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Cabrera S, García-Vicente Á, Gutiérrez P, Sánchez A, Gaxiola M, Rodríguez-Bobadilla C, Selman M, Pardo A. Increased ER Stress and Unfolded Protein Response Activation in Epithelial and Inflammatory Cells in Hypersensitivity Pneumonitis. J Histochem Cytochem 2024; 72:289-307. [PMID: 38725414 PMCID: PMC11107439 DOI: 10.1369/00221554241251915] [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: 10/24/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024] Open
Abstract
Several types of cytotoxic insults disrupt endoplasmic reticulum (ER) homeostasis, cause ER stress, and activate the unfolded protein response (UPR). The role of ER stress and UPR activation in hypersensitivity pneumonitis (HP) has not been described. HP is an immune-mediated interstitial lung disease that develops following repeated inhalation of various antigens in susceptible and sensitized individuals. The aim of this study was to investigate the lung expression and localization of the key effectors of the UPR, BiP/GRP78, CHOP, and sXBP1 in HP patients compared with control subjects. Furthermore, we developed a mouse model of HP to determine whether ER stress and UPR pathway are induced during this pathogenesis. In human control lungs, we observed weak positive staining for BiP in some epithelial cells and macrophages, while sXBP1 and CHOP were negative. Conversely, strong BiP, sXBP1- and CHOP-positive alveolar and bronchial epithelial, and inflammatory cells were identified in HP lungs. We also found apoptosis and autophagy markers colocalization with UPR proteins in HP lungs. Similar results were obtained in lungs from an HP mouse model. Our findings suggest that the UPR pathway is associated with the pathogenesis of HP.
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Affiliation(s)
- Sandra Cabrera
- Laboratorio de Fibrosis, Unidad de Biopatología Pulmonar, Ciencias-INER, Universidad Nacional Autónoma de México, México City, México
| | - Ángeles García-Vicente
- Laboratorio de Fibrosis, Unidad de Biopatología Pulmonar, Ciencias-INER, Universidad Nacional Autónoma de México, México City, México
| | - Pamela Gutiérrez
- Laboratorio de Fibrosis, Unidad de Biopatología Pulmonar, Ciencias-INER, Universidad Nacional Autónoma de México, México City, México
| | - Andrea Sánchez
- Laboratorio de Fibrosis, Unidad de Biopatología Pulmonar, Ciencias-INER, Universidad Nacional Autónoma de México, México City, México
| | - Miguel Gaxiola
- Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas,” Mexico City, México
| | - Carolina Rodríguez-Bobadilla
- Laboratorio de Fibrosis, Unidad de Biopatología Pulmonar, Ciencias-INER, Universidad Nacional Autónoma de México, México City, México
| | - Moisés Selman
- Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas,” Mexico City, México
| | - Annie Pardo
- Laboratorio de Fibrosis, Unidad de Biopatología Pulmonar, Ciencias-INER, Universidad Nacional Autónoma de México, México City, México
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Liu W, Huang K, Yang XZ, Wang P. Transcriptomic and network analysis identifies shared and unique pathways and immune changes across fibrotic interstitial lung diseases. Aging (Albany NY) 2024; 16:3200-3230. [PMID: 38349858 DOI: 10.18632/aging.205530] [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: 08/07/2023] [Accepted: 12/01/2023] [Indexed: 02/15/2024]
Abstract
BACKGROUND Interstitial lung disease (ILD) encompasses a diverse group of disorders characterized by chronic inflammation and fibrosis of the pulmonary interstitium. Three ILDs, namely idiopathic pulmonary fibrosis (IPF), fibrotic hypersensitivity pneumonitis (fHP), and connective tissue disease-associated ILD (CTD-ILD), exhibit similar progressive fibrosis phenotypes, yet possess distinct etiologies, encouraging us to explore their different underlying mechanisms. METHODS Transcriptome data of fibrotic lung tissues from patients with IPF, fHP, and CTD-ILD were subjected to functional annotation, network, and pathway analyses. Additionally, we employed the xCell deconvolution algorithm to predict immune cell infiltration in patients with fibrotic ILDs and healthy controls. RESULTS We identified a shared progressive fibrosis-related module in these diseases which was related to extracellular matrix (ECM) degradation and production and potentially regulated by the p53 family transcription factors. In IPF, neuron-related processes emerged as a critical specific mechanism in functional enrichment. In fHP, we observed that B cell signaling and immunoglobulin A (IgA) production may act as predominant processes, which was further verified by B cell infiltration and the central role of CD19 gene. In CTD-ILD, active chemokine processes were enriched, and active dendritic cells (aDCs) were predicted to infiltrate the lung tissues. CONCLUSIONS This study revealed shared and specific molecular and cellular pathways among IPF, fHP, and CTD-ILD, providing a basis for understanding their pathogenesis and identifying potential therapeutic targets.
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Affiliation(s)
- Wenhao Liu
- Eight-Year Program of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Kangping Huang
- Eight-Year Program of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xin-Zhuang Yang
- Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine and Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Ping Wang
- Department of Pulmonary and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
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3
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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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4
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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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5
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Zheng Y, Schupp JC, Adams T, Clair G, Justet A, Ahangari F, Yan X, Hansen P, Carlon M, Cortesi E, Vermant M, Vos R, De Sadeleer LJ, Rosas IO, Pineda R, Sembrat J, Königshoff M, McDonough JE, Vanaudenaerde BM, Wuyts WA, Kaminski N, Ding J. Unagi: Deep Generative Model for Deciphering Cellular Dynamics and In-Silico Drug Discovery in Complex Diseases. RESEARCH SQUARE 2023:rs.3.rs-3676579. [PMID: 38196613 PMCID: PMC10775382 DOI: 10.21203/rs.3.rs-3676579/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Human diseases are characterized by intricate cellular dynamics. Single-cell sequencing provides critical insights, yet a persistent gap remains in computational tools for detailed disease progression analysis and targeted in-silico drug interventions. Here, we introduce UNAGI, a deep generative neural network tailored to analyze time-series single-cell transcriptomic data. This tool captures the complex cellular dynamics underlying disease progression, enhancing drug perturbation modeling and discovery. When applied to a dataset from patients with Idiopathic Pulmonary Fibrosis (IPF), UNAGI learns disease-informed cell embeddings that sharpen our understanding of disease progression, leading to the identification of potential therapeutic drug candidates. Validation via proteomics reveals the accuracy of UNAGI's cellular dynamics analyses, and the use of the Fibrotic Cocktail treated human Precision-cut Lung Slices confirms UNAGI's predictions that Nifedipine, an antihypertensive drug, may have antifibrotic effects on human tissues. UNAGI's versatility extends to other diseases, including a COVID dataset, demonstrating adaptability and confirming its broader applicability in decoding complex cellular dynamics beyond IPF, amplifying its utility in the quest for therapeutic solutions across diverse pathological landscapes.
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Affiliation(s)
- Yumin Zheng
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, QC, Canada
- Meakins-Christie Laboratories, Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Jonas C. Schupp
- Pulmonary, Critical Care and Sleep Medicine, Yale University, School of Medicine, New Haven, CT, United States
| | - Taylor Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale University, School of Medicine, New Haven, CT, United States
| | - Geremy Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Aurelien Justet
- Pulmonary, Critical Care and Sleep Medicine, Yale University, School of Medicine, New Haven, CT, United States
| | - Farida Ahangari
- Pulmonary, Critical Care and Sleep Medicine, Yale University, School of Medicine, New Haven, CT, United States
| | - Xiting Yan
- Pulmonary, Critical Care and Sleep Medicine, Yale University, School of Medicine, New Haven, CT, United States
| | - Paul Hansen
- Meakins-Christie Laboratories, Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Marianne Carlon
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium
| | - Emanuela Cortesi
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium
| | - Marie Vermant
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium
| | - Robin Vos
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium
| | - Laurens J. De Sadeleer
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium
| | - Ivan O Rosas
- Division of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Ricardo Pineda
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John Sembrat
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Melanie Königshoff
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John E. McDonough
- Pulmonary, Critical Care and Sleep Medicine, Yale University, School of Medicine, New Haven, CT, United States
| | - Bart M. Vanaudenaerde
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium
| | - Wim A. Wuyts
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale University, School of Medicine, New Haven, CT, United States
| | - Jun Ding
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, QC, Canada
- Meakins-Christie Laboratories, Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Mila - Quebec AI Institute, Montreal, QC, Canada
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6
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Lang NJ, Gote-Schniering J, Porras-Gonzalez D, Yang L, De Sadeleer LJ, Jentzsch RC, Shitov VA, Zhou S, Ansari M, Agami A, Mayr CH, Hooshiar Kashani B, Chen Y, Heumos L, Pestoni JC, Molnar ES, Geeraerts E, Anquetil V, Saniere L, Wögrath M, Gerckens M, Lehmann M, Yildirim AÖ, Hatz R, Kneidinger N, Behr J, Wuyts WA, Stoleriu MG, Luecken MD, Theis FJ, Burgstaller G, Schiller HB. Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis. Sci Transl Med 2023; 15:eadh0908. [PMID: 38055803 DOI: 10.1126/scitranslmed.adh0908] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 11/16/2023] [Indexed: 12/08/2023]
Abstract
Pulmonary fibrosis develops as a consequence of failed regeneration after injury. Analyzing mechanisms of regeneration and fibrogenesis directly in human tissue has been hampered by the lack of organotypic models and analytical techniques. In this work, we coupled ex vivo cytokine and drug perturbations of human precision-cut lung slices (hPCLS) with single-cell RNA sequencing and induced a multilineage circuit of fibrogenic cell states in hPCLS. We showed that these cell states were highly similar to the in vivo cell circuit in a multicohort lung cell atlas from patients with pulmonary fibrosis. Using micro-CT-staged patient tissues, we characterized the appearance and interaction of myofibroblasts, an ectopic endothelial cell state, and basaloid epithelial cells in the thickened alveolar septum of early-stage lung fibrosis. Induction of these states in the hPCLS model provided evidence that the basaloid cell state was derived from alveolar type 2 cells, whereas the ectopic endothelial cell state emerged from capillary cell plasticity. Cell-cell communication routes in patients were largely conserved in hPCLS, and antifibrotic drug treatments showed highly cell type-specific effects. Our work provides an experimental framework for perturbational single-cell genomics directly in human lung tissue that enables analysis of tissue homeostasis, regeneration, and pathology. We further demonstrate that hPCLS offer an avenue for scalable, high-resolution drug testing to accelerate antifibrotic drug development and translation.
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Affiliation(s)
- Niklas J Lang
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Janine Gote-Schniering
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Rheumatology and Immunology, Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
- Lung Precision Medicine Program, Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Diana Porras-Gonzalez
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Lin Yang
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Laurens J De Sadeleer
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, 3000 Leuven, Belgium
| | - R Christoph Jentzsch
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Vladimir A Shitov
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Shuhong Zhou
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Meshal Ansari
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Ahmed Agami
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Christoph H Mayr
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Baharak Hooshiar Kashani
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Yuexin Chen
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Lukas Heumos
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Jeanine C Pestoni
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Eszter Sarolta Molnar
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | | | | | | | - Melanie Wögrath
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Michael Gerckens
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Mareike Lehmann
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute for Lung Research, Philipps-University Marburg, Universities of Giessen and Marburg Lung Center, Member of the German Center for Lung Research (DZL), 35043 Marburg, Germany
| | - Ali Önder Yildirim
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, 81377 Munich, Germany
| | - Rudolf Hatz
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich-Gauting, 82131 Gauting, Germany
| | - Nikolaus Kneidinger
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Jürgen Behr
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Wim A Wuyts
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, 3000 Leuven, Belgium
| | - Mircea-Gabriel Stoleriu
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich-Gauting, 82131 Gauting, Germany
| | - Malte D Luecken
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
- Department of Mathematics, Technische Universität München, 85748 Garching bei München, Germany
| | - Gerald Burgstaller
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Herbert B Schiller
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, 81377 Munich, Germany
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7
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He J, Hu J, Liu H. A three-gene random forest model for diagnosing idiopathic pulmonary fibrosis based on circadian rhythm-related genes in lung tissue. Expert Rev Respir Med 2023; 17:1307-1320. [PMID: 38285622 DOI: 10.1080/17476348.2024.2311262] [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: 12/13/2023] [Accepted: 01/24/2024] [Indexed: 01/31/2024]
Abstract
BACKGROUND The disorder of circadian rhythm could be a key factor mediating fibrotic lung disease Therefore, our study aims to determine the diagnostic value of circadian rhythm-related genes (CRRGs) in IPF. METHODS We retrieved the data on CRRGs from previous studies and the GSE150910 dataset. The participants from the GSE150910 dataset were divided into training and internal validation sets. Next, we used several various bioinformatics methods and machine learning algorithms to screen genes. Next, we identified SEMA5A, COL7A1, and TUBB3, which were included in the random forest (RF) diagnostic model. Finally, external validation was conducted on data retrieved from the GSE184316 datasets. RESULTS The results revealed that the RF diagnostic model could diagnose patients with IPF in the internal validation set with the area under the ROC curve (AUC) value of 0.905 and in the external validation with the AUC value of 0.767. Furthermore, real-time quantitative PCR and western blotting results revealed a significant decrease in SEMA5A (p < 0.05) expression level and an increase in COL7A1 and TUBB3 expression levels in TGF-β1-treated normal human lung fibroblasts. CONCLUSION We constructed an RF diagnostic model based on SEMA5A, COL7A1, and TUBB3 expression in lung tissue for diagnosing patients with IPF.
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Affiliation(s)
- Jie He
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Jun Hu
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Otolaryngology - Head and Neck Surgery, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Hairong Liu
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Geriatric Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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de Fays C, Geudens V, Gyselinck I, Kerckhof P, Vermaut A, Goos T, Vermant M, Beeckmans H, Kaes J, Van Slambrouck J, Mohamady Y, Willems L, Aversa L, Cortesi EE, Hooft C, Aerts G, Aelbrecht C, Everaerts S, McDonough JE, De Sadeleer LJ, Gohy S, Ambroise J, Janssens W, Ceulemans LJ, Van Raemdonck D, Vos R, Hackett TL, Hogg JC, Kaminski N, Gayan-Ramirez G, Pilette C, Vanaudenaerde BM. Mucosal immune alterations at the early onset of tissue destruction in chronic obstructive pulmonary disease. Front Immunol 2023; 14:1275845. [PMID: 37915582 PMCID: PMC10616299 DOI: 10.3389/fimmu.2023.1275845] [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: 08/10/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
Rationale COPD is characterized by chronic airway inflammation, small airways changes, with disappearance and obstruction, and also distal/alveolar destruction (emphysema). The chronology by which these three features evolve with altered mucosal immunity remains elusive. This study assessed the mucosal immune defense in human control and end-stage COPD lungs, by detailed microCT and RNA transcriptomic analysis of diversely affected zones. Methods In 11 control (non-used donors) and 11 COPD (end-stage) explant frozen lungs, 4 cylinders/cores were processed per lung for microCT and tissue transcriptomics. MicroCT was used to quantify tissue percentage and alveolar surface density to classify the COPD cores in mild, moderate and severe alveolar destruction groups, as well as to quantify terminal bronchioles in each group. Transcriptomics of each core assessed fold changes in innate and adaptive cells and pathway enrichment score between control and COPD cores. Immunostainings of immune cells were performed for validation. Results In mildly affected zones, decreased defensins and increased mucus production were observed, along CD8+ T cell accumulation and activation of the IgA pathway. In more severely affected zones, CD68+ myeloid antigen-presenting cells, CD4+ T cells and B cells, as well as MHCII and IgA pathway genes were upregulated. In contrast, terminal bronchioles were decreased in all COPD cores. Conclusion Spatial investigation of end-stage COPD lungs show that mucosal defense dysregulation with decreased defensins and increased mucus and IgA responses, start concomitantly with CD8+ T-cell accumulation in mild emphysema zones, where terminal bronchioles are already decreased. In contrast, adaptive Th and B cell activation is observed in areas with more advanced tissue destruction. This study suggests that in COPD innate immune alterations occur early in the tissue destruction process, which affects both the alveoli and the terminal bronchioles, before the onset of an adaptive immune response.
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Affiliation(s)
- Charlotte de Fays
- Pole of Pneumology, ENT, and Dermatology, Institute of Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Vincent Geudens
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Iwein Gyselinck
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Pieterjan Kerckhof
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Astrid Vermaut
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Tinne Goos
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Marie Vermant
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Hanne Beeckmans
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Janne Kaes
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Jan Van Slambrouck
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Yousry Mohamady
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Lynn Willems
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Lucia Aversa
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Emanuela E. Cortesi
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Charlotte Hooft
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Gitte Aerts
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Celine Aelbrecht
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Stephanie Everaerts
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - John E. McDonough
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Laurens J. De Sadeleer
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Sophie Gohy
- Pole of Pneumology, ENT, and Dermatology, Institute of Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium
- Department of Pneumology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Jerome Ambroise
- Centre de Technologies Moléculaires Appliquées, Institute of Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium
| | - Wim Janssens
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Laurens J. Ceulemans
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Dirk Van Raemdonck
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Robin Vos
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Tillie L. Hackett
- Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
| | - James C. Hogg
- Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Ghislaine Gayan-Ramirez
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Charles Pilette
- Pole of Pneumology, ENT, and Dermatology, Institute of Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium
- Department of Pneumology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Bart M. Vanaudenaerde
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
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Li F, Yang J, Li Y, Tan Z, Li H, Zhang N. Long non-coding RNA FENDRR suppresses cancer-associated fibroblasts and serves as a prognostic indicator in colorectal cancer. Transl Oncol 2023; 36:101740. [PMID: 37487432 PMCID: PMC10369470 DOI: 10.1016/j.tranon.2023.101740] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 07/26/2023] Open
Abstract
Genetically abnormal fibroblasts are notably more prevalent in colorectal cancer (CRC) than in adjacent normal tissue, emphasizing their significance in driving the heterogeneity of the tumor microenvironment. Functioning as a significant regulatory gene in the context of fibrosis, FOXF1 adjacent non-coding developmental regulatory RNA (FENDRR) has exhibited abnormal expression in colorectal cancer and interstitial localization in our experiments. However, current research on the role of FENDRR in cancer has focused solely on its impact on cancer cells. Its crucial role in the tumor stroma is yet to be explored. The goal of this study was to understand the relationship between atypical FENDRR expression, its distinct localization, and genetically abnormal fibroblasts in CRC. We aimed to establish the function of FENDRR within the stromal compartment of patients through bioinformatics. Our study confirmed that FENDRR suppresses cancer-associated fibroblasts by inhibiting their activation and collagen generation in CRC. Furthermore, our findings suggest that low FENDRR expression indicates a poor prognosis. Therefore, we propose that FENDRR is a promising therapeutic target for future studies in CRC.
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Affiliation(s)
- Fengxia Li
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jing Yang
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China
| | - Yankun Li
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Zhenyu Tan
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China
| | - Hui Li
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
| | - Nong Zhang
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
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10
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Adams TN, Batra K, Kypreos M, Glazer CS. Impact of radiographic honeycombing on transplant free survival and efficacy of immunosuppression in fibrotic hypersensitivity pneumonitis. BMC Pulm Med 2023; 23:224. [PMID: 37349780 DOI: 10.1186/s12890-023-02523-3] [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: 03/15/2023] [Accepted: 06/17/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND The distinction between hypersensitivity pneumonitis (HP) and idiopathic pulmonary fibrosis (IPF) was thought to be important due to the difference in mortality between the conditions as well as the response to treatment. However, recent work suggests that the clinical diagnosis may matter less than certain radiographic features, namely usual interstitial pneumonia (UIP) pattern. The purpose of this study is to evaluate whether radiographic honeycombing is more predictive of transplant-free survival (TFS) than other clinical, radiographic, or histologic findings that distinguish HP from IPF in the current guidelines and to evaluate the impact of radiographic honeycombing on the efficacy of immunosuppression in fibrotic HP. METHODS We retrospectively identified IPF and fibrotic HP patients evaluated between 2003 and 2019. Univariable and multivariable logistic regression was performed for patients with fibrotic HP and IPF to evaluate TFS. To assess the impact of treatment with immunosuppression on TFS in fibrotic HP, a cox proportional hazard model adjusted for known predictors of survival in HP including age, gender, and baseline pulmonary function testing results was constructed, and p-interaction for the presence of honeycombing on high resolution computed tomography and use of immunosuppression was calculated. RESULTS Our cohort included 178 with IPF and 198 with fibrotic HP. In a multivariable analysis, the presence of honeycombing had a greater impact on the TFS than the diagnosis of HP vs. IPF. Among the criteria used in the HP diagnostic guidelines, only typical HP scan impacted survival in a multivariable model, while identification of antigen and surgical lung biopsy findings had no impact on survival. We identified a trend toward worse survival on immunosuppression in those with HP with radiographic honeycombing. CONCLUSION Our data suggests that honeycombing and baseline pulmonary function testing have a greater impact on TFS than the clinical diagnosis of IPF vs. fibrotic HP and that radiographic honeycombing is a predictor of poor TFS in fibrotic HP. We suggest that invasive diagnostic testing including surgical lung biopsy may not be useful in predicting mortality in HP patients with honeycombing and may potentially increase risk of immunosuppression.
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Affiliation(s)
- Traci N Adams
- Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75219, USA.
| | - Kiran Batra
- Department of Radiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75219, USA
| | - Margaret Kypreos
- Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75219, USA
| | - Craig S Glazer
- Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75219, USA
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11
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Effendi WI, Nagano T. Epigenetics Approaches toward Precision Medicine for Idiopathic Pulmonary Fibrosis: Focus on DNA Methylation. Biomedicines 2023; 11:biomedicines11041047. [PMID: 37189665 DOI: 10.3390/biomedicines11041047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Genetic information is not transmitted solely by DNA but by the epigenetics process. Epigenetics describes molecular missing link pathways that could bridge the gap between the genetic background and environmental risk factors that contribute to the pathogenesis of pulmonary fibrosis. Specific epigenetic patterns, especially DNA methylation, histone modifications, long non-coding, and microRNA (miRNAs), affect the endophenotypes underlying the development of idiopathic pulmonary fibrosis (IPF). Among all the epigenetic marks, DNA methylation modifications have been the most widely studied in IPF. This review summarizes the current knowledge concerning DNA methylation changes in pulmonary fibrosis and demonstrates a promising novel epigenetics-based precision medicine.
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12
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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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13
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An integrative approach for identification of smoking-related genes involving bladder cancer. Arch Toxicol 2023; 97:177-188. [PMID: 36220961 DOI: 10.1007/s00204-022-03380-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/08/2022] [Indexed: 01/19/2023]
Abstract
Tobacco smoking is one of the most important environmental risk factors involving bladder tumorigenesis. However, smoking-related genes in bladder carcinogenesis and corresponding genetic effects on bladder cancer risk remain unclear. Weighted correlation network analysis (WGCNA) underlying transcriptome of bladder cancer tissues was applied to identify smoking-related genes. The logistic regression model was utilized to estimate genetic effects of single nucleotide polymorphisms (SNPs) in smoking-related genes on bladder cancer risk in the Chinese and European populations with a total of 6510 cases and 6569 controls, as well as the interaction with smoking status. Transcriptome of cells and tissues was used to profile the expression pattern of candidate genes and their genetic variants. Our results demonstrated that a total of 24 SNPs in 14 smoking-related genes were associated with the risk of bladder cancer, of which rs9348451 in CDKAL1 exhibited an interaction with smoking status (ORinteraction = 1.38, Pinteraction = 1.08 × 10-2) and tobacco smoking might combine with CDKAL1 rs9348451 to increase the risk of bladder cancer (Ptrend = 4.27 × 10-4). Moreover, rs9348451 was associated with CDKAL1 expression in bladder cancer, especially in smokers (P < 0.001). Besides, CDKAL1 was upregulated in bladder cancer compared to normal adjacent tissues, as well as upregulated via treatment of cigarette smoke extracts. This study highlights the important role of nurture and nature, as well as their interaction on tumorigenesis, which provides a new way to decipher the etiology of bladder cancer with smoking status.
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14
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Liu Q, Dong Y, Escames G, Wu X, Ren J, Yang W, Zhang S, Zhu Y, Tian Y, Acuña‐Castroviejo D, Yang Y. Identification of PIK3CG as a hub in septic myocardial injury using network pharmacology and weighted gene co-expression network analysis. Bioeng Transl Med 2022; 8:e10384. [PMID: 36684068 PMCID: PMC9842026 DOI: 10.1002/btm2.10384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/13/2022] [Accepted: 07/16/2022] [Indexed: 01/25/2023] Open
Abstract
Sepsis causes multiple organ injuries, among which the heart is one most severely damaged organ. Melatonin (MEL) alleviates septic myocardial injury, although a systematic and comprehensive approach is still lacking to understand the precise protective machinery of MEL. This study aimed to examine the underlying mechanisms of MEL on improvement of septic myocardial injury at a systematic level. This study integrated three analytic modalities including database investigations, RNA-seq analysis, and weighted gene co-expression network analysis (WCGNA), in order to acquire a set of genes associated with the pathogenesis of sepsis. The Drugbank database was employed to predict genes that may serve as pharmacological targets for MEL-elicited benefits, if any. A pharmacological protein-protein interaction network was subsequently constructed, and 66 hub genes were captured which were enriched in a variety of immune response pathways. Notably, PIK3CG, one of the hub genes, displayed high topological characteristic values, strongly suggesting its promise as a novel target for MEL-evoked treatment of septic myocardial injury. Importantly, molecular docking simulation experiments as well as in vitro and in vivo studies supported an essential role for PIK3CG in MEL-elicited effect on septic myocardial injury. This study systematically clarified the mechanisms of MEL intervention in septic myocardial injury involved multiple targets and multiple pathways. Moreover, PIK3CG-governed signaling cascade plays an important role in the etiology of sepsis and septic myocardial injury. Findings from our study provide valuable information on novel intervention targets for the management of septic myocardial injury. More importantly, this study has indicated the utility of combining a series of techniques for disease target discovery and exploration of possible drug targets, which should shed some light on elucidation of experimental and clinical drug action mechanisms systematically.
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Affiliation(s)
- Qiong Liu
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of Education, Faculty of life Science and Medicine, Northwest UniversityXi'anChina,Xi'an Key Laboratory of Cardiovascular and Cerebrovascular DiseasesXi'an No. 3 Hospital, The Affiliated Hospital of Northwest University, Faculty of life Science and Medicine, Northwest UniversityXi'anChina
| | - Yushu Dong
- Institute of Neuroscience, General Hospital of Northern Theater CommandShenyangChina
| | - Germaine Escames
- Biomedical Research Center, Health Sciences Technology ParkUniversity of GranadaGranadaSpain,Ibs. Granada, CIBERfesGranadaSpain,UGC of Clinical LaboratoriesUniversitu San Cecilio's HospitalGranadaSpain
| | - Xue Wu
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of Education, Faculty of life Science and Medicine, Northwest UniversityXi'anChina,Xi'an Key Laboratory of Cardiovascular and Cerebrovascular DiseasesXi'an No. 3 Hospital, The Affiliated Hospital of Northwest University, Faculty of life Science and Medicine, Northwest UniversityXi'anChina
| | - Jun Ren
- Department of CardiologyZhongshan Hospital, Fudan UniversityShanghaiChina,Shanghai Institute of Cardiovascular DiseasesShanghaiChina,Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Wenwen Yang
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of Education, Faculty of life Science and Medicine, Northwest UniversityXi'anChina,Xi'an Key Laboratory of Cardiovascular and Cerebrovascular DiseasesXi'an No. 3 Hospital, The Affiliated Hospital of Northwest University, Faculty of life Science and Medicine, Northwest UniversityXi'anChina
| | - Shaofei Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of Education, Faculty of life Science and Medicine, Northwest UniversityXi'anChina,Xi'an Key Laboratory of Cardiovascular and Cerebrovascular DiseasesXi'an No. 3 Hospital, The Affiliated Hospital of Northwest University, Faculty of life Science and Medicine, Northwest UniversityXi'anChina
| | - Yanli Zhu
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of Education, Faculty of life Science and Medicine, Northwest UniversityXi'anChina,Xi'an Key Laboratory of Cardiovascular and Cerebrovascular DiseasesXi'an No. 3 Hospital, The Affiliated Hospital of Northwest University, Faculty of life Science and Medicine, Northwest UniversityXi'anChina
| | - Ye Tian
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of Education, Faculty of life Science and Medicine, Northwest UniversityXi'anChina,Xi'an Key Laboratory of Cardiovascular and Cerebrovascular DiseasesXi'an No. 3 Hospital, The Affiliated Hospital of Northwest University, Faculty of life Science and Medicine, Northwest UniversityXi'anChina
| | - Darío Acuña‐Castroviejo
- Biomedical Research Center, Health Sciences Technology ParkUniversity of GranadaGranadaSpain,Ibs. Granada, CIBERfesGranadaSpain,UGC of Clinical LaboratoriesUniversitu San Cecilio's HospitalGranadaSpain
| | - Yang Yang
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of Education, Faculty of life Science and Medicine, Northwest UniversityXi'anChina,Xi'an Key Laboratory of Cardiovascular and Cerebrovascular DiseasesXi'an No. 3 Hospital, The Affiliated Hospital of Northwest University, Faculty of life Science and Medicine, Northwest UniversityXi'anChina
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15
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Exogen allergische Alveolitis und Transkriptom. Pneumologie 2022. [DOI: 10.1055/a-1697-9898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Verleden SE, Braubach P, Werlein C, Plucinski E, Kuhnel MP, Snoeckx A, El Addouli H, Welte T, Haverich A, Laenger FP, Dettmer S, Pauwels P, Verplancke V, Van Schil PE, Lapperre T, Kwakkel-Van-Erp JM, Ackermann M, Hendriks JMH, Jonigk D. From Macroscopy to Ultrastructure: An Integrative Approach to Pulmonary Pathology. Front Med (Lausanne) 2022; 9:859337. [PMID: 35372395 PMCID: PMC8965844 DOI: 10.3389/fmed.2022.859337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022] Open
Abstract
Pathology and radiology are complimentary tools, and their joint application is often crucial in obtaining an accurate diagnosis in non-neoplastic pulmonary diseases. However, both come with significant limitations of their own: Computed Tomography (CT) can only visualize larger structures due to its inherent–relatively–poor resolution, while (histo) pathology is often limited due to small sample size and sampling error and only allows for a 2D investigation. An innovative approach of inflating whole lung specimens and subjecting these subsequently to CT and whole lung microCT allows for an accurate matching of CT-imaging and histopathology data of exactly the same areas. Systematic application of this approach allows for a more targeted assessment of localized disease extent and more specifically can be used to investigate early mechanisms of lung diseases on a morphological and molecular level. Therefore, this technique is suitable to selectively investigate changes in the large and small airways, as well as the pulmonary arteries, veins and capillaries in relation to the disease extent in the same lung specimen. In this perspective we provide an overview of the different strategies that are currently being used, as well as how this growing field could further evolve.
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Affiliation(s)
- Stijn E. Verleden
- Antwerp Surgical Training, Anatomy and Research Centre (ASTARC), Antwerp University, Antwerp, Belgium
- Division of Pneumology, University Hospital Antwerp, Edegem, Belgium
- Department of Thoracic and Vascular Surgery, University Hospital Antwerp, Edegem, Belgium
| | - Peter Braubach
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Institute for Pathology, Hannover Medical School, Hannover, Germany
| | | | - Edith Plucinski
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Institute for Pathology, Hannover Medical School, Hannover, Germany
| | - Mark P. Kuhnel
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Institute for Pathology, Hannover Medical School, Hannover, Germany
| | - Annemiek Snoeckx
- Division of Radiology, University Hospital Antwerp and University of Antwerp, Edegem, Belgium
| | - Haroun El Addouli
- Division of Radiology, University Hospital Antwerp and University of Antwerp, Edegem, Belgium
| | - Tobias Welte
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Division of Pneumology, Hannover Medical School, Hannover, Germany
| | - Axel Haverich
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Division of Thoracic Surgery, Hannover Medical School, Hannover, Germany
| | - Florian P. Laenger
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Institute for Pathology, Hannover Medical School, Hannover, Germany
| | - Sabine Dettmer
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Department of Radiology, Hannover Medical School, Hannover, Germany
| | - Patrick Pauwels
- Division of Pathology, University Hospital Antwerp, Edegem, Belgium
| | | | - Paul E. Van Schil
- Antwerp Surgical Training, Anatomy and Research Centre (ASTARC), Antwerp University, Antwerp, Belgium
- Department of Thoracic and Vascular Surgery, University Hospital Antwerp, Edegem, Belgium
| | - Therese Lapperre
- Division of Pneumology, University Hospital Antwerp, Edegem, Belgium
- Laboratory of Experimental Medicine and Pediatrics (LEMP), Antwerp University, Antwerp, Belgium
| | - Johanna M. Kwakkel-Van-Erp
- Division of Pneumology, University Hospital Antwerp, Edegem, Belgium
- Laboratory of Experimental Medicine and Pediatrics (LEMP), Antwerp University, Antwerp, Belgium
| | - Maximilian Ackermann
- Institute of Pathology and Department of Molecular Pathology, Helios University Clinic Wuppertal, University of Witten-Herdecke, Witten, Germany
- Institute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jeroen M. H. Hendriks
- Antwerp Surgical Training, Anatomy and Research Centre (ASTARC), Antwerp University, Antwerp, Belgium
- Department of Thoracic and Vascular Surgery, University Hospital Antwerp, Edegem, Belgium
| | - Danny Jonigk
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Institute for Pathology, Hannover Medical School, Hannover, Germany
- *Correspondence: Danny Jonigk
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17
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Yang MM, Wolters PJ. Cut from the Same Cloth: Similarities between Hypersensitivity Pneumonitis and Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2022; 205:4-6. [PMID: 34748715 PMCID: PMC8865579 DOI: 10.1164/rccm.202109-2211ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Monica M Yang
- Department of Medicine University of California San Francisco San Francisco, California
| | - Paul J Wolters
- Department of Medicine University of California San Francisco San Francisco, California
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