Accurate detection of cholangiocarcinoma in primary sclerosing cholangitis by DNA methylation biomarkers in bile and plasma

Hege Marie Vedeld; Sigurd Breder; Heidi Pharo; Hans Petter Brodal; Evy Marie Adolfsen; Sara Brandt-Winge; Erik von Seth; Marit Mæhle Grimsrud; Sheraz Yaqub; Tom H Karlsen; Krzyztof Grzyb; Vemund Paulsen; Martti A Färkkilä; Annika Bergquist; Lars Aabakken; Kirsten M Boberg; Trine Folseraas; Guro E Lind

doi:10.1016/j.jhepr.2026.101876

Accurate detection of cholangiocarcinoma in primary sclerosing cholangitis by DNA methylation biomarkers in bile and plasma

JHEP Rep. 2026 Apr 29:101876. doi: 10.1016/j.jhepr.2026.101876. Online ahead of print.

Authors

Hege Marie Vedeld¹, Sigurd Breder², Heidi Pharo¹, Hans Petter Brodal¹, Evy Marie Adolfsen¹, Sara Brandt-Winge¹, Erik von Seth³, Marit Mæhle Grimsrud⁴, Sheraz Yaqub⁵, Tom H Karlsen⁶, Krzyztof Grzyb⁷, Vemund Paulsen⁸, Martti A Färkkilä⁹, Annika Bergquist³, Lars Aabakken¹⁰, Kirsten M Boberg⁶, Trine Folseraas¹¹, Guro E Lind¹²

Affiliations

¹ Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - the Norwegian Radium Hospital, Oslo, Norway.
² Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital. Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
³ Department of Medicine Huddinge, Unit of Gastroenterology and Nutrition (GUT), Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
⁴ Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital. Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Oncology, Akershus University Hospital, Lørenskog, Norway.
⁵ Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Hepato-Pancreato-Biliary (HPB) Surgery, Department of Gastrointestinal and Pediatric Surgery, Oslo University Hospital, Oslo, Norway.
⁶ Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital. Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital - Rikshospitalet, Oslo, Norway.
⁷ Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
⁸ Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital - Rikshospitalet, Oslo, Norway.
⁹ Helsinki University and Department of Medicine, Division of Gastroenterology, Helsinki University Hospital, Helsinki, Finland.
¹⁰ Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital - Rikshospitalet, Oslo, Norway.
¹¹ Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital. Oslo, Norway; Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital - Rikshospitalet, Oslo, Norway.
¹² Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - the Norwegian Radium Hospital, Oslo, Norway; Department of Biosciences, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0371, Norway. Electronic address: g.e.lind@ibv.uio.no.

PMID: 42067191
DOI: 10.1016/j.jhepr.2026.101876

Abstract

Background & aims: Current methods for cholangiocarcinoma (CCA) detection in primary sclerosing cholangitis (PSC) lack accuracy, often leading to late, non-curative diagnoses. This study aimed to identify DNA methylation biomarkers in liquid biopsies for earlier and more accurate CCA detection.

Methods: Reduced representation bisulfite sequencing (RRBS) was used to analyze tissue samples from individuals with CCA (n=10) and PSC (n=9), yielding 12 candidate DNA methylation biomarkers. Following droplet digital PCR (ddPCR) assay development, quality control, and verification in tissue, four biomarkers were selected for evaluation in bile (n = 272) and plasma (n = 128) samples from individuals with PSC and/or CCA collected across three different hospitals.

Results: Four biomarkers demonstrated perfect discrimination (AUC=1.00) between PSC-associated CCA (PSC-CCA) and PSC alone in tissue samples. In bile, all four biomarkers achieved an AUC >0.9 for distinguishing PSC-CCA (n=20) from PSC alone (n=207). A two-biomarker panel (5-42952178 and PRKCB) achieved 95% sensitivity and 90% specificity, while adding KCNA6 and ZFP82 increased specificity to 97% with sensitivity maintained at 90%. Notably, the two-biomarker bile panel successfully detected all eight CCA cases (100% sensitivity) in samples collected 3-12 months prior to diagnosis by conventional methods. Performance was lower in plasma, where an alternative two-biomarker panel (KCNA6 and PRKCB) achieved 70% sensitivity and 90% specificity for distinguishing PSC-CCA (n=17) and PSC alone (n=101).

Conclusions: Four DNA methylation biomarkers accurately discriminate CCA from PSC in bile, with lower performance in plasma. Their ability to detect CCA months before clinical diagnosis supports further evaluation in prospective studies to enable earlier, potentially curative intervention in PSC.

Impact and implications: This study demonstrates that liquid biopsy-based DNA methylation biomarkers offer high sensitivity and specificity for early detection of CCA in individuals with PSC, directly addressing a critical unmet need. Early and accurate detection may enable timely surgical intervention, with the potential to significantly improve survival in this high-risk group. Both bile and plasma samples are accessible via routine clinical care, and implementation of such biomarkers would not introduce additional procedural risk. If validated in prospective studies, these biomarkers could transform standard CCA surveillance in PSC by providing a minimally invasive, reliable tool for longitudinal monitoring and earlier detection and intervention.

Keywords: Bile; biliary tract cancer; biomarker; cholangiocarcinoma; ctDNA; ddPCR; epigenetics; plasma; primary sclerosing cholangitis; surveillance.