Abstract
BackgroundCrohn’s disease (CD) is characterized by persistent inflammation and ulceration of the small or large bowel, and expansion of mesenteric adipose tissue, termed creeping fat (CF). We previously demonstrated that human adipose-derived stem cells (hASCs) from CF of patients with CD exhibit dysfunctional phenotypes, including a pro-inflammatory profile, high phagocytic capacity, and weak immunosuppressive properties. Importantly, these phenotypes persist in patients in remission and are found in all adipose depots explored including subcutaneous fat. We hypothesized that changes in hASCs are a consequence of epigenetic modifications.MethodsWe applied epigenome-wide profiling with a methylation array (Illumina EPIC/850k array) and gene expression analysis to explore the impact of CD on the methylation signature of hASCs isolated from the subcutaneous fat of patients with CD and healthy controls (n = 7 and 5, respectively; cohort I). Differentially methylated positions (p value cutoff < 1 × 10−4 and ten or more DMPs per gene) and regions (inclusion threshold 0.2, p value cutoff < 1 × 10−2 and more than 2 DMRs per gene) were identified using dmpfinder and Bumphunter (minfi), respectively. Changes in the expression of differentially methylated genes in hASCs were validated in a second cohort (n = 10/10 inactive and active CD and 10 controls; including patients from cohort I) and also in peripheral blood mononuclear cells (PBMCs) of patients with active/inactive CD and of healthy controls (cohort III; n = 30 independent subjects).ResultsWe found a distinct DNA methylation landscape in hASCs from patients with CD, leading to changes in the expression of differentially methylated genes involved in immune response, metabolic, cell differentiation, and development processes. Notably, the expression of several of these genes in hASCs and PBMCs such as tumor necrosis factor alpha (TNFA) and PR domain zinc finger protein 16 (PRDM16) were not restored to normal (healthy) levels after disease remission.ConclusionshASCs of patients with CD exhibit a unique DNA methylation and gene expression profile, but the expression of several genes are only partially restored in patients with inactive CD, both in hASCs and PBMCs. Understanding how CD shapes the functionality of hASCs is critical for investigating the complex pathophysiology of this disease, as well as for the success of cell-based therapies.Graphical abstractHuman adipose-stem cells isolated from subcutaneous fat of patients with Crohn’s disease exhibit an altered DNA methylation pattern and gene expression profile compared with those isolated from healthy individuals, with immune system, cell differentiation, metabolic and development processes identified as the main pathways affected. Interestingly, the gene expression of several genes involved in these pathways is only partially restored to control levels in patients with inactive Crohn’s disease, both in human adipose-stem cells and peripheral blood mononuclear cells. Understanding how Crohn’s disease shapes the functionality of human adipose-stem cells is critical for investigating the complex pathophysiology of this disease, as well as for the success of cell-based therapies.
Highlights
Crohn’s disease (CD) is characterized by persistent inflammation and ulceration of the small or large bowel, and expansion of mesenteric adipose tissue, termed creeping fat (CF)
Methylation signature of adipose stem cells from subcutaneous fat in patients with Crohn’s We first assessed genome-wide patterns of DNA methylation in human adipose-derived stem cells (hASCs) isolated from subcutaneous fat depots of patients with CD and compared them with those from hASCs isolated from healthy controls (n = 7 patients with CD and 5 healthy controls; cohort I)
Development process We studied the expression of genes related to development process, such as the homeobox B5 (HOXB5), homeobox B6 (HOXB6), and shroom family member 3 (SHROOM3), finding that they were all significantly downregulated in hASCs from patients with active or inactive disease compared with controls (Fig. 4d)
Summary
Crohn’s disease (CD) is characterized by persistent inflammation and ulceration of the small or large bowel, and expansion of mesenteric adipose tissue, termed creeping fat (CF). The altered properties of hASCs persist even when patients with CD are in remission, in all AT depots explored including subcutaneous fat [18] The constancy of this dysfunctional phenotype might reflect changes at the epigenetic level, which hamper the resolution of the inflammatory events in the sinus of the affected mesenteric AT. In support of this proposition, recent DNA methylation studies in peripheral blood mononuclear cells (PBMCs) revealed that patients with CD have a distinct DNA methylome linked to the expression of differentially methylated genes associated with immune response and inflammation [19,20,21]. We hypothesized that hASCs from patients with CD are conditioned by a chronic inflammatory milieu, which may alter their DNA methylome and influence their antiinflammatory and regenerative capacity
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