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Ma Y, Jiang T, Zhu X, Xu Y, Wan K, Zhang T, Xie M. Efferocytosis in dendritic cells: an overlooked immunoregulatory process. Front Immunol 2024; 15:1415573. [PMID: 38835772 PMCID: PMC11148234 DOI: 10.3389/fimmu.2024.1415573] [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: 04/10/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024] Open
Abstract
Efferocytosis, the process of engulfing and removing apoptotic cells, plays an essential role in preserving tissue health and averting undue inflammation. While macrophages are primarily known for this task, dendritic cells (DCs) also play a significant role. This review delves into the unique contributions of various DC subsets to efferocytosis, highlighting the distinctions in how DCs and macrophages recognize and handle apoptotic cells. It further explores how efferocytosis influences DC maturation, thereby affecting immune tolerance. This underscores the pivotal role of DCs in orchestrating immune responses and sustaining immune equilibrium, providing new insights into their function in immune regulation.
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Affiliation(s)
- Yanyan Ma
- Department of Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Tangxing Jiang
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xun Zhu
- Department of Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yizhou Xu
- Department of Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Ke Wan
- Department of Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Tingxuan Zhang
- Department of Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Miaorong Xie
- Department of Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
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2
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Faure-Dupuy S, Jubrail J, Depierre M, Africano-Gomez K, Öberg L, Israelsson E, Thörn K, Delevoye C, Castellano F, Herit F, Guilbert T, Russell DG, Mayer G, Cunoosamy DM, Kurian N, Niedergang F. ARL5b inhibits human rhinovirus 16 propagation and impairs macrophage-mediated bacterial clearance. EMBO Rep 2024; 25:1156-1175. [PMID: 38332148 PMCID: PMC10933434 DOI: 10.1038/s44319-024-00069-x] [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: 05/01/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 02/10/2024] Open
Abstract
Human rhinovirus is the most frequently isolated virus during severe exacerbations of chronic respiratory diseases, like chronic obstructive pulmonary disease. In this disease, alveolar macrophages display significantly diminished phagocytic functions that could be associated with bacterial superinfections. However, how human rhinovirus affects the functions of macrophages is largely unknown. Macrophages treated with HRV16 demonstrate deficient bacteria-killing activity, impaired phagolysosome biogenesis, and altered intracellular compartments. Using RNA sequencing, we identify the small GTPase ARL5b to be upregulated by the virus in primary human macrophages. Importantly, depletion of ARL5b rescues bacterial clearance and localization of endosomal markers in macrophages upon HRV16 exposure. In permissive cells, depletion of ARL5b increases the secretion of HRV16 virions. Thus, we identify ARL5b as a novel regulator of intracellular trafficking dynamics and phagolysosomal biogenesis in macrophages and as a restriction factor of HRV16 in permissive cells.
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Affiliation(s)
| | - Jamil Jubrail
- Université Paris Cité, CNRS, Inserm, Institut Cochin, Paris, 75014, France
- Southampton Solent University, East Park Terrace, Southampton, SO14 0YN, UK
| | - Manon Depierre
- Université Paris Cité, CNRS, Inserm, Institut Cochin, Paris, 75014, France
| | | | - Lisa Öberg
- Translational Science & Experimental Medicine, Research & Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 413 14, Sweden
| | - Elisabeth Israelsson
- Translational Science & Experimental Medicine, Research & Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 413 14, Sweden
| | - Kristofer Thörn
- Translational Science & Experimental Medicine, Research & Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 413 14, Sweden
| | - Cédric Delevoye
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France
- Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Flavia Castellano
- Université Paris Cité, CNRS, Inserm, Institut Cochin, Paris, 75014, France
- Université Paris Est Creteil, INSERM, IMRB, Creteil, 94010, France
| | - Floriane Herit
- Université Paris Cité, CNRS, Inserm, Institut Cochin, Paris, 75014, France
| | - Thomas Guilbert
- Université Paris Cité, CNRS, Inserm, Institut Cochin, Paris, 75014, France
| | - David G Russell
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gaell Mayer
- Immunology, Late stage Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 413 14, Sweden
| | - Danen M Cunoosamy
- Research & Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 413 14, Sweden
| | - Nisha Kurian
- Research & Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 413 14, Sweden
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3
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Zhang Z, Yu H, Wang Q, Ding Y, Wang Z, Zhao S, Bian T. A Macrophage-Related Gene Signature for Identifying COPD Based on Bioinformatics and ex vivo Experiments. J Inflamm Res 2023; 16:5647-5665. [PMID: 38050560 PMCID: PMC10693783 DOI: 10.2147/jir.s438308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/21/2023] [Indexed: 12/06/2023] Open
Abstract
Background This study aims to investigate the association between immune cells and the development of COPD, while providing a new method for the diagnosis of COPD according to the changes in immune microenvironment. Methods In this study, the "CIBERSORT" algorithm was used to estimate the tissue infiltration of 22 types of immune cells in GSE20257 and GSE10006. The "limma" package was used for differentially expressed analysis. The key modules associated with vital immune cells were identified using WGCNA. GO and KEGG enrichment analysis revealed the biological functions of the candidate genes. Ultimately, a novel diagnostic prediction model was constructed via machine learning methods and multivariate logistic regression analysis based on GSE20257. Furthermore, we examined the stability of the model on one internal test set (GSE10006), three external test sets (GSE8545, GSE57148 and GSE76925), one single-cell transcriptome dataset (GSE167295), macrophages (THP-M cells) and lung tissue from COPD patients. Results M0 macrophages (AUC > 0.7 in GSE20257 and GSE10006) were considered as the most important immune cells through exploring the immune microenvironment landscapes in COPD patients and healthy controls. The differentially expressed genes from GSE20257 and GSE10006 were divided into six and five modules via WGCNA, respectively. The green module in GSE20257 (cor = 0.41, P < 0.001) and the brown module in GSE10006 (cor = 0.67, P < 0.001) were highly correlated with M0 macrophages and were selected as key modules. Forty-one intersected genes obtained from two modules were primarily involved in regulation of cytokine production, regulation of innate immune response, specific granule, phagosome, lysosome, ferroptosis, and other biological processes. On the basis of the candidate genetic markers further characterized via the "Boruta" and "LASSO" algorithm for COPD, a diagnostic model comprising CLEC5A, FTL and SLC2A3 was constructed, which could accurately distinguish COPD patients from healthy controls in multiple datasets. GSE20257 as the training set has an AUC of 0.916. The AUCs of the internal test set and three external test sets were 0.873, 0.932, 0.675 and 0.688, respectively. Single-cell sequencing analysis suggested that CLEC5A, FTL and SLC2A3 were expressed in macrophages from COPD patients. The expressions of CLEC5A, FTL and SLC2A3 were up-regulated in THP-M cells and lung tissue from COPD patients. Conclusion According to the variations of immune microenvironment in COPD patients, we constructed and validated a novel macrophage M0-associated diagnostic model with satisfactory predictive value. CLEC5A, FTL and SLC2A3 are expected to be promising targets of immunotherapy in COPD.
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Affiliation(s)
- Zheming Zhang
- Wuxi Medical Center of Nanjing Medical University, Wuxi, People’s Republic of China
- Department of Respiratory Medicine, Wuxi People’s Hospital, Nanjing Medical University, Wuxi, People’s Republic of China
| | - Haoda Yu
- Wuxi Medical Center of Nanjing Medical University, Wuxi, People’s Republic of China
- Department of Respiratory Medicine, Wuxi People’s Hospital, Nanjing Medical University, Wuxi, People’s Republic of China
| | - Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, People’s Republic of China
| | - Yu Ding
- Wuxi Medical Center of Nanjing Medical University, Wuxi, People’s Republic of China
- Department of Respiratory Medicine, Wuxi People’s Hospital, Nanjing Medical University, Wuxi, People’s Republic of China
| | - Ziteng Wang
- Wuxi Medical Center of Nanjing Medical University, Wuxi, People’s Republic of China
- Department of Respiratory Medicine, Wuxi People’s Hospital, Nanjing Medical University, Wuxi, People’s Republic of China
| | - Songyun Zhao
- Wuxi Medical Center of Nanjing Medical University, Wuxi, People’s Republic of China
| | - Tao Bian
- Wuxi Medical Center of Nanjing Medical University, Wuxi, People’s Republic of China
- Department of Respiratory Medicine, Wuxi People’s Hospital, Nanjing Medical University, Wuxi, People’s Republic of China
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4
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Odendall C, Sa Pessoa J, Mesquita FS. Meeting report - Cell dynamics: host-pathogen interface. J Cell Sci 2022; 135:276364. [PMID: 35979931 DOI: 10.1242/jcs.260456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two years into the most significant infectious disease event of our generation, infections have populated every conversation and in-depth understanding of host-pathogen interactions has, perhaps, never been more important. In a successful return to in-person conferences, the host-pathogen interface was the focus of the third Cell Dynamics meeting, which took place at the glorious Wotton House in Surrey, UK. The meeting organised by Michaela Gack, Maximiliano Gutierrez, Dominique Soldati-Favre and Michael Way gathered an international group of scientists who shared their recent discoveries and views on numerous aspects, including cell-autonomous defence mechanisms, pathogen interactions with host cytoskeletal or membrane dynamics, and cellular immune regulation. More than 30 years into the beginning of cellular microbiology as a field, the meeting exhibited the unique aspect of the host-pathogen interface in uncovering the fundamentals of both pathogens and their hosts.
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Affiliation(s)
- Charlotte Odendall
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, SE1 9RT London, UK
| | - Joana Sa Pessoa
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL Belfast, UK
| | - Francisco S Mesquita
- Global Health Institute, School of Life Sciences, EPFL, CH-1015 Lausanne, Switzerland
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5
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Delgado MG, Rivera CA, Lennon-Duménil AM. Macropinocytosis and Cell Migration: Don't Drink and Drive…. Subcell Biochem 2022; 98:85-102. [PMID: 35378704 DOI: 10.1007/978-3-030-94004-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Macropinocytosis is a nonspecific mechanism by which cells compulsively "drink" the surrounding extracellular fluids in order to feed themselves or sample the molecules therein, hence gaining information about their environment. This process is cell-intrinsically incompatible with the migration of many cells, implying that the two functions are antagonistic. The migrating cell uses a molecular switch to stop and explore its surrounding fluid by macropinocytosis, after which it employs the same molecular machinery to start migrating again to examine another location. This cycle of migration/macropinocytosis allows cells to explore tissues, and it is key to a range of physiological processes. Evidence of this evolutionarily conserved antagonism between the two processes can be found in several cell types-immune cells, for example, being particularly adept-and ancient organisms (e.g., the social amoeba Dictyostelium discoideum). How macropinocytosis and migration are negatively coupled is the subject of this chapter.
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6
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Molecular epidemiology and clinical characterization of human rhinoviruses circulating in Shanghai, 2012-2020. Arch Virol 2022; 167:1111-1123. [PMID: 35303167 PMCID: PMC8931777 DOI: 10.1007/s00705-022-05405-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/22/2022] [Indexed: 12/30/2022]
Abstract
Human rhinoviruses (HRVs) cause acute upper and lower respiratory tract infections and aggravation of asthma and chronic obstructive pulmonary disease. The 5’ untranslated region (5' UTR) and the VP4/VP2 region are widely used for genotyping of HRVs. Members of the species Rhinovirus A and Rhinovirus C have been reported to be more frequently associated with severe disease than members of the species Rhinovirus B. We report the clinical and molecular epidemiological characteristics of HRVs circulating from 2012 to 2020 in Shanghai. A total of 5832 nasopharyngeal swabs from patients with acute respiratory infections were collected. A real-time reverse transcription polymerase chain reaction assay was used for virus detection. The 5' untranslated region and VP4/VP2 region were amplified and sequenced for genotyping and phylogenetic analysis. The overall rate of rhinovirus detection was 2.74% (160/5832), with members of species A, B, and C accounting for 68.13% (109/160), 20.00% (32/160), and 11.88% (19/160) of the total, respectively. A peak of HRV infection was observed in autumn (5.34%, 58/1087). Patients in the 3- to 14-year-old age group were the most susceptible to HRV infection (χ2 = 23.88, P = 0.017). Influenza virus and Streptococcus pneumoniae were detected more frequently than other pathogens in cases of coinfection. Recombination events were identified in 10 strains, which were successfully genotyped by phylogenetic analysis based on the 5’ UTR-VP4/VP2 region but not the 5’ UTR region alone. We observed a high degree of variability in the relative distribution of HRV genotypes and the prevalence of HRV infection in Shanghai and found evidence of recombination events in the portion of the genome containing the 5’ UTR and the VP4/VP2 region between HRV-C strains and HRV-A-like strains. This study is important for surveillance of the spread of HRVs and the emergence of new variants.
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7
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Chánez-Paredes S, Montoya-García A, Castro-Ochoa KF, García-Cordero J, Cedillo-Barrón L, Shibayama M, Nava P, Flemming S, Schlegel N, Gautreau AM, Vargas-Robles H, Mondragón-Flores R, Schnoor M. The Arp2/3 Inhibitory Protein Arpin Is Required for Intestinal Epithelial Barrier Integrity. Front Cell Dev Biol 2021; 9:625719. [PMID: 34012961 PMCID: PMC8128147 DOI: 10.3389/fcell.2021.625719] [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: 11/03/2020] [Accepted: 03/17/2021] [Indexed: 12/23/2022] Open
Abstract
The intestinal epithelial barrier (IEB) depends on stable interepithelial protein complexes such as tight junctions (TJ), adherens junctions (AJ), and the actin cytoskeleton. During inflammation, the IEB is compromised due to TJ protein internalization and actin remodeling. An important actin regulator is the actin-related protein 2/3 (Arp2/3) complex, which induces actin branching. Activation of Arp2/3 by nucleation-promoting factors is required for the formation of epithelial monolayers, but little is known about the relevance of Arp2/3 inhibition and endogenous Arp2/3 inhibitory proteins for IEB regulation. We found that the recently identified Arp2/3 inhibitory protein arpin was strongly expressed in intestinal epithelial cells. Arpin expression decreased in response to tumor necrosis factor (TNF)α and interferon (IFN)γ treatment, whereas the expression of gadkin and protein interacting with protein C-kinase α-subunit 1 (PICK1), other Arp2/3 inhibitors, remained unchanged. Of note, arpin coprecipitated with the TJ proteins occludin and claudin-1 and the AJ protein E-cadherin. Arpin depletion altered the architecture of both AJ and TJ, increased actin filament content and actomyosin contractility, and significantly increased epithelial permeability, demonstrating that arpin is indeed required for maintaining IEB integrity. During experimental colitis in mice, arpin expression was also decreased. Analyzing colon tissues from ulcerative colitis patients by Western blot, we found different arpin levels with overall no significant changes. However, in acutely inflamed areas, arpin was significantly reduced compared to non-inflamed areas. Importantly, patients receiving mesalazine had significantly higher arpin levels than untreated patients. As arpin depletion (theoretically meaning more active Arp2/3) increased permeability, we wanted to know whether Arp2/3 inhibition would show the opposite. Indeed, the specific Arp2/3 inhibitor CK666 ameliorated TNFα/IFNγ-induced permeability in established Caco-2 monolayers by preventing TJ disruption. CK666 treatment also attenuated colitis development, colon tissue damage, TJ disruption, and permeability in dextran sulphate sodium (DSS)-treated mice. Our results demonstrate that loss of arpin triggers IEB dysfunction during inflammation and that low arpin levels can be considered a novel hallmark of acute inflammation.
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Affiliation(s)
| | | | | | | | | | - Mineko Shibayama
- Department of Infectomics and Molecular Pathogenesis, CINVESTAV-IPN, Mexico City, Mexico
| | - Porfirio Nava
- Department of Physiology, Biophysics and Neurosciences, CINVESTAV-IPN, Mexico City, Mexico
| | - Sven Flemming
- Department of Surgery I, University Hospital Würzburg, Würzburg, Germany
| | - Nicolas Schlegel
- Department of Surgery I, University Hospital Würzburg, Würzburg, Germany
| | | | | | | | - Michael Schnoor
- Department of Molecular Biomedicine, CINVESTAV-IPN, Mexico City, Mexico
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8
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Coleman A, Bialasiewicz S, Marsh RL, Grahn Håkansson E, Cottrell K, Wood A, Jayasundara N, Ware RS, Zaugg J, Sidjabat HE, Adams J, Ferguson J, Brown M, Roos K, Cervin A. Upper Respiratory Microbiota in Relation to Ear and Nose Health Among Australian Aboriginal and Torres Strait Islander Children. J Pediatric Infect Dis Soc 2021; 10:468-476. [PMID: 33393596 DOI: 10.1093/jpids/piaa141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/06/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND We explored the nasal microbiota in Indigenous Australian children in relation to ear and nasal health. METHODS In total, 103 Indigenous Australian children aged 2-7 years (mean 4.7 years) were recruited from 2 Queensland communities. Children's ears, nose, and throats were examined and upper respiratory tract (URT) swabs collected. Clinical histories were obtained from parents/medical records. URT microbiota were characterized using culturomics with Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification. Real-time PCR was used to quantify otopathogen (Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis) loads and detect respiratory viruses. Data were analyzed using beta diversity measures, regression modeling, and a correlation network analysis. RESULTS Children with historical/current otitis media (OM) or URT infection (URTI) had higher nasal otopathogen detection and loads and rhinovirus detection compared with healthy children (all P < .04). Children with purulent rhinorrhea had higher nasal otopathogen detection and loads and rhinovirus detection (P < .04) compared with healthy children. High otopathogen loads were correlated in children with historical/current OM or URTI, whereas Corynebacterium pseudodiphtheriticum and Dolosigranulum pigrum were correlated in healthy children. CONCLUSIONS Corynebacterium pseudodiphtheriticum and D. pigrum are associated with URT and ear health. The importance of the main otopathogens in URT disease/OM was confirmed, and their role relates to co-colonization and high otopathogens loads.
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Affiliation(s)
- Andrea Coleman
- Children's Health Research Centre, The University of Queensland Centre for Clinical Research, South Brisbane, Australia.,Department of Surgery-Otolaryngology, Head and Neck Surgery, Townsville University Hospital, Townsville, Australia
| | - Seweryn Bialasiewicz
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Australia.,Queensland Pediatric Infectious Diseases Laboratory, Queensland Children's Hospital, South Brisbane, Australia
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Eva Grahn Håkansson
- Department of Clinical Microbiology, Umeå University and Essum AB, Umeå, Sweden
| | - Kyra Cottrell
- The University of Queensland Centre for Clinical Research, Herston, Australia
| | - Amanda Wood
- Queensland Health Deadly Ears Program, Brisbane, Australia
| | - Nadeesha Jayasundara
- Queensland Pediatric Infectious Diseases Laboratory, Queensland Children's Hospital, South Brisbane, Australia
| | - Robert S Ware
- Menzies Health Institute Queensland, Griffith University, Brisbane, Australia
| | - Julian Zaugg
- Children's Health Research Centre, The University of Queensland Centre for Clinical Research, South Brisbane, Australia
| | - Hanna E Sidjabat
- The University of Queensland Centre for Clinical Research, Herston, Australia
| | - Jasmyn Adams
- Queensland Health Deadly Ears Program, Brisbane, Australia
| | | | - Matthew Brown
- Queensland Health Deadly Ears Program, Brisbane, Australia
| | | | - Anders Cervin
- The University of Queensland Centre for Clinical Research, Herston, Australia.,Department of Otolaryngology, Head and Neck Surgery, The Royal Brisbane and Women's Hospital, Brisbane, Australia
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9
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Tarim EA, Karakuzu B, Oksuz C, Sarigil O, Kizilkaya M, Al-Ruweidi MKAA, Yalcin HC, Ozcivici E, Tekin HC. Microfluidic-based virus detection methods for respiratory diseases. EMERGENT MATERIALS 2021; 4:143-168. [PMID: 33786415 PMCID: PMC7992628 DOI: 10.1007/s42247-021-00169-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
With the recent SARS-CoV-2 outbreak, the importance of rapid and direct detection of respiratory disease viruses has been well recognized. The detection of these viruses with novel technologies is vital in timely prevention and treatment strategies for epidemics and pandemics. Respiratory viruses can be detected from saliva, swab samples, nasal fluid, and blood, and collected samples can be analyzed by various techniques. Conventional methods for virus detection are based on techniques relying on cell culture, antigen-antibody interactions, and nucleic acids. However, these methods require trained personnel as well as expensive equipment. Microfluidic technologies, on the other hand, are one of the most accurate and specific methods to directly detect respiratory tract viruses. During viral infections, the production of detectable amounts of relevant antibodies takes a few days to weeks, hampering the aim of prevention. Alternatively, nucleic acid-based methods can directly detect the virus-specific RNA or DNA region, even before the immune response. There are numerous methods to detect respiratory viruses, but direct detection techniques have higher specificity and sensitivity than other techniques. This review aims to summarize the methods and technologies developed for microfluidic-based direct detection of viruses that cause respiratory infection using different detection techniques. Microfluidics enables the use of minimal sample volumes and thereby leading to a time, cost, and labor effective operation. Microfluidic-based detection technologies provide affordable, portable, rapid, and sensitive analysis of intact virus or virus genetic material, which is very important in pandemic and epidemic events to control outbreaks with an effective diagnosis.
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Affiliation(s)
- E. Alperay Tarim
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Betul Karakuzu
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Cemre Oksuz
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Oyku Sarigil
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Melike Kizilkaya
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | | | | | - Engin Ozcivici
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - H. Cumhur Tekin
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
- METU MEMS Center, Ankara, Turkey
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10
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Rigano A, Ehmsen S, Öztürk SU, Ryan J, Balashov A, Hammer M, Kirli K, Boehm U, Brown CM, Bellve K, Chambers JJ, Cosolo A, Coleman RA, Faklaris O, Fogarty KE, Guilbert T, Hamacher AB, Itano MS, Keeley DP, Kunis S, Lacoste J, Laude A, Ma WY, Marcello M, Montero-Llopis P, Nelson G, Nitschke R, Pimentel JA, Weidtkamp-Peters S, Park PJ, Alver BH, Grunwald D, Strambio-De-Castillia C. Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nat Methods 2021; 18:1489-1495. [PMID: 34862503 PMCID: PMC8648560 DOI: 10.1038/s41592-021-01315-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/30/2021] [Indexed: 12/31/2022]
Abstract
For quality, interpretation, reproducibility and sharing value, microscopy images should be accompanied by detailed descriptions of the conditions that were used to produce them. Micro-Meta App is an intuitive, highly interoperable, open-source software tool that was developed in the context of the 4D Nucleome (4DN) consortium and is designed to facilitate the extraction and collection of relevant microscopy metadata as specified by the recent 4DN-BINA-OME tiered-system of Microscopy Metadata specifications. In addition to substantially lowering the burden of quality assurance, the visual nature of Micro-Meta App makes it particularly suited for training purposes.
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Affiliation(s)
- Alessandro Rigano
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA USA
| | - Shannon Ehmsen
- grid.38142.3c000000041936754XDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA USA
| | - Serkan Utku Öztürk
- grid.38142.3c000000041936754XDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA USA
| | - Joel Ryan
- grid.14709.3b0000 0004 1936 8649Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec Canada
| | - Alexander Balashov
- grid.38142.3c000000041936754XDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA USA
| | - Mathias Hammer
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA USA
| | - Koray Kirli
- grid.38142.3c000000041936754XDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA USA
| | - Ulrike Boehm
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA
| | - Claire M. Brown
- grid.14709.3b0000 0004 1936 8649Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec Canada
| | - Karl Bellve
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA USA
| | - James J. Chambers
- grid.266683.f0000 0001 2166 5835Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA USA
| | - Andrea Cosolo
- grid.38142.3c000000041936754XDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA USA
| | - Robert A. Coleman
- grid.251993.50000000121791997Department of Anatomy and Structural Biology, Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY USA
| | - Orestis Faklaris
- grid.121334.60000 0001 2097 0141BioCampus Montpellier (BCM), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Kevin E. Fogarty
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA USA
| | - Thomas Guilbert
- grid.508487.60000 0004 7885 7602Institut Cochin, Inserm U1016-CNRS UMR8104-Université de Paris, Paris, France
| | - Anna B. Hamacher
- grid.411327.20000 0001 2176 9917Center for Advanced Imaging, Heinrich-Heine University Duesseldorf, Düsseldorf, Germany
| | - Michelle S. Itano
- grid.10698.360000000122483208UNC Neuroscience Microscopy Core Facility, Department of Cell Biology and Physiology, Carolina Institute for Developmental Disabilities, and UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC USA
| | - Daniel P. Keeley
- grid.10698.360000000122483208UNC Neuroscience Microscopy Core Facility, Department of Cell Biology and Physiology, Carolina Institute for Developmental Disabilities, and UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC USA
| | - Susanne Kunis
- grid.10854.380000 0001 0672 4366Department of Biology/Chemistry and Center for Cellular Nanoanalytics, University Osnabrück, Osnabrück, Germany
| | | | - Alex Laude
- grid.1006.70000 0001 0462 7212Bioimaging Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Willa Y. Ma
- grid.10698.360000000122483208UNC Neuroscience Microscopy Core Facility, Carolina Institute for Developmental Disabilities, and UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC USA
| | - Marco Marcello
- grid.10025.360000 0004 1936 8470Center for Cell Imaging, University of Liverpool, Liverpool, UK
| | - Paula Montero-Llopis
- grid.38142.3c000000041936754XMicroscopy Resources of the North Quad, University of Harvard Medical School, Boston, MA USA
| | - Glyn Nelson
- grid.1006.70000 0001 0462 7212Bioimaging Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Roland Nitschke
- grid.5963.9Life Imaging Center and Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Freiburg, Germany
| | - Jaime A. Pimentel
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Stefanie Weidtkamp-Peters
- grid.411327.20000 0001 2176 9917Center for Advanced Imaging, Heinrich-Heine University Duesseldorf, Düsseldorf, Germany
| | - Peter J. Park
- grid.38142.3c000000041936754XDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA USA
| | - Burak H. Alver
- grid.38142.3c000000041936754XDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA USA
| | - David Grunwald
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA USA
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11
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Jaumouillé V, Waterman CM. Physical Constraints and Forces Involved in Phagocytosis. Front Immunol 2020; 11:1097. [PMID: 32595635 PMCID: PMC7304309 DOI: 10.3389/fimmu.2020.01097] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023] Open
Abstract
Phagocytosis is a specialized process that enables cellular ingestion and clearance of microbes, dead cells and tissue debris that are too large for other endocytic routes. As such, it is an essential component of tissue homeostasis and the innate immune response, and also provides a link to the adaptive immune response. However, ingestion of large particulate materials represents a monumental task for phagocytic cells. It requires profound reorganization of the cell morphology around the target in a controlled manner, which is limited by biophysical constraints. Experimental and theoretical studies have identified critical aspects associated with the interconnected biophysical properties of the receptors, the membrane, and the actin cytoskeleton that can determine the success of large particle internalization. In this review, we will discuss the major physical constraints involved in the formation of a phagosome. Focusing on two of the most-studied types of phagocytic receptors, the Fcγ receptors and the complement receptor 3 (αMβ2 integrin), we will describe the complex molecular mechanisms employed by phagocytes to overcome these physical constraints.
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Affiliation(s)
- Valentin Jaumouillé
- Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Clare M Waterman
- Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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12
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Cafferkey J, Coultas JA, Mallia P. Human rhinovirus infection and COPD: role in exacerbations and potential for therapeutic targets. Expert Rev Respir Med 2020; 14:777-789. [PMID: 32498634 DOI: 10.1080/17476348.2020.1764354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Respiratory virus infections (predominantly rhinoviruses) are the commonly identified in COPD exacerbations but debate about their role as a trigger of exacerbations continues. Experimental infection studies have provided significant new evidence establishing a causal relationship between virus infection and COPD exacerbations and contributed to a better understanding of the mechanisms of virus-induced exacerbations. However as yet no anti-viral treatments have undergone clinical trials in COPD patients. AREAS COVERED This review discusses the evidence for and against respiratory viruses being the main trigger of COPD exacerbations from both epidemiological studies and experimental infection studies. The host immune response to rhinovirus infection and how abnormalities in host immunity may underlie increased susceptibility to virus infection in COPD are discussed and the role of dual viral-bacterial infection in COPD exacerbations. Finally the current state of anti-viral therapy is discussed and how these may be used in the future treatment of COPD exacerbations. EXPERT OPINION Respiratory virus infections are the trigger of a substantial proportion of COPD exacerbations and rhinoviruses are the most common virus type. Clinical trials of anti-viral agents are needed in COPD patients to determine whether they are effective in virus-induced COPD exacerbations.
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Affiliation(s)
- John Cafferkey
- Department of Respiratory Medicine, Imperial College Healthcare NHS Trust , London, UK
| | | | - Patrick Mallia
- Department of Respiratory Medicine, Imperial College Healthcare NHS Trust , London, UK.,National Heart and Lung Institute, Imperial College London , London, UK
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13
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Wei H, Zhao H, Li R, Yang F, Wu Y. Rhinovirus impairs the immune response of alveolar macrophages to facilitate Streptococcus pneumonia infection. Pathog Dis 2020; 78:5828079. [PMID: 32358959 DOI: 10.1093/femspd/ftaa020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/01/2020] [Indexed: 12/27/2022] Open
Abstract
Pneumonia is one important cause of mortality in neonates. However, the mechanism remains still unclear. Viral infection greatly enhances the morbidity of Streptococcus pneumonia. In this study, we tried to understand how human rhinovirus (HRV) would accelerate Streptococcus pneumonia infection. Alveolar macrophages (AMs) were isolated from neonatal mice. Cytokine concentrations were detected using ELISA. The phagocytosis of Streptococcus pneumonia by AMs was indicated by immunofluorescence. Toll-like receptor 3 (TLR3) and CD68 expression in isolated AMs or infected mice were determined by western blot or immunochemistry. The mortality was explored using Kaplan-Meier analysis. HRV infection enhanced cytokine release by AMs, and decreased Streptococcus pneumonia-induced TNF-α, IL-1β and IL-6 release by AMs, while has no influence on IL-10 release. HRV infection impaired phagocytosis of Streptococcus pneumonia in AMs. Mechanically, HRV infection up-regulated TLR3 expression in AMs. Mortality and pneumococcal burden decreased in TLR3-/- neonatal mice and inflammation and phagocytosis were restored in TLR3-/- AMs. Neonatal rhinovirus impairs the immune response of alveolar macrophages to facilitate Streptococcus pneumonia infection via TLR3 signaling.
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Affiliation(s)
- Huiping Wei
- Department of Emergency, Hubei Maternal and Child Health Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 745 Wuluo Road, Hongshan District, Wuhan 430070, Hubei, China
| | - Hui Zhao
- Department of Emergency, Hubei Maternal and Child Health Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 745 Wuluo Road, Hongshan District, Wuhan 430070, Hubei, China
| | - Ruifang Li
- Department of Neurology, the Third People's Hospital of Hubei Province, No. 26 Zhongshan Road, Qiaokou District, Wuhan 430030, Hubei, China
| | - Feiyun Yang
- Department of Emergency, the First Affiliated Hospital of Xinxiang Medical College, No. 88 Jiankang Road, Weihui 453100, Henan, China
| | - Yan Wu
- Department of Emergency, Hubei Maternal and Child Health Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 745 Wuluo Road, Hongshan District, Wuhan 430070, Hubei, China
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14
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Abstract
Phagocytosis is a specialized process that enables cellular ingestion and clearance of microbes, dead cells and tissue debris that are too large for other endocytic routes. As such, it is an essential component of tissue homeostasis and the innate immune response, and also provides a link to the adaptive immune response. However, ingestion of large particulate materials represents a monumental task for phagocytic cells. It requires profound reorganization of the cell morphology around the target in a controlled manner, which is limited by biophysical constraints. Experimental and theoretical studies have identified critical aspects associated with the interconnected biophysical properties of the receptors, the membrane, and the actin cytoskeleton that can determine the success of large particle internalization. In this review, we will discuss the major physical constraints involved in the formation of a phagosome. Focusing on two of the most-studied types of phagocytic receptors, the Fcγ receptors and the complement receptor 3 (αMβ2 integrin), we will describe the complex molecular mechanisms employed by phagocytes to overcome these physical constraints.
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Affiliation(s)
- Valentin Jaumouillé
- Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Clare M Waterman
- Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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