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Mahoney KJ, Bowie JS, Ford AE, Perera N, Sekiguchi Y, Fothergill DM, Lee EC. Plasma Proteomics-Based Discovery of Mechanistic Biomarkers of Hyperbaric Stress and Pulmonary Oxygen Toxicity. Metabolites 2023; 13:970. [PMID: 37755249 PMCID: PMC10534745 DOI: 10.3390/metabo13090970] [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: 06/30/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 09/28/2023] Open
Abstract
Our aim was to identify proteins that reflect an acute systemic response to prolonged hyperbaric stress and discover potential biomarker pathways for pulmonary O2 toxicity. The study was a double-blind, randomized, crossover design in trained male Navy diver subjects. Each subject completed two dry resting hyperbaric chamber dives separated by a minimum of one week. One dive exposed the subject to 6.5 h of 100% oxygen (O2) at 2ATA. The alternate dive exposed the subjects to an enhanced air nitrox mixture (EAN) containing 30.6% O2 at the same depth for the same duration. Venous blood samples collected before (PRE) and after (POST) each dive were prepared and submitted to LC-MS/MS analysis (2 h runs). A total of 346 total proteins were detected and analyzed. A total of 12 proteins were significantly increased at EANPOST (vs. EANPRE), including proteins in hemostasis and immune signaling and activation. Significantly increased proteins at O2PRE (vs. O2POST) included neural cell adhesion molecule 1, glycoprotein Ib, catalase, hemoglobin subunit beta, fibulin-like proteins, and complement proteins. EANPOST and O2POST differed in biomarkers related to coagulation, immune signaling and activation, and metabolism. Of particular interest is (EANPOST vs. O2POST), which is protective against oxidative stress.
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Affiliation(s)
- Kyle J. Mahoney
- Department of Kinesiology, University of Connecticut, Storrs, CT 06269, USA; (K.J.M.); (J.S.B.); (N.P.)
| | - Jacob S. Bowie
- Department of Kinesiology, University of Connecticut, Storrs, CT 06269, USA; (K.J.M.); (J.S.B.); (N.P.)
| | - Austin E. Ford
- Department of Kinesiology, University of Connecticut, Storrs, CT 06269, USA; (K.J.M.); (J.S.B.); (N.P.)
| | - Neranjan Perera
- Department of Kinesiology, University of Connecticut, Storrs, CT 06269, USA; (K.J.M.); (J.S.B.); (N.P.)
| | - Yasuki Sekiguchi
- Department of Kinesiology, University of Connecticut, Storrs, CT 06269, USA; (K.J.M.); (J.S.B.); (N.P.)
| | | | - Elaine C. Lee
- Department of Kinesiology, University of Connecticut, Storrs, CT 06269, USA; (K.J.M.); (J.S.B.); (N.P.)
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Yie TA, Loomis CA, Nowatzky J, Khodadadi-Jamayran A, Lin Z, Cammer M, Barnett C, Mezzano V, Alu M, Novick JA, Munger JS, Kugler MC. Hedgehog and Platelet-derived Growth Factor Signaling Intersect during Postnatal Lung Development. Am J Respir Cell Mol Biol 2023; 68:523-536. [PMID: 36693140 PMCID: PMC10174164 DOI: 10.1165/rcmb.2022-0269oc] [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: 07/10/2021] [Accepted: 01/24/2023] [Indexed: 01/26/2023] Open
Abstract
Normal lung development critically depends on HH (Hedgehog) and PDGF (platelet-derived growth factor) signaling, which coordinate mesenchymal differentiation and proliferation. PDGF signaling is required for postnatal alveolar septum formation by myofibroblasts. Recently, we demonstrated a requirement for HH in postnatal lung development involving alveolar myofibroblast differentiation. Given shared features of HH signaling and PDGF signaling and their impact on this key cell type, we sought to clarify their relationship during murine postnatal lung development. Timed experiments revealed that HH inhibition phenocopies the key lung myofibroblast phenotypes of Pdgfa (platelet-derived growth factor subunit A) and Pdgfra (platelet-derived growth factor receptor alpha) knockouts during secondary alveolar septation. Using a dual signaling reporter, Gli1lZ;PdgfraEGFP, we show that HH and PDGF pathway intermediates are concurrently expressed during alveolar septal myofibroblast accumulation, suggesting pathway convergence in the generation of lung myofibroblasts. Consistent with this hypothesis, HH inhibition reduces Pdgfra expression and diminishes the number of Pdgfra-positive and Pdgfra-lineage cells in postnatal lungs. Bulk RNA sequencing data of Pdgfra-expressing cells from Postnatal Day 8 (P8) lungs show that HH inhibition alters the expression not only of well-established HH targets but also of several putative PDGF target genes. This, together with the presence of Gli-binding sites in PDGF target genes, suggests HH input into PDGF signaling. We identified these HH/PDGF targets in several postnatal lung mesenchymal cell populations, including myofibroblasts, using single-cell transcriptomic analysis. Collectively, our data indicate that HH signaling and PDGF signaling intersect to support myofibroblast/fibroblast function during secondary alveolar septum formation. Moreover, they provide a molecular foundation relevant to perinatal lung diseases associated with impaired alveolarization.
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Affiliation(s)
- Ting-An Yie
- Division of Pulmonary, Critical Care and Sleep Medicine and
| | | | - Johannes Nowatzky
- Division of Rheumatology, Department of Medicine
- Department of Pathology
| | | | | | | | - Clea Barnett
- Division of Pulmonary, Critical Care and Sleep Medicine and
| | | | | | | | - John S. Munger
- Division of Pulmonary, Critical Care and Sleep Medicine and
- Department of Cell Biology, School of Medicine and Langone Medical Center, New York University, New York, New York
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An optical pH-sensor integrated microfluidic platform multilayered with bacterial cellulose and gelatin methacrylate to mimic drug-induced lung injury. J IND ENG CHEM 2023. [DOI: 10.1016/j.jiec.2023.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Yuan Y, Qiao G, Zhou J, Zhou Y, Li Y, Li X, Jiang Z, Wang Y. Integrated analysis reveals the protective mechanism and therapeutic potential of hyperbaric oxygen against pulmonary fibrosis. Genes Dis 2022; 10:1029-1039. [DOI: 10.1016/j.gendis.2022.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Saygili E, Devamoglu U, Goker-Bagca B, Goksel O, Biray-Avci C, Goksel T, Yesil-Celiktas O. A drug-responsive multicellular human spheroid model to recapitulate drug-induced pulmonary fibrosis. Biomed Mater 2022; 17. [PMID: 35617946 DOI: 10.1088/1748-605x/ac73cd] [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: 12/31/2021] [Accepted: 05/26/2022] [Indexed: 11/12/2022]
Abstract
Associated with a high mortality rate, pulmonary fibrosis (PF) is the end stage of several interstitial lung diseases. Although many factors are linked to PF progression, initiation of the fibrotic process remains to be studied. Current research focused on generating new strategies to gain a better understanding of the underlying disease mechanism as the animal models remain insufficient to reflect human physiology. Herein, to account complex cellular interactions within the fibrotic tissue, a multicellular spheroid (MCS) model where human bronchial epithelial cells incorporated with human lung fibroblasts was generated and treated with bleomycin (BLM) to emulate drug-induced PF. Recapitulating the epithelial-interstitial microenvironment, the findings successfully reflected the PF disease, where excessive alpha smooth muscle actin (α-SMA) and collagen type I secretion were noted along with the morphological changes in response to BLM. Moreover, increased levels of fibrotic linked COL13A1, MMP2, WNT3 and decreased expression level of CDH1 provide evidence for the model reliability on fibrosis modelling. Subsequent administration of the FDA approved nintedanib and pirfenidone anti-fibrotic drugs proved the drug-responsiveness of the model.
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Affiliation(s)
- Ecem Saygili
- Department of Bioengineering, Ege University, Department of Bioengineering, Bornova, Izmir, 35040, TURKEY
| | - Utku Devamoglu
- Department of Bioengineering, Ege University, Department of Bioengineering, Bornova, Izmir, 35040, TURKEY
| | - Bakiye Goker-Bagca
- Department of Medical Biology, Adnan Menderes University, Department of Medical Biology, Aydin, Aydin, 09010, TURKEY
| | - Ozlem Goksel
- Department of Pulmonary Medicine / EgeSAM-Ege University Translational Pulmonary Research Center, Ege University, Bornova, Izmir, 35040, TURKEY
| | - Cigir Biray-Avci
- Department of Medical Biology, Ege University, Bornova, Izmir, 35040, TURKEY
| | - Tuncay Goksel
- Department of Pulmonary Medicine / EgeSAM-Ege University Translational Pulmonary Research Center, Ege University, Bornova, Izmir, 35040, TURKEY
| | - Ozlem Yesil-Celiktas
- Department of Bioengineering / EgeSAM-Ege University Translational Pulmonary Research Center, Ege University, Bornova, Izmir, 35040, TURKEY
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Mennen R, Hallmark N, Pallardy M, Bars R, Tinwell H, Piersma A. Genome-wide expression screening in the cardiac embryonic stem cell test shows additional differentiation routes that are regulated by morpholines and piperidines. Curr Res Toxicol 2022; 3:100086. [PMID: 36157598 PMCID: PMC9489494 DOI: 10.1016/j.crtox.2022.100086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 08/08/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
The cardiac embryonic stem cell test showed additional differentiation routes. Morpholines and piperidines regulated the alternative differentiation routes. The gene expression levels help in understanding the applicability domain.
The cardiac embryonic stem cell test (ESTc) is a well-studied non-animal alternative test method based on cardiac cell differentiation inhibition as a measure for developmental toxicity of tested chemicals. In the ESTc, a heterogenic cell population is generated besides cardiomyocytes. Using the full biological domain of ESTc may improve the sensitivity of the test system, possibly broadening the range of chemicals for which developmental effects can be detected in the test. In order to improve our knowledge of the biological and chemical applicability domains of the ESTc, we applied a hypothesis-generating data-driven approach on control samples as follows. A genome-wide expression screening was performed, using Next Generation Sequencing (NGS), to map the range of developmental pathways in the ESTc and to search for a predictive embryotoxicity biomarker profile, instead of the conventional read-out of beating cardiomyocytes. The detected developmental pathways included circulatory system development, skeletal system development, heart development, muscle and organ tissue development, and nervous system and cell development. Two pesticidal chemical classes, the morpholines and piperidines, were assessed for perturbation of differentiation in the ESTc using NGS. In addition to the anticipated impact on cardiomyocyte differentiation, the other developmental pathways were also regulated, in a concentration–response fashion. Despite the structural differences between the morpholine and piperidine pairs, their gene expression effect patterns were largely comparable. In addition, some chemical-specific gene regulation was also observed, which may help with future mechanistic understanding of specific effects with individual test compounds. These similar and unique regulations of gene expression profiles by the test compounds, adds to our knowledge of the chemical applicability domain, specificity and sensitivity of the ESTc. Knowledge of both the biological and chemical applicability domain contributes to the optimal placement of ESTc in test batteries and in Integrated Approaches to Testing and Assessment (IATA).
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Affiliation(s)
- R.H. Mennen
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Corresponding author at: National Institute for Public Health and Environment (RIVM), Centre for Health Protection (GZB), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands.
| | - N. Hallmark
- Bayer AG Crop Science Division, Monheim, Germany
| | - M. Pallardy
- Inflammation, Microbiome and Immunosurveillance, Université Paris-Saclay, INSERM UMR996, Châtenay-Malabry 92296, France
| | - R. Bars
- Bayer Crop Science, Sophia-Antipolis, France
| | - H. Tinwell
- Bayer Crop Science, Sophia-Antipolis, France
| | - A.H. Piersma
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, the Netherlands
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Yuan Y, Li Y, Qiao G, Zhou Y, Xu Z, Hill C, Jiang Z, Wang Y. Hyperbaric Oxygen Ameliorates Bleomycin-Induced Pulmonary Fibrosis in Mice. Front Mol Biosci 2021; 8:675437. [PMID: 34150851 PMCID: PMC8211992 DOI: 10.3389/fmolb.2021.675437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/30/2021] [Indexed: 11/25/2022] Open
Abstract
The prevalence of pulmonary fibrosis is increasing with an aging population and its burden is likely to increase following COVID-19, with large financial and medical implications. As approved therapies in pulmonary fibrosis only slow disease progression, there is a significant unmet medical need. Hyperbaric oxygen (HBO) is the inhaling of pure oxygen, under the pressure of greater than one atmosphere absolute, and it has been reported to improve pulmonary function in patients with pulmonary fibrosis. Our recent study suggested that repetitive HBO exposure may affect biological processes in mice lungs such as response to wounding and extracellular matrix. To extend these findings, a bleomycin-induced pulmonary fibrosis mouse model was used to evaluate the effect of repetitive HBO exposure on pulmonary fibrosis. Building on our previous findings, we provide evidence that HBO exposure attenuates bleomycin-induced pulmonary fibrosis in mice. In vitro, HBO exposure could reverse, at least partially, transforming growth factor (TGF)-β-induced fibroblast activation, and this effect may be mediated by downregulating TGF-β-induced expression of hypoxia inducible factor (HIF)-1α. These findings support HBO as a potentially life-changing therapy for patients with pulmonary fibrosis, although further research is needed to fully evaluate this.
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Affiliation(s)
- Yuan Yuan
- Department of Neurophysiology and Neuropharmacology, Institute of Special Environmental Medicine and Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Yali Li
- Department of Neurophysiology and Neuropharmacology, Institute of Special Environmental Medicine and Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Guoqiang Qiao
- Department of Neurophysiology and Neuropharmacology, Institute of Special Environmental Medicine and Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Yilu Zhou
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Zijian Xu
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Charlotte Hill
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Zhenglin Jiang
- Department of Neurophysiology and Neuropharmacology, Institute of Special Environmental Medicine and Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Yihua Wang
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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Koenitzer JR, Wu H, Atkinson JJ, Brody SL, Humphreys BD. Single-Nucleus RNA-Sequencing Profiling of Mouse Lung. Reduced Dissociation Bias and Improved Rare Cell-Type Detection Compared with Single-Cell RNA Sequencing. Am J Respir Cell Mol Biol 2021; 63:739-747. [PMID: 32804550 DOI: 10.1165/rcmb.2020-0095ma] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Single-cell RNA sequencing (scRNASeq) has advanced our understanding of lung biology, but its utility is limited by the need for fresh samples, loss of cell types by death or inadequate dissociation, and transcriptional stress responses induced during tissue digestion. Single-nucleus RNA sequencing (snRNASeq) has addressed these deficiencies in other tissues, but no protocol exists for lung tissue. We present a snRNASeq protocol and compare its results with those of scRNASeq. Two nuclear suspensions were prepared in lysis buffer on ice while one cell suspension was generated using enzymatic and mechanical dissociation. Cells and nuclei were processed using the 10× Genomics platform, and sequencing data were analyzed by Seurat. A total of 16,110 single-nucleus and 11,934 single-cell transcriptomes were generated. Gene detection rates were equivalent in snRNASeq and scRNASeq (∼1,700 genes and 3,000 unique molecular identifiers per cell) when mapping intronic and exonic reads. In the combined data, 89% of epithelial cells were identified by snRNASeq versus 22.2% of immune cells. snRNASeq transcriptomes are enriched for transcription factors and signaling proteins, with reduction in mitochondrial and stress-response genes. Both techniques improved mesenchymal cell detection over previous studies. Homeostatic signaling relationships among alveolar cell types were defined by receptor-ligand mapping using snRNASeq data, revealing interplay among epithelial, mesenchymal, and capillary endothelial cells. snRNASeq can be applied to archival murine lung samples, improves dissociation bias, eliminates artifactual gene expression, and provides similar gene detection compared with scRNASeq.
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Affiliation(s)
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, and
| | | | - Steven L Brody
- Division of Pulmonary and Critical Care, Department of Medicine
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, and.,Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
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