DNA methylation of the TPMT gene and azathioprine pharmacokinetics in children with very early onset inflammatory bowel disease

NLRP3 promoter methylation as a predictive biomarker for glucocorticoid response in patients with inflammatory bowel disease

Glucocorticoids are used for inflammatory bowel disease (IBD) therapy; however nearly 50 % of IBD patients exhibit resistance or dependence. This study evaluates the relationship between methylation level at two CpG sites (cg21991396 and cg00448525) within NLRP3 promoter and glucocorticoid response of 94 IBD pediatrics (39 with Crohn's disease (40.4 %)) and 47 IBD adults (26 with Crohn's disease (55.3 %)). Disease activity scores were collected before the treatment, after the first full-dose reduction and after 3 months of therapy. Patients with active disease despite receiving a standard dose of prednisone were considered resistant, while those who initially responded but relapsed upon dose reduction were classified as dependent. The DNA methylation was investigated through sodium bisulfite conversion followed by pyrosequencing. In IBD adults, methylation levels at both NLRP3 CpG sites increased with patients' age (p = 0.0038 and p = 0.0018, respectively). In IBD pediatrics, the methylation level at both CpG sites negatively correlated with the disease activity score before treatment (p = 0.031 and p = 0.072, respectively) and after 1 month of therapy (p = 0.037 and p = 0.067, respectively). Furthermore, poor glucocorticoid response after one month of therapy in pediatric patients was associated with lower methylation levels at both CpG sites (p = 0.045 and p = 0.038, respectively). Crohn's disease patients had higher percentage of good responders compared to ulcerative colitis patients (p = 0.06). These findings indicate that NLRP3 methylation might change through patients' lifespan and could have different clinical implications for pediatric and adult IBD forms.

DNA methylation fine-tunes pro-and anti-inflammatory signalling pathways in inactive ulcerative colitis tissue biopsies

DNA methylation has been implied to play a role in the immune dysfunction associated with inflammatory bowel disease (IBD) and the disease development of ulcerative colitis (UC). Changes of the DNA methylation and correlated gene expression in patient samples with inactive UC might reveal possible regulatory features important for further treatment options for UC. Targeted bisulfite sequencing and whole transcriptome sequencing were performed on mucosal biopsies from patients with active UC (UC, n = 14), inactive UC (RM, n = 20), and non-IBD patients which served as controls (NN, n = 11). The differentially methylated regions (DMRs) were identified by DMRseq. Correlation analysis was performed between DMRs and their nearest differentially expressed genes (DEGs). Principal component analysis (PCA) was performed based on correlated DMR regulated genes. DMR regulated genes then were functional annotated. Cell-type deconvolutions were performed based on methylation levels. The comparisons revealed a total of 38 methylation-regulated genes in inactive UC that are potentially regulated by DMRs (correlation p value < 0.1). Several methylation-regulated genes could be identified in inactive UC participating in IL-10 and cytokine signalling pathways such as IL1B and STAT3. DNA methylation events in inactive UC seem to be fine-tuned by the balancing pro- and anti- inflammatory pathways to maintain a prevailed healing process to restore dynamic epithelium homeostasis.