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.
- hepatobiliary cancer
- hepatocellular carcinoma
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JC, LC, ZZ and XZ contributed equally.
CH, HW, WZ and JF contributed equally.
Contributors Conceptualisation: JF, WZ, HW and CH; Methodology: XL, JN and CH; Collection of samples and clinical data: JC, LC, XZ, WL, GS, YG, PG, YY, AK, LX, RD, YZ, XY, JW, TZ, DY, XH, HS, SQ, FS, CS, WZ and JZ; Formal data analysis: ZZ, CZ, XZ and WZ; Writing original draft: JC, LC, ZZ, XZ, XL, EKS, BCHC, CH, WZ and JF; Funding acquisition: GS, AK, JC, HW, and LC, CH, WZ, and JF.
Funding National Institutes of Health (U01CA217078 and R01CA223662); Chinese State Key Project for Liver Cancer (2018ZX10732202-001); National Natural Science Foundation of China (81790633, 91729303, 81672860, 81572061, 81602513, 81472840, 81530077 and 81672825); The University of Chicago Ludwig Center; and The Howard Hughes Medical Institute.
Competing interests The 5hmC-Seal technology was invented by CH and was licensed by Shanghai Epican Genetech Co. Ltd. for clinical applications in human diseases from the University of Chicago. XL is a co-founder of Shanghai Epican Genetech Co. Ltd. CH and WZ are shareholders of Shanghai Epican Genetech Co. Ltd. CH is a scientific founder of Accent Therapeutics, Inc. and a member of its scientific advisory board. All other authors report no potential conflicts of interest.
Ethics approval The human research ethics committees at The Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, China; Zhongshan Hospital, Fudan University, Shanghai, China; The Tenth People’s Hospital of Shanghai, Tongji University, Shanghai, China.
Provenance and peer review Not commissioned; externally peer reviewed.
Patient consent for publication Not required.
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