Volume 25, No 11, Nov 2015
ISSN: 1001-0602
EISSN: 1748-7838 2018
impact factor 17.848*
(Clarivate Analytics, 2019)
Volume 25 Issue 11, November 2015: 1250-1264 | Open Access
ORIGINAL ARTICLES
Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients
Lu Wen1,*, Jingyi Li1,*, Huahu Guo2,4,5,*, Xiaomeng Liu1,*, Shengmin Zheng3, Dafang Zhang3, Weihua Zhu3, Jianhui Qu6, Limin Guo7, Dexiao Du2,4,5, Xiao Jin1,9, Yuhao Zhang1,9, Yun Gao1, Jie Shen1,10, Hao Ge1,9, Fuchou Tang1,8,10, Yanyi Huang1,10,11 and Jirun Peng2,4,5
1Biodynamic Optical Imaging Center (BIOPIC), College of Life Sciences, Peking University, Beijing 100871, China
2Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
3Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing 100044, China
4Ninth School of Clinical Medicine, Peking University, Beijing 100044, China
5School of Oncology, Capital Medical University, Beijing 100069, China
6Center of Therapeutic Research for Liver Cancer, Beijing 302 Hospital, Beijing 100039, China
7Department of Hepatobiliary Surgery, Beijing DiTan Hospital, Capital Medical University, Beijing 100015, China
8Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China
9BIMCR, Peking University, Beijing 100871, China
10Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
11College of Engineering, Peking University, Beijing 100871, China
Correspondence: Fuchou Tang, E-mail: tangfuchou@pku.edu.cn; Yanyi Huang, E-mail: yanyi@pku.edu.cn; Jirun Peng,(pengjr@medmail.com.cn)
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.
10.1038/cr.2015.126
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