Integrating Murine Gene Expression Studies to Understand Obstructive Lung Disease Due to Chronic Inhaled Endotoxin

Rationale
Endotoxin is a near ubiquitous environmental exposure that that has been associated with both asthma and chronic obstructive pulmonary disease (COPD). These obstructive lung diseases have a complex pathophysiology, making them difficult to study comprehensively in the context of endotoxin. Genome-wide gene expression studies have been used to identify a molecular snapshot of the response to environmental exposures. Identification of differentially expressed genes shared across all published murine models of chronic inhaled endotoxin will provide insight into the biology underlying endotoxin-associated lung disease.
Methods
We identified three published murine models with gene expression profiling after repeated low-dose inhaled endotoxin. All array data from these experiments were re-analyzed, annotated consistently, and tested for shared genes found to be differentially expressed. Additional functional comparison was conducted by testing for significant enrichment of differentially expressed genes in known pathways. The importance of this gene signature in smoking-related lung disease was assessed using hierarchical clustering in an independent experiment where mice were exposed to endotoxin, smoke, and endotoxin plus smoke.
Results
A 101-gene signature was detected in three murine models, more than expected by chance. The three model systems exhibit additional similarity beyond shared genes when compared at the pathway level, with increasing enrichment of inflammatory pathways associated with longer duration of endotoxin exposure. Genes and pathways important in both asthma and COPD were shared across all endotoxin models. Mice exposed to endotoxin, smoke, and smoke plus endotoxin were accurately classified with the endotoxin gene signature.
Conclusions
Despite the differences in laboratory, duration of exposure, and strain of mouse used in three experimental models of chronic inhaled endotoxin, surprising similarities in gene expression were observed. The endotoxin component of tobacco smoke may play an important role in disease development.

研究依据
内毒素（Endotoxin）是一种几乎无处不在的环境暴露物，与哮喘及慢性阻塞性肺疾病（chronic obstructive pulmonary disease, COPD）均存在关联。这类阻塞性肺部疾病的病理生理学机制复杂，使得在该内毒素暴露情境下开展全面研究颇具挑战。全基因组基因表达研究已被用于识别机体对环境暴露的分子应答快照。鉴定出在所有已发表的慢性吸入内毒素小鼠模型（murine models）中共享的差异表达基因（differentially expressed genes），将有助于深入解析内毒素相关性肺部疾病的潜在生物学机制。

研究方法
我们筛选出3项经公开报道的、采用反复低剂量吸入内毒素处理后的小鼠模型基因表达谱分析（gene expression profiling）数据。对上述实验的所有芯片阵列数据进行了重新分析、统一注释，并针对其中共享的差异表达基因进行了检验。此外，我们通过检验差异表达基因在已知通路（pathways）中的显著富集情况，开展了额外的功能比较分析。为评估该基因特征在吸烟相关性肺部疾病中的重要性，我们在一项独立实验中采用层次聚类（hierarchical clustering）方法对暴露于内毒素、香烟烟雾以及内毒素联合香烟烟雾的小鼠数据进行了分析。

研究结果
我们在3项小鼠模型中检测到了由101个基因组成的特征基因集，其数量远超随机预期。在通路层面进行比较时，这3个模型系统除共享基因外还存在更多相似性，且随着内毒素暴露时长的增加，炎症通路的富集程度逐渐升高。所有内毒素模型均共享了在哮喘和COPD中发挥重要作用的基因及通路。通过该内毒素特征基因集，可准确对暴露于内毒素、香烟烟雾以及内毒素联合香烟烟雾的小鼠进行分类。

研究结论
尽管3项慢性吸入内毒素的实验模型在实验实验室、暴露时长以及小鼠品系方面均存在差异，但我们仍观察到了令人意外的基因表达相似性。烟草烟雾中的内毒素成分可能在疾病发生发展中发挥重要作用。