验证了这类高甲基化的肿瘤特异性。这类携带肿瘤特异性高甲基化的大量基因组区域，可为全年龄段女性结直肠肿瘤的早期无创检测提供丰富的潜在生物标志物。