Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients.
Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients.
复制标题
肝细胞癌患者循环游离DNA中高甲基化CpG岛的基因组规模检测
DOI：
10.1038/cr.2015.126
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发表时间：
2015-11
期刊：
影响因子：
44.1
通讯作者：
Peng J
中科院分区：
文献类型：
--
作者：
Wen L;Li J;Guo H;Liu X;Zheng S;Zhang D;Zhu W;Qu J;Guo L;Du D;Jin X;Zhang Y;Gao Y;Shen J;Ge H;Tang F;Huang Y;Peng J
尽管细胞和组织的DNA甲基化分析取得了进展，但目前用于循环无细胞DNA （ccfDNA）中DNA甲基化的基因组级分析技术仍然有限。在这里，我们描述了一种甲基化CpG串联扩增和测序（MCTA-Seq）方法，可以同时检测ccfDNA中数千个高甲基化CpG岛。这种高度敏感的技术可以处理低至7.5 pg的基因组DNA，相当于2.5个单倍体基因组拷贝。我们分析了一组肝细胞癌（HCC）患者和对照组的组织和血浆样本（n = 151），在血液中鉴定了数十种用于检测小肝癌（≤3 cm）的高效标志物。其中4个（RGS10、ST8SIA6、RUNX2和VIM）主要是癌症检测的特异性标记，而另外15个被归类为一组新标记，在正常肝组织中已经高甲基化。已经建立了两种相应的分类器，对HCC患者（n = 36）和对照组(包括肝硬化患者（n = 17）和正常人（n = 38）的血浆样本的敏感性为94%，特异性为89%。值得注意的是，所有15例甲胎蛋白阴性的HCC患者均被成功识别。匹配的血浆和组织样本之间的比较表明，癌症和非癌组织都有助于血浆中甲基化标记物的升高。MCTA-Seq将促进ccfDNA甲基化生物标志物的开发，并有助于改善临床环境中的癌症检测。
Despite advances in DNA methylome analyses of cells and tissues, current techniques for genome-scale profiling of DNA methylation in circulating cell-free DNA (ccfDNA) remain limited. Here we describe a methylated CpG tandems amplification and sequencing (MCTA-Seq) method that can detect thousands of hypermethylated CpG islands simultaneously in ccfDNA. This highly sensitive technique can work with genomic DNA as little as 7.5 pg, which is equivalent to 2.5 copies of the haploid genome. We have analyzed a cohort of tissue and plasma samples (n = 151) of hepatocellular carcinoma (HCC) patients and control subjects, identifying dozens of high-performance markers in blood for detecting small HCC (≤ 3 cm). Among these markers, 4 (RGS10, ST8SIA6, RUNX2 and VIM) are mostly specific for cancer detection, while the other 15, classified as a novel set, are already hypermethylated in the normal liver tissues. Two corresponding classifiers have been established, combination of which achieves a sensitivity of 94% with a specificity of 89% for the plasma samples from HCC patients (n = 36) and control subjects including cirrhosis patients (n = 17) and normal individuals (n = 38). Notably, all 15 alpha-fetoprotein-negative HCC patients were successfully identified. Comparison between matched plasma and tissue samples indicates that both the cancer and noncancerous tissues contribute to elevation of the methylation markers in plasma. MCTA-Seq will facilitate the development of ccfDNA methylation biomarkers and contribute to the improvement of cancer detection in a clinical setting.