Circulating cell-free DNA methylation analysis of pancreatic cancer patients for early noninvasive diagnosis

Wenzhe Hu; Xudong Zhao; Nan Luo; Mengmeng Xiao; Feng Feng; Yuan An; Jianfei Chen; Long Rong; Yinmo Yang; Jirun Peng

doi:10.3389/fonc.2025.1552426

Circulating cell-free DNA methylation analysis of pancreatic cancer patients for early noninvasive diagnosis

Front Oncol. 2025 Mar 10:15:1552426. doi: 10.3389/fonc.2025.1552426. eCollection 2025.

Authors

Wenzhe Hu^#^{1

2}, Xudong Zhao^#³, Nan Luo^#^{1

2

4}, Mengmeng Xiao⁵, Feng Feng^{1

2}, Yuan An^{1

2}, Jianfei Chen^{1

2}, Long Rong³, Yinmo Yang⁶, Jirun Peng^{1

2

4}

Affiliations

¹ Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.
² School of Oncology, Capital Medical University, Beijing, China.
³ Department of Endoscopy Center, Peking University First Hospital, Peking University, Beijing, China.
⁴ Ninth School of Clinical Medicine, Peking University, Beijing, China.
⁵ Department of General Surgery, Peking University People's Hospital, Peking University, Beijing, China.
⁶ Department of General Surgery, Peking University First Hospital, Peking University, Beijing, China.

^# Contributed equally.

Abstract

Background: Aberrant hypermethylation of genomic DNA CpG islands (CGIs) is frequently observed in human pancreatic cancer (PAC). A plasma cell-free DNA (cfDNA) methylation analysis method can be utilized for the early and noninvasive detection of PAC. This study also aimed to differentiate PAC from other cancer types.

Methods: We employed the methylated CpG tandem amplification and sequencing (MCTA-Seq) method, which targets approximately one-third of CGIs, on plasma samples from PAC patients (n = 50) and healthy controls (n = 52), as well as from cancerous and adjacent noncancerous tissue samples (n = 66). The method's efficacy in detecting PAC and distinguishing it from hepatocellular carcinoma (HCC), colorectal cancer (CRC), and gastric cancer (GC) was evaluated. Additionally, a methylation score and typing system for PAC was also established.

Results: We identified a total of 120 cfDNA methylation biomarkers, including IRX4, KCNS2, and RIMS4, for the detection of PAC in blood. A panel comprising these biomarkers achieved a sensitivity of 97% and 86% for patients in the discovery and validation cohorts, respectively, with a specificity of 100% in both cohorts. The methylation scoring and typing systems were clinically applicable. Furthermore, we identified hundreds of differentially methylated cfDNA biomarkers between PAC and HCC, CRC, and GC. Certain combinations of these markers can be used in a highly specific (approximately 100%) algorithm to differentiate PAC from HCC, CRC, and GC in blood.

Conclusions: Our study identified cfDNA methylation markers for PAC, offering a novel approach for the early, noninvasive diagnosis of PAC.

Keywords: DNA methylation; circulating cell-free DNA; colorectal cancer; early noninvasive diagnosis; gastric cancer; hepatocellular carcinoma; pancreatic cancer.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This research was funded by the Capital’s Funds for Health Improvement and Research of China (No. 2020-2-2083), the Natural Science Foundation of China (No. 82072601), the Natural Science Foundation of China (No. 82171722), the National Science and Technology Major Project (2023ZD0500902), and the Young Elite Scientists Sponsorship Program by CAST (2023QNRC001).