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Biomedicines
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Phenotypes and Endotypes in Interstitial Lung Diseases
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Phenotypes and Endotypes in Interstitial Lung Diseases

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Molecular and Translational Medicine".

Deadline for manuscript submissions: 31 March 2025 | Viewed by 8737

Special Issue Editor

Dr. Francesco Amati

E-Mail Website
Guest Editor
Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Milan, Italy
Interests: interstitial lung disease; pulmonary fibrosis; orphan lung diseases; non-cystic fibrosis bronchiectasis; pneumonia/ pulmonary infection; sarcoidosis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Interstitial lung diseases (ILDs) represent a heterogeneous group of more than 200 entities of either known or unknown etiology. ILD heterogeneity manifests at many levels, including symptoms, disease course, radiological and histological features, and biological underpinnings. This heterogeneity has been a substantial barrier to understanding disease mechanisms and developing effective and personalized treatments. Despite the growing interest and clinical research in ILDs, patients’ management remains sub-optimal, mainly because of the limited knowledge of disease pathogenesis, the highly variable and unpredictable disease behavior, and the heterogeneous response to treatment. Recent data suggest that different ILDs can share similar pathogenetic and biological pathways and thus be amenable to the same treatment. A paradigmatic example is the progressive pulmonary fibrosis (PPF) phenotype in which nintedanib, a tyrosine kinase inhibitor targeting the PDGF and other several growth factors, has shown efficacy regardless of ILD etiology. A growing amount of evidence points towards subgroups characterization of ILDs through endotypes, defined by specific genetic and molecular biomarkers. Thus, the future of ILDs lies in precision medicine approaches based on phenotypic and endotypic features. The aim of the Special Issue “Phenotypes and Endotypes in Interstitial Lung Diseases” is to outline the status of knowledge in this field.

Dr. Francesco Amati
Guest Editor

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Published Papers (5 papers)

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Research

13 pages, 3486 KiB  
Article
Expression of HOXB7 in the Lung of Patients with Idiopathic Pulmonary Fibrosis: A Proof-of-Concept Study
by Anna Valeria Samarelli, Roberto Tonelli, Giulia Raineri, Ilenia Mastrolia, Matteo Costantini, Luca Fabbiani, Virginia Catani, Tiziana Petrachi, Giulia Bruzzi, Dario Andrisani, Filippo Gozzi, Alessandro Marchioni, Valentina Masciale, Beatrice Aramini, Valentina Ruggieri, Giulia Grisendi, Massimo Dominici, Stefania Cerri and Enrico Clini
Biomedicines 2024, 12(6), 1321; https://doi.org/10.3390/biomedicines12061321 - 13 Jun 2024
Viewed by 1178
Abstract
Background: The molecular pathways involved in the onset and progression of idiopathic pulmonary fibrosis (IPF) still need to be fully clarified as some are shared with lung cancer development. HOXB7, a member of the homeobox (Hox) gene family, has been found [...] Read more.
Background: The molecular pathways involved in the onset and progression of idiopathic pulmonary fibrosis (IPF) still need to be fully clarified as some are shared with lung cancer development. HOXB7, a member of the homeobox (Hox) gene family, has been found involved in various cancers. Methods: Immunohistochemical (IHC) analysis was run on lung tissue samples from surgical lung biopsy (SLB) of 19 patients with IPF, retrospectively selected from the IPF database of the University Hospital of Modena. HOXB7 expression was analyzed and compared with that of five patients with no evidence of pulmonary fibrosis as controls. Results: The semi-quantitative analysis of IHC showed that HOXB7 protein expression was higher in IPF patients compared to controls (difference between means = 6.2 ± 2.37, p = 0.0157). Further, HOXB7 expression was higher in IPF patients with a higher extent of fibrosis (50–75%)—measured with high-resolution computer tomography—compared to those with a lower extent (0–25%) (difference between means = 25.74 ± 6.72, p = 0.004). Conclusions: The expression of HOXB7 is higher in the lung of IPF patients compared to controls, and was represented in different cellular compartments within the lung niche. Further investigations are needed to clarify its role in the pathogenesis and progression of IPF. Full article
(This article belongs to the Special Issue Phenotypes and Endotypes in Interstitial Lung Diseases)
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10 pages, 264 KiB  
Article
First Report of the Prevalence at Baseline and after 1-Year Follow-Up of Treatable Traits in Interstitial Lung Diseases
by Francesco Amati, Anna Stainer, Giacomo Maruca, Maria De Santis, Giuseppe Mangiameli, Chiara Torrisi, Paola Bossi, Veronica Polelli, Francesco Blasi, Carlo Selmi, Giuseppe Marulli, Luca Balzarini, Luigi Maria Terracciano, Roberto Gatti and Stefano Aliberti
Biomedicines 2024, 12(5), 1047; https://doi.org/10.3390/biomedicines12051047 - 9 May 2024
Viewed by 1211
Abstract
Different factors, not limited to the lung, influence the progression of ILDs. A “treatable trait” strategy was recently proposed for ILD patients as a precision model of care to improve outcomes. However, no data have been published so far on the prevalence of [...] Read more.
Different factors, not limited to the lung, influence the progression of ILDs. A “treatable trait” strategy was recently proposed for ILD patients as a precision model of care to improve outcomes. However, no data have been published so far on the prevalence of TTs in ILD. A prospective, observational, cohort study was conducted within the ILD Program at the IRCCS Humanitas Research Hospital (Milan, Italy) between November 2021 and November 2023. TTs were selected according to recent literature and assigned during multidisciplinary discussion (MDD) to one of the following categories: pulmonary, etiological, comorbidities, and lifestyle. Patients were further divided into four groups according to their post-MDD diagnosis: idiopathic ILD, sarcoidosis, connective tissue disease–ILD, and other ILD. The primary study outcome was the prevalence of each TT in the study population. A total of 116 patients with ILD [63.9% male; median (IQR) age: 69 (54–78) years] were included in the study. All the TTs identified in the literature were found in our cohort, except for intractable chronic cough. We also recognized differences in TTs across the ILD groups, with less TTs in patients with sarcoidosis. This analysis provides the first ancillary characterization of TTs in ILD patients in a real setting to date. Full article
(This article belongs to the Special Issue Phenotypes and Endotypes in Interstitial Lung Diseases)
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14 pages, 2588 KiB  
Article
A Protective Effect of Pirfenidone in Lung Fibroblast–Endothelial Cell Network via Inhibition of Rho-Kinase Activity
by Yusuke Nakamura, Yasuo Shimizu, Mio Fujimaki-Shiraishi, Nobuhiko Uchida, Akihiro Takemasa and Seiji Niho
Biomedicines 2023, 11(8), 2259; https://doi.org/10.3390/biomedicines11082259 - 12 Aug 2023
Cited by 3 | Viewed by 1597
Abstract
Pulmonary fibrosis is a life-threatening disease that has been attributed to several causes. Specifically, vascular injury is thought to be involved in the pathogenesis of fibrosis. The effects of the antifibrotic drug pirfenidone on angiogenesis have not been fully elucidated. This study aimed [...] Read more.
Pulmonary fibrosis is a life-threatening disease that has been attributed to several causes. Specifically, vascular injury is thought to be involved in the pathogenesis of fibrosis. The effects of the antifibrotic drug pirfenidone on angiogenesis have not been fully elucidated. This study aimed to investigate the effects of pirfenidone in human lung fibroblast–endothelial cell co-culture network formation and to analyze the underlying molecular mechanisms. Human lung fibroblasts were co-cultured with human umbilical vein endothelial cells to establish a co-culture network cell sheet. The influence of pirfenidone was evaluated for protective effect on the endothelial network in cell sheets stimulated with transforming growth factor β (TGF-β). Results indicated that TGF-β disrupted the network formation. Pirfenidone and Y27632 (Rho-associated coiled-coil containing protein kinase [Rho-kinase or ROCK] inhibitor) protected against the TGF-β–induced endothelial network disruption. TGF-β activated Rho-kinase signaling in cells composing the co-culture cell sheet, whereas pirfenidone and Y27632 inhibited these effects. In conclusion, TGF-β–induced Rho-kinase activation and disrupted endothelial network formation. Pirfenidone suppressed TGF-β–induced Rho-kinase activity in cell sheets, thereby enabling vascular endothelial cells networks to be preserved in the cell sheets. These findings suggest that pirfenidone has potential vascular network–preserving effect via inhibiting Rho-kinase activity in vascular injury, which is a precursor to pulmonary fibrosis. Full article
(This article belongs to the Special Issue Phenotypes and Endotypes in Interstitial Lung Diseases)
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12 pages, 2575 KiB  
Article
Hyperpolarized Xenon-129: A New Tool to Assess Pulmonary Physiology in Patients with Pulmonary Fibrosis
by Kun Qing, Talissa A. Altes, John P. Mugler III, Jaime F. Mata, Nicholas J. Tustison, Kai Ruppert, Juliana Bueno, Lucia Flors, Yun M. Shim, Li Zhao, Joanne Cassani, William G. Teague, John S. Kim, Zhixing Wang, Iulian C. Ruset, F. William Hersman and Borna Mehrad
Biomedicines 2023, 11(6), 1533; https://doi.org/10.3390/biomedicines11061533 - 25 May 2023
Cited by 1 | Viewed by 2006
Abstract
Purpose: The existing tools to quantify lung function in interstitial lung diseases have significant limitations. Lung MRI imaging using inhaled hyperpolarized xenon-129 gas (129Xe) as a contrast agent is a new technology for measuring regional lung physiology. We sought to assess [...] Read more.
Purpose: The existing tools to quantify lung function in interstitial lung diseases have significant limitations. Lung MRI imaging using inhaled hyperpolarized xenon-129 gas (129Xe) as a contrast agent is a new technology for measuring regional lung physiology. We sought to assess the utility of the 129Xe MRI in detecting impaired lung physiology in usual interstitial pneumonia (UIP). Materials and methods: After institutional review board approval and informed consent and in compliance with HIPAA regulations, we performed chest CT, pulmonary function tests (PFTs), and 129Xe MRI in 10 UIP subjects and 10 healthy controls. Results: The 129Xe MRI detected highly heterogeneous abnormalities within individual UIP subjects as compared to controls. Subjects with UIP had markedly impaired ventilation (ventilation defect fraction: UIP: 30 ± 9%; healthy: 21 ± 9%; p = 0.026), a greater amount of 129Xe dissolved in the lung interstitium (tissue-to-gas ratio: UIP: 1.45 ± 0.35%; healthy: 1.10 ± 0.17%; p = 0.014), and impaired 129Xe diffusion into the blood (RBC-to-tissue ratio: UIP: 0.20 ± 0.06; healthy: 0.28 ± 0.05; p = 0.004). Most MRI variables had no correlation with the CT and PFT measurements. The elevated level of 129Xe dissolved in the lung interstitium, in particular, was detectable even in subjects with normal or mildly impaired PFTs, suggesting that this measurement may represent a new method for detecting early fibrosis. Conclusion: The hyperpolarized 129Xe MRI was highly sensitive to regional functional changes in subjects with UIP and may represent a new tool for understanding the pathophysiology, monitoring the progression, and assessing the effectiveness of treatment in UIP. Full article
(This article belongs to the Special Issue Phenotypes and Endotypes in Interstitial Lung Diseases)
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10 pages, 3348 KiB  
Article
Histologic Analysis of Idiopathic Pulmonary Fibrosis by Morphometric and Fractal Analysis
by Massimiliano Mancini, Lavinia Bargiacchi, Claudia De Vitis, Michela D’Ascanio, Chiara De Dominicis, Mohsen Ibrahim, Erino Angelo Rendina, Alberto Ricci, Arianna Di Napoli, Rita Mancini and Andrea Vecchione
Biomedicines 2023, 11(5), 1483; https://doi.org/10.3390/biomedicines11051483 - 19 May 2023
Cited by 4 | Viewed by 1807
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive fibrotic lung disorder, ultimately leading to respiratory failure and death. Despite great research advances in understanding the mechanisms underlying the disease, its diagnosis, and its treatment, IPF still remains idiopathic without known biological or histological [...] Read more.
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive fibrotic lung disorder, ultimately leading to respiratory failure and death. Despite great research advances in understanding the mechanisms underlying the disease, its diagnosis, and its treatment, IPF still remains idiopathic without known biological or histological markers able to predict disease progression or response to treatment. The histologic hallmark of IPF is usual interstitial pneumonia (UIP), with its intricate architectural distortion and temporal inhomogeneity. We hypothesize that normal lung alveolar architecture can be compared to fractals, such as the Pythagoras tree with its fractal dimension (Df), and every pathological insult, distorting the normal lung structure, could result in Df variations. In this study, we aimed to assess the UIP histologic fractal dimension in relationship to other morphometric parameters in newly diagnosed IPF patients and its possible role in the prognostic stratification of the disease. Clinical data and lung tissue specimens were obtained from twelve patients with IPF, twelve patients with non-specific interstitial pneumonia (NSIP), and age-matched “healthy” control lung tissue from patients undergoing lung surgery for other causes. Histology and histomorphometry were performed to evaluate Df and lacunarity measures, using the box counting method on the FracLac ImageJ plugin. The results showed that Df was significantly higher in IPF patients compared to controls and fibrotic NSIP patients, indicating greater architectural distortion in IPF. Additionally, high Df values were associated with higher fibroblastic foci density and worse prognostic outcomes in IPF, suggesting that Df may serve as a potential novel prognostic marker for IPF. The scalability of Df measurements was demonstrated through repeated measurements on smaller portions from the same surgical biopsies, which were selected to mimic a cryobiopsy. Our study provides further evidence to support the use of fractal morphometry as a tool for quantifying and determining lung tissue remodeling in IPF, and we demonstrated a significant correlation between histological and radiological Df in UIP pattern, as well as a significant association between Df and FF density. Furthermore, our study demonstrates the scalability and self-similarity of Df measurements across different biopsy types, including surgical and smaller specimens. Full article
(This article belongs to the Special Issue Phenotypes and Endotypes in Interstitial Lung Diseases)
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