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). 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. We 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). We 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. hASCs 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. Human 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.

中文翻译：

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克罗恩病患者的脂肪干细胞显示出独特的DNA甲基化模式。

克罗恩氏病（CD）的特征是持续存在的小肠或大肠发炎和溃疡，以及肠系膜脂肪组织（称为蠕动脂肪（CF））扩张。我们以前证明，患有CD的患者CF的人类脂肪干细胞（hASCs）表现出功能异常的表型，包括促炎性，高吞噬能力和弱免疫抑制特性。重要的是，这些表型在缓解的患者中仍然存在，并且在所有探索的脂肪库中都发现，包括皮下脂肪。我们假设hASCs的变化是表观遗传修饰的结果。我们使用甲基化阵列（Illumina EPIC / 850k阵列）进行了表观基因组范围的分析和基因表达分析，以探讨CD对从患有CD的患者和健康对照组的皮下脂肪中分离出的hASC的甲基化特征的影响（n = 7和5，分别；同类群组I）。使用dmpfinder和dmpfinder识别差异甲基化位置（p值截止值<1×10-4和每个基因10个或更多DMP）和区域（包含阈值0.2，p值截止值<1×10-2和每个基因2个以上DMR）。 Bumphunter（minfi）分别。在第二个队列中验证了hASC中差异甲基化基因表达的变化（n = 10/10无活性和活性CD和10个对照；（包括群组I的患者），以及患有活动性/非活动性CD的患者和健康对照者的外周血单核细胞（PBMC）（群组III； n = 30个独立受试者）。我们从患有CD的患者中在hASCs中发现了一个独特的DNA甲基化态势，导致涉及免疫应答，代谢，细胞分化和发育过程的差异甲基化基因的表达发生了变化。值得注意的是，疾病缓解后，hASCs和PBMC中的这些基因中的一些表达（如肿瘤坏死因子α（TNFA）和PR域锌指蛋白16（PRDM16））并未恢复到正常（健康）水平。患有CD的患者的hASC表现出独特的DNA甲基化和基因表达谱，但是在患有非活动性CD的患者中，某些基因的表达只能部分恢复，在hASC和PBMC中都是如此。了解CD如何塑造hASC的功能对于研究该疾病的复杂病理生理以及基于细胞的疗法的成功至关重要。从克罗恩氏病患者的皮下脂肪中分离出的人脂肪干细胞与从健康个体中分离出的人类脂肪干细胞相比，具有改变的DNA甲基化模式和基因表达谱，其中免疫系统，细胞分化，代谢和发育过程被确定为受影响的主要途径。有趣的是，在人类脂肪干细胞和外周血单核细胞中，与这些途径有关的几个基因的基因表达仅部分恢复到控制非活动性克罗恩病患者的水平。