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Moos PJ, Cheminant JR, Cowman S, Noll J, Wang Q, Musci T, Venosa A. Spatial and phenotypic heterogeneity of resident and monocyte-derived macrophages during inflammatory exacerbations leading to pulmonary fibrosis. Front Immunol 2024; 15:1425466. [PMID: 39100672 PMCID: PMC11294112 DOI: 10.3389/fimmu.2024.1425466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/28/2024] [Indexed: 08/06/2024] Open
Abstract
Introduction Genetic mutations in critical nodes of pulmonary epithelial function are linked to the pathogenesis of pulmonary fibrosis (PF) and other interstitial lung diseases. The slow progression of these pathologies is often intermitted and accelerated by acute exacerbations, complex non-resolving cycles of inflammation and parenchymal damage, resulting in lung function decline and death. Excess monocyte mobilization during the initial phase of an acute exacerbation, and their long-term persistence in the lung, is linked to poor disease outcome. Methods The present work leverages a clinical idiopathic PF dataset and a murine model of acute inflammatory exacerbations triggered by mutation in the alveolar type-2 cell-restricted Surfactant Protein-C [SP-C] gene to spatially and phenotypically define monocyte/macrophage changes in the fibrosing lung. Results SP-C mutation triggered heterogeneous CD68+ macrophage activation, with highly active peri-injured cells relative to those sampled from fully remodeled and healthy regions. Ingenuity pathway analysis of sorted CD11b-SigF+CD11c+ alveolar macrophages defined asynchronous activation of extracellular matrix re-organization, cellular mobilization, and Apolipoprotein E (Apoe) signaling in the fibrosing lung. Cell-cell communication analysis of single cell sequencing datasets predicted pro-fibrogenic signaling (fibronectin/Fn1, osteopontin/Spp1, and Tgfb1) emanating from Trem2/TREM2 + interstitial macrophages. These cells also produced a distinct lipid signature from alveolar macrophages and monocytes, characterized by Apoe expression. Mono- and di-allelic genetic deletion of ApoE in SP-C mutant mice had limited impact on inflammation and mortality up to 42 day after injury. Discussion Together, these results provide a detailed spatio-temporal picture of resident, interstitial, and monocyte-derived macrophages during SP-C induced inflammatory exacerbations and end-stage clinical PF, and propose ApoE as a biomarker to identify activated macrophages involved in tissue remodeling.
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Affiliation(s)
| | | | | | | | | | | | - Alessandro Venosa
- Department of Pharmacology and Toxicology, University of Utah College of Pharmacy, Salt Lake City, UT, United States
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Piga I, Magni F, Smith A. The journey towards clinical adoption of MALDI-MS-based imaging proteomics: from current challenges to future expectations. FEBS Lett 2024; 598:621-634. [PMID: 38140823 DOI: 10.1002/1873-3468.14795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/06/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023]
Abstract
Among the spatial omics techniques available, mass spectrometry imaging (MSI) represents one of the most promising owing to its capability to map the distribution of hundreds of peptides and proteins, as well as other classes of biomolecules, within a complex sample background in a multiplexed and relatively high-throughput manner. In particular, matrix-assisted laser desorption/ionisation (MALDI-MSI) has come to the fore and established itself as the most widely used technique in clinical research. However, the march of this technique towards clinical utility has been hindered by issues related to method reproducibility, appropriate biocomputational tools, and data storage. Notwithstanding these challenges, significant progress has been achieved in recent years regarding multiple facets of the technology and has rendered it more suitable for a possible clinical role. As such, there is now more robust and extensive evidence to suggest that the technology has the potential to support clinical decision-making processes under appropriate circumstances. In this review, we will discuss some of the recent developments that have facilitated this progress and outline some of the more promising clinical proteomics applications which have been developed with a clear goal towards implementation in mind.
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Affiliation(s)
- Isabella Piga
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Andrew Smith
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
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Bolognesi MM, Antoranz A, Bosisio FM, Cattoretti G. Quantitative multiplex immunohistochemistry with colorimetric staining (QUIVER) may still benefit from MILAN. Acta Neuropathol Commun 2023; 11:91. [PMID: 37287032 DOI: 10.1186/s40478-023-01585-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/09/2023] Open
Affiliation(s)
- Maddalena M Bolognesi
- Pathology, Department of Medicine and Surgery, Università di Milano-Bicocca, Via Cadore 48, Monza, MI, Italy
| | - Asier Antoranz
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- The Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Francesca Maria Bosisio
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Giorgio Cattoretti
- Pathology, Department of Medicine and Surgery, Università di Milano-Bicocca, Via Cadore 48, Monza, MI, Italy.
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Buccardi M, Ferrini E, Pennati F, Vincenzi E, Ledda RE, Grandi A, Buseghin D, Villetti G, Sverzellati N, Aliverti A, Stellari FF. A fully automated micro‑CT deep learning approach for precision preclinical investigation of lung fibrosis progression and response to therapy. Respir Res 2023; 24:126. [PMID: 37161569 PMCID: PMC10170869 DOI: 10.1186/s12931-023-02432-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/24/2023] [Indexed: 05/11/2023] Open
Abstract
Micro-computed tomography (µCT)-based imaging plays a key role in monitoring disease progression and response to candidate drugs in various animal models of human disease, but manual image processing is still highly time-consuming and prone to operator bias. Focusing on an established mouse model of bleomycin (BLM)-induced lung fibrosis we document, here, the ability of a fully automated deep-learning (DL)-based model to improve and speed-up lung segmentation and the precise measurement of morphological and functional biomarkers in both the whole lung and in individual lobes. µCT-DL whose results were overall highly consistent with those of more conventional, especially histological, analyses, allowed to cut down by approximately 45-fold the time required to analyze the entire dataset and to longitudinally follow fibrosis evolution and response to the human-use-approved drug Nintedanib, using both inspiratory and expiratory μCT. Particularly significant advantages of this µCT-DL approach, are: (i) its reduced experimental variability, due to the fact that each animal acts as its own control and the measured, operator bias-free biomarkers can be quantitatively compared across experiments; (ii) its ability to monitor longitudinally the spatial distribution of fibrotic lesions, thus eliminating potential confounding effects associated with the more severe fibrosis observed in the apical region of the left lung and the compensatory effects taking place in the right lung; (iii) the animal sparing afforded by its non-invasive nature and high reliability; and (iv) the fact that it can be integrated into different drug discovery pipelines with a substantial increase in both the speed and robustness of the evaluation of new candidate drugs. The µCT-DL approach thus lends itself as a powerful new tool for the precision preclinical monitoring of BLM-induced lung fibrosis and other disease models as well. Its ease of operation and use of standard imaging instrumentation make it easily transferable to other laboratories and to other experimental settings, including clinical diagnostic applications.
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Affiliation(s)
- Martina Buccardi
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, Italy
- Experimental Pharmacology & Translational Science Department, Chiesi Farmaceutici S.P.A, 43122, Parma, Italy
| | - Erica Ferrini
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Francesca Pennati
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico Di Milano, Milan, Italy
| | - Elena Vincenzi
- Department of Computer Science, Bioengineering, Robotics and Systems Engineering, University of Genoa, Genoa, Italy
- Camelot Biomedical System S.R.L, Via Al Ponte Reale 2/20, 16124, Genoa, Italy
| | | | - Andrea Grandi
- Experimental Pharmacology & Translational Science Department, Chiesi Farmaceutici S.P.A, 43122, Parma, Italy
| | - Davide Buseghin
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Gino Villetti
- Experimental Pharmacology & Translational Science Department, Chiesi Farmaceutici S.P.A, 43122, Parma, Italy
| | | | - Andrea Aliverti
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico Di Milano, Milan, Italy
| | - Franco Fabio Stellari
- Experimental Pharmacology & Translational Science Department, Chiesi Farmaceutici S.P.A, 43122, Parma, Italy.
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Principi L, Ferrini E, Ciccimarra R, Pagani L, Chinello C, Previtali P, Smith A, Villetti G, Zoboli M, Ravanetti F, Stellari FF, Magni F, Piga I. Proteomic Fingerprint of Lung Fibrosis Progression and Response to Therapy in Bleomycin-Induced Mouse Model. Int J Mol Sci 2023; 24:ijms24054410. [PMID: 36901840 PMCID: PMC10002924 DOI: 10.3390/ijms24054410] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease characterized by the aberrant accumulation of extracellular matrix in the lungs. nintedanib is one of the two FDA-approved drugs for IPF treatment; however, the exact pathophysiological mechanisms of fibrosis progression and response to therapy are still poorly understood. In this work, the molecular fingerprint of fibrosis progression and response to nintedanib treatment have been investigated by mass spectrometry-based bottom-up proteomics in paraffin-embedded lung tissues from bleomycin-induced (BLM) pulmonary fibrosis mice. Our proteomics results unveiled that (i) samples clustered depending on the tissue fibrotic grade (mild, moderate, and severe) and not on the time course after BLM treatment; (ii) the dysregulation of different pathways involved in fibrosis progression such as the complement coagulation cascades, advanced glycation end products (AGEs) and their receptors (RAGEs) signaling, the extracellular matrix-receptor interaction, the regulation of actin cytoskeleton, and ribosomes; (iii) Coronin 1A (Coro1a) as the protein with the highest correlation when evaluating the progression of fibrosis, with an increased expression from mild to severe fibrosis; and (iv) a total of 10 differentially expressed proteins (padj-value ≤ 0.05 and Fold change ≤-1.5 or ≥1.5), whose abundance varied in the base of the severity of fibrosis (mild and moderate), were modulated by the antifibrotic treatment with nintedanib, reverting their trend. Notably, nintedanib significantly restored lactate dehydrogenase B (Ldhb) expression but not lactate dehydrogenase A (Ldha). Notwithstanding the need for further investigations to validate the roles of both Coro1a and Ldhb, our findings provide an extensive proteomic characterization with a strong relationship with histomorphometric measurements. These results unveil some biological processes in pulmonary fibrosis and drug-mediated fibrosis therapy.
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Affiliation(s)
- Lucrezia Principi
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Erica Ferrini
- Department of Veterinary Science, University of Parma, 43122 Parma, Italy
| | - Roberta Ciccimarra
- Department of Veterinary Science, University of Parma, 43122 Parma, Italy
| | - Lisa Pagani
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Clizia Chinello
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Paolo Previtali
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Andrew Smith
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Gino Villetti
- Experimental Pharmacology & Translational Science Department, Chiesi Farmaceutici S.p.A., 43122 Parma, Italy
| | - Matteo Zoboli
- Department of Veterinary Science, University of Parma, 43122 Parma, Italy
| | | | - Franco Fabio Stellari
- Experimental Pharmacology & Translational Science Department, Chiesi Farmaceutici S.p.A., 43122 Parma, Italy
- Correspondence: (F.F.S.); (I.P.)
| | - Fulvio Magni
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Isabella Piga
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
- Correspondence: (F.F.S.); (I.P.)
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Grandi A, Ferrini E, Mecozzi L, Ciccimarra R, Zoboli M, Leo L, Khalajzeyqami Z, Kleinjan A, Löwik CWGM, Donofrio G, Villetti G, Stellari FF. Indocyanine-enhanced mouse model of bleomycin-induced lung fibrosis with hallmarks of progressive emphysema. Am J Physiol Lung Cell Mol Physiol 2023; 324:L211-L227. [PMID: 36625471 PMCID: PMC9925167 DOI: 10.1152/ajplung.00180.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The development of new drugs for idiopathic pulmonary fibrosis strongly relies on preclinical experimentation, which requires the continuous improvement of animal models and integration with in vivo imaging data. Here, we investigated the lung distribution of bleomycin (BLM) associated with the indocyanine green (ICG) dye by fluorescence imaging. A long-lasting lung retention (up to 21 days) was observed upon oropharyngeal aspiration (OA) of either ICG or BLM + ICG, with significantly more severe pulmonary fibrosis, accompanied by the progressive appearance of emphysema-like features, uniquely associated with the latter combination. More severe and persistent lung fibrosis, together with a progressive air space enlargement uniquely associated with the BLM + ICG group, was confirmed by longitudinal micro-computed tomography (CT) and histological analyses. Multiple inflammation and fibrosis biomarkers were found to be increased in the bronchoalveolar lavage fluid of BLM- and BLM + ICG-treated animals, but with a clear trend toward a much stronger increase in the latter group. Similarly, in vitro assays performed on macrophage and epithelial cell lines revealed a significantly more marked cytotoxicity in the case of BLM + ICG-treated mice. Also unique to this group was the synergistic upregulation of apoptotic markers both in lung sections and cell lines. Although the exact mechanism underlying the more intense lung fibrosis phenotype with emphysema-like features induced by BLM + ICG remains to be elucidated, we believe that this combination treatment, whose overall effects more closely resemble the human disease, represents a valuable alternative model for studying fibrosis development and for the identification of new antifibrotic compounds.
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Affiliation(s)
- Andrea Grandi
- 1Chiesi Farmaceutici S.p.A., Corporate Pre-Clinical R&D, Parma, Italy
| | - Erica Ferrini
- 2Department of Veterinary Science, University of Parma, Parma, Italy
| | - Laura Mecozzi
- 3Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | - Matteo Zoboli
- 2Department of Veterinary Science, University of Parma, Parma, Italy
| | - Ludovica Leo
- 3Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Zahra Khalajzeyqami
- 4Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Alex Kleinjan
- 5Department of Pulmonary Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Clemens W. G. M. Löwik
- 6Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Gaetano Donofrio
- 2Department of Veterinary Science, University of Parma, Parma, Italy
| | - Gino Villetti
- 1Chiesi Farmaceutici S.p.A., Corporate Pre-Clinical R&D, Parma, Italy
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Promises and Challenges of Cell-Based Therapies to Promote Lung Regeneration in Idiopathic Pulmonary Fibrosis. Cells 2022; 11:cells11162595. [PMID: 36010671 PMCID: PMC9406501 DOI: 10.3390/cells11162595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 12/17/2022] Open
Abstract
The lung epithelium is constantly exposed to harmful agents present in the air that we breathe making it highly susceptible to damage. However, in instances of injury to the lung, it exhibits a remarkable capacity to regenerate injured tissue thanks to the presence of distinct stem and progenitor cell populations along the airway and alveolar epithelium. Mechanisms of repair are affected in chronic lung diseases such as idiopathic pulmonary fibrosis (IPF), a progressive life-threatening disorder characterized by the loss of alveolar structures, wherein excessive deposition of extracellular matrix components cause the distortion of tissue architecture that limits lung function and impairs tissue repair. Here, we review the most recent findings of a study of epithelial cells with progenitor behavior that contribute to tissue repair as well as the mechanisms involved in mouse and human lung regeneration. In addition, we describe therapeutic strategies to promote or induce lung regeneration and the cell-based strategies tested in clinical trials for the treatment of IPF. Finally, we discuss the challenges, concerns and limitations of applying these therapies of cell transplantation in IPF patients. Further research is still required to develop successful strategies focused on cell-based therapies to promote lung regeneration to restore lung architecture and function.
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