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Published on: June 16, 2017
A Pathway Analysis Based on Genome-Wide DNA Methylation of Chinese Patients with Graves' Orbitopathy
Zhong Xin1, Lin Hua2, Yi-Lin Yang1
1Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China.
Background:
The pathogenesis Graves' Orbitopathy (GO) is not yet fully understood. Here, we conducted a pathway analysis based on genome-wide DNA methylation data of Chinese GO patients to explore GO-related pathways and potential feature genes.
Methods:
Six GO patients and 6 age-matched control individuals were recruited, and a genome-scale screen of DNA methylation was measured using their peripheral blood sample. After extracting the differentially methylated regions (DMRs), we classified DMRs into three clusters with respect to median absolute deviation (MAD) for GO and control group, respectively. Then the extract tests were performed to identify significant pathways by comparing the counts of genes in each cluster between GO and control group in a pathway. For each significant pathway, we calculated the Methylation-based Inference of Regulatory Activity (MIRA) score to infer the regulatory activity of genes involved in the pathway. Furthermore, we took the significant pathways as the subsets and applied Random forests (RF) method to extract GO-related feature genes.
Results:
We identified four potential significant pathways associated with the occurrence and development of GO disease. There were Toxoplasmosis, Axon guidance, Focal adhesion, and Proteoglycans in cancer (p<0.001 or p=0.007). The identified genes involved in the significant pathways, such as LDLR (p=0.019), CDK5 (p=0.036), and PIK3CB (p=0.020), were found to be correlated with GO phenotype.
Conclusion:
Our study suggested pathway analyses can help understand the potential relationships between the DNA methylation level of some certain genes and their regulation in Chinese GO patients.
Insights
This study explored DNA methylation in Chinese Graves' Orbitopathy (GO) patients, identifying key pathways like Toxoplasmosis and Axon guidance. These findings enhance understanding of GO pathogenesis and potential therapeutic targets.
Area of Science:
- Genomics
- Epigenetics
- Ophthalmology
Background:
- The exact causes of Graves' Orbitopathy (GO) remain unclear.
- This research investigates genome-wide DNA methylation patterns in Chinese GO patients.
Purpose of the Study:
- To identify GO-related pathways through pathway analysis.
- To discover potential feature genes associated with GO pathogenesis.
Main Methods:
- Genome-wide DNA methylation screening was performed on peripheral blood from 6 GO patients and 6 controls.
- Differentially methylated regions (DMRs) were identified, clustered, and analyzed for significant pathway enrichment.
- Random forests (RF) method was used to extract feature genes from significant pathways.
Main Results:
- Four significant pathways were identified: Toxoplasmosis, Axon guidance, Focal adhesion, and Proteoglycans in cancer (p<0.001 or p=0.007).
- Genes such as LDLR, CDK5, and PIK3CB within these pathways showed correlation with GO phenotype.
Conclusions:
- Pathway analysis of DNA methylation data provides insights into gene regulation in Chinese GO patients.
- This approach can elucidate the relationship between DNA methylation and GO development.
