Alexis Overs, Paul Peixoto, Eric Hervouet, Chloé Molimard, Franck Monnien, Jules Durand, Michael Guittaut, Angélique Vienot, Julien Viot, Michael Herfs, Christophe Borg, Jean-Paul Feugeas, Zohair Selmani
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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.</p><p><strong>Methods: </strong>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).</p><p><strong>Results: </strong>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.</p><p><strong>Conclusion: </strong>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.</p>","PeriodicalId":10366,"journal":{"name":"Clinical Epigenetics","volume":null,"pages":null},"PeriodicalIF":4.8000,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11490026/pdf/","citationCount":"0","resultStr":"{\"title\":\"COL25A1 and METAP1D DNA methylation are promising liquid biopsy epigenetic biomarkers of colorectal cancer using digital PCR.\",\"authors\":\"Alexis Overs, Paul Peixoto, Eric Hervouet, Chloé Molimard, Franck Monnien, Jules Durand, Michael Guittaut, Angélique Vienot, Julien Viot, Michael Herfs, Christophe Borg, Jean-Paul Feugeas, Zohair Selmani\",\"doi\":\"10.1186/s13148-024-01748-1\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Colorectal cancer is a public health issue and was the third leading cause of cancer-related death worldwide in 2022. 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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).</p><p><strong>Results: </strong>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.</p><p><strong>Conclusion: </strong>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. 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引用次数: 0
摘要
背景:结直肠癌是一个公共卫生问题,2022 年在全球癌症相关死亡原因中排名第三。早期诊断可改善预后,因此筛查是结直肠癌治疗的核心部分。通过对无细胞循环肿瘤 DNA 的研究,可以对结直肠癌患者进行基于血液的筛查、诊断和随访。本研究旨在确定新型的结直肠癌DNA甲基化生物标志物,用于对结直肠癌患者进行随访:方法:通过生物信息学分析,在基因表达总库(GEO)数据库(n = 507)中建立了DNA甲基化图谱,随后在癌症基因组图谱(TCGA)数据库(n = 348)中进行了确认。然后,利用甲基化特异性数字 PCR 技术在结直肠癌患者(35 人)和健康供体(35 人)的局部组织和无细胞 DNA 样本上验证了硅图特征:结果:生物信息学分析预测 COL25A1 和 METAP1D 的 DNA 甲基化是结直肠癌生物标志物(ROC AUC = 1,95% CI [0.999-1])。这两个生物标记物经组织样本证实,COL25A1和METAP1D的组合对无细胞DNA的敏感性为49%,特异性为100%:对公共数据库的生物信息学分析表明,COL25A1和METAP1D的DNA甲基化是适用于临床的液体活检DNA甲基化生物标记物。其特异性意味着对随访具有极好的阳性预测价值,而基于血液的检测具有高灵敏度和相对无创的特点,因此这些生物标记物可用于结直肠癌筛查。不过,这些生物标志物对结直肠癌筛查和随访的临床影响还需要进一步的前瞻性研究来确定。
COL25A1 and METAP1D DNA methylation are promising liquid biopsy epigenetic biomarkers of colorectal cancer using digital PCR.
Background: 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.
Methods: 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).
Results: 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.
Conclusion: 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.
期刊介绍:
Clinical Epigenetics, the official journal of the Clinical Epigenetics Society, is an open access, peer-reviewed journal that encompasses all aspects of epigenetic principles and mechanisms in relation to human disease, diagnosis and therapy. Clinical trials and research in disease model organisms are particularly welcome.