Bekker Nicolaas J, van Pijkeren Alienke, Wolters Justina C, Sánchez Brotons Alejandro, Guryev Victor, Woldhuis Roy R, Bischoff Rainer, Alkema Wynand, Horvatovich Peter, van Nijnatten Johannes L L, van den Berge Maarten, Timens Wim, Brandsma Corry-Anke
Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Am J Physiol Lung Cell Mol Physiol. 2023 Apr 1;324(4):L521-L535. doi: 10.1152/ajplung.00105.2022. Epub 2023 Feb 21.
Lung fibroblasts are implicated in abnormal tissue repair in chronic obstructive pulmonary disease (COPD). The exact mechanisms are unknown and comprehensive analysis comparing COPD- and control fibroblasts is lacking. The aim of this study is to gain insight into the role of lung fibroblasts in COPD pathology using unbiased proteomic and transcriptomic analysis. Protein and RNA were isolated from cultured parenchymal lung fibroblasts of 17 patients with stage IV COPD and 16 non-COPD controls. Proteins were analyzed using LC-MS/MS and RNA through RNA sequencing. Differential protein and gene expression in COPD was assessed via linear regression, followed by pathway enrichment, correlation analysis, and immunohistological staining in lung tissue. Proteomic and transcriptomic data were compared to investigate the overlap and correlation between both levels of data. We identified 40 differentially expressed (DE) proteins and zero DE genes between COPD and control fibroblasts. The most significant DE proteins were HNRNPA2B1 and FHL1. Thirteen of the 40 proteins were previously associated with COPD, including FHL1 and GSTP1. Six of the 40 proteins were related to telomere maintenance pathways, and were positively correlated with the senescence marker LMNB1. No significant correlation between gene and protein expression was observed for the 40 proteins. We hereby describe 40 DE proteins in COPD fibroblasts including previously described COPD proteins (FHL1, GSTP1) and new COPD research targets like HNRNPA2B1. Lack of overlap and correlation between gene and protein data supports the use of unbiased proteomics analysis and indicates that different types of information are generated with both methods.
肺成纤维细胞与慢性阻塞性肺疾病（COPD）中异常的组织修复有关。确切机制尚不清楚，且缺乏对COPD成纤维细胞与对照成纤维细胞的全面分析。本研究的目的是通过无偏倚的蛋白质组学和转录组学分析，深入了解肺成纤维细胞在COPD病理中的作用。从17例IV期COPD患者和16例非COPD对照者的培养肺实质成纤维细胞中分离蛋白质和RNA。使用液相色谱-串联质谱法（LC-MS/MS）分析蛋白质，通过RNA测序分析RNA。通过线性回归评估COPD中差异蛋白质和基因表达，随后进行通路富集、相关性分析以及肺组织免疫组织化学染色。比较蛋白质组学和转录组学数据，以研究两种数据水平之间的重叠和相关性。我们鉴定出COPD成纤维细胞与对照成纤维细胞之间有40种差异表达（DE）蛋白质和零种DE基因。最显著的DE蛋白质是HNRNPA2B1和FHL1。40种蛋白质中有13种先前与COPD相关，包括FHL1和GSTP1。40种蛋白质中有6种与端粒维持通路相关，并与衰老标志物LMNB1呈正相关。对于这40种蛋白质，未观察到基因与蛋白质表达之间的显著相关性。我们在此描述了COPD成纤维细胞中的40种DE蛋白质，包括先前描述的COPD相关蛋白质（FHL1、GSTP1）以及新的COPD研究靶点如HNRNPA2B1。基因和蛋白质数据之间缺乏重叠和相关性支持使用无偏倚蛋白质组学分析，并表明两种方法产生了不同类型的信息。
