Department of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut, USA.
Thorax. 2021 Feb;76(2):134-143. doi: 10.1136/thoraxjnl-2019-214301. Epub 2020 Dec 10.
Alpha-1 antitrypsin deficiency (AATD) is a genetic condition that causes early onset pulmonary emphysema and airways obstruction. The complete mechanisms via which AATD causes lung disease are not fully understood. To improve our understanding of the pathogenesis of AATD, we investigated gene expression profiles of bronchoalveolar lavage (BAL) and peripheral blood mononuclear cells (PBMCs) in AATD individuals.
We performed RNA-Seq on RNA extracted from matched BAL and PBMC samples isolated from 89 subjects enrolled in the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Subjects were stratified by genotype and augmentation therapy. Supervised and unsupervised differential gene expression analyses were performed using Weighted Gene Co-expression Network Analysis (WGCNA) to identify gene profiles associated with subjects' clinical variables. The genes in the most significant WGCNA module were used to cluster AATD individuals. Gene validation was performed by NanoString nCounter Gene Expression Assay.
We observed modest effects of AATD genotype and augmentation therapy on gene expression. When WGCNA was applied to BAL transcriptome, one gene module, ME31 (2312 genes), correlated with the highest number of clinical variables and was functionally enriched with numerous immune T-lymphocyte related pathways. This gene module identified two distinct clusters of AATD individuals with different disease severity and distinct PBMC gene expression patterns.
We successfully identified novel clusters of AATD individuals where severity correlated with increased immune response independent of individuals' genotype and augmentation therapy. These findings may suggest the presence of previously unrecognised disease endotypes in AATD that associate with T-lymphocyte immunity and disease severity.
α-1 抗胰蛋白酶缺乏症（AATD）是一种遗传疾病，可导致早发性肺气肿和气道阻塞。AATD 导致肺部疾病的确切机制尚未完全阐明。为了深入了解 AATD 的发病机制，我们研究了 AATD 个体支气管肺泡灌洗液（BAL）和外周血单核细胞（PBMC）的基因表达谱。
我们对来自参与基因组研究在 α-1 抗胰蛋白酶缺乏症和结节病（GRADS）研究的 89 名受试者的匹配 BAL 和 PBMC 样本中提取的 RNA 进行了 RNA-Seq。根据基因型和增敏治疗对受试者进行分层。使用加权基因共表达网络分析（WGCNA）对受监督和不受监督的差异基因表达分析进行分析，以确定与受试者临床变量相关的基因谱。最显著的 WGCNA 模块中的基因用于对 AATD 个体进行聚类。通过 NanoString nCounter 基因表达分析验证基因。
我们观察到 AATD 基因型和增敏治疗对基因表达有适度影响。当 WGCNA 应用于 BAL 转录组时，一个基因模块 ME31（2312 个基因）与最多数量的临床变量相关，并且功能上富含许多免疫 T 淋巴细胞相关途径。该基因模块确定了 AATD 个体的两个不同簇，具有不同的疾病严重程度和不同的 PBMC 基因表达模式。
我们成功地识别了 AATD 个体的新簇，其中严重程度与免疫反应的增加相关，与个体的基因型和增敏治疗无关。这些发现可能表明 AATD 中存在以前未被识别的疾病亚型，与 T 淋巴细胞免疫和疾病严重程度相关。
