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Updated: Aug 19, 2025
Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
Consequences of aberrated DNA methylation in Colon Adenocarcinoma: a bioinformatic-based multi-approach
Arash Moradi1, Milad Shahsavari2, Erfan Gowdini1
1Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-E Pajoohesh, Km 15, P.O. Box 14965/161, Tehran - Karaj Highway, Tehran, Iran.
Introduction:
The biology of colorectal cancer (CRC) is remained to be elucidated. Numerous genetic and epigenetic modifications are in concert to create and progress CRC. DNA methylation as a principal epigenetic factor has gained increased attention and could be utilized for biological studies. This study aims to find novel methylated and downregulated genes with a focus on HAND2 in CRC and decipher the biological consequences.
Material And Method:
Data on DNA methylation from GEO and SMART databases and the expression GEPIA2 database were downloaded. Afterward, a set of hypermethylated and downregulated genes in CRC was chosen by overlapping genes. Consequently, HAND2 was selected as a key gene for further investigation and confirmed with cell lines methylation and expression data. The functions of HAND2 were further analyzed using gene ontology analyses and the protein-protein interaction network.
Results:
The methylation (p < 0.01) and expression (p < 0.01) of HAND2 are significantly varied in CRC compared to normal control. The correlation analysis (Pearson's correlation coefficient = -0.44, p = 6.6e-14) conveys that HAND2 significantly downregulated and has a reverse correlation with the methylation status of CpG islands. The biological process analysis of HAND2 target genes conveyed that disruption in HAND2 expression could dysregulate ERK1 and ERK2 signaling pathways.
Conclusion:
Together, the findings showed that DNA hypermethylation of HAND2 was critical evidence in CRC. Further validation and prospective studies are needed to utilize HAND2 methylation as a promising biomarker.
Insights
DNA hypermethylation of HAND2 is a key factor in colorectal cancer (CRC) development. This finding suggests HAND2 methylation could serve as a promising biomarker for CRC, warranting further investigation.
Area of Science:
- Molecular Biology
- Cancer Research
- Epigenetics
Background:
- Colorectal cancer (CRC) biology involves complex genetic and epigenetic changes.
- DNA methylation is a key epigenetic mechanism influencing cancer progression.
- Identifying novel methylated and downregulated genes in CRC is crucial for understanding its development.
Purpose of the Study:
- To identify novel methylated and downregulated genes in colorectal cancer (CRC).
- To investigate the role of the HAND2 gene in CRC.
- To decipher the biological consequences of HAND2 alterations in CRC.
Main Methods:
- Downloaded DNA methylation and gene expression data from public databases (GEO, SMART, GEPIA2).
- Selected hypermethylated and downregulated genes by overlapping datasets.
- Confirmed HAND2 methylation and expression in CRC cell lines.
- Performed gene ontology and protein-protein interaction network analyses for HAND2.
Main Results:
- HAND2 showed significant methylation and downregulation in CRC compared to normal tissues (p < 0.01).
- A significant inverse correlation was observed between HAND2 methylation and expression (Pearson's r = -0.44, p = 6.6e-14).
- Disruption of HAND2 expression was linked to dysregulation of ERK1 and ERK2 signaling pathways.
Conclusions:
- DNA hypermethylation of HAND2 is a critical finding in colorectal cancer.
- HAND2 methylation presents potential as a promising biomarker for CRC.
- Further validation and prospective studies are necessary to confirm HAND2's utility as a biomarker.
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