Biomarker Discovery and Early Detection in CCA

At the 2025 Annual Cholangiocarcinoma Foundation Conference, a working group that included co-chairs Jesus Bañales and Zack Foda, as well as Jennifer Knox, Tomasz Beer, Stephanie Roessler, Pashtoon Kasi, Trine Folseraas, Luis Diaz, Ainhoa Lapitz, Lisa Craine, and Jennifer Wild, discussed biomarkers for early detection and screening of cholangiocarcinoma (CCA) and the potential roadmap for translating biomarkers into clinical practice.

Jesus Bañales first discussed who should be the target group for early diagnosis and screening. There are several factors that increase the risk of CCA development. Conditions with low to moderate prevalence, such as primary sclerosing cholangitis (PSC), Caroli’s disease, choledochal cysts, liver fluke disease, and cirrhosis, are associated with a high risk of CCA. In contrast, conditions with higher prevalence, including hepatitis B, hepatitis C, biliary stones, alcohol-related liver disease, metabolic liver disease, type 2 diabetes mellitus, intrahepatic and extrahepatic CCA, and smoking, are linked to a moderate risk of developing CCA.

The diagnosis of CCA combines the use of imaging techniques, the analysis of nonspecific tumor markers, and biopsy/cytology confirmation. Serum tumor biomarkers CA19.9 and CEA correlate with metastatic disease; if both biomarkers are found elevated, there is a higher risk of development of metastatic disease compared with a singular elevation of either biomarker. Some of the most promising biomarkers and technologies for CCA detection include assays using circulating tumor DNA (ctDNA), cell-free noncoding RNAs, cytokines/proteins, metabolites, circulating tumor cells, extracellular vesicles, imaging biomarkers, and integration of different biomarkers by artificial intelligence tools. One study conducted by the Mayo Clinic found that methylated DNA markers, including TWIST1, HOXA1, VSTM2B, and CLEC11A, from biliary brushings improve the detection of malignant biliary strictures. Another diagnostic strategy is the analysis of ctDNA levels. A recent study evaluated the potential value of evaluating ctDNA levels for the early detection of CCA in patients with PSC. A total of 63 patients with PSC and 20 healthy individuals were included. Interestingly, approximately one-third of patients with PSC and without cancer presented with ctDNA levels measurable in bile; a mutant allele frequency value of ≥0.1% was considered suggestive of the presence of a mutation. The patients with PSC and without cancer also had different degrees of dysplasia, which are difficult to detect and analyze. Additionally, ≤4 patients with CCA did not have measurable ctDNA levels present in bile.

Accurate noninvasive biomarkers can predict CCA development in surveillance and early detection efforts. The CCA registry was used to conduct a study that evaluated the effect of chronic liver disease on the overall survival (OS) of patients with cholangiocarcinoma. In this study, patients in the CCA registry diagnosed with cholangiocarcinoma and chronic liver disease were compared with patients with cholangiocarcinoma and healthy livers. It was found that those with CCA and chronic liver disease survived longer than those with a healthy liver. This may be due to patients with chronic liver disease undergoing more routine surveillance and monitoring, which increases the likelihood of detecting tumors at an earlier stage and contributes to longer survival. This in turn leads to patients being eligible for surgical interventions with a curative intent, leading to a higher OS compared with patients with a healthy liver. These data strongly highlight the importance of generating a standardized surveillance program and the importance of biomarker identification toward early identification of CCA.

The panel also discussed clinical implementation of biomarkers, where several key considerations were outlined to bridge the gap between biomarker discovery and their practical application in clinical settings. The panelists discussed that it is important to note that biomarker discovery includes advanced technologies, high-throughput platforms, high sensitivity and specificity, and expensive techniques. Clinical implementation, however, involves applying discovered biomarkers in routine clinical practice. For clinical implementation to be successful, methods should be utilized that are commonly available techniques in most laboratories, through potential central lab analysis, and report results that are easily quantifiable and interpretable. Methods should also be cost-effective and potentially tailored to specific risk conditions.

Despite advancements in biomarker research, several critical gaps remain in addressing unmet clinical needs, particularly in identifying and validating biomarkers for improved risk assessment and early diagnosis. Some of these gaps include the need for 2 types of biomarkers, risk-prediction markers in high-risk conditions and early diagnostic markers. In addition, high-throughput omics-based discovery studies, including all or specific etiologies, are needed as well as validation of available results from already performed omics studies. Addressing these gaps, particularly in the area of risk prediction, will be crucial for advancing personalized medicine, improving patient outcomes, and improving clinical implementation.

There are some questions that should be addressed early in the process of biomarker translation. These include addressing if industry partners should be involved, and if so, when? It is also important to include patient groups early in these studies to increase the number of patients and to address required regulations for the biomarker.

Next steps needed to advance biomarker research and improve their clinical trial implementation are to select biomarkers that are accurate, reproducible, well-validated, easy to quantify, and cost-effective. It is also important to involve experts in other research areas who have successfully translated a biomarker. In terms of research priorities, protocols need to be established for broad clinical application, and performance standards need to be established before translation into clinical practice.

Source

Foda ZH, Bañales JM. WG9-Biomarker Discovery & Early Detection. Presented at: 2025 Annual Cholangiocarcinoma Foundation Conference. April 9-11, 2025; Salt Lake City, UT.