Pan-cancer methylation analysis of circulating cell-free DNA

• Published in: Cancer genetics Vol. 296-297; pp. 182 - 195
• Main Authors: Dong, Wenjiao, Lau, Cia-Hin, Li, Jiaqi, Huang, Zhihao, Li, Jiahui, Wu, Weidong, Chen, Xiaoqing, Huang, Yumei, Huang, Xiaojun, Xu, Meijing, Zhu, Haibao, Ding, Yuanlin
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.09.2025
• Subjects: Cancer screening; Cell Line, Tumor; Cell-Free Nucleic Acids - blood; Cysteine Dioxygenase; DNA Methylation; DNA Restriction Enzymes; Healthy Volunteers; Humans; Multi-cancer; Neoplasms - blood; Neoplasms - diagnosis; Pan-cancer; POCT; Promoter Regions, Genetic; Sequence Analysis, DNA; DNA methylation; Multi-cancer; Pan-cancer; POCT; Cancer screening
• ISSN: 2210-7762
• DOI: 10.1016/j.cancergen.2025.07.014

•establish a gene methylation panel (HIST1H4F and CDO1) for pan-cancer analysis.•multi-organ cancers early detection with blood cfDNA.•high detection sensitivity and specificity in diverse cancer types.•universal cancer screening with only a few markers. Universal cancer screening based on methylation analysis of circulating cell-free DNA (cfDNA) enables multi-organ cancer detection, thereby reducing all-cause mortality and preventing cancer misdiagnosed by guideline-based cancer-specific screening. This study aims to establish a gene methylation panel for blood-based multi-cancer early detection. Bioinformatics analysis and in-house DNA sequencing of various human cancer cell lines and blood from healthy persons were carried out to identify candidate pan-cancer methylation sites. Methylation-sensitive restriction enzymes-quantitative PCR (MSRE-qPCR) was then used for DNA methylation analysis. Blood cfDNA from 103 patients with diverse cancer types and 40 healthy subjects was extracted for methylation analysis. By bioinformatics analysis and in-house DNA sequencing, we identified two candidates pan-cancer methylation sites, HIST1H4F and CDO1. A long stretch of methylation was found on the promoters of HIST1H4F and CDO1 across various cancer cell lines, while these genomic regions are unmethylated in healthy persons. When tested with clinical samples, the detection sensitivity and specificity of our gene methylation panel in detecting pan-cancer were 47.57 % and 90.00 %, respectively. When analyzed by cancer subtypes, the detection sensitivity was the highest in lung cancer (76.92 %), followed by colorectal cancer (63.64 %) and gastric cancer (50.00 %). Our newly established gene methylation panel provides an alternative assay for multi-cancer screening tests. As no bisulfite conversion and invasive procedures are required, it can accelerate cancer diagnosis and streamline the operation for pan-cancer screening. [Display omitted]