Intest Res.  2020 Jul;18(3):297-305. 10.5217/ir.2019.00105.

Hypermethylated promoters of tumor suppressor genes were identified in Crohn’s disease patients

• Kim TO
• Han YK
• Yi JM

• KMID: 2504585
• DOI: http://doi.org/10.5217/ir.2019.00105

Abstract

Background/Aims
Overwhelming evidence suggests that inflammatory bowel disease (IBD) is caused by a complicated interplay between the multiple genes and abnormal epigenetic regulation in response to environmental factors. It is becoming apparent that epigenetic factors are significantly associated with the development of the disease. DNA methylation remains the most studied epigenetic modification, and hypermethylation of gene promoters is associated with gene silencing.
Methods
DNA methylation alterations may contribute to the many complex diseases development by regulating the interplay between external and internal environmental factors and gene transcriptional expression. In this study, we used 15 tumor suppressor genes (TSGs), originally identified in colon cancer, to detect promoter methylation in patients with Crohn’s disease (CD). Methylation specific polymerase chain reaction and bisulfite sequencing analyses were performed to assess methylation level of TSGs in CD patients.
Results
We found 6 TSGs (sFRP1, sFRP2, sFRP5, TFPI2, Sox17, and GATA4) are robustly hypermethylated in CD patient samples. Bisulfite sequencing analysis confirmed the methylation levels of the sFRP1, sFRP2, sFRP5, TFPI2, Sox17, and GATA4 promoters in the representative CD patient samples.
Conclusions
In this study, the promoter hypermethylation of the TSGs observed indicates that CD exhibits specific DNA methylation signatures with potential clinical applications for the noninvasive diagnosis of IBD and the prognosis for patients with IBD.

Keyword

DNA methylation; Promoter; Crohn disease; Genes, Tumor suppressor

Figure

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  Fig. 1. Summarized results from the methylation analyses on the tumor suppressor genes identified from colon cancer and obtained from patients with CD. Each square and number indicates a single CD patient blood sample. The white square indicates the unmethylated CpG sites. The black square indicates the methylated CpG sites. The Bar graph presents methylation frequencies of tested genes. E-cad, Ecadherin.

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  Fig. 2. The methylation level of the promoter region of the sFRP1, sFRP2, and sFRP5 genes in CD patient samples (patient #1, #2, and #3) as determined by bisulfite sequencing analysis. The location of each CpG site related to the transcription start site is shown at the bottom of the panels. Open and filled squares indicate methylation and no methylation, respectively.

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  Fig. 3. The methylation levels of the promoter regions of the GATA4, Sox17, and TFPI2 genes in CD patient samples (patient #1, #2, and #3) as determined by bisulfite sequencing analysis. The location of each CpG site related to the transcription start site is shown at the bottom of the panels. Open and filled squares indicate methylation and no methylation, respectively.

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