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Cao JB, Zhu ST, Huang XS, Wang XY, Wu ML, Li X, Liu FL, Chen L, Zheng YT, Wang JH. Mast cell degranulation-triggered by SARS-CoV-2 induces tracheal-bronchial epithelial inflammation and injury. Virol Sin 2024; 39:309-318. [PMID: 38458399 DOI: 10.1016/j.virs.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/27/2024] [Indexed: 03/10/2024] Open
Abstract
SARS-CoV-2 infection-induced hyper-inflammation is a key pathogenic factor of COVID-19. Our research, along with others', has demonstrated that mast cells (MCs) play a vital role in the initiation of hyper-inflammation caused by SARS-CoV-2. In previous study, we observed that SARS-CoV-2 infection induced the accumulation of MCs in the peri-bronchus and bronchioalveolar-duct junction in humanized mice. Additionally, we found that MC degranulation triggered by the spike protein resulted in inflammation in alveolar epithelial cells and capillary endothelial cells, leading to subsequent lung injury. The trachea and bronchus are the routes for SARS-CoV-2 transmission after virus inhalation, and inflammation in these regions could promote viral spread. MCs are widely distributed throughout the respiratory tract. Thus, in this study, we investigated the role of MCs and their degranulation in the development of inflammation in tracheal-bronchial epithelium. Histological analyses showed the accumulation and degranulation of MCs in the peri-trachea of humanized mice infected with SARS-CoV-2. MC degranulation caused lesions in trachea, and the formation of papillary hyperplasia was observed. Through transcriptome analysis in bronchial epithelial cells, we found that MC degranulation significantly altered multiple cellular signaling, particularly, leading to upregulated immune responses and inflammation. The administration of ebastine or loratadine effectively suppressed the induction of inflammatory factors in bronchial epithelial cells and alleviated tracheal injury in mice. Taken together, our findings confirm the essential role of MC degranulation in SARS-CoV-2-induced hyper-inflammation and the subsequent tissue lesions. Furthermore, our results support the use of ebastine or loratadine to inhibit SARS-CoV-2-triggered degranulation, thereby preventing tissue damage caused by hyper-inflammation.
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Affiliation(s)
- Jian-Bo Cao
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; School of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Shu-Tong Zhu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiao-Shan Huang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xing-Yuan Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Meng-Li Wu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xin Li
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Feng-Liang Liu
- Key Laboratory of Bioactive Peptides of Yunnan Province, Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ling Chen
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yong-Tang Zheng
- Key Laboratory of Bioactive Peptides of Yunnan Province, Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| | - Jian-Hua Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 101408, China.
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2
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Natri HM, Del Azodi CB, Peter L, Taylor CJ, Chugh S, Kendle R, Chung MI, Flaherty DK, Matlock BK, Calvi CL, Blackwell TS, Ware LB, Bacchetta M, Walia R, Shaver CM, Kropski JA, McCarthy DJ, Banovich NE. Cell-type-specific and disease-associated expression quantitative trait loci in the human lung. Nat Genet 2024; 56:595-604. [PMID: 38548990 PMCID: PMC11018522 DOI: 10.1038/s41588-024-01702-0] [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: 03/21/2023] [Accepted: 02/28/2024] [Indexed: 04/04/2024]
Abstract
Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis. Defining the genetic control of gene expression in a cell-type-specific and context-dependent manner is critical for understanding the mechanisms through which genetic variation influences complex traits and disease pathobiology. To this end, we performed single-cell RNA sequencing of lung tissue from 66 individuals with pulmonary fibrosis and 48 unaffected donors. Using a pseudobulk approach, we mapped expression quantitative trait loci (eQTLs) across 38 cell types, observing both shared and cell-type-specific regulatory effects. Furthermore, we identified disease interaction eQTLs and demonstrated that this class of associations is more likely to be cell-type-specific and linked to cellular dysregulation in pulmonary fibrosis. Finally, we connected lung disease risk variants to their regulatory targets in disease-relevant cell types. These results indicate that cellular context determines the impact of genetic variation on gene expression and implicates context-specific eQTLs as key regulators of lung homeostasis and disease.
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Affiliation(s)
- Heini M Natri
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Christina B Del Azodi
- St. Vincent's Institute of Medical Research, Melbourne, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Lance Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J Taylor
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sagrika Chugh
- St. Vincent's Institute of Medical Research, Melbourne, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Melbourne, Victoria, Australia
- School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, Victoria, Australia
| | - Robert Kendle
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - David K Flaherty
- Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brittany K Matlock
- Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Carla L Calvi
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy S Blackwell
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
| | - Lorraine B Ware
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew Bacchetta
- Department of Cardiac Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rajat Walia
- Department of Thoracic Disease and Transplantation, Norton Thoracic Institute, Phoenix, AZ, USA
| | - Ciara M Shaver
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan A Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
| | - Davis J McCarthy
- St. Vincent's Institute of Medical Research, Melbourne, Victoria, Australia
- Melbourne Integrative Genomics, University of Melbourne, Melbourne, Victoria, Australia
- School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, Victoria, Australia
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3
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Vannan A, Lyu R, Williams AL, Negretti NM, Mee ED, Hirsh J, Hirsh S, Nichols DS, Calvi CL, Taylor CJ, Polosukhin VV, Serezani APM, McCall AS, Gokey JJ, Shim H, Ware LB, Bacchetta MJ, Shaver CM, Blackwell TS, Walia R, Sucre JMS, Kropski JA, McCarthy DJ, Banovich NE. Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571954. [PMID: 38168317 PMCID: PMC10760144 DOI: 10.1101/2023.12.15.571954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The human lung is structurally complex, with a diversity of specialized epithelial, stromal and immune cells playing specific functional roles in anatomically distinct locations, and large-scale changes in the structure and cellular makeup of this distal lung is a hallmark of pulmonary fibrosis (PF) and other progressive chronic lung diseases. Single-cell transcriptomic studies have revealed numerous disease-emergent/enriched cell types/states in PF lungs, but the spatial contexts wherein these cells contribute to disease pathogenesis has remained uncertain. Using sub-cellular resolution image-based spatial transcriptomics, we analyzed the gene expression of more than 1 million cells from 19 unique lungs. Through complementary cell-based and innovative cell-agnostic analyses, we characterized the localization of PF-emergent cell-types, established the cellular and molecular basis of classical PF histopathologic disease features, and identified a diversity of distinct molecularly-defined spatial niches in control and PF lungs. Using machine-learning and trajectory analysis methods to segment and rank airspaces on a gradient from normal to most severely remodeled, we identified a sequence of compositional and molecular changes that associate with progressive distal lung pathology, beginning with alveolar epithelial dysregulation and culminating with changes in macrophage polarization. Together, these results provide a unique, spatially-resolved characterization of the cellular and molecular programs of PF and control lungs, provide new insights into the heterogeneous pathobiology of PF, and establish analytical approaches which should be broadly applicable to other imaging-based spatial transcriptomic studies.
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Affiliation(s)
- Annika Vannan
- Translational Genomics Research Institute, Phoenix, AZ
| | - Ruqian Lyu
- St. Vincent’s Institute of Medical Research, Fitzroy, VIC, AUS
- Melbourne Integrative Genomics, University of Melbourne, Parkville, VIC, AUS
| | | | - Nicholas M. Negretti
- Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Evan D. Mee
- Translational Genomics Research Institute, Phoenix, AZ
| | - Joseph Hirsh
- Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Samuel Hirsh
- Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - David S. Nichols
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Carla L. Calvi
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Chase J. Taylor
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Vasiliy. V. Polosukhin
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ana PM Serezani
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - A. Scott McCall
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jason J. Gokey
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Heejung Shim
- Melbourne Integrative Genomics, University of Melbourne, Parkville, VIC, AUS
| | - Lorraine B. Ware
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew J. Bacchetta
- Department of Cardiac Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ciara M. Shaver
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy S. Blackwell
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
- Department of Veterans Affairs Medical Center, Nashville, TN
| | - Rajat Walia
- Department of Thoracic Disease and Transplantation, Norton Thoracic Institute, Phoenix, AZ, USA
| | - Jennifer MS Sucre
- Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Jonathan A. Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
- Department of Veterans Affairs Medical Center, Nashville, TN
| | - Davis J McCarthy
- St. Vincent’s Institute of Medical Research, Fitzroy, VIC, AUS
- Melbourne Integrative Genomics, University of Melbourne, Parkville, VIC, AUS
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4
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Urday P, Gayen nee’ Betal S, Sequeira Gomes R, Al-Kouatly HB, Solarin K, Chan JSY, Li D, Rahman I, Addya S, Boelig RC, Aghai ZH. SARS-CoV-2 Covid-19 Infection During Pregnancy and Differential DNA Methylation in Human Cord Blood Cells From Term Neonates. Epigenet Insights 2023; 16:25168657231184665. [PMID: 37425024 PMCID: PMC10328022 DOI: 10.1177/25168657231184665] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023] Open
Abstract
Background The global pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). About 18.4% of total Covid-19 cases were reported in children. Even though vertical transmission from mother to infant is likely to occur at a low rate, exposure to COVID-19 during fetal life may alter DNA methylation patterns with potential long-term effects. Objective To determine if COVID-19 infection during pregnancy alters the DNA methylation patterns in umbilical cord blood cells from term infants and to identify potential pathways and genes affected by exposure to COVID-19 infection. Methods Umbilical cord blood was collected from 8 infants exposed to COVID-19 during pregnancy and 8 control infants with no COVID-19 exposure. Genomic DNA was isolated from umbilical cord blood cells and genome-wide DNA methylation was performed using Illumina Methylation EPIC Array. Results 119 differentially methylated loci were identified at the FDR level of 0.20 (64 hypermethylated loci and 55 hypomethylated loci) in umbilical cord blood cells of COVID-19 exposed neonates compared to the control group. Important canonical pathways identified by Ingenuity Pathway Analysis (IPA) were related to stress response (corticotropin releasing hormone signaling, glucocorticoid receptor signaling, and oxytocin in brain signaling pathway), and cardiovascular disease and development (nitric oxide signaling in the cardiovascular system, apelin cardiomyocyte signaling pathways, factors promoting cardiogenesis, and renin-angiotensin signaling). The genes affected by the differential methylations were associated with cardiac, renal, hepatic, neurological diseases, developmental and immunological disorders. Conclusions COVID-19 induces differential DNA methylation in umbilical cord blood cells. The differentially methylated genes may contribute to hepatic, renal, cardiac, developmental and immunological disorders in offspring born to mothers with COVID-19 infection during pregnancy, and their developmental regulation.
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Affiliation(s)
- Pedro Urday
- Neonatology, Thomas Jefferson University/Nemours, Philadelphia, PA, USA
| | | | | | - Huda B Al-Kouatly
- Division of Maternal Fetal Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Kolawole Solarin
- Neonatology, Thomas Jefferson University/Nemours, Philadelphia, PA, USA
| | - Joanna SY Chan
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Dongmei Li
- Department of Clinical and Translational Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Sankar Addya
- Laboratory of Cancer Genomics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Rupsa C Boelig
- Division of Maternal Fetal Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zubair H Aghai
- Neonatology, Thomas Jefferson University/Nemours, Philadelphia, PA, USA
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5
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Natri HM, Del Azodi CB, Peter L, Taylor CJ, Chugh S, Kendle R, Chung MI, Flaherty DK, Matlock BK, Calvi CL, Blackwell TS, Ware LB, Bacchetta M, Walia R, Shaver CM, Kropski JA, McCarthy DJ, Banovich NE. Cell type-specific and disease-associated eQTL in the human lung. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533161. [PMID: 36993211 PMCID: PMC10055257 DOI: 10.1101/2023.03.17.533161] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis (PF). Defining the genetic control of gene expression in a cell-type-specific and context-dependent manner is critical for understanding the mechanisms through which genetic variation influences complex traits and disease pathobiology. To this end, we performed single-cell RNA-sequencing of lung tissue from 67 PF and 49 unaffected donors. Employing a pseudo-bulk approach, we mapped expression quantitative trait loci (eQTL) across 38 cell types, observing both shared and cell type-specific regulatory effects. Further, we identified disease-interaction eQTL and demonstrated that this class of associations is more likely to be cell-type specific and linked to cellular dysregulation in PF. Finally, we connected PF risk variants to their regulatory targets in disease-relevant cell types. These results indicate that cellular context determines the impact of genetic variation on gene expression, and implicates context-specific eQTL as key regulators of lung homeostasis and disease.
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6
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Oldham JM, Allen RJ, Lorenzo-Salazar JM, Molyneaux PL, Ma SF, Joseph C, Kim JS, Guillen-Guio B, Hernández-Beeftink T, Kropski JA, Huang Y, Lee CT, Adegunsoye A, Pugashetti JV, Linderholm AL, Vo V, Strek ME, Jou J, Muñoz-Barrera A, Rubio-Rodriguez LA, Hubbard R, Hirani N, Whyte MKB, Hart S, Nicholson AG, Lancaster L, Parfrey H, Rassl D, Wallace W, Valenzi E, Zhang Y, Mychaleckyj J, Stockwell A, Kaminski N, Wolters PJ, Molina-Molina M, Banovich NE, Fahy WA, Martinez FJ, Hall IP, Tobin MD, Maher TM, Blackwell TS, Yaspan BL, Jenkins RG, Flores C, Wain LV, Noth I. PCSK6 and Survival in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2023; 207:1515-1524. [PMID: 36780644 PMCID: PMC10263132 DOI: 10.1164/rccm.202205-0845oc] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 02/13/2023] [Indexed: 02/15/2023] Open
Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) is a devastating disease characterized by limited treatment options and high mortality. A better understanding of the molecular drivers of IPF progression is needed. Objectives: To identify and validate molecular determinants of IPF survival. Methods: A staged genome-wide association study was performed using paired genomic and survival data. Stage I cases were drawn from centers across the United States and Europe and stage II cases from Vanderbilt University. Cox proportional hazards regression was used to identify gene variants associated with differential transplantation-free survival (TFS). Stage I variants with nominal significance (P < 5 × 10-5) were advanced for stage II testing and meta-analyzed to identify those reaching genome-wide significance (P < 5 × 10-8). Downstream analyses were performed for genes and proteins associated with variants reaching genome-wide significance. Measurements and Main Results: After quality controls, 1,481 stage I cases and 397 stage II cases were included in the analysis. After filtering, 9,075,629 variants were tested in stage I, with 158 meeting advancement criteria. Four variants associated with TFS with consistent effect direction were identified in stage II, including one in an intron of PCSK6 (proprotein convertase subtilisin/kexin type 6) reaching genome-wide significance (hazard ratio, 4.11 [95% confidence interval, 2.54-6.67]; P = 9.45 × 10-9). PCSK6 protein was highly expressed in IPF lung parenchyma. PCSK6 lung staining intensity, peripheral blood gene expression, and plasma concentration were associated with reduced TFS. Conclusions: We identified four novel variants associated with IPF survival, including one in PCSK6 that reached genome-wide significance. Downstream analyses suggested that PCSK6 protein plays a potentially important role in IPF progression.
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Affiliation(s)
- Justin M. Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | - Richard J. Allen
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Jose M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Shwu-Fan Ma
- Division of Pulmonary and Critical Care Medicine and
| | | | - John S. Kim
- Division of Pulmonary and Critical Care Medicine and
| | - Beatriz Guillen-Guio
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Tamara Hernández-Beeftink
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Jonathan A. Kropski
- Division of Pulmonary and Critical Care Medicine, Vanderbilt University, Nashville, Tennessee
| | - Yong Huang
- Division of Pulmonary and Critical Care Medicine and
| | - Cathryn T. Lee
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Ayodeji Adegunsoye
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Janelle Vu Pugashetti
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Angela L. Linderholm
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Vivian Vo
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Mary E. Strek
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Jonathan Jou
- Department of Surgery, College of Medicine, University of Illinois, Peoria, Illinois
| | - Adrian Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodriguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Richard Hubbard
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Nik Hirani
- Medical Research Council Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Moira K. B. Whyte
- Medical Research Council Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Simon Hart
- Respiratory Research Group, Hull York Medical School, Castle Hill Hospital, Cottingham, United Kingdom
| | - Andrew G. Nicholson
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Lisa Lancaster
- Division of Pulmonary and Critical Care Medicine, Vanderbilt University, Nashville, Tennessee
| | - Helen Parfrey
- Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital, Cambridge, United Kingdom
| | - Doris Rassl
- Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital, Cambridge, United Kingdom
| | - William Wallace
- Medical Research Council Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Eleanor Valenzi
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Josyf Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | | | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, Yale University, New Haven, Connecticut
| | - Paul J. Wolters
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, California
| | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge, Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | | | - William A. Fahy
- Discovery Medicine, GlaxoSmithKline, Stevenage, United Kingdom
| | | | - Ian P. Hall
- Division of Respiratory Medicine and
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, California; and
| | - Timothy S. Blackwell
- Division of Pulmonary and Critical Care Medicine, Vanderbilt University, Nashville, Tennessee
| | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine and
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7
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Cury S, Oliveira J, Biagi-Júnior C, Silva Jr W, Reis P, Cabral-Marques O, Hasimoto E, Freire P, Carvalho R. Transcriptional profiles and common genes link lung cancer with the development and severity of COVID-19. Gene 2023; 852:147047. [PMID: 36379381 PMCID: PMC9659360 DOI: 10.1016/j.gene.2022.147047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/14/2022]
Abstract
Lung cancer patients with COVID-19 present an increased risk of developing severe disease and, consequently, have poor outcomes. Determining SARS-CoV-2-host interactome in lung cancer cells and tissues, infected or uninfected with SARS-CoV-2, may reveal molecular mechanisms associated with COVID-19 development and severity in lung cancer patients. Here, we integrated transcriptome data of lung tumors from patients with small- or non-small cell lung cancer (SCLC and NSCLC) and normal lung and lung cancer cells infected with SARS-CoV-2. We aimed to characterize molecular mechanisms potentially associated with COVID-19 development and severity in lung cancer patients and to predict the SARS-CoV-2-host cell interactome. We found that the gene expression profiles of lung cell lines infected with SARS-CoV-2 resemble more primary lung tumors than non-malignant lung tissues. In addition, the transcriptomic-based interactome analysis of SCLC and NSCLC revealed increased expression of cancer genes BRCA1 and CENPF, whose proteins are known or predicted to interact with the SARS-CoV-2 spike glycoprotein and helicase, respectively. We also found that TRIB3, a gene coding a putative host-SARS-CoV-2 interacting protein associated with COVID-19 infection, is co-expressed with the up-regulated genes MTHFD2, ADM2, and GPT2 in all tested conditions. Our analysis identified biological processes such as amino acid metabolism and angiogenesis and 22 host mediators of SARS-CoV-2 infection and replication that may contribute to the development and severity of COVID-19 in lung cancers.
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Affiliation(s)
- S.S. Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - J.S. Oliveira
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - C.A.O. Biagi-Júnior
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil,Institute for Cancer Research (IPEC), Guarapuava, PR, Brazil
| | - W.A. Silva Jr
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil,Institute for Cancer Research (IPEC), Guarapuava, PR, Brazil
| | - P.P. Reis
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - O. Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil,Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil,Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo, SP, Brazil,Department of Pharmacy and Postgraduate Program of Health and Science, Federal University of Rio Grande do Norte (UFRN), Natal, RN, Brazil
| | - E.N. Hasimoto
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - P.P. Freire
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil,Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil,Corresponding authors at: Department of Immunology, Institute of Biomedical Sciences - University of São Paulo, Lineu Prestes Avenue, 1730 São Paulo, Brazil (P.P. Freire). Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), CEP: 18.618-689, Botucatu, São Paulo, Brazil (R.F. Carvalho)
| | - R.F. Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil,Lead Contact,Corresponding authors at: Department of Immunology, Institute of Biomedical Sciences - University of São Paulo, Lineu Prestes Avenue, 1730 São Paulo, Brazil (P.P. Freire). Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), CEP: 18.618-689, Botucatu, São Paulo, Brazil (R.F. Carvalho)
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8
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Li F, Deng J, Song Y, Wu C, Yu B, Wang G, Li J, Zhong Y, Liang F. Pulmonary fibrosis in patients with COVID-19: A retrospective study. Front Cell Infect Microbiol 2022; 12:1013526. [PMID: 36619759 PMCID: PMC9811255 DOI: 10.3389/fcimb.2022.1013526] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) pandemic has caused substantial threats to people's physical health and lives, claiming the lives of over 6 million people worldwide. Although the mortality rate of COVID-19 is very low, many survivors may have different degrees and various sequelae. Previous studies have shown that pulmonary fibrosis (PF) were common on discharged COVID-19 patients, and PF itself is a poor prognostic factor. Methods 227 COVID-19 hospitalized patients' clinical and laboratory data from the first 15 days following admission were collected in this retrospective study. Groups were based on with or without PF of COVID-19. Categorical variables were compared with the chi-square test or Fisher's exact test. Continuous variables were tested by Wilcoxon rank-sum test for the non-normal distribution. Spearman correlations were used to assess the correlations between PF with clinic parameters of multiple time points. Univariate and multivariate logistic regression were used to analyze for risk factors of COVID-19 patients with pulmonary fibrosis. Results Sixty cases of COVID-19 patients were diagnosed with PF. Compared with 167 non-PF patients, those with PF were older and had higher proportions of fever, shortness of breath, hemoptysis, abdominal pain, hypertension, cardiovascular, diabetes, high flow nasal cannula (HFNC), severe disease, and virus shedding duration. Furthermore, the correlation analysis between PF and clinic parameters showed that PF were positively related to the C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR), and negatively correlated with hemoglobin (HGB) and albumin (ALB) at all time points in the first 15 days after admission. Moreover, We found that PF were significantly correlated with coagulation indexes prothrombin time (PT), activated partial thromboplastin time (APTT), fibrinogen (Fib) and fibrinolysis index D-Dimer at some phases. In addition, Univariate logistic regression analyses showed that age, fever, shortness of breath, hemoptysis, hypertension, cardiovascular, diabetes, HFNC, severe disease were the risk factors of COVID-19 patients with PF. However, multivariate logistic regression showed that age was the risk factor of COVID-19 patients with PF. Conclusion Combining various factors, advanced age is an independent risk factor of COVID-19 patients with PF. PF was significantly related with clinic parameter of inflammation/coagulopathy/fibrinolysis.
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Affiliation(s)
- Fanglin Li
- Department of Hematology and Key Laboratory of Non-resolving Inflammation and Cancer of Hunan Province, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiayi Deng
- Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yongqiang Song
- Critical Care Medicine, Renmin Hospital of Yiyang, Yiyang, Hunan, China
| | - Chenfang Wu
- Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bo Yu
- Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guyi Wang
- Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jinxiu Li
- Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yanjun Zhong
- Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Yanjun Zhong, ; Fang Liang,
| | - Fang Liang
- Department of Hematology and Key Laboratory of Non-resolving Inflammation and Cancer of Hunan Province, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Yanjun Zhong, ; Fang Liang,
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9
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Miura Y, Ohkubo H, Nakano A, Bourke JE, Kanazawa S. Pathophysiological conditions induced by SARS-CoV-2 infection reduce ACE2 expression in the lung. Front Immunol 2022; 13:1028613. [PMID: 36405683 PMCID: PMC9673245 DOI: 10.3389/fimmu.2022.1028613] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/14/2022] [Indexed: 04/03/2024] Open
Abstract
SARS-CoV-2 infection causes a variety of physiological responses in the lung, and understanding how the expression of SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE2), and its proteolytic activator, transmembrane serine protease 2 (TMPRSS2), are affected in patients with underlying disease such as interstitial pneumonia will be important in considering COVID-19 progression. We examined the expression of ACE2 and TMPRSS2 in an induced usual interstitial pneumonia (iUIP) mouse model and patients with IPF as well as the changes in whole-lung ACE2 and TMPRSS2 expression under physiological conditions caused by viral infection. Histopathological and biochemical characteristics were analyzed using human specimens from patients with IPF and precision-cut lung slices (PCLS) from iUIP mouse model showing UIP with honeycombing and severe fibrosis after non-specific interstitial pneumonia. ACE2 expression decreased with acute lung inflammation and increased in the abnormal lung epithelium of the iUIP mouse model. ACE2 is also expressed in metaplastic epithelial cells. Poly(I:C), interferons, and cytokines associated with fibrosis decreased ACE2 expression in PCLS in the iUIP model. Hypoxia also decreases ACE2 via HIF1α in PCLS. Antifibrotic agent, nintedanib attenuates ACE2 expression in invasive epithelial cells. Patients with IPF are at a higher risk of SARS-CoV-2 infection due to the high expression of ACE2. However, ACE2 and TMPRSS2 expression is decreased by immune intermediaries, including interferons and cytokines that are associated with viral infection and upon administration of antifibrotic agents, suggesting that most of the viral infection-induced pathophysiological responses aid the development of resistance against SARS-CoV-2 infection.
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Affiliation(s)
- Yoko Miura
- Department of Neurodevelopmental Disorder Genetics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Hirotsugu Ohkubo
- Department of Respiratory Medicine, Allergy and Clinical Immunology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Akiko Nakano
- Department of Respiratory Medicine, Allergy and Clinical Immunology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Jane E. Bourke
- Department of Pharmacology, Biomedicine Discovery Institute, Monash University, Clayton, VA, Australia
| | - Satoshi Kanazawa
- Department of Neurodevelopmental Disorder Genetics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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10
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COVID-19 in patients with chronic lung disease. Clin Chest Med 2022; 44:385-393. [PMID: 37085227 PMCID: PMC9678841 DOI: 10.1016/j.ccm.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that causes an acute respiratory tract infection known as coronavirus disease 2019 (COVID-19). SARS-CoV-2 enters cells by binding the ACE2 receptor and coreceptors notably TMPRSS2 or Cathepsin L. Severe COVID-19 infection can lead to acute lung injury. Below we describe the current evidence of the impact of common chronic lung diseases (CLDs) on the development of COVID-19. The impact of treatment of CLD on COVID-19 and any risk of vaccination in patients with CLD are considered.
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11
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Johansen MD, Mahbub RM, Idrees S, Nguyen DH, Miemczyk S, Pathinayake P, Nichol K, Hansbro NG, Gearing LJ, Hertzog PJ, Gallego-Ortega D, Britton WJ, Saunders BM, Wark PA, Faiz A, Hansbro PM. Increased SARS-CoV-2 Infection, Protease, and Inflammatory Responses in Chronic Obstructive Pulmonary Disease Primary Bronchial Epithelial Cells Defined with Single-Cell RNA Sequencing. Am J Respir Crit Care Med 2022; 206:712-729. [PMID: 35549656 PMCID: PMC9799113 DOI: 10.1164/rccm.202108-1901oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Rationale: Patients with chronic obstructive pulmonary disease (COPD) develop more severe coronavirus disease (COVID-19); however, it is unclear whether they are more susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and what mechanisms are responsible for severe disease. Objectives: To determine whether SARS-CoV-2 inoculated primary bronchial epithelial cells (pBECs) from patients with COPD support greater infection and elucidate the effects and mechanisms involved. Methods: We performed single-cell RNA sequencing analysis on differentiated pBECs from healthy subjects and patients with COPD 7 days after SARS-CoV-2 inoculation. We correlated changes with viral titers, proinflammatory responses, and IFN production. Measurements and Main Results: Single-cell RNA sequencing revealed that COPD pBECs had 24-fold greater infection than healthy cells, which was supported by plaque assays. Club/goblet and basal cells were the predominant populations infected and expressed mRNAs involved in viral replication. Proteases involved in SARS-CoV-2 entry/infection (TMPRSS2 and CTSB) were increased, and protease inhibitors (serpins) were downregulated more so in COPD. Inflammatory cytokines linked to COPD exacerbations and severe COVID-19 were increased, whereas IFN responses were blunted. Coexpression analysis revealed a prominent population of club/goblet cells with high type 1/2 IFN responses that were important drivers of immune responses to infection in both healthy and COPD pBECs. Therapeutic inhibition of proteases and inflammatory imbalances reduced viral titers and cytokine responses, particularly in COPD pBECs. Conclusions: COPD pBECs are more susceptible to SARS-CoV-2 infection because of increases in coreceptor expression and protease imbalances and have greater inflammatory responses. A prominent cluster of IFN-responsive club/goblet cells emerges during infection, which may be important drivers of immunity. Therapeutic interventions suppress SARS-CoV-2 replication and consequent inflammation.
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Affiliation(s)
- Matt D. Johansen
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Rashad M. Mahbub
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Sobia Idrees
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Duc H. Nguyen
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Stefan Miemczyk
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Prabuddha Pathinayake
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, Australia
| | - Kristy Nichol
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, Australia
| | - Nicole G. Hansbro
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Linden J. Gearing
- Department of Molecular and Translational Sciences, School of Clinical Sciences at Monash Health, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Monash University, Clayton, Victoria, Australia
| | - Paul J. Hertzog
- Department of Molecular and Translational Sciences, School of Clinical Sciences at Monash Health, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Monash University, Clayton, Victoria, Australia
| | - David Gallego-Ortega
- Faculty of Engineering and Information Technology, School of Biomedical Engineering, Centre for Single Cell Technology, University of Technology Sydney, Ultimo, New South Wales, Australia;,Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia;,St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales Sydney, Kensington, New South Wales, Australia; and
| | - Warwick J. Britton
- Centenary Institute, University of Sydney and Department of Clinical Immunology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Bernadette M. Saunders
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Peter A. Wark
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, Australia
| | - Alen Faiz
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Philip M. Hansbro
- Faculty of Science, School of Life Sciences, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, New South Wales, Australia;,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, Australia
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12
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Ikonomou L, Magnusson M, Dries R, Herzog EL, Hynds RE, Borok Z, Park JA, Skolasinski S, Burgess JK, Turner L, Mojarad SM, Mahoney JE, Lynch T, Lehmann M, Thannickal VJ, Hook JL, Vaughan AE, Hoffman ET, Weiss DJ, Ryan AL. Stem cells, cell therapies, and bioengineering in lung biology and disease 2021. Am J Physiol Lung Cell Mol Physiol 2022; 323:L341-L354. [PMID: 35762622 PMCID: PMC9484991 DOI: 10.1152/ajplung.00113.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/14/2022] [Accepted: 06/23/2022] [Indexed: 12/15/2022] Open
Abstract
The 9th biennial conference titled "Stem Cells, Cell Therapies, and Bioengineering in Lung Biology and Diseases" was hosted virtually, due to the ongoing COVID-19 pandemic, in collaboration with the University of Vermont Larner College of Medicine, the National Heart, Lung, and Blood Institute, the Alpha-1 Foundation, the Cystic Fibrosis Foundation, and the International Society for Cell & Gene Therapy. The event was held from July 12th through 15th, 2021 with a pre-conference workshop held on July 9th. As in previous years, the objectives remained to review and discuss the status of active research areas involving stem cells (SCs), cellular therapeutics, and bioengineering as they relate to the human lung. Topics included 1) technological advancements in the in situ analysis of lung tissues, 2) new insights into stem cell signaling and plasticity in lung remodeling and regeneration, 3) the impact of extracellular matrix in stem cell regulation and airway engineering in lung regeneration, 4) differentiating and delivering stem cell therapeutics to the lung, 5) regeneration in response to viral infection, and 6) ethical development of cell-based treatments for lung diseases. This selection of topics represents some of the most dynamic and current research areas in lung biology. The virtual workshop included active discussion on state-of-the-art methods relating to the core features of the 2021 conference, including in situ proteomics, lung-on-chip, induced pluripotent stem cell (iPSC)-airway differentiation, and light sheet microscopy. The conference concluded with an open discussion to suggest funding priorities and recommendations for future research directions in basic and translational lung biology.
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Affiliation(s)
- Laertis Ikonomou
- Department of Oral Biology, University at Buffalo, State University of New York, Buffalo, New York
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University at Buffalo, State University of New York, Buffalo, New York
| | - Mattias Magnusson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Ruben Dries
- Section of Hematology and Medical Oncology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Erica L Herzog
- Yale Interstitial Lung Disease Center of Excellence, Pulmonary and Critical Care Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Robert E Hynds
- Epithelial Cell Biology in ENT Research Group, Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Zea Borok
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, San Diego, California
| | - Jin-Ah Park
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | | | - Janette K Burgess
- Department of Pathology and Medical Biology, Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Leigh Turner
- Department of Health, Society, and Behavior, University of California, Irvine Program In Public Health, Irvine, California
| | - Sarah M Mojarad
- Engineering in Society Program, Viterbi School of Engineering, University of Southern California, Los Angeles, California
| | | | - Thomas Lynch
- Department of Surgery, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Mareike Lehmann
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center Munich, Helmholtz Zentrum München, Munich, Germany
| | - Victor J Thannickal
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Jamie L Hook
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York
- Global Health and Emerging Pathogens Institute, Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Andrew E Vaughan
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Evan T Hoffman
- Department of Medicine, University of Vermont, Burlington, Vermont
| | - Daniel J Weiss
- Department of Medicine, University of Vermont, Burlington, Vermont
| | - Amy L Ryan
- Hastings Center for Pulmonary Research, Department of Medicine, University of Southern California, Los Angeles, California
- Department of Stem Cell and Regenerative Medicine, University of Southern California, Los Angeles, California
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
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13
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Hoque MN, Sarkar MMH, Khan MA, Hossain MA, Hasan MI, Rahman MH, Habib MA, Akter S, Banu TA, Goswami B, Jahan I, Nafisa T, Molla MMA, Soliman ME, Araf Y, Khan MS, Zheng C, Islam T. Differential gene expression profiling reveals potential biomarkers and pharmacological compounds against SARS-CoV-2: Insights from machine learning and bioinformatics approaches. Front Immunol 2022; 13:918692. [PMID: 36059456 PMCID: PMC9429819 DOI: 10.3389/fimmu.2022.918692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/27/2022] [Indexed: 12/02/2022] Open
Abstract
The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has created an urgent global situation. Therefore, it is necessary to identify the differentially expressed genes (DEGs) in COVID-19 patients to understand disease pathogenesis and the genetic factor(s) responsible for inter-individual variability and disease comorbidities. The pandemic continues to spread worldwide, despite intense efforts to develop multiple vaccines and therapeutic options against COVID-19. However, the precise role of SARS-CoV-2 in the pathophysiology of the nasopharyngeal tract (NT) is still unfathomable. This study utilized machine learning approaches to analyze 22 RNA-seq data from COVID-19 patients (n = 8), recovered individuals (n = 7), and healthy individuals (n = 7) to find disease-related differentially expressed genes (DEGs). We compared dysregulated DEGs to detect critical pathways and gene ontology (GO) connected to COVID-19 comorbidities. We found 1960 and 153 DEG signatures in COVID-19 patients and recovered individuals compared to healthy controls. In COVID-19 patients, the DEG–miRNA, and DEG–transcription factors (TFs) interactions network analysis revealed that E2F1, MAX, EGR1, YY1, and SRF were the highly expressed TFs, whereas hsa-miR-19b, hsa-miR-495, hsa-miR-340, hsa-miR-101, and hsa-miR-19a were the overexpressed miRNAs. Three chemical agents (Valproic Acid, Alfatoxin B1, and Cyclosporine) were abundant in COVID-19 patients and recovered individuals. Mental retardation, mental deficit, intellectual disability, muscle hypotonia, micrognathism, and cleft palate were the significant diseases associated with COVID-19 by sharing DEGs. Finally, the detected DEGs mediated by TFs and miRNA expression indicated that SARS-CoV-2 infection might contribute to various comorbidities. Our results provide the common DEGs between COVID-19 patients and recovered humans, which suggests some crucial insights into the complex interplay between COVID-19 progression and the recovery stage, and offer some suggestions on therapeutic target identification in COVID-19 caused by the SARS-CoV-2.
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Affiliation(s)
- M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | | | - Md. Arif Khan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Md. Arju Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Md. Imran Hasan
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
| | - Md. Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
| | - Md. Ahashan Habib
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Shahina Akter
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Iffat Jahan
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Tasnim Nafisa
- National Institute of Laboratory Medicine and Referral Center, Dhaka, Bangladesh
| | | | - Mahmoud E. Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Yusha Araf
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - M. Salim Khan
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
- *Correspondence: Tofazzal Islam, ; Chunfu Zheng, ; Md. Salim Khan,
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
- *Correspondence: Tofazzal Islam, ; Chunfu Zheng, ; Md. Salim Khan,
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
- *Correspondence: Tofazzal Islam, ; Chunfu Zheng, ; Md. Salim Khan,
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14
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Eyres M, Bell JA, Davies ER, Fabre A, Alzetani A, Jogai S, Marshall BG, Johnston DA, Xu Z, Fletcher SV, Wang Y, Marshall G, Davies DE, Offer E, Jones MG. Spatially resolved deconvolution of the fibrotic niche in lung fibrosis. Cell Rep 2022; 40:111230. [PMID: 35977489 PMCID: PMC10073410 DOI: 10.1016/j.celrep.2022.111230] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/07/2022] [Accepted: 07/26/2022] [Indexed: 11/03/2022] Open
Abstract
A defining pathological feature of human lung fibrosis is localized tissue heterogeneity, which challenges the interpretation of transcriptomic studies that typically lose spatial information. Here we investigate spatial gene expression in diagnostic tissue using digital profiling technology. We identify distinct, region-specific gene expression signatures as well as shared gene signatures. By integration with single-cell data, we spatially map the cellular composition within and distant from the fibrotic niche, demonstrating discrete changes in homeostatic and pathologic cell populations even in morphologically preserved lung, while through ligand-receptor analysis, we investigate cellular cross-talk within the fibrotic niche. We confirm findings through bioinformatic, tissue, and in vitro analyses, identifying that loss of NFKB inhibitor zeta in alveolar epithelial cells dysregulates the TGFβ/IL-6 signaling axis, which may impair homeostatic responses to environmental stress. Thus, spatially resolved deconvolution advances understanding of cell composition and microenvironment in human lung fibrogenesis.
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Affiliation(s)
- Michael Eyres
- Medicines Discovery Catapult, Alderley Park, Cheshire, UK
| | - Joseph A Bell
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - Elizabeth R Davies
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK; Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Aurelie Fabre
- Department of Histopathology, St. Vincent's University Hospital & UCD School of Medicine, University College Dublin, Dublin, Ireland
| | - Aiman Alzetani
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK; University Hospital Southampton, Southampton, UK
| | - Sanjay Jogai
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK; University Hospital Southampton, Southampton, UK
| | - Ben G Marshall
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK; University Hospital Southampton, Southampton, UK
| | - David A Johnston
- Biomedical Imaging Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Zijian Xu
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK; Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Sophie V Fletcher
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK; University Hospital Southampton, Southampton, UK
| | - Yihua Wang
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK; Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK; Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Gayle Marshall
- Medicines Discovery Catapult, Alderley Park, Cheshire, UK
| | - Donna E Davies
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK; Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Emily Offer
- Medicines Discovery Catapult, Alderley Park, Cheshire, UK
| | - Mark G Jones
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK; Institute for Life Sciences, University of Southampton, Southampton, UK.
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15
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Kim SH, Jhun BW, Jeong BH, Park HY, Kim H, Kwon OJ, Shin SH. The Higher Incidence of COVID-19 in Patients With Non-Tuberculous Mycobacterial Pulmonary Disease: A Single Center Experience in Korea. J Korean Med Sci 2022; 37:e250. [PMID: 35971764 PMCID: PMC9424694 DOI: 10.3346/jkms.2022.37.e250] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/05/2022] [Indexed: 11/20/2022] Open
Abstract
The aim of our study was to investigate the incidence of and risk factors for coronavirus disease 2019 (COVID-19) in patients with non-tuberculous mycobacterial-pulmonary disease (NTM-PD). A total of 3,866 patients with NTM-PD were retrospectively identified from a single center. Compared to the general population of Korea, patients with NTM-PD had a substantially increased age-standardized incidence of COVID-19 from January 2020 to February 2021 (2.1% vs. 0.2%). The odds of being infected with COVID-19 was particularly higher in patients who received treatment for NTM-PD than in those who did not receive treatment for NTM-PD (adjusted odd ratio = 1.99, 95% confidence interval = 1.09-3.64, P = 0.026). Patients with NTM-PD might be regarded as a high-risk group for COVID-19 and may need a more proactive preventive strategy for COVID-19 and other pandemics in the future.
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Affiliation(s)
- Sang Hyuk Kim
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Seoul, Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Byeong-Ho Jeong
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hye Yun Park
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hojoong Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - O Jung Kwon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun Hye Shin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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16
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Cinti F, Cinti S. The Endocrine Adipose Organ: A System Playing a Central Role in COVID-19. Cells 2022; 11:cells11132109. [PMID: 35805193 PMCID: PMC9265618 DOI: 10.3390/cells11132109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/26/2022] [Accepted: 06/30/2022] [Indexed: 02/01/2023] Open
Abstract
In the last 30 years the adipose cell has been object of several studies, turning its reputation from an inert cell into the main character involved in the pathophysiology of multiple diseases, including the ongoing COVID-19 pandemic, which has changed the clinical scenario of the last two years. Composed by two types of tissue (white and brown), with opposite roles, the adipose organ is now classified as a real endocrine organ whose dysfunction is involved in different diseases, mainly obesity and type 2 diabetes. In this mini-review we aim to retrace the adipose organ history from physiology to physiopathology, to provide therapeutic perspectives for the prevention and treatment of its two main related diseases (obesity and type 2 diabetes) and to summarize the most recent discoveries linking adipose tissue to COVID-19.
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Affiliation(s)
- Francesca Cinti
- UOS Centro Malattie Endocrine e Metaboliche, UOC Endocrinologia e Diabetologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Roma, Italy;
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
| | - Saverio Cinti
- Center of Obesity, Department of Experimental and Clinical Medicine, Marche Polytechnic University, 60126 Ancona, Italy
- Correspondence: or ; Tel.: +39-3396936172
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17
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Mortality among Patients with SARS-CoV-2 and Different Interstitial Lung Disease Subtypes: A Multicenter Cohort Study. Ann Am Thorac Soc 2022; 19:1435-1437. [PMID: 35499867 PMCID: PMC9353962 DOI: 10.1513/annalsats.202202-137rl] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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18
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Basolo A, Poma AM, Bonuccelli D, Proietti A, Macerola E, Ugolini C, Torregrossa L, Giannini R, Vignali P, Basolo F, Santini F, Toniolo A. Adipose tissue in COVID-19: detection of SARS-CoV-2 in adipocytes and activation of the interferon-alpha response. J Endocrinol Invest 2022; 45:1021-1029. [PMID: 35169984 PMCID: PMC8852916 DOI: 10.1007/s40618-022-01742-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/07/2022] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Obesity is a recognized risk factor for the progression to severe forms of COVID-19, yet the mechanisms of the association are unclear. METHODS Subcutaneous abdominal adipose tissue specimens of subjects deceased from COVID-19 (n = 23) were compared to those of controls dying abruptly from causes other than infectious (accidental trauma, sudden cardiac death). Alterations of lung parenchyma consistent with moderate to severe disease were detected in all COVID-19 cases, not in controls. Investigations included: histopathologic features, detection of virus antigens and genome, characterization of infiltrating leukocytes, transcription levels of immune-related genes. RESULTS By RT-PCR, the SARS-CoV-2 genome was detected in the adipose tissue of 13/23 (56%) cases of the COVID-19 cohort. The virus nucleocapsid antigen was detected in the cytoplasm of 1-5% adipocytes in 12/12 COVID-19 cases that were virus-positive by PCR in the adipose tissue (one case could not be assessed due insufficient tissue). The adipose tissue of COVID-19 cases showed leukocyte infiltrates and upregulation of the interferon-alpha pathway. After adjusting for age and sex, the activation score of IFN-alpha was directly related with transcription levels of the ACE2 gene, a key entry factor of SARS-CoV-2. CONCLUSIONS In lethal COVID-19 cases, the SARS-CoV-2 nucleocapsid antigen has been detected in a sizeable proportion of adipocytes, showing that the virus may directly infect the parenchymal cells of subcutaneous fat. Infection appears to activate the IFN alpha pathway and to attract infiltrating leukocytes. Due to the huge numbers of adipocytes in adults, the adipose tissue represents a significant reservoir for SARS-CoV-2 and an important source of inflammatory mediators.
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Affiliation(s)
- A. Basolo
- Obesity and Lipodystrophy Center, Endocrinology Unit, University Hospital of Pisa, 56124 Pisa, Italy
| | - A. M. Poma
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - D. Bonuccelli
- Department of Forensic Medicine, Azienda USL Toscana Nordovest, Lucca, Italy
| | - A. Proietti
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - E. Macerola
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - C. Ugolini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - L. Torregrossa
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - R. Giannini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - P. Vignali
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - F. Basolo
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, Pisa, Italy
| | - F. Santini
- Obesity and Lipodystrophy Center, Endocrinology Unit, University Hospital of Pisa, 56124 Pisa, Italy
| | - A. Toniolo
- Global Virus Network, University of Insubria, 21100 Varese, Italy
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19
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Serezani AP, Pascoalino BD, Bazzano J, Vowell KN, Tanjore H, Taylor CJ, Calvi CL, Mccall SA, Bacchetta MD, Shaver CM, Ware LB, Salisbury ML, Banovich NE, Kendall PL, Kropski JA, Blackwell TS. Multi-Platform Single-Cell Analysis Identifies Immune Cell Types Enhanced in Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2022; 67:50-60. [PMID: 35468042 PMCID: PMC9273229 DOI: 10.1165/rcmb.2021-0418oc] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Immune cells have been implicated in Idiopathic Pulmonary Fibrosis (IPF), but the phenotypes and effector mechanisms of these cells remain incompletely characterized. We performed mass cytometry to quantify immune/inflammatory cell subsets in lungs of 12 patients with IPF and 15 organ donors without chronic lung disease and utilized existing single-cell RNA-sequencing (scRNA-seq) data to investigate transcriptional profiles of immune cells over-represented in IPF. Among myeloid cells, we found increased numbers of alveolar macrophages (AMØs) and dendritic cells (DCs) in IPF, as well as a subset of monocyte-derived DC. In contrast, monocyte-like cells and interstitial macrophages were reduced in IPF. Transcriptomic profiling identified an enrichment for interferon-γ (IFN-γ) response pathways in AMØs and DCs from IPF, as well as antigen processing in DCs and phagocytosis in AMØs. Among T cells, we identified three subset of memory T cells that were increased in IPF, including CD4+ and CD8+ resident memory T cells (TRM), and CD8+ effector memory (TEMRA) cells. The response to IFN-γ pathway was enriched in CD4 TRM and CD8 TRM cells in IPF, along with T cell activation and immune response-regulating signaling pathways. Increased AMØs, DCs, and memory T cells were present in IPF lungs compared to control subjects. In IPF, these cells possess an activation profile indicating increased IFN-γ signaling and up-regulation of adaptive immunity in the lungs. Together, these studies highlight critical features of the immunopathogenesis of IPF.
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Affiliation(s)
- Ana Pm Serezani
- Vanderbilt University Medical Center, 12328, Medicine, Nashville, Tennessee, United States;
| | | | - Julia Bazzano
- Vanderbilt University Medical Center, 12328, Nashville, Tennessee, United States
| | - Katherine N Vowell
- Vanderbilt University Medical Center, 12328, Nashville, Tennessee, United States
| | - Harikrishna Tanjore
- Vanderbilt University Medical Center, 12328, Medicine, Nashville, Tennessee, United States
| | - Chase J Taylor
- Vanderbilt University Medical Center, 12328, Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Nashville, Tennessee, United States
| | - Carla L Calvi
- Vanderbilt University Medical Center, 12328, Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Nashville, Tennessee, United States
| | - Scott A Mccall
- Vanderbilt University Medical Center, 12328, Medicine, Nashville, Tennessee, United States
| | - Matthew D Bacchetta
- Vanderbilt University Medical Center, 12328, Thoracic and Cardiac Surgery and Biomedical Engineering, Nashville, Tennessee, United States
| | - Ciara M Shaver
- Vanderbilt University Medical Center, 12328, Medicine, Nashville, Tennessee, United States
| | - Lorraine B Ware
- Vanderbilt University, 5718, Department of Internal Medicine, Division of Allergy, Pulmonary, and Critical Care, and Department of Pathology, Microbiology and Immunology, Nashville, Tennessee, United States
| | - Margaret L Salisbury
- Vanderbilt University Medical Center, 12328, Medicine, Nashville, Tennessee, United States
| | - Nicholas E Banovich
- Translational Genomics Research Institute, 10897, Phoenix, Arizona, United States
| | - Peggy L Kendall
- Washington University in St Louis, 7548, Internal Medicine, St Louis, Missouri, United States
| | - Jonathan A Kropski
- Vanderbilt University Medical Center, 12328, Medicine, Nashville, Tennessee, United States
| | - Timothy S Blackwell
- Vanderbilt University Medical Center, 12328, Medicine, Nashville, Tennessee, United States
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20
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Ravaglia C, Doglioni C, Chilosi M, Piciucchi S, Dubini A, Rossi G, Pedica F, Puglisi S, Donati L, Tomassetti S, Poletti V. Clinical, radiological, and pathological findings in patients with persistent lung disease following SARS-CoV-2 infection. Eur Respir J 2022; 60:13993003.02411-2021. [PMID: 35301248 PMCID: PMC8932282 DOI: 10.1183/13993003.02411-2021] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 02/13/2022] [Indexed: 12/18/2022]
Abstract
Some patients experience pulmonary sequelae after SARS-CoV-2 infection, ranging from self-limited abnormalities to major lung diseases. Morphological analysis of lung tissue may help our understanding of pathogenic mechanisms and help to provide consistent personalised management. The aim of this study was to ascertain morphological and immunomolecular features of lung tissue. Transbronchial lung cryobiopsy was carried out in patients with persistent symptoms and computed tomography suggestive of residual lung disease after recovery from SARS-CoV-2 infection. 164 patients were referred for suspected pulmonary sequelae after COVID-19; 10 patients with >5% parenchymal lung disease underwent lung biopsy. The histological pattern of lung disease was not homogeneous and three different case clusters could be identified, which was mirrored by their clinical and radiological features. Cluster 1 (“chronic fibrosing”) was characterised by post-infection progression of pre-existing interstitial pneumonias. Cluster 2 (“acute/subacute injury”) was characterised by different types and grades of lung injury, ranging from organising pneumonia and fibrosing nonspecific interstitial pneumonia to diffuse alveolar damage. Cluster 3 (“vascular changes”) was characterised by diffuse vascular increase, dilatation and distortion (capillaries and venules) within otherwise normal parenchyma. Clusters 2 and 3 had immunophenotypical changes similar to those observed in early/mild COVID-19 pneumonias (abnormal expression of STAT3 in hyperplastic pneumocytes and PD-L1, IDO and STAT3 in endothelial cells). This is the first study correlating histological/immunohistochemical patterns with clinical and radiological pictures of patients with post-COVID lung disease. Different phenotypes with potentially different underlying pathogenic mechanisms have been identified. Post-COVID lung disease is not a single entity, but includes different subtypes, each of them potentially requiring separate and different managementhttps://bit.ly/3BJDeUF
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Affiliation(s)
- Claudia Ravaglia
- Department of Thoracic Diseases, G.B. Morgagni Hospital/University of Bologna, Forlì, Italy
| | - Claudio Doglioni
- Department of Pathology, University Vita-Salute, Milan and San Raffaele Scientific Institute, Milan, Italy
| | - Marco Chilosi
- Department of Pathology, Pederzoli Hospital, Peschiera del Garda, Verona, Italy
| | - Sara Piciucchi
- Department of Radiology, G.B. Morgagni Hospital/University of Bologna, Forlì, Italy
| | - Alessandra Dubini
- Department of Pathology, G.B. Morgagni Hospital/University of Bologna, Forlì, Italy
| | - Giulio Rossi
- Department of Pathology, Fondazione Poliambulanza Istituto Ospedaliero Multispecialistico, Brescia, Italy
| | - Federica Pedica
- Department of Pathology, San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Puglisi
- Department of Thoracic Diseases, G.B. Morgagni Hospital/University of Bologna, Forlì, Italy
| | - Luca Donati
- Biostatistics and Clinical Trial Unit, Istituto Romagnolo per lo Studio dei Tumori "Dino Amadori"-IRST S.r.l., IRCCS, Meldola, Italy
| | - Sara Tomassetti
- Department of Experimental and Clinical Medicine, Careggi University Hospital, Firenze, Italy
| | - Venerino Poletti
- Department of Thoracic Diseases, G.B. Morgagni Hospital/University of Bologna, Forlì, Italy.,DIMES, University of Bologna, Bologna, Italy.,Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Aarhus, Denmark
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21
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Jin X, Zhang J, Li Y, Zhang Z, Cui T, Wang Y, Yao L, Yang X, Qu G, Zheng Y, Jiang G. Exogenous Chemical Exposure Increased Transcription Levels of the Host Virus Receptor Involving Coronavirus Infection. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:1854-1863. [PMID: 35049283 PMCID: PMC8790821 DOI: 10.1021/acs.est.1c07172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 05/28/2023]
Abstract
Virus receptors are highly involved in mediating the entrance of infectious viruses into host cells. Here, we found that typical chemical exposure caused the upregulation of virus receptor mRNA levels. Chemicals with the same structural characteristics can affect the transcription of angiotensin-converting enzyme 2 (ACE2), a dominant receptor of SARS-CoV-2. Some chemicals can also regulate the transcription of ACE2 by similar regulatory mechanisms, such as multilayer biological responses and the crucial role of TATA-box binding protein associated factor 6. The abovementioned finding suggested that chemical mixtures may have a joint effect on the ACE2 mRNA level in the real scenario, where humans are exposed to numerous chemicals simultaneously in daily life. Chemically regulated virus receptor transcription was in a tissue-dependent manner, with the highest sensitivity in pulmonary epithelial cells. Therefore, in addition to genetic factors, exogenous chemical exposure can be an emerging nongenetic factor that stimulates the transcription of virus receptor abundance and may elevate the protein expression. These alterations could ultimately give rise to the susceptibility to virus infection and disease severity. This finding highlights new requirements for sufficient epidemiological data about exposomes on pathogen receptors in the host.
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Affiliation(s)
- Xiaoting Jin
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, P. R. China
- Department
of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, P. R. China
| | - Jingxu Zhang
- Department
of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, P. R. China
| | - Yanting Li
- Department
of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, P. R. China
| | - Ze Zhang
- Department
of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, P. R. China
| | - Tenglong Cui
- Department
of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, P. R. China
| | - Yuanyuan Wang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, P. R. China
| | - Linlin Yao
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, P. R. China
| | - Xiaoxi Yang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, P. R. China
| | - Guangbo Qu
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, P. R. China
- College
of Resources and Environment, University
of Chinese Academy of Sciences, Beijing 100049, P. R.
China
- School
of Environment, Hangzhou Institute for Advanced
Study, UCAS, Hangzhou 310000, P. R. China
| | - Yuxin Zheng
- Department
of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, P. R. China
| | - Guibin Jiang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, P. R. China
- College
of Resources and Environment, University
of Chinese Academy of Sciences, Beijing 100049, P. R.
China
- School
of Environment, Hangzhou Institute for Advanced
Study, UCAS, Hangzhou 310000, P. R. China
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22
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Implications of testicular ACE2 and the renin-angiotensin system for SARS-CoV-2 on testis function. Nat Rev Urol 2022; 19:116-127. [PMID: 34837081 PMCID: PMC8622117 DOI: 10.1038/s41585-021-00542-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 12/16/2022]
Abstract
Although many studies have focused on SARS-CoV-2 infection in the lungs, comparatively little is known about the potential effects of the virus on male fertility. SARS-CoV-2 infection of target cells requires the presence of furin, angiotensin-converting enzyme 2 (ACE2) receptors, and transmembrane protease serine 2 (TMPRSS2). Thus, cells in the body that express these proteins might be highly susceptible to viral entry and downstream effects. Currently, reports regarding the expression of the viral entry proteins in the testes are conflicting; however, other members of the SARS-CoV family of viruses - such as SARS-CoV - have been suspected to cause testicular dysfunction and/or orchitis. SARS-CoV-2, which displays many similarities to SARS-CoV, could potentially cause similar adverse effects. Commonalities between SARS family members, taken in combination with sparse reports of testicular discomfort and altered hormone levels in patients with SARS-CoV-2, might indicate possible testicular dysfunction. Thus, SARS-CoV-2 infection has the potential for effects on testis somatic and germline cells and experimental approaches might be required to help identify potential short-term and long-term effects of SARS-CoV-2 on male fertility.
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23
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Giacomelli C, Piccarducci R, Marchetti L, Romei C, Martini C. Pulmonary fibrosis from molecular mechanisms to therapeutic interventions: lessons from post-COVID-19 patients. Biochem Pharmacol 2021; 193:114812. [PMID: 34687672 PMCID: PMC8546906 DOI: 10.1016/j.bcp.2021.114812] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 02/07/2023]
Abstract
Pulmonary fibrosis (PF) is characterised by several grades of chronic inflammation and collagen deposition in the interalveolar space and is a hallmark of interstitial lung diseases (ILDs). Recently, infectious agents have emerged as driving causes for PF development; however, the role of viral/bacterial infections in the initiation and propagation of PF is still debated. In this context, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the current coronavirus disease 2019 (COVID-19) pandemic, has been associated with acute respiratory distress syndrome (ARDS) and PF development. Although the infection by SARS-CoV-2 can be eradicated in most cases, the development of fibrotic lesions cannot be precluded; furthermore, whether these lesions are stable or progressive fibrotic events is still unknown. Herein, an overview of the main molecular mechanisms driving the fibrotic process together with the currently approved and newly proposed therapeutic solutions was given. Then, the most recent data that emerged from post-COVID-19 patients was discussed, in order to compare PF and COVID-19-dependent PF, highlighting shared and specific mechanisms. A better understanding of PF aetiology is certainly needed, also to develop effective therapeutic strategies and COVID-19 pathology is offering one more chance to do it. Overall, the work reported here could help to define new approaches for therapeutic intervention in the diversity of the ILD spectrum.
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Affiliation(s)
- Chiara Giacomelli
- Department of Pharmacy, University of Pisa, Via Bonanno 6, Pisa 56126, Italy
| | - Rebecca Piccarducci
- Department of Pharmacy, University of Pisa, Via Bonanno 6, Pisa 56126, Italy
| | - Laura Marchetti
- Department of Pharmacy, University of Pisa, Via Bonanno 6, Pisa 56126, Italy
| | - Chiara Romei
- Multidisciplinary Team of Interstitial Lung Disease, Radiology Department, Pisa University Hospital, Via Paradisa 2, Pisa 56124, Italy
| | - Claudia Martini
- Department of Pharmacy, University of Pisa, Via Bonanno 6, Pisa 56126, Italy,Corresponding author
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24
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Liberti DC, Morrisey EE. Organoid models: assessing lung cell fate decisions and disease responses. Trends Mol Med 2021; 27:1159-1174. [PMID: 34674972 DOI: 10.1016/j.molmed.2021.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 12/17/2022]
Abstract
Organoids can be derived from various cell types in the lung, and they provide a reproducible and tractable model for understanding the complex signals driving cell fate decisions in a regenerative context. In this review, we provide a retrospective account of organoid methodologies and outline new opportunities for optimizing these methods to further explore emerging concepts in lung biology. Moreover, we examine the benefits of integrating organoid assays with in vivo modeling to explore how the various niches and compartments in the respiratory system respond to both acute and chronic lung disease. The strategic implementation and improvement of organoid techniques will provide exciting new opportunities to understand and identify new therapeutic approaches to ameliorate lung disease states.
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Affiliation(s)
- Derek C Liberti
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Edward E Morrisey
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Yang J, Yan Y, Zhong W. Application of omics technology to combat the COVID-19 pandemic. MedComm (Beijing) 2021; 2:381-401. [PMID: 34766152 PMCID: PMC8554664 DOI: 10.1002/mco2.90] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022] Open
Abstract
As of August 27, 2021, the ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread to over 220 countries, areas, and territories. Thus far, 214,468,601 confirmed cases, including 4,470,969 deaths, have been reported to the World Health Organization. To combat the COVID-19 pandemic, multiomics-based strategies, including genomics, transcriptomics, proteomics, and metabolomics, have been used to study the diagnosis methods, pathogenesis, prognosis, and potential drug targets of COVID-19. In order to help researchers and clinicians to keep up with the knowledge of COVID-19, we summarized the most recent progresses reported in omics-based research papers. This review discusses omics-based approaches for studying COVID-19, summarizing newly emerged SARS-CoV-2 variants as well as potential diagnostic methods, risk factors, and pathological features of COVID-19. This review can help researchers and clinicians gain insight into COVID-19 features, providing direction for future drug development and guidance for clinical treatment, so that patients can receive appropriate treatment as soon as possible to reduce the risk of disease progression.
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Affiliation(s)
- Jingjing Yang
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
- School of Pharmaceutical SciencesHainan UniversityHaikouHainanChina
| | - Yunzheng Yan
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Wu Zhong
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
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Acevedo N, Escamilla-Gil JM, Espinoza H, Regino R, Ramírez J, Florez de Arco L, Dennis R, Torres-Duque CA, Caraballo L. Chronic Obstructive Pulmonary Disease Patients Have Increased Levels of Plasma Inflammatory Mediators Reported Upregulated in Severe COVID-19. Front Immunol 2021; 12:678661. [PMID: 34335580 PMCID: PMC8320593 DOI: 10.3389/fimmu.2021.678661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/28/2021] [Indexed: 12/29/2022] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is associated with increased risk of severe COVID-19, but the mechanisms are unclear. Besides, patients with severe COVID-19 have been reported to have increased levels of several immune mediators. Methods Ninety-two proteins were quantified in 315 plasma samples from 118 asthmatics, 99 COPD patients and 98 healthy controls (age 40-90 years), who were recruited in Colombia before the COVID-19 pandemic. Protein levels were compared between each disease group and healthy controls. Significant proteins were compared to the gene signatures of SARS-CoV-2 infection reported in the “COVID-19 Drug and Gene Set Library” and with experimentally tested protein biomarkers of severe COVID-19. Results Forty-one plasma proteins showed differences between patients and controls. Asthmatic patients have increased levels in IL-6 while COPD patients have a broader systemic inflammatory dysregulation driven by HGF, OPG, and several chemokines (CXCL9, CXCL10, CXCL11, CX3CL1, CXCL1, MCP-3, MCP-4, CCL3, CCL4 and CCL11). These proteins are involved in chemokine signaling pathways related with response to viral infections and some, were found up-regulated upon SARS-CoV-2 experimental infection of Calu-3 cells as reported in the COVID-19 Related Gene Sets database. An increase of HPG, CXCL9, CXCL10, IL-6, MCP-3, TNF and EN-RAGE has also been experimentally detected in patients with severe COVID-19. Conclusions COPD patients have altered levels of plasma proteins that have been reported increased in patients with severe COVID-19. Our study suggests that COPD patients have a systemic dysregulation in chemokine networks (including HGF and CXCL9) that could make them more susceptible to severe COVID-19. Also, that IL-6 levels are increased in some asthmatic patients (especially in females) and this may influence their response to COVID-19. The findings in this study depict a novel panel of inflammatory plasma proteins in COPD patients that may potentially associate with increased susceptibility to severe COVID-19 and might be useful as a biomarker signature after future experimental validation.
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Affiliation(s)
- Nathalie Acevedo
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
| | | | - Héctor Espinoza
- Informatic Unit, INMEDIT SAS and Faculty of Engineering, University of Cartagena, Cartagena, Colombia
| | - Ronald Regino
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
| | - Jonathan Ramírez
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
| | | | - Rodolfo Dennis
- Departamento de Investigaciones, Fundación Cardioinfantil, Bogotá, Colombia
| | - Carlos A Torres-Duque
- Research Department - CINEUMO, Fundación Neumológica Colombiana, Bogotá, Colombia.,Research Department and Specialization Program in Pulmonology, Universidad de la Sabana, Bogotá, Colombia
| | - Luis Caraballo
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
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