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Adewale AT, Sharma S, Mouawad J, Nguyen XX, Bradshaw AD, Feghali-Bostwick C. IGF-II Regulates Lysyl Oxidase Propeptide and Mediates its Effects in part via Basic Helix-Loop-Helix E40. Matrix Biol 2024:S0945-053X(24)00078-7. [PMID: 38852924 DOI: 10.1016/j.matbio.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/31/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Pulmonary fibrosis (PF) is a clinically severe and commonly fatal complication of Systemic Sclerosis (SSc). Our group has previously reported profibrotic roles for Insulin-like Growth Factor II (IGF-II) and Lysyl Oxidase (LOX) in SSc-PF. We sought to identify downstream regulatory mediators of IGF-II. In the present work, we show that SSc lung tissues have higher baseline levels of the total (N-glycosylated/unglycosylated) LOX-Propeptide (LOX-PP) than normal lung tissues. LOX-PP-mediated changes were consistent with the extracellular matrix (ECM) deregulation implicated in SSc-PF progression. Furthermore, Tolloid-like 1 (TLL1) and Bone Morphogenetic Protein 1 (BMP1), enzymes that can cleave ProLOX to release LOX-PP, were increased in SSc lung fibrosis and the bleomycin (BLM)-induced murine lung fibrosis model, respectively. In addition, IGF-II regulated the levels of ProLOX, active LOX, LOX-PP, BMP1, and isoforms of TLL1. The Class E Basic Helix-Loop-Helix protein 40 (BHLHE40) transcription factor localized to the nucleus in response to IGF-II. BHLHE40 silencing downregulated TLL1 isoforms and LOX-PP, and restored significant features of ECM deregulation triggered by IGF-II. Our findings indicate that IGF-II, BHLHE40, and LOX-PP may serve as targets of therapeutic intervention to halt SSc-PF progression.
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Affiliation(s)
- Adegboyega Timothy Adewale
- Medical Scientist Training Program; Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Shailza Sharma
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
| | - Joe Mouawad
- Medical Scientist Training Program; Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Xinh-Xinh Nguyen
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Amy D Bradshaw
- Medical Scientist Training Program; Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Carol Feghali-Bostwick
- Medical Scientist Training Program; Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
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2
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Xu K, Ding L, Li W, Wang Y, Ma S, Lian H, Pan X, Wan R, Zhao W, Yang J, Rosas I, Wang L, Yu G. Aging-Associated Metabolite Methylmalonic Acid Increases Susceptibility to Pulmonary Fibrosis. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00198-6. [PMID: 38849030 DOI: 10.1016/j.ajpath.2024.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 06/09/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease characterized by pulmonary fibroblast overactivation, resulting in the accumulation of abnormal extracellular matrix and lung parenchymal damage. Although the pathogenesis of IPF remains unclear, aging was proposed as the most prominent nongenetic risk factor. Previous studies have indicated that propionate metabolism undergoes reprogramming in the aging population, leading to the accumulation of the by-product methylmalonic acid (MMA). This study aims to explore alterations in propionate metabolism in IPF and the impact of the by-product MMA on pulmonary fibrosis. The present study revealed alterations in the expression of enzymes involved in propionate metabolism within IPF lung tissues, characterized by an increase in propionyl-CoA carboxylase and methylmalonyl-CoA epimerase expression, and a decrease in methylmalonyl-CoA mutase expression. Knockdown of methylmalonyl-CoA mutase, the key enzyme in propionate metabolism, in A549 cells induced a profibrotic phenotype and activated co-cultured fibroblasts. MMA exacerbated bleomycin-induced mouse lung fibrosis and induced a profibrotic phenotype in both epithelial cells and fibroblasts through activation of the canonical transforming growth factor-β/Smad pathway. Overall, our findings unveil an alteration of propionate metabolism in IPF, leading to MMA accumulation, thus exacerbating lung fibrosis through promoting profibrotic phenotypic transitions via the canonical transforming growth factor-β/Smad signaling pathway.
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Affiliation(s)
- Kai Xu
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Organ Fibrosis, Pingyuan Laboratory, College of Life Science, Henan Normal University, Xinxiang, China
| | - Linke Ding
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Organ Fibrosis, Pingyuan Laboratory, College of Life Science, Henan Normal University, Xinxiang, China
| | - Wenwen Li
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Organ Fibrosis, Pingyuan Laboratory, College of Life Science, Henan Normal University, Xinxiang, China
| | - Yaxuan Wang
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Organ Fibrosis, Pingyuan Laboratory, College of Life Science, Henan Normal University, Xinxiang, China
| | - Shuaichen Ma
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Organ Fibrosis, Pingyuan Laboratory, College of Life Science, Henan Normal University, Xinxiang, China
| | - Hui Lian
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Organ Fibrosis, Pingyuan Laboratory, College of Life Science, Henan Normal University, Xinxiang, China
| | - Xiaoyue Pan
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Organ Fibrosis, Pingyuan Laboratory, College of Life Science, Henan Normal University, Xinxiang, China
| | - Ruyan Wan
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Organ Fibrosis, Pingyuan Laboratory, College of Life Science, Henan Normal University, Xinxiang, China
| | - Weiming Zhao
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Organ Fibrosis, Pingyuan Laboratory, College of Life Science, Henan Normal University, Xinxiang, China
| | - Juntang Yang
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Organ Fibrosis, Pingyuan Laboratory, College of Life Science, Henan Normal University, Xinxiang, China
| | - Ivan Rosas
- Division of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, Texas
| | - Lan Wang
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Organ Fibrosis, Pingyuan Laboratory, College of Life Science, Henan Normal University, Xinxiang, China.
| | - Guoying Yu
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Organ Fibrosis, Pingyuan Laboratory, College of Life Science, Henan Normal University, Xinxiang, China.
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3
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Arvind M, Pattnaik B, Gheware A, Prakash YS, Srivastava M, Agrawal A, Bhatraju NK. Plausible role of INPP4A dysregulation in idiopathic pulmonary fibrosis. Physiol Rep 2024; 12:e16032. [PMID: 38720166 PMCID: PMC11078778 DOI: 10.14814/phy2.16032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/02/2024] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
INPP4A has been shown to be involved in the regulation of cell proliferation and apoptosis of multiple cell types including fibroblasts. Previous reports from our group have demonstrated the role of inositol polyphosphate 4-phosphatase Type I A (INPP4A) in these functions. Though existing evidences suggest a critical role for INPP4A in the maintenance of lung homeostasis, its role in chronic lung diseases is relatively under explored. In the current study, we made an attempt to understand the regulation of INPP4A in idiopathic pulmonary fibrosis (IPF). Through integration of relevant INPP4A gene expression data from public repositories with our results from in vitro experiments and mouse models, we show that INPP4A is altered in IPF. Interestingly, the direction of the change is dependent both on the disease stage and the region of the lung used. INPP4A was found to be upregulated when analyzed in lung sample representative of the whole lung, but was downregulated in the fibrotic regions of the lung. Similarly, INPP4A was found to be high, compared to controls, only in the early stage of the disease. Though the observed increase in INPP4A was found to be negatively correlated to physiological indices, FVC, and DLCO, of lung function, treatment with anti-INPP4A antibody worsened the condition in bleomycin treated mice. These contrasting results taken together are suggestive of a nuanced regulation of INPP4A in IPF which is dependent on the disease stage, cellular state and extent of fibrosis in the lung region being analyzed.
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Affiliation(s)
- Meghana Arvind
- Centre of Excellence for Translational Research In Asthma and Lung diseases (TRIAL)CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | - Bijay Pattnaik
- Centre of Excellence for Translational Research In Asthma and Lung diseases (TRIAL)CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Department of Pulmonary Critical Care and Sleep MedicineAll India Institute of Medical SciencesNew DelhiIndia
| | - Atish Gheware
- Centre of Excellence for Translational Research In Asthma and Lung diseases (TRIAL)CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
- Division of Pulmonary and Critical Care Medicine, Department of MedicineWashington University in St. LouisSt. LouisMissouriUSA
| | - Y. S. Prakash
- Department of Anaesthesiology and Perioperative MedicineMayo ClinicRochesterMinnesotaUSA
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
| | - Mousami Srivastava
- Centre of Excellence for Translational Research In Asthma and Lung diseases (TRIAL)CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Symbiosis Statistical Institute (SSI)Symbiosis International University (SIU)PuneMaharashtraIndia
| | - Anurag Agrawal
- Centre of Excellence for Translational Research In Asthma and Lung diseases (TRIAL)CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
- Trivedi School of BiosciencesAshoka UniversitySonipatHaryanaIndia
| | - Naveen Kumar Bhatraju
- Centre of Excellence for Translational Research In Asthma and Lung diseases (TRIAL)CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Trivedi School of BiosciencesAshoka UniversitySonipatHaryanaIndia
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Duch P, Díaz‐Valdivia N, Gabasa M, Ikemori R, Arshakyan M, Fernández‐Nogueira P, Llorente A, Teixido C, Ramírez J, Pereda J, Chuliá‐Peris L, Galbis JM, Hilberg F, Reguart N, Radisky DC, Alcaraz J. Aberrant TIMP-1 production in tumor-associated fibroblasts drives the selective benefits of nintedanib in lung adenocarcinoma. Cancer Sci 2024; 115:1505-1519. [PMID: 38476010 PMCID: PMC11093210 DOI: 10.1111/cas.16141] [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: 10/03/2023] [Revised: 02/01/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
The fibrotic tumor microenvironment is a pivotal therapeutic target. Nintedanib, a clinically approved multikinase antifibrotic inhibitor, is effective against lung adenocarcinoma (ADC) but not squamous cell carcinoma (SCC). Previous studies have implicated the secretome of tumor-associated fibroblasts (TAFs) in the selective effects of nintedanib in ADC, but the driving factor(s) remained unidentified. Here we examined the role of tissue inhibitor of metalloproteinase-1 (TIMP-1), a tumor-promoting cytokine overproduced in ADC-TAFs. To this aim, we combined genetic approaches with in vitro and in vivo preclinical models based on patient-derived TAFs. Nintedanib reduced TIMP-1 production more efficiently in ADC-TAFs than SCC-TAFs through a SMAD3-dependent mechanism. Cell culture experiments indicated that silencing TIMP1 in ADC-TAFs abolished the therapeutic effects of nintedanib on cancer cell growth and invasion, which were otherwise enhanced by the TAF secretome. Consistently, co-injecting ADC cells with TIMP1-knockdown ADC-TAFs into immunocompromised mice elicited a less effective reduction of tumor growth and invasion under nintedanib treatment compared to tumors bearing unmodified fibroblasts. Our results unveil a key mechanism underlying the selective mode of action of nintedanib in ADC based on the excessive production of TIMP-1 in ADC-TAFs. We further pinpoint reduced SMAD3 expression and consequent limited TIMP-1 production in SCC-TAFs as key for the resistance of SCC to nintedanib. These observations strongly support the emerging role of TIMP-1 as a critical regulator of therapy response in solid tumors.
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Affiliation(s)
- Paula Duch
- Department of Biomedicine, School of Medicine and Health Sciences, Unit of Biophysics and BioengineeringUniversity of BarcelonaBarcelonaSpain
| | - Natalia Díaz‐Valdivia
- Department of Biomedicine, School of Medicine and Health Sciences, Unit of Biophysics and BioengineeringUniversity of BarcelonaBarcelonaSpain
| | - Marta Gabasa
- Department of Biomedicine, School of Medicine and Health Sciences, Unit of Biophysics and BioengineeringUniversity of BarcelonaBarcelonaSpain
- Thoracic Oncology UnitHospital Clinic BarcelonaBarcelonaSpain
| | - Rafael Ikemori
- Department of Biomedicine, School of Medicine and Health Sciences, Unit of Biophysics and BioengineeringUniversity of BarcelonaBarcelonaSpain
| | - Marselina Arshakyan
- Department of Biomedicine, School of Medicine and Health Sciences, Unit of Biophysics and BioengineeringUniversity of BarcelonaBarcelonaSpain
| | - Patricia Fernández‐Nogueira
- Department of Biomedicine, School of Medicine and Health Sciences, Unit of Biophysics and BioengineeringUniversity of BarcelonaBarcelonaSpain
| | - Alejandro Llorente
- Department of Biomedicine, School of Medicine and Health Sciences, Unit of Biophysics and BioengineeringUniversity of BarcelonaBarcelonaSpain
| | - Cristina Teixido
- Thoracic Oncology UnitHospital Clinic BarcelonaBarcelonaSpain
- Pathology ServiceHospital Clinic BarcelonaBarcelonaSpain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
| | - Josep Ramírez
- Thoracic Oncology UnitHospital Clinic BarcelonaBarcelonaSpain
- Pathology ServiceHospital Clinic BarcelonaBarcelonaSpain
- Biomedical Research Center Network for Respiratory Diseases (CIBERES)Carlos III Health InstituteMadridSpain
| | - Javier Pereda
- Department of Physiology, Faculty of PharmacyUniversity of ValenciaBurjassotSpain
| | - Lourdes Chuliá‐Peris
- Department of Physiology, Faculty of PharmacyUniversity of ValenciaBurjassotSpain
| | | | - Frank Hilberg
- Boehringer Ingelheim Austria RCV GmbH & Co. KGViennaAustria
| | - Noemí Reguart
- Thoracic Oncology UnitHospital Clinic BarcelonaBarcelonaSpain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
| | | | - Jordi Alcaraz
- Department of Biomedicine, School of Medicine and Health Sciences, Unit of Biophysics and BioengineeringUniversity of BarcelonaBarcelonaSpain
- Thoracic Oncology UnitHospital Clinic BarcelonaBarcelonaSpain
- Biomedical Research Center Network for Respiratory Diseases (CIBERES)Carlos III Health InstituteMadridSpain
- Institute for Bioengineering of Catalonia (IBEC)The Barcelona Institute for Science and Technology (BIST)BarcelonaSpain
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5
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Sage SE, Leeb T, Jagannathan V, Gerber V. Single-cell profiling of bronchoalveolar cells reveals a Th17 signature in neutrophilic severe equine asthma. Immunology 2024; 171:549-565. [PMID: 38153159 DOI: 10.1111/imm.13745] [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: 08/03/2023] [Accepted: 12/10/2023] [Indexed: 12/29/2023] Open
Abstract
Severe equine asthma (SEA) is a complex respiratory condition characterized by chronic airway inflammation. It shares many clinical and pathological features with human neutrophilic asthma, making it a valuable model for studying this condition. However, the immune mechanisms driving SEA have remained elusive. Although SEA has been primarily associated with a Th2 response, there have also been reports of Th1, Th17, or mixed-mediated responses. To uncover the elusive immune mechanisms driving SEA, we performed single-cell mRNA sequencing (scRNA-seq) on cryopreserved bronchoalveolar cells from 11 Warmblood horses, 5 controls and 6 with SEA. We identified six major cell types, including B cells, T cells, monocytes-macrophages, dendritic cells, neutrophils, and mast cells. All cell types exhibited significant heterogeneity, with previously identified and novel cell subtypes. Notably, we observed monocyte-lymphocyte complexes and detected a robust Th17 signature in SEA, with CXCL13 upregulation in intermediate monocytes. Asthmatic horses exhibited expansion of the B-cell population, Th17 polarization of the T-cell populations, and dysregulation of genes associated with T-cell function. Neutrophils demonstrated enhanced migratory capacity and heightened aptitude for neutrophil extracellular trap formation. These findings provide compelling evidence for a predominant Th17 immune response in neutrophilic SEA, driven by dysregulation of monocyte and T-cell genes. The dysregulated genes identified through scRNA-seq have potential as biomarkers and therapeutic targets for SEA and provide insights into human neutrophilic asthma.
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Affiliation(s)
- Sophie E Sage
- Department of Clinical Veterinary Medicine, Vetsuisse Faculty, Swiss Institute of Equine Medicine, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Vinzenz Gerber
- Department of Clinical Veterinary Medicine, Vetsuisse Faculty, Swiss Institute of Equine Medicine, University of Bern, Bern, Switzerland
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6
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Pattaroni C, Begka C, Cardwell B, Jaffar J, Macowan M, Harris NL, Westall GP, Marsland BJ. Multi-omics integration reveals a nonlinear signature that precedes progression of lung fibrosis. Clin Transl Immunology 2024; 13:e1485. [PMID: 38269243 PMCID: PMC10807351 DOI: 10.1002/cti2.1485] [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: 08/28/2023] [Revised: 12/11/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
Objectives Idiopathic pulmonary fibrosis (IPF) is a devastating progressive interstitial lung disease with poor outcomes. While decades of research have shed light on pathophysiological mechanisms associated with the disease, our understanding of the early molecular events driving IPF and its progression is limited. With this study, we aimed to model the leading edge of fibrosis using a data-driven approach. Methods Multiple omics modalities (transcriptomics, metabolomics and lipidomics) of healthy and IPF lung explants representing different stages of fibrosis were combined using an unbiased approach. Multi-Omics Factor Analysis of datasets revealed latent factors specifically linked with established fibrotic disease (Factor1) and disease progression (Factor2). Results Features characterising Factor1 comprised well-established hallmarks of fibrotic disease such as defects in surfactant, epithelial-mesenchymal transition, extracellular matrix deposition, mitochondrial dysfunction and purine metabolism. Comparatively, Factor2 identified a signature revealing a nonlinear trajectory towards disease progression. Molecular features characterising Factor2 included genes related to transcriptional regulation of cell differentiation, ciliogenesis and a subset of lipids from the endocannabinoid class. Machine learning models, trained upon the top transcriptomics features of each factor, accurately predicted disease status and progression when tested on two independent datasets. Conclusion This multi-omics integrative approach has revealed a unique signature which may represent the inflection point in disease progression, representing a promising avenue for the identification of therapeutic targets aimed at addressing the progressive nature of the disease.
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Affiliation(s)
- Céline Pattaroni
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Christina Begka
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Bailey Cardwell
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Jade Jaffar
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Matthew Macowan
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Nicola L Harris
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Glen P Westall
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
- Department of Respiratory MedicineAlfred HospitalMelbourneVICAustralia
| | - Benjamin J Marsland
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
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7
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Zhang C, Chen L, Xie C, Wang F, Wang J, Zhou H, Liu Q, Zeng Z, Li N, Huang J, Zhao Y, Liu H. YTHDC1 delays cellular senescence and pulmonary fibrosis by activating ATR in an m6A-independent manner. EMBO J 2024; 43:61-86. [PMID: 38177310 PMCID: PMC10883269 DOI: 10.1038/s44318-023-00003-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 09/23/2023] [Accepted: 10/26/2023] [Indexed: 01/06/2024] Open
Abstract
Accumulation of DNA damage in the lung induces cellular senescence and promotes age-related diseases such as idiopathic pulmonary fibrosis (IPF). Hence, understanding the mechanistic regulation of DNA damage repair is important for anti-aging therapies and disease control. Here, we identified an m6A-independent role of the RNA-binding protein YTHDC1 in counteracting stress-induced pulmonary senescence and fibrosis. YTHDC1 is primarily expressed in pulmonary alveolar epithelial type 2 (AECII) cells and its AECII expression is significantly decreased in AECIIs during fibrosis. Exogenous overexpression of YTHDC1 alleviates pulmonary senescence and fibrosis independent of its m6A-binding ability, while YTHDC1 deletion enhances disease progression in mice. Mechanistically, YTHDC1 promotes the interaction between TopBP1 and MRE11, thereby activating ATR and facilitating DNA damage repair. These findings reveal a noncanonical function of YTHDC1 in delaying cellular senescence, and suggest that enhancing YTHDC1 expression in the lung could be an effective treatment strategy for pulmonary fibrosis.
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Affiliation(s)
- Canfeng Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Liping Chen
- The Center for Medical Research, The First People's Hospital of Nanning City, Nanning, 530021, China
| | - Chen Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Fengwei Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Juan Wang
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Haoxian Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Qianyi Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhuo Zeng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Na Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Haiying Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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8
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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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9
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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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10
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Islam MA, Getz M, Macklin P, Ford Versypt AN. An agent-based modeling approach for lung fibrosis in response to COVID-19. PLoS Comput Biol 2023; 19:e1011741. [PMID: 38127835 PMCID: PMC10769079 DOI: 10.1371/journal.pcbi.1011741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 01/05/2024] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
The severity of the COVID-19 pandemic has created an emerging need to investigate the long-term effects of infection on patients. Many individuals are at risk of suffering pulmonary fibrosis due to the pathogenesis of lung injury and impairment in the healing mechanism. Fibroblasts are the central mediators of extracellular matrix (ECM) deposition during tissue regeneration, regulated by anti-inflammatory cytokines including transforming growth factor beta (TGF-β). The TGF-β-dependent accumulation of fibroblasts at the damaged site and excess fibrillar collagen deposition lead to fibrosis. We developed an open-source, multiscale tissue simulator to investigate the role of TGF-β sources in the progression of lung fibrosis after SARS-CoV-2 exposure, intracellular viral replication, infection of epithelial cells, and host immune response. Using the model, we predicted the dynamics of fibroblasts, TGF-β, and collagen deposition for 15 days post-infection in virtual lung tissue. Our results showed variation in collagen area fractions between 2% and 40% depending on the spatial behavior of the sources (stationary or mobile), the rate of activation of TGF-β, and the duration of TGF-β sources. We identified M2 macrophages as primary contributors to higher collagen area fraction. Our simulation results also predicted fibrotic outcomes even with lower collagen area fraction when spatially-localized latent TGF-β sources were active for longer times. We validated our model by comparing simulated dynamics for TGF-β, collagen area fraction, and macrophage cell population with independent experimental data from mouse models. Our results showed that partial removal of TGF-β sources changed the fibrotic patterns; in the presence of persistent TGF-β sources, partial removal of TGF-β from the ECM significantly increased collagen area fraction due to maintenance of chemotactic gradients driving fibroblast movement. The computational findings are consistent with independent experimental and clinical observations of collagen area fractions and cell population dynamics not used in developing the model. These critical insights into the activity of TGF-β sources may find applications in the current clinical trials targeting TGF-β for the resolution of lung fibrosis.
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Affiliation(s)
- Mohammad Aminul Islam
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York, United States of America
| | - Michael Getz
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America
| | - Paul Macklin
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America
| | - Ashlee N. Ford Versypt
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York, United States of America
- Department of Biomedical Engineering, University at Buffalo, The State University of New York, Buffalo, New York, United States of America
- Institute for Artificial Intelligence and Data Science, University at Buffalo, The State University of New York, Buffalo, New York, United States of America
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11
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Blumhagen RZ, Kurche JS, Cool CD, Walts AD, Heinz D, Fingerlin TE, Yang IV, Schwartz DA. Spatially distinct molecular patterns of gene expression in idiopathic pulmonary fibrosis. Respir Res 2023; 24:287. [PMID: 37978501 PMCID: PMC10655274 DOI: 10.1186/s12931-023-02572-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/21/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a heterogeneous disease that is pathologically characterized by areas of normal-appearing lung parenchyma, active fibrosis (transition zones including fibroblastic foci) and dense fibrosis. Defining transcriptional differences between these pathologically heterogeneous regions of the IPF lung is critical to understanding the distribution and extent of fibrotic lung disease and identifying potential therapeutic targets. Application of a spatial transcriptomics platform would provide more detailed spatial resolution of transcriptional signals compared to previous single cell or bulk RNA-Seq studies. METHODS We performed spatial transcriptomics using GeoMx Nanostring Digital Spatial Profiling on formalin-fixed paraffin-embedded (FFPE) tissue from 32 IPF and 12 control subjects and identified 231 regions of interest (ROIs). We compared normal-appearing lung parenchyma and airways between IPF and controls with histologically normal lung tissue, as well as histologically distinct regions within IPF (normal-appearing lung parenchyma, transition zones containing fibroblastic foci, areas of dense fibrosis, and honeycomb epithelium metaplasia). RESULTS We identified 254 differentially expressed genes (DEGs) between IPF and controls in histologically normal-appearing regions of lung parenchyma; pathway analysis identified disease processes such as EIF2 signaling (important for cap-dependent mRNA translation), epithelial adherens junction signaling, HIF1α signaling, and integrin signaling. Within IPF, we identified 173 DEGs between transition and normal-appearing lung parenchyma and 198 DEGs between dense fibrosis and normal lung parenchyma; pathways dysregulated in both transition and dense fibrotic areas include EIF2 signaling pathway activation (upstream of endoplasmic reticulum (ER) stress proteins ATF4 and CHOP) and wound healing signaling pathway deactivation. Through cell deconvolution of transcriptome data and immunofluorescence staining, we confirmed loss of alveolar parenchymal signals (AGER, SFTPB, SFTPC), gain of secretory cell markers (SCGB3A2, MUC5B) as well as dysregulation of the upstream regulator ATF4, in histologically normal-appearing tissue in IPF. CONCLUSIONS Our findings demonstrate that histologically normal-appearing regions from the IPF lung are transcriptionally distinct when compared to similar lung tissue from controls with histologically normal lung tissue, and that transition zones and areas of dense fibrosis within the IPF lung demonstrate activation of ER stress and deactivation of wound healing pathways.
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Affiliation(s)
- Rachel Z Blumhagen
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St, Office M222D, Denver, CO, 80206, USA.
| | - Jonathan S Kurche
- Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO, 80045, USA
- Medical Service, Rocky Mountain Regional Veterans Administration Medical Center, 1700 N Wheeling St, Aurora, CO, 80045, USA
| | - Carlyne D Cool
- Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO, 80045, USA
- Department of Medicine, National Jewish Health, 1400 Jackson St, Denver, CO, 80206, USA
| | - Avram D Walts
- Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO, 80045, USA
| | - David Heinz
- Pathology Laboratory, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Tasha E Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St, Office M222D, Denver, CO, 80206, USA
| | - Ivana V Yang
- Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO, 80045, USA
| | - David A Schwartz
- Department of Medicine, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, Aurora, CO, 80045, USA
- Medical Service, Rocky Mountain Regional Veterans Administration Medical Center, 1700 N Wheeling St, Aurora, CO, 80045, USA
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12
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Islam MA, Getz M, Macklin P, Versypt ANF. An agent-based modeling approach for lung fibrosis in response to COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.10.03.510677. [PMID: 36238719 PMCID: PMC9558432 DOI: 10.1101/2022.10.03.510677] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The severity of the COVID-19 pandemic has created an emerging need to investigate the long-term effects of infection on patients. Many individuals are at risk of suffering pulmonary fibrosis due to the pathogenesis of lung injury and impairment in the healing mechanism. Fibroblasts are the central mediators of extracellular matrix (ECM) deposition during tissue regeneration, regulated by anti-inflammatory cytokines including transforming growth factor beta (TGF-β). The TGF-β-dependent accumulation of fibroblasts at the damaged site and excess fibrillar collagen deposition lead to fibrosis. We developed an open-source, multiscale tissue simulator to investigate the role of TGF-β sources in the progression of lung fibrosis after SARS-CoV-2 exposure, intracellular viral replication, infection of epithelial cells, and host immune response. Using the model, we predicted the dynamics of fibroblasts, TGF-β, and collagen deposition for 15 days post-infection in virtual lung tissue. Our results showed variation in collagen area fractions between 2% and 40% depending on the spatial behavior of the sources (stationary or mobile), the rate of activation of TGF-β, and the duration of TGF-β sources. We identified M2 macrophages as primary contributors to higher collagen area fraction. Our simulation results also predicted fibrotic outcomes even with lower collagen area fraction when spatially-localized latent TGF-β sources were active for longer times. We validated our model by comparing simulated dynamics for TGF-β, collagen area fraction, and macrophage cell population with independent experimental data from mouse models. Our results showed that partial removal of TGF-β sources changed the fibrotic patterns; in the presence of persistent TGF-β sources, partial removal of TGF-β from the ECM significantly increased collagen area fraction due to maintenance of chemotactic gradients driving fibroblast movement. The computational findings are consistent with independent experimental and clinical observations of collagen area fractions and cell population dynamics not used in developing the model. These critical insights into the activity of TGF-β sources may find applications in the current clinical trials targeting TGF-β for the resolution of lung fibrosis. Author summary COVID-19 survivors are at risk of lung fibrosis as a long-term effect. Lung fibrosis is the excess deposition of tissue materials in the lung that hinder gas exchange and can collapse the whole organ. We identified TGF-β as a critical regulator of fibrosis. We built a model to investigate the mechanisms of TGF-β sources in the process of fibrosis. Our results showed spatial behavior of sources (stationary or mobile) and their activity (activation rate of TGF-β, longer activation of sources) could lead to lung fibrosis. Current clinical trials for fibrosis that target TGF-β need to consider TGF-β sources' spatial properties and activity to develop better treatment strategies.
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13
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Yang DC, Hsu SW, Li JM, Oldham J, Chen CH. Spatial Decoding of Immune Cell Contribution to Fibroblastic Foci in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2023; 208:728-731. [PMID: 37487177 PMCID: PMC10515576 DOI: 10.1164/rccm.202303-0372le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/24/2023] [Indexed: 07/26/2023] Open
Affiliation(s)
- David C. Yang
- Division of Pulmonary, Critical Care, and Sleep Medicine and
| | - Ssu-Wei Hsu
- Division of Pulmonary, Critical Care, and Sleep Medicine and
- Division of Nephrology, Department of Internal Medicine, University of California, Davis, Davis, California; and
| | - Ji-Min Li
- Division of Pulmonary, Critical Care, and Sleep Medicine and
- Division of Nephrology, Department of Internal Medicine, University of California, Davis, Davis, California; and
| | - Justin Oldham
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Ching-Hsien Chen
- Division of Pulmonary, Critical Care, and Sleep Medicine and
- Division of Nephrology, Department of Internal Medicine, University of California, Davis, Davis, California; and
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14
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Bonatti M, Pitozzi V, Caruso P, Pontis S, Pittelli MG, Frati C, Mangiaracina C, Lagrasta CAM, Quaini F, Cantarella S, Ottonello S, Villetti G, Civelli M, Montanini B, Trevisani M. Time-course transcriptome analysis of a double challenge bleomycin-induced lung fibrosis rat model uncovers ECM homoeostasis-related translationally relevant genes. BMJ Open Respir Res 2023; 10:e001476. [PMID: 37730279 PMCID: PMC10510891 DOI: 10.1136/bmjresp-2022-001476] [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: 09/28/2022] [Accepted: 08/30/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is an irreversible disorder with a poor prognosis. The incomplete understanding of IPF pathogenesis and the lack of accurate animal models is limiting the development of effective treatments. Thus, the selection of clinically relevant animal models endowed with similarities with the human disease in terms of lung anatomy, cell biology, pathways involved and genetics is essential. The bleomycin (BLM) intratracheal murine model is the most commonly used preclinical assay to evaluate new potential therapies for IPF. Here, we present the findings derived from an integrated histomorphometric and transcriptomic analysis to investigate the development of lung fibrosis in a time-course study in a BLM rat model and to evaluate its translational value in relation to IPF. METHODS Rats were intratracheally injected with a double dose of BLM (days 0-4) and sacrificed at days 7, 14, 21, 28 and 56. Histomorphometric analysis of lung fibrosis was performed on left lung sections. Transcriptome profiling by RNAseq was performed on the right lung lobes and results were compared with nine independent human gene-expression IPF studies. RESULTS The histomorphometric and transcriptomic analyses provided a detailed overview in terms of temporal gene-expression regulation during the establishment and repair of the fibrotic lesions. Moreover, the transcriptomic analysis identified three clusters of differentially coregulated genes whose expression was modulated in a time-dependent manner in response to BLM. One of these clusters, centred on extracellular matrix (ECM)-related process, was significantly correlated with histological parameters and gene sets derived from human IPF studies. CONCLUSIONS The model of lung fibrosis presented in this study lends itself as a valuable tool for preclinical efficacy evaluation of new potential drug candidates. The main finding was the identification of a group of persistently dysregulated genes, mostly related to ECM homoeostasis, which are shared with human IPF.
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Affiliation(s)
- Martina Bonatti
- Department of Chemistry Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Department of Medicine Solna (MedS) and Center for Molecular Medicine (CMM), Karolinska Institutet, Solna, Sweden
| | - Vanessa Pitozzi
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | - Paola Caruso
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | - Silvia Pontis
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | | | - Caterina Frati
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | - Federico Quaini
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Simona Cantarella
- Department of Chemistry Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- DKFZ - German Cancer Research Center, Heidelberg, Germany
| | - Simone Ottonello
- Department of Chemistry Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gino Villetti
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | - Maurizio Civelli
- Corporate Preclinical R&D, Chiesi Farmaceutici SpA, Parma, Italy
| | - Barbara Montanini
- Department of Chemistry Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Interdepartmental Research Centre Biopharmanet-Tec, University of Parma, Parma, Italy
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15
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Moshkovitz N, Epstein Shochet G, Shitrit D. Prostaglandin E2 (PGE2) and Roflumilast Involvement in IPF Progression. Int J Mol Sci 2023; 24:12393. [PMID: 37569768 PMCID: PMC10418473 DOI: 10.3390/ijms241512393] [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: 06/29/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
The ECM propagates processes in idiopathic pulmonary fibrosis (IPF), leading to progressive lung scarring. We established an IPF-conditioned matrix (IPF-CM) system as a platform for testing drug candidates. Here, we tested the involvement of a PGE2 and PDE4 inhibitor, Roflumilast, in the IPF-CM system. Primary normal/IPF tissue-derived human lung fibroblasts (N/IPF-HLFs) were cultured on Matrigel and then removed to create the IPF-CM. N-HLFs were exposed to the IPF-CM/N-CM with/without PGE2 (1 nM) and Roflumilast (1 µM) for 24 h. The effect of the IPF-CM on cell phenotype and pro-fibrotic gene expression was tested. In addition, electronic records of 107 patients with up to 15-year follow-up were retrospectively reviewed. Patients were defined as slow/rapid progressors using forced vital capacity (FVC) annual decline. Medication exposure was examined. N-HLFs cultured on IPF-CM were arranged in large aggregates as a result of increased proliferation, migration and differentiation. A PGE2 and Roflumilast combination blocked the large aggregate formation induced by the IPF-CM (p < 0.001) as well as cell migration, proliferation, and pro-fibrotic gene expression. A review of patient records showed that significantly more slow-progressing patients were exposed to NSAIDs (p = 0.003). PGE2/PDE4 signaling may be involved in IPF progression. These findings should be further studied.
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Affiliation(s)
- Noa Moshkovitz
- Pulmonary Department, Meir Medical Center, Kfar Saba 44281, Israel; (N.M.); (G.E.S.)
| | - Gali Epstein Shochet
- Pulmonary Department, Meir Medical Center, Kfar Saba 44281, Israel; (N.M.); (G.E.S.)
| | - David Shitrit
- Pulmonary Department, Meir Medical Center, Kfar Saba 44281, Israel; (N.M.); (G.E.S.)
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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16
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Zhou H, Xie C, Xie Y, He Y, Chen Y, Zhang C, Zhang Y, Zhao Y, Liu H. UBQLN1 deficiency mediates telomere shortening and IPF through interacting with RPA1. PLoS Genet 2023; 19:e1010856. [PMID: 37463174 PMCID: PMC10381042 DOI: 10.1371/journal.pgen.1010856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
Premature telomere shortening is a known factor correlated to idiopathic pulmonary fibrosis (IPF) occurrence, which is a chronic, progressive, age-related disease with high mortality. The etiology of IPF is still unknown. Here, we found that UBQLN1 plays a key role in telomere length maintenance and is potentially relevant to IPF. UBQLN1 involves in DNA replication by interacting with RPA1 and shuttling it off from the replication fork. The deficiency of UBQLN1 retains RPA1 at replication fork, hinders replication and thus causes cell cycle arrest and genome instability. Especially at telomere regions of the genome, where more endogenous replication stress exists because of G rich sequences, UBQLN1 depletion leads to rapid telomere shortening in HeLa cells. It revealed that UBQLN1 depletion also shortens telomere length at mouse lung and accelerates mouse lung fibrosis. In addition, the UBQLN1 expression level in IPF patients is downregulated and correlated to poor prognosis. Altogether, these results uncover a new role of UBQLN1 in ensuring DNA replication and maintaining telomere stability, which may shed light on IPF pathogenesis and prevention.
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Affiliation(s)
- Haoxian Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Department of Cardiology, Guangdong Provincial Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Chen Xie
- Cardiovascular Department, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yujie Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yunru He
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanlian Chen
- Cardiovascular Department, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Canfeng Zhang
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yan Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Haiying Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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17
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Waldrep KM, Rodgers JI, Garrett SM, Wolf BJ, Feghali-Bostwick CA. The Role of SOX9 in IGF-II-Mediated Pulmonary Fibrosis. Int J Mol Sci 2023; 24:11234. [PMID: 37510994 PMCID: PMC10378869 DOI: 10.3390/ijms241411234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/29/2023] [Accepted: 07/02/2023] [Indexed: 07/30/2023] Open
Abstract
Pulmonary fibrosis (PF) associated with systemic sclerosis (SSc) results in significant morbidity and mortality. We previously reported that insulin-like growth factor-II (IGF-II) is overexpressed in lung tissues and fibroblasts from SSc patients, and IGF-II fosters fibrosis by upregulating collagen type I, fibronectin, and TGFβ. We now show that IGF-II augments mRNA levels of profibrotic signaling molecules TGFβ2 (p ≤ 0.01) and TGFβ3 (p ≤ 0.05), collagen type III (p ≤ 0.01), and the collagen posttranslational modification enzymes P4HA2 (p ≤ 0.05), P3H2 (p ≤ 0.05), LOX (p = 0.065), LOXL2 (p ≤ 0.05), LOXL4 (p ≤ 0.05) in primary human lung fibroblasts. IGF-II increases protein levels of TGFβ2 (p ≤ 0.01), as well as COL3A1, P4HA2, P4Hβ, and LOXL4 (p ≤ 0.05). In contrast, IGF-II decreases mRNA levels of the collagen degradation enzymes cathepsin (CTS) K, CTSB, and CTSL and protein levels of CTSK (p ≤ 0.05). The SRY-box transcription factor 9 (SOX9) is overexpressed in SSc lung tissues at the mRNA (p ≤ 0.05) and protein (p ≤ 0.01) levels compared to healthy controls. IGF-II induces SOX9 in lung fibroblasts (p ≤ 0.05) via the IGF1R/IR hybrid receptor, and SOX9 regulates TGFβ2 (p ≤ 0.05), TGFβ3 (p ≤ 0.05), COL3A1 (p ≤ 0.01), and P4HA2 (p ≤ 0.001) downstream of IGF-II. Our results identify a novel IGF-II signaling axis and downstream targets that are regulated in a SOX9-dependent and -independent manner. Our findings provide novel insights on the role of IGF-II in promoting pulmonary fibrosis.
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Affiliation(s)
- Kristy M Waldrep
- Department of Medicine, Rheumatology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Jessalyn I Rodgers
- Department of Medicine, Rheumatology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Sara M Garrett
- Department of Medicine, Rheumatology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Bethany J Wolf
- Department of Public Health Sciences, Biostatistics and Bioinformatics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Carol A Feghali-Bostwick
- Department of Medicine, Rheumatology, Medical University of South Carolina, Charleston, SC 29425, USA
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18
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Arif M, Basu A, Wolf KM, Park JK, Pommerolle L, Behee M, Gochuico BR, Cinar R. An Integrative Multiomics Framework for Identification of Therapeutic Targets in Pulmonary Fibrosis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207454. [PMID: 37038090 PMCID: PMC10238219 DOI: 10.1002/advs.202207454] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/26/2023] [Indexed: 06/04/2023]
Abstract
Pulmonary fibrosis (PF) is a heterogeneous disease with a poor prognosis. Therefore, identifying additional therapeutic modalities is required to improve outcome. However, the lack of biomarkers of disease progression hampers the preclinical to clinical translational process. Here, this work assesses and identifies progressive alterations in pulmonary function, transcriptomics, and metabolomics in the mouse lung at 7, 14, 21, and 28 days after a single dose of oropharyngeal bleomycin. By integrating multi-omics data, this work identifies two central gene subnetworks associated with multiple critical pathological changes in transcriptomics and metabolomics as well as pulmonary function. This work presents a multi-omics-based framework to establish a translational link between the bleomycin-induced PF model in mice and human idiopathic pulmonary fibrosis to identify druggable targets and test therapeutic candidates. This work also indicates peripheral cannabinoid receptor 1 (CB1 R) antagonism as a rational therapeutic target for clinical translation in PF. Mouse Lung Fibrosis Atlas can be accessed freely at https://niaaa.nih.gov/mouselungfibrosisatlas.
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Affiliation(s)
- Muhammad Arif
- Section on Fibrotic DisordersNational Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthRockvilleMD20852USA
- Laboratory of Cardiovascular Physiology and Tissue InjuryNational Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthRockvilleMD20852USA
| | - Abhishek Basu
- Section on Fibrotic DisordersNational Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthRockvilleMD20852USA
| | - Kaelin M. Wolf
- Section on Fibrotic DisordersNational Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthRockvilleMD20852USA
| | - Joshua K. Park
- Laboratory of Physiologic StudiesNational Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthRockvilleMD20852USA
| | - Lenny Pommerolle
- Section on Fibrotic DisordersNational Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthRockvilleMD20852USA
| | - Madeline Behee
- Section on Fibrotic DisordersNational Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthRockvilleMD20852USA
| | - Bernadette R. Gochuico
- Medical Genetics BranchNational Human Genome Research InstituteNational Institutes of Health (NIH)BethesdaMD20892USA
| | - Resat Cinar
- Section on Fibrotic DisordersNational Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthRockvilleMD20852USA
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19
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Zhang L, Huang Z, Wang F, Xue M, Zhang X, Wan Y, Ma L. POU Class 2 Associating Factor 1 Exerts a Protective Effect on the Respiratory Syncytial Virus-Induced Acute Bronchiolitis by the NF- κB Pathway. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2023; 2023:2815219. [PMID: 37260522 PMCID: PMC10229246 DOI: 10.1155/2023/2815219] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/11/2022] [Accepted: 07/29/2022] [Indexed: 06/02/2023]
Abstract
Background Respiratory syncytial virus (RSV) is the main pathogen causing acute bronchiolitis, which is common in infants and young children. A previous study revealed the possible involvement of POU class 2 associating factor 1 (POU2AF1) in RSV-triggered acute bronchiolitis. We attempted to clarify the specific action mechanism of POU2AF1 underlying RSV-triggered inflammation. Methods RT-qPCR measured POU2AF1 levels in RSV-infected children, mice, and airway epithelial cell lines (HBECs). HE staining showed histopathological features in the lung tissue of RSV-infected mice. ELISA examined the contents of proinflammatory cytokines in RSV-infected mice. Western blotting evaluated the protein abundance of proinflammatory cytokines in RSV-infected HBECs and assessed NF-κB pathway-associated protein expression in RSV-infected mice and RSV-treated HBECs. Results POU2AF1 presented depletion in RSV-infected children, mice, and HBECs. RSV-infected triggered lung injury and inflammatory cell infiltration in the mouse lung tissue, while POU2AF1 overexpression rescued these changes. RSV-infected induced inflammatory impairment in HBECs, whereas POU2AF1 reversed this effect. POU2AF1 suppressed the upregulated NF-κB pathway-associated protein expression in mice and HBECs under RSV infection. Conclusion POU2AF1 exerts a protective impact on RSV-induced acute bronchiolitis in vitro and in vivo through the NF-κB pathway. Our research may provide a novel direction for better therapy of RSV-triggered acute bronchiolitis.
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Affiliation(s)
- Liwen Zhang
- Department of Pediatrics, The Second People's Hospital of Changzhou, Affiliated Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| | - Zhiying Huang
- Department of Pediatrics, The Second People's Hospital of Changzhou, Affiliated Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| | - Fei Wang
- Department of Pediatrics, The Second People's Hospital of Changzhou, Affiliated Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| | - Mei Xue
- Department of Pediatrics, The Second People's Hospital of Changzhou, Affiliated Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| | - Xiaoyu Zhang
- Department of Pediatrics, The Second People's Hospital of Changzhou, Affiliated Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| | - Yu Wan
- Department of Pediatrics, The Second People's Hospital of Changzhou, Affiliated Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
| | - Liang Ma
- Department of Gastroenterology, The First People's Hospital of Changzhou, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
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20
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Jia M, Rosas L, Kapetanaki MG, Tabib T, Sebrat J, Cruz T, Bondonese A, Mora AL, Lafyatis R, Rojas M, Benos PV. Early events marking lung fibroblast transition to profibrotic state in idiopathic pulmonary fibrosis. Respir Res 2023; 24:116. [PMID: 37085855 PMCID: PMC10122312 DOI: 10.1186/s12931-023-02419-0] [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: 09/24/2022] [Accepted: 04/12/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Idiopathic Pulmonary Fibrosis (IPF) is an age-associated progressive lung disease with accumulation of scar tissue impairing gas exchange. Previous high-throughput studies elucidated the role of cellular heterogeneity and molecular pathways in advanced disease. However, critical pathogenic pathways occurring in the transition of fibroblasts from normal to profibrotic have been largely overlooked. METHODS We used single cell transcriptomics (scRNA-seq) from lungs of healthy controls and IPF patients (lower and upper lobes). We identified fibroblast subclusters, genes and pathways associated with early disease. Immunofluorescence assays validated the role of MOXD1 early in fibrosis. RESULTS We identified four distinct fibroblast subgroups, including one marking the normal-to-profibrotic state transition. Our results show for the first time that global downregulation of ribosomal proteins and significant upregulation of the majority of copper-binding proteins, including MOXD1, mark the IPF transition. We find no significant differences in gene expression in IPF upper and lower lobe samples, which were selected to have low and high degree of fibrosis, respectively. CONCLUSIONS Early events during IPF onset in fibroblasts include dysregulation of ribosomal and copper-binding proteins. Fibroblasts in early stage IPF may have already acquired a profibrotic phenotype while hallmarks of advanced disease, including fibroblast foci and honeycomb formation, are still not evident. The new transitional fibroblasts we discover could prove very important for studying the role of fibroblast plasticity in disease progression and help develop early diagnosis tools and therapeutic interventions targeting earlier disease states.
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Affiliation(s)
- Minxue Jia
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
- Joint Carnegie Mellon University – University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, USA
| | - Lorena Rosas
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Maria G. Kapetanaki
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - John Sebrat
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Tamara Cruz
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Anna Bondonese
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Ana L. Mora
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Mauricio Rojas
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
- Joint Carnegie Mellon University – University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, USA
- Department of Epidemiology, University of Florida, 2004 Mowry Rd, Gainesville, FL 32610 USA
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21
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Verleden SE, Vanstapel A, Jacob J, Goos T, Hendriks J, Ceulemans LJ, Van Raemdonck DE, De Sadeleer L, Vos R, Kwakkel-van Erp JM, Neyrinck AP, Verleden GM, Boone MN, Janssens W, Wauters E, Weynand B, Jonigk DD, Verschakelen J, Wuyts WA. Radiologic and Histologic Correlates of Early Interstitial Lung Changes in Explanted Lungs. Radiology 2023; 307:e221145. [PMID: 36537894 PMCID: PMC7614383 DOI: 10.1148/radiol.221145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/13/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022]
Abstract
Background Interstitial lung abnormalities (ILAs) reflect imaging features on lung CT scans that are compatible with (early) interstitial lung disease. Despite accumulating evidence regarding the incidence, risk factors, and prognosis of ILAs, the histopathologic correlates of ILAs remain elusive. Purpose To determine the correlation between radiologic and histopathologic findings in CT-defined ILAs in human lung explants. Materials and Methods Explanted lungs or lobes from participants with radiologically documented ILAs were prospectively collected from 2010 to 2021. These specimens were air-inflated, frozen, and scanned with CT and micro-CT (spatial resolution of 0.7 mm and 90 μm, respectively). Subsequently, the lungs were cut and sampled with core biopsies. At least five samples per lung underwent micro-CT and subsequent histopathologic assessment with semiquantitative remodeling scorings. Based on area-specific radiologic scoring, the association between radiologic and histopathologic findings was assessed. Results Eight lung explants from six donors (median age at explantation, 71 years [range, 60-83 years]; four men) were included (unused donor lungs, n = 4; pre-emptive lobectomy for oncologic indications, n = 2). Ex vivo CT demonstrated ground-glass opacification, reticulation, and bronchiectasis. Micro-CT and histopathologic examination demonstrated that lung abnormalities were frequently paraseptal and associated with fibrosis and lymphocytic inflammation. The histopathologic results showed varying degrees of fibrosis in areas that appeared normal on CT scans. Regions of reticulation on CT scans generally had greater fibrosis at histopathologic analysis. Vasculopathy and bronchiectasis were also often present at histopathologic examination of lungs with ILAs. Fully developed fibroblastic foci were rarely observed. Conclusion This study demonstrated direct histologic correlates of CT-defined interstitial lung abnormalities. © RSNA, 2022 Supplemental material is available for this article. See also the editorial by Jeudy in this issue.
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Affiliation(s)
- Stijn E. Verleden
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Arno Vanstapel
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Joseph Jacob
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Tinne Goos
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Jeroen Hendriks
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Laurens J. Ceulemans
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Dirk E. Van Raemdonck
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Laurens De Sadeleer
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Robin Vos
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Johanna M. Kwakkel-van Erp
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Arne P. Neyrinck
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Geert M. Verleden
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Matthieu N. Boone
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Wim Janssens
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Els Wauters
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Birgit Weynand
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Danny D. Jonigk
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Johny Verschakelen
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
| | - Wim A. Wuyts
- From the Department of Chronic Diseases and Metabolism, BREATHE
(S.E.V., A.V., T.G., L.J.C., D.E.V.R., L.D.S., R.V., G.M.V., W.J., E.W.,
W.A.W.), Department of Cardiovascular Sciences (A.P.N.), and Department of
Imaging and Pathology (B.W., J.V.), KU Leuven, Herestraat 49, 3000 Leuven,
Belgium; Department of ASTARC, University of Antwerp, Antwerp, Belgium (S.E.V.,
J.H.); Department of Respiratory Medicine (S.E.V., J.M.K.v.E.) and Department of
Thoracic and Vascular Surgery (S.E.V., J.H.), University Hospital Antwerp,
Antwerp, Belgium; Department of Respiratory Medicine (J.J.) and Centre for
Medical Image Computing (J.J.), University College London, London, UK;
Department of Thoracic Surgery, University Hospital Leuven, Leuven, Belgium
(L.J.C., D.E.V.R.); Department of Physics and Astronomy, Ghent University,
Ghent, Belgium (M.N.B.); Institute of Pathology, Hannover Medical School,
Hannover, Germany (D.D.J.); and Biomedical Research in Endstage and Obstructive
Lung Disease Hannover (BREATH), Member of the German Center for Lung Research
(DZL), Hannover, Germany (D.D.J.)
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22
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Sarkar A, Das S, Bone H, DeVengencie I, Prasad J, Farkas D, Londino JD, Nho RS, Rojas M, Horowitz JC. Regulation of Mesenchymal Cell Fate by Transfer of Active Gasdermin-D via Monocyte-Derived Extracellular Vesicles. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:832-841. [PMID: 36688687 PMCID: PMC9998362 DOI: 10.4049/jimmunol.2200511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/03/2023] [Indexed: 01/24/2023]
Abstract
Fibrosis is characterized by inappropriately persistent myofibroblast accumulation and excessive extracellular matrix deposition with the disruption of tissue architecture and organ dysfunction. Regulated death of reparative mesenchymal cells is critical for normal wound repair, but profibrotic signaling promotes myofibroblast resistance to apoptotic stimuli. A complex interplay between immune cells and structural cells underlies lung fibrogenesis. However, there is a paucity of knowledge on how these cell populations interact to orchestrate physiologic and pathologic repair of the injured lung. In this context, gasdermin-D (GsdmD) is a cytoplasmic protein that is activated following cleavage by inflammatory caspases and induces regulated cell death by forming pores in cell membranes. This study was undertaken to evaluate the impact of human (Thp-1) monocyte-derived extracellular vesicles and GsdmD on human lung fibroblast death. Our data show that active GsdmD delivered by monocyte-derived extracellular vesicles induces caspase-independent fibroblast and myofibroblast death. This cell death was partly mediated by GsdmD-independent induction of cellular inhibitor of apoptosis 2 (cIAP-2) in the recipient fibroblast population. Our findings, to our knowledge, define a novel paradigm by which inflammatory monocytes may orchestrate the death of mesenchymal cells in physiologic wound healing, illustrating the potential to leverage this mechanism to eliminate mesenchymal cells and facilitate the resolution of fibrotic repair.
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Affiliation(s)
- Anasuya Sarkar
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH; and The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Srabani Das
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH; and The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Hannah Bone
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH; and The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Ivana DeVengencie
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH; and The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Jayendra Prasad
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH; and The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Daniela Farkas
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH; and The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - James D Londino
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH; and The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Richard S Nho
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH; and The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Mauricio Rojas
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH; and The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Jeffrey C Horowitz
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH; and The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH
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23
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Papazoglou AS, Karagiannidis E, Liatsos A, Bompoti A, Moysidis DV, Arvanitidis C, Tsolaki F, Tsagkaropoulos S, Theocharis S, Tagarakis G, Michaelson JS, Herrmann MD. Volumetric Tissue Imaging of Surgical Tissue Specimens Using Micro-Computed Tomography: An Emerging Digital Pathology Modality for Nondestructive, Slide-Free Microscopy-Clinical Applications of Digital Pathology in 3 Dimensions. Am J Clin Pathol 2023; 159:242-254. [PMID: 36478204 DOI: 10.1093/ajcp/aqac143] [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: 08/16/2022] [Accepted: 10/14/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES Micro-computed tomography (micro-CT) is a novel, nondestructive, slide-free digital imaging modality that enables the acquisition of high-resolution, volumetric images of intact surgical tissue specimens. The aim of this systematic mapping review is to provide a comprehensive overview of the available literature on clinical applications of micro-CT tissue imaging and to assess its relevance and readiness for pathology practice. METHODS A computerized literature search was performed in the PubMed, Scopus, Web of Science, and CENTRAL databases. To gain insight into regulatory and financial considerations for performing and examining micro-CT imaging procedures in a clinical setting, additional searches were performed in medical device databases. RESULTS Our search identified 141 scientific articles published between 2000 and 2021 that described clinical applications of micro-CT tissue imaging. The number of relevant publications is progressively increasing, with the specialties of pulmonology, cardiology, otolaryngology, and oncology being most commonly concerned. The included studies were mostly performed in pathology departments. Current micro-CT devices have already been cleared for clinical use, and a Current Procedural Terminology (CPT) code exists for reimbursement of micro-CT imaging procedures. CONCLUSIONS Micro-CT tissue imaging enables accurate volumetric measurements and evaluations of entire surgical specimens at microscopic resolution across a wide range of clinical applications.
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Affiliation(s)
| | - Efstratios Karagiannidis
- First Department of Cardiology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Alexandros Liatsos
- First Department of Cardiology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreana Bompoti
- Diagnostic Imaging, Peterborough City Hospital, North West Anglia NHS Foundation Trust, Peterborough, UK
| | - Dimitrios V Moysidis
- First Department of Cardiology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Christos Arvanitidis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.,LifeWatch ERIC, Sector II-II, Seville, Spain
| | - Fani Tsolaki
- Department of Cardiothoracic Surgery, AHEPA University Hospital, Thessaloniki, Greece
| | | | - Stamatios Theocharis
- First Department of Pathology, National and Kapoditrian University of Athens, Athens, Greece
| | - Georgios Tagarakis
- Department of Cardiothoracic Surgery, AHEPA University Hospital, Thessaloniki, Greece
| | - James S Michaelson
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Markus D Herrmann
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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24
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Huang Y, Guzy R, Ma SF, Bonham CA, Jou J, Schulte JJ, Kim JS, Barros AJ, Espindola MS, Husain AN, Hogaboam CM, Sperling AI, Noth I. Central lung gene expression associates with myofibroblast features in idiopathic pulmonary fibrosis. BMJ Open Respir Res 2023; 10:10/1/e001391. [PMID: 36725082 PMCID: PMC9896241 DOI: 10.1136/bmjresp-2022-001391] [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: 08/04/2022] [Accepted: 01/13/2023] [Indexed: 02/03/2023] Open
Abstract
RATIONALE Contribution of central lung tissues to pathogenesis of idiopathic pulmonary fibrosis (IPF) remains unknown. OBJECTIVE To ascertain the relationship between cell types of IPF-central and IPF-peripheral lung explants using RNA sequencing (RNA-seq) transcriptome. METHODS Biopsies of paired IPF-central and IPF-peripheral along with non-IPF lungs were selected by reviewing H&E data. Criteria for differentially expressed genes (DEG) were set at false discovery rate <5% and fold change >2. Computational cell composition deconvolution was performed. Signature scores were computed for each cell type. FINDINGS Comparison of central IPF versus non-IPF identified 1723 DEG (1522 upregulated and 201 downregulated). Sixty-two per cent (938/1522) of the mutually upregulated genes in central IPF genes were also upregulated in peripheral IPF versus non-IPF. Moreover, 85 IPF central-associated genes (CAG) were upregulated in central IPF versus both peripheral IPF and central non-IPF. IPF single-cell RNA-seq analysis revealed the highest CAG signature score in myofibroblasts and significantly correlated with a previously published activated fibroblasts signature (r=0.88, p=1.6×10-4). CAG signature scores were significantly higher in IPF than in non-IPF myofibroblasts (p=0.013). Network analysis of central-IPF genes identified a module significantly correlated with the deconvoluted proportion of myofibroblasts in central IPF and anti-correlated with inflammation foci trait in peripheral IPF. The module genes were over-represented in idiopathic pulmonary fibrosis signalling pathways. INTERPRETATION Gene expression in central IPF lung regions demonstrates active myofibroblast features that contributes to disease progression. Further elucidation of pathological transcriptomic state of cells in the central regions of the IPF lung that are relatively spared from morphological rearrangements may provide insights into molecular changes in the IPF progression.
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Affiliation(s)
- Yong Huang
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Rob Guzy
- Section of Pulmonary & Critical Care Medicine, University of Chicago, Chicago, Illinois, USA
| | - Shwu-Fan Ma
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Catherine A Bonham
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Jonathan Jou
- Department of Surgery, University of Illinois, Peoria, Illinois, USA
| | - Jefree J Schulte
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - John S Kim
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Andrew J Barros
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Milena S Espindola
- Division of Pulmonary & Critical Care Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Aliya N Husain
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Cory M Hogaboam
- Division of Pulmonary & Critical Care Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Anne I Sperling
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Imre Noth
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
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25
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Cellular and Molecular Mechanisms in Idiopathic Pulmonary Fibrosis. Adv Respir Med 2023; 91:26-48. [PMID: 36825939 PMCID: PMC9952569 DOI: 10.3390/arm91010005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/06/2023] [Accepted: 01/12/2023] [Indexed: 02/04/2023]
Abstract
The respiratory system is a well-organized multicellular organ, and disruption of cellular homeostasis or abnormal tissue repair caused by genetic deficiency and exposure to risk factors lead to life-threatening pulmonary disease including idiopathic pulmonary fibrosis (IPF). Although there is no clear etiology as the name reflected, its pathological progress is closely related to uncoordinated cellular and molecular signals. Here, we review the advances in our understanding of the role of lung tissue cells in IPF pathology including epithelial cells, mesenchymal stem cells, fibroblasts, immune cells, and endothelial cells. These advances summarize the role of various cell components and signaling pathways in the pathogenesis of idiopathic pulmonary fibrosis, which is helpful to further study the pathological mechanism of the disease, provide new opportunities for disease prevention and treatment, and is expected to improve the survival rate and quality of life of patients.
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26
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Sabater L, Gossart JB, Hernandez I, Rico D, Blanchard A, Borthwick LA, Fisher AJ, Majo J, Jiwa K, Collins A, Abbate G, Oakley F, Mann DA, Mann J. miRNA Expression in Fibroblastic Foci within Idiopathic Pulmonary Fibrosis Lungs Reveals Novel Disease-Relevant Pathways. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:417-429. [PMID: 36690076 DOI: 10.1016/j.ajpath.2022.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/22/2023]
Abstract
miRNAs are a class of noncoding RNAs of approximately 22 nucleotides long that play an important role in regulating gene expression at a post-transcriptional level. Aberrant levels of miRNAs have been associated with profibrotic processes in idiopathic pulmonary fibrosis (IPF). However, most of these studies used whole IPF tissue or in vitro monocultures in which fibrosis has been artificially induced. In this study, we used laser microdissection to collect fibroblastic foci (FF), the key pathologic lesion in IPF, then isolate miRNAs and compare their expression levels with those found in whole IPF lung tissue and/or in vitro cultured fibroblast from IPF or normal lungs. Sequencing libraries were generated, and data generated were bioinformatically analyzed. A total of 18 miRNAs were significantly overexpressed in FF tissue when compared with whole IPF tissue; of these molecules, 15 were unique to FF. Comparison of FF with cultured IPF fibroblasts also revealed differences in miRNA composition that impact on several signaling pathways. The miRNA composition of FF is both overlapping and distinct from that of whole IPF tissue or cultured IPF fibroblasts and highlights the importance of characterizing FF biology as a phenotypically and functionally discrete tissue microenvironment.
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Affiliation(s)
- Laura Sabater
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jean B Gossart
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Inmaculada Hernandez
- Computational Epigenomics Laboratory, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Daniel Rico
- Computational Epigenomics Laboratory, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andy Blanchard
- GlaxoSmithKline Medicines Research Centre, Stevenage, United Kingdom
| | - Lee A Borthwick
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andrew J Fisher
- Institute of Transplantation, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Joaquim Majo
- Institute of Transplantation, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Kasim Jiwa
- Institute of Transplantation, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Amy Collins
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; FibroFind Ltd, FibroFind Laboratories, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Giuseppe Abbate
- FibroFind Ltd, FibroFind Laboratories, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Fiona Oakley
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; FibroFind Ltd, FibroFind Laboratories, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Derek A Mann
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; FibroFind Ltd, FibroFind Laboratories, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jelena Mann
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; FibroFind Ltd, FibroFind Laboratories, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom.
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27
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LIU JIA, WANG FAPING, YUAN BO, LUO FENGMING. Transcriptional factor RUNX1: A potential therapeutic target for fibrotic pulmonary disease. BIOCELL 2023. [DOI: 10.32604/biocell.2023.026148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
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Glenn LM, Troy LK, Corte TJ. Novel diagnostic techniques in interstitial lung disease. Front Med (Lausanne) 2023; 10:1174443. [PMID: 37188089 PMCID: PMC10175799 DOI: 10.3389/fmed.2023.1174443] [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: 02/26/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Research into novel diagnostic techniques and targeted therapeutics in interstitial lung disease (ILD) is moving the field toward increased precision and improved patient outcomes. An array of molecular techniques, machine learning approaches and other innovative methods including electronic nose technology and endobronchial optical coherence tomography are promising tools with potential to increase diagnostic accuracy. This review provides a comprehensive overview of the current evidence regarding evolving diagnostic methods in ILD and to consider their future role in routine clinical care.
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Affiliation(s)
- Laura M. Glenn
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
- *Correspondence: Laura M. Glenn,
| | - Lauren K. Troy
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
| | - Tamera J. Corte
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
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Zou S, Khoo BL. Subtyping based on immune cell fractions reveal heterogeneity of cardiac fibrosis in end-stage heart failure. Front Immunol 2023; 14:1053793. [PMID: 36875078 PMCID: PMC9975711 DOI: 10.3389/fimmu.2023.1053793] [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: 09/26/2022] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Background A central issue hindering the development of effective anti-fibrosis drugs for heart failure is the unclear interrelationship between fibrosis and the immune cells. This study aims at providing precise subtyping of heart failure based on immune cell fractions, elaborating their differences in fibrotic mechanisms, and proposing a biomarker panel for evaluating intrinsic features of patients' physiological statuses through subtype classification, thereby promoting the precision medicine for cardiac fibrosis. Methods We inferred immune cell type abundance of the ventricular samples by a computational method (CIBERSORTx) based on ventricular tissue samples from 103 patients with heart failure, and applied K-means clustering to divide patients into two subtypes based on their immune cell type abundance. We also designed a novel analytic strategy: Large-Scale Functional Score and Association Analysis (LAFSAA), to study fibrotic mechanisms in the two subtypes. Results Two subtypes of immune cell fractions: pro-inflammatory and pro-remodeling subtypes, were identified. LAFSAA identified 11 subtype-specific pro-fibrotic functional gene sets as the basis for personalised targeted treatments. Based on feature selection, a 30-gene biomarker panel (ImmunCard30) established for diagnosing patient subtypes achieved high classification performance, with the area under the receiver operator characteristic curve corresponding to 0.954 and 0.803 for the discovery and validation sets, respectively. Conclusion Patients with the two subtypes of cardiac immune cell fractions were likely having different fibrotic mechanisms. Patients' subtypes can be predicted based on the ImmunCard30 biomarker panel. We envision that our unique stratification strategy revealed in this study will unravel advance diagnostic techniques for personalised anti-fibrotic therapy.
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Affiliation(s)
- Shangjie Zou
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, Hong Kong SAR, China.,Hong Kong Center for Cerebro-Cardiovascular Health Engineering (COCHE), Hong Kong, Hong Kong SAR, China
| | - Bee Luan Khoo
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, Hong Kong SAR, China.,Hong Kong Center for Cerebro-Cardiovascular Health Engineering (COCHE), Hong Kong, Hong Kong SAR, China.,Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong-Shenzhen Futian Research Institute, Shenzhen, China
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30
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Nanri Y, Nunomura S, Honda Y, Takedomi H, Yamaguchi Y, Izuhara K. A positive loop formed by SOX11 and periostin upregulates TGF-β signals leading to skin fibrosis. J Invest Dermatol 2022; 143:989-998.e7. [PMID: 36584910 DOI: 10.1016/j.jid.2022.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/28/2022] [Accepted: 12/14/2022] [Indexed: 12/29/2022]
Abstract
Systemic sclerosis (SSc) is a chronic, heterogenous disease of connective tissue characterized by organ fibrosis together with vascular injury and autoimmunity. Transforming growth factor (TGF)-β plays a central role in generating fibrosis, including SSc. Periostin is a matricellular protein playing a key role in the generation of fibrosis by amplifying the TGF-β signals. SOX (SRY-related HMG box) 11 is a transcription factor playing several important roles in organ development in embryos. We have previously shown that SOX11 induces periostin expression. However, the roles of the interactions among the TGF-β signals, periostin, and SOX11 remain unknown in the pathogenesis of SSc. In this study, we found that most clones of dermal fibroblasts derived from SSc patients showed constitutive, high expression of SOX11, which is significantly induced by TGF-β1. SOX11 forms a positive loop with periostin to activate the TGF-β signals in SSc dermal fibroblasts. Genetic deletion of Sox11 in Postn-expressing fibroblasts impairs dermal fibrosis by bleomycin. Moreover, using the DNA microarray method, we identified several fibrotic factors dependent on the TGF-β/SOX11/periostin pathway in SSc dermal fibroblasts. Our findings, taken together, show that a positive loop formed by SOX11 and periostin in fibroblasts upregulates the TGF-β signals, leading to skin fibrosis.
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Affiliation(s)
- Yasuhiro Nanri
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga, Japan
| | - Satoshi Nunomura
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga, Japan
| | - Yuko Honda
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga, Japan
| | | | - Yukie Yamaguchi
- Department of Environmental Immuno-Dermatology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kenji Izuhara
- Division of Medical Biochemistry, Department of Biomolecular Sciences, Saga, Japan.
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31
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Parker AL, Bowman E, Zingone A, Ryan BM, Cooper WA, Kohonen-Corish M, Harris CC, Cox TR. Extracellular matrix profiles determine risk and prognosis of the squamous cell carcinoma subtype of non-small cell lung carcinoma. Genome Med 2022; 14:126. [PMID: 36404344 PMCID: PMC9677915 DOI: 10.1186/s13073-022-01127-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/14/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Squamous cell carcinoma (SqCC) is a subtype of non-small cell lung cancer for which patient prognosis remains poor. The extracellular matrix (ECM) is critical in regulating cell behavior; however, its importance in tumor aggressiveness remains to be comprehensively characterized. METHODS Multi-omics data of SqCC human tumor specimens was combined to characterize ECM features associated with initiation and recurrence. Penalized logistic regression was used to define a matrix risk signature for SqCC tumors and its performance across a panel of tumor types and in SqCC premalignant lesions was evaluated. Consensus clustering was used to define prognostic matreotypes for SqCC tumors. Matreotype-specific tumor biology was defined by integration of bulk RNAseq with scRNAseq data, cell type deconvolution, analysis of ligand-receptor interactions and enriched biological pathways, and through cross comparison of matreotype expression profiles with aging and idiopathic pulmonary fibrosis lung profiles. RESULTS This analysis revealed subtype-specific ECM signatures associated with tumor initiation that were predictive of premalignant progression. We identified an ECM-enriched tumor subtype associated with the poorest prognosis. In silico analysis indicates that matrix remodeling programs differentially activate intracellular signaling in tumor and stromal cells to reinforce matrix remodeling associated with resistance and progression. The matrix subtype with the poorest prognosis resembles ECM remodeling in idiopathic pulmonary fibrosis and may represent a field of cancerization associated with elevated cancer risk. CONCLUSIONS Collectively, this analysis defines matrix-driven features of poor prognosis to inform precision medicine prevention and treatment strategies towards improving SqCC patient outcome.
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Affiliation(s)
- Amelia L. Parker
- grid.415306.50000 0000 9983 6924Matrix and Metastasis Lab, Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, 384 Victoria St, Darlinghurst, NSW 2052 Australia ,grid.1005.40000 0004 4902 0432School of Clinical Medicine, UNSW Sydney, Sydney, 2052 Australia
| | - Elise Bowman
- grid.48336.3a0000 0004 1936 8075Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA
| | - Adriana Zingone
- grid.48336.3a0000 0004 1936 8075Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA
| | - Brid M. Ryan
- grid.48336.3a0000 0004 1936 8075Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA ,Present address: MiNA Therapeutics, London, UK
| | - Wendy A. Cooper
- grid.413249.90000 0004 0385 0051Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050 Australia ,grid.1013.30000 0004 1936 834XSydney Medical School, University of Sydney, Sydney, NSW 2050 Australia ,grid.1029.a0000 0000 9939 5719Discipline of Pathology, School of Medicine, Western Sydney University, Liverpool, NSW 2170 Australia
| | - Maija Kohonen-Corish
- grid.417229.b0000 0000 8945 8472Woolcock Institute of Medical Research, Sydney, NSW 2037 Australia ,grid.1005.40000 0004 4902 0432Microbiome Research Centre, School of Clinical Medicine, UNSW Sydney, Sydney, 2052 Australia ,grid.415306.50000 0000 9983 6924Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
| | - Curtis C. Harris
- grid.48336.3a0000 0004 1936 8075Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA
| | - Thomas R. Cox
- grid.415306.50000 0000 9983 6924Matrix and Metastasis Lab, Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, 384 Victoria St, Darlinghurst, NSW 2052 Australia ,grid.1005.40000 0004 4902 0432School of Clinical Medicine, UNSW Sydney, Sydney, 2052 Australia
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32
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Moll SA, Platenburg MGJP, Platteel ACM, Vorselaars ADM, Janssen Bonàs M, Kraaijvanger R, Roodenburg-Benschop C, Meek B, van Moorsel CHM, Grutters JC. Prevalence and clinical associations of myositis antibodies in a large cohort of interstitial lung diseases. PLoS One 2022; 17:e0277007. [PMID: 36327336 PMCID: PMC9632801 DOI: 10.1371/journal.pone.0277007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background Serologic testing for autoantibodies is recommended in interstitial lung diseases (ILDs), as connective tissue diseases (CTDs) are an important secondary cause. Myositis antibodies are associated with CTD-ILD, but clinical associations with other ILDs are unclear. In this study, associations of myositis antibodies in various ILDs were evaluated. Methods 1463 ILD patients and 116 healthy subjects were screened for myositis antibodies with a line-blot assay on serum available at time of diagnosis. Additionally, bronchoalveolar lavage fluid (BALf) was analysed. Results A total of 394 patients demonstrated reactivity to at least one antibody, including anti-Ro52 (36.0%), anti-Mi-2β (17.3%) and anti-Jo-1 (10.9%). Anti-Jo-1 (OR 6.4; p<0.100) and anti-Ro52 (OR 6.0; p<0.001) were associated with CTD-ILD. Interestingly, anti-Mi-2β was associated with idiopathic pulmonary fibrosis (IPF; OR 5.3; p = 0.001) and hypersensitivity pneumonitis (HP; OR 5.9; p<0.001). Furthermore, anti-Mi-2β was strongly associated with a histological usual interstitial pneumonia (UIP) pattern (OR 6.5; p < 0.001). Moreover, anti-Mi-2β reactivity was identified in BALf and correlated with serum anti-Mi-2β (r = 0.64; p = 0.002). No differences were found in survival rates between ILD patients with and without serum Mi-2β reactivity (hazard ratio 0.835; 95% CI 0.442–1.575; p = 0.577). Conclusion In conclusion, novel associations of antibody Mi-2β with fibrotic ILD were found. Furthermore, serum anti-Mi-2β was associated with a histological UIP pattern and presence of anti-Mi-2β in BALf. Possibly, anti-Mi-2β could be implemented as a future diagnostic biomarker for fibrotic ILD.
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Affiliation(s)
- Sofia A. Moll
- Department of Pulmonology, St. Antonius Hospital Nieuwegein, Centre for Interstitial Lung Diseases, Nieuwegein, The Netherlands
- * E-mail:
| | - Mark G. J. P. Platenburg
- Department of Pulmonology, St. Antonius Hospital Nieuwegein, Centre for Interstitial Lung Diseases, Nieuwegein, The Netherlands
| | - Anouk C. M. Platteel
- Department of Medical Microbiology and Immunology, St. Antonius Hospital Nieuwegein, Nieuwegein, The Netherlands
| | - Adriane D. M. Vorselaars
- Department of Pulmonology, St. Antonius Hospital Nieuwegein, Centre for Interstitial Lung Diseases, Nieuwegein, The Netherlands
| | - Montse Janssen Bonàs
- Department of Pulmonology, St. Antonius Hospital Nieuwegein, Centre for Interstitial Lung Diseases, Nieuwegein, The Netherlands
| | - Raisa Kraaijvanger
- Department of Pulmonology, St. Antonius Hospital Nieuwegein, Centre for Interstitial Lung Diseases, Nieuwegein, The Netherlands
| | - Claudia Roodenburg-Benschop
- Department of Pulmonology, St. Antonius Hospital Nieuwegein, Centre for Interstitial Lung Diseases, Nieuwegein, The Netherlands
| | - Bob Meek
- Department of Medical Microbiology and Immunology, St. Antonius Hospital Nieuwegein, Nieuwegein, The Netherlands
| | - Coline H. M. van Moorsel
- Department of Pulmonology, St. Antonius Hospital Nieuwegein, Centre for Interstitial Lung Diseases, Nieuwegein, The Netherlands
| | - Jan C. Grutters
- Department of Pulmonology, St. Antonius Hospital Nieuwegein, Centre for Interstitial Lung Diseases, Nieuwegein, The Netherlands
- Division Heart & Lungs, University Medical Centre Utrecht, Utrecht, The Netherlands
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Chioccioli M, Roy S, Newell R, Pestano L, Dickinson B, Rigby K, Herazo-Maya J, Jenkins G, Ian S, Saini G, Johnson SR, Braybrooke R, Yu G, Sauler M, Ahangari F, Ding S, DeIuliis J, Aurelien N, Montgomery RL, Kaminski N. A lung targeted miR-29 mimic as a therapy for pulmonary fibrosis. EBioMedicine 2022; 85:104304. [PMID: 36265417 PMCID: PMC9587275 DOI: 10.1016/j.ebiom.2022.104304] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/22/2022] [Accepted: 09/25/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND MicroRNAs are non-coding RNAs that negatively regulate gene networks. Previously, we reported that systemically delivered miR-29 mimic MRG-201 reduced fibrosis in animal models, supporting the consideration of miR-29-based therapies for idiopathic pulmonary fibrosis (IPF). METHODS We generated MRG-229, a next-generation miR-29 mimic based on MRG-201 with improved chemical stability due to additional sugar modifications and conjugation with the internalization moiety BiPPB (PDGFbetaR-specific bicyclic peptide)1. We investigated the anti-fibrotic efficacy of MRG-229 on TGF-β1 treated human lung fibroblasts (NHLFs), human precision cut lung slices (hPCLS), and in vivo bleomycin studies; toxicology was assessed in two animal models, rats, and non-human primates. Finally, we examined miR-29b levels in a cohort of 46 and 213 patients with IPF diagnosis recruited from Yale and Nottingham Universities (Profile Cohort), respectively. FINDINGS The peptide-conjugated MRG-229 mimic decreased expression of pro-fibrotic genes and reduced collagen production in each model. In bleomycin-treated mice, the peptide-conjugated MRG-229 mimic downregulated profibrotic gene programs at doses more than ten-fold lower than the original compound. In rats and non-human primates, the peptide-conjugated MRG-229 mimic was well tolerated at clinically relevant doses with no adverse findings observed. In human peripheral blood from IPF patients decreased miR-29 concentrations were associated with increased mortality in two cohorts potentially identified as a target population for treatment. INTERPRETATION Collectively, our results provide support for the development of the peptide-conjugated MRG-229 mimic as a potential therapy in humans with IPF. FUNDING This work was supported by NIH NHLBI grants UH3HL123886, R01HL127349, R01HL141852, U01HL145567.
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Affiliation(s)
- Maurizio Chioccioli
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | | | | | | | | | | | - Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Steward Ian
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | | | | | - Guying Yu
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang, CN, China
| | - Maor Sauler
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Farida Ahangari
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Shuizi Ding
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Joseph DeIuliis
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | | | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA.
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Elitist random swapped particle swarm optimization embedded with variable k-nearest neighbour classification: a new PSO variant applied to gene identification. Soft comput 2022. [DOI: 10.1007/s00500-022-07515-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
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Kadefors M, Berlin F, Wildt M, Dellgren G, Rolandsson Enes S, Aspberg A, Westergren-Thorsson G. Dipeptidyl peptidase 4 expression is not associated with an activated fibroblast phenotype in idiopathic pulmonary fibrosis. Front Pharmacol 2022; 13:953771. [PMID: 36120350 PMCID: PMC9473336 DOI: 10.3389/fphar.2022.953771] [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: 05/27/2022] [Accepted: 08/01/2022] [Indexed: 11/24/2022] Open
Abstract
Dipeptidyl peptidase 4 (DPP4) has been proposed as a marker for activated fibroblasts in fibrotic disease. We aimed to investigate whether a profibrotic DPP4 phenotype is present in lung tissue from patients with idiopathic pulmonary fibrosis (IPF). The presence of DPP4+ fibroblasts in normal and IPF lung tissue was investigated using flow cytometry and immunohistology. In addition, the involvement of DPP4 in fibroblast activation was examined in vitro, using CRISPR/Cas9 mediated genetic inactivation to generate primary DPP4 knockout lung fibroblasts. We observed a reduced frequency of primary DPP4+ fibroblasts in IPF tissue using flow cytometry, and an absence of DPP4+ fibroblasts in pathohistological features of IPF. The in vivo observations were supported by results in vitro showing a decreased expression of DPP4 on normal and IPF fibroblasts after profibrotic stimuli (transforming growth factor β) and no effect on the expression of activation markers (α-smooth muscle actin, collagen I and connective tissue growth factor) upon knockout of DPP4 in lung fibroblasts with or without activation with profibrotic stimuli.
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Affiliation(s)
- Måns Kadefors
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- *Correspondence: Måns Kadefors,
| | - Frida Berlin
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Marie Wildt
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Göran Dellgren
- Transplant Institute and Department of Cardiothoracic Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Anders Aspberg
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden
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36
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Herrera JA, Dingle L, Montero MA, Venkateswaran RV, Blaikley JF, Lawless C, Schwartz MA. The UIP/IPF fibroblastic focus is a collagen biosynthesis factory embedded in a distinct extracellular matrix. JCI Insight 2022; 7:e156115. [PMID: 35852874 PMCID: PMC9462507 DOI: 10.1172/jci.insight.156115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
Usual interstitial pneumonia (UIP) is a histological pattern characteristic of idiopathic pulmonary fibrosis (IPF). The UIP pattern is patchy with histologically normal lung adjacent to dense fibrotic tissue. At this interface, fibroblastic foci (FF) are present and are sites where myofibroblasts and extracellular matrix (ECM) accumulate. Utilizing laser capture microdissection-coupled mass spectrometry, we interrogated the FF, adjacent mature scar, and adjacent alveoli in 6 fibrotic (UIP/IPF) specimens plus 6 nonfibrotic alveolar specimens as controls. The data were subjected to qualitative and quantitative analysis and histologically validated. We found that the fibrotic alveoli protein signature is defined by immune deregulation as the strongest category. The fibrotic mature scar classified as end-stage fibrosis whereas the FF contained an overabundance of a distinctive ECM compared with the nonfibrotic control. Furthermore, FF were positive for both TGFB1 and TGFB3, whereas the aberrant basaloid cell lining of FF was predominantly positive for TGFB2. In conclusion, spatial proteomics demonstrated distinct protein compositions in the histologically defined regions of UIP/IPF tissue. These data revealed that FF are the main site of collagen biosynthesis and that the adjacent alveoli are abnormal. This essential information will inform future mechanistic studies on fibrosis progression.
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Affiliation(s)
| | - Lewis Dingle
- Blond McIndoe Laboratories, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - M. Angeles Montero
- Department of Histopathology, Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
| | - Rajamiyer V. Venkateswaran
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Department of Transplant, Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
| | - John F. Blaikley
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Department of Transplant, Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
| | | | - Martin A. Schwartz
- The Wellcome Centre for Cell-Matrix Research and
- Yale Cardiovascular Research Center and
- Departments of Internal Medicine (Cardiology) and Cell Biology, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut, USA
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37
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Cadena-Suárez AR, Hernández-Hernández HA, Alvarado-Vásquez N, Rangel-Escareño C, Sommer B, Negrete-García MC. Role of MicroRNAs in Signaling Pathways Associated with the Pathogenesis of Idiopathic Pulmonary Fibrosis: A Focus on Epithelial-Mesenchymal Transition. Int J Mol Sci 2022; 23:ijms23126613. [PMID: 35743055 PMCID: PMC9224458 DOI: 10.3390/ijms23126613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 12/15/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive disease with high mortality and unclear etiology. Previous evidence supports that the origin of this disease is associated with epigenetic alterations, age, and environmental factors. IPF initiates with chronic epithelial lung injuries, followed by basal membrane destruction, which promotes the activation of myofibroblasts and excessive synthesis of extracellular matrix (ECM) proteins, as well as epithelial-mesenchymal transition (EMT). Due to miRNAs’ role as regulators of apoptosis, proliferation, differentiation, and cell-cell interaction processes, some studies have involved miRNAs in the biogenesis and progression of IPF. In this context, the analysis and discussion of the probable association of miRNAs with the signaling pathways involved in the development of IPF would improve our knowledge of the associated molecular mechanisms, thereby facilitating its evaluation as a therapeutic target for this severe lung disease. In this work, the most recent publications evaluating the role of miRNAs as regulators or activators of signal pathways associated with the pathogenesis of IPF were analyzed. The search in Pubmed was made using the following terms: “miRNAs and idiopathic pulmonary fibrosis (IPF)”; “miRNAs and IPF and signaling pathways (SP)”; and “miRNAs and IPF and SP and IPF pathogenesis”. Additionally, we focus mainly on those works where the signaling pathways involved with EMT, fibroblast differentiation, and synthesis of ECM components were assessed. Finally, the importance and significance of miRNAs as potential therapeutic or diagnostic tools for the treatment of IPF are discussed.
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Affiliation(s)
- Ana Ruth Cadena-Suárez
- Laboratorio de Biología Molecular, Instituto Nacional de Enfermedades Respiratorias (INER) “Ismael Cosío Villegas”, Calz. Tlalpan 4502, Col. Sección XVI, Mexico City 14080, Mexico; (A.R.C.-S.); (H.A.H.-H.)
| | - Hilda Arely Hernández-Hernández
- Laboratorio de Biología Molecular, Instituto Nacional de Enfermedades Respiratorias (INER) “Ismael Cosío Villegas”, Calz. Tlalpan 4502, Col. Sección XVI, Mexico City 14080, Mexico; (A.R.C.-S.); (H.A.H.-H.)
| | - Noé Alvarado-Vásquez
- Departamento de Bioquímica, Instituto Nacional de Enfermedades Respiratorias (INER) “Ismael Cosío Villegas”, Calz. Tlalpan 4502, Col. Sección XVI, Mexico City 14080, Mexico;
| | - Claudia Rangel-Escareño
- Departamento de Genomica Computacional, Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Col. Arenal Tepepan, Mexico City 14610, Mexico;
- Escuela de Ingenieria y Ciencias, Tecnológico de Monterrey, Epigmenio González 500, San Pablo 76130, Mexico
| | - Bettina Sommer
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias (INER) “Ismael Cosío Villegas”, Calz. Tlalpan 4502, Col. Sección XVI, Mexico City 14080, Mexico;
| | - María Cristina Negrete-García
- Laboratorio de Biología Molecular, Instituto Nacional de Enfermedades Respiratorias (INER) “Ismael Cosío Villegas”, Calz. Tlalpan 4502, Col. Sección XVI, Mexico City 14080, Mexico; (A.R.C.-S.); (H.A.H.-H.)
- Correspondence:
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Qiao X, Hou G, He YL, Song DF, An Y, Altawil A, Zhou XM, Wang QY, Kang J, Yin Y. The Novel Regulatory Role of the lncRNA–miRNA–mRNA Axis in Chronic Inflammatory Airway Diseases. Front Mol Biosci 2022; 9:927549. [PMID: 35769905 PMCID: PMC9234692 DOI: 10.3389/fmolb.2022.927549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 05/19/2022] [Indexed: 12/28/2022] Open
Abstract
Chronic inflammatory airway diseases, characterized by airway inflammation and airway remodelling, are increasing as a cause of morbidity and mortality for all age groups and races across the world. The underlying molecular mechanisms involved in chronic inflammatory airway diseases have not been fully explored. MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs) have recently attracted much attention for their roles in the regulation of a variety of biological processes. A number of studies have confirmed that both lncRNAs and miRNAs can regulate the initiation and progression of chronic airway diseases by targeting mRNAs and regulating different cellular processes, such as proliferation, apoptosis, inflammation, migration, and epithelial–mesenchymal transition (EMT). Recently, accumulative evidence has shown that the novel regulatory mechanism underlying the interaction among lncRNAs, miRNAs and messenger RNAs (mRNAs) plays a critical role in the pathophysiological processes of chronic inflammatory airway diseases. In this review, we comprehensively summarized the regulatory roles of the lncRNA–miRNA–mRNA network in different cell types and their potential roles as biomarkers, indicators of comorbidities or therapeutic targets for chronic inflammatory airway diseases, particularly chronic obstructive pulmonary disease (COPD) and asthma.
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Affiliation(s)
- Xin Qiao
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Gang Hou
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Yu-Lin He
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Dong-Fang Song
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yi An
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Abdullah Altawil
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiao-Ming Zhou
- Respiratory Department, Center for Pulmonary Vascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- *Correspondence: Xiao-Ming Zhou, ; Yan Yin,
| | - Qiu-Yue Wang
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Jian Kang
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yan Yin
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
- *Correspondence: Xiao-Ming Zhou, ; Yan Yin,
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Immunity, Ciliated Epithelium, and Mortality. Chest 2022; 161:1440-1441. [DOI: 10.1016/j.chest.2022.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 11/21/2022] Open
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Wilson C, Mertens TC, Shivshankar P, Bi W, Collum SD, Wareing N, Ko J, Weng T, Naikawadi RP, Wolters PJ, Maire P, Jyothula SS, Thandavarayan RA, Ren D, Elrod ND, Wagner EJ, Huang HJ, Dickey BF, Ford HL, Karmouty-Quintana H. Sine oculis homeobox homolog 1 plays a critical role in pulmonary fibrosis. JCI Insight 2022; 7:e142984. [PMID: 35420997 PMCID: PMC9220956 DOI: 10.1172/jci.insight.142984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/12/2022] [Indexed: 11/30/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal disease with limited treatment options. The role of the developmental transcription factor Sine oculis homeobox homolog 1 (SIX1) in the pathophysiology of lung fibrosis is not known. IPF lung tissue samples and IPF-derived alveolar type II cells (AT2) showed a significant increase in SIX1 mRNA and protein levels, and the SIX1 transcriptional coactivators EYA1 and EYA2 were elevated. Six1 was also upregulated in bleomycin-treated (BLM-treated) mice and in a model of spontaneous lung fibrosis driven by deletion of Telomeric Repeat Binding Factor 1 (Trf1) in AT2 cells. Conditional deletion of Six1 in AT2 cells prevented or halted BLM-induced lung fibrosis, as measured by a significant reduction in histological burden of fibrosis, reduced fibrotic mediator expression, and improved lung function. These effects were associated with increased macrophage migration inhibitory factor (MIF) in lung epithelial cells in vivo following SIX1 overexpression in BLM-induced fibrosis. A MIF promoter-driven luciferase assay demonstrated direct binding of Six1 to the 5'-TCAGG-3' consensus sequence of the MIF promoter, identifying a likely mechanism of SIX1-driven MIF expression in the pathogenesis of lung fibrosis and providing a potentially novel pathway for targeting in IPF therapy.
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Affiliation(s)
- Cory Wilson
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Tinne C.J. Mertens
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Pooja Shivshankar
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Weizen Bi
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Scott D. Collum
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Nancy Wareing
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Junsuk Ko
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Tingting Weng
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
| | - Ram P. Naikawadi
- Pulmonary, Critical Care, Allergy and Sleep Medicine, UCSF, San Francisco, California, USA
| | - Paul J. Wolters
- Pulmonary, Critical Care, Allergy and Sleep Medicine, UCSF, San Francisco, California, USA
| | - Pascal Maire
- Université de Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Soma S.K. Jyothula
- Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, McGovern Medical School, UTHealth, Houston, Texas, USA
| | | | - Dewei Ren
- Methodist J.C. Walter Jr. Transplant Center, Houston Methodist Hospital, Houston, Texas, USA
| | - Nathan D. Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Eric J. Wagner
- Department of Biochemistry and Biophysics, Center for RNA Biology, Wilmot Cancer Institute, University of Rochester School of Medicine and Dentistry, KMRB G.9629, Rochester, New York, USA
| | - Howard J. Huang
- Methodist J.C. Walter Jr. Transplant Center, Houston Methodist Hospital, Houston, Texas, USA
| | - Burton F. Dickey
- Department of Pulmonary Medicine, Division of Internal Medicine, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Heide L. Ford
- Department of Pharmacology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, Texas, USA
- Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, McGovern Medical School, UTHealth, Houston, Texas, USA
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Consensus Gene Co-Expression Network Analysis Identifies Novel Genes Associated with Severity of Fibrotic Lung Disease. Int J Mol Sci 2022; 23:ijms23105447. [PMID: 35628257 PMCID: PMC9141193 DOI: 10.3390/ijms23105447] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/07/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a severe fibrotic lung disease characterized by irreversible scarring of the lung parenchyma leading to dyspnea, progressive decline in lung function, and respiratory failure. We analyzed lung transcriptomic data from independent IPF cohorts using weighted gene co-expression network analysis (WGCNA) to identify gene modules based on their preservation status in these cohorts. The consensus gene modules were characterized by leveraging existing clinical and molecular data such as lung function, biological processes, pathways, and lung cell types. From a total of 32 consensus gene modules identified, two modules were found to be significantly correlated with the disease, lung function, and preserved in other IPF datasets. The upregulated gene module was enriched for extracellular matrix, collagen metabolic process, and BMP signaling while the downregulated module consisted of genes associated with tube morphogenesis, blood vessel development, and cell migration. Using a combination of connectivity-based and trait-based significance measures, we identified and prioritized 103 "hub" genes (including 25 secretory candidate biomarkers) by their similarity to known IPF genetic markers. Our validation studies demonstrate the dysregulated expression of CRABP2, a retinol-binding protein, in multiple lung cells of IPF, and its correlation with the decline in lung function.
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Fernandez RJ, Gardner ZJG, Slovik KJ, Liberti DC, Estep KN, Yang W, Chen Q, Santini GT, Perez JV, Root S, Bhatia R, Tobias JW, Babu A, Morley MP, Frank DB, Morrisey EE, Lengner CJ, Johnson FB. GSK3 inhibition rescues growth and telomere dysfunction in dyskeratosis congenita iPSC-derived type II alveolar epithelial cells. eLife 2022; 11:64430. [PMID: 35559731 PMCID: PMC9200405 DOI: 10.7554/elife.64430] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 05/11/2022] [Indexed: 11/27/2022] Open
Abstract
Dyskeratosis congenita (DC) is a rare genetic disorder characterized by deficiencies in telomere maintenance leading to very short telomeres and the premature onset of certain age-related diseases, including pulmonary fibrosis (PF). PF is thought to derive from epithelial failure, particularly that of type II alveolar epithelial (AT2) cells, which are highly dependent on Wnt signaling during development and adult regeneration. We use human induced pluripotent stem cell-derived AT2 (iAT2) cells to model how short telomeres affect AT2 cells. Cultured DC mutant iAT2 cells accumulate shortened, uncapped telomeres and manifest defects in the growth of alveolospheres, hallmarks of senescence, and apparent defects in Wnt signaling. The GSK3 inhibitor, CHIR99021, which mimics the output of canonical Wnt signaling, enhances telomerase activity and rescues the defects. These findings support further investigation of Wnt agonists as potential therapies for DC-related pathologies.
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Affiliation(s)
- Rafael Jesus Fernandez
- Medical Scientist Training Program, University of Pennsylvania, Philadelphia, United States
| | - Zachary J G Gardner
- Medical Scientist Training Program, University of Pennsylvania, Philadelphia, United States
| | - Katherine J Slovik
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, United States
| | - Derek C Liberti
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, United States
| | - Katrina N Estep
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, United States
| | - Wenli Yang
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, United States
| | - Qijun Chen
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, United States
| | - Garrett T Santini
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Javier V Perez
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, United States
| | - Sarah Root
- College of Arts and Sciences and Vagelos Scholars Program, University of Pennsylvania, Philadelphia, United States
| | - Ranvir Bhatia
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - John W Tobias
- Penn Genomic Analysis Core, University of Pennsylvania, Philadelphia, United States
| | - Apoorva Babu
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, United States
| | - Michael P Morley
- Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, United States
| | - David B Frank
- Penn-CHOP Lung Biology Institute, Children's Hospital of Philadelphia, Philadelphia, United States
| | - Edward E Morrisey
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, United States
| | - Christopher J Lengner
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, United States
| | - F Brad Johnson
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, United States
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Zhang DW, Ye JJ, Sun Y, Ji S, Kang JY, Wei YY, Fei GH. CD19 and POU2AF1 are Potential Immune-Related Biomarkers Involved in the Emphysema of COPD: On Multiple Microarray Analysis. J Inflamm Res 2022; 15:2491-2507. [PMID: 35479834 PMCID: PMC9035466 DOI: 10.2147/jir.s355764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/05/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Emphysema is the main cause of the progression of chronic obstructive pulmonary disease (COPD). This study aimed to identify the key genes involved in COPD-related emphysema. Patients and Methods GSE76925 was downloaded from Gene Expression Omnibus database. Protein–protein interaction networks of differentially expressed genes (DEGs) between control and COPD groups were constructed to identify hub genes using Cytoscape. Diagnostic performance of hub genes was evaluated using receiver operating characteristic analysis. Correlation analysis was performed to identify the key genes by analyzing the relationship between the hub genes and lung function and computed tomography (CT) indexes of emphysema. COPD patients were then divided into two groups based on the median expression of key genes and DEGs between these two groups were identified. Enrichment analysis of DEGs and correlation analysis between key genes and the infiltration of the immune cells were also analyzed. Finally, the role of key genes was evaluated in a lung tissues dataset (GSE47460) and a blood dataset (GSE76705). Additionally, the expression of key genes was validated by quantitative real-time polymerase chain reaction and immunohistochemistry. Results CD19 and POU2AF1 had diagnostic efficacy for COPD and were significantly correlated with lung function and CT indexes of emphysema. Enrichment and immune analyses revealed that CD19 and POU2AF1 were correlated with the B cells in COPD. These results were consistent in GSE47460. The expression of CD19 and POU2AF1 in blood was the opposite of that in lung tissues, and CD19 and POU2AF1 were both significantly upregulated in COPD lung tissues at both the mRNA and protein levels. Conclusion CD19 and POU2AF1 may serve as key regulators of emphysema and contribute to the progression of COPD by regulating the B-cell immunology. Targeting B cells may be a promising strategy for treating COPD.
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Affiliation(s)
- Da-Wei Zhang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Jing-Jing Ye
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Ying Sun
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Shuang Ji
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Jia-Ying Kang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Yuan-Yuan Wei
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Guang-He Fei
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
- Correspondence: Guang-He Fei, Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China, Tel +86 551 6292 2013, Fax +86 551 6363 5578, Email
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Pham TX, Lee J, Guan J, Caporarello N, Meridew JA, Jones DL, Tan Q, Huang SK, Tschumperlin DJ, Ligresti G. Transcriptional analysis of lung fibroblasts identifies PIM1 signaling as a driver of aging-associated persistent fibrosis. JCI Insight 2022; 7:153672. [PMID: 35167499 PMCID: PMC8986080 DOI: 10.1172/jci.insight.153672] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 02/09/2022] [Indexed: 01/18/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is an aging-associated disease characterized by myofibroblast accumulation and progressive lung scarring. To identify transcriptional gene programs driving persistent lung fibrosis in aging, we performed RNA-Seq on lung fibroblasts isolated from young and aged mice during the early resolution phase after bleomycin injury. We discovered that, relative to injured young fibroblasts, injured aged fibroblasts exhibited a profibrotic state characterized by elevated expression of genes implicated in inflammation, matrix remodeling, and cell survival. We identified the proviral integration site for Moloney murine leukemia virus 1 (PIM1) and its target nuclear factor of activated T cells-1 (NFATc1) as putative drivers of the sustained profibrotic gene signatures in injured aged fibroblasts. PIM1 and NFATc1 transcripts were enriched in a pathogenic fibroblast population recently discovered in IPF lungs, and their protein expression was abundant in fibroblastic foci. Overexpression of PIM1 in normal human lung fibroblasts potentiated their fibrogenic activation, and this effect was attenuated by NFATc1 inhibition. Pharmacological inhibition of PIM1 attenuated IPF fibroblast activation and sensitized them to apoptotic stimuli. Interruption of PIM1 signaling in IPF lung explants ex vivo inhibited prosurvival gene expression and collagen secretion, suggesting that targeting this pathway may represent a therapeutic strategy to block IPF progression.
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Affiliation(s)
- Tho X. Pham
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Jisu Lee
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Jiazhen Guan
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Nunzia Caporarello
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Jeffrey A. Meridew
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Dakota L. Jones
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Qi Tan
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Steven K. Huang
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Daniel J. Tschumperlin
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Giovanni Ligresti
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
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RNA Sequencing of Epithelial Cell/Fibroblastic Foci Sandwich in Idiopathic Pulmonary Fibrosis: New Insights on the Signaling Pathway. Int J Mol Sci 2022; 23:ijms23063323. [PMID: 35328744 PMCID: PMC8954546 DOI: 10.3390/ijms23063323] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 12/27/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease characterized by irreversible scarring of the distal lung. IPF is best described by its histopathological pattern of usual interstitial pneumonia (UIP), characterized by spatial heterogeneity with alternating interstitial fibrosis and areas of normal lung, and temporal heterogeneity of fibrosis characterized by scattered fibroblastic foci (FF), dense acellular collagen and honeycomb changes. FF, comprising aggregated fibroblasts/myofibroblasts surrounded by metaplastic epithelial cells (EC), are the cardinal pathological lesion and their presence strongly correlates with disease progression and mortality. We hypothesized that the EC/FF sandwich from patients with UIP/IPF has a distinct molecular signature which could offer new insights into the crosstalk of these two crucial actors in the disease. Laser capture microdissection with RNAseq was used to investigate the transcriptome of the EC/FF sandwich from IPF patients versus controls (primary spontaneous pneumothorax). Differentially expressed gene analysis identified 23 up-regulated genes mainly related to epithelial dysfunction. Gene ontology analysis highlighted the activation of different pathways, mainly related to EC, immune response and programmed cell death. This study provides novel insights into the IPF pathogenetic pathways and suggests that targeting some of these up-regulated pathways (particularly those related to secreto-protein/mucin dysfunction) may be beneficial in IPF. Further studies in a larger number of lung samples, ideally from patients with early and advanced disease, are needed to validate these findings.
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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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47
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Shi XF, He X, Sun ZR, Wang JX, Gu YH, Xie YB, Duo J. Different expression of circulating microRNA profile and plasma SP-D in Tibetan COPD patients. Sci Rep 2022; 12:3388. [PMID: 35232961 PMCID: PMC8888752 DOI: 10.1038/s41598-022-05592-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 01/14/2022] [Indexed: 02/07/2023] Open
Abstract
COPD is the fourth leading cause of mortality, and is predicted to be the third leading cause of death worldwide by 2020. But few studies on Tibetan COPD of China. This study identifies distinctive miRNA signatures in Tibetan COPD patients from Tibetan healthy subjects that could serve as diagnostic biomarkers or describe differential molecular mechanisms with potential therapeutic implications. In this study, a total of 210 differentially expressed miRNAs were screened. Analysis of the functions of target genes of differentially expressed miRNAs via GO enrichment analysis revealed that they mainly influenced guanyl-nucleotide exchange factor activity, cell morphogenesis and the positive regulation of GTPase activity. KEGG pathway enrichment analysis showed that these target genes were mainly enriched in signaling by NGF, Axon guidance, developmental biology, ubiquitin mediated proteolysis, and PDGF signaling pathways. MiR-106-5p and miR-486-5p expression was validated in the complete cohort. Age, plasma miR-106-5p, miR-486-5p, SP-D protein levels, and SP-D mRNA level were also determined to be correlated with FEV1%Pred, and may as the risk factors of Tibetan COPD. The combination of plasma miR-106-5p, miR-486-5p and SP-D mRNA expression may be the best model to assist the diagnosis of Tibetan COPD.
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Affiliation(s)
- Xue-Feng Shi
- Department of Respiratory Medicine, Qinghai Provincial People's Hospital, Xining, Qinghai, 810007, People's Republic of China
| | - Xiang He
- Department of Respiratory Medicine, Qinghai Provincial People's Hospital, Xining, Qinghai, 810007, People's Republic of China
| | - Ze-Rui Sun
- Department of Respiratory Medicine, Qinghai Provincial People's Hospital, Xining, Qinghai, 810007, People's Republic of China
| | - Jian-Xiang Wang
- Department of Respiratory Medicine, Qinghai Provincial People's Hospital, Xining, Qinghai, 810007, People's Republic of China
| | - Yu-Hai Gu
- Department of Respiratory Medicine, Qinghai Provincial People's Hospital, Xining, Qinghai, 810007, People's Republic of China
| | - You-Bang Xie
- Department of Hematology and Rheumatology, Qinghai Provincial People's Hospital, Xining, Qinghai, 810007, People's Republic of China.
| | - Jie Duo
- Department of Respiratory Medicine, Qinghai Provincial People's Hospital, Xining, Qinghai, 810007, People's Republic of China.
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Moog MT, Hinze C, Bormann T, Aschenbrenner F, Knudsen L, DeLuca DS, Jonigk D, Neubert L, Welte T, Gauldie J, Kolb M, Maus UA. B Cells Are Not Involved in the Regulation of Adenoviral TGF-β1- or Bleomycin-Induced Lung Fibrosis in Mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1259-1271. [PMID: 35149532 DOI: 10.4049/jimmunol.2100767] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is an irreversible, age-related diffuse parenchymal lung disease of poorly defined etiology. Many patients with IPF demonstrate distinctive lymphocytic interstitial infiltrations within remodeled lung tissue with uncertain pathogenetic relevance. Histopathological examination of explant lung tissue of patients with IPF revealed accentuated lymphoplasmacellular accumulations in close vicinity to, or even infiltrating, remodeled lung tissue. Similarly, we found significant accumulations of B cells interfused with T cells within remodeled lung tissue in two murine models of adenoviral TGF-β1 or bleomycin (BLM)-induced lung fibrosis. Such B cell accumulations coincided with significantly increased lung collagen deposition, lung histopathology, and worsened lung function in wild-type (WT) mice. Surprisingly, B cell-deficient µMT knockout mice exhibited similar lung tissue remodeling and worsened lung function upon either AdTGF-β1 or BLM as for WT mice. Comparative transcriptomic profiling of sorted B cells collected from lungs of AdTGF-β1- and BLM-exposed WT mice identified a large set of commonly regulated genes, but with significant enrichment observed for Gene Ontology terms apparently not related to lung fibrogenesis. Collectively, although we observed B cell accumulations in lungs of IPF patients as well as two experimental models of lung fibrosis, comparative profiling of characteristic features of lung fibrosis between WT and B cell-deficient mice did not support a major involvement of B cells in lung fibrogenesis in mice.
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Affiliation(s)
- Marie T Moog
- Division of Experimental Pneumology, Hannover Medical School, Hannover, Germany
| | - Christopher Hinze
- Division of Experimental Pneumology, Hannover Medical School, Hannover, Germany
| | - Tina Bormann
- Division of Experimental Pneumology, Hannover Medical School, Hannover, Germany
| | | | - Lars Knudsen
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany
| | - David S DeLuca
- German Center for Lung Research, partner site Biomedical Research in Endstage and Obstructive Lung Disease Hanover, Hannover, Germany
| | - Danny Jonigk
- German Center for Lung Research, partner site Biomedical Research in Endstage and Obstructive Lung Disease Hanover, Hannover, Germany
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Lavinia Neubert
- German Center for Lung Research, partner site Biomedical Research in Endstage and Obstructive Lung Disease Hanover, Hannover, Germany
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Tobias Welte
- German Center for Lung Research, partner site Biomedical Research in Endstage and Obstructive Lung Disease Hanover, Hannover, Germany
- Clinic for Pneumology, Hannover Medical School, Hannover, Germany; and
| | - Jack Gauldie
- Department of Medicine, Pathology, and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Martin Kolb
- Department of Medicine, Pathology, and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Ulrich A Maus
- Division of Experimental Pneumology, Hannover Medical School, Hannover, Germany;
- German Center for Lung Research, partner site Biomedical Research in Endstage and Obstructive Lung Disease Hanover, Hannover, Germany
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49
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Wong BH, Mei D, Chua GL, Galam DL, Wenk MR, Torta F, Silver DL. The lipid transporter Mfsd2a maintains pulmonary surfactant homeostasis. J Biol Chem 2022; 298:101709. [PMID: 35150739 PMCID: PMC8914330 DOI: 10.1016/j.jbc.2022.101709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/18/2022] Open
Abstract
Pulmonary surfactant is a lipoprotein complex essential for lung function, and insufficiency or altered surfactant composition is associated with major lung diseases, such as acute respiratory distress syndromes, idiopathic pulmonary fibrosis, and chronic obstructive pulmonary disease. Pulmonary surfactant is primarily composed of phosphatidylcholine (PC) in complex with specialized surfactant proteins and secreted by alveolar type 2 (AT2) cells. Surfactant homeostasis on the alveolar surface is balanced by the rates of synthesis and secretion with reuptake and recycling by AT2 cells, with some degradation by pulmonary macrophages and loss up the bronchial tree. However, whether phospholipid (PL) transporters exist in AT2 cells to mediate reuptake of surfactant PL remains to be identified. Here, we demonstrate that major facilitator superfamily domain containing 2a (Mfsd2a), a sodium-dependent lysophosphatidylcholine (LPC) transporter, is expressed at the apical surface of AT2 cells. A mouse model with inducible AT2 cell–specific deficiency of Mfsd2a exhibited AT2 cell hypertrophy with reduced total surfactant PL levels because of reductions in the most abundant surfactants, PC containing dipalmitic acid, and PC species containing the omega-3 fatty acid docosahexaenoic acid. These changes in surfactant levels and composition were mirrored by similar changes in the AT2 cell lipidome. Mechanistically, direct tracheal instillation of fluorescent LPC and PC probes indicated that Mfsd2a mediates the uptake of LPC generated by pulmonary phospholipase activity in the alveolar space. These studies reveal that Mfsd2a-mediated LPC uptake is quantitatively important in maintaining surfactant homeostasis and identify this lipid transporter as a physiological component of surfactant recycling.
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Affiliation(s)
- Bernice H Wong
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Ding Mei
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Geok Lin Chua
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Dwight L Galam
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - David L Silver
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.
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50
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Haider MZ, Al-Mannai A, Al-Sirhan S, Elsabagh A, Nasser N, Al-Quraishi N, Ouda A, Erradi K, Ashour AA, Gupta I, Abdulmajeed J, Al-Romaihi HE, Bansal D, Musa OAH, Abd Farag EAB, Al-Thani MHJ, Al Moustafa AE. Impact of Smoking on COVID-19 Symptoms in Non-Vaccinated Patients: A Matched Observational Study from Qatar. J Multidiscip Healthc 2022; 15:531-540. [PMID: 35321233 PMCID: PMC8937311 DOI: 10.2147/jmdh.s347130] [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: 11/01/2021] [Accepted: 12/10/2021] [Indexed: 01/08/2023] Open
Abstract
Purpose Predisposition to acute illness from COVID-19 is suggested to correlate with cigarette smoking as it augments the risk of developing cardiovascular and respiratory illnesses, including infections. However, the effects of smoking on COVID-19 symptoms are not well described and controversial. In this study, we aim to explore the associations between smoking and COVID-19 symptoms. Subjects and Methods A cross-sectional study using the Ministry of Public Health (MoPH), Qatar database was administered to a Qatari population with confirmed COVID-19 disease who filled in pre-defined phone-call questionnaire between 27th February 2020 and 31st December 2020. We analyzed 11,701 non-vaccinated COVID-19 individuals (2952 smokers and 8749 non-smokers) with confirmed RT-PCR test results. The association of smoking and the presence of symptoms as well as patient characteristics was calculated using Pearson’s Chi-square and Fisher’s exact tests, adjusting for potential covariates. Results Compared with the non-smokers, symptomatic COVID-19 infection is significantly higher in smokers. In addition, we found fever as the most common symptom developed in COVID-19 patients followed by cough, headache, muscle ache, and sore throat. As compared to other symptoms, association of smoking with chills and abdominal pain was less evident (P < 0.05 and P < 0.001, respectively). However, both groups showed similar rates of developing cough. Conclusion In conclusion, smoking is associated with COVID-19 symptoms frequency in non-vaccinated patients; nevertheless, further investigations are necessary to understand the mechanism of this association which could generate new targets for the management of COVID-19 in smoker patients.
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Affiliation(s)
| | - Amna Al-Mannai
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Sally Al-Sirhan
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Ahmed Elsabagh
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Nasser Nasser
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | | | - Amr Ouda
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Khadija Erradi
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Anas A Ashour
- Department of Internal Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Ishita Gupta
- College of Medicine, QU Health, Qatar University, Doha, Qatar
- Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar
| | | | | | | | | | | | | | - Ala-Eddin Al Moustafa
- College of Medicine, QU Health, Qatar University, Doha, Qatar
- Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar
- Biomedical Research Centre, Qatar University, Doha, Qatar
- Correspondence: Ala-Eddin Al Moustafa, College of Medicine, QU Health, Qatar University, PO Box 2713, Doha, Qatar, Tel +974 4403 7817, Fax +974 4403-3333, Email
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