Department of Oncobiology, University Hospital of Besançon, 3 Boulevard Alexandre Fleming, 25000, Besançon, France.
UMR1098, INSERM, University of Bourgogne Franche-Comté, Besançon, France.
Clin Epigenetics. 2024 Oct 18;16(1):146. doi: 10.1186/s13148-024-01748-1.
Colorectal cancer is a public health issue and was the third leading cause of cancer-related death worldwide in 2022. Early diagnosis can improve prognosis, making screening a central part of colorectal cancer management. Blood-based screening, diagnosis and follow-up of colorectal cancer patients are possible with the study of cell-free circulating tumor DNA. This study aimed to identify novel DNA methylation biomarkers of colorectal cancer that can be used for the follow-up of patients with colorectal cancer.
A DNA methylation profile was established in the Gene Expression Omnibus (GEO) database (n = 507) using bioinformatics analysis and subsequently confirmed using The Cancer Genome Atlas (TCGA) database (n = 348). The in silico profile was then validated on local tissue and cell-free DNA samples using methylation-specific digital PCR in colorectal cancer patients (n = 35) and healthy donors (n = 35).
The DNA methylation of COL25A1 and METAP1D was predicted to be a colorectal cancer biomarker by bioinformatics analysis (ROC AUC = 1, 95% CI [0.999-1]). The two biomarkers were confirmed with tissue samples, and the combination of COL25A1 and METAP1D yielded 49% sensitivity and 100% specificity for cell-free DNA.
Bioinformatics analysis of public databases revealed COL25A1 and METAP1D DNA methylation as clinically applicable liquid biopsies DNA methylation biomarkers. The specificity implies an excellent positive predictive value for follow-up, and the high sensitivity and relative noninvasiveness of a blood-based test make these biomarkers compatible with colorectal cancer screening. However, the clinical impact of these biomarkers in colorectal cancer screening and follow-up needs to be established in further prospective studies.
结直肠癌是一个公共卫生问题，也是 2022 年全球导致癌症死亡的第三大原因。早期诊断可以改善预后，使筛查成为结直肠癌管理的核心部分。通过研究无细胞循环肿瘤 DNA，可以对结直肠癌患者进行血液筛查、诊断和随访。本研究旨在鉴定结直肠癌的新型 DNA 甲基化生物标志物，可用于结直肠癌患者的随访。
使用生物信息学分析在基因表达综合数据库（GEO）（n=507）中建立 DNA 甲基化图谱，随后在癌症基因组图谱（TCGA）数据库（n=348）中进行验证。然后在结直肠癌患者（n=35）和健康供体（n=35）的局部组织和无细胞 DNA 样本中使用甲基化特异性数字 PCR 对该图谱进行验证。
通过生物信息学分析预测 COL25A1 和 METAP1D 的 DNA 甲基化是结直肠癌的生物标志物（ROC AUC=1，95%CI [0.999-1]）。这两个生物标志物在组织样本中得到验证，COL25A1 和 METAP1D 的组合对无细胞 DNA 的灵敏度为 49%，特异性为 100%。
对公共数据库的生物信息学分析揭示了 COL25A1 和 METAP1D 的 DNA 甲基化为具有临床应用价值的液体活检 DNA 甲基化生物标志物。特异性意味着随访的阳性预测值极好，基于血液的检测具有较高的灵敏度和相对无创性，使这些生物标志物与结直肠癌筛查兼容。然而，这些生物标志物在结直肠癌筛查和随访中的临床影响需要在进一步的前瞻性研究中确定。
