Samarelli Anna Valeria, Tonelli Roberto, Raineri Giulia, Bruzzi Giulia, Andrisani Dario, Gozzi Filippo, Marchioni Alessandro, Costantini Matteo, Fabbiani Luca, Genovese Filippo, Pinetti Diego, Manicardi Linda, Castaniere Ivana, Masciale Valentina, Aramini Beatrice, Tabbì Luca, Rizzato Simone, Bettelli Stefania, Manfredini Samantha, Dominici Massimo, Clini Enrico, Cerri Stefania
Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy.
Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy.
Front Oncol. 2024 Jan 23;13:1275346. doi: 10.3389/fonc.2023.1275346. eCollection 2023.
Idiopathic pulmonary fibrosis (IPF) severely affects the lung leading to aberrant deposition of extracellular matrix and parenchymal stiffness with progressive functional derangement. The limited availability of fresh tissues represents one of the major limitations to study the molecular profiling of IPF lung tissue. The primary aim of this study was to explore the proteomic profiling yield of archived formalin-fixed paraffin-embedded (FFPE) specimens of IPF lung tissues.
We further determined the protein expression according to respiratory functional decline at the time of biopsy. The total proteins isolated from 11 FFPE samples of IPF patients compared to 3 FFPE samples from a non-fibrotic lung defined as controls, were subjected to label-free quantitative proteomic analysis by liquid chromatography-mass spectrometry (LC-MS/MS) and resulted in the detection of about 400 proteins.
After the pairwise comparison between controls and IPF, functional enrichment analysis identified differentially expressed proteins that were involved in extracellular matrix signaling pathways, focal adhesion and transforming growth factor β (TGF-β) signaling pathways strongly associated with IPF onset and progression. Five proteins were significantly over- expressed in the lung of IPF patients with either advanced disease stage (Stage II) or impaired pulmonary function (FVC<75, DLCO<55) compared to controls; these were lymphocyte cytosolic protein 1 (LCP1), peroxiredoxin-2 (PRDX2), transgelin 2 (TAGLN2), lumican (LUM) and mimecan (OGN) that might play a key role in the fibrogenic processes.
Our work showed that the analysis of FFPE samples was able to identify key proteins that might be crucial for the IPF pathogenesis. These proteins are correlated with lung carcinogenesis or involved in the immune landscape of lung cancer, thus making possible common mechanisms between lung carcinogenesis and fibrosis progression, two pathological conditions at risk for each other in the real life.
特发性肺纤维化（IPF）严重影响肺部，导致细胞外基质异常沉积和实质僵硬，并伴有进行性功能紊乱。新鲜组织的获取有限是研究IPF肺组织分子图谱的主要限制之一。本研究的主要目的是探索IPF肺组织存档福尔马林固定石蜡包埋（FFPE）标本的蛋白质组学图谱产量。
我们根据活检时呼吸功能下降情况进一步确定蛋白质表达。从11例IPF患者的FFPE样本中分离出的总蛋白与3例非纤维化肺的FFPE样本（定义为对照）进行比较，通过液相色谱 - 质谱联用（LC-MS/MS）进行无标记定量蛋白质组分析，检测到约400种蛋白质。
在对照与IPF之间进行成对比较后，功能富集分析确定了差异表达的蛋白质，这些蛋白质参与细胞外基质信号通路、粘着斑和转化生长因子β（TGF-β）信号通路，这些通路与IPF的发生和进展密切相关。与对照相比，在疾病晚期（II期）或肺功能受损（FVC<75，DLCO<55）的IPF患者肺中，有5种蛋白质显著过表达；这些蛋白质分别是淋巴细胞胞质蛋白1（LCP1）、过氧化物酶体增殖物激活受体2（PRDX2）、转胶蛋白2（TAGLN2）、核纤蛋白（LUM）和 mimecan（OGN），它们可能在纤维化过程中起关键作用。
我们的工作表明，对FFPE样本的分析能够识别出对IPF发病机制可能至关重要的关键蛋白质。这些蛋白质与肺癌发生相关或参与肺癌的免疫格局，从而使肺癌发生和纤维化进展之间存在共同机制成为可能，这两种病理状况在现实生活中相互关联。
