Section of Pulmonary, Critical Care and Sleep Medicine, Dept of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA.
Dept of Medicine, Division of Respirology, McMaster University, Hamilton, ON, Canada.
Eur Respir J. 2021 Dec 2;58(6). doi: 10.1183/13993003.02950-2020. Print 2021 Dec.
Sarcoidosis is a multisystem granulomatous disease of unknown origin with a variable and often unpredictable course and pattern of organ involvement. In this study we sought to identify specific bronchoalveolar lavage (BAL) cell gene expression patterns indicative of distinct disease phenotypic traits.
RNA sequencing by Ion Torrent Proton was performed on BAL cells obtained from 215 well-characterised patients with pulmonary sarcoidosis enrolled in the multicentre Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Weighted gene co-expression network analysis and nonparametric statistics were used to analyse genome-wide BAL transcriptome. Validation of results was performed using a microarray expression dataset of an independent sarcoidosis cohort (Freiburg, Germany; n=50).
Our supervised analysis found associations between distinct transcriptional programmes and major pulmonary phenotypic manifestations of sarcoidosis including T-helper type 1 (Th1) and Th17 pathways associated with hilar lymphadenopathy, transforming growth factor-β1 (TGFB1) and mechanistic target of rapamycin (MTOR) signalling with parenchymal involvement, and interleukin (IL)-7 and IL-2 with airway involvement. Our unsupervised analysis revealed gene modules that uncovered four potential sarcoidosis endotypes including hilar lymphadenopathy with increased acute T-cell immune response; extraocular organ involvement with PI3K activation pathways; chronic and multiorgan disease with increased immune response pathways; and multiorgan involvement, with increased IL-1 and IL-18 immune and inflammatory responses. We validated the occurrence of these endotypes using gene expression, pulmonary function tests and cell differentials from Freiburg.
Taken together, our results identify BAL gene expression programmes that characterise major pulmonary sarcoidosis phenotypes and suggest the presence of distinct disease molecular endotypes.
结节病是一种病因不明的多系统肉芽肿性疾病，其病程和器官受累模式具有多变性和不可预测性。在本研究中，我们试图确定特定的支气管肺泡灌洗液（BAL）细胞基因表达模式，这些模式表明存在不同的疾病表型特征。
对 215 名患有肺结节病的患者的支气管肺泡灌洗液（BAL）细胞进行 Ion Torrent Proton 测序，这些患者是多中心α-1 抗胰蛋白酶缺乏症和结节病的基因组研究（GRADS）中的一部分。使用加权基因共表达网络分析和非参数统计分析对全基因组 BAL 转录组进行分析。使用来自德国弗莱堡的独立结节病队列（n=50）的微阵列表达数据集对结果进行验证。
我们的监督分析发现了特定转录程序与结节病的主要肺部表型表现之间的关联，包括与肺门淋巴结病相关的 Th1 和 Th17 途径、与实质受累相关的转化生长因子-β1（TGFB1）和机械靶点雷帕霉素（MTOR）信号、与气道受累相关的白细胞介素（IL）-7 和 IL-2。我们的非监督分析揭示了基因模块，这些模块揭示了四种潜在的结节病内型，包括伴有急性 T 细胞免疫反应的肺门淋巴结病；伴有 PI3K 激活途径的眼外器官受累；伴有免疫反应途径增加的慢性和多器官疾病；以及伴有 IL-1 和 IL-18 免疫和炎症反应增加的多器官受累。我们使用弗莱堡的基因表达、肺功能测试和细胞差异验证了这些内型的发生。
综上所述，我们的研究结果确定了支气管肺泡灌洗液（BAL）基因表达程序，这些程序可用于描述主要的肺部结节病表型，并提示存在不同的疾病分子内型。
