Genome-wide mapping of 5-hydroxymethylcytosines in circulating cell-free DNA as a non-invasive approach for early detection of hepatocellular carcinoma

Jiabin Cai; Lei Chen; Zhou Zhang; Xinyu Zhang; Xingyu Lu; Weiwei Liu; Guoming Shi; Yang Ge; Pingting Gao; Yuan Yang; Aiwu Ke; Linlin Xiao; Ruizhao Dong; Yanjing Zhu; Xuan Yang; Jiefei Wang; Tongyu Zhu; Deping Yang; Xiaowu Huang; Chengjun Sui; Shuangjian Qiu; Feng Shen; Huichuan Sun; Weiping Zhou; Jian Zhou; Ji Nie; Chang Zeng; Emily Kunce Stroup; Xu Zhang; Brian C-H Chiu; Wan Yee Lau; Chuan He; Hongyang Wang; Wei Zhang; Jia Fan

doi:10.1136/gutjnl-2019-318882

Genome-wide mapping of 5-hydroxymethylcytosines in circulating cell-free DNA as a non-invasive approach for early detection of hepatocellular carcinoma

Gut. 2019 Dec;68(12):2195-2205. doi: 10.1136/gutjnl-2019-318882. Epub 2019 Jul 29.

Authors

Jiabin Cai^#^{1

2

3}, Lei Chen^#^{4

5}, Zhou Zhang^#⁶, Xinyu Zhang^#^{1

2}, Xingyu Lu⁷, Weiwei Liu⁸, Guoming Shi^{1

2}, Yang Ge⁹, Pingting Gao^{1

2}, Yuan Yang¹⁰, Aiwu Ke^{1

2}, Linlin Xiao¹¹, Ruizhao Dong^{1

2}, Yanjing Zhu⁴, Xuan Yang^{1

2}, Jiefei Wang¹², Tongyu Zhu¹², Deping Yang¹³, Xiaowu Huang^{1

2}, Chengjun Sui¹⁰, Shuangjian Qiu^{1

2}, Feng Shen¹⁰, Huichuan Sun^{1

2}, Weiping Zhou¹⁰, Jian Zhou^{1

2

3}, Ji Nie¹⁴, Chang Zeng^{6

15}, Emily Kunce Stroup¹⁵, Xu Zhang¹⁶, Brian C-H Chiu¹⁷, Wan Yee Lau¹⁸, Chuan He^#^{14

19

20

21}, Hongyang Wang^#^{4

5

22}, Wei Zhang^#^{6

23}, Jia Fan^#^{1

2

3}

Affiliations

¹ Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
² Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University & Ministry of Education, Shanghai, China.
³ Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, Fudan University, Shanghai, China.
⁴ The International Cooperation Laboratory on Signal Transduction, The Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, China.
⁵ National Center for Liver Cancer, Shanghai, China.
⁶ Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
⁷ Shanghai Epican Genetech Co. Ltd., Shanghai, China.
⁸ Department of Laboratory Medicine, The Tenth People's Hospital of Shanghai, Tongji University, Shanghai, China.
⁹ School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
¹⁰ Department of Hepatobiliary Surgery, The Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, China.
¹¹ Department of Laboratory Medicine, Shanghai Jiao Tong University, Shanghai, China.
¹² Shanghai Public Health Clinic Center, Fudan University, Shanghai, China.
¹³ Department of Laboratory Medicine, Zhoupu Hospital, Shanghai University of Medicine & Health Sciences, Shanghai, China.
¹⁴ Department of Chemistry, University of Chicago, Chicago, Illinois, USA.
¹⁵ Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, Illinois, Chicago.
¹⁶ Department of Medicine, University of Illinois, Chicago, Illinois, USA.
¹⁷ Department of Public Health Sciences, University of Chicago, Chicago, Illinois, USA.
¹⁸ Faculty of Medicine, The Chinese University of Hong Kong, New Territories, Hong Kong, China.
¹⁹ Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.
²⁰ Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA.
²¹ The Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, USA.
²² Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, The Second Military Medical University & Ministry of Education, Shanghai, China.
²³ The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.

^# Contributed equally.

Abstract

Objective: The lack of highly sensitive and specific diagnostic biomarkers is a major contributor to the poor outcomes of patients with hepatocellular carcinoma (HCC). We sought to develop a non-invasive diagnostic approach using circulating cell-free DNA (cfDNA) for the early detection of HCC.

Design: Applying the 5hmC-Seal technique, we obtained genome-wide 5-hydroxymethylcytosines (5hmC) in cfDNA samples from 2554 Chinese subjects: 1204 patients with HCC, 392 patients with chronic hepatitis B virus infection (CHB) or liver cirrhosis (LC) and 958 healthy individuals and patients with benign liver lesions. A diagnostic model for early HCC was developed through case-control analyses using the elastic net regularisation for feature selection.

Results: The 5hmC-Seal data from patients with HCC showed a genome-wide distribution enriched with liver-derived enhancer marks. We developed a 32-gene diagnostic model that accurately distinguished early HCC (stage 0/A) based on the Barcelona Clinic Liver Cancer staging system from non-HCC (validation set: area under curve (AUC)=88.4%; (95% CI 85.8% to 91.1%)), showing superior performance over α-fetoprotein (AFP). Besides detecting patients with early stage or small tumours (eg, ≤2.0 cm) from non-HCC, the 5hmC model showed high capacity for distinguishing early HCC from high risk subjects with CHB or LC history (validation set: AUC=84.6%; (95% CI 80.6% to 88.7%)), also significantly outperforming AFP. Furthermore, the 5hmC diagnostic model appeared to be independent from potential confounders (eg, smoking/alcohol intake history).

Conclusion: We have developed and validated a non-invasive approach with clinical application potential for the early detection of HCC that are still surgically resectable in high risk individuals.

Keywords: cancer; hepatobiliary cancer; hepatocellular carcinoma.

Publication types

Multicenter Study
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

5-Methylcytosine / analogs & derivatives*
5-Methylcytosine / blood
Biomarkers, Tumor / blood
Carcinoma, Hepatocellular / blood
Carcinoma, Hepatocellular / diagnosis
Carcinoma, Hepatocellular / genetics*
Cell-Free Nucleic Acids / blood*
DNA, Neoplasm / analysis*
Early Detection of Cancer / methods*
Female
Genome-Wide Association Study / methods*
Humans
Liver Neoplasms / blood
Liver Neoplasms / diagnosis
Liver Neoplasms / genetics*
Male
Middle Aged
Prospective Studies
ROC Curve

Substances

Biomarkers, Tumor
Cell-Free Nucleic Acids
DNA, Neoplasm
5-hydroxymethylcytosine
5-Methylcytosine

Abstract

Publication types

MeSH terms

Substances

Grants and funding