Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
Eur J Hum Genet. 2011 Mar;19(3):307-12. doi: 10.1038/ejhg.2010.187. Epub 2010 Dec 8.
DNA methylation is a hallmark in a subset of right-sided colorectal cancers. Methylation-based screening may improve prevention and survival rate for this type of cancer, which is often clinically asymptomatic in the early stages. We aimed to discover prognostic or diagnostic biomarkers for colon cancer by comparing DNA methylation profiles of right-sided colon tumours and paired normal colon mucosa using an 8.5 k CpG island microarray. We identified a diagnostic CpG-rich region, located in the first intron of the protein-tyrosine phosphatase gamma gene (PTPRG) gene, with altered methylation already in the adenoma stage, that is, before the carcinoma transition. Validation of this region in an additional cohort of 103 sporadic colorectal tumours and 58 paired normal mucosa tissue samples showed 94% sensitivity and 96% specificity. Interestingly, comparable results were obtained when screening a cohort of Lynch syndrome-associated cancers. Functional studies showed that PTPRG intron 1 methylation did not directly affect PTPRG expression, however, the methylated region overlapped with a binding site of the insulator protein CTCF. Chromatin immunoprecipitation (ChIP) showed that methylation of the locus was associated with absence of CTCF binding. Methylation-associated changes in CTCF binding to PTPRG intron 1 could have implications on tumour gene expression by enhancer blocking, chromosome loop formation or abrogation of its insulator function. The high sensitivity and specificity for the PTPRG intron 1 methylation in both sporadic and hereditary colon cancers support biomarker potential for early detection of colon cancer.
DNA 甲基化是右半结直肠肿瘤的一个特征。基于甲基化的筛查可能会提高这种癌症的预防和生存率，因为这种癌症在早期阶段通常没有临床症状。我们旨在通过比较使用 8.5 kCpG 岛微阵列的右侧结肠癌肿瘤和配对正常结肠粘膜的 DNA 甲基化谱，发现结肠癌的预后或诊断生物标志物。我们确定了一个诊断性富含 CpG 的区域，位于蛋白酪氨酸磷酸酶γ基因（PTPRG）基因的第一个内含子中，在腺瘤阶段（即在癌前过渡之前）就已经发生了甲基化改变。在另外一组 103 例散发性结直肠肿瘤和 58 对配对正常粘膜组织样本中对该区域进行验证，结果显示 94%的敏感性和 96%的特异性。有趣的是，当筛选一组林奇综合征相关癌症时，也得到了类似的结果。功能研究表明，PTPRG 内含子 1 甲基化并没有直接影响 PTPRG 的表达，但是，甲基化区域与绝缘子蛋白 CTCF 的结合位点重叠。染色质免疫沉淀（ChIP）表明，该基因座的甲基化与 CTCF 结合的缺失有关。PTPRG 内含子 1 上 CTCF 结合的甲基化相关变化可能通过增强子阻断、染色体环形成或其绝缘子功能的缺失对肿瘤基因表达产生影响。PTPRG 内含子 1 甲基化在散发性和遗传性结肠癌中的高敏感性和特异性支持了其作为结肠癌早期检测的生物标志物的潜力。
