1
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Taivans I, Grima L, Jurka N, Zvaigzne L, Gordjušina V, Strazda G. FOT Technique Applied for Monitoring of COVID-19 Pneumonia Reveals Small Airways Involvement. Diagnostics (Basel) 2024; 14:1160. [PMID: 38893686 PMCID: PMC11171776 DOI: 10.3390/diagnostics14111160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
The fact that some SARS-CoV-2 pneumonia patients benefit from changing body position, and some from continuous positive airways pressure (CPAP), indicates the functional character of hypoxia. We hypothesize that such effects could be explained by the closure of small airways. To prove the hypothesis, we evaluated the patency of small airways in 30 oxygen-dependent, spontaneously breathing patients with SARS-CoV-2 pneumonia during their hospital stay using the FOT method and then compared the results with data obtained three months later. During the acute period, total resistance (R5) and peripheral resistance (R5-20) rose above the upper limit of normal (ULN) in 28% and 50% of all patients, respectively. Reactance indices X5, AX and Fres exceeded ULN in 55%, 68% and 66% of cases. Significant correlations were observed between PaO2/FiO2, the time spent in the hospital and R5, X5, AX and Fres. After 3 months, 18 patients were re-examined. During the hospital stay, 11 of them had risen above the upper limit of normal (ULN), for both resistance (R5-20) and reactance (X5, AX) values. Three months later, ULN for R5-20 was exceeded in only four individuals, but ULN for X5 and AX was exceeded in five individuals. Lung function examination revealed a combined restrictive/obstructive ventilatory failure and reduced CO transfer factor. We interpret these changes as lung tissue remodeling due to the process of fibrosis. We conclude that during acute period of SARS-CoV-2 pneumonia, dilated pulmonary blood vessels and parenchymal oedema induce functional closure of small airways, which in turn induce atelectasis with pulmonary right-to-left shunting, followed by the resulting hypoxemia.
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Affiliation(s)
- Immanuels Taivans
- Medical Faculty, University of Latvia, LV1050 Riga, Latvia; (L.G.); (N.J.); (V.G.); (G.S.)
| | - Laura Grima
- Medical Faculty, University of Latvia, LV1050 Riga, Latvia; (L.G.); (N.J.); (V.G.); (G.S.)
| | - Normunds Jurka
- Medical Faculty, University of Latvia, LV1050 Riga, Latvia; (L.G.); (N.J.); (V.G.); (G.S.)
| | | | - Valentina Gordjušina
- Medical Faculty, University of Latvia, LV1050 Riga, Latvia; (L.G.); (N.J.); (V.G.); (G.S.)
| | - Gunta Strazda
- Medical Faculty, University of Latvia, LV1050 Riga, Latvia; (L.G.); (N.J.); (V.G.); (G.S.)
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2
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Miyamori D, Kamitani T, Yoshida S, Kikuchi Y, Shigenobu Y, Ikeda K, Yamamoto Y, Ito M. Effects of the Coronavirus disease 2019 pandemic on mortality in patients with lung cancer: A multiple mediation analysis in Japan. Int J Cancer 2024. [PMID: 38794791 DOI: 10.1002/ijc.35042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/20/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024]
Abstract
COVID-19 pandemic has had a substantial effect on healthcare systems worldwide, including the care of patients with lung cancer. The impact of healthcare disruptions and behavioral changes on lung cancer mortality is unclear. Patients newly diagnosed with lung cancer during the pandemic period 2020-2021 were compared with those diagnosed in the pre-pandemic 2018-2019. The primary outcome was all-cause mortality within 1 year. Cox proportional hazards regression analyses were conducted to estimate the changes in mortality between pandemic and pre-pandemic. Multiple mediation analyses were performed to determine the factors that accounted for the changes in mortality. In total, 5785 patients with lung cancer were included in this study. The overall mortality rate was significantly higher during the pandemic compared with the pre-pandemic (crude hazard ratio [HR]: 1.19, 95% confidence interval [CI]: 1.05, 1.29). Mediation analyses showed that not receiving tumor-directed treatment, diagnosis at an older age, and decreased diagnosis through cancer screening significantly accounted for 17.5% (95%CI: 4.2, 30.7), 13.9% (95%CI: 0.8, 27.0), and 12.4% (95%CI: 3.0, 21.8) of the increased mortality, respectively. This study revealed a significant increase in mortality risk in patients with lung cancer who have not received tumor-directed treatment or cancer screening, despite potential selection bias for follow-up status. Efforts should be focused on ensuring timely access to healthcare services, optimizing treatment delivery, and addressing the unique challenges faced by patients with lung cancer during the pandemic to mitigate the impact of the pandemic on lung cancer outcomes and provide clinical care to vulnerable populations.
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Affiliation(s)
- Daisuke Miyamori
- Department of General Internal Medicine, Hiroshima University Hospital, Hiroshima, Japan
| | - Tsukasa Kamitani
- Section of Education for Clinical Research, Kyoto University Hospital, Kyoto, Japan
| | - Shuhei Yoshida
- Department of General Internal Medicine, Hiroshima University Hospital, Hiroshima, Japan
| | - Yuka Kikuchi
- Department of General Internal Medicine, Hiroshima University Hospital, Hiroshima, Japan
| | - Yuya Shigenobu
- Department of General Internal Medicine, Hiroshima University Hospital, Hiroshima, Japan
| | - Kotaro Ikeda
- Department of General Internal Medicine, Hiroshima University Hospital, Hiroshima, Japan
| | - Yosuke Yamamoto
- Department of Healthcare Epidemiology, School of Public Health in the Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masanori Ito
- Department of General Internal Medicine, Hiroshima University Hospital, Hiroshima, Japan
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3
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Woodall MNJ, Cujba AM, Worlock KB, Case KM, Masonou T, Yoshida M, Polanski K, Huang N, Lindeboom RGH, Mamanova L, Bolt L, Richardson L, Cakir B, Ellis S, Palor M, Burgoyne T, Pinto A, Moulding D, McHugh TD, Saleh A, Kilich E, Mehta P, O'Callaghan C, Zhou J, Barclay W, De Coppi P, Butler CR, Cortina-Borja M, Vinette H, Roy S, Breuer J, Chambers RC, Heywood WE, Mills K, Hynds RE, Teichmann SA, Meyer KB, Nikolić MZ, Smith CM. Age-specific nasal epithelial responses to SARS-CoV-2 infection. Nat Microbiol 2024; 9:1293-1311. [PMID: 38622380 PMCID: PMC11087271 DOI: 10.1038/s41564-024-01658-1] [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: 03/24/2023] [Accepted: 03/04/2024] [Indexed: 04/17/2024]
Abstract
Children infected with SARS-CoV-2 rarely progress to respiratory failure. However, the risk of mortality in infected people over 85 years of age remains high. Here we investigate differences in the cellular landscape and function of paediatric (<12 years), adult (30-50 years) and older adult (>70 years) ex vivo cultured nasal epithelial cells in response to infection with SARS-CoV-2. We show that cell tropism of SARS-CoV-2, and expression of ACE2 and TMPRSS2 in nasal epithelial cell subtypes, differ between age groups. While ciliated cells are viral replication centres across all age groups, a distinct goblet inflammatory subtype emerges in infected paediatric cultures and shows high expression of interferon-stimulated genes and incomplete viral replication. In contrast, older adult cultures infected with SARS-CoV-2 show a proportional increase in basaloid-like cells, which facilitate viral spread and are associated with altered epithelial repair pathways. We confirm age-specific induction of these cell types by integrating data from in vivo COVID-19 studies and validate that our in vitro model recapitulates early epithelial responses to SARS-CoV-2 infection.
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Affiliation(s)
| | | | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Tereza Masonou
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Ni Huang
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Liam Bolt
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Samuel Ellis
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Machaela Palor
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Thomas Burgoyne
- UCL Institute of Ophthalmology, University College London, London, UK
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Andreia Pinto
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Dale Moulding
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Timothy D McHugh
- UCL Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, UK
| | - Aarash Saleh
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Eliz Kilich
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Puja Mehta
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Jie Zhou
- Department of Infectious Disease, Imperial College London, London, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Paolo De Coppi
- Great Ormond Street UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Colin R Butler
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
| | | | - Heloise Vinette
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Sunando Roy
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Judith Breuer
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Rachel C Chambers
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Wendy E Heywood
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Kevin Mills
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Robert E Hynds
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory/Dept Physics, University of Cambridge, Cambridge, UK.
| | | | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK.
- University College London Hospitals NHS Foundation Trust, London, UK.
| | - Claire M Smith
- Great Ormond Street UCL Institute of Child Health, London, UK.
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4
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Behboudi E, Nooreddin Faraji S, Daryabor G, Mohammad Ali Hashemi S, Asadi M, Edalat F, Javad Raee M, Hatam G. SARS-CoV-2 mechanisms of cell tropism in various organs considering host factors. Heliyon 2024; 10:e26577. [PMID: 38420467 PMCID: PMC10901034 DOI: 10.1016/j.heliyon.2024.e26577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 01/30/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
A critical step in the drug design for SARS-CoV-2 is to discover its molecular targets. This study comprehensively reviewed the molecular mechanisms of SARS-CoV-2, exploring host cell tropism and interaction targets crucial for cell entry. The findings revealed that beyond ACE2 as the primary entry receptor, alternative receptors, co-receptors, and several proteases such as TMPRSS2, Furin, Cathepsin L, and ADAM play critical roles in virus entry and subsequent pathogenesis. Additionally, SARS-CoV-2 displays tropism in various human organs due to its diverse receptors. This review delves into the intricate details of receptors, host proteases, and the involvement of each organ. Polymorphisms in the ACE2 receptor and mutations in the spike or its RBD region contribute to the emergence of variants like Alpha, Beta, Gamma, Delta, and Omicron, impacting the pathogenicity of SARS-CoV-2. The challenge posed by mutations raises questions about the effectiveness of existing vaccines and drugs, necessitating consideration for updates in their formulations. In the urgency of these critical situations, repurposed drugs such as Camostat Mesylate and Nafamostat Mesylate emerge as viable pharmaceutical options. Numerous drugs are involved in inhibiting receptors and host factors crucial for SARS-CoV-2 entry, with most discussed in this review. In conclusion, this study may provide valuable insights to inform decisions in therapeutic approaches.
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Affiliation(s)
- Emad Behboudi
- Department of Basic Medical Sciences, Khoy University of Medical Sciences, Khoy, Iran
| | - Seyed Nooreddin Faraji
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamreza Daryabor
- Autoimmune Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Ali Hashemi
- Department of Bacteriology & Virology, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Maryam Asadi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fahime Edalat
- Department of Bacteriology & Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Javad Raee
- Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamreza Hatam
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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5
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Silverman JB, Vega PN, Tyska MJ, Lau KS. Intestinal Tuft Cells: Morphology, Function, and Implications for Human Health. Annu Rev Physiol 2024; 86:479-504. [PMID: 37863104 PMCID: PMC11193883 DOI: 10.1146/annurev-physiol-042022-030310] [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] [Indexed: 10/22/2023]
Abstract
Tuft cells are a rare and morphologically distinct chemosensory cell type found throughout many organs, including the gastrointestinal tract. These cells were identified by their unique morphologies distinguished by large apical protrusions. Ultrastructural data have begun to describe the molecular underpinnings of their cytoskeletal features, and tuft cell-enriched cytoskeletal proteins have been identified, although the connection of tuft cell morphology to tuft cell functionality has not yet been established. Furthermore, tuft cells display variations in function and identity between and within tissues, leading to the delineation of distinct tuft cell populations. As a chemosensory cell type, they display receptors that are responsive to ligands specific for their environment. While many studies have demonstrated the tuft cell response to protists and helminths in the intestine, recent research has highlighted other roles of tuft cells as well as implicated tuft cells in other disease processes including inflammation, cancer, and viral infections. Here, we review the literature on the cytoskeletal structure of tuft cells. Additionally, we focus on new research discussing tuft cell lineage, ligand-receptor interactions, tuft cell tropism, and the role of tuft cells in intestinal disease. Finally, we discuss the implication of tuft cell-targeted therapies in human health and how the morphology of tuft cells may contribute to their functionality.
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Affiliation(s)
- Jennifer B Silverman
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; ,
| | - Paige N Vega
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; ,
| | - Matthew J Tyska
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; ,
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; ,
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6
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Ciszewski WM, Wozniak LA, Sobierajska K. SARS-CoV-2 S and N protein peptides drive invasion abilities of colon cancer cells through TGF-β1 regulation. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119541. [PMID: 37468071 DOI: 10.1016/j.bbamcr.2023.119541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023]
Abstract
The COVID-19 pandemic led to the delay of colorectal cancer (CRC) diagnosis, which causes CRC to be treated at more advanced, often metastatic stages. Unfortunately, there is no effective treatment for metastatic CRC stages, which are considered the leading cause of patients' death. The mortality induced by SARS-CoV-2 is significantly higher in cancer patients than in patients with other diseases. Interestingly, COVID-19 patients often develop fibrosis which depends on epithelial-mesenchymal transition (EMT) - the process also involved in cancer progression. The study aimed to verify whether SARS-CoV-2 induces EMT and consequently increases the invasion potential of colon cancer cells. CRC cells were stimulated with SARS-CoV-2 S and N protein peptides and epithelial and mesenchymal markers were analysed with Western blotting to detect the occurrence of the EMT. The migration, invasion assays and MMP-7 secretion were employed to evaluate the potential of SARS-CoV-2 to stimulate the cells invasion in vitro. ELISA assay, TGF-β1 neutralizing antibodies, TGF-βR silencing and inhibitors were used to investigate the role of the TGF-β1 signalling pathways in the SARS-CoV-2-dependent CRC stimulation. The SARS-CoV-2 induced EMT, which increased the invasion ability of CRC cells. Moreover, the SARS-CoV-2 proteins drive colon cancer cell invasion through TGF-β1. Additionally, secreted TGF-β1 induced a bystander effect in colon cancer cells. However, blocking TGF-β1/Smad- and -non-Smad-dependent pathways suppressed the SARS-CoV-2-induced invasiveness of CRC. In conclusion, we revealed that SARS-CoV-2 stimulates the invasion abilities of CRC by regulating TGF-β1-induced EMT. Our results provide a theoretical basis for using anti-TGF-β1 therapy to reduce the risk of CRC metastasis during SARS-CoV-2 infection.
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Affiliation(s)
- Wojciech M Ciszewski
- Department of Molecular Cell Mechanisms, Medical University of Lodz, Mazowiecka 6/8, 92-215, Lodz, Poland.
| | - Lucyna A Wozniak
- Department of Structural Biology, Medical University of Lodz, Zeligowskiego 7/9, 90-752, Lodz, Poland
| | - Katarzyna Sobierajska
- Department of Molecular Cell Mechanisms, Medical University of Lodz, Mazowiecka 6/8, 92-215, Lodz, Poland
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7
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Eshetie S, Jullian P, Benyamin B, Lee SH. Host genetic determinants of COVID-19 susceptibility and severity: A systematic review and meta-analysis. Rev Med Virol 2023; 33:e2466. [PMID: 37303119 DOI: 10.1002/rmv.2466] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/29/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023]
Abstract
Genome-wide association studies (GWASs) have identified single nucleotide polymorphisms (SNPs) associated with susceptibility and severity of coronavirus disease 2019 (COVID-19). However, identified SNPs are inconsistent across studies, and there is no compelling consensus that COVID-19 status is determined by genetic factors. Here, we conducted a systematic review and meta-analysis to determine the effect of genetic factors on COVID-19. A random-effect meta-analysis was performed to estimate pooled odds ratios (ORs) of SNP effects, and SNP-based heritability (SNP-h2 ) of COVID-19. The analyses were performed using meta-R package, and Stata version 17. The meta-analysis included a total of 96,817 COVID-19 cases and 6,414,916 negative controls. The meta-analysis showed that a cluster of highly correlated 9 SNPs (R2 > 0.9) at 3p21.31 gene locus covering LZTFL1 and SLC6A20 genes was significantly associated with COVID-19 severity, with a pooled OR of 1.8 [1.5-2.0]. Meanwhile, another 3 SNPs (rs2531743-G, rs2271616-T, and rs73062389-A) within the locus was associated with COVID-19 susceptibility, with pooled estimates of 0.95 [0.93-0.96], 1.23 [1.19-1.27] and 1.15 [1.13-1.17], respectively. Interestingly, SNPs associated with susceptibility and SNPs associated with severity in this locus are in linkage equilibrium (R2 < 0.026). The SNP-h2 on the liability scale for severity and susceptibility was estimated at 7.6% (Se = 3.2%) and 4.6% (Se = 1.5%), respectively. Genetic factors contribute to COVID-19 susceptibility and severity. In the 3p21.31 locus, SNPs that are associated with susceptibility are not in linkage disequilibrium (LD) with SNPs that are associated with severity, indicating within-locus heterogeneity.
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Affiliation(s)
- Setegn Eshetie
- Australian Centre for Precision Health and UniSA Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
- Department of Medical Microbiology, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
- South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Adelaide, South Australia, Australia
| | - Pastor Jullian
- Australian Centre for Precision Health and UniSA Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Adelaide, South Australia, Australia
| | - Beben Benyamin
- Australian Centre for Precision Health and UniSA Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Adelaide, South Australia, Australia
| | - S Hong Lee
- Australian Centre for Precision Health and UniSA Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Adelaide, South Australia, Australia
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8
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Liu W, Lu JY, Wang YJ, Xu XX, Chen YC, Yu SX, Xiang XW, Chen XZ, Jiu Y, Gao H, Sheng M, Chen ZJ, Hu X, Li D, Maiuri P, Huang X, Ying T, Xu GL, Pang DW, Zhang ZL, Liu B, Liu YJ. Vaccinia virus induces EMT-like transformation and RhoA-mediated mesenchymal migration. J Med Virol 2023; 95:e29041. [PMID: 37621182 DOI: 10.1002/jmv.29041] [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: 05/24/2023] [Revised: 07/17/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
The emerging outbreak of monkeypox is closely associated with the viral infection and spreading, threatening global public health. Virus-induced cell migration facilitates viral transmission. However, the mechanism underlying this type of cell migration remains unclear. Here we investigate the motility of cells infected by vaccinia virus (VACV), a close relative of monkeypox, through combining multi-omics analyses and high-resolution live-cell imaging. We find that, upon VACV infection, the epithelial cells undergo epithelial-mesenchymal transition-like transformation, during which they lose intercellular junctions and acquire the migratory capacity to promote viral spreading. After transformation, VACV-hijacked RhoA signaling significantly alters cellular morphology and rearranges the actin cytoskeleton involving the depolymerization of robust actin stress fibers, leading-edge protrusion formation, and the rear-edge recontraction, which coordinates VACV-induced cell migration. Our study reveals how poxviruses alter the epithelial phenotype and regulate RhoA signaling to induce fast migration, providing a unique perspective to understand the pathogenesis of poxviruses.
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Affiliation(s)
- Wei Liu
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Department of Chemistry, Fudan University, Shanghai, China
| | - Jia-Yin Lu
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Department of Chemistry, Fudan University, Shanghai, China
| | - Ya-Jun Wang
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Department of Chemistry, Fudan University, Shanghai, China
| | - Xin-Xin Xu
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Department of Chemistry, Fudan University, Shanghai, China
| | - Yu-Chen Chen
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Department of Chemistry, Fudan University, Shanghai, China
| | - Sai-Xi Yu
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Department of Chemistry, Fudan University, Shanghai, China
| | - Xiao-Wei Xiang
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Department of Chemistry, Fudan University, Shanghai, China
| | - Xue-Zhu Chen
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Department of Chemistry, Fudan University, Shanghai, China
| | - Yaming Jiu
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Hai Gao
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Department of Chemistry, Fudan University, Shanghai, China
| | - Mengyao Sheng
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Department of Chemistry, Fudan University, Shanghai, China
| | - Zheng-Jun Chen
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xinyao Hu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, College of Life Sciences, Institute of Biophysics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Dong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, College of Life Sciences, Institute of Biophysics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Paolo Maiuri
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Xinxin Huang
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Tianlei Ying
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Guo-Liang Xu
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Dai-Wen Pang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, Research Center for Analytical Sciences, Frontiers Science Center for Cell Responses, College of Chemistry, Nankai University, Tianjin, China
| | - Zhi-Ling Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Baohong Liu
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Department of Chemistry, Fudan University, Shanghai, China
| | - Yan-Jun Liu
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Department of Chemistry, Fudan University, Shanghai, China
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9
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Talukdar SN, McGregor B, Osan JK, Hur J, Mehedi M. RSV infection does not induce EMT. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532506. [PMID: 36993657 PMCID: PMC10055011 DOI: 10.1101/2023.03.13.532506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Respiratory syncytial virus (RSV) infection does not cause severe disease in most of us despite suffering from multiple RSV infections in our lives. However, infants, young children, older adults, and immunocompromised patients are unfortunately vulnerable to RSV-associated severe diseases. A recent study suggested that RSV infection causes cell expansion, resulting in bronchial wall thickening in vitro. Whether the virus-induced changes in the lung airway resemble epithelial-mesenchymal transition (EMT) is still unknown. Here, we report that RSV does not induce EMT in three different in vitro lung models: the epithelial A549 cell line, primary normal human bronchial epithelial cells, and pseudostratified airway epithelium. We found that RSV increases the cell surface area and perimeter in the infected airway epithelium, which is distinct from the effects of a potent EMT inducer, TGF-β1-driven cell elongation-indicative of cell motility. A genome-wide transcriptome analysis revealed that both RSV and TGF-β1 have distinct modulation patterns of the transcriptome, which suggests that RSV-induced changes are distinct from EMT.
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Affiliation(s)
- Sattya N. Talukdar
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, North Dakota, United States of America
| | - Brett McGregor
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, North Dakota, United States of America
| | - Jaspreet K. Osan
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, North Dakota, United States of America
| | - Junguk Hur
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, North Dakota, United States of America
| | - Masfique Mehedi
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, North Dakota, United States of America
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10
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Sen'kova AV, Savin IA, Odarenko KV, Salomatina OV, Salakhutdinov NF, Zenkova MA, Markov AV. Protective effect of soloxolone derivatives in carrageenan- and LPS-driven acute inflammation: Pharmacological profiling and their effects on key inflammation-related processes. Biomed Pharmacother 2023; 159:114231. [PMID: 36640672 DOI: 10.1016/j.biopha.2023.114231] [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: 10/17/2022] [Revised: 12/21/2022] [Accepted: 01/08/2023] [Indexed: 01/13/2023] Open
Abstract
The anti-inflammatory potential of three cyanoenone-containing triterpenoids, including soloxolone methyl (SM), soloxolone (S) and its novel derivative bearing at the C-30 amidoxime moiety (SAO), was studied in murine models of acute inflammation. It was found that the compounds effectively suppressed the development of carrageenan-induced paw edema and peritonitis as well as lipopolysaccharide (LPS)-driven acute lung injury (ALI) with therapeutic outcomes comparable with that of the reference drugs indomethacin and dexamethasone. Non-immunogenic carrageenan-stimulated inflammation was more sensitive to the transformation of C-30 of SM compared with immunogenic LPS-induced inflammation: the anti-inflammatory properties of the studied compounds against carrageenan-induced paw edema and peritonitis decreased in the order of SAO > S > > SM, whereas the efficiency of these triterpenoids against LPS-driven ALI was similar (SAO ≈ S ≈ SM). Further studies demonstrated that soloxolone derivatives significantly inhibited a range of immune-related processes, including granulocyte influx and the expression of key pro-inflammatory cytokines and chemokines in the inflamed sites as well as the functional activity of macrophages. Moreover, SM was found to prevent inflammation-associated apoptosis of A549 pneumocytes and effectively inhibited the protease activity of thrombin (IC50 = 10.3 µM) tightly associated with rodent inflammatome. Taken together, our findings demonstrate that soloxolone derivatives can be considered as novel promising anti-inflammatory drug candidates with multi-targeted mechanism of action.
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Affiliation(s)
- Aleksandra V Sen'kova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent'ev avenue, 8, 630090 Novosibirsk, Russia.
| | - Innokenty A Savin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrent'ev avenue, 9, 630090 Novosibirsk, Russia.
| | - Kirill V Odarenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent'ev avenue, 8, 630090 Novosibirsk, Russia.
| | - Oksana V Salomatina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrent'ev avenue, 9, 630090 Novosibirsk, Russia.
| | - Nariman F Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrent'ev avenue, 9, 630090 Novosibirsk, Russia.
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent'ev avenue, 8, 630090 Novosibirsk, Russia.
| | - Andrey V Markov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrent'ev avenue, 8, 630090 Novosibirsk, Russia.
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11
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Brown B, Ojha V, Fricke I, Al-Sheboul SA, Imarogbe C, Gravier T, Green M, Peterson L, Koutsaroff IP, Demir A, Andrieu J, Leow CY, Leow CH. Innate and Adaptive Immunity during SARS-CoV-2 Infection: Biomolecular Cellular Markers and Mechanisms. Vaccines (Basel) 2023; 11:408. [PMID: 36851285 PMCID: PMC9962967 DOI: 10.3390/vaccines11020408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/16/2023] Open
Abstract
The coronavirus 2019 (COVID-19) pandemic was caused by a positive sense single-stranded RNA (ssRNA) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, other human coronaviruses (hCoVs) exist. Historical pandemics include smallpox and influenza, with efficacious therapeutics utilized to reduce overall disease burden through effectively targeting a competent host immune system response. The immune system is composed of primary/secondary lymphoid structures with initially eight types of immune cell types, and many other subtypes, traversing cell membranes utilizing cell signaling cascades that contribute towards clearance of pathogenic proteins. Other proteins discussed include cluster of differentiation (CD) markers, major histocompatibility complexes (MHC), pleiotropic interleukins (IL), and chemokines (CXC). The historical concepts of host immunity are the innate and adaptive immune systems. The adaptive immune system is represented by T cells, B cells, and antibodies. The innate immune system is represented by macrophages, neutrophils, dendritic cells, and the complement system. Other viruses can affect and regulate cell cycle progression for example, in cancers that include human papillomavirus (HPV: cervical carcinoma), Epstein-Barr virus (EBV: lymphoma), Hepatitis B and C (HB/HC: hepatocellular carcinoma) and human T cell Leukemia Virus-1 (T cell leukemia). Bacterial infections also increase the risk of developing cancer (e.g., Helicobacter pylori). Viral and bacterial factors can cause both morbidity and mortality alongside being transmitted within clinical and community settings through affecting a host immune response. Therefore, it is appropriate to contextualize advances in single cell sequencing in conjunction with other laboratory techniques allowing insights into immune cell characterization. These developments offer improved clarity and understanding that overlap with autoimmune conditions that could be affected by innate B cells (B1+ or marginal zone cells) or adaptive T cell responses to SARS-CoV-2 infection and other pathologies. Thus, this review starts with an introduction into host respiratory infection before examining invaluable cellular messenger proteins and then individual immune cell markers.
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Affiliation(s)
| | | | - Ingo Fricke
- Independent Immunologist and Researcher, 311995 Lamspringe, Germany
| | - Suhaila A Al-Sheboul
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
- Department of Medical Microbiology, International School of Medicine, Medipol University-Istanbul, Istanbul 34810, Turkey
| | | | - Tanya Gravier
- Independent Researcher, MPH, San Francisco, CA 94131, USA
| | | | | | | | - Ayça Demir
- Faculty of Medicine, Afyonkarahisar University, Istanbul 03030, Turkey
| | - Jonatane Andrieu
- Faculté de Médecine, Aix–Marseille University, 13005 Marseille, France
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, USM, Penang 11800, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine, (INFORMM), Universiti Sains Malaysia, USM, Penang 11800, Malaysia
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12
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Linjawi M, Shakoor H, Hilary S, Ali HI, Al-Dhaheri AS, Ismail LC, Apostolopoulos V, Stojanovska L. Cancer Patients during COVID-19 Pandemic: A Mini-Review. Healthcare (Basel) 2023; 11:healthcare11020248. [PMID: 36673615 PMCID: PMC9859465 DOI: 10.3390/healthcare11020248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Since its emergence, coronavirus disease 2019 (COVID-19) has affected the entire world and all commerce and industries, including healthcare systems. COVID-19 adversely affects cancer patients because they are immunocompromised. Increased COVID-19 infection and shortage of medical supplies, beds and healthcare workers in hospitals affect cancer care. This paper includes a description of the existing research that shows the impact of COVID-19 on the management of cancer patients. Aged people with various chronic conditions such as cancer and comorbidities face more challenges as they have a greater risk of disease severity. COVID-19 has affected care delivery, including patient management, and has been responsible for increased mortality among cancer patients. Cancer patients with severe symptoms require regular therapies and treatment; therefore, they have a higher risk of exposure. Due to the risk of transmission, various steps were taken to combat this disease; however, they have affected the existing operational efficiency. Herein, we present the changing priorities during COVID-19, which also affected cancer care, including delayed diagnosis, treatment, and surgeries.
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Affiliation(s)
- Maryam Linjawi
- Department of Nutrition and Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Hira Shakoor
- Department of Nutrition and Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Serene Hilary
- Department of Nutrition and Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Correspondence: (S.H.); (L.S.)
| | - Habiba I. Ali
- Department of Nutrition and Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Ayesha S. Al-Dhaheri
- Department of Nutrition and Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Leila Cheikh Ismail
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, Research Institute of Medical and Health Sciences (RIMHS), University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, OX3 9DU, UK
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia
| | - Lily Stojanovska
- Department of Nutrition and Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia
- Correspondence: (S.H.); (L.S.)
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13
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Rizzi M, Tonello S, D’Onghia D, Sainaghi PP. Gas6/TAM Axis Involvement in Modulating Inflammation and Fibrosis in COVID-19 Patients. Int J Mol Sci 2023; 24:ijms24020951. [PMID: 36674471 PMCID: PMC9861142 DOI: 10.3390/ijms24020951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
Gas6 (growth arrest-specific gene 6) is a widely expressed vitamin K-dependent protein that is involved in many biological processes such as homeostatic regulation, inflammation and repair/fibrotic processes. It is known that it is the main ligand of TAMs, a tyrosine kinase receptor family of three members, namely MerTK, Tyro-3 and Axl, for which it displays the highest affinity. Gas6/TAM axis activation is known to be involved in modulating inflammatory responses as well as fibrotic evolution in many different pathological conditions. Due to the rapidly evolving COVID-19 pandemic, this review will focus on Gas6/TAM axis activation in SARS-CoV-2 infection, where de-regulated inflammatory responses and fibrosis represent a relevant feature of severe disease manifestation. Furthermore, this review will highlight the most recent scientific evidence supporting an unsuspected role of Axl as a SARS-CoV-2 infection driver, and the potential therapeutic advantages of the use of existing Axl inhibitors in COVID-19 management. From a physiological point of view, the Gas6/TAM axis plays a dual role, fostering the tissue repair processes or leading to organ damage and loss of function, depending on the prevalence of its anti-inflammatory or profibrotic properties. This review makes a strong case for further research focusing on the Gas6/TAM axis as a pharmacological target to manage different disease conditions, such as chronic fibrosis or COVID-19.
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14
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Barmania F, Mellet J, Holborn MA, Pepper MS. Genetic Associations with Coronavirus Susceptibility and Disease Severity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:119-140. [PMID: 37378764 DOI: 10.1007/978-3-031-28012-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19) global public health emergency, and the disease it causes is highly variable in its clinical presentation. Host genetic factors are increasingly recognised as a determinant of infection susceptibility and disease severity. Several initiatives and groups have been established to analyse and review host genetic epidemiology associated with COVID-19 outcomes. Here, we review the genetic loci associated with COVID-19 susceptibility and severity focusing on the common variants identified in genome-wide association studies.
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Affiliation(s)
- Fatima Barmania
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juanita Mellet
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Megan A Holborn
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Michael S Pepper
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
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15
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Traspov AA, Minashkin MM, Poyarkov SV, Komarov AG, Shtinova IA, Speshilov GI, Karbyshev IA, Pozdniakova NV, Godkov MA. The rs17713054 and rs1800629 polymorphisms of genes LZTFL1 and TNF are associated with COVID-19 severity. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2022. [DOI: 10.24075/brsmu.2022.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Both genetic and non-genetic factors are responsible for high interindividual variability in response to SARS-CoV-2. Despite the fact that multiple genetic polymorphisms have been identified as risk factors of severe COVID-19, such polymorphisms are still insufficiently studied in the Russian population. The study was aimed to identify genetic determinants associated with severe COVID-19 in the sample of patients from the Russian Federation. The correlation of the rs17713054 polymorphism in gene LZTFL1 and rs1800629 polymorphism in gene TNF (tumor necrosis factor) with the COVID-19 severity was assessed. DNA samples obtained from 713 patients (324 males and 389 females) aged 18‒95 with COVID-19 of varying severity were analyzed. The rs1800629 polymorphism of gene TNF (OR = 1.5; p = 0.02) and rs17713054 polymorphism of gene LZTFL1 (OR = 1.60; p = 0.0043) were identified as risk factors of severe disease. The TNF polymorphism rs1800629 and LZTFL1 polymorphism rs17713054 could be considered as potential predictive biomarkers. The rs17713054 G > A polymorphism was strongly associated with severe disease. In the future the findings may provide the basis for the development of test-systems for prediction of the risk of severe viral respiratory diseases.
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Affiliation(s)
| | | | | | - AG Komarov
- State Budget Institution Of Health Of The City Of Moscow "Diagnostic Center (Center For Laboratory Research) Of The Department Of Health Of The City Of Moscow" Russian Federation, , Moscow
| | - IA Shtinova
- State Budget Institution Of Health Of The City Of Moscow "Diagnostic Center (Center For Laboratory Research) Of The Department Of Health Of The City Of Moscow" Russian Federation, , Moscow
| | - GI Speshilov
- State Budget Institution Of Health Of The City Of Moscow "Diagnostic Center (Center For Laboratory Research) Of The Department Of Health Of The City Of Moscow" Russian Federation, , Moscow
| | - IA Karbyshev
- State Budget Institution Of Health Of The City Of Moscow "Diagnostic Center (Center For Laboratory Research) Of The Department Of Health Of The City Of Moscow" Russian Federation, , Moscow
| | | | - MA Godkov
- Sklifosovsky Research Institute for Emergency Medicine, Moscow, Russia
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16
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Bradic M, Taleb S, Thomas B, Chidiac O, Robay A, Hassan N, Malek J, Ait Hssain A, Abi Khalil C. DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome. J Transl Med 2022; 20:526. [PMID: 36371196 PMCID: PMC9652914 DOI: 10.1186/s12967-022-03737-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/30/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND COVID-19 infections could be complicated by acute respiratory distress syndrome (ARDS), increasing mortality risk. We sought to assess the methylome of peripheral blood mononuclear cells in COVID-19 with ARDS. METHODS We recruited 100 COVID-19 patients with ARDS under mechanical ventilation and 33 non-COVID-19 controls between April and July 2020. COVID-19 patients were followed at four time points for 60 days. DNA methylation and immune cell populations were measured at each time point. A multivariate cox proportional risk regression analysis was conducted to identify predictive signatures according to survival. RESULTS The comparison of COVID-19 to controls at inclusion revealed the presence of a 14.4% difference in promoter-associated CpGs in genes that control immune-related pathways such as interferon-gamma and interferon-alpha responses. On day 60, 24% of patients died. The inter-comparison of baseline DNA methylation to the last recorded time point in both COVID-19 groups or the intra-comparison between inclusion and the end of follow-up in every group showed that most changes occurred as the disease progressed, mainly in the AIM gene, which is associated with an intensified immune response in those who recovered. The multivariate Cox proportional risk regression analysis showed that higher methylation of the "Apoptotic execution Pathway" genes (ROC1, ZNF789, and H1F0) at inclusion increases mortality risk by over twofold. CONCLUSION We observed an epigenetic signature of immune-related genes in COVID-19 patients with ARDS. Further, Hypermethylation of the apoptotic execution pathway genes predicts the outcome. TRIAL REGISTRATION IMRPOVIE study, NCT04473131.
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Affiliation(s)
- Martina Bradic
- grid.5386.8000000041936877XDepartment of Genetic Medicine, Weill Cornell Medicine, New York, USA ,grid.51462.340000 0001 2171 9952Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Sarah Taleb
- grid.452146.00000 0004 1789 3191Division of Genomics and Translational Biomedicine, College of Health and Life Sciences- HBKU, Doha, Qatar
| | - Binitha Thomas
- grid.416973.e0000 0004 0582 4340Epigenetics Cardiovascular Lab, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Omar Chidiac
- grid.416973.e0000 0004 0582 4340Epigenetics Cardiovascular Lab, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Amal Robay
- grid.416973.e0000 0004 0582 4340Epigenetics Cardiovascular Lab, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Nessiya Hassan
- grid.413548.f0000 0004 0571 546XNursery and midwifery research department, Hamad Medical Corporation., Doha, Qatar
| | - Joel Malek
- grid.416973.e0000 0004 0582 4340Genomics Core. Weill Cornell Medicine-Qatar., Doha, Qatar
| | - Ali Ait Hssain
- grid.413548.f0000 0004 0571 546XMedical Intensive Care Unit, Hamad Medical Corporation., Doha, Qatar
| | - Charbel Abi Khalil
- Department of Genetic Medicine, Weill Cornell Medicine, New York, USA. .,Epigenetics Cardiovascular Lab, Weill Cornell Medicine-Qatar, Doha, Qatar. .,Joan and Sanford I. Weill Department of Medicine., Weill Cornell Medicine, New York, USA.
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17
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Abstract
Human genetics can inform the biology and epidemiology of coronavirus disease 2019 (COVID-19) by pinpointing causal mechanisms that explain why some individuals become more severely affected by the disease upon infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Large-scale genetic association studies, encompassing both rare and common genetic variants, have used different study designs and multiple disease phenotype definitions to identify several genomic regions associated with COVID-19. Along with a multitude of follow-up studies, these findings have increased our understanding of disease aetiology and provided routes for management of COVID-19. Important emergent opportunities include the clinical translatability of genetic risk prediction, the repurposing of existing drugs, exploration of variable host effects of different viral strains, study of inter-individual variability in vaccination response and understanding the long-term consequences of SARS-CoV-2 infection. Beyond the current pandemic, these transferrable opportunities are likely to affect the study of many infectious diseases.
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Affiliation(s)
- Mari E K Niemi
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Mark J Daly
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Broad Institute, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.
- Broad Institute, Cambridge, MA, USA.
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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18
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Yip KM, Lee KM, Ng TB, Xu S, Yung KKL, Qu S, Cheung AKL, Sze SCW. An anti-inflammatory and anti-fibrotic proprietary Chinese medicine nasal spray designated as Allergic Rhinitis Nose Drops (ARND) with potential to prevent SARS-CoV-2 coronavirus infection by targeting RBD (Delta)- angiotensin converting enzyme 2 (ACE2) binding. Chin Med 2022; 17:88. [PMID: 35897044 PMCID: PMC9328017 DOI: 10.1186/s13020-022-00635-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/18/2022] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Since the outbreak of COVID-19 has resulted in over 313,000,000 confirmed cases of infection and over 5,500,000 deaths, substantial research work has been conducted to discover agents/ vaccines against COVID-19. Undesired adverse effects were observed in clinical practice and common vaccines do not protect the nasal tissue. An increasing volume of direct evidence based on clinical studies of traditional Chinese medicines (TCM) in the treatment of COVID-19 has been reported. However, the safe anti-inflammatory and anti-fibrotic proprietary Chinese medicines nasal spray, designated as Allergic Rhinitis Nose Drops (ARND), and its potential of re-purposing for suppressing viral infection via SARS-CoV-2 RBD (Delta)- angiotensin converting enzyme 2 (ACE2) binding have not been elucidated. PURPOSE To characterize ARND as a potential SARS-CoV-2 entry inhibitor for its possible preventive application in anti-virus hygienic agent. METHODS Network pharmacology analysis of ARND was adopted to asacertain gene targets which were commonly affected by COVID-19. The inhibitory effect of ARND on viral infection was determined by an in vitro pseudovirus assay. Furthermore, ARND was confirmed to have a strong binding affinity with ACE2 and SARS-CoV-2 spike-RBD (Delta) by ELISA. Finally, inflammatory and fibrotic cell models were used in conjunction in this study. RESULTS The results suggested ARND not only inhibited pseudovirus infection and undermined the binding affinity between ACE2 and the Spike protein (Delta), but also attenuated the inflammatory response upon infection and may lead to a better prognosis with a lower risk of pulmonary fibrosis. The data in this study also provide a basis for further development of ARND as an antiviral hygienic product and further investigations on ARND in the live virus, in vivo and COVID-19 patients. ARND holds promise for use in the current COVID-19 outbreak as well as in future pandemics. CONCLUSION ARND could be considered as a safe anti-SARS-CoV-2 agent with potential to prevent SARS-CoV-2 coronavirus infection.
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Affiliation(s)
- Ka Man Yip
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong, Special Administrative Region, China.,Golden Meditech Center for NeuroRegeneration Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong, Special Administrative Region, China
| | - Kwan Ming Lee
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong, Special Administrative Region, China.,Golden Meditech Center for NeuroRegeneration Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong, Special Administrative Region, China
| | - Tzi Bun Ng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region, China
| | - Shujun Xu
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong, Special Administrative Region, China.,Golden Meditech Center for NeuroRegeneration Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong, Special Administrative Region, China
| | - Ken Kin Lam Yung
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong, Special Administrative Region, China. .,Golden Meditech Center for NeuroRegeneration Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong, Special Administrative Region, China.
| | - Shaogang Qu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China. .,Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou, 510515, Guangdong, China. .,Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| | - Allen Ka Loon Cheung
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong, Special Administrative Region, China.
| | - Stephen Cho Wing Sze
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong, Special Administrative Region, China. .,Golden Meditech Center for NeuroRegeneration Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong, Special Administrative Region, China.
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19
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Zhang WN, Li XP, Wang PF, Zhu L, Xiao XH, Dai YJ. Comprehensive Analysis of the Novel Omicron Receptor AXL in Cancers. Comput Struct Biotechnol J 2022; 20:3304-3312. [PMID: 35782741 PMCID: PMC9234055 DOI: 10.1016/j.csbj.2022.06.051] [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: 02/28/2022] [Revised: 06/23/2022] [Accepted: 06/23/2022] [Indexed: 11/25/2022] Open
Abstract
The SARS-CoV-2 is constantly mutating, and the new coronavirus such as Omicron has spread to many countries around the world. Anexelekto (AXL) is a transmembrane protein with biological functions such as promoting cell growth, migration, aggregation, metastasis and adhesion, and plays an important role in cancers and coronavirus disease 2019 (COVID-19). Unlike angiotensin-converting enzyme 2 (ACE2), AXL was highly expressed in respiratory system cells. In this study, we verified the AXL expression in cancer and normal tissues and found AXL expression was strongly correlated with cancer prognosis, tumor mutation burden (TMB), the microsatellite instability (MSI) in most tumor types. Immune infiltration analysis also demonstrated that there was an inextricable link between AXL expression and immune scores in cancer patients, especially in BLCA, BRCA and CESC. The NK-cells, plasmacytoid dendritic cells, myeloid dendritic cells, as one of the important components of the tumor microenvironment, were highly expressed AXL. In addition, AXL-related tumor neoantigens were identified and might provide the novel potential targets for tumor vaccines or SARS-Cov-2 vaccines research in cancer patients.
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20
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Huang Y, Jiang L, Liu Y, Liu L, Wang J, Shi L. Long non-coding RNAs in virus-related cancers. Rev Med Virol 2022; 32:e2364. [PMID: 35607835 DOI: 10.1002/rmv.2364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/30/2022] [Accepted: 05/06/2022] [Indexed: 12/12/2022]
Abstract
Some viral infections lead to tumourigenesis explained by a variety of underlying molecular mechanisms. Long non-coding RNAs (lncRNAs) have the potential to be added to this list due to their diverse mechanisms in biological functions and disease processes via gene alternation, transcriptional regulation, protein modification, microRNA sponging and interaction with RNA/DNA/proteins. In this review, we summarise the dysregulation and mechanism of lncRNAs in virus-related cancers focussing on Hepatitis B virus, Epstein-Barr virus, Human Papillomavirus. We will also discuss the potential implications of lncRNAs in COVID-19.
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Affiliation(s)
- Yushan Huang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Longchang Jiang
- Department of Vascular Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yang Liu
- Gansu Provincial People's Hospital, Lanzhou, China
| | - Lixian Liu
- Shijiangzhuang City Zoo, Shijiazhuang, China
| | - Junling Wang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Lei Shi
- School of Public Health, Lanzhou University, Lanzhou, China
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21
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Manfioletti G, Fedele M. Epithelial-Mesenchymal Transition (EMT) 2021. Int J Mol Sci 2022; 23:ijms23105848. [PMID: 35628655 PMCID: PMC9145979 DOI: 10.3390/ijms23105848] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/27/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a transdifferentiation process wherein epithelial cells acquire characteristics typical of mesenchymal cells [...].
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Affiliation(s)
| | - Monica Fedele
- National Research Council (CNR), Institute of Experimental Endocrinology and Oncology (IEOS), 80145 Naples, Italy
- Correspondence: or ; Tel.: +39-(081)-545-5751
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22
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Prognostic serum biomarkers in cancer patients with COVID-19: a systematic review. Transl Oncol 2022; 21:101443. [PMID: 35523009 PMCID: PMC9057983 DOI: 10.1016/j.tranon.2022.101443] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/05/2021] [Accepted: 04/27/2022] [Indexed: 12/23/2022] Open
Abstract
Albumin, CRP, d-dimer, ferritin, hemoglobin, IL-2R, IL-6, LDH, and PCT were identified as commonly changed biomarkers in three different comparison groups. Increased levels of CRP, d-dimer, ferritin, IL-2R, IL-6, LDH, and PCT are positively correlated to the COVID-19 severity and cancer surveillance in cancer patients with COVID-19. High levels of CRP, ferritin, and LDH after immunotherapy for COVID-19 in cancer patients indicate a poor prognosis. Cancer patients who had lower levels of CRP, ferritin, and LDH exhibit a good prognosis after antivirals/antibiotic treatment for SARS-CoV-2 infection.
Purpose Methods Results Conclusion
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23
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Healthy Immunity on Preventive Medicine for Combating COVID-19. Nutrients 2022; 14:nu14051004. [PMID: 35267980 PMCID: PMC8912522 DOI: 10.3390/nu14051004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
Immunomodulation is influenced by the consumption of nutrients, and healthy immunity is pivotal to defending an individual from a variety of pathogens. The immune system is a network of intricately regulated biological processes that is comprised of many organs, cellular structures, and signaling molecules. A balanced diet, rich in vitamins, minerals, and antioxidants, is key to a strengthened immune system and, thus, crucial to proper functioning of various physiological activities. Conversely, deficiencies of these micronutrients, involving impaired immunity, are linked to numerous health complications, along with a host of pathologies. Coronavirus disease 2019 (COVID-19) is a dangerous infectious disease caused by a β-form of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its genomic variants, which enter host cells upon binding to the angiotensin converting enzyme 2 receptors, and is associated with substantial morbidities and mortalities globally. Patients afflicted with COVID-19 display asymptomatic to severe symptoms, occurrences of which are multifactorial and include diverse immune responses, sex and gender differences, aging, and underlying medical conditions. Geriatric populations, especially men in comparison to women, regardless of their states, are most vulnerable to severe COVID-19-associated infections and complications, with fatal outcomes. Advances in genomic and proteomic technologies help one understand molecular events, including host–pathogen interactions and pathogenesis of COVID-19 and, subsequently, have developed a variety of preventive measures urgently, ranging from mask wearing to vaccination to medication. Despite these approaches, no unique strategy is available today that can effectively prevent and/or treat this hostile disease. As a consequence, the maintenance of a boosted immune system could be considered a high priority of preventive medicine for combating COVID-19. Herein, we discuss the current level of understanding underlining the contribution of healthy immunity and its relevance to COVID-19 molecular pathogenesis, and potential therapeutic strategies, in the management of this devastating disease.
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24
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Role of glycosyltransferases in carcinogenesis; growth factor signaling and EMT/MET programs. Glycoconj J 2022; 39:167-176. [PMID: 35089466 PMCID: PMC8795723 DOI: 10.1007/s10719-022-10041-3] [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] [Received: 12/02/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 02/06/2023]
Abstract
The glycosylation of cell surface receptors has been shown to regulate each step of signal transduction, including receptor trafficking to the cell surface, ligand binding, dimerization, phosphorylation, and endocytosis. In this review we focus on the role of glycosyltransferases that are involved in the modification of N-glycans, such as the effect of branching and elongation in signaling by various cell surface receptors. In addition, the role of those enzymes in the EMT/MET programs, as related to differentiation and cancer development, progress and therapy resistance is discussed.
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25
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Abdo Cuza AA, Ávila JP, Martínez RM, González JJ, Aspuro GP, Gutiérrez Martínez JA, Suzarte MR, Hernández DS, Añé-Kouri AL, Ramos TC. Nimotuzumab for COVID-19: case series. Immunotherapy 2021; 14:10.2217/imt-2021-0269. [PMID: 34806405 PMCID: PMC8628863 DOI: 10.2217/imt-2021-0269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/08/2021] [Indexed: 12/15/2022] Open
Abstract
Background: In COVID-19, EGFR production is upregulated in the alveolar epithelial cells. EGFR overexpression further activates STAT-3 and increases lung pathology. The EGFR pathway is also one of the major nodes in pulmonary fibrosis. Methods: Nimotuzumab, a humanized anti-EGFR antibody, was used to treat three patients with severe or moderate COVID-19. The antibody was administered in combination with other drugs included in the national COVID-19 protocol. Results: Nimotuzumab was well tolerated. IL-6 decreased from the first antibody infusion. Clinical symptoms significantly improved after nimotuzumab administration, and the CT scans at discharge showed major resolution of the lung lesions and no signs of fibrosis. Conclusion: Safe anti-EGFR antibodies like nimotuzumab may modulate COVID-19-associated hyperinflammation and prevent fibrosis. Clinical Trial Registration: RPCEC00000369 (RPCEC rpcec.sld.cu).
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Affiliation(s)
- Anselmo A Abdo Cuza
- Intensive Care Unit. Medical & Surgical Research Center (CIMEQ), Havana, Cuba
| | - Jonathan Pi Ávila
- Intensive Care Unit. Medical & Surgical Research Center (CIMEQ), Havana, Cuba
| | | | | | | | | | - Mayra Ramos Suzarte
- Clinical Research Direction. Center of Molecular Immunology (CIM), Havana, Cuba
| | | | - Ana L Añé-Kouri
- Clinical Research Direction. Center of Molecular Immunology (CIM), Havana, Cuba
| | - Tania Crombet Ramos
- Clinical Research Direction. Center of Molecular Immunology (CIM), Havana, Cuba
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26
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Downes DJ, Cross AR, Hua P, Roberts N, Schwessinger R, Cutler AJ, Munis AM, Brown J, Mielczarek O, de Andrea CE, Melero I, Gill DR, Hyde SC, Knight JC, Todd JA, Sansom SN, Issa F, Davies JOJ, Hughes JR. Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus. Nat Genet 2021; 53:1606-1615. [PMID: 34737427 PMCID: PMC7611960 DOI: 10.1038/s41588-021-00955-3] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 09/22/2021] [Indexed: 12/21/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) disease (COVID-19) pandemic has caused millions of deaths worldwide. Genome-wide association studies identified the 3p21.31 region as conferring a twofold increased risk of respiratory failure. Here, using a combined multiomics and machine learning approach, we identify the gain-of-function risk A allele of an SNP, rs17713054G>A, as a probable causative variant. We show with chromosome conformation capture and gene-expression analysis that the rs17713054-affected enhancer upregulates the interacting gene, leucine zipper transcription factor like 1 (LZTFL1). Selective spatial transcriptomic analysis of lung biopsies from patients with COVID-19 shows the presence of signals associated with epithelial-mesenchymal transition (EMT), a viral response pathway that is regulated by LZTFL1. We conclude that pulmonary epithelial cells undergoing EMT, rather than immune cells, are likely responsible for the 3p21.31-associated risk. Since the 3p21.31 effect is conferred by a gain-of-function, LZTFL1 may represent a therapeutic target.
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Affiliation(s)
- Damien J Downes
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Amy R Cross
- Nuffield Department of Surgical Sciences, Transplantation Research and Immunology Group,University of Oxford, Oxford, UK
| | - Peng Hua
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nigel Roberts
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine Centre for Computational Biology, University of Oxford, Oxford, UK
| | - Antony J Cutler
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Immunology Research Unit, GlaxoSmithKline, Stevenage, UK
| | - Altar M Munis
- Department of Medicine, Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe University of Oxford, Oxford, UK
| | - Jill Brown
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Olga Mielczarek
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Carlos E de Andrea
- Department of Pathology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ignacio Melero
- Division of Immunology and Immunotherapy, Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Deborah R Gill
- Department of Medicine, Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe University of Oxford, Oxford, UK
| | - Stephen C Hyde
- Department of Medicine, Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe University of Oxford, Oxford, UK
| | - Julian C Knight
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - John A Todd
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen N Sansom
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Fadi Issa
- Nuffield Department of Surgical Sciences, Transplantation Research and Immunology Group,University of Oxford, Oxford, UK
- Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - James O J Davies
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK.
| | - Jim R Hughes
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine Centre for Computational Biology, University of Oxford, Oxford, UK.
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27
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Yang C, Li Y, Xiao SY. Do We Really Understand the Relationship Between Expression of ACE2 and Coronavirus Disease 2019 Lung Pathophysiology? J Thorac Oncol 2021; 16:1785-1787. [PMID: 34716001 PMCID: PMC8547761 DOI: 10.1016/j.jtho.2021.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Chunxiu Yang
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China; Wuhan University Center for Pathology and Molecular Diagnostics, Wuhan, People's Republic of China
| | - Yueying Li
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China; Wuhan University Center for Pathology and Molecular Diagnostics, Wuhan, People's Republic of China
| | - Shu-Yuan Xiao
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China; Wuhan University Center for Pathology and Molecular Diagnostics, Wuhan, People's Republic of China; Department of Pathology, University of Chicago Medicine, Chicago, Illinois.
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28
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Alfaro-García JP, Granados-Alzate MC, Vicente-Manzanares M, Gallego-Gómez JC. An Integrated View of Virus-Triggered Cellular Plasticity Using Boolean Networks. Cells 2021; 10:cells10112863. [PMID: 34831086 PMCID: PMC8616224 DOI: 10.3390/cells10112863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/18/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Virus-related mortality and morbidity are due to cell/tissue damage caused by replicative pressure and resource exhaustion, e.g., HBV or HIV; exaggerated immune responses, e.g., SARS-CoV-2; and cancer, e.g., EBV or HPV. In this context, oncogenic and other types of viruses drive genetic and epigenetic changes that expand the tumorigenic program, including modifications to the ability of cancer cells to migrate. The best-characterized group of changes is collectively known as the epithelial–mesenchymal transition, or EMT. This is a complex phenomenon classically described using biochemistry, cell biology and genetics. However, these methods require enormous, often slow, efforts to identify and validate novel therapeutic targets. Systems biology can complement and accelerate discoveries in this field. One example of such an approach is Boolean networks, which make complex biological problems tractable by modeling data (“nodes”) connected by logical operators. Here, we focus on virus-induced cellular plasticity and cell reprogramming in mammals, and how Boolean networks could provide novel insights into the ability of some viruses to trigger uncontrolled cell proliferation and EMT, two key hallmarks of cancer.
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Affiliation(s)
- Jenny Paola Alfaro-García
- Molecular and Translation Medicine Group, Faculty of Medicine, University of Antioquia, Medellin 050010, Colombia; (J.P.A.-G.); (M.C.G.-A.)
| | - María Camila Granados-Alzate
- Molecular and Translation Medicine Group, Faculty of Medicine, University of Antioquia, Medellin 050010, Colombia; (J.P.A.-G.); (M.C.G.-A.)
| | - Miguel Vicente-Manzanares
- Molecular Mechanisms Program, Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain
- Correspondence: (M.V.-M.); (J.C.G.-G.)
| | - Juan Carlos Gallego-Gómez
- Molecular and Translation Medicine Group, Faculty of Medicine, University of Antioquia, Medellin 050010, Colombia; (J.P.A.-G.); (M.C.G.-A.)
- Correspondence: (M.V.-M.); (J.C.G.-G.)
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29
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Vázquez-Jiménez A, Avila-Ponce De León UE, Matadamas-Guzman M, Muciño-Olmos EA, Martínez-López YE, Escobedo-Tapia T, Resendis-Antonio O. On Deep Landscape Exploration of COVID-19 Patients Cells and Severity Markers. Front Immunol 2021; 12:705646. [PMID: 34603282 PMCID: PMC8481922 DOI: 10.3389/fimmu.2021.705646] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
COVID-19 is a disease with a spectrum of clinical responses ranging from moderate to critical. To study and control its effects, a large number of researchers are focused on two substantial aims. On the one hand, the discovery of diverse biomarkers to classify and potentially anticipate the disease severity of patients. These biomarkers could serve as a medical criterion to prioritize attention to those patients with higher prone to severe responses. On the other hand, understanding how the immune system orchestrates its responses in this spectrum of disease severities is a fundamental issue required to design new and optimized therapeutic strategies. In this work, using single-cell RNAseq of bronchoalveolar lavage fluid of nine patients with COVID-19 and three healthy controls, we contribute to both aspects. First, we presented computational supervised machine-learning models with high accuracy in classifying the disease severity (moderate and severe) in patients with COVID-19 starting from single-cell data from bronchoalveolar lavage fluid. Second, we identified regulatory mechanisms from the heterogeneous cell populations in the lungs microenvironment that correlated with different clinical responses. Given the results, patients with moderate COVID-19 symptoms showed an activation/inactivation profile for their analyzed cells leading to a sequential and innocuous immune response. In comparison, severe patients might be promoting cytotoxic and pro-inflammatory responses in a systemic fashion involving epithelial and immune cells without the possibility to develop viral clearance and immune memory. Consequently, we present an in-depth landscape analysis of how transcriptional factors and pathways from these heterogeneous populations can regulate their expression to promote or restrain an effective immune response directly linked to the patients prognosis.
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Affiliation(s)
- Aarón Vázquez-Jiménez
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Ugo Enrique Avila-Ponce De León
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado en Ciencias Biológicas, UNAM, Mexico City, Mexico
| | - Meztli Matadamas-Guzman
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado en Ciencias Biomédicas, UNAM, Mexico City, Mexico
| | - Erick Andrés Muciño-Olmos
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado en Ciencias Biomédicas, UNAM, Mexico City, Mexico
| | - Yoscelina E. Martínez-López
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado en Ciencias Médicas y de la Salud, UNAM, Mexico City, Mexico
| | - Thelma Escobedo-Tapia
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, UNAM, Mexico City, Mexico
| | - Osbaldo Resendis-Antonio
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Coordinación de la Investigación Científica - Red de Apoyo a la Investigación, UNAM, Mexico City, Mexico
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