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Espina-Ordoñez M, Balderas-Martínez YI, Torres-Machorro AL, Herrera I, Maldonado M, Romero Y, Toscano-Marquez F, Pardo A, Selman M, Cisneros J. Mir-155-5p targets TP53INP1 to promote proliferative phenotype in hypersensitivity pneumonitis lung fibroblasts. Noncoding RNA Res 2024; 9:865-875. [PMID: 38586316 PMCID: PMC10997802 DOI: 10.1016/j.ncrna.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/11/2024] [Accepted: 02/19/2024] [Indexed: 04/09/2024] Open
Abstract
Background Hypersensitivity pneumonitis (HP) is an inflammatory disorder affecting lung parenchyma and often evolves into fibrosis (fHP). The altered regulation of genes involved in the pathogenesis of the disease is not well comprehended, while the role of microRNAs in lung fibroblasts remains unexplored. Methods We used integrated bulk RNA-Seq and enrichment pathway bioinformatic analyses to identify differentially expressed (DE)-miRNAs and genes (DEGs) associated with HP lungs. In vitro, we evaluated the expression and potential role of miR-155-5p in the phenotype of fHP lung fibroblasts. Loss and gain assays were used to demonstrate the impact of miR-155-5p on fibroblast functions. In addition, mir-155-5p and its target TP53INP1 were analyzed after treatment with TGF-β, IL-4, and IL-17A. Results We found around 50 DEGs shared by several databases that differentiate HP from control and IPF lungs, constituting a unique HP lung transcriptional signature. Additionally, we reveal 18 DE-miRNAs that may regulate these DEGs. Among the candidates likely associated with HP pathogenesis was miR-155-5p. Our findings indicate that increased miR-155-5p in fHP fibroblasts coincides with reduced TP53INP1 expression, high proliferative capacity, and a lack of senescence markers compared to IPF fibroblasts. Induced overexpression of miR-155-5p in normal fibroblasts remarkably increases the proliferation rate and decreases TP53INP1 expression. Conversely, miR-155-5p inhibition reduces proliferation and increases senescence markers. TGF-β, IL-4, and IL-17A stimulated miR-155-5p overexpression in HP lung fibroblasts. Conclusion Our findings suggest a distinctive signature of 53 DEGs in HP, including CLDN18, EEF2, CXCL9, PLA2G2D, and ZNF683, as potential targets for future studies. Likewise, 18 miRNAs, including miR-155-5p, could be helpful to establish differences between these two pathologies. The overexpression of miR-155-5p and downregulation of TP53INP1 in fHP lung fibroblasts may be involved in his proliferative and profibrotic phenotype. These findings may help differentiate and characterize their pathogenic features and understand their role in the disease.
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Affiliation(s)
- Marco Espina-Ordoñez
- Laboratorio de Biopatología Pulmonar INER-Ciencias-UNAM, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, 14080, Mexico
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio D, Piso 1, Circuito de Posgrados, Ciudad Universidad, Coyoacán, C.P 04510, CDMX, Mexico
| | - Yalbi Itzel Balderas-Martínez
- Laboratorio de Biología Computacional, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, 14080, Mexico
| | - Ana Lilia Torres-Machorro
- Laboratorio de Biología Celular, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, 14080, Mexico
| | - Iliana Herrera
- Laboratorio de Biopatología Pulmonar INER-Ciencias-UNAM, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, 14080, Mexico
| | - Mariel Maldonado
- Laboratorio de Biopatología Pulmonar INER-Ciencias-UNAM, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, 14080, Mexico
| | - Yair Romero
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Fernanda Toscano-Marquez
- Laboratorio de Biopatología Pulmonar INER-Ciencias-UNAM, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, 14080, Mexico
| | - Annie Pardo
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Moisés Selman
- Laboratorio de Biopatología Pulmonar INER-Ciencias-UNAM, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, 14080, Mexico
| | - José Cisneros
- Departamento de Investigación en Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, 14080, Mexico
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Wu J, Wang J, Duan C, Han C, Hou X. Identifying MS4A6A + macrophages as potential contributors to the pathogenesis of nonalcoholic fatty liver disease, periodontitis, and type 2 diabetes mellitus. Heliyon 2024; 10:e29340. [PMID: 38644829 PMCID: PMC11033123 DOI: 10.1016/j.heliyon.2024.e29340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/14/2024] [Accepted: 04/05/2024] [Indexed: 04/23/2024] Open
Abstract
Purpose Concrete epidemiological evidence has suggested the mutually-contributing effect respectively between nonalcoholic fatty liver disease (NAFLD), type 2 diabetes mellitus (T2DM), and periodontitis (PD); however, their shared crosstalk mechanism remains an open issue. Method The NAFLD, PD, and T2DM-related datasets were obtained from the NCBI GEO repository. Their common differentially expressed genes (DEGs) were identified and the functional enrichment analysis performed by the DAVID platform determined relevant biological processes and pathways. Then, the STRING database established a PPI network of such DEGs and topological analysis through Cytoscape 3.7.1 software along with the machine-learning analysis by the least absolute shrinkage and selection operator (LASSO) algorithm screened out hub characteristic genes. Their efficacy was validated by external datasets using the receiver operating characteristic (ROC) curve, and gene expression and location of the most robust one was determined using single-cell sequencing and immunohistochemical staining. Finally, the promising drugs were predicted through the CTD database, and the CB-DOCK 2 and Pymol platform mimicked molecular docking. Result Intersection of differentially expressed genes from three datasets identified 25 shared DEGs of the three diseases, which were enriched in MHC II-mediated antigen presenting process. PPI network and LASSO machine-learning analysis determined 4 feature genes, of which the MS4A6A gene mainly expressed by macrophages was the hub gene and key immune cell type. Molecular docking simulation chosen fenretinide as the most promising medicant for MS4A6A+ macrophages. Conclusion MS4A6A+ macrophages were suggested to be important immune-related mediators in the progression of NAFLD, PD, and T2DM pathologies.
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Affiliation(s)
- Junhao Wu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jinsheng Wang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Caihan Duan
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Chaoqun Han
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiaohua Hou
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
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Luo L, Jiang M, Xiong Y, Xiong A, Zhang L, Wu D, Liu Y, Ran Q, Liu J, Zhang Y, Li J, He X, Wang J, Li G. Fine particulate matter 2.5 induces susceptibility to Pseudomonas aeruginosa infection via expansion of PD-L1 high neutrophils in mice. Respir Res 2024; 25:90. [PMID: 38355515 PMCID: PMC10865610 DOI: 10.1186/s12931-023-02640-x] [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: 07/10/2023] [Accepted: 12/15/2023] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Exposure to PM2.5 has been implicated in a range of detrimental health effects, particularly affecting the respiratory system. However, the precise underlying mechanisms remain elusive. METHODS To address this objective, we collected ambient PM2.5 and administered intranasal challenges to mice, followed by single-cell RNA sequencing (scRNA-seq) to unravel the heterogeneity of neutrophils and unveil their gene expression profiles. Flow cytometry and immunofluorescence staining were subsequently conducted to validate the obtained results. Furthermore, we assessed the phagocytic potential of neutrophils upon PM2.5 exposure using gene analysis of phagocytosis signatures and bacterial uptake assays. Additionally, we utilized a mouse pneumonia model to evaluate the susceptibility of PM2.5-exposed mice to Pseudomonas aeruginosa infection. RESULTS Our study revealed a significant increase in neutrophil recruitment within the lungs of PM2.5-exposed mice, with subclustering of neutrophils uncovering subsets with distinct gene expression profiles. Notably, exposure to PM2.5 was associated with an expansion of PD-L1high neutrophils, which exhibited impaired phagocytic function dependent upon PD-L1 expression. Furthermore, PM2.5 exposure was found to increase the susceptibility of mice to Pseudomonas aeruginosa, due in part to increased PD-L1 expression on neutrophils. Importantly, monoclonal antibody targeting of PD-L1 significantly reduced bacterial burden, dissemination, and lung inflammation in PM2.5-exposed mice upon Pseudomonas aeruginosa infection. CONCLUSIONS Our study suggests that PM2.5 exposure promotes expansion of PD-L1high neutrophils with impaired phagocytic function in mouse lungs, contributing to increased vulnerability to bacterial infection, and therefore targeting PD-L1 may be a therapeutic strategy for reducing the harmful effects of PM2.5 exposure on the immune system.
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Affiliation(s)
- Li Luo
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China
| | - Manling Jiang
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology, Macao Special Administrative Region, Taipa, China
| | - Ying Xiong
- Department of Pulmonary and Critical Care Medicine, Sichuan Friendship Hospital, Chengdu, China
| | - Anying Xiong
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China
| | - Lei Zhang
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology, Macao Special Administrative Region, Taipa, China
| | - Dehong Wu
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China
| | - Yao Liu
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology, Macao Special Administrative Region, Taipa, China
| | - Qin Ran
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China
| | - Jiliu Liu
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China
| | - Yi Zhang
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China
| | - Jiahuan Li
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China
- North Sichuan Medical College, Nanchong, China
| | - Xiang He
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China.
| | - Junyi Wang
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology, Macao Special Administrative Region, Taipa, China.
| | - Guoping Li
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, 610031, China.
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Alarcon-Dionet A, Ruiz A, Chavez-Galan L, Buendia-Roldan I, Selman M. GDF15 as a potential biomarker to distinguish fibrotic from non-fibrotic hypersensitivity pneumonitis. Sci Rep 2024; 14:859. [PMID: 38195721 PMCID: PMC10776671 DOI: 10.1038/s41598-023-49459-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 12/08/2023] [Indexed: 01/11/2024] Open
Abstract
Hypersensitivity Pneumonitis (HP) is an immune-mediated interstitial lung disease (ILD) characterized by fibrotic HP (fHP) or non-fibrotic HP (non-fHP). Fibrosis is associated with poor prognosis, emphasizing the need for biomarkers to distinguish fHP from non-fHP. This study aimed to determine the plasma levels of GDF15 in HP patients and assess its association with lung function and phenotype classification. GDF15 levels were quantified by ELISA in HP (n = 64), idiopathic pulmonary fibrosis (n = 54), and healthy control (n = 128) groups. Clinical, demographic, and functional data were obtained from medical records. High-resolution chest CT scans were used to classify HP patients into fHP and non-fHP groups. In addition, receiver operating characteristic analysis was performed to determine the cut-off point, sensitivity, and specificity. Our results revealed significantly elevated GDF15 levels in fHP compared to non-fHP (2539 ± 821 pg/ml versus 1783 ± 801 pg/ml; p = 0.009). The estimated cut-off point for plasma GDF15 levels to distinguish fHP from non-fHP was 2193.4 pg/ml (AUC 0.75). These findings suggest that GDF15 may serve as a valuable biomarker for differentiating between fHP and non-fHP, potentially indicating its involvement in lung fibrosis development in HP.
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Affiliation(s)
- A Alarcon-Dionet
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, 14080, Mexico City, Mexico
| | - A Ruiz
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, 14080, Mexico City, Mexico
| | - L Chavez-Galan
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, 14080, Mexico City, Mexico
| | - I Buendia-Roldan
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, 14080, Mexico City, Mexico.
| | - M Selman
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, 14080, Mexico City, Mexico
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Fernández Pérez ER, Leach SM, Vestal B. Rationale and design of the prognostic transcriptomic signature in fibrotic hypersensitivity pneumonitis (PREDICT) study. ERJ Open Res 2024; 10:00625-2023. [PMID: 38264150 PMCID: PMC10805267 DOI: 10.1183/23120541.00625-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/17/2023] [Indexed: 01/25/2024] Open
Abstract
Hypersensitivity pneumonitis is an immunologically mediated form of lung disease, resulting from inhalational exposure to a large variety of antigens. A subgroup of patients with fibrotic hypersensitivity pneumonitis (FHP) develop symptomatic, functional and radiographic disease progression. Mortality occurs primarily from respiratory failure as a result of progressive and self-sustaining lung injury that often occurs despite immunosuppression and removal of the inciting antigen. The development and validation of a prognostic transcriptomic signature for FHP (PREDICT-HP) is an observational multicentre cohort study designed to explore a transcriptomic signature from peripheral blood mononuclear cells in patients with FHP that is predictive of disease progression. This article describes the design and rationale of the PREDICT-HP study. This study will enrol ∼135 patients with FHP at approximately seven academic medical sites. Participants with a confirmed diagnosis of FHP are followed over 24 months and undergo physical examinations, self-administered questionnaires, chest computed tomography, pulmonary function tests, a 6-min walk test and blood testing for transcriptomic analyses. At each 6-month follow-up visit the study will assess the participants' clinical course and clinical events including hospitalisations and respiratory exacerbations. The PREDICT study has the potential to enhance our ability to predict disease progression and fundamentally advance our understanding of the pathobiology of FHP disease progression.
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Affiliation(s)
- Evans R. Fernández Pérez
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - Sonia M. Leach
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Brian Vestal
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
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Joannes A, Voisin T, Morzadec C, Letellier A, Gutierrez FL, Chiforeanu DC, Le Naoures C, Guillot S, De Latour BR, Rouze S, Jaillet M, Crestani B, Wollin L, Jouneau S, Vernhet L. Anti-fibrotic effects of nintedanib on lung fibroblasts derived from patients with Progressive Fibrosing Interstitial Lung Diseases (PF-ILDs). Pulm Pharmacol Ther 2023; 83:102267. [PMID: 37972706 DOI: 10.1016/j.pupt.2023.102267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/22/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
The tyrosine kinase inhibitor nintedanib has been recently approved for the treatment of Interstitial Lung Diseases (ILDs) that manifest a progressive fibrosis phenotype other than Idiopathic pulmonary Fibrosis (IPF). Nintedanib reduces the development of lung fibrosis in various animal models resembling features of PF-ILD and in vitro, it inhibits the fibrosing phenotype of human lung fibroblasts (HLFs) isolated from patients with IPF. To get insight on the cellular and molecular mechanisms that drive the clinical efficiency of nintedanib in patients with non-IPF PF-ILD, we investigated its effects on the fibrosing functions of HLFs derived from patients with PF-hypersensitivity pneumonitis (PF-HP, n = 7), PF-sarcoidosis (n = 5) and pleuroparenchymal fibroelastosis (PPFE, n = 4). HLFs were treated with nintedanib (10 nM-1 μM) and then stimulated with PDGF-BB (25-50 ng/ml) or TGF-β1 (1 ng/ml) for 24-72 h to assess proliferation and migration or differentiation. At nanomolar concentrations, nintedanib reduced the levels of PDGF receptor and ERK1/2 phosphorylation, the proliferation and the migration of PF-HP, PF-sarcoidosis and PPFE HLFs stimulated with PDGF-BB. Moreover, nintedanib also attenuates the myofibroblastic differentiation driven by TGF-β1 but only when it is used at 1 μM. The drug reduced the phosphorylation of SMAD2/3 and decreased the induction of collagen, fibronectin and α-smooth muscle actin expression induced by TGF-β1. In conclusion, our results demonstrate that nintedanib counteracts fundamental fibrosing functions of lung fibroblasts derived from patients with PF-HP, PF-sarcoidosis and PPFE, at concentrations previously reported to inhibit control and IPF HLFs. Such effects may contribute to its clinical benefit in patients suffering from these irreversible ILDs.
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Affiliation(s)
- Audrey Joannes
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000, Rennes, France.
| | - Tom Voisin
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000, Rennes, France
| | - Claudie Morzadec
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000, Rennes, France
| | - Alice Letellier
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000, Rennes, France
| | | | | | - Cécile Le Naoures
- Department of Pathology and Cytology, Rennes University Hospital, 35033, Rennes, France
| | - Stéphanie Guillot
- Department of Respiratory Physiology, Rennes University Hospital, 35033, Rennes, France
| | | | - Simon Rouze
- Department of Thoracic, Cardiac and Vascular Surgery, Rennes University Hospital, 35033, Rennes, France
| | - Madeleine Jaillet
- Faculté de Médecine Xavier Bichat, Université de Paris, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR1152, FHU APOLLO, Labex INFLAMEX, Paris, France
| | - Bruno Crestani
- Faculté de Médecine Xavier Bichat, Université de Paris, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR1152, FHU APOLLO, Labex INFLAMEX, Paris, France; Department of Pulmonology, AP-HP, Hôpital Bichat, FHU APOLLO, Inserm 1152, University of Paris, Paris, France
| | - Lutz Wollin
- Boehringer Ingelheim Pharma GmbH & Co, KG, Biberach an der Riss, Germany
| | - Stéphane Jouneau
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000, Rennes, France; Department of Respiratory Diseases, Competence Center for Rare Pulmonary Disease, Rennes University Hospital, 35033, Rennes, France
| | - Laurent Vernhet
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000, Rennes, France
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Mutsaers SE, Miles T, Prêle CM, Hoyne GF. Emerging role of immune cells as drivers of pulmonary fibrosis. Pharmacol Ther 2023; 252:108562. [PMID: 37952904 DOI: 10.1016/j.pharmthera.2023.108562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
The pathogenesis of pulmonary fibrosis, including idiopathic pulmonary fibrosis (IPF) and other forms of interstitial lung disease, involves a complex interplay of various factors including host genetics, environmental pollutants, infection, aberrant repair and dysregulated immune responses. Highly variable clinical outcomes of some ILDs, in particular IPF, have made it difficult to identify the precise mechanisms involved in disease pathogenesis and thus the development of a specific cure or treatment to halt and reverse the decline in patient health. With the advent of in-depth molecular diagnostics, it is becoming evident that the pathogenesis of IPF is unlikely to be the same for all patients and therefore will likely require different treatment approaches. Chronic inflammation is a cardinal feature of IPF and is driven by both innate and adaptive immune responses. Inflammatory cells and activated fibroblasts secrete various pro-inflammatory cytokines and chemokines that perpetuate the inflammatory response and contribute to the recruitment and activation of more immune cells and fibroblasts. The balance between pro-inflammatory and regulatory immune cell subsets, as well as the interactions between immune cell types and resident cells within the lung microenvironment, ultimately determines the extent of fibrosis and the potential for resolution. This review examines the role of the innate and adaptive immune responses in pulmonary fibrosis, with an emphasis on IPF. The role of different immune cell types is discussed as well as novel anti-inflammatory and immunotherapy approaches currently in clinical trial or in preclinical development.
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Affiliation(s)
- Steven E Mutsaers
- Institute for Respiratory Health, The University of Western Australia, Nedlands, WA, Australia.
| | - Tylah Miles
- Institute for Respiratory Health, The University of Western Australia, Nedlands, WA, Australia
| | - Cecilia M Prêle
- Institute for Respiratory Health, The University of Western Australia, Nedlands, WA, Australia; School of Medical, Molecular and Forensic Sciences, Murdoch University, WA, Australia
| | - Gerard F Hoyne
- Institute for Respiratory Health, The University of Western Australia, Nedlands, WA, Australia; The School of Health Sciences and Physiotherapy, University of Notre Dame Australia, Fremantle, WA, Australia
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8
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Russo RC, Quesniaux VFJ, Ryffel B. Homeostatic chemokines as putative therapeutic targets in idiopathic pulmonary fibrosis. Trends Immunol 2023; 44:1014-1030. [PMID: 37951789 DOI: 10.1016/j.it.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal chronic interstitial lung disease (ILD) that affects lung mechanical functions and gas exchange. IPF is caused by increased fibroblast activity and collagen deposition that compromise the alveolar-capillary barrier. Identifying an effective therapy for IPF remains a clinical challenge. Chemokines are key proteins in cell communication that have functions in immunity as well as in tissue homeostasis, damage, and repair. Chemokine receptor signaling induces the activation and proliferation of lung-resident cells, including alveolar macrophages (AMs) and fibroblasts. AMs are an important source of chemokines and cytokines during IPF. We highlight the complexity of this system and, based on insights from genetic and transcriptomic studies, propose a new role for homeostatic chemokine imbalance in IPF, with implications for putative therapeutic targets.
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Affiliation(s)
- Remo C Russo
- Laboratory of Pulmonary Immunology and Mechanics, Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil.
| | - Valerie F J Quesniaux
- Experimental and Molecular Immunology and Neurogenetics (INEM), Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7355, University of Orleans, Orleans 45071, France.
| | - Bernhard Ryffel
- Experimental and Molecular Immunology and Neurogenetics (INEM), Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7355, University of Orleans, Orleans 45071, France.
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Lv W, Mao H, Ruan Y, Li S, Shimizu K, Zhang L, Zhang C. Identification and immunological characterization of PLA2G2A and cell death-associated molecular clusters in idiopathic pulmonary fibrosis. Life Sci 2023; 331:122071. [PMID: 37673297 DOI: 10.1016/j.lfs.2023.122071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/31/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
AIMS Idiopathic pulmonary fibrosis (IPF) is a severe pulmonary interstitial pneumonia. Our study focuses on the role of PLA2 enzyme in the IPF to explore a more effective diagnosis and treatment mechanism of IPF. MAIN METHODS Transcriptome data of IPF from GEO database and bleomycin-induced pulmonary fibrosis mice were analyzed to identify PLA2 enzyme and their metabolite, lysophosphatidylcholines 18:0, in IPF. Based on PLA2G2A and PLA2G2D / PLA2G2A-associated cell death genes (PCDs), the consensus clustering analysis was used to identify the subtypes of IPF and the correlation between PLA2G2A and prognosis was analyzed. The machine learning (ML) models and artificial neural network (ANN) model was used to validate the diagnostic accuracy of PLA2s and PCDs in diagnosing IPF. The gene and protein expression of NLRP3, GSDMD, and CASP-1 was estimated in recombinant PLA2G2A protein induced MLE-12 cells. KEY FINDINGS The expression of PLA2G2D, PLA2G2A, and LPC18 significantly changed in IPF. Furtherly, PLA2G2A has a significant correlation with poor patient prognosis, which could predict the 2 or 3-years mortality rates of IPF. Two subtypes of IPF patients, identified based on PCDs, showed significant different immunoinfiltration. Recombinant PLA2G2A protein could induce the pyrotosis in the MLE-12 cell. The generalized linear model and ANN model of PLA2s or PCDs accurate diagnosis IPF. SIGNIFICANCE PLA2G2A is the most robustly associated gene with IPF among the PLA2s, which demonstrates a potential in diagnosing and prognostic value in IPF, and provides a foundation for further understanding and breakthroughs in IPF diagnosis and treatment.
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Affiliation(s)
- Weichao Lv
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Hongcai Mao
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yang Ruan
- Laboratory of Systematic Forest and Forest Products Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Shuaiyu Li
- Saigo Laboratory, School of Information Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Kuniyoshi Shimizu
- Laboratory of Systematic Forest and Forest Products Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Louqian Zhang
- Department of Thoratic Surgery, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, Jiangsu, China.
| | - Chaofeng Zhang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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10
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WANG J, LU L, HE X, MA L, CHEN T, LI G, YU H. [Identification of SULF1 as a Shared Gene in Idiopathic Pulmonary Fibrosis
and Lung Adenocarcinoma]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2023; 26:669-683. [PMID: 37985153 PMCID: PMC10600753 DOI: 10.3779/j.issn.1009-3419.2023.101.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is an idiopathic chronic, progressive interstitial lung disease with a diagnosed median survival of 3-5 years. IPF is associated with an increased risk of lung cancer. Therefore, exploring the shared pathogenic genes and molecular pathways between IPF and lung adenocarcinoma (LUAD) holds significant importance for the development of novel therapeutic approaches and personalized precision treatment strategies for IPF combined with lung cancer. METHODS Bioinformatics analysis was conducted using publicly available gene expression datasets of IPF and LUAD from the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis was employed to identify common genes involved in the progression of both diseases, followed by functional enrichment analysis. Subsequently, additional datasets were used to pinpoint the core shared genes between the two diseases. The relationship between core shared genes and prognosis, as well as their expression patterns, clinical relevance, genetic characteristics, and immune-related functions in LUAD, were analyzed using The Cancer Genome Atlas (TCGA) database and single-cell RNA sequencing datasets. Finally, potential therapeutic drugs related to the identified genes were screened through drug databases. RESULTS A total of 529 shared genes between IPF and LUAD were identified. Among them, SULF1 emerged as a core shared gene associated with poor prognosis. It exhibited significantly elevated expression levels in LUAD tissues, concomitant with high mutation rates, genomic heterogeneity, and an immunosuppressive microenvironment. Subsequent single-cell RNA-seq analysis revealed that the high expression of SULF1 primarily originated from tumor-associated fibroblasts. This study further demonstrated an association between SULF1 expression and tumor drug sensitivity, and it identified potential small-molecule drugs targeting SULF1 highly expressed fibroblasts. CONCLUSIONS This study identified a set of shared molecular pathways and core genes between IPF and LUAD. Notably, SULF1 may serve as a potential immune-related biomarker and therapeutic target for both diseases.
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11
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Lv J, Gao H, Ma J, Liu J, Tian Y, Yang C, Li M, Zhao Y, Li Z, Zhang X, Zhu Y, Zhang J, Wu L. Dynamic atlas of immune cells reveals multiple functional features of macrophages associated with progression of pulmonary fibrosis. Front Immunol 2023; 14:1230266. [PMID: 37771586 PMCID: PMC10525351 DOI: 10.3389/fimmu.2023.1230266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/24/2023] [Indexed: 09/30/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial lung disease with a high mortality rate and unclarified aetiology. Immune response is elaborately regulated during the progression of IPF, but immune cells subsets are complicated which has not been detailed described during IPF progression. Therefore, in the current study, we sought to investigate the role of immune regulation by elaborately characterize the heterogeneous of immune cells during the progression of IPF. To this end, we performed single-cell profiling of lung immune cells isolated from four stages of bleomycin-induced pulmonary fibrosis-a classical mouse model that mimics human IPF. The results revealed distinct components of immune cells in different phases of pulmonary fibrosis and close communication between macrophages and other immune cells along with pulmonary fibrosis progression. Enriched signals of SPP1, CCL5 and CXCL2 were found between macrophages and other immune cells. The more detailed definition of the subpopulations of macrophages defined alveolar macrophages (AMs) and monocyte-derived macrophages (mo-Macs)-the two major types of primary lung macrophages-exhibited the highest heterogeneity and dynamic changes in expression of profibrotic genes during disease progression. Our analysis suggested that Gpnmb and Trem2 were both upregulated in macrophages and may play important roles in pulmonary fibrosis progression. Additionally, the metabolic status of AMs and mo-Macs varied with disease progression. In line with the published data on human IPF, macrophages in the mouse model shared some features regarding gene expression and metabolic status with that of macrophages in IPF patients. Our study provides new insights into the pathological features of profibrotic macrophages in the lung that will facilitate the identification of new targets for disease intervention and treatment of IPF.
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Affiliation(s)
- Jiaoyan Lv
- Institute for Immunology, Tsinghua-Peking Joint Centre for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Haoxiang Gao
- Department of Automation, Ministry of Education (MOE) Key Laboratory of Bioinformatics, Bioinformatics Division and Centre for Synthetic & Systems Biology, BNRist, Tsinghua University, Beijing, China
| | - Jie Ma
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Jiachen Liu
- Institute for Immunology, Tsinghua-Peking Joint Centre for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yujie Tian
- Institute for Immunology, Tsinghua-Peking Joint Centre for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Chunyuan Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Mansheng Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yue Zhao
- Annoroad Gene Technology (Beijing) Co., Ltd., Beijing, China
| | - Zhimin Li
- Annoroad Gene Technology (Beijing) Co., Ltd., Beijing, China
| | - Xuegong Zhang
- Department of Automation, Ministry of Education (MOE) Key Laboratory of Bioinformatics, Bioinformatics Division and Centre for Synthetic & Systems Biology, BNRist, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Jianhong Zhang
- Institute for Immunology, Tsinghua-Peking Joint Centre for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
| | - Li Wu
- Institute for Immunology, Tsinghua-Peking Joint Centre for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Beijing, China
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12
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Frommer ML, Langridge BJ, Awad L, Jasionowska S, Denton CP, Abraham DJ, Abu-Hanna J, Butler PEM. Single-Cell Analysis of ADSC Interactions with Fibroblasts and Endothelial Cells in Scleroderma Skin. Cells 2023; 12:1784. [PMID: 37443817 PMCID: PMC10341100 DOI: 10.3390/cells12131784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Adipose-derived stem cells (ADSCs) as part of autologous fat grafting have anti-fibrotic and anti-inflammatory effects, but the exact mechanisms of action remain unknown. By simulating the interaction of ADSCs with fibroblasts and endothelial cells (EC) from scleroderma (SSc) skin in silico, we aim to unravel these mechanisms. Publicly available single-cell RNA sequencing data from the stromal vascular fraction of 3 lean patients and biopsies from the skin of 10 control and 12 patients with SSc were obtained from the GEO and analysed using R and Seurat. Differentially expressed genes were used to compare the fibroblast and EC transcriptome between controls and SSc. GO and KEGG functional enrichment was performed. Ligand-receptor interactions of ADSCs with fibroblasts and ECs were explored with LIANA. Pro-inflammatory and extracellular matrix (ECM) interacting fibroblasts were identified in SSc. Arterial, capillary, venous and lymphatic ECs showed a pro-fibrotic and pro-inflammatory transcriptome. Most interactions with both cell types were based on ECM proteins. Differential interactions identified included NTN1, VEGFD, MMP2, FGF2, and FNDC5. The ADSC secretome may disrupt vascular and perivascular inflammation hubs in scleroderma by promoting angiogenesis and especially lymphangiogenesis. Key phenomena observed after fat grafting remain unexplained, including modulation of fibroblast behaviour.
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Affiliation(s)
- Marvin L. Frommer
- Charles Wolfson Centre for Reconstructive Surgery, Royal Free Hospital, London NW3 2QG, UK; (B.J.L.); (J.A.-H.); (P.E.M.B.)
- Department of Surgical Biotechnology, Division of Surgery & Interventional Science, University College London, London NW3 2QG, UK
- Department of Plastic Surgery, Royal Free Hospital, London NW3 2QG, UK
| | - Benjamin J. Langridge
- Charles Wolfson Centre for Reconstructive Surgery, Royal Free Hospital, London NW3 2QG, UK; (B.J.L.); (J.A.-H.); (P.E.M.B.)
- Department of Surgical Biotechnology, Division of Surgery & Interventional Science, University College London, London NW3 2QG, UK
- Department of Plastic Surgery, Royal Free Hospital, London NW3 2QG, UK
| | - Laura Awad
- Charles Wolfson Centre for Reconstructive Surgery, Royal Free Hospital, London NW3 2QG, UK; (B.J.L.); (J.A.-H.); (P.E.M.B.)
- Department of Plastic Surgery, Royal Free Hospital, London NW3 2QG, UK
| | - Sara Jasionowska
- Charles Wolfson Centre for Reconstructive Surgery, Royal Free Hospital, London NW3 2QG, UK; (B.J.L.); (J.A.-H.); (P.E.M.B.)
- Department of Plastic Surgery, Royal Free Hospital, London NW3 2QG, UK
| | - Christopher P. Denton
- Centre for Rheumatology, Department of Inflammation, Division of Medicine, University College London, London NW3 2QG, UK
| | - David J. Abraham
- Centre for Rheumatology, Department of Inflammation, Division of Medicine, University College London, London NW3 2QG, UK
| | - Jeries Abu-Hanna
- Charles Wolfson Centre for Reconstructive Surgery, Royal Free Hospital, London NW3 2QG, UK; (B.J.L.); (J.A.-H.); (P.E.M.B.)
- Division of Medical Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Peter E. M. Butler
- Charles Wolfson Centre for Reconstructive Surgery, Royal Free Hospital, London NW3 2QG, UK; (B.J.L.); (J.A.-H.); (P.E.M.B.)
- Department of Surgical Biotechnology, Division of Surgery & Interventional Science, University College London, London NW3 2QG, UK
- Department of Plastic Surgery, Royal Free Hospital, London NW3 2QG, UK
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13
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Dasgupta S, Das SS, Patidar S, Kajaria V, Chowdhury SR, Chaudhury K. Identification of Common Dysregulated Genes in COVID-19 and Hypersensitivity Pneumonitis: A Systems Biology and Machine Learning Approach. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:205-214. [PMID: 37062762 DOI: 10.1089/omi.2022.0171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
A comprehensive knowledge on systems biology of severe acute respiratory syndrome coronavirus 2 is crucial for differential diagnosis of COVID-19. Interestingly, the radiological and pathological features of COVID-19 mimic that of hypersensitivity pneumonitis (HP), another pulmonary fibrotic phenotype. This motivated us to explore the overlapping pathophysiology of COVID-19 and HP, if any, and using a systems biology approach. Two datasets were obtained from the Gene Expression Omnibus database (GSE147507 and GSE150910) and common differentially expressed genes (DEGs) for both diseases identified. Fourteen common DEGs, significantly altered in both diseases, were found to be implicated in complement activation and growth factor activity. A total of five microRNAs (hsa-miR-1-3p, hsa-miR-20a-5p, hsa-miR-107, hsa-miR-16-5p, and hsa-miR-34b-5p) and five transcription factors (KLF6, ZBTB7A, ELF1, NFIL3, and ZBT33) exhibited highest interaction with these common genes. Next, C3, CFB, MMP-9, and IL1A were identified as common hub genes for both COVID-19 and HP. Finally, these top-ranked genes (hub genes) were evaluated using random forest classifier to discriminate between the disease and control group (coronavirus disease 2019 [COVID-19] vs. controls, and HP vs. controls). This supervised machine learning approach demonstrated 100% and 87.6% accuracy in differentiating COVID-19 from controls, and HP from controls, respectively. These findings provide new molecular leads that inform COVID-19 and HP diagnostics and therapeutics research and innovation.
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Affiliation(s)
- Sanjukta Dasgupta
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Sankha Subhra Das
- Department of Human Genetics, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Sankalp Patidar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Vaibhav Kajaria
- Department of Pulmonology, Fortis Hospital Anandapur, Kolkata, India
| | | | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
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14
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Abstract
The human lung cellular portfolio, traditionally characterized by cellular morphology and individual markers, is highly diverse, with over 40 cell types and a complex branching structure highly adapted for agile airflow and gas exchange. While constant during adulthood, lung cellular content changes in response to exposure, injury, and infection. Some changes are temporary, but others are persistent, leading to structural changes and progressive lung disease. The recent advance of single-cell profiling technologies allows an unprecedented level of detail and scale to cellular measurements, leading to the rise of comprehensive cell atlas styles of reporting. In this review, we chronical the rise of cell atlases and explore their contributions to human lung biology in health and disease.
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Affiliation(s)
- Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, USA;
| | - Arnaud Marlier
- Department of Neurosurgery, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, USA;
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15
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Sakr N, Glazova O, Shevkova L, Onyanov N, Kaziakhmedova S, Shilova A, Vorontsova MV, Volchkov P. Characterizing and Quenching Autofluorescence in Fixed Mouse Adrenal Cortex Tissue. Int J Mol Sci 2023; 24:ijms24043432. [PMID: 36834842 PMCID: PMC9968082 DOI: 10.3390/ijms24043432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Tissue autofluorescence of fixed tissue sections is a major concern of fluorescence microscopy. The adrenal cortex emits intense intrinsic fluorescence that interferes with signals from fluorescent labels, resulting in poor-quality images and complicating data analysis. We used confocal scanning laser microscopy imaging and lambda scanning to characterize the mouse adrenal cortex autofluorescence. We evaluated the efficacy of tissue treatment methods in reducing the intensity of the observed autofluorescence, such as trypan blue, copper sulfate, ammonia/ethanol, Sudan Black B, TrueVIEWTM Autofluorescence Quenching Kit, MaxBlockTM Autofluorescence Reducing Reagent Kit, and TrueBlackTM Lipofuscin Autofluorescence Quencher. Quantitative analysis demonstrated autofluorescence reduction by 12-95%, depending on the tissue treatment method and excitation wavelength. TrueBlackTM Lipofuscin Autofluorescence Quencher and MaxBlockTM Autofluorescence Reducing Reagent Kit were the most effective treatments, reducing the autofluorescence intensity by 89-93% and 90-95%, respectively. The treatment with TrueBlackTM Lipofuscin Autofluorescence Quencher preserved the specific fluorescence signals and tissue integrity, allowing reliable detection of fluorescent labels in the adrenal cortex tissue. This study demonstrates a feasible, easy-to-perform, and cost-effective method to quench tissue autofluorescence and improve the signal-to-noise ratio in adrenal tissue sections for fluorescence microscopy.
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Affiliation(s)
- Nawar Sakr
- Endocrinology Research Centre, Moscow 117292, Russia
- Genome Engineering Lab, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
| | - Olga Glazova
- Endocrinology Research Centre, Moscow 117292, Russia
- Genome Engineering Lab, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
| | - Liudmila Shevkova
- Endocrinology Research Centre, Moscow 117292, Russia
- Genome Engineering Lab, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
| | - Nikita Onyanov
- Genome Engineering Lab, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
| | - Samira Kaziakhmedova
- Genome Engineering Lab, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
| | - Alena Shilova
- Faculty of Medicine, M.V. Lomonosov Moscow State University, 27-1, Lomonosovsky Prospect, Moscow 117192, Russia
| | - Maria V. Vorontsova
- Endocrinology Research Centre, Moscow 117292, Russia
- Genome Engineering Lab, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
| | - Pavel Volchkov
- Endocrinology Research Centre, Moscow 117292, Russia
- Genome Engineering Lab, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russia
- Correspondence:
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16
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Usual interstitial pneumonia as a stand-alone diagnostic entity: the case for a paradigm shift? THE LANCET. RESPIRATORY MEDICINE 2023; 11:188-196. [PMID: 36640788 DOI: 10.1016/s2213-2600(22)00475-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 01/13/2023]
Abstract
Usual interstitial pneumonia (UIP) is characterised by a distinctive morphological and radiological appearance that was considered the pathognomonic hallmark of idiopathic pulmonary fibrosis (IPF). However, this peculiar lung remodelling pattern is also seen in other fibrotic interstitial lung diseases, including hypersensitivity pneumonitis, and connective tissue diseases. In this Personal View, we advocate the designation of a UIP pattern as a single, discrete diagnostic entity, amalgamating its primary form and secondary processes in disorders such as hypersensitivity pneumonitis (hypersensitivity pneumonitis with UIP), rheumatoid arthritis (rheumatoid arthritis with UIP), and others. The current separation between primary and secondary UIP is in keeping with the view that every individual interstitial lung disease must be viewed as a separate entity but does not reflect striking similarities between primary and secondary UIP in the morphological or radiological appearance, clinical behaviour, pathogenic pathways, and the efficacy of anti-fibrotic therapy. We believe that the unification of UIP as a single diagnostic entity has undeniable advantages.
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17
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Chen JY, Yiu WH, Tang PMK, Tang SCW. New insights into fibrotic signaling in renal cell carcinoma. Front Cell Dev Biol 2023; 11:1056964. [PMID: 36910160 PMCID: PMC9996540 DOI: 10.3389/fcell.2023.1056964] [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: 09/29/2022] [Accepted: 01/17/2023] [Indexed: 02/23/2023] Open
Abstract
Fibrotic signaling plays a pivotal role in the development and progression of solid cancers including renal cell carcinoma (RCC). Intratumoral fibrosis (ITF) and pseudo-capsule (PC) fibrosis are significantly correlated to the disease progression of renal cell carcinoma. Targeting classic fibrotic signaling processes such as TGF-β signaling and epithelial-to-mesenchymal transition (EMT) shows promising antitumor effects both preclinically and clinically. Therefore, a better understanding of the pathogenic mechanisms of fibrotic signaling in renal cell carcinoma at molecular resolution can facilitate the development of precision therapies against solid cancers. In this review, we systematically summarized the latest updates on fibrotic signaling, from clinical correlation and molecular mechanisms to its therapeutic strategies for renal cell carcinoma. Importantly, we examined the reported fibrotic signaling on the human renal cell carcinoma dataset at the transcriptome level with single-cell resolution to assess its translational potential in the clinic.
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Affiliation(s)
- Jiao-Yi Chen
- Division of Nephrology, Department of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Wai-Han Yiu
- Division of Nephrology, Department of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Patrick Ming-Kuen Tang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Sydney Chi-Wai Tang
- Division of Nephrology, Department of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
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18
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Sirtuins and Hypoxia in EMT Control. Pharmaceuticals (Basel) 2022; 15:ph15060737. [PMID: 35745656 PMCID: PMC9228842 DOI: 10.3390/ph15060737] [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: 11/04/2021] [Revised: 05/25/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
Epithelial–mesenchymal transition (EMT), a physiological process during embryogenesis, can become pathological in the presence of different driving forces. Reduced oxygen tension or hypoxia is one of these forces, triggering a large number of molecular pathways with aberrant EMT induction, resulting in cancer and fibrosis onset. Both hypoxia-induced factors, HIF-1α and HIF-2α, act as master transcription factors implicated in EMT. On the other hand, hypoxia-dependent HIF-independent EMT has also been described. Recently, a new class of seven proteins with deacylase activity, called sirtuins, have been implicated in the control of both hypoxia responses, HIF-1α and HIF-2α activation, as well as EMT induction. Intriguingly, different sirtuins have different effects on hypoxia and EMT, acting as either activators or inhibitors, depending on the tissue and cell type. Interestingly, sirtuins and HIF can be activated or inhibited with natural or synthetic molecules. Moreover, recent studies have shown that these natural or synthetic molecules can be better conveyed using nanoparticles, representing a valid strategy for EMT modulation. The following review, by detailing the aspects listed above, summarizes the interplay between hypoxia, sirtuins, and EMT, as well as the possible strategies to modulate them by using a nanoparticle-based approach.
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19
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Wang J, Jiang M, Xiong A, Zhang L, Luo L, Liu Y, Liu S, Ran Q, Wu D, Xiong Y, He X, Leung ELH, Li G. Integrated analysis of single-cell and bulk RNA sequencing reveals pro-fibrotic PLA2G7 high macrophages in pulmonary fibrosis. Pharmacol Res 2022; 182:106286. [PMID: 35662628 DOI: 10.1016/j.phrs.2022.106286] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/09/2022] [Accepted: 05/29/2022] [Indexed: 10/18/2022]
Abstract
Pulmonary fibrosis (PF) is the pathological change of end-stage interstitial lung diseases with high mortality and limited therapeutic options. Lung macrophages have distinct subsets with divergent functions, and play critical roles in the pathogenesis of PF. In this study, integrative analysis of lung single-cell and bulk RNA-seq data from patients with fibrotic hypersensitivity pneumonitis and idiopathic pulmonary fibrosis was utilized to identify particular macrophage subsets during the development of PF. We find a specific macrophage subpopulation highly expressing PLA2G7 in fibrotic lungs. We performed additional single-cell RNA-seq analysis to identify analogous macrophage population in bleomycin (BLM)-induced mouse pulmonary fibrosis models. By in vitro and in vivo experiments, we further reveal the pro-fibrotic role for this PLA2G7high macrophage subset in fibroblast-to-myofibroblast transition (FMT) during pulmonary fibrosis. PLA2G7 promotes FMT via LPC/ATX/LPA/LPA2 axis in macrophages. Moreover, PLA2G7 is regulated by STAT1, and pharmacological inhibition of PLA2G7 by Darapladib ameliorates pulmonary fibrosis in BLM-induced mice. The results of this study support the view that PLA2G7high macrophage subpopulation contributes importantly to the pathogenesis of PF, which provides a potential way for targeted therapy.
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Affiliation(s)
- Junyi Wang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China; Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology, Taipa, Macao Special Administrative Region of China
| | - Manling Jiang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China; Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China
| | - Anying Xiong
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China; Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China
| | - Lei Zhang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China; Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology, Taipa, Macao Special Administrative Region of China
| | - Li Luo
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Yao Liu
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Shengbin Liu
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Qin Ran
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China; Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China
| | - Dehong Wu
- Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China
| | - Ying Xiong
- Department of Pulmonary and Critical Care Medicine, Sichuan Friendship Hospital, Chengdu, China
| | - Xiang He
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China; Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China.
| | - Elaine Lai-Han Leung
- Faculty of Health Sciences, University of Macau, Taipa, Macao Special Administrative Region of China.
| | - Guoping Li
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China; Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, Chengdu Third People's Hospital Branch of National Clinical Research Center for Respiratory Disease, Chengdu, China.
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