{
  "abstract": "Background Advanced gastric cancer (aGC) exhibits substantial heterogeneity in response to combination immunotherapy. Circulating cell-free DNA (cfDNA) enables non-invasive profiling of tumor dynamics and may provide biomarkers for response prediction.Methods We enrolled 94 patients with aGC undergoing combination immunotherapy and assigned them to a discovery set (n=49) and an internal validation set (n=45). Plasma cfDNA was collected pre-treatment and post-treatment and profiled by low-pass whole-genome sequencing and whole-genome bisulfite sequencing in the discovery set, with targeted bisulfite sequencing used in the validation set.Results The discovery set included 34 responders and 15 non-responders, and the validation set included 30 responders and 15 non-responders. We found that responders showed longer cfDNA, lower cfDNA tumor fraction (median: 0.06 vs 0.01, p<0.001), reduced chromosomal instability (median genomic instability index: 0.026 vs 0.007, p<0.001), and higher global methylation (median: 0.715 vs 0.724, p=0.007). Additionally, the differentially methylated region (DMR) at chr20:25849353-25849490 consistently showed higher methylation in responders in both the discovery (adjusted p=0.006) and validation sets (adjusted p=0.049). A predictor based on this DMR outperformed programmed death-ligand 1 (PD-L1) combined positive score (CPS) with area under the curve (AUCs) of 0.79 (discovery: 95% CI 0.65 to 0.93) and 0.72 (validation: 95% CI 0.54 to 0.91). When integrating PD-L1 CPS with this DMR, the AUCs were 0.81 (discovery: 95% CI 0.67 to 0.95) and 0.75 (validation: 95% CI 0.56 to 0.94), respectively. For on-treatment monitoring, three DMRs increased specifically in responders; among them, increased methylation of chr8:110479193-110480324 and chr8:50891437-50892120 was associated with improved progression-free survival (median: 4.90 vs 11.57 months, p<0.001; median: 5.20 vs 10.20 months, p=0.007).Conclusion Integrated cfDNA profiling captures immunotherapy-associated molecular dynamics in aGC. A single pretreatment cfDNA methylation marker (chr20:25849353-25849490) improves response prediction beyond PD-L1 CPS and represents a potential predictive biomarker for combination immunotherapy.",
  "authors": [
    {
      "affiliations": [
        "School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China",
        "Department of Epidemiology, School of Public Health, State Key Laboratory Cultivation Base of Biomarkers for Cancer Precision Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China",
        "The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Center, Wuxi, Shanghai, China"
      ],
      "name": "Jingshuai Fang"
    },
    {
      "affiliations": [
        "Department of Epidemiology, School of Public Health, State Key Laboratory Cultivation Base of Biomarkers for Cancer Precision Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China"
      ],
      "name": "Yuhui Yu"
    },
    {
      "affiliations": [
        "Department of Epidemiology, School of Public Health, State Key Laboratory Cultivation Base of Biomarkers for Cancer Precision Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China",
        "Department of Medical Oncology, Jiangsu Key Laboratory of Innovative Cancer Diagnosis & Therapeutics, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, China"
      ],
      "name": "Yan Sun"
    },
    {
      "affiliations": [
        "Innovation Center of Suzhou, Nanjing Medical University, Suzhou, Jiangsu, China",
        "National Center of Technology Innovation for Biopharmaceuticals, Suzhou, Jiangsu, China"
      ],
      "name": "Mengmeng Ji"
    },
    {
      "affiliations": [
        "Department of Epidemiology, School of Public Health, State Key Laboratory Cultivation Base of Biomarkers for Cancer Precision Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China"
      ],
      "name": "Yue Jiang"
    },
    {
      "affiliations": [
        "Department of Oncology, The First Affiliated Hospital With Nanjing Medical University, Nanjing, Jiangsu, China",
        "Gastric Cancer Center, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China"
      ],
      "name": "Xiaofeng Chen"
    },
    {
      "affiliations": [
        "School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China",
        "Department of Epidemiology, School of Public Health, State Key Laboratory Cultivation Base of Biomarkers for Cancer Precision Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China",
        "The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Center, Wuxi, Shanghai, China"
      ],
      "name": "Caiwang Yan"
    },
    {
      "affiliations": [
        "School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China",
        "Department of Epidemiology, School of Public Health, State Key Laboratory Cultivation Base of Biomarkers for Cancer Precision Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China",
        "Department of Medical Oncology, Jiangsu Key Laboratory of Innovative Cancer Diagnosis & Therapeutics, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, China"
      ],
      "name": "Guangfu Jin"
    }
  ],
  "title": "Comprehensive molecular characterization of cfDNA as predictive and monitoring biomarkers in advanced gastric cancer receiving immunotherapy",
  "uid": "a7e15de1-26a8-5e3a-9fcd-0e9a466c2aae"
}