Integrative genome-wide DNA methylome and transcriptome data reveals key genes involved in the dysregulation of adipose-stem cells linked to Crohn’s disease [RNA-seq]. Integrative genome-wide DNA methylome and transcriptome data reveals key genes involved in the dysregulation of adipose-stem cells linked to Crohn’s disease [RNA-seq]

Creeping fat, also known as mesenteric fat, which is connected to the inflamed segments of the intestine and is a hallmark of Crohn's disease (CD), appears to be correlated with disease activity. Adipose-stem cells isolated from the creeping fat of CD subjects were found to be dysfunctional (exhibiting a high inflammatory profile, high invasive and phagocytic capacities, and worse immunosuppressive properties), and this dysfunction persisted in hASCs taken from CD subjects who were in remission of the disease. We hypothesized that the abnormal behavior of adipose stem cells is caused by the accumulation of epigenetic modifications due to the inflammatory environment underlying active CD. DNA methylation and transcriptomics were performed in adipose-derived stem cells (ASCs) isolated from visceral adipose tissue biopsies of active and inactive CD patients and non-IBD patients. An integrative analysis of both omics was performed to obtain the best gene candidates. Overall design: Total RNA extracted from human adipocyte stem cells (hASCs) derived 21 Crohn’s disease (CD) patients samples and 7 healthy individual samples were processed using the TruSeq mRNA library preparation kit (Illumna) and sequenced using 1x50 single reads. CD samples were derived from different tissues and disease states: 7 creeping fat samples from active Crohn’s disease (CF_aCD), 7 mesenteric samples from active Crohn’s disease (hMES_aCD), and 7 mesenteric samples from inactive Crohn’s disease (hMES_iCD).

爬行脂肪（creeping fat）又称肠系膜脂肪，与炎症肠段相连，是克罗恩病（Crohn's disease, CD）的标志性病理特征，且似乎与疾病活动度密切相关。从克罗恩病患者的爬行脂肪中分离得到的脂肪干细胞（adipose-stem cells）功能异常，表现为高炎症表型、较强的侵袭与吞噬能力，以及更弱的免疫抑制特性；且这种功能异常在处于疾病缓解期的克罗恩病患者的人类脂肪干细胞（human adipocyte stem cells, hASCs）中仍持续存在。本研究推测，脂肪干细胞的异常行为是由活动性克罗恩病相关炎症环境所诱导的表观遗传修饰积累所致。研究人员对从活动性、非活动性克罗恩病患者以及非炎症性肠病（non-inflammatory bowel disease, non-IBD）患者的内脏脂肪组织活检样本中分离得到的脂肪来源干细胞（adipose-derived stem cells, ASCs）进行了DNA甲基化与转录组学检测。通过对两组组学数据进行整合分析，筛选出最优的候选基因。总实验设计：从21例克罗恩病患者及7例健康个体中分离得到的人类脂肪干细胞（hASCs）所提取的总RNA，采用TruSeq mRNA文库制备试剂盒（Illumina）进行文库构建，并以1×50单端读长模式进行测序。克罗恩病样本源自不同组织与疾病状态：7例活动性克罗恩病患者的爬行脂肪样本（CF_aCD）、7例活动性克罗恩病患者的肠系膜样本（hMES_aCD）以及7例非活动性克罗恩病患者的肠系膜样本（hMES_iCD）。