Huang Steven K, Scruggs Anne M, McEachin Richard C, White Eric S, Peters-Golden Marc
Division of Pulmonary and Critical Care Medicine in the Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America.
PLoS One. 2014 Sep 12;9(9):e107055. doi: 10.1371/journal.pone.0107055. eCollection 2014.
Excessive fibroproliferation is a central hallmark of idiopathic pulmonary fibrosis (IPF), a chronic, progressive disorder that results in impaired gas exchange and respiratory failure. Fibroblasts are the key effector cells in IPF, and aberrant expression of multiple genes contributes to their excessive fibroproliferative phenotype. DNA methylation changes are critical to the development of many diseases, but the DNA methylome of IPF fibroblasts has never been characterized. Here, we utilized the HumanMethylation 27 array, which assays the DNA methylation level of 27,568 CpG sites across the genome, to compare the DNA methylation patterns of IPF fibroblasts (n = 6) with those of nonfibrotic patient controls (n = 3) and commercially available normal lung fibroblast cell lines (n = 3). We found that multiple CpG sites across the genome are differentially methylated (as defined by P value less than 0.05 and fold change greater than 2) in IPF fibroblasts compared to fibroblasts from nonfibrotic controls. These methylation differences occurred both in genes recognized to be important in fibroproliferation and extracellular matrix generation, as well as in genes not previously recognized to participate in those processes (including organ morphogenesis and potassium ion channels). We used bisulfite sequencing to independently verify DNA methylation differences in 3 genes (CDKN2B, CARD10, and MGMT); these methylation changes corresponded with differences in gene expression at the mRNA and protein level. These differences in DNA methylation were stable throughout multiple cell passages. DNA methylation differences may thus help to explain a proportion of the differences in gene expression previously observed in studies of IPF fibroblasts. Moreover, significant variability in DNA methylation was observed among individual IPF cell lines, suggesting that differences in DNA methylation may contribute to fibroblast heterogeneity among patients with IPF. These results demonstrate that IPF fibroblasts exhibit global differences in DNA methylation that may contribute to the excessive fibroproliferation associated with this disease.
过度的纤维增生是特发性肺纤维化(IPF)的核心特征,这是一种慢性进行性疾病,会导致气体交换受损和呼吸衰竭。成纤维细胞是IPF中的关键效应细胞,多个基因的异常表达导致其过度的纤维增生表型。DNA甲基化变化对许多疾病的发生发展至关重要,但IPF成纤维细胞的DNA甲基化组从未被表征过。在此,我们利用人类甲基化27芯片,该芯片可检测全基因组27568个CpG位点的DNA甲基化水平,以比较IPF成纤维细胞(n = 6)与非纤维化患者对照(n = 3)以及市售正常肺成纤维细胞系(n = 3)的DNA甲基化模式。我们发现,与非纤维化对照的成纤维细胞相比,IPF成纤维细胞中全基因组多个CpG位点存在差异甲基化(定义为P值小于0.05且变化倍数大于2)。这些甲基化差异既发生在已知对纤维增生和细胞外基质生成重要的基因中,也发生在先前未被认为参与这些过程的基因中(包括器官形态发生和钾离子通道)。我们使用亚硫酸氢盐测序独立验证了3个基因(CDKN2B、CARD10和MGMT)的DNA甲基化差异;这些甲基化变化与mRNA和蛋白质水平的基因表达差异相对应。这些DNA甲基化差异在多个细胞传代过程中是稳定的。因此,DNA甲基化差异可能有助于解释先前在IPF成纤维细胞研究中观察到的部分基因表达差异。此外,在各个IPF细胞系中观察到DNA甲基化存在显著变异性,表明DNA甲基化差异可能导致IPF患者成纤维细胞的异质性。这些结果表明,IPF成纤维细胞在DNA甲基化方面表现出全局差异,这可能导致与该疾病相关的过度纤维增生。