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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
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Genome-wide 5-hydroxymethylcytosines in circulating cell-free DNA as noninvasive diagnostic markers for gastric
Yingli Fu1, Jing Jiang1, Yanhua Wu1
1Division of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China.
Summary
Early detection of gastric cancer may be possible using cell-free DNA 5-hydroxymethylcytosine (5hmC) features. A diagnostic model based on five 5hmC genes effectively identified gastric cancer patients, showing promise for early diagnosis.
Area of Science:
- Epigenetics
- Genomics
- Cancer Biomarkers
Background:
- 5-Hydroxymethylcytosine (5hmC) profiles are tissue-specific and tumor-specific.
- 5hmC features in cell-free DNA (cfDNA) hold potential for early gastric cancer detection.
Purpose of the Study:
- To explore the potential of cfDNA 5hmC features as biomarkers for early gastric cancer detection.
- To develop and validate a diagnostic model for gastric cancer using cfDNA 5hmC modification patterns.
Main Methods:
- A case-control study sequenced cfDNA 5hmC modifications in 50 gastric cancer patients and 50 controls.
- Identified significantly differential 5hmC modification genes to construct a diagnostic model.
- Validated the model's robustness using an external dataset from the Gene Expression Omnibus (GEO).
Main Results:
- Over 90% of 5hmC peaks were located in gene bodies in both groups.
- A diagnostic model based on five 5hmC genes (FBXL7, PDE3A, TPO, SNTG2, STXBP5) demonstrated high accuracy (AUC 0.87–0.95) across training, validation, and testing sets.
- The model effectively distinguished gastric cancer patients from controls, with no significant difference observed between healthy controls and benign gastric disease patients in the testing set.
Conclusions:
- cfDNA 5hmC characteristics are specific to gastric cancer patients.
- A diagnostic model utilizing five genes' 5hmC features can effectively identify gastric cancer, supporting its potential for early detection.
