粪便 DNA 中 SDC2、SEPT9 和 VIM 基因的甲基化分析用于结直肠癌的诊断。

DNA methylation analysis of the SDC2, SEPT9 and VIM genes in fecal DNA for colorectal cancer diagnosis.

机构信息

Dalian Gentalker Biotech Co., Ltd., 9-2, Jinqi Road, Jinpu New District , Dalian, Liaoning, 116635, China.

Department of Laboratory, The Second Affiliated Hospital of Dalian Medical University, 216 Zhongshan Street, Ganjingzi District, Dalian, Liaoning, 116031, China.

出版信息

BMC Cancer. 2024 Sep 30;24(1):1205. doi: 10.1186/s12885-024-12990-4.

DOI:10.1186/s12885-024-12990-4

PMID:39350171

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11440654/

Abstract

BACKGROUND

Colorectal cancer is one of the most common cancers worldwide. DNA methylation sites may serve as a new gene signature for colorectal cancer diagnosis. The search for representative DNA methylation sites is urgently needed. This study aimed to systematically identify a methylation gene panel for colorectal cancer diagnosis via tissue and fecal samples.

METHODS

A total of 181 fecal and 50 tumor tissue samples were collected. They were obtained from 83 colorectal cancer patients and 98 healthy subjects. These samples were evaluated for DNA methylation of 9 target genes via quantitative bisulfite next-generation sequencing. We employed the rank-sum test to screen the colorectal cancer-specific methylation sites in the tissue and fecal cohorts. A data model was subsequently constructed and validated via the dedicated validation dataset.

RESULTS

Compared with the fecal and negative control samples, the colorectal cancer tissue samples presented significantly higher methylation rates for all the selected gene sites. The methylation rates of the tissue and preoperative fecal samples showed the same high and low rates at the same sites. After screening, a panel of 29 loci in the SDC2, SEPT9, and VIM genes proved to be reliable biomarkers for colorectal cancer diagnosis in fecal samples. Logistic regression models were then constructed and validated using this panel. The sensitivity of the model was 91.43% (95% CI = [89.69, 93.17]), the specificity was 100% (95% CI = [100,100]), and the AUC value is 99.31% (95% CI = [99,99.62]). The diagnostic accuracy of the model for stage I and stage II colorectal cancer was 100% (11/11) and 91.3% (21/23), respectively. Overall, this study confirms that the gene locus panel and the model can be used to diagnose colorectal cancer effectively through feces.

CONCLUSIONS

Our study identified a set of key methylation sites for colorectal cancer diagnosis from fecal samples, highlighting the importance of using tissue and fecal samples to accurately assess DNA methylation levels to screen for methylation sites, and developing an effective diagnostic model for colorectal cancer.

摘要

背景

结直肠癌是全球最常见的癌症之一。DNA 甲基化位点可能成为结直肠癌诊断的新基因标志物。因此，迫切需要寻找有代表性的 DNA 甲基化位点。本研究旨在通过组织和粪便样本系统地鉴定用于结直肠癌诊断的甲基化基因谱。

方法

共收集了 181 份粪便和 50 份肿瘤组织样本，来自 83 例结直肠癌患者和 98 例健康受试者。采用定量亚硫酸氢盐二代测序法评估 9 个靶基因的 DNA 甲基化情况。采用秩和检验筛选组织和粪便队列中结直肠癌特异性甲基化位点。然后，使用专门的验证数据集构建和验证数据模型。

结果

与粪便和阴性对照样本相比，结直肠癌组织样本中所有选定基因位点的甲基化率明显更高。组织和术前粪便样本的甲基化率在相同的位点表现出相同的高低水平。筛选后，SDC2、SEPT9 和 VIM 基因中的 29 个基因座组成的基因谱被证明是粪便样本中结直肠癌诊断的可靠生物标志物。然后使用该基因谱构建和验证了逻辑回归模型。该模型的灵敏度为 91.43%（95%CI=[89.69,93.17]），特异性为 100%（95%CI=[100,100]），AUC 值为 99.31%（95%CI=[99,99.62]）。该模型对Ⅰ期和Ⅱ期结直肠癌的诊断准确率分别为 100%（11/11）和 91.3%（21/23）。总之，本研究证实，通过粪便可以有效地使用基因座谱和模型来诊断结直肠癌。