1
|
Dai J, Xu D, Yang C, Wang H, Chen D, Lin Z, Qiu S, Zhang L, Li X, Tian X, Liu Q, Cui Y, Zhou R, Liu W. Severe pneumonia and pathogenic damage in human airway epithelium caused by Coxsackievirus B4. Emerg Microbes Infect 2023; 12:2261560. [PMID: 37725516 PMCID: PMC10538465 DOI: 10.1080/22221751.2023.2261560] [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: 07/23/2023] [Accepted: 09/17/2023] [Indexed: 09/21/2023]
Abstract
Coxsackievirus B4 (CVB4) has one of the highest proportions of fatal outcomes of other enterovirus serotypes. However, the pathogenesis of severe respiratory disease caused by CVB4 infection remains unclear. In this study, 3 of 42 (7.2%, GZ-R6, GZ-R7 and GZ-R8) patients with severe pneumonia tested positive for CVB4 infection in southern China. Three full-length genomes of pneumonia-derived CVB4 were sequenced and annotated for the first time, showing their high nucleotide similarity and clustering within genotype V. To analyze the pathogenic damage caused by CVB4 in the lungs, a well-differentiated human airway epithelium (HAE) was established and infected with the pneumonia-derived CVB4 isolate GZ-R6. The outcome was compared with that of a severe hand-foot-mouth disease (HFMD)-derived CVB4 strain GZ-HFM01. Compared with HFMD-derived CVB4, pneumonia-derived CVB4 caused more intense and rapid disruption of HAE polarity, leading to tight-junction barrier disruption, loss of cilia, and airway epithelial cell hypertrophy. More pneumonia-derived CVB4 were released from the basolateral side of the HAE than HFMD-derived CVB4. Of the 18 cytokines tested, only IL-6 and IL-1b secretion significantly increased on bilateral sides of HAE during the early stage of pneumonia-derived CVB4 infection, while multiple cytokine secretions significantly increased in HFMD-derived CVB4-infected HAE. HFMD-derived CVB4 exhibited stronger neurovirulence in the human neuroblastoma cells SH-SY5Y than pneumonia-derived CVB4, which is consistent with the clinical manifestations of patients infected with these two viruses. This study has increased the depth of our knowledge of severe pneumonia infection caused by CVB4 and will benefit its prevention and treatment.
Collapse
Affiliation(s)
- Jing Dai
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Duo Xu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Chao Yang
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Huan Wang
- Scientific Research Center, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Dehui Chen
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zhengshi Lin
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Shuyan Qiu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Li Zhang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Xiao Li
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Xingui Tian
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Qian Liu
- Scientific Research Center, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Rong Zhou
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, People’s Republic of China
| |
Collapse
|
2
|
Leach T, Gandhi U, Reeves KD, Stumpf K, Okuda K, Marini FC, Walker SJ, Boucher R, Chan J, Cox LA, Atala A, Murphy SV. Development of a novel air-liquid interface airway tissue equivalent model for in vitro respiratory modeling studies. Sci Rep 2023; 13:10137. [PMID: 37349353 PMCID: PMC10287689 DOI: 10.1038/s41598-023-36863-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/12/2023] [Indexed: 06/24/2023] Open
Abstract
The human airways are complex structures with important interactions between cells, extracellular matrix (ECM) proteins and the biomechanical microenvironment. A robust, well-differentiated in vitro culture system that accurately models these interactions would provide a useful tool for studying normal and pathological airway biology. Here, we report the development and characterization of a physiologically relevant air-liquid interface (ALI) 3D airway 'organ tissue equivalent' (OTE) model with three novel features: native pulmonary fibroblasts, solubilized lung ECM, and hydrogel substrate with tunable stiffness and porosity. We demonstrate the versatility of the OTE model by evaluating the impact of these features on human bronchial epithelial (HBE) cell phenotype. Variations of this model were analyzed during 28 days of ALI culture by evaluating epithelial confluence, trans-epithelial electrical resistance, and epithelial phenotype via multispectral immuno-histochemistry and next-generation sequencing. Cultures that included both solubilized lung ECM and native pulmonary fibroblasts within the hydrogel substrate formed well-differentiated ALI cultures that maintained a barrier function and expressed mature epithelial markers relating to goblet, club, and ciliated cells. Modulation of hydrogel stiffness did not negatively impact HBE differentiation and could be a valuable variable to alter epithelial phenotype. This study highlights the feasibility and versatility of a 3D airway OTE model to model the multiple components of the human airway 3D microenvironment.
Collapse
Affiliation(s)
- Timothy Leach
- Wake Forest School of Medicine, Medical Center, Wake Forest Institute for Regenerative Medicine, 391 Technology Way, Winston-Salem, NC, 27101, USA
- Wake Forest School of Medicine, Medical Center Boulevard, Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Winston-Salem, NC, 27157, USA
| | - Uma Gandhi
- Wake Forest School of Medicine, Medical Center, Wake Forest Institute for Regenerative Medicine, 391 Technology Way, Winston-Salem, NC, 27101, USA
| | - Kimberly D Reeves
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Kristina Stumpf
- Wake Forest School of Medicine, Medical Center, Wake Forest Institute for Regenerative Medicine, 391 Technology Way, Winston-Salem, NC, 27101, USA
| | - Kenichi Okuda
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Frank C Marini
- Wake Forest School of Medicine, Medical Center, Wake Forest Institute for Regenerative Medicine, 391 Technology Way, Winston-Salem, NC, 27101, USA
| | - Stephen J Walker
- Wake Forest School of Medicine, Medical Center, Wake Forest Institute for Regenerative Medicine, 391 Technology Way, Winston-Salem, NC, 27101, USA
| | - Richard Boucher
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeannie Chan
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Laura A Cox
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Anthony Atala
- Wake Forest School of Medicine, Medical Center, Wake Forest Institute for Regenerative Medicine, 391 Technology Way, Winston-Salem, NC, 27101, USA
- Wake Forest School of Medicine, Medical Center Boulevard, Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Winston-Salem, NC, 27157, USA
| | - Sean V Murphy
- Wake Forest School of Medicine, Medical Center, Wake Forest Institute for Regenerative Medicine, 391 Technology Way, Winston-Salem, NC, 27101, USA.
- Wake Forest School of Medicine, Medical Center Boulevard, Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Winston-Salem, NC, 27157, USA.
| |
Collapse
|
3
|
Bukowy-Bieryłło Z, Daca-Roszak P, Jurczak J, Przystałowska-Macioła H, Jaksik R, Witt M, Ziętkiewicz E. In vitro differentiation of ciliated cells in ALI-cultured human airway epithelium - The framework for functional studies on airway differentiation in ciliopathies. Eur J Cell Biol 2021; 101:151189. [PMID: 34896770 DOI: 10.1016/j.ejcb.2021.151189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 12/22/2022] Open
Abstract
Primary cultures of the human airway epithelium (AE) cells are an indispensable tool in studies of pathophysiology of genetic and environmental pulmonary diseases, including cystic fibrosis (CF), primary ciliary dyskinesia (PCD) and chronic obstructive pulmonary disease (COPD). Air-liquid interface (ALI) culture is the best method to follow the differentiation of ciliated cells, whose dysfunction forms the basis of PCD. Here, we used custom-designed Taqman Low Density Array (TLDA), qRT-PCR-based assay, to analyze expression of 14 AE genes in cells from healthy donors, cultured in ALI settings using Pneumacult medium, with the focus on genes involved in cilia differentiation and in PCD pathogenesis. The results of TLDA assay were compared with the bulk RNAseq analysis, and placed in the cellular context using immunofluorescent staining (IF) of ALI cultured cells. Expression analysis revealed culture time-related upregulation of the majority of cilia-related genes, followed by the appearance of respective protein signals visualized by IF. Strong correlation of TLDA with RNAseq results indicated that TLDA assay is a reliable and scalable approach to analyze expression of selected genes specific for different AE cell types. Characterization of temporal and inter-donor changes in the expression of these genes, performed in healthy donors and in well-defined ALI/Pnemacult culture conditions, provides a useful reference relevant for a broad spectrum of functional studies where the in vitro AE differentiation is in focus.
Collapse
Affiliation(s)
| | | | - Joanna Jurczak
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Roman Jaksik
- Systems Biology Group, Faculty of Automatic Control, Electronics and Informatics, Silesian University of Technology, Gliwice, Poland
| | - Michał Witt
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Ewa Ziętkiewicz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| |
Collapse
|
4
|
Rajczewski AT, Mehta S, Nguyen DDA, Grüning B, Johnson JE, McGowan T, Griffin TJ, Jagtap PD. A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19). Clin Proteomics 2021; 18:15. [PMID: 33971807 PMCID: PMC8107781 DOI: 10.1186/s12014-021-09321-1] [Citation(s) in RCA: 6] [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: 03/01/2021] [Accepted: 05/01/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. METHODS: In this study we have compiled a list of 636 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). RESULTS Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639-peptide possibilities to 87 peptides that were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Through stringent p-value cutoff combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. CONCLUSION We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from patient samples. We also contend that samples harvested from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.
Collapse
Affiliation(s)
- Andrew T Rajczewski
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Dinh Duy An Nguyen
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Björn Grüning
- Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Thomas McGowan
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular and Cell Biology Building, University of Minnesota, 420 Washington Ave SE 7-129, Minneapolis, MN, 55455, USA.
| |
Collapse
|
5
|
Rajczewski AT, Mehta S, Nguyen DDA, Grüning BA, Johnson JE, McGowan T, Griffin TJ, Jagtap PD. A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19). MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.09.21251427. [PMID: 33688669 PMCID: PMC7941646 DOI: 10.1101/2021.02.09.21251427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. In this study we have compiled a list of 639 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639 peptide possibilities to 87 peptides which were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Applying stringent statistical scoring thresholds, combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from a variety of sample types. We also contend that samples taken from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.
Collapse
Affiliation(s)
- Andrew T. Rajczewski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dinh Duy An Nguyen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Björn A. Grüning
- Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - James E. Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Thomas McGowan
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Pratik D. Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|