Using cell-free DNA tumor methylation score to detect and monitor cholangiocarcinoma

IF 3.3 3区医学 Q2 GASTROENTEROLOGY & HEPATOLOGY

Hpb Pub Date : 2026-08-01 Epub Date: 2026-05-19 DOI:10.1016/j.hpb.2026.05.004

Salar Javanshir, Isabella Angeli-Pahim, Pavan Iyengar, Anastasia Chambers, Iulia M. Smarandache, Rishiraj Ganguli, Abhishek Shrestha, Jessica Squadrito, Adriana Abreu, Gabrielle Suchan, Carl Rizk, Fahreddin Palaz, Steven J. Hughes, Ilyas Sahin, Joseph R. Grajo, Sergio Duarte, Ali Zarrinpar

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引用次数: 0

Abstract

Background

Cholangiocarcinoma (CCA) is characterized by late or unclear diagnosis, high recurrence rates, and limited options for noninvasive disease monitoring. The widely used serum biomarker CA 19-9 has suboptimal sensitivity and specificity, underscoring the need for more accurate and reliable quantitative measures of tumor burden. Cell-free DNA (cfDNA) methylation represents a promising approach for longitudinal disease monitoring.

Methods

In this single-center cohort study, we evaluated a cfDNA methylation-based Tumor Methylation Score (TMS) for detecting and monitoring CCA. Twenty-five patients with histologically confirmed CCA and twelve controls with benign hepatobiliary conditions were enrolled, yielding 100 plasma samples and 26 tissue samples. cfDNA methylation was quantified across 537 cancer-associated CpG loci by qPCR method, and TMS was calculated from the difference in methylation in paired plasma and buffy coat samples. For tissue samples, TMS was calculated by quantifying methylation in tumor and background liver separately. Response to treatment was assessed using blinded radiographic review. Tissue-based validation was performed using The Cancer Genome Atlas and 4 additional GEO cohorts. Finally, cellular pathways associated with the panel genes were explored using the Ingenuity Pathway Analysis (IPA).

Results

TMS was significantly elevated in CCA samples compared with controls in both tissue (P = 0.007) and plasma (P < 0.0001). Plasma TMS distinguished CCA from controls with a sensitivity of 74.3% and specificity of 80% (AUC = 0.823), while CA 19-9 showed no discriminatory value. TMS decreased consistently following curative resection. Longitudinal changes in TMS (ΔTMS) robustly distinguished radiographic progression from non-progression during systemic therapy (AUC = 0.968), outperforming ΔCA 19–9. Tissue-based analyses across independent cohorts confirmed cancer specificity and association with adverse outcomes. IPA identified HOXA9 as a significantly altered gene implicated in CCA carcinogenesis.

Conclusions

Quantitative cfDNA methylation monitoring using TMS is feasible and accurately reflects dynamic tumor burden in CCA. TMS may serve as a complementary adjunct to imaging and CA 19–9 for diagnosis, prognosis, and longitudinal disease monitoring, warranting validation in larger prospective studies.

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应用游离DNA肿瘤甲基化评分检测和监测胆管癌。

背景：胆管癌（CCA）的特点是诊断晚或不明确，复发率高，无创疾病监测选择有限。广泛使用的血清生物标志物CA 19-9具有次优的敏感性和特异性，强调需要更准确和可靠的肿瘤负荷定量测量。无细胞DNA （cfDNA）甲基化是一种很有前途的纵向疾病监测方法。方法：在这项单中心队列研究中，我们评估了基于cfDNA甲基化的肿瘤甲基化评分（TMS）用于检测和监测CCA。纳入25例组织学证实的CCA患者和12例肝胆良性疾病对照，获得100份血浆样本和26份组织样本。通过qPCR方法对537个与癌症相关的CpG位点的cfDNA甲基化进行量化，并根据配对血浆和黄皮毛样品的甲基化差异计算TMS。对于组织样本，分别通过量化肿瘤和背景肝脏的甲基化来计算TMS。采用盲法放射学评价对治疗的反应。使用癌症基因组图谱和另外4个GEO队列进行基于组织的验证。最后，使用独创性途径分析（IPA）探索了与面板基因相关的细胞途径。结果：与对照组相比，CCA样品在组织（P = 0.007）和血浆（P < 0.0001）中TMS均显著升高。血浆TMS区分CCA与对照组的敏感性为74.3%，特异性为80% (AUC = 0.823)，而CA 19-9无区别价值。TMS在治愈性切除后持续下降。TMS的纵向变化（ΔTMS）有力地区分了全身治疗期间放射学进展与非进展（AUC = 0.968），优于ΔCA 19-9。独立队列的基于组织的分析证实了癌症特异性和与不良结局的关联。IPA发现HOXA9是一个显著改变的基因，与CCA致癌有关。结论：TMS定量监测cfDNA甲基化是可行的，能准确反映CCA的动态肿瘤负荷。经颅磁刺激可作为影像学和CA 19-9诊断、预后和纵向疾病监测的辅助手段，在更大规模的前瞻性研究中得到验证。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Hpb GASTROENTEROLOGY & HEPATOLOGY-SURGERY

CiteScore

5.60

自引率

3.40%

发文量

244

审稿时长

57 days

期刊介绍： HPB is an international forum for clinical, scientific and educational communication. Twelve issues a year bring the reader leading articles, expert reviews, original articles, images, editorials, and reader correspondence encompassing all aspects of benign and malignant hepatobiliary disease and its management. HPB features relevant aspects of clinical and translational research and practice. Specific areas of interest include HPB diseases encountered globally by clinical practitioners in this specialist field of gastrointestinal surgery. The journal addresses the challenges faced in the management of cancer involving the liver, biliary system and pancreas. While surgical oncology represents a large part of HPB practice, submission of manuscripts relating to liver and pancreas transplantation, the treatment of benign conditions such as acute and chronic pancreatitis, and those relating to hepatobiliary infection and inflammation are also welcomed. There will be a focus on developing a multidisciplinary approach to diagnosis and treatment with endoscopic and laparoscopic approaches, radiological interventions and surgical techniques being strongly represented. HPB welcomes submission of manuscripts in all these areas and in scientific focused research that has clear clinical relevance to HPB surgical practice. HPB aims to help its readers - surgeons, physicians, radiologists and basic scientists - to develop their knowledge and practice. HPB will be of interest to specialists involved in the management of hepatobiliary and pancreatic disease however will also inform those working in related fields. Abstracted and Indexed in: MEDLINE® EMBASE PubMed Science Citation Index Expanded Academic Search (EBSCO) HPB is owned by the International Hepato-Pancreato-Biliary Association (IHPBA) and is also the official Journal of the American Hepato-Pancreato-Biliary Association (AHPBA), the Asian-Pacific Hepato Pancreatic Biliary Association (A-PHPBA) and the European-African Hepato-Pancreatic Biliary Association (E-AHPBA).