Whole-Genome DNA Methylation Profiling of CD14+ Monocytes Reveals Disease Status and Activity Differences in Crohn’s Disease Patients

Abstract

Crohn’s disease (CD) is a multifactorial incurable chronic disorder. Current medical treatment seeks to induce and maintain a state of remission. During episodes of inflammation, monocytes infiltrate the inflamed mucosa whereupon they differentiate into macrophages with a pro-inflammatory phenotype. Here, we sought to characterize the circulating monocytes by profiling their DNA methylome and relate it to the level of CD activity. We gathered an all-female age-matched cohort of 16 CD patients and 7 non-CD volunteers. CD patients were further subdivided into 8 CD patients with active disease (CD-active) and 8 CD patients in remission (CD-remissive) as determined by the physician global assessment. We identified 15 and 12 differentially methylated genes (DMGs) when comparing CD with non-CD and CD-active with CD-remissive, respectively. Differential methylation was predominantly found in the promoter regions of inflammatory genes. Comparing our observations with gene expression data on classical (CD14++CD16-), non-classical (CD14+CD16++) and intermediate (CD14++CD16+) monocytes indicated that while 7 DMGs were differentially expressed across the 3 subsets, the remaining DMGs could not immediately be associated with differences in known populations. We conclude that CD activity is associated with differences in DNA methylation at the promoter region of inflammation-associated genes.

Nutritional Therapy Strategies in Pediatric Crohn’s Disease

“…Crohn’s disease (CD) is a chronic disorder that belongs to the group of inflammatory bowel diseases (IBD); it is characterized by transmural inflammation that can affect any area along the proximal-distal axis of the gastrointestinal tract (GI) [ 1 , 2 , 3 ]. Symptoms often involve abdominal pain, diarrhea, rectal blood loss, and fatigue, and the disease often leads to weight loss and malnutrition [ 4 ].…”

The role of epigenetic modifications for the pathogenesis of Crohn's disease

“…DNA methylation studies on blood samples from CD patients with inactive or active disease are diverse and included analyses on whole blood samples [ 54 ], peripheral blood cells [ 55 , 56 ], peripheral leukocytes [ 57 – 59 ], including peripheral blood mononuclear cells (PBMCs) [ 60 , 61 ], serum samples [ 62 ], or separated B cells [ 63 ], T cells [ 64 ], and monocytes [ 65 ] (Table 1 ). The majority of studies involve adult patients [ 54 – 56 , 58 , 60 , 62 , 63 , 65 ], while a few articles describe the DNA methylation in pediatric donors [ 57 , 59 , 61 , 64 ]. A comparison between these studies is difficult because DNA methylation is strongly affected by age, or environmental conditions, such as medication or nutrition [ 66 ].…”

“…Thus, it is assumed that the epigenetic modifications more likely reflect the disease state. In addition to age, gender also influences methylation status, which is why some studies include only subjects of the same sex [ 54 , 58 , 65 ]. This leads to better comparability of results between patients and control subjects.…”

“…Cell-specific patterns in DNA methylation of CD patients were described in different subpopulations of blood cells [ 55 , 63 – 65 ], enabling, for instance, the clustering of monocytes by their methylation profile [ 55 ]. Therefore, the validity of epigenetic analyses in whole blood samples is limited since individual cell-specific signals may disappear against the background of other present cells.…”

“…The fact that epigenetic modifications were described in monocytes of CD patients but not in T cells supports previous findings that transcriptional altered monocytes play a central role in CD pathogenesis that might be investigated in more detail by using single-cell technologies [ 71 ]. Interestingly, the methylation profile of CD14 + monocytes in female CD patients also differed at the level of the subpopulations (classical, intermediate, non-classical) [ 65 ], indicating different gene regulation according to the defined function of the respective subpopulation. However, on a genome-wide level, they did not identify statistically significant methylation differences when comparing CD patients vs. healthy subjects or CD patients with active disease vs. inactive disease patients [ 65 ], possibly due to the small number of subjects or high individual variances (Table 1 ).…”