Epigenetic profiling identifies markers of aggressive cancer subtype using a targeted methylation-based multi-cancer early detection (MCED) blood test
Presenter: Yue An, BS;MS Session: Early Detection Biomarkers 1 Time: 4/19/2026 2:00:00 PM → 4/19/2026 5:00:00 PM
Authors
Kezhong Chen 1 , Jian Huang 2 , Dahong Zhang 3 , Shu Wang 4 , Hongxu Liu 5 , Wenzhao Zhong 6 , Xiangnan Li 7 , Qiang Zhang 5 , Zhigao Li 8 , Jiaqi Liu 9 , Ziqing Tian 10 , Fei Zhou 11 , Gongsheng Jin 12 , Xudong Xiang 13 , Zhigang Li 14 , Hui Xie 15 , Ya Wei 16 , Guochun Zhang 17 , Guolin Ye 18 , Ming Cai 19 , Junfeng Wang 8 , Yan Zhang 20 , Chao Cheng 21 , Hefei Li 22 , Desong Yang 23 , Jianhong Lian 24 , Sheng Huang 25 , Tao Xu 26 , Zengjun Wang 27 , Xi Guo 28 , Zhuowei Liu 29 , Minfeng Chen 30 , Yang Wang 31 , Yue An 31 , Yanzhan Yang 31 , Min Li 31 , Jing Liu 31 , Baoliang Zhu 31 , Yonghui Li 31 , Xiaohui Wu 31 , Fan Yang 1 , Jun Wang 1 1 Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People’s Hospital, Beijing, China, 2 The Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 3 Urology & Nephrology Center, Department of Urology, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, China, 4 Breast Disease Center, Peking University People’s Hospital, Beijing, China, 5 Liaoning Provincial Cancer Hospital, Shenyang, China, 6 Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China, 7 The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China, 8 Harbin Medical University Cancer Hospital, Harbin, China, 9 Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China, 10 Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China, 11 Shanghai Pulmonary Hospital, Shanghai, China, 12 The First Affiliated Hospital of Bengbu Medical College, Bengbu, China, 13 Department of Thoracic Surgery, Yunnan Cancer Hospital, Kunming, China, 14 Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of medicine, Shanghai, China, 15 Department of Breast Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China, 16 Anyang Tumor Hospital, Anyang, China, 17 Department of Breast Surgery, Guangdong Provincial People’s Hospital, Guangzhou, China, 18 Department of Breast Cancer, The First People’s Hospital of Foshan, Foshan, China, 19 Department of Urology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China, 20 Department of Oncology, Shijiazhuang People’s Hospital, Shijiazhuang, China, 21 Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China, 22 Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China, 23 Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China, 24 Department of General Surgery,Shanxi Cancer Hospital, Taiyuan, China, 25 Department of Breast Surgical Oncology,Yunnan Cancer Hospital, Kunming, China, 26 Peking University People’s Hospital, Beijing, China, 27 Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China, 28 Department of Urology, Hunan Provincial People’s Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, China, 29 Sun Yat-sen University Cancer Center, Guangzhou, China, 30 Department of urology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China, 31 Shanghai Xiaohe Medical Laboratory Co. Ltd., Shanghai, China
Abstract
Background: Previous MCED studies have shown differences in detection performance across different aggressiveness cancer subtypes. However, the methylation profiles and ctDNA shedding patterns across different aggressiveness subtypes have not been analyzed. We systematically compared cell-free DNA (cfDNA) tumor fraction and methylation profiles across aggressiveness subtypes in three cancers to identify epigenetic biomarkers that differentiate tumor aggressiveness. Methods: Blood samples from a case-control study (NCT06217900) including 757 cancer cases were analyzed using a targeted methylation-based MCED test. We compared cfDNA tumor fraction and methylation profiles between aggressiveness subtypes, stage-matched small cell lung cancer (SCLC) (n=137) versus (vs) non-small cell lung cancer (NSCLC) (n=137), stage I invasive lung adenocarcinoma (IAC) (n=81) vs minimally invasive adenocarcinoma (MIA) (n=81), triple-negative breast cancer (TNBC) (n=151) vs non-TNBC (n=151), and intermediate/high-grade prostate cancer (Gleason Grade Group[GG] 2-5)(n=14) vs low-grade prostate cancer(GG1)(n=6). Tumor fraction was estimated using zero-inflated Negative Binomial model based on the distribution of methylation signals, and methylation profiles were assessed by calculating methylated/unmethylated (M/U) ratios between different aggressiveness subtypes. Marker comparisons were conducted using the Mann-Whitney U test with multiple testing corrections. Results: The sensitivity is higher in more aggressive subtypes (lung cancer 93.73% vs SCLC 99.27%; breast cancer 70.76% vs TNBC 81.46%; prostate cancer 40% vs intermediate and high-grad prostate cancer 42.86%). In lung cancer, SCLC exhibited a significantly higher cfDNA tumor fraction than NSCLC (Wilcoxon p = 2.24×10⁻²⁴), with 41,136 markers (79.18% hypomethylated) showing elevated M/U ratios. In stage I lung adenocarcinoma, IAC demonstrated a higher cfDNA tumor fraction (Wilcoxon p = 2.55×10⁻⁶) and systematic methylation differences compared to MIA. In breast cancer, TNBC had a significantly higher cfDNA tumor fraction than non-TNBC (Wilcoxon p = 2.55×10⁻⁶), with 25,717 markers (80.32% hypomethylated) displaying increased M/U ratios. Among prostate cancers of the same stage, GG2-5 cases exhibited higher cfDNA tumor fraction (Wilcoxon p = 0.038) and systematic methylation alterations compared to GG1. Conclusion: Aggressive tumor subtypes consistently display elevated cfDNA tumor fraction and characteristic methylation profiles marked by increased M/U ratios. These findings suggest cfDNA methylation patterns are promising epigenetic biomarkers for distinguishing tumor aggressiveness, potentially improving cancer screening precision and reducing overdiagnosis.
Disclosure
K. Chen, None.. J. Huang, None.. D. Zhang, None.. S. Wang, None.. H. Liu, None.. W. Zhong, None.. X. Li, None.. Q. Zhang, None.. Z. Li, None.. J. Liu, None.. Z. Tian, None.. F. Zhou, None.. G. Jin, None.. X. Xiang, None.. Z. Li, None.. H. Xie, None.. Y. Wei, None.. G. Zhang, None.. G. Ye, None.. M. Cai, None.. J. Wang, None.. Y. Zhang, None.. C. Cheng, None.. H. Li, None.. D. Yang, None.. J. Lian, None.. S. Huang, None.. T. Xu, None.. Z. Wang, None.. X. Guo, None.. Z. Liu, None.. M. Chen, None. Y. Wang, Shanghai Xiaohe Medical Laboratory Co. Ltd. Employment. Y. An, Shanghai Xiaohe Medical Laboratory Co. Ltd. Employment. Y. Yang, Shanghai Xiaohe Medical Laboratory Co. Ltd. Employment. M. Li, Shanghai Xiaohe Medical Laboratory Co. Ltd. Employment. J. Liu, Shanghai Xiaohe Medical Laboratory Co. Ltd. Employment. B. Zhu, Shanghai Xiaohe Medical Laboratory Co. Ltd. Employment. Y. Li, Shanghai Xiaohe Medical Laboratory Co. Ltd. Employment. X. Wu, Shanghai Xiaohe Medical Laboratory Co. Ltd. Employment. F. Yang, None.. J. Wang, None.
Cited in
Control: 2337 · Presentation Id: 10155 · Meeting 21436