1 Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado.
2 Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado.
Am J Respir Cell Mol Biol. 2019 Jan;60(1):96-105. doi: 10.1165/rcmb.2018-0177OC.
Epigenetic marks are likely to explain variability of response to antigen in granulomatous lung disease. The objective of this study was to identify DNA methylation and gene expression changes associated with chronic beryllium disease (CBD) and sarcoidosis in lung cells obtained by BAL. BAL cells from CBD (n = 8), beryllium-sensitized (n = 8), sarcoidosis (n = 8), and additional progressive sarcoidosis (n = 9) and remitting (n = 15) sarcoidosis were profiled on the Illumina 450k methylation and Affymetrix/Agilent gene expression microarrays. Statistical analyses were performed to identify DNA methylation and gene expression changes associated with CBD, sarcoidosis, and disease progression in sarcoidosis. DNA methylation array findings were validated by pyrosequencing. We identified 52,860 significant (P < 0.005 and q < 0.05) CpGs associated with CBD; 2,726 CpGs near 1,944 unique genes have greater than 25% methylation change. A total of 69% of differentially methylated genes are significantly (q < 0.05) differentially expressed in CBD, with many canonical inverse relationships of methylation and expression in genes critical to T-helper cell type 1 differentiation, chemokines and their receptors, and other genes involved in immunity. Testing of these CBD-associated CpGs in sarcoidosis reveals that methylation changes only approach significance, but are methylated in the same direction, suggesting similarities between the two diseases with more heterogeneity in sarcoidosis that limits power with the current sample size. Analysis of progressive versus remitting sarcoidosis identified 15,215 CpGs (P < 0.005 and q < 0.05), but only 801 of them have greater than 5% methylation change, demonstrating that DNA methylation marks of disease progression changes are more subtle. Our study highlights the significance of epigenetic marks in lung immune response in granulomatous lung disease.
表观遗传标记可能解释了肉芽肿性肺部疾病中对抗原反应的可变性。本研究的目的是确定通过 BAL 获得的肺细胞中与慢性铍病 (CBD) 和结节病相关的 DNA 甲基化和基因表达变化。CBD(n=8)、铍致敏(n=8)、结节病(n=8)以及另外的进展性结节病(n=9)和缓解性结节病(n=15)的 BAL 细胞在 Illumina 450k 甲基化和 Affymetrix/Agilent 基因表达微阵列上进行了分析。进行了统计分析以确定与 CBD、结节病和结节病进展相关的 DNA 甲基化和基因表达变化。通过焦磷酸测序验证了 DNA 甲基化阵列的发现。我们确定了 52860 个与 CBD 相关的显著 (P<0.005 和 q<0.05) CpG；2726 个 CpG 位于 1944 个独特基因附近，其甲基化变化超过 25%。在 CBD 中，有 69%的差异甲基化基因的表达显著 (q<0.05) 不同，许多与 T 辅助细胞 1 分化、趋化因子及其受体以及其他参与免疫的基因相关的关键基因的甲基化和表达呈相反关系。在结节病中测试这些与 CBD 相关的 CpG 表明，甲基化变化仅接近显著水平，但方向相同，这表明两种疾病具有相似性，而结节病的异质性更大，限制了当前样本量的功效。对进展性与缓解性结节病的分析确定了 15215 个 CpG (P<0.005 和 q<0.05)，但其中只有 801 个具有超过 5%的甲基化变化，这表明疾病进展变化的 DNA 甲基化标记更为微妙。我们的研究强调了表观遗传标记在肉芽肿性肺部疾病中肺部免疫反应中的重要性。
