Gene Expression Profiling in the Lungs of Patients with Chronic Obstructive Pulmonary Disease (COPD) and Lung Cancer. Homo sapiens

COPD is a common and disabling lung disease for which very few therapeutic options are currently available. We reasoned that global gene expression profiling of COPD lungs could reveal previously unidentified disease pathways for potential therapeutic interventions. Forty-eight human lung samples were obtained from lungs or lobes resected for small peripheral lung lesions (5 non-smokers, 21 GOLD 0, 9 GOLD 1, 10 GOLD 2 and 3 GOLD 3 patients). mRNA from the specimens was profiled using Agilent’s Functional ID v2.0 array which contains 23,720 sequences. Quantitative morphometric analysis of the specimens revealed that the samples contained a variable proportion of airways, blood vessels and parenchyma. Incorporating these data into a model relating gene expression to % predicted forced expiratory flow between 25 and 75% of forced expiratory volume (FEF 25-75 % P) revealed a signature gene set of 203 transcripts. Genes involved in extracellular matrix synthesis/degradation, oxidative stress and cell proliferation were among the up-regulated genes whereas genes which participate in nicotine metabolism, elastic fiber homeostasis and anti-inflammatory response were down-regulated. Immunohistochemistry confirmed expression of urokinase (PLAU), urokinanse receptor (PLAUR) and thrombospondin (THBS1) by alveolar macrophages and small airway epithelial cells. Genes in this pathway have been shown to be involved in transforming growth factor beta-1 (TGFβ1) and matrix metalloproteinase (MMP) activation and are subject to inhibition by serpin E2. Interestingly, both TGFβ1 and serpin E2 have been identified as candidate genes in COPD genetic linkage and association studies. The results thus provide a possible link between these two powerful approaches to identify potential therapeutic targets. (255 words) Keywords: Pulmonary emphysema, phenotype, transcriptional analysis, cigarette smoking Overall design: Forty-eight human lung samples were obtained from lungs or lobes resected for small peripheral lung lesions (5 non-smokers, 21 GOLD 0, 9 GOLD 1, 10 GOLD 2 and 3 GOLD 3 patients). mRNA from the specimens was profiled using Agilent’s Functional ID v2.0 array which contains 23,720 sequences. Quantitative morphometric analysis of the specimens revealed that the samples contained a variable proportion of airways, blood vessels and parenchyma. Incorporating these data into a model relating gene expression to % predicted forced expiratory flow between 25 and 75% of forced expiratory volume (FEF 25-75 % P) revealed a signature gene set of 203 transcripts.

慢性阻塞性肺疾病（Chronic Obstructive Pulmonary Disease, COPD）是一种常见且致残性肺部疾病，目前可供选择的治疗方案极为有限。我们推测，对慢阻肺患者的肺部组织开展全基因表达谱分析，或可揭示此前未被探明的疾病通路，为潜在治疗干预提供新方向。
本研究共收集48份人类肺部样本，均来自因小型外周肺部病变接受切除手术的肺组织或肺叶，其中包含5名非吸烟者、21名全球慢性阻塞性肺疾病倡议（Global Initiative for Chronic Obstructive Lung Disease, GOLD）0级、9名GOLD 1级、10名GOLD 2级及3名GOLD 3级患者。
样本的信使核糖核酸（messenger RNA, mRNA）通过安捷伦（Agilent）Functional ID v2.0芯片完成表达谱检测，该芯片涵盖23720条序列。对样本进行定量形态计量分析后发现，各样本中气道、血管及肺实质的占比存在差异。将上述数据整合至关联基因表达与预测用力肺活量25%~75%时用力呼气流速百分比（FEF 25-75 % P）的模型中，最终筛选得到包含203条转录本的特征基因集。
上调基因涉及细胞外基质合成/降解、氧化应激及细胞增殖相关通路，而下调基因则参与尼古丁代谢、弹性纤维稳态及抗炎应答过程。免疫组织化学实验证实，尿激酶（urokinase, PLAU）、尿激酶受体（urokinase receptor, PLAUR）及血小板反应蛋白1（thrombospondin 1, THBS1）可由肺泡巨噬细胞与小气道上皮细胞表达。该通路中的基因已被证实参与转化生长因子β1（transforming growth factor-β1, TGFβ1）与基质金属蛋白酶（matrix metalloproteinase, MMP）的激活过程，且可受到丝氨酸蛋白酶抑制剂E2（serpin E2）的调控。值得注意的是，TGFβ1与serpin E2均已在慢阻肺的遗传连锁及关联研究中被鉴定为候选基因。综上，本研究结果为两种筛选潜在治疗靶点的有效手段搭建起潜在的关联桥梁。

关键词：肺气肿、表型、转录组分析、吸烟
整体实验设计：本研究共收集48份人类肺部样本，均来自因小型外周肺部病变接受切除手术的肺组织或肺叶，其中包含5名非吸烟者、21名GOLD 0级、9名GOLD 1级、10名GOLD 2级及3名GOLD 3级患者。样本的mRNA通过安捷伦（Agilent）Functional ID v2.0芯片完成表达谱检测，该芯片涵盖23720条序列。对样本进行定量形态计量分析后发现，各样本中气道、血管及肺实质的占比存在差异。将上述数据整合至关联基因表达与预测用力肺活量25%~75%时用力呼气流速百分比（FEF 25-75 % P）的模型中，最终筛选得到包含203条转录本的特征基因集。