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Martín-Galiano AJ, López D. Conservation of HLA Spike Protein Epitopes Supports T Cell Cross-Protection in SARS-CoV-2 Vaccinated Individuals against the Potentially Zoonotic Coronavirus Khosta-2. Int J Mol Sci 2024; 25:6087. [PMID: 38892276 PMCID: PMC11172828 DOI: 10.3390/ijms25116087] [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: 04/25/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Heterologous vaccines, which induce immunity against several related pathogens, can be a very useful and rapid way to deal with new pandemics. In this study, the potential impact of licensed COVID-19 vaccines on cytotoxic and helper cell immune responses against Khosta-2, a novel sarbecovirus that productively infects human cells, was analyzed for the 567 and 41 most common HLA class I and II alleles, respectively. Computational predictions indicated that most of these 608 alleles, covering more than 90% of the human population, contain sufficient fully conserved T-cell epitopes between the Khosta-2 and SARS-CoV-2 spike-in proteins. Ninety percent of these fully conserved peptides for class I and 93% for class II HLA molecules were verified as epitopes recognized by CD8+ or CD4+ T lymphocytes, respectively. These results show a very high correlation between bioinformatic prediction and experimental assays, which strongly validates this study. This immunoinformatics analysis allowed a broader assessment of the alleles that recognize these peptides, a global approach at the population level that is not possible with experimental assays. In summary, these findings suggest that both cytotoxic and helper cell immune protection elicited by currently licensed COVID-19 vaccines should be effective against Khosta-2 virus infection. Finally, by being rapidly adaptable to future coronavirus pandemics, this study has potential public health implications.
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Affiliation(s)
- Antonio J. Martín-Galiano
- Core Scientific and Technical Units, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain;
| | - Daniel López
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
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Peled Y, Patel JK, Raanani E, Eilon R, Fardman A, Beigel R, Atari N, Kliker L, Elkader BA, Mandelboim M, Afek A. BNT162b2-vaccine-induced neutralization responses are immune correlates of clinical protection against SARS-CoV-2 in heart transplant recipients. Clin Transplant 2023; 37:e15091. [PMID: 37572313 DOI: 10.1111/ctr.15091] [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: 06/22/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/14/2023]
Abstract
BACKGROUND Defining immune correlates of protection against COVID-19 is pivotal for optimizing the use of COVID-19 vaccines, predicting the impact of novel variants on clinical outcomes, and advancing the development of immunotherapies and next-generation vaccines. We aimed to identify vaccine-induced immune correlates of protection against COVID-19-related hospitalizations in a highly vaccinated heart transplant (HT) cohort. METHODS In a case-control study of HT recipients vaccinated with the BNT162b2 vaccine, patients were prospectively assessed for vaccine-induced neutralization of the wild-type virus, and the Delta and Omicron BA.1, BA.2, BA.4, and BA.5 variants. Comparative analyses with controls were conducted to identify correlates of protection against COVID-19 hospitalization. ROC analyses were performed. Primary outcomes were COVID-19 hospitalizations and severity of SARS-CoV-2 breakthrough infection. RESULTS The study cohort comprised 59 HT recipients aged 58 (49,65) years with breakthrough infections after three or four monovalent BNT162b2 doses; 41 (69.5%) were men. Thirty-six (61%) patients with COVID-19 were hospitalized; most cases were non-severe (58, 98%). For hospitalized (vs. non-hospitalized) COVID-19 patients, vaccine-induced neutralization titers were significantly lower against all SARS-CoV-2 variants (p < .005). Vaccine-induced neutralization of the wild-type virus and delta and omicron BA.1, BA.2, BA.4, and BA.5 variants was associated with a reduced risk for COVID-19-related hospitalization. The optimal neutralization titer thresholds that were predictive of COVID-19 hospitalizations were 96 (wild-type), 48 (delta), 12 (BA.1), 96 (BA.2), 96 (BA.4), and 48 (BA.5). CONCLUSIONS BNT162b2-vaccine-induced neutralization responses are immune correlates of protection and confer clinical protection against COVID-19 hospitalizations.
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Affiliation(s)
- Yael Peled
- Leviev Cardiothoracic and Vascular Center, Sheba Medical Center, Tel Hashomer, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jignesh K Patel
- Cedars-Sinai Heart Institute and David Geffen School of Medicine at the University of California, Los Angeles, California, USA
| | - Ehud Raanani
- Leviev Cardiothoracic and Vascular Center, Sheba Medical Center, Tel Hashomer, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ram Eilon
- Leviev Cardiothoracic and Vascular Center, Sheba Medical Center, Tel Hashomer, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alexander Fardman
- Leviev Cardiothoracic and Vascular Center, Sheba Medical Center, Tel Hashomer, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Roy Beigel
- Leviev Cardiothoracic and Vascular Center, Sheba Medical Center, Tel Hashomer, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nofar Atari
- Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Israel
| | - Limor Kliker
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Israel
| | - Bayan Abd Elkader
- Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Israel
| | - Michal Mandelboim
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Israel
| | - Arnon Afek
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- General Management, Sheba Medical Center, Tel Hashomer, Israel
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Ramasamy R. COVID-19 Vaccines for Optimizing Immunity in the Upper Respiratory Tract. Viruses 2023; 15:2203. [PMID: 38005881 PMCID: PMC10674974 DOI: 10.3390/v15112203] [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: 10/09/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Rapid development and deployment of vaccines greatly reduced mortality and morbidity during the COVID-19 pandemic. The most widely used COVID-19 vaccines approved by national regulatory authorities require intramuscular administration. SARS-CoV-2 initially infects the upper respiratory tract, where the infection can be eliminated with little or no symptoms by an effective immune response. Failure to eliminate SARS-CoV-2 in the upper respiratory tract results in lower respiratory tract infections that can lead to severe disease and death. Presently used intramuscularly administered COVID-19 vaccines are effective in reducing severe disease and mortality, but are not entirely able to prevent asymptomatic and mild infections as well as person-to-person transmission of the virus. Individual and population differences also influence susceptibility to infection and the propensity to develop severe disease. This article provides a perspective on the nature and the mode of delivery of COVID-19 vaccines that can optimize protective immunity in the upper respiratory tract to reduce infections and virus transmission as well as severe disease.
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Affiliation(s)
- Ranjan Ramasamy
- ID-FISH Technology Inc., 556 Gibraltar Drive, Milpitas, CA 95035, USA
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Pita-Martínez C, Pérez-García F, Virseda Berdices A, Martin-Vicente M, Castilla-García L, Hervás Fernández I, González Ventosa V, Muñoz-Gómez MJ, Cuadros-González J, Bermejo-Martin JF, Resino S, Martínez I. A deficient immune response to SARS-CoV-2 in the nasopharynx is associated with severe COVID-19 pneumonia. Int J Infect Dis 2023; 134:126-132. [PMID: 37290572 PMCID: PMC10245280 DOI: 10.1016/j.ijid.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023] Open
Abstract
OBJECTIVES We analyzed the expression of inflammatory and antiviral genes in the nasopharynx of SARS-CoV-2 infected patients and their association with the severity of COVID-19 pneumonia. METHODS We conducted a cross-sectional study on 223 SARS-CoV-2 infected patients. Clinical data were collected from medical records, and nasopharyngeal samples were collected in the first 24 hours after admission to the emergency room. The gene expression of eight proinflammatory/antiviral genes (plasminogen activator urokinase receptor [PLAUR], interleukin [IL]-6, IL-8, interferon [IFN]-β, IFN-stimulated gene 15 [ISG15], retinoic acid-inducible gene I [RIG-I], C-C motif ligand 5 [CCL5], and chemokine C-X-C motif ligand 10 [CXCL10]) were quantified by real-time polymerase chain reaction. Outcome variables were: (i) pneumonia; (ii) severe pneumonia or acute respiratory distress syndrome. Statistical analysis was performed using multivariate logistic regression analyses. RESULTS We enrolled 84 mild, 88 moderate, and 51 severe/critical cases. High expression of PLAUR (adjusted odds ratio [aOR] = 1.25; P = 0.032, risk factor) and low expression of CXCL10 (aOR = 0.89; P = 0.048, protective factor) were associated with pneumonia. Furthermore, lower values of ISG15 (aOR = 0.88, P = 0.021), RIG-I (aOR = 0.87, P = 0.034), CCL5 (aOR = 0.73, P <0.001), and CXCL10 (aOR = 0.84, P = 0.002) were risk factors for severe pneumonia/acute respiratory distress syndrome. CONCLUSION An unbalanced early innate immune response to SARS-CoV-2 in the nasopharynx, characterized by high expression of PLAUR and low expression of antiviral genes (ISG15 and RIG-I), and chemokines (CCL5 and CXCL10), was associated with COVID-19 severity.
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Affiliation(s)
- Carlos Pita-Martínez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Felipe Pérez-García
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología Clínica, Hospital Universitario Príncipe de Asturias, Madrid, Spain; Universidad de Alcalá, Facultad de Medicina, Departamento de Biomedicina y Biotecnología, Madrid, Spain
| | - Ana Virseda Berdices
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - María Martin-Vicente
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Lucía Castilla-García
- Servicio de Hematología y Hemoterapia, Hospital Universitario Príncipe de Asturias, Madrid, Spain
| | - Irene Hervás Fernández
- Servicio de Microbiología Clínica, Hospital Universitario Príncipe de Asturias, Madrid, Spain
| | | | - María José Muñoz-Gómez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Cuadros-González
- Servicio de Microbiología Clínica, Hospital Universitario Príncipe de Asturias, Madrid, Spain; Universidad de Alcalá, Facultad de Medicina, Departamento de Biomedicina y Biotecnología, Madrid, Spain
| | - Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigación Biomédica de Salamanca, (IBSAL), Salamanca, Spain; Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Salvador Resino
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Isidoro Martínez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
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Ramasamy R. Overview of immunological & virological factors driving the evolution & global spread of SARS-CoV-2 variants. Indian J Med Res 2023; 158:257-268. [PMID: 37815068 PMCID: PMC10720969 DOI: 10.4103/ijmr.ijmr_2591_22] [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: 12/21/2022] [Indexed: 10/11/2023] Open
Abstract
The SARS-CoV-2, a highly infectious positive strand RNA virus first identified in December 2019, has produced multiple genetic variants that have rapidly and sequentially spread worldwide during the coronavirus disease 2019 (COVID-19) pandemic. Genetic changes in SARS-CoV-2 for greater infectivity, replication and transmission were selected during the early stages of the pandemic. More recently, after widespread infection and vaccination, SARS-CoV-2 variants that evade antigen-specific adaptive immunity, have begun to be selected. This article provides an overview of the molecular immunological and virological factors underlying the origin and global spread of important SARS-CoV-2 variant lineages.
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Luo M, Xia G, Gan T, Zhao Z, Wu J, Hu T, Wang L, Zhang Y. Influencing factors of hospital-acquired COVID-19 prevention and control status among emergency support frontline healthcare workers under closed-loop management: a cross-sectional study. Front Public Health 2023; 11:1209646. [PMID: 37575121 PMCID: PMC10413553 DOI: 10.3389/fpubh.2023.1209646] [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: 04/21/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Background This study aimed to understand the hospital-acquired COVID-19 infection rate and infection prevention and control status of emergency support frontline healthcare workers (ESFHCWs) under closed-loop management, and to explore the related factors affecting hospital-acquired COVID-19 prevention and control status. Methods The study site was a provincial-level tertiary hospital in the Xinjiang Uygur Autonomous Region specializing in treating COVID-19 patients. ESFHCWs were assigned from different hospitals in Zhejiang Province to provide emergency medical support in this specialized hospital. All ESFHCWs were managed using a closed loop. A self-designed questionnaire was used to estimate basic information, work experience, and the status of infection prevention and control (SIPC). A total of 269 ESFHCWs responded to the questionnaire. A generalized linear regression model was used to estimate the factors influencing SIPC. Results There were six hospital-acquired COVID-19 cases, with an infection rate of 2.23%. The independent risk factors influencing COVID-19 prevention and control status were work seniority, anxiety disorder, and consumption of gastrointestinal, anti-inflammatory and anti-asthmatic, and hypnotic sedative drugs. Compared with ESFHCWs with more than 10 years of work seniority, ESFHCWs with less than 5 years of work seniority and 5-10 years of work seniority had lower COVID-19 SIPC scores. Among ESFHCWs with anxiety disorder, the SIPC score was significantly lower than that of ESFHCWs without anxiety disorder. The SIPC scores of ESFHCWs taking other medications (gastrointestinal, anti-inflammatory and anti-asthmatic, and hypnotic sedative drugs) were lower than those of ESFHCWs who did not. Conclusion The closed-loop management method may be effective in reducing the infection rate of hospital-acquired COVID-19 among ESFHCWs. HCWs with less than 10 years of work seniority, anxiety disorder, and other medications (gastrointestinal, anti-inflammatory and anti-asthmatic, and hypnotic sedative drugs) were probably not suitable for participating in emergency assistant actions because of their poor SIPC scores. Further studies are needed to develop the selection criteria for ESFHCWs.
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Affiliation(s)
- Man Luo
- Department of Hospital Infection Control, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Guoqin Xia
- Department of Hospital Infection Control, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Tieer Gan
- Department of Hospital Infection Control, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, China
| | - Zhifang Zhao
- Department of Hospital Infection Control, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Jiannong Wu
- Department of Critical Care, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, China
| | - Ting Hu
- Department of Hospital Infection Control, Hangzhou Red Cross Hospital, Hangzhou, China
| | - Lucong Wang
- Department of Hospital Infection Control, Jindong District Chisong Town Central Hospital, Jinhua, China
| | - Yiyin Zhang
- Department of Hospital Infection Control, Ningbo Traditional Chinese Medicine Hospital, Ningbo, China
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7
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Feng Y, Yang M, Fan Z, Zhao W, Kim P, Zhou X. COVIDanno, COVID-19 annotation in human. Front Microbiol 2023; 14:1129103. [PMID: 37497545 PMCID: PMC10366449 DOI: 10.3389/fmicb.2023.1129103] [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: 12/21/2022] [Accepted: 06/26/2023] [Indexed: 07/28/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 19 (COVID-19), has caused a global health crisis. Despite ongoing efforts to treat patients, there is no universal prevention or cure available. One of the feasible approaches will be identifying the key genes from SARS-CoV-2-infected cells. SARS-CoV-2-infected in vitro model, allows easy control of the experimental conditions, obtaining reproducible results, and monitoring of infection progression. Currently, accumulating RNA-seq data from SARS-CoV-2 in vitro models urgently needs systematic translation and interpretation. To fill this gap, we built COVIDanno, COVID-19 annotation in humans, available at http://biomedbdc.wchscu.cn/COVIDanno/. The aim of this resource is to provide a reference resource of intensive functional annotations of differentially expressed genes (DEGs) among different time points of COVID-19 infection in human in vitro models. To do this, we performed differential expression analysis for 136 individual datasets across 13 tissue types. In total, we identified 4,935 DEGs. We performed multiple bioinformatics/computational biology studies for these DEGs. Furthermore, we developed a novel tool to help users predict the status of SARS-CoV-2 infection for a given sample. COVIDanno will be a valuable resource for identifying SARS-CoV-2-related genes and understanding their potential functional roles in different time points and multiple tissue types.
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Affiliation(s)
- Yuzhou Feng
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
- Med-X Center for Informatics, Sichuan University, Chengdu, China
| | - Mengyuan Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhiwei Fan
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States
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8
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Liu L, Jiao Y, Yang M, Wu L, Long G, Hu W. Network Pharmacology, Molecular Docking and Molecular Dynamics to Explore the Potential Immunomodulatory Mechanisms of Deer Antler. Int J Mol Sci 2023; 24:10370. [PMID: 37373516 DOI: 10.3390/ijms241210370] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/29/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The use of deer antlers dates back thousands of years in Chinese history. Deer antlers have antitumor, anti-inflammatory, and immunomodulatory properties and can be used in treating neurological diseases. However, only a few studies have reported the immunomodulatory mechanism of deer antler active compounds. Using network pharmacology, molecular docking, and molecular dynamics simulation techniques, we analyzed the underlying mechanism by which deer antlers regulate the immune response. We identified 4 substances and 130 core targets that may play immunomodulatory roles, and the beneficial and non-beneficial effects in the process of immune regulation were analyzed. The targets were enriched in pathways related to cancer, human cytomegalovirus infection, the PI3K-Akt signaling pathway, human T cell leukemia virus 1 infection, and lipids and atherosclerosis. Molecular docking showed that AKT1, MAPK3, and SRC have good binding activity with 17 beta estradiol and estrone. Additionally, the molecular dynamics simulation of the molecular docking result using GROMACS software (version: 2021.2) was performed and we found that the AKT1-estrone complex, 17 beta estradiol-AKT1 complex, estrone-MAPK3 complex, and 17 beta estradiol-MAPK3 complex had relatively good binding stability. Our research sheds light on the immunomodulatory mechanism of deer antlers and provides a theoretical foundation for further exploration of their active compounds.
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Affiliation(s)
- Lingyu Liu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Yu Jiao
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Mei Yang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Lei Wu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Guohui Long
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Wei Hu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
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Otter C, Fausto A, Tan L, Khosla A, Cohen N, Weiss S. Infection of primary nasal epithelial cells differentiates among lethal and seasonal human coronaviruses. Proc Natl Acad Sci U S A 2023; 120:e2218083120. [PMID: 37023127 PMCID: PMC10104492 DOI: 10.1073/pnas.2218083120] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/27/2023] [Indexed: 04/07/2023] Open
Abstract
The nasal epithelium is the initial entry portal and primary barrier to infection by all human coronaviruses (HCoVs). We utilize primary human nasal epithelial cells grown at air-liquid interface, which recapitulate the heterogeneous cellular population as well as mucociliary clearance functions of the in vivo nasal epithelium, to compare lethal [Severe acute respiratory syndrome (SARS)-CoV-2 and Middle East respiratory syndrome-CoV (MERS-CoV)] and seasonal (HCoV-NL63 and HCoV-229E) HCoVs. All four HCoVs replicate productively in nasal cultures, though replication is differentially modulated by temperature. Infections conducted at 33 °C vs. 37 °C (reflective of temperatures in the upper and lower airway, respectively) revealed that replication of both seasonal HCoVs (HCoV-NL63 and -229E) is significantly attenuated at 37 °C. In contrast, SARS-CoV-2 and MERS-CoV replicate at both temperatures, though SARS-CoV-2 replication is enhanced at 33 °C late in infection. These HCoVs also diverge significantly in terms of cytotoxicity induced following infection, as the seasonal HCoVs as well as SARS-CoV-2 cause cellular cytotoxicity as well as epithelial barrier disruption, while MERS-CoV does not. Treatment of nasal cultures with type 2 cytokine IL-13 to mimic asthmatic airways differentially impacts HCoV receptor availability as well as replication. MERS-CoV receptor DPP4 expression increases with IL-13 treatment, whereas ACE2, the receptor used by SARS-CoV-2 and HCoV-NL63, is down-regulated. IL-13 treatment enhances MERS-CoV and HCoV-229E replication but reduces that of SARS-CoV-2 and HCoV-NL63, reflecting the impact of IL-13 on HCoV receptor availability. This study highlights diversity among HCoVs during infection of the nasal epithelium, which is likely to influence downstream infection outcomes such as disease severity and transmissibility.
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Affiliation(s)
- Clayton J. Otter
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Alejandra Fausto
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Li Hui Tan
- Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Surgery, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA19104
| | - Alisha S. Khosla
- Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Surgery, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA19104
| | - Noam A. Cohen
- Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Surgery, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA19104
| | - Susan R. Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
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10
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Blood leukocyte transcriptional modules and differentially expressed genes associated with disease severity and age in COVID-19 patients. Sci Rep 2023; 13:898. [PMID: 36650374 PMCID: PMC9844197 DOI: 10.1038/s41598-023-28227-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
Since the molecular mechanisms determining COVID-19 severity are not yet well understood, there is a demand for biomarkers derived from comparative transcriptome analyses of mild and severe cases, combined with patients' clinico-demographic and laboratory data. Here the transcriptomic response of human leukocytes to SARS-CoV-2 infection was investigated by focusing on the differences between mild and severe cases and between age subgroups (younger and older adults). Three transcriptional modules correlated with these traits were functionally characterized, as well as 23 differentially expressed genes (DEGs) associated to disease severity. One module, correlated with severe cases and older patients, had an overrepresentation of genes involved in innate immune response and in neutrophil activation, whereas two other modules, correlated with disease severity and younger patients, harbored genes involved in the innate immune response to viral infections, and in the regulation of this response. This transcriptomic mechanism could be related to the better outcome observed in younger COVID-19 patients. The DEGs, all hyper-expressed in the group of severe cases, were mostly involved in neutrophil activation and in the p53 pathway, therefore related to inflammation and lymphopenia. These biomarkers may be useful for getting a better stratification of risk factors in COVID-19.
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11
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Special Issue "SARS-CoV-2 Innate and Adaptive Immune Responses". Viruses 2022; 14:v14112363. [PMID: 36366460 PMCID: PMC9695004 DOI: 10.3390/v14112363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 01/31/2023] Open
Abstract
Since the end of 2019, humanity has been facing the emergence of a new large positive-sense, single-stranded RNA virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes a respiratory disease with substantial morbidity and mortality called coronavirus disease 19 (COVID-19) [...]
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Otter CJ, Fausto A, Tan LH, Cohen NA, Weiss SR. Infection of primary nasal epithelial cells differentiates among lethal and seasonal human coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.17.512617. [PMID: 36299422 PMCID: PMC9603826 DOI: 10.1101/2022.10.17.512617] [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: 11/05/2022]
Abstract
The nasal epithelium is the initial entry portal and primary barrier to infection by all human coronaviruses (HCoVs). We utilize primary nasal epithelial cells grown at air-liquid interface, which recapitulate the heterogeneous cellular population as well as mucociliary clearance functions of the in vivo nasal epithelium, to compare lethal (SARS-CoV-2 and MERS-CoV) and seasonal (HCoV-NL63 and HCoV-229E) HCoVs. All four HCoVs replicate productively in nasal cultures but diverge significantly in terms of cytotoxicity induced following infection, as the seasonal HCoVs as well as SARS-CoV-2 cause cellular cytotoxicity as well as epithelial barrier disruption, while MERS-CoV does not. Treatment of nasal cultures with type 2 cytokine IL-13 to mimic asthmatic airways differentially impacts HCoV replication, enhancing MERS-CoV replication but reducing that of SARS-CoV-2 and HCoV-NL63. This study highlights diversity among HCoVs during infection of the nasal epithelium, which is likely to influence downstream infection outcomes such as disease severity and transmissibility.
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Affiliation(s)
- Clayton J. Otter
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alejandra Fausto
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Li Hui Tan
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Noam A. Cohen
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Susan R. Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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