Proteomic profiling of formalin-fixed paraffine-embedded tissue reveals key proteins related to lung dysfunction in idiopathic pulmonary fibrosis

Anna Valeria Samarelli; Roberto Tonelli; Giulia Raineri; Giulia Bruzzi; Dario Andrisani; Filippo Gozzi; Alessandro Marchioni; Matteo Costantini; Luca Fabbiani; Filippo Genovese; Diego Pinetti; Linda Manicardi; Ivana Castaniere; Valentina Masciale; Beatrice Aramini; Luca Tabbì; Simone Rizzato; Stefania Bettelli; Samantha Manfredini; Massimo Dominici; Enrico Clini; Stefania Cerri

doi:10.3389/fonc.2023.1275346

Proteomic profiling of formalin-fixed paraffine-embedded tissue reveals key proteins related to lung dysfunction in idiopathic pulmonary fibrosis

Front Oncol. 2024 Jan 23:13:1275346. doi: 10.3389/fonc.2023.1275346. eCollection 2023.

Authors

Anna Valeria Samarelli¹, Roberto Tonelli^{1

2}, Giulia Raineri¹, Giulia Bruzzi^{1

2}, Dario Andrisani^{1

2}, Filippo Gozzi^{1

2}, Alessandro Marchioni^{1

2}, Matteo Costantini³, Luca Fabbiani^{3

4}, Filippo Genovese⁵, Diego Pinetti⁵, Linda Manicardi², Ivana Castaniere^{1

2}, Valentina Masciale^{6

7}, Beatrice Aramini⁸, Luca Tabbì², Simone Rizzato², Stefania Bettelli⁹, Samantha Manfredini⁹, Massimo Dominici^{6

7}, Enrico Clini^{1

2}, Stefania Cerri^{1

2}

Affiliations

¹ Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy.
² Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy.
³ Pathology Institute, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy.
⁴ Immunohistochemistry Lab, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy.
⁵ Centro Interdipartimentale Grandi Strumenti (C.I.G.S.), University of Modena and Reggio Emilia, Modena, Italy.
⁶ Laboratory of Cellular Therapy, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, Modena, Italy.
⁷ Oncology Unit, University Hospital of Modena and Reggio Emilia, University of Modena and Reggio Emilia, Modena, Italy.
⁸ Division of Thoracic Surgery, Department of Medical and Surgical Sciences-Diagnostic and Specialty Medicine (DIMEC) of the Alma Mater Studiorum, University of Bologna G.B. Morgagni-L. Pierantoni Hospital, Forlì, Italy.
⁹ Molecular Pathology and Predictive Medicine Unit, Modena Cancer Center, University Hospital of Modena, Modena, Italy.

Abstract

Introduction: 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.

Methods: 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.

Results: 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.

Discussion: 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.

Keywords: IPF; lung function decline; mass spectrometry; molecular profiling; pulmonary fibrosis; rare disease.

Copyright © 2024 Samarelli, Tonelli, Raineri, Bruzzi, Andrisani, Gozzi, Marchioni, Costantini, Fabbiani, Genovese, Pinetti, Manicardi, Castaniere, Masciale, Aramini, Tabbì, Rizzato, Bettelli, Manfredini, Dominici, Clini and Cerri.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The realization of this project produced as part of the research program at Experimental Pneumology, University of Modena and Reggio Emilia (www.experimentalpneumology.unimore.it) was made possible thanks to the valuable contribution of “Federazione Italiana Malattie dell’Apparato Respiratorio (FIMARP), Modena Golf Country Club, AMMI (Associazione Mogli di Medici Italiani and B-PER Banca; it was carried out within the framework of the HEAL Italia project funded by the PNRR. The research leading to these results has received funding from the European Union-NextGenerationEU through the Italian Ministry of University and Research under PNRR-M4C2-l1.3 Project PE_00000019“HEAL ITALIA” to prof. Enrico Clini, CUP E93C22001860006. The views and opinions expressed are those of the authors only and do not necessarily felect those of the European Union or the European Commission. Neither the European Union nor the European Commission can be held responsible for them.