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Bishop CR, Yan K, Nguyen W, Rawle DJ, Tang B, Larcher T, Suhrbier A. Microplastics dysregulate innate immunity in the SARS-CoV-2 infected lung. Front Immunol 2024; 15:1382655. [PMID: 38803494 PMCID: PMC11128561 DOI: 10.3389/fimmu.2024.1382655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Global microplastic (MP) pollution is now well recognized, with humans and animals consuming and inhaling MPs on a daily basis, with a growing body of concern surrounding the potential impacts on human health. Methods Using a mouse model of mild COVID-19, we describe herein the effects of azide-free 1 μm polystyrene MP beads, co-delivered into lungs with a SARS-CoV-2 omicron BA.5 inoculum. The effect of MPs on the host response to SARS-CoV-2 infection was analysed using histopathology and RNA-Seq at 2 and 6 days post-infection (dpi). Results Although infection reduced clearance of MPs from the lung, virus titres and viral RNA levels were not significantly affected by MPs, and overt MP-associated clinical or histopathological changes were not observed. However, RNA-Seq of infected lungs revealed that MP exposure suppressed innate immune responses at 2 dpi and increased pro-inflammatory signatures at 6 dpi. The cytokine profile at 6 dpi showed a significant correlation with the 'cytokine release syndrome' signature observed in some COVID-19 patients. Discussion The findings are consistent with the recent finding that MPs can inhibit phagocytosis of apoptotic cells via binding of Tim4. They also add to a growing body of literature suggesting that MPs can dysregulate inflammatory processes in specific disease settings.
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Affiliation(s)
- Cameron R. Bishop
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Kexin Yan
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Wilson Nguyen
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Daniel J. Rawle
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Bing Tang
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Thibaut Larcher
- Institut National de Recherche Agronomique, Unité Mixte de Recherche, Oniris, Nantes, France
| | - Andreas Suhrbier
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Australian Infectious Disease Research Centre, Global Virus Network (GVN) Center of Excellence, Brisbane, QLD, Australia
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2
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Brown AP, Parameswaran S, Cai L, Elston S, Pham C, Barski A, Weirauch MT, Ji H. TET1 regulates responses to house dust mite by altering chromatin accessibility, DNA methylation, and gene expression in airway epithelial cells. RESEARCH SQUARE 2023:rs.3.rs-3726852. [PMID: 38168374 PMCID: PMC10760239 DOI: 10.21203/rs.3.rs-3726852/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background Previous studies have identified TET1 as a potential key regulator of genes linked to asthma. TET1 has been shown to transcriptionally respond to house dust mite extract, an allergen known to directly cause allergic asthma development, and regulate the expression of genes involved in asthma. How TET1 regulates expression of these genes, however, is unknown. TET1 is a DNA demethylase; therefore, most prior research on TET1-based gene regulation has focused on how TET1 affects methylation. However, TET1 can also interact directly with transcription factors and histone modifiers to regulate gene expression. Understanding how TET1 regulates expression to contribute to allergic responses and asthma development thus requires a comprehensive approach. To this end, we measured mRNA expression, DNA methylation, chromatin accessibility and histone modifications in control and TET1 knockdown human bronchial epithelial cells treated or untreated with house dust mite extract. Results Throughout our analyses, we detected strong similarities between the effects of TET1 knockdown alone and the effects of HDM treatment alone. One especially striking pattern was that both TET1 knockdown and HDM treatment generally led to decreased chromatin accessibility at largely the same genomic loci. Transcription factor enrichment analyses indicated that altered chromatin accessibility following the loss of TET1 may affect, or be affected by, CTCF and CEBP binding. TET1 loss also led to changes in DNA methylation, but these changes were generally in regions where accessibility was not changing. Conclusions TET1 regulates gene expression through different mechanisms (DNA methylation and chromatin accessibility) in different parts of the genome in the airway epithelial cells, which mediates inflammatory responses to allergen. Collectively, our data suggest novel molecular mechanisms through which TET1 regulates critical pathways following allergen challenges and contributes to the development of asthma.
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Affiliation(s)
| | | | | | | | | | | | | | - Hong Ji
- University of California Davis
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Gazzinelli-Guimaraes PH, Golec DP, Karmele EP, Sciurba J, Bara-Garcia P, Hill T, Kang B, Bennuru S, Schwartzberg PL, Nutman TB. Eosinophil trafficking in allergen-mediated pulmonary inflammation relies on IL-13-driven CCL-11 and CCL-24 production by tissue fibroblasts and myeloid cells. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2023; 2:100131. [PMID: 37781651 PMCID: PMC10509988 DOI: 10.1016/j.jacig.2023.100131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/19/2023] [Accepted: 04/30/2023] [Indexed: 10/03/2023]
Abstract
Background The immunologic mechanisms underlying pulmonary type 2 inflammation, including the dynamics of eosinophil recruitment to the lungs, still need to be elucidated. Objective We sought to investigate how IL-13-producing TH2 effector cells trigger eosinophil migration in house dust mite (HDM)-driven allergic pulmonary inflammation. Methods Multiparameter and molecular profiling of murine lungs with HDM-induced allergy was investigated in the absence of IL-13 signaling by using IL-13Rα1-deficient mice and separately through adoptive transfer of CD4+ T cells from IL-5-deficient mice into TCRα-/- mice before allergic inflammation. Results We demonstrated through single-cell techniques that HDM-driven pulmonary inflammation displays a profile characterized by TH2 effector cell-induced IL-13-dominated eosinophilic inflammation. Using HDM-sensitized IL-13Rα1-/- mice, we found a marked reduction in the influx of eosinophils into the lungs along with a significant downregulation of both CCL-11 and CCL-24. We further found that eosinophil trafficking to the lung relies on production of IL-13-driven CCL-11 and CCL-24 by fibroblasts and Ly6C+ (so-called classical) monocytes. Moreover, this IL-13-mediated eotaxin-dependent eosinophil influx to the lung tissue required IL-5-induced eosinophilia. Finally, we demonstrated that this IL-13-driven eosinophil-dominated pulmonary inflammation was critical for limiting bystander lung transiting Ascaris parasites in a model of allergy and helminth interaction. Conclusion Our data suggest that IL-5-dependent allergen-specific TH2 effector cell response and subsequent signaling through the IL-13/IL-13Rα1 axis in fibroblasts and myeloid cells regulate the eotaxin-dependent recruitment of eosinophils to the lungs, with multiple downstream consequences, including bystander control of lung transiting parasitic helminths.
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Affiliation(s)
| | - Dominic P. Golec
- Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, MD
| | - Erik P. Karmele
- Laboratory of Molecular Immunology, NIAID, National Institutes of Health, Bethesda, MD
| | - Joshua Sciurba
- Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, MD
| | - Pablo Bara-Garcia
- Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, MD
| | - Tom Hill
- National Institute of Allergy and Infectious Diseases (NIAID) Collaborative Bioinformatics Resource, NIAID, National Institutes of Health, Bethesda, MD
| | - Byunghyun Kang
- Laboratory of Molecular Immunology, NIAID, National Institutes of Health, Bethesda, MD
| | - Sasisekhar Bennuru
- Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, MD
| | | | - Thomas B. Nutman
- Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, MD
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Ji H, Brown AP, Henson SN, Haczku A. The "epiTet" of Air Pollution: Epigenetic Regulation of Airway Inflammation by Tet1. Int Arch Allergy Immunol 2023; 184:949-952. [PMID: 37276849 PMCID: PMC10530385 DOI: 10.1159/000530272] [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: 02/02/2023] [Accepted: 03/17/2023] [Indexed: 06/07/2023] Open
Affiliation(s)
- Hong Ji
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, California, USA
- California National Primate Research Center, University of California, Davis, California, USA
| | - Anthony P Brown
- California National Primate Research Center, University of California, Davis, California, USA
| | - Stephanie N Henson
- California National Primate Research Center, University of California, Davis, California, USA
| | - Angela Haczku
- California National Primate Research Center, University of California, Davis, California, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Lung Center, Department of Internal Medicine, School of Medicine, University of California, Davis, California, USA
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Osborn RM, Leach J, Zanche M, Ashton JM, Chu C, Thakar J, Dewhurst S, Rosenberger S, Pavelka M, Pryhuber GS, Mariani TJ, Anderson CS. Preparation of noninfectious scRNAseq samples from SARS-CoV-2-infected epithelial cells. PLoS One 2023; 18:e0281898. [PMID: 36827401 PMCID: PMC9956660 DOI: 10.1371/journal.pone.0281898] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/03/2023] [Indexed: 02/26/2023] Open
Abstract
Coronavirus disease (COVID-19) is an infectious disease caused by the SARS coronavirus 2 (SARS-CoV-2) virus. Direct assessment, detection, and quantitative analysis using high throughput methods like single-cell RNA sequencing (scRNAseq) is imperative to understanding the host response to SARS-CoV-2. One barrier to studying SARS-CoV-2 in the laboratory setting is the requirement to process virus-infected cell cultures, and potentially infectious materials derived therefrom, under Biosafety Level 3 (BSL-3) containment. However, there are only 190 BSL3 laboratory facilities registered with the U.S. Federal Select Agent Program, as of 2020, and only a subset of these are outfitted with the equipment needed to perform high-throughput molecular assays. Here, we describe a method for preparing non-hazardous RNA samples from SARS-CoV-2 infected cells, that enables scRNAseq analyses to be conducted safely in a BSL2 facility-thereby making molecular assays of SARS-CoV-2 cells accessible to a much larger community of researchers. Briefly, we infected African green monkey kidney epithelial cells (Vero-E6) with SARS-CoV-2 for 96 hours, trypsin-dissociated the cells, and inactivated them with methanol-acetone in a single-cell suspension. Fixed cells were tested for the presence of infectious SARS-CoV-2 virions using the Tissue Culture Infectious Dose Assay (TCID50), and also tested for viability using flow cytometry. We then tested the dissociation and methanol-acetone inactivation method on primary human lung epithelial cells that had been differentiated on an air-liquid interface. Finally, we performed scRNAseq quality control analysis on the resulting cell populations to evaluate the effects of our virus inactivation and sample preparation protocol on the quality of the cDNA produced. We found that methanol-acetone inactivated SARS-CoV-2, fixed the lung epithelial cells, and could be used to obtain noninfectious, high-quality cDNA libraries. This methodology makes investigating SARS-CoV-2, and related high-containment RNA viruses at a single-cell level more accessible to an expanded community of researchers.
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Affiliation(s)
- Raven M. Osborn
- Translational Biomedical Sciences Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Clinical and Translational Sciences Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Justin Leach
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Michelle Zanche
- Genomics Research Center, Center for Advanced Research Technologies, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - John M. Ashton
- Genomics Research Center, Center for Advanced Research Technologies, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - ChinYi Chu
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Juilee Thakar
- Translational Biomedical Sciences Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Clinical and Translational Sciences Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Stephen Dewhurst
- Clinical and Translational Sciences Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Sonia Rosenberger
- Department of Environmental Health and Safety, University of Rochester, Rochester, New York, United States of America
- Biosafety Level 3 Facility, Center for Advanced Research Technologies, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Martin Pavelka
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Biosafety Level 3 Facility, Center for Advanced Research Technologies, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Gloria S. Pryhuber
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Thomas J. Mariani
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Christopher S. Anderson
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
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Wang Y, Dong X, Pan C, Zhu C, Qi H, Wang Y, Wei H, Xie Q, Wu L, Shen H, Li S, Xie Y. Single-cell transcriptomic characterization reveals the landscape of airway remodeling and inflammation in a cynomolgus monkey model of asthma. Front Immunol 2022; 13:1040442. [PMID: 36439114 PMCID: PMC9685410 DOI: 10.3389/fimmu.2022.1040442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/20/2022] [Indexed: 06/22/2024] Open
Abstract
Monkey disease models, which are comparable to humans in terms of genetic, anatomical, and physiological characteristics, are important for understanding disease mechanisms and evaluating the efficiency of biological treatments. Here, we established an A.suum-induced model of asthma in cynomolgus monkeys to profile airway inflammation and remodeling in the lungs by single-cell RNA sequencing (scRNA-seq). The asthma model results in airway hyperresponsiveness and remodeling, demonstrated by pulmonary function test and histological characterization. scRNA-seq reveals that the model elevates the numbers of stromal, epithelial and mesenchymal cells (MCs). Particularly, the model increases the numbers of endothelial cells (ECs), fibroblasts (Fibs) and smooth muscle cells (SMCs) in the lungs, with upregulated gene expression associated with cell functions enriched in cell migration and angiogenesis in ECs and Fibs, and VEGF-driven cell proliferation, apoptotic process and complement activation in SMCs. Interestingly, we discover a novel Fib subtype that mediates type I inflammation in the asthmatic lungs. Moreover, MCs in the asthmatic lungs are found to regulate airway remodeling and immunological responses, with elevated gene expression enriched in cell migration, proliferation, angiogenesis and innate immunological responses. Not only the numbers of epithelial cells in the asthmatic lungs change at the time of lung tissue collection, but also their gene expressions are significantly altered, with an enrichment in the biological processes of IL-17 signaling pathway and apoptosis in the majority of subtypes of epithelial cells. Moreover, the ubiquitin process and DNA repair are more prevalent in ciliated epithelial cells. Last, cell-to-cell interaction analysis reveals a complex network among stromal cells, MCs and macrophages that contribute to the development of asthma and airway remodeling. Our findings provide a critical resource for understanding the principle underlying airway remodeling and inflammation in a monkey model of asthma, as well as valuable hints for the future treatment of asthma, especially the airway remodeling-characterized refractory asthma.
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Affiliation(s)
- Yingshuo Wang
- Department of Pulmonology, The Children’s Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyan Dong
- Department of Pulmonology, The Children’s Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Caizhe Pan
- Department of Pulmonology, The Children’s Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Cihang Zhu
- Department of Pulmonology, The Children’s Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Hantao Qi
- Department of Pulmonology, The Children’s Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Yifan Wang
- Department of Pulmonology, The Children’s Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Wei
- Department of Pulmonology, The Children’s Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiangmin Xie
- Department of Pulmonology, The Children’s Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Respiratory Drugs Research, Zhejiang University School of Medicine, Hangzhou, China
| | - Lei Wu
- Department of Pulmonology, The Children’s Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Huijuan Shen
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuxian Li
- Department of Pulmonology, The Children’s Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Yicheng Xie
- Department of Pulmonology, The Children’s Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, China
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