Genome-Wide DNA Methylation Markers Associated With Metabolic Liver Cancer

Samuel O Antwi; Ampem Darko Jnr Siaw; Sebastian M Armasu; Jacob A Frank; Irene K Yan; Fowsiyo Y Ahmed; Laura Izquierdo-Sanchez; Loreto Boix; Angela Rojas; Jesus M Banales; Maria Reig; Per Stål; Manuel Romero Gómez; Kirk J Wangensteen; Amit G Singal; Lewis R Roberts; Tushar Patel

doi:10.1016/j.gastha.2025.100621

Genome-Wide DNA Methylation Markers Associated With Metabolic Liver Cancer

Gastro Hep Adv. 2025 Jan 23;4(5):100621. doi: 10.1016/j.gastha.2025.100621. eCollection 2025.

Authors

Samuel O Antwi^{1

2}, Ampem Darko Jnr Siaw¹, Sebastian M Armasu³, Jacob A Frank³, Irene K Yan⁴, Fowsiyo Y Ahmed⁵, Laura Izquierdo-Sanchez⁶, Loreto Boix⁷, Angela Rojas^{8

9}, Jesus M Banales^{6

10

11}, Maria Reig⁷, Per Stål¹², Manuel Romero Gómez^{8

9}, Kirk J Wangensteen⁵, Amit G Singal¹³, Lewis R Roberts⁵, Tushar Patel^{4

14}

Affiliations

¹ Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, Florida.
² Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Jacksonville, Florida.
³ Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota.
⁴ Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida.
⁵ Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota.
⁶ Department of Liver and Gastrointestinal Diseases, Biogipuzkoa Health Research Institute-Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain.
⁷ BCLC Group, Liver Unit, ICMDM, IDIBAPS, Hospital Clinic of Barcelona, University of Barcelona. Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD); Barcelona University, Barcelona, Spain.
⁸ SeLiver Group, UCM Digestive Diseases, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital/CSIC/University of Seville, Seville, Spain.
⁹ Hepatic and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Madrid, Spain.
¹⁰ Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain.
¹¹ Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
¹² Department of Upper GI Diseases, Karolinska University Hospital, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
¹³ Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.
¹⁴ Department of Transplantation, Mayo Clinic, Jacksonville, Florida.

Abstract

Background and aims: Metabolic liver disease is the fastest-rising cause of hepatocellular carcinoma (HCC), but the underlying molecular processes that drive HCC development in the setting of metabolic perturbations are unclear. We investigated the role of aberrant DNA methylation in metabolic HCC development in a multicenter international study.

Methods: We used a case-control design, frequency-matched on age, sex, and study site. Genome-wide profiling of peripheral blood leukocyte DNA was performed using the 850k EPIC array. The study sample was split 80% and 20% for training and validation. Cell type proportions were estimated from the methylation data. Differential methylation analysis was performed adjusting for cell type, generating area under the receiver-operating characteristic curves (AUC-ROC).

Results: We enrolled 272 metabolic HCC patients and 316 control patients with metabolic liver disease from 6 sites. Fifty-five differentially methylated CpGs were identified; 33 hypermethylated and 22 hypomethylated in cases vs controls. The panel of 55 CpGs discriminated between the cases and controls with AUC = 0.79 (95% confidence interval [CI] = 0.71-0.87), sensitivity = 0.77 (95% CI = 0.66-0.89), and specificity = 0.74 (95% CI = 0.64-0.85). The 55-CpG classifier panel performed better than a base model that comprised age, sex, race, and diabetes mellitus (AUC = 0.65, 95% CI = 0.55-0.75; sensitivity = 0.62, 95% CI = 0.49-0.75; and specificity = 0.64, 95% CI = 0.52-0.75). A multifactorial model that combined the 55 CpGs with age, sex, race, and diabetes yielded AUC = 0.78 (95% CI = 0.70-0.86), sensitivity = 0.81 (95% CI = 0.71-0.92), and specificity = 0.67 (95% CI = 0.55-0.78).

Conclusion: A panel of 55 blood leukocyte DNA methylation markers differentiates patients with metabolic HCC from control patients with benign metabolic liver disease, with a slightly higher sensitivity when combined with demographic and clinical information.

Keywords: HCC; Liver Cancer; MASLD; Metabolic Dysfunction-Associated Steatotic Liver Disease; NAFLD.