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Updated: Sep 26, 2025
Targeted DNA Methylation Analysis by Next-generation Sequencing
Published on: February 24, 2015
CpG Island Methylation of the Rap1Gap Gene in Medullary Thyroid Cancer
Bita Faam1, Ata A Ghadiri1,2, Mohammad Ali Ghaffari1
1Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
Background:
Medullary thyroid cancer (MTC) is a rare type of neuroendocrine tumor. This study aimed to investigate the gene and protein expression of RAP1GAP and DNA methylation patterns of its CpG74a , CpG74b , and CpG24 in an Iranian population with MTC.
Methods:
In this case-control study, we selected 55 individuals who underwent thyroidectomy in Erfan hospital, Tehran, between 2018 and 2020. Samples were divided into normal thyroid tissues (control; n=20), benign nodule (n=20), and MTC (n=15). DNA methylation patterns were investigated using MSP (methylation-specific PCR). The protein level and mRNA expression of RAP1GAP were also evaluated using western blotting and real-time PCR, respectively.
Results:
The hyper-methylation rates of CpG24 and CpG74a in the MTC samples were considerably higher than the controls (83% versus 15% and 74% versus 17%, respectively; P<0.001). The methylation/unmethylation ratio of CpG74a , and CpG24 was considerably higher than the controls (P<0.001). The methylation/unmethylation ratio of CpG24 in the benign nodules was also considerably greater than the controls (P<0.001). The mRNA expression and the protein level of RAP1GAP in the MTC group were considerably lower than the controls (P=0.005 and P=0.035, respectively). In the MTC group, aberrant methylation of CpG74a and CpG24 was significantly correlated with decreasing expression of the Rap1Gap gene (R2 : 0.23; P=0.032 and R2 : 0.56; P=0.001, respectively).
Conclusion:
Hyper-methylation in CpG24 and CpG74a and decreasing expression of RAP1GAP can be considered as diagnostic biomarkers for MTC.
Insights
Medullary thyroid cancer (MTC) shows higher CpG24 and CpG74a hyper-methylation and lower RAP1GAP gene and protein expression. These changes can serve as diagnostic biomarkers for MTC.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Medullary thyroid cancer (MTC) is a rare neuroendocrine tumor.
- Investigating genetic and epigenetic alterations in MTC is crucial for understanding its development.
- RAP1GAP gene expression and DNA methylation patterns are potential factors in MTC pathogenesis.
Purpose of the Study:
- To examine the gene and protein expression of RAP1GAP in an Iranian MTC population.
- To analyze DNA methylation patterns of CpG74a, CpG74b, and CpG24 in MTC.
- To correlate methylation status with RAP1GAP expression in MTC.
Main Methods:
- Case-control study involving 55 thyroid tissue samples (20 normal, 20 benign nodules, 15 MTC).
- DNA methylation patterns assessed using methylation-specific PCR (MSP).
- RAP1GAP mRNA and protein levels determined by real-time PCR and western blotting, respectively.
Main Results:
- Significantly higher hyper-methylation rates of CpG24 and CpG74a were observed in MTC tissues compared to controls.
- The methylation/unmethylation ratio for CpG74a and CpG24 was significantly elevated in MTC.
- RAP1GAP mRNA and protein expression were significantly lower in MTC samples.
- Aberrant methylation of CpG74a and CpG24 correlated with decreased RAP1GAP gene expression in MTC.
Conclusions:
- Hyper-methylation of CpG24 and CpG74a, along with decreased RAP1GAP expression, are significant findings in MTC.
- These molecular alterations show potential as diagnostic biomarkers for medullary thyroid cancer.
- The study highlights the role of epigenetic modifications and gene expression changes in MTC development.
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