Genome-wide DNA methylation profiling in differentiating Crohn's disease from intestinal tuberculosis

Differential diagnosis of Crohn's disease (CD) and intestinal tuberculosis (ITB) is still difficult in clinical pratice. DNA methylation has been considered as a favorable area for biomarker exploration and identification.

The purpose of the current study was to evaluate DNA methylation changes between CD and ITB.

We performed a genome-wide association study to identify differentially methylated positions (DMPs), including 8 CD patients (before the initial of biologics or immunomodulators), 6 ITB patients, and 8 healthy controls (HCs), in whole blood DNA using the Infinium HumanMethylation850 BeadChip.

Patients in the CD group and ITB group were all observed with hypo-methylated changes compared with HCs. However, the CD group overlaps with the ITB group in DNA methylation, suggesting a stable epigenetic profile between the two diseases. The pathway enrichment analysis showed the alternation in inflammation-related pathway, immune system, and signal transduction. Focused on the DMPs located in the promoter region, further analysis indicated hypermethylation of cg03122532 (5'UTR of KCNJ15) could be a potential CD-specific biomarker.

We identified specific differential methylation loci related to CD and ITB in blood DNA. DNA metylation as a important epigenetic modification could contribute to the pathogenesis study and biomarker exploration of the diseases.