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Tsujino S, Deguchi S, Nomai T, Padilla-Blanco M, Plianchaisuk A, Wang L, Begum MM, Uriu K, Mizuma K, Nao N, Kojima I, Tsubo T, Li J, Matsumura Y, Nagao M, Oda Y, Tsuda M, Anraku Y, Kita S, Yajima H, Sasaki-Tabata K, Guo Z, Hinay AA, Yoshimatsu K, Yamamoto Y, Nagamoto T, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Nasser H, Jonathan M, Putri O, Kim Y, Chen L, Suzuki R, Tamura T, Maenaka K, Irie T, Matsuno K, Tanaka S, Ito J, Ikeda T, Takayama K, Zahradnik J, Hashiguchi T, Fukuhara T, Sato K. Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant. Microbiol Immunol 2024. [PMID: 38961765 DOI: 10.1111/1348-0421.13165] [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: 03/27/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/05/2024]
Abstract
In middle to late 2023, a sublineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. We performed multiscale investigations, including phylogenetic analysis, epidemic dynamics modeling, infection experiments using pseudoviruses, clinical isolates, and recombinant viruses in cell cultures and experimental animals, and the use of human sera and antiviral compounds, to reveal the virological features of the newly emerging EG.5.1 variant. Our phylogenetic analysis and epidemic dynamics modeling suggested that two hallmark substitutions of EG.5.1, S:F456L and ORF9b:I5T are critical to its increased viral fitness. Experimental investigations on the growth kinetics, sensitivity to clinically available antivirals, fusogenicity, and pathogenicity of EG.5.1 suggested that the virological features of EG.5.1 are comparable to those of XBB.1.5. However, cryo-electron microscopy revealed structural differences between the spike proteins of EG.5.1 and XBB.1.5. We further assessed the impact of ORF9b:I5T on viral features, but it was almost negligible in our experimental setup. Our multiscale investigations provide knowledge for understanding the evolutionary traits of newly emerging pathogenic viruses, including EG.5.1, in the human population.
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Affiliation(s)
- Shuhei Tsujino
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Tomo Nomai
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Miguel Padilla-Blanco
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
- Departamento de Farmacia, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU (UCH-CEU), CEU Universities, Valencia, Spain
| | - Arnon Plianchaisuk
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keita Mizuma
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Isshu Kojima
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Tomoya Tsubo
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Jingshu Li
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Yuki Anraku
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Shunsuke Kita
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hisano Yajima
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kaori Sasaki-Tabata
- Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Ziyi Guo
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Alfredo A Hinay
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | | | | | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Michael Jonathan
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Olivia Putri
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | - Yoonjin Kim
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Life Sciences, Faculty of Natural Science, Imperial College London, London, UK
| | - Luo Chen
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan
- Division of Pathogen Structure, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Takashi Irie
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Keita Matsuno
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Jiri Zahradnik
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
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2
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López-Ayllón BD, Marin S, Fernández MF, García-García T, Fernández-Rodríguez R, de Lucas-Rius A, Redondo N, Mendoza-García L, Foguet C, Grigas J, Calvet A, Villalba JM, Gómez MJR, Megías D, Mandracchia B, Luque D, Lozano JJ, Calvo C, Herrán UM, Thomson TM, Garrido JJ, Cascante M, Montoya M. Metabolic and mitochondria alterations induced by SARS-CoV-2 accessory proteins ORF3a, ORF9b, ORF9c and ORF10. J Med Virol 2024; 96:e29752. [PMID: 38949191 DOI: 10.1002/jmv.29752] [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: 11/10/2023] [Revised: 06/07/2024] [Accepted: 06/08/2024] [Indexed: 07/02/2024]
Abstract
Antiviral signaling, immune response and cell metabolism are dysregulated by SARS-CoV-2, the causative agent of COVID-19. Here, we show that SARS-CoV-2 accessory proteins ORF3a, ORF9b, ORF9c and ORF10 induce a significant mitochondrial and metabolic reprogramming in A549 lung epithelial cells. While ORF9b, ORF9c and ORF10 induced largely overlapping transcriptomes, ORF3a induced a distinct transcriptome, including the downregulation of numerous genes with critical roles in mitochondrial function and morphology. On the other hand, all four ORFs altered mitochondrial dynamics and function, but only ORF3a and ORF9c induced a marked alteration in mitochondrial cristae structure. Genome-Scale Metabolic Models identified both metabolic flux reprogramming features both shared across all accessory proteins and specific for each accessory protein. Notably, a downregulated amino acid metabolism was observed in ORF9b, ORF9c and ORF10, while an upregulated lipid metabolism was distinctly induced by ORF3a. These findings reveal metabolic dependencies and vulnerabilities prompted by SARS-CoV-2 accessory proteins that may be exploited to identify new targets for intervention.
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Affiliation(s)
- Blanca D López-Ayllón
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Silvia Marin
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - Marco Fariñas Fernández
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- Department of Biomedical Laboratory Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Tránsito García-García
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research, Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Raúl Fernández-Rodríguez
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research, Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Ana de Lucas-Rius
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Natalia Redondo
- Unit of Infectious Diseases, University Hospital '12 de Octubre', Institute for Health Research Hospital '12 de Octubre' (imas12), Madrid, Spain
- Centre for Biomedical Research Network on Infectious Diseases (CIBERINFEC), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Laura Mendoza-García
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Carles Foguet
- British Heart Foundation Cardiovascular Epidemiology Unit and Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Juozas Grigas
- Laboratory of Immunology, Department of Anatomy and Physiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alba Calvet
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - José Manuel Villalba
- Department of Cell Biology, Physiology and Immunology, Agrifood Campus of International Excellence, University of Córdoba, Córdoba, Spain
| | - María Josefa Rodríguez Gómez
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Diego Megías
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
| | - Biagio Mandracchia
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- ETSI Telecommunication, University of Valladolid, Valladolid, Spain
| | - Daniel Luque
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- Electron Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Juan José Lozano
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Cristina Calvo
- Barcelona Institute for Molecular Biology (IBMB-CSIC), Barcelona, Spain
| | - Unai Merino Herrán
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Timothy M Thomson
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
- Barcelona Institute for Molecular Biology (IBMB-CSIC), Barcelona, Spain
- Translational Research and Computational Biology Laboratory, Faculty of Science and Engineering, Peruvian University Cayetano Heredia, Lima, Perú
| | - Juan J Garrido
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research, Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - María Montoya
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
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Zhou Y, Chen Z, Liu S, Liu S, Liao Y, Du A, Dong Z, Zhang Y, Chen X, Tao S, Wu X, Razzaq A, Xu G, Tan DA, Li S, Deng Y, Peng J, Dai S, Deng X, Zhang X, Jiang T, Zhang Z, Cheng G, Zhao J, Xia Z. A Cullin 5-based complex serves as an essential modulator of ORF9b stability in SARS-CoV-2 replication. Signal Transduct Target Ther 2024; 9:159. [PMID: 38937432 PMCID: PMC11211426 DOI: 10.1038/s41392-024-01874-5] [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: 10/29/2023] [Revised: 04/12/2024] [Accepted: 05/15/2024] [Indexed: 06/29/2024] Open
Abstract
The ORF9b protein, derived from the nucleocapsid's open-reading frame in both SARS-CoV and SARS-CoV-2, serves as an accessory protein crucial for viral immune evasion by inhibiting the innate immune response. Despite its significance, the precise regulatory mechanisms underlying its function remain elusive. In the present study, we unveil that the ORF9b protein of SARS-CoV-2, including emerging mutant strains like Delta and Omicron, can undergo ubiquitination at the K67 site and subsequent degradation via the proteasome pathway, despite certain mutations present among these strains. Moreover, our investigation further uncovers the pivotal role of the translocase of the outer mitochondrial membrane 70 (TOM70) as a substrate receptor, bridging ORF9b with heat shock protein 90 alpha (HSP90α) and Cullin 5 (CUL5) to form a complex. Within this complex, CUL5 triggers the ubiquitination and degradation of ORF9b, acting as a host antiviral factor, while HSP90α functions to stabilize it. Notably, treatment with HSP90 inhibitors such as GA or 17-AAG accelerates the degradation of ORF9b, leading to a pronounced inhibition of SARS-CoV-2 replication. Single-cell sequencing data revealed an up-regulation of HSP90α in lung epithelial cells from COVID-19 patients, suggesting a potential mechanism by which SARS-CoV-2 may exploit HSP90α to evade the host immunity. Our study identifies the CUL5-TOM70-HSP90α complex as a critical regulator of ORF9b protein stability, shedding light on the intricate host-virus immune response dynamics and offering promising avenues for drug development against SARS-CoV-2 in clinical settings.
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Affiliation(s)
- Yuzheng Zhou
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, China
| | - Zongpeng Chen
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Sijie Liu
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Sixu Liu
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Yujie Liao
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Ashuai Du
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Zijun Dong
- Department of Basic Medicine, School of Medicine, Hunan Normal University, 410081, Changsha, China
| | - Yongxing Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Xuan Chen
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Siyi Tao
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Xin Wu
- Department of spine surgery, The Third Xiangya Hospital, Central South University, 410013, Changsha, China
| | - Aroona Razzaq
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Gang Xu
- School of Basic Medical Sciences, Anhui Medical University, 230032, Hefei, China
| | - De-An Tan
- Hunan Key Laboratory of Neurorestoratology, 921 Hospital of Joint Logistics Support Force People's Liberation Army of China (The Second Affiliated Hospital of Hunan Normal University), 410003, Changsha, Hunan, China
| | - Shanni Li
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Youwen Deng
- Department of spine surgery, The Third Xiangya Hospital, Central South University, 410013, Changsha, China
| | - Jian Peng
- Department of Geriatric Surgery, Xiangya Hospital, Central South University, 410008, Changsha, China
| | - Shuyan Dai
- Xiangya School of Pharmaceutical Sciences, Central South University, 410013, Changsha, China
| | - Xu Deng
- Xiangya School of Pharmaceutical Sciences, Central South University, 410013, Changsha, China
| | - Xianwen Zhang
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | | | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, China
| | - Gong Cheng
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, 518132, Shenzhen, China
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Jincun Zhao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, China
- Guangzhou Laboratory, 510005, Guangzhou, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, China
| | - Zanxian Xia
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, Hunan Key Laboratory of Medical Genetics & Center for Medical Genetics, School of Life Sciences, Central South University, 410008, Changsha, China.
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4
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Ferdoush J, Abdul Kadir R, Simay Kaplanoglu S, Osborn M. SARS-CoV-2 and UPS with potentials for therapeutic interventions. Gene 2024; 912:148377. [PMID: 38490508 DOI: 10.1016/j.gene.2024.148377] [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: 01/19/2024] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
The Ubiquitin proteasome system (UPS), an essential eukaryotic/host/cellular post-translational modification (PTM), plays a critical role in the regulation of diverse cellular functions including regulation of protein stability, immune signaling, antiviral activity, as well as virus replication. Although UPS regulation of viral proteins may be utilized by the host as a defense mechanism to invade viruses, viruses may have adapted to take advantage of the host UPS. This system can be manipulated by viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) to stimulate various steps of the viral replication cycle and facilitate pathogenesis, thereby causing the respiratory disease COVID-19. Many SARS-CoV-2 encoded proteins including open reading frame 3a (ORF3a), ORF6, ORF7a, ORF9b, and ORF10 interact with the host's UPS machinery, influencing host immune signaling and apoptosis. Moreover, SARS-CoV-2 encoded papain-like protease (PLpro) interferes with the host UPS to facilitate viral replication and to evade the host's immune system. These alterations in SARS-CoV-2 infected cells have been revealed by various proteomic studies, suggesting potential targets for clinical treatment. To provide insight into the underlying causes of COVID-19 and suggest possible directions for therapeutic interventions, this paper reviews the intricate relationship between SARS-CoV-2 and UPS. Promising treatment strategies are also investigated in this paper including targeting PLpro with zinc-ejector drugs, as well as targeting viral non-structural protein (nsp12) via heat treatment associated ubiquitin-mediated proteasomal degradation to reduce viral pathogenesis.
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Affiliation(s)
- Jannatul Ferdoush
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA.
| | - Rizwaan Abdul Kadir
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Selin Simay Kaplanoglu
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Morgan Osborn
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
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5
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Yu M, Li J, Gao W, Li Z, Zhang W. Multiple E3 ligases act as antiviral factors against SARS-CoV-2 via inducing the ubiquitination and degradation of ORF9b. J Virol 2024; 98:e0162423. [PMID: 38709105 PMCID: PMC11237466 DOI: 10.1128/jvi.01624-23] [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: 10/18/2023] [Accepted: 04/07/2024] [Indexed: 05/07/2024] Open
Abstract
Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) open reading frame 9b (ORF9b) antagonizes the antiviral type I and III interferon (IFN) responses and is ubiquitinated and degraded via the ubiquitin-proteasome pathway. However, E3 ubiquitin ligases that mediate the polyubiquitination and degradation of ORF9b remain unknown. In this study, we identified 14 E3 ligases that specifically bind to SARS-CoV-2 ORF9b. Specifically, three E3 ligases, HECT, UBA, and WWE domain-containing E3 ubiquitin protein ligase 1 (HUWE1), ubiquitin protein ligase E3 component n-recognin 4 (UBR4), and UBR5, induced K48-linked polyubiquitination and degradation of ORF9b, thereby attenuating ORF9b-mediated inhibition of the IFN response and SARS-CoV-2 replication. Moreover, each E3 ligase performed this function independent of the other two E3 ligases. Therefore, the three E3 ligases identified in this study as anti-SARS-CoV-2 host factors provide novel molecular insight into the virus-host interaction.IMPORTANCEUbiquitination is an important post-translational modification that regulates multiple biological processes, including viral replication. Identification of E3 ubiquitin ligases that target viral proteins for degradation can provide novel targets for antagonizing viral infections. Here, we identified multiple E3 ligases, including HECT, UBA, and WWE domain-containing E3 ubiquitin protein ligase 1 (HUWE1), ubiquitin protein ligase E3 component n-recognin 4 (UBR4), and UBR5, that ubiquitinated and induced the degradation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) open reading frame 9b (ORF9b), an interferon (IFN) antagonist, thereby enhancing IFN production and attenuating SARS-CoV-2 replication. Our study provides new possibilities for drug development targeting the interaction between E3 ligases and ORF9b.
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Affiliation(s)
- Miao Yu
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China
- Department of Geriatrics and Special medical treatment, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Jie Li
- Department of Geriatrics and Special medical treatment, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wenying Gao
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhaolong Li
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wenyan Zhang
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
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6
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Carvajal JJ, García-Castillo V, Cuellar SV, Campillay-Véliz CP, Salazar-Ardiles C, Avellaneda AM, Muñoz CA, Retamal-Díaz A, Bueno SM, González PA, Kalergis AM, Lay MK. New insights into the pathogenesis of SARS-CoV-2 during and after the COVID-19 pandemic. Front Immunol 2024; 15:1363572. [PMID: 38911850 PMCID: PMC11190347 DOI: 10.3389/fimmu.2024.1363572] [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: 12/31/2023] [Accepted: 04/24/2024] [Indexed: 06/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the respiratory distress condition known as COVID-19. This disease broadly affects several physiological systems, including the gastrointestinal, renal, and central nervous (CNS) systems, significantly influencing the patient's overall quality of life. Additionally, numerous risk factors have been suggested, including gender, body weight, age, metabolic status, renal health, preexisting cardiomyopathies, and inflammatory conditions. Despite advances in understanding the genome and pathophysiological ramifications of COVID-19, its precise origins remain elusive. SARS-CoV-2 interacts with a receptor-binding domain within angiotensin-converting enzyme 2 (ACE2). This receptor is expressed in various organs of different species, including humans, with different abundance. Although COVID-19 has multiorgan manifestations, the main pathologies occur in the lung, including pulmonary fibrosis, respiratory failure, pulmonary embolism, and secondary bacterial pneumonia. In the post-COVID-19 period, different sequelae may occur, which may have various causes, including the direct action of the virus, alteration of the immune response, and metabolic alterations during infection, among others. Recognizing the serious adverse health effects associated with COVID-19, it becomes imperative to comprehensively elucidate and discuss the existing evidence surrounding this viral infection, including those related to the pathophysiological effects of the disease and the subsequent consequences. This review aims to contribute to a comprehensive understanding of the impact of COVID-19 and its long-term effects on human health.
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Affiliation(s)
- Jonatan J. Carvajal
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Valeria García-Castillo
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Shelsy V. Cuellar
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | | | - Camila Salazar-Ardiles
- Center for Research in Physiology and Altitude Medicine (FIMEDALT), Biomedical Department, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Andrea M. Avellaneda
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Department of Basic Sciences, Faculty of Sciences, Universidad Santo Tomás, Antofagasta, Chile
| | - Christian A. Muñoz
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Angello Retamal-Díaz
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Susan M. Bueno
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo A. González
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Margarita K. Lay
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
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7
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Rezabakhsh A, Sadaie MR, Ala A, Roosta Y, Habtemariam S, Sahebnasagh A, Khezri MR. STING agonists as promising vaccine adjuvants to boost immunogenicity against SARS-related coronavirus derived infection: possible role of autophagy. Cell Commun Signal 2024; 22:305. [PMID: 38831299 PMCID: PMC11145937 DOI: 10.1186/s12964-024-01680-0] [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: 01/23/2024] [Accepted: 05/26/2024] [Indexed: 06/05/2024] Open
Abstract
As a major component of innate immunity and a positive regulator of interferons, the Stimulator of interferon gene (STING) has an immunotherapy potential to govern a variety of infectious diseases. Despite the recent advances regarding vaccines against COVID-19, nontoxic novel adjuvants with the potential to enhance vaccine efficacy are urgently desired. In this connection, it has been well-documented that STING agonists are applied to combat COVID-19. This approach is of major significance for boosting immune responses most likely through an autophagy-dependent manner in susceptible individuals against infection induced by severe acute respiratory syndrome Coronavirus (SARS‑CoV‑2). Given that STING agonists exert substantial immunomodulatory impacts under a wide array of pathologic conditions, these agents could be considered novel adjuvants for enhancing immunogenicity against the SARS-related coronavirus. Here, we intend to discuss the recent advances in STING agonists' recruitment to boost innate immune responses upon vaccination against SARS-related coronavirus infections. In light of the primordial role of autophagy modulation, the potential of being an antiviral vaccine adjuvant was also explored.
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Affiliation(s)
- Aysa Rezabakhsh
- Cardiovascular Research Center, Shahid Madani specialized Heart Hospita, Tabriz University of Medical Sciences, University St, Tabriz, 5166615573, Iran.
| | - M Reza Sadaie
- NovoMed Consulting, Biomedical Sciences, Germantown, Maryland, USA
| | - Alireza Ala
- Emergency and Trauma Care Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yousef Roosta
- Hematology, Immune Cell Therapy, and Stem Cells Transplantation Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Solomon Habtemariam
- Pharmacognosy Research and Herbal Analysis Services UK, University of Greenwich, Kent, UK
| | - Adeleh Sahebnasagh
- Clinical Research Center, Department of Internal Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mohammad Rafi Khezri
- Reproductive Health Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, 5715799313, Iran.
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8
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Caobi A, Saeed M. Upping the ante: enhanced expression of interferon-antagonizing ORF6 and ORF9b proteins by SARS-CoV-2 variants of concern. Curr Opin Microbiol 2024; 79:102454. [PMID: 38518551 PMCID: PMC11162932 DOI: 10.1016/j.mib.2024.102454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/24/2024]
Abstract
SARS-CoV-2 exhibits a remarkable capability to subvert the host antiviral innate immune system. This adeptness is orchestrated by viral proteins, which initially attempt to obstruct the activation of the antiviral immune program and then act as a fail-safe mechanism to mitigate the downstream effects of the activated immune response. This dual strategy leads to delayed expression and enfeebled action of type-I and -III interferons at the infection site, enabling the virus to replicate extensively in the lungs and subsequently disseminate to other organs. Throughout the course of the COVID-19 pandemic, SARS-CoV-2 has undergone evolution, giving rise to several variants of concern, some with exceedingly higher transmission and virulence. These improved features have been linked, at least in part, to the heightened expression or activity of specific viral proteins involved in circumventing host defense mechanisms. In this review, we aim to provide a concise summary of two SARS-CoV-2 proteins, ORF6 and ORF9b, which provided selective advantage to certain variants, affecting their biology and pathogenesis.
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Affiliation(s)
- Allen Caobi
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Mohsan Saeed
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA.
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9
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David P, Sinha S, Iqbal K, De Marco G, Taheri S, McLaren E, Maisuria S, Arumugakani G, Ash Z, Buckley C, Coles L, Hettiarachchi C, Payne E, Savic S, Smithson G, Slade M, Shah R, Marzo-Ortega H, Keen M, Lawson C, Mclorinan J, Nizam S, Reddy H, Sharif O, Sultan S, Tran G, Wood M, Wood S, Ghosh P, McGonagle D. MDA5-autoimmunity and interstitial pneumonitis contemporaneous with the COVID-19 pandemic (MIP-C). EBioMedicine 2024; 104:105136. [PMID: 38723554 PMCID: PMC11090026 DOI: 10.1016/j.ebiom.2024.105136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Anti-MDA5 (Melanoma differentiation-associated protein-5) positive dermatomyositis (MDA5+-DM) is characterised by rapidly progressive interstitial lung disease (ILD) and high mortality. MDA5 is an RNA sensor and a key pattern recognition receptor for the SARS-CoV-2 virus. METHODS This is a retrospective observational study of a surge in MDA5 autoimmunity, as determined using a 15 muscle-specific autoantibodies (MSAs) panel, between Janurary 2018 and December 2022 in Yorkshire, UK. MDA5-positivity was correlated with clinical features and outcome, and regional SARS-CoV-2 positivity and vaccination rates. Gene expression patterns in COVID-19 were compared with autoimmune lung disease and idiopathic pulmonary fibrosis (IPF) to gain clues into the genesis of the observed MDA5+-DM outbreak. FINDINGS Sixty new anti-MDA5+, but not other MSAs surged between 2020 and 2022, increasing from 0.4% in 2019 to 2.1% (2020), 4.8% (2021) and 1.7% (2022). Few (8/60) had a prior history of confirmed COVID-19, peak rates overlapped with regional SARS-COV-2 community positivity rates in 2021, and 58% (35/60) had received anti-SARS-CoV-2 vaccines. 25/60 cases developed ILD which rapidly progression with death in 8 cases. Among the 35/60 non-ILD cases, 14 had myositis, 17 Raynaud phenomena and 10 had dermatomyositis spectrum rashes. Transcriptomic studies showed strong IFIH1 (gene encoding for MDA5) induction in COVID-19 and autoimmune-ILD, but not IPF, and IFIH1 strongly correlated with an IL-15-centric type-1 interferon response and an activated CD8+ T cell signature that is an immunologic hallmark of progressive ILD in the setting of systemic autoimmune rheumatic diseases. The IFIH1 rs1990760TT variant blunted such response. INTERPRETATION A distinct pattern of MDA5-autoimmunity cases surged contemporaneously with circulation of the SARS-COV-2 virus during COVID-19. Bioinformatic insights suggest a shared immunopathology with known autoimmune lung disease mechanisms. FUNDING This work was supported in part by the National Institute for Health Research (NIHR) Leeds Biomedical Research Centre (BRC), and in part by the National Institutes of Health (NIH) grant R01-AI155696 and pilot awards from the UC Office of the President (UCOP)-RGPO (R00RG2628, R00RG2642 and R01RG3780) to P.G. S.S was supported in part by R01-AI141630 (to P.G) and in part through funds from the American Association of Immunologists (AAI) Intersect Fellowship Program for Computational Scientists and Immunologists.
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Affiliation(s)
- Paula David
- Leeds Teaching Hospitals NHS Trust, Rheumatology Department, Leeds, United Kingdom; University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, United Kingdom; Internal Medicine B, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Saptarshi Sinha
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Khizer Iqbal
- Leeds Teaching Hospitals NHS Trust, Rheumatology Department, Leeds, United Kingdom
| | - Gabriele De Marco
- University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, United Kingdom; Mid Yorkshire Teaching NHS Trust, Rheumatology, Wakefield, United Kingdom; NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Sahar Taheri
- Department of Computer Science and Engineering, Jacob's School of Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ella McLaren
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sheetal Maisuria
- Leeds Teaching Hospitals NHS Trust, Pathology, Leeds, United Kingdom
| | - Gururaj Arumugakani
- Leeds Teaching Hospitals NHS Trust, Pathology, Leeds, United Kingdom; University of Leeds, Immunology, Leeds, United Kingdom
| | - Zoe Ash
- Bradford Teaching Hospitals NHS Foundation Trust, Rheumatology, Bradford, United Kingdom
| | - Catrin Buckley
- Leeds Teaching Hospitals NHS Trust, Rheumatology Department, Leeds, United Kingdom
| | - Lauren Coles
- Leeds Teaching Hospitals NHS Trust, Rheumatology Department, Leeds, United Kingdom
| | | | - Emma Payne
- Leeds Teaching Hospitals NHS Trust, Pathology, Leeds, United Kingdom
| | - Sinisa Savic
- University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, United Kingdom; NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom; Department of Clinical Immunology and Allergy, Leeds Teaching Hospitals, NHS Trust, Leeds, UK
| | - Gayle Smithson
- Mid Yorkshire Teaching NHS Trust, Rheumatology, Wakefield, United Kingdom
| | - Maria Slade
- Mid Yorkshire Teaching NHS Trust, Rheumatology, Wakefield, United Kingdom
| | - Rahul Shah
- Leeds Teaching Hospitals NHS Trust, Rheumatology Department, Leeds, United Kingdom
| | - Helena Marzo-Ortega
- Leeds Teaching Hospitals NHS Trust, Rheumatology Department, Leeds, United Kingdom; University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, United Kingdom; NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Mansoor Keen
- Bradford Teaching Hospitals NHS Foundation Trust, Rheumatology, Bradford, United Kingdom
| | - Catherine Lawson
- Harrogate and District NHS Foundation Trust, Rheumatology, Harrogate, United Kingdom
| | - Joanna Mclorinan
- Leeds Teaching Hospitals NHS Trust, Rheumatology Department, Leeds, United Kingdom
| | - Sharmin Nizam
- Mid Yorkshire Teaching NHS Trust, Rheumatology, Wakefield, United Kingdom
| | - Hanu Reddy
- Airedale NHS Foundation Trust, Rheumatology, Steeton with Eastburn, United Kingdom
| | - Omer Sharif
- Calderdale and Huddersfield NHS Foundation Trust, Rheumatology, Huddersfield and Halifax, United Kingdom
| | - Shabina Sultan
- Airedale NHS Foundation Trust, Rheumatology, Steeton with Eastburn, United Kingdom
| | - Gui Tran
- Harrogate and District NHS Foundation Trust, Rheumatology, Harrogate, United Kingdom
| | - Mark Wood
- Leeds Teaching Hospitals NHS Trust, Rheumatology Department, Leeds, United Kingdom
| | - Samuel Wood
- Leeds Teaching Hospitals NHS Trust, Rheumatology Department, Leeds, United Kingdom
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA; Department of Medicine, School of Medicine, and Veterans Affairs Medical Center, University of University of California San Diego, La Jolla, CA, 92093, USA.
| | - Dennis McGonagle
- Leeds Teaching Hospitals NHS Trust, Rheumatology Department, Leeds, United Kingdom; University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, United Kingdom.
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10
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Li Y, Tang Y, Wang X, Zhu A, Liu D, He Y, Guo H, Zheng J, Liu X, Chi F, Wang Y, Zhuang Z, Zhang Z, Liu D, Chen Z, Li F, Ran W, Yu K, Wang D, Wen L, Zhuo J, Zhang Y, Xi Y, Zhao J, Zhao J, Sun J. Characterization of humoral immune responses against SARS-CoV-2 accessory proteins in infected patients and mouse model. Virol Sin 2024; 39:414-421. [PMID: 38677713 DOI: 10.1016/j.virs.2024.04.005] [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: 11/05/2023] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, encodes several accessory proteins that have been shown to play crucial roles in regulating the innate immune response. However, their expressions in infected cells and immunogenicity in infected humans and mice are still not fully understood. This study utilized various techniques such as luciferase immunoprecipitation system (LIPS), immunofluorescence assay (IFA), and western blot (WB) to detect accessory protein-specific antibodies in sera of COVID-19 patients. Specific antibodies to proteins 3a, 3b, 7b, 8 and 9c can be detected by LIPS, but only protein 3a antibody was detected by IFA or WB. Antibodies against proteins 3a and 7b were only detected in ICU patients, which may serve as a marker for predicting disease progression. Further, we investigated the expression of accessory proteins in SARS-CoV-2-infected cells and identified the expressions of proteins 3a, 6, 7a, 8, and 9b. We also analyzed their ability to induce antibodies in immunized mice and found that only proteins 3a, 6, 7a, 8, 9b and 9c were able to induce measurable antibody productions, but these antibodies lacked neutralizing activities and did not protect mice from SARS-CoV-2 infection. Our findings validate the expression of SARS-CoV-2 accessory proteins and elucidate their humoral immune response, providing a basis for protein detection assays and their role in pathogenesis.
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Affiliation(s)
- Yuming Li
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Yanhong Tang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China; Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Hunan Normal University, Changsha, 410005, China
| | - Xiaoqian Wang
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Dongdong Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Yiyun He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Hu Guo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Jie Zheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Xinzhuo Liu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Fengyu Chi
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Zhen Zhuang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Donglan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Zhao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Fang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Wei Ran
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Kuai Yu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Dong Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Liyan Wen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Jianfen Zhuo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Yin Xi
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China.
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China; Guangzhou National Laboratory, Guangzhou, Guangdong, 510005, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China; Guangzhou National Laboratory, Guangzhou, Guangdong, 510005, China; Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China; Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, 518005, China.
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China.
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11
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Wang MM, Zhao Y, Liu J, Fan RR, Tang YQ, Guo ZY, Li T. The role of the cGAS-STING signaling pathway in viral infections, inflammatory and autoimmune diseases. Acta Pharmacol Sin 2024:10.1038/s41401-023-01185-5. [PMID: 38822084 DOI: 10.1038/s41401-023-01185-5] [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: 08/06/2023] [Accepted: 10/18/2023] [Indexed: 06/02/2024] Open
Abstract
Pattern recognition receptors are an essential part of the immune system, which detect pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs) and help shape both innate and adaptive immune responses. When dsDNA is present, cyclic GMP-AMP Synthase (cGAS) produces a second messenger called cyclic GMP-AMP (cGAMP), which then triggers an adaptor protein called STING, and eventually activates the expression of type I interferon (IFN) and pro-inflammatory cytokines in immune cells. The cGAS-STING signaling pathway has been receiving a lot of attention lately as a key immune-surveillance mediator. In this review, we summarize the present circumstances of the cGAS-STING signaling pathway in viral infections and inflammatory diseases, as well as autoimmune diseases. Modulation of the cGAS-STING signaling pathway provides potential strategies for treating viral infections, inflammatory diseases, and autoimmune diseases.
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Affiliation(s)
- Ming-Ming Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, 999078, China
| | - Yue Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, 999078, China
| | - Juan Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, 999078, China
| | - Rong-Rong Fan
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, 14183, Sweden
| | - Yan-Qing Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, 999078, China
| | - Zheng-Yang Guo
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, 999078, China
| | - Ting Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, 999078, China.
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12
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Xiao X, Fu Y, You W, Huang C, Zeng F, Gu X, Sun X, Li J, Zhang Q, Du W, Cheng G, Liu Z, Liu L. Inhibition of the RLR signaling pathway by SARS-CoV-2 ORF7b is mediated by MAVS and abrogated by ORF7b-homologous interfering peptide. J Virol 2024; 98:e0157323. [PMID: 38572974 PMCID: PMC11092349 DOI: 10.1128/jvi.01573-23] [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: 10/09/2023] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and characterized by dysregulated immune response. Studies have shown that the SARS-CoV-2 accessory protein ORF7b induces host cell apoptosis through the tumor necrosis factor alpha (TNF-α) pathway and blocks the production of interferon beta (IFN-β). The underlying mechanism remains to be investigated. In this study, we found that ORF7b facilitated viral infection and production, and inhibited the RIG-I-like receptor (RLR) signaling pathway through selectively interacting with mitochondrial antiviral-signaling protein (MAVS). MAVS439-466 region and MAVS Lys461 were essential for the physical association between MAVS and ORF7b, and the inhibition of the RLR signaling pathway by ORF7b. MAVSK461/K63 ubiquitination was essential for the RLR signaling regulated by the MAVS-ORF7b complex. ORF7b interfered with the recruitment of tumor necrosis factor receptor-related factor 6 (TRAF6) and the activation of the RLR signaling pathway by MAVS. Furthermore, interfering peptides targeting the ORF7b complex reversed the ORF7b-suppressed MAVS-RLR signaling pathway. The most potent interfering peptide V disrupts the formation of ORF7b tetramers, reverses the levels of the ORF7b-inhibited physical association between MAVS and TRAF6, leading to the suppression of viral growth and infection. Overall, this study provides a mechanism for the suppression of innate immunity by SARS-CoV-2 infection and the mechanism-based approach via interfering peptides to potentially prevent SARS-CoV-2 infection.IMPORTANCEThe pandemic coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and continues to be a threat to public health. It is imperative to understand the biology of SARS-CoV-2 infection and find approaches to prevent SARS-CoV-2 infection and ameliorate COVID-19. Multiple SARS-CoV-2 proteins are known to function on the innate immune response, but the underlying mechanism remains unknown. This study shows that ORF7b inhibits the RIG-I-like receptor (RLR) signaling pathway through the physical association between ORF7b and mitochondrial antiviral-signaling protein (MAVS), impairing the K63-linked MAVS polyubiquitination and its recruitment of tumor necrosis factor receptor-related factor 6 (TRAF6) to MAVS. The most potent interfering peptide V targeting the ORF7b-MAVS complex may reverse the suppression of the MAVS-mediated RLR signaling pathway by ORF7b and prevent viral infection and production. This study may provide new insights into the pathogenic mechanism of SARS-CoV-2 and a strategy to develop new drugs to prevent SARS-CoV-2 infection.
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Affiliation(s)
- Xiao Xiao
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Yanan Fu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Wanling You
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Congcong Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Feng Zeng
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Xinsheng Gu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Xiaoguang Sun
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Jian Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Qiwei Zhang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Weixing Du
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Zhixin Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Long Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
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13
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Xie F, Zhu Q. The regulation of cGAS-STING signaling by RNA virus-derived components. Virol J 2024; 21:101. [PMID: 38693578 PMCID: PMC11064393 DOI: 10.1186/s12985-024-02359-1] [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: 02/04/2024] [Accepted: 04/04/2024] [Indexed: 05/03/2024] Open
Abstract
The Cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) serves as a key innate immune signaling axis involved in the regulation of various human diseases. It has been found that cGAS-STING pathway can recognize a variety of cytosolic double-stranded DNA (dsDNA), contributing to cause a robust type I interferon response thereby affecting the occurrence and progression of viral infection. Accumulating evidence indicates RNA virus-derived components play an important role in regulating cGAS-STING signaling, either as protective or pathogenic factors in the pathogenesis of diseases. Thus, a comprehensive understanding of the function of RNA virus-derived components in regulating cGAS-STING signaling will provide insights into developing novel therapies. Here, we review the existing literature on cGAS-STING pathway regulated by RNA virus-derived components to propose insights into pharmacologic strategies targeting the cGAS-STING pathway.
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Affiliation(s)
- Feiting Xie
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, 310006, Hangzhou, China.
| | - Qiugang Zhu
- Department of Laboratory Medicine, Shangyu People's Hospital of Shaoxing, Shaoxing, China
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14
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Fracella M, Mancino E, Nenna R, Virgillito C, Frasca F, D'Auria A, Sorrentino L, Petrarca L, La Regina D, Matera L, Di Mattia G, Caputo B, Antonelli G, Pierangeli A, Viscidi RP, Midulla F, Scagnolari C. Age-related transcript changes in type I interferon signaling in children and adolescents with long COVID. Eur J Immunol 2024; 54:e2350682. [PMID: 38522030 DOI: 10.1002/eji.202350682] [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: 07/25/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/25/2024]
Abstract
SARS-CoV-2 typically causes mild symptoms in children, but evidence suggests that persistent immunopathological changes may lead to long COVID (LC). To explore the interplay between LC and innate immunity, we assessed the type I interferon (IFN-I) response in children and adolescents with LC symptoms (LC; n = 28). This was compared with age-matched SARS-CoV-2 recovered participants without LC symptoms (MC; n = 28) and healthy controls (HC; n = 18). We measured the mRNA expression of IFN-I (IFN-α/β/ε/ω), IFN-I receptor (IFNAR1/2), and ISGs (ISG15, ISG56, MxA, IFI27, BST2, LY6E, OAS1, OAS2, OAS3, and MDA5) in PBMCs collected 3-6 months after COVID-19. LC adolescents (12-17 years) had higher transcript levels of IFN-β, IFN-ε, and IFN-ω than HC, whereas LC children (6-11 years) had lower levels than HC. In adolescents, increased levels of IFN-α, IFN-β, and IFN-ω mRNAs were found in the LC group compared with MC, while lower levels were observed in LC children than MC. Adolescents with neurological symptoms had higher IFN-α/β mRNA levels than MC. LC and MC participants showed decreased expression of ISGs and IFNAR1, but increased expression of IFNAR2, than HC. Our results show age-related changes in the expression of transcripts involved in the IFN-I signaling pathway in children and adolescents with LC.
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Affiliation(s)
- Matteo Fracella
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Enrica Mancino
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Raffaella Nenna
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Chiara Virgillito
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Federica Frasca
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Alessandra D'Auria
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Leonardo Sorrentino
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Laura Petrarca
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Domenico La Regina
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Luigi Matera
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Greta Di Mattia
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Beniamino Caputo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Alessandra Pierangeli
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Raphael P Viscidi
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Fabio Midulla
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Carolina Scagnolari
- Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
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15
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Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
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Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
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16
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Sun YK, Wang C, Lin PQ, Hu L, Ye J, Gao ZG, Lin R, Li HM, Shu Q, Huang LS, Tan LH. Severe pediatric COVID-19: a review from the clinical and immunopathophysiological perspectives. World J Pediatr 2024; 20:307-324. [PMID: 38321331 PMCID: PMC11052880 DOI: 10.1007/s12519-023-00790-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/14/2023] [Indexed: 02/08/2024]
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) tends to have mild presentations in children. However, severe and critical cases do arise in the pediatric population with debilitating systemic impacts and can be fatal at times, meriting further attention from clinicians. Meanwhile, the intricate interactions between the pathogen virulence factors and host defense mechanisms are believed to play indispensable roles in severe COVID-19 pathophysiology but remain incompletely understood. DATA SOURCES A comprehensive literature review was conducted for pertinent publications by reviewers independently using the PubMed, Embase, and Wanfang databases. Searched keywords included "COVID-19 in children", "severe pediatric COVID-19", and "critical illness in children with COVID-19". RESULTS Risks of developing severe COVID-19 in children escalate with increasing numbers of co-morbidities and an unvaccinated status. Acute respiratory distress stress and necrotizing pneumonia are prominent pulmonary manifestations, while various forms of cardiovascular and neurological involvement may also be seen. Multiple immunological processes are implicated in the host response to COVID-19 including the type I interferon and inflammasome pathways, whose dysregulation in severe and critical diseases translates into adverse clinical manifestations. Multisystem inflammatory syndrome in children (MIS-C), a potentially life-threatening immune-mediated condition chronologically associated with COVID-19 exposure, denotes another scientific and clinical conundrum that exemplifies the complexity of pediatric immunity. Despite the considerable dissimilarities between the pediatric and adult immune systems, clinical trials dedicated to children are lacking and current management recommendations are largely adapted from adult guidelines. CONCLUSIONS Severe pediatric COVID-19 can affect multiple organ systems. The dysregulated immune pathways in severe COVID-19 shape the disease course, epitomize the vast functional diversity of the pediatric immune system and highlight the immunophenotypical differences between children and adults. Consequently, further research may be warranted to adequately address them in pediatric-specific clinical practice guidelines.
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Affiliation(s)
- Yi-Kan Sun
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310030, China
| | - Can Wang
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Pei-Quan Lin
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Lei Hu
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Jing Ye
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Zhi-Gang Gao
- Department of General Surgery, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Ru Lin
- Department of Cardiopulmonary and Extracorporeal Life Support, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Hao-Min Li
- Clinical Data Center, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Qiang Shu
- Department of Cardiac Surgery, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
- National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Li-Su Huang
- National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China.
- Department of Infectious Diseases, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China.
| | - Lin-Hua Tan
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China.
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17
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Liang S, Zheng YY, Pan Y. Blood transcriptome analysis uncovered COVID-19-myocarditis crosstalk. Microb Pathog 2024; 189:106587. [PMID: 38373644 DOI: 10.1016/j.micpath.2024.106587] [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: 10/12/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND The condition of COVID-19-related myocarditis has emerged as a prominent contributor to COVID-19 mortality. As the epidemic persists, its incidence continues to rise. Despite ongoing efforts, the elucidation of COVID-19-related myocarditis underlying molecular mechanisms still requires further investigation. METHODS Hub genes for COVID-19-related myocarditis were screened by integrating gene expression profile analysis via differential expression in COVID-19 (GSE196822) and myocarditis (GSE148153 and GSE147517). After verification with independent datasets (GSE211979, GSE167028, GSE178491 and GSE215865), the hub genes were studied using a range of systems-biology approaches, such as ceRNA, TF-mRNA networks and PPI networks, as well as gene ontology, pathway enrichment, immune infiltration analysis and drug target identification. RESULTS TBKBP1 and ERGIC1 were identified as COVID-19-related myocarditis hub genes via integrated bioinformatics analysis. In addition, receiver operating characteristic curves constructed based on the expression levels of TBKBP1 and ERGIC1 could effectively distinguish healthy control individuals from patients with COVID-19. Functional enrichment analysis suggested several enriched biological pathways related to inflammation and immune response. Immune cell changes correlated with TBKBP1 and ERGIC1 levels in patients with COVID-19 or patients with COVID-19 and myocarditis. Tamibarotene, methotrexate and theophylline were identified as a potential drug targeting TBKBP1 and ERGIC1. CONCLUSION TBKBP1 and ERGIC1 were identified as crucial genes in the development of COVID-19-related myocarditis and have demonstrated a strong association with innate antiviral immunity. The present work may be helpful for further investigation of the molecular mechanisms and new therapeutic drug targets correlated with myocarditis in COVID-19.
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Affiliation(s)
- Shuang Liang
- Pharmacy Department, Hebei Medical University Third Hospital, Shijiazhuang, 050000, China.
| | - Ying-Ying Zheng
- Pharmacy Department, Hebei Medical University Third Hospital, Shijiazhuang, 050000, China
| | - Ying Pan
- Pharmacy Department, Hebei Medical University Third Hospital, Shijiazhuang, 050000, China
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18
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Jia Y, Li F, Liu Z, Liu S, Huang M, Gao X, Su X, Wang Z, Wang T. Interaction between the SFTSV envelope glycoprotein Gn and STING inhibits the formation of the STING-TBK1 complex and suppresses the NF-κB signaling pathway. J Virol 2024; 98:e0181523. [PMID: 38421179 PMCID: PMC10949458 DOI: 10.1128/jvi.01815-23] [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: 12/22/2023] [Accepted: 02/11/2024] [Indexed: 03/02/2024] Open
Abstract
Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne bunyavirus with high pathogenicity. There has been a gradual increase in the number of reported cases in recent years, with high morbidity and mortality rates. The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling pathway plays an important role in the innate immune defense activated by viral infection; however, the role of the cGAS-STING signaling pathway during SFTSV infection is still unclear. In this study, we investigated the relationship between SFTSV infection and cGAS-STING signaling. We found that SFTSV infection caused the release of mitochondrial DNA into the cytoplasm and inhibits downstream innate immune signaling pathways by activating the cytoplasmic DNA receptor cGAS. We found that the SFTSV envelope glycoprotein Gn was a potent inhibitor of the cGAS-STING pathway and blocked the nuclear accumulation of interferon regulatory factor 3 and p65 to inhibit downstream innate immune signaling. Gn of SFTSV interacted with STING to inhibit STING dimerization and inhibited K27-ubiquitin modification of STING to disrupt the assembly of the STING-TANK-binding kinase 1 complex and downstream signaling. In addition, Gn was found to be involved in inducing STING degradation, further inhibiting the downstream immune response. In conclusion, this study identified the important role of the glycoprotein Gn in the antiviral innate immune response and revealed a novel mechanism of immune escape for SFTSV. Moreover, this study increases the understanding of the pathogenic mechanism of SFTSV and provides new insights for further treatment of SFTS. IMPORTANCE Severe fever with thrombocytopenia syndrome virus (SFTSV) is a newly discovered virus associated with severe hemorrhagic fever in humans. However, the role of the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling pathway during SFTSV infection is still unclear. We found that SFTSV infection inhibits downstream innate immune signaling pathways by activating the cytoplasmic DNA receptor cGAS. In addition, SFTSV Gn blocked the nuclear accumulation of interferon regulatory factor 3 and p65 to inhibit downstream innate immune signaling. Moreover, we determined that Gn of SFTSV inhibited K27-ubiquitin modification of STING to disrupt the assembly of the STING-TANK-binding kinase 1 complex and downstream signaling. We found that the SFTSV envelope glycoprotein Gn is a potent inhibitor of the cGAS-STING pathway. In conclusion, this study highlights the crucial function of the glycoprotein Gn in the antiviral innate immune response and reveals a new method of immune escape of SFTSV.
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Affiliation(s)
- Yupei Jia
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Feifei Li
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Zixiang Liu
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Sihua Liu
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Mengqian Huang
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Xiaoning Gao
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Xin Su
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Zhiyun Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Tao Wang
- School of Life Sciences, Tianjin University, Tianjin, China
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19
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Mahmoodi M, Mohammadi Henjeroei F, Hassanshahi G, Nosratabadi R. Do chemokine/chemokine receptor axes play paramount parts in trafficking and oriented locomotion of monocytes/macrophages toward the lungs of COVID-19 infected patients? A systematic review. Cytokine 2024; 175:156497. [PMID: 38190792 DOI: 10.1016/j.cyto.2023.156497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/19/2023] [Accepted: 12/31/2023] [Indexed: 01/10/2024]
Abstract
The COVID-19 (coronavirus disease 2019) is a well-defined viral infection, resulting from SARS-CoV-2 (severe acute respiratory syndrome- coronavirus-2). The innate immune system serves as the first line of defense to limit viral spreading and subsequently stimulate adaptive immune responses by the prominent aids of its cellular and molecular arms. Monocytes are defined as the most prominent innate immune cells (IICs) that are reactive against invading pathogens. These cells support host protection against the virus that is mediated by several non-specific mechanisms such as phagocytosis, producing antiviral enzymes, and recruitment of immune cells toward and into the infected tissues. They have the ability to egress from blood and migrate to the SARS-CoV-2 infected regions by the aid of some defense-related functions like chemotaxis, which is mediated by chemical compounds, e.g., chemokines. Chemokines, in addition to their related ligands are categorized within the most important and deserved agents involved in oriented trafficking of monocytes/macrophages towards and within the lung parenchyma in both steady state and pathological circumstances, including COVID-19-raised infection. However, the overexpression of chemokines could have deleterious effects on various organs through the induction of cytokine storm and may be the most important leading mechanisms in the pathogenesis of COVID-19. Authors have aimed the current review article to describe present knowledge about the interplay between monocytes/macrophages and SARS-CoV-2 with a focus on the ability of IICs to migrate and home into the lung of COVID-19 patients through various chemokine-chemokine receptor axes to promote our understanding regarding this disease.
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Affiliation(s)
- Merat Mahmoodi
- Department of Medical Immunology, Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Fatemeh Mohammadi Henjeroei
- Department of Medical Immunology, Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Gholamhossein Hassanshahi
- Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, RafsanjanUniversity of Medical Sciences, Rafsanjan, Iran
| | - Reza Nosratabadi
- Department of Medical Immunology, Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran; Gastroenterology and Hepatology Research Center, Kerman University of Medical Sciences, Kerman, Iran.
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20
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Andreakos E. Type I and type III interferons: From basic biology and genetics to clinical development for COVID-19 and beyond. Semin Immunol 2024; 72:101863. [PMID: 38271892 DOI: 10.1016/j.smim.2024.101863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/11/2023] [Accepted: 01/02/2024] [Indexed: 01/27/2024]
Abstract
Type I and type III interferons (IFNs) constitute a key antiviral defense systems of the body, inducing viral resistance to cells and mediating diverse innate and adaptive immune functions. Defective type I and type III IFN responses have recently emerged as the 'Achilles heel' in COVID-19, with such patients developing severe disease and exhibiting a high risk for critical pneumonia and death. Here, we review the biology of type I and type III IFNs, their similarities and important functional differences, and their roles in SARS-CoV-2 infection. We also appraise the various mechanisms proposed to drive defective IFN responses in COVID-19 with particular emphasis to the ability of SARS-CoV-2 to suppress IFN production and activities, the genetic factors involved and the presence of autoantibodies neutralizing IFNs and accounting for a large proportion of individuals with severe COVID-19. Finally, we discuss the long history of the type I IFN therapeutics for the treatment of viral diseases, cancer and multiple sclerosis, the various efforts to use them in respiratory infections, and the newly emerging type III IFN therapeutics, with emphasis to the more recent studies on COVID-19 and their potential use as broad spectrum antivirals for future epidemics or pandemics.
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Affiliation(s)
- Evangelos Andreakos
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, BRFAA, Athens, Greece.
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21
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Rosas-Murrieta NH, Rodríguez-Enríquez A, Herrera-Camacho I, Millán-Pérez-Peña L, Santos-López G, Rivera-Benítez JF. Comparative Review of the State of the Art in Research on the Porcine Epidemic Diarrhea Virus and SARS-CoV-2, Scope of Knowledge between Coronaviruses. Viruses 2024; 16:238. [PMID: 38400014 PMCID: PMC10892376 DOI: 10.3390/v16020238] [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: 12/13/2023] [Revised: 01/17/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
This review presents comparative information corresponding to the progress in knowledge of some aspects of infection by the porcine epidemic diarrhea virus (PEDV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronaviruses. PEDV is an alphacoronavirus of great economic importance due to the million-dollar losses it generates in the pig industry. PEDV has many similarities to the SARS-CoV-2 betacoronavirus that causes COVID-19 disease. This review presents possible scenarios for SARS-CoV-2 based on the collected literature on PEDV and the tools or strategies currently developed for SARS-CoV-2 that would be useful in PEDV research. The speed of the study of SARS-CoV-2 and the generation of strategies to control the pandemic was possible due to the knowledge derived from infections caused by other human coronaviruses such as severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS). Therefore, from the information obtained from several coronaviruses, the current and future behavior of SARS-CoV-2 could be inferred and, with the large amount of information on the virus that causes COVID-19, the study of PEDV could be improved and probably that of new emerging and re-emerging coronaviruses.
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Affiliation(s)
- Nora H. Rosas-Murrieta
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Alan Rodríguez-Enríquez
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
- Posgrado en Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Irma Herrera-Camacho
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Lourdes Millán-Pérez-Peña
- Centro de Química, Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (A.R.-E.); (I.H.-C.); (L.M.-P.-P.)
| | - Gerardo Santos-López
- Centro de Investigación Biomédica de Oriente, Laboratorio de Biología Molecular y Virología, Instituto Mexicano del Seguro Social (IMSS), Metepec 74360, Mexico;
| | - José F. Rivera-Benítez
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Ciudad de México 38110, Mexico;
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22
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Noh HE, Rha MS. Mucosal Immunity against SARS-CoV-2 in the Respiratory Tract. Pathogens 2024; 13:113. [PMID: 38392851 PMCID: PMC10892713 DOI: 10.3390/pathogens13020113] [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: 12/11/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
The respiratory tract, the first-line defense, is constantly exposed to inhaled allergens, pollutants, and pathogens such as respiratory viruses. Emerging evidence has demonstrated that the coordination of innate and adaptive immune responses in the respiratory tract plays a crucial role in the protection against invading respiratory pathogens. Therefore, a better understanding of mucosal immunity in the airways is critical for the development of novel therapeutics and next-generation vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses. Since the coronavirus disease 2019 pandemic, our knowledge of mucosal immune responses in the airways has expanded. In this review, we describe the latest knowledge regarding the key components of the mucosal immune system in the respiratory tract. In addition, we summarize the host immune responses in the upper and lower airways following SARS-CoV-2 infection and vaccination, and discuss the impact of allergic airway inflammation on mucosal immune responses against SARS-CoV-2.
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Affiliation(s)
- Hae-Eun Noh
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea;
| | - Min-Seok Rha
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea;
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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23
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Pang Y, Zhou Y, Wang Y, Fang L, Xiao S. Lactate-lactylation-HSPA6 axis promotes PRRSV replication by impairing IFN-β production. J Virol 2024; 98:e0167023. [PMID: 38088561 PMCID: PMC10804950 DOI: 10.1128/jvi.01670-23] [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: 10/24/2023] [Accepted: 11/27/2023] [Indexed: 01/24/2024] Open
Abstract
Lactate, traditionally considered a metabolic by-product, has recently been identified as a substrate for the induction of lactylation, a newly identified epigenetic modification that plays an important role in the regulation of host gene expression. Our previous study showed that lactate levels were significantly elevated in cells infected with the porcine reproductive and respiratory syndrome virus (PRRSV), an Arterivirus that has devastated the swine industry worldwide for over 30 years. However, the role of elevated lactate in PRRSV infections remains unknown. In this study, we found that lactate was required for optimal PRRSV proliferation, and PRRSV infection increased cellular lactylation in a dose-dependent manner. Using the Cleavage Under Targets and Tagmentation (CUT&Tag) combined with RNA sequencing (RNA-seq) to screen the downstream genes regulated by lactylation in PRRSV-infected cells, we found that PRRSV-induced lactylation activated the expression of heat shock 70 kDa protein 6 (HSPA6). Follow-up experiments showed that HSPA6 is important for PRRSV proliferation by negatively modulating interferon (IFN)-β induction. Mechanistically, HSPA6 impeded the interaction between TNF-receptor-associated factor 3 (TRAF3) and inhibitor of nuclear factor kappa-B kinase subunit epsilon (IKKε), thereby hindering the production of IFN-β. Taken together, these results indicate that the activated lactate-lactylation-HSPA6 axis promotes viral growth by impairing IFN-β induction, providing new therapeutic targets for the prevention and control of PRRSV infection. The results presented here also link lactylation to the virus life cycle, improving our understanding of epigenetic regulation in viral infection.IMPORTANCEAs a newly identified epigenetic modification, lactate-induced lactylation has received attentions because it plays important roles in gene expression and contributes to tumorigenesis and the innate immune response. Previous studies showed that many viruses upregulate cellular lactate levels; however, whether virus-elevated lactate induces lactylation and the subsequent biological significance of the modification to viral infection have not been reported. In this study, we demonstrated that porcine reproductive and respiratory syndrome virus (PRRSV) infection induced cellular lactylation, which, in turn, upregulated the expression of HSPA6, an IFN-negative regulator. We also dissected the mechanism by which HSPA6 negatively regulates IFN-β production. To our knowledge, this is the first report to study virus-induced lactylation and establish the relationship between lactylation and virus infection.
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Affiliation(s)
- Yu Pang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yanrong Zhou
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Yucheng Wang
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Liurong Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shaobo Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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24
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Zhang J, Xia Y, Li X, He R, Xie X. Case report: A case of Acute Macular Neuroretinopathy secondary to Influenza A virus during Long COVID. Front Immunol 2024; 14:1302504. [PMID: 38288123 PMCID: PMC10822910 DOI: 10.3389/fimmu.2023.1302504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/18/2023] [Indexed: 01/31/2024] Open
Abstract
Ocular abnormalities have been reported in association with viral infections, including Long COVID, a debilitating illness caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This report presents a case of a female patient diagnosed with Acute Macular Neuroretinopathy (AMN) following an Influenza A virus infection during Long COVID who experienced severe inflammation symptoms and ocular complications. We hypothesize that the rare occurrence of AMN in this patient could be associated with the immune storm secondary to the viral infection during Long COVID.
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Affiliation(s)
- Jiaqi Zhang
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Eye School of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yihao Xia
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Eye School of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaodong Li
- The First Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Runxi He
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Eye School of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xuejun Xie
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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25
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Mihaescu G, Chifiriuc MC, Filip R, Bleotu C, Ditu LM, Constantin M, Cristian RE, Grigore R, Bertesteanu SV, Bertesteanu G, Vrancianu CO. Role of interferons in the antiviral battle: from virus-host crosstalk to prophylactic and therapeutic potential in SARS-CoV-2 infection. Front Immunol 2024; 14:1273604. [PMID: 38288121 PMCID: PMC10822962 DOI: 10.3389/fimmu.2023.1273604] [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: 08/06/2023] [Accepted: 12/29/2023] [Indexed: 01/31/2024] Open
Abstract
Mammalians sense antigenic messages from infectious agents that penetrate the respiratory and digestive epithelium, as well as signals from damaged host cells through membrane and cytosolic receptors. The transduction of these signals triggers a personalized response, depending on the nature of the stimulus and the host's genetics, physiological condition, and comorbidities. Interferons (IFNs) are the primary effectors of the innate immune response, and their synthesis is activated in most cells within a few hours after pathogen invasion. IFNs are primarily synthesized in infected cells, but their anti-infective effect is extended to the neighboring cells by autocrine and paracrine action. The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in 2019 was a stark reminder of the potential threat posed by newly emerging viruses. This pandemic has also triggered an overwhelming influx of research studies aiming to unveil the mechanisms of protective versus pathogenic host immune responses induced by SARS-CoV-2. The purpose of this review is to describe the role of IFNs as vital players in the battle against SARS-CoV-2 infection. We will briefly characterize and classify IFNs, present the inductors of IFN synthesis, their sensors, and signaling pathways, and then discuss the role of IFNs in controlling the evolution of SARS-CoV-2 infection and its clinical outcome. Finally, we will present the perspectives and controversies regarding the prophylactic and therapeutic potential of IFNs in SARS-CoV-2 infection.
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Affiliation(s)
- Grigore Mihaescu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Department of Life, Medical and Agricultural Sciences, Biological Sciences Section, Academy of Romanian Scientists, Bucharest, Romania
| | - Roxana Filip
- Faculty of Medicine and Biological Sciences, Stefan cel Mare University of Suceava, Suceava, Romania
- Microbiology Department, Suceava Emergency County Hospital, Suceava, Romania
| | - Coralia Bleotu
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Cellular and Molecular Pathology Department, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Lia Mara Ditu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Marian Constantin
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Institute of Biology of Romanian Academy, Bucharest, Romania
| | - Roxana-Elena Cristian
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Raluca Grigore
- ENT Department, University of Medicine and Pharmacy Carol Davila and Coltea Clinical Hospital, Bucharest, Romania
| | - Serban Vifor Bertesteanu
- ENT Department, University of Medicine and Pharmacy Carol Davila and Coltea Clinical Hospital, Bucharest, Romania
| | - Gloria Bertesteanu
- ENT Department, University of Medicine and Pharmacy Carol Davila and Coltea Clinical Hospital, Bucharest, Romania
| | - Corneliu Ovidiu Vrancianu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- DANUBIUS Department, National Institute of Research and Development for Biological Sciences, Bucharest, Romania
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26
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Anand A, Long C, Chandran K. NYC metropolitan wastewater reveals links between SARS-CoV-2 amino acid mutations and disease outcomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:167971. [PMID: 37914132 DOI: 10.1016/j.scitotenv.2023.167971] [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: 02/17/2023] [Revised: 10/01/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
Since late 2020, diverse SARS-CoV-2 variants with enhanced infectivity and transmissibility have emerged. In contrast to the focus on amino acid mutations in the spike protein, mutations in non-spike proteins and their associated impacts remain relatively understudied. New York City metropolitan wastewater revealed over 60 % of the most frequently occurring amino acid mutations in regions outside the spike protein. Strikingly, ~50 % of the mutations detected herein remain uncharacterized for functional impacts. Our results suggest that there are several understudied mutations within non-spike proteins N, ORF1a, ORF1b, ORF9b, and ORF9c, that could increase transmissibility, and infectivity among human populations. We also demonstrate significant correlations of P314L, D614G, T95I, G50E, G50R, G204R, R203K, G662S, P10S, and P13L with documented mortality rates, hospitalization rates, and percent positivity suggesting that amino acid mutations are likely to be indicators of COVID-19 infection outcomes.
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Affiliation(s)
- Archana Anand
- Department of Earth and Environmental Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, United States of America
| | - Chenghua Long
- Department of Earth and Environmental Engineering, Columbia University, 500 W. 120th Street, New York, NY 10027, United States of America
| | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University, 500 W. 120th Street, New York, NY 10027, United States of America.
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27
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Uribe FR, González VPI, Kalergis AM, Soto JA, Bohmwald K. Understanding the Neurotrophic Virus Mechanisms and Their Potential Effect on Systemic Lupus Erythematosus Development. Brain Sci 2024; 14:59. [PMID: 38248274 PMCID: PMC10813552 DOI: 10.3390/brainsci14010059] [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: 11/07/2023] [Revised: 12/24/2023] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
Central nervous system (CNS) pathologies are a public health concern, with viral infections one of their principal causes. These viruses are known as neurotropic pathogens, characterized by their ability to infiltrate the CNS and thus interact with various cell populations, inducing several diseases. The immune response elicited by neurotropic viruses in the CNS is commanded mainly by microglia, which, together with other local cells, can secrete inflammatory cytokines to fight the infection. The most relevant neurotropic viruses are adenovirus (AdV), cytomegalovirus (CMV), enterovirus (EV), Epstein-Barr Virus (EBV), herpes simplex virus type 1 (HSV-1), and herpes simplex virus type 2 (HSV-2), lymphocytic choriomeningitis virus (LCMV), and the newly discovered SARS-CoV-2. Several studies have associated a viral infection with systemic lupus erythematosus (SLE) and neuropsychiatric lupus (NPSLE) manifestations. This article will review the knowledge about viral infections, CNS pathologies, and the immune response against them. Also, it allows us to understand the relevance of the different viral proteins in developing neuronal pathologies, SLE and NPSLE.
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Affiliation(s)
- Felipe R. Uribe
- Millennium Institute on Immunology and Immunotherapy, Laboratorio de Inmunología Traslacional, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile; (F.R.U.); (V.P.I.G.)
| | - Valentina P. I. González
- Millennium Institute on Immunology and Immunotherapy, Laboratorio de Inmunología Traslacional, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile; (F.R.U.); (V.P.I.G.)
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8330025, Chile;
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Jorge A. Soto
- Millennium Institute on Immunology and Immunotherapy, Laboratorio de Inmunología Traslacional, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile; (F.R.U.); (V.P.I.G.)
| | - Karen Bohmwald
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma, Santiago 8910060, Chile
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28
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Chio CC, Chan HW, Chen SH, Huang HI. Enterovirus D68 vRNA induces type III IFN production via MDA5. Virus Res 2024; 339:199284. [PMID: 38040125 PMCID: PMC10704515 DOI: 10.1016/j.virusres.2023.199284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/03/2023]
Abstract
Enterovirus D68 (EV-D68) primarily spreads through the respiratory tract and causes respiratory symptoms in children and acute flaccid myelitis (AFM). Type III interferons (IFNs) play a critical role in inhibiting viral growth in respiratory epithelial cells. However, the mechanism by which EV-D68 induces type III IFN production is not yet fully understood. In this study, we show that EV-D68 infection stimulates Calu-3 cells to secrete IFN-λ. The transfection of EV-D68 viral RNA (vRNA) stimulated IFN-λ via MDA5. Furthermore, our findings provide evidence that EV-D68 infection also induces MDA5-IRF3/IRF7-mediated IFN-λ. In addition, we discovered that EV-D68 infection downregulated MDA5 expression. Knockdown of MDA5 increased EV-D68 replication in Calu-3 cells. Finally, we demonstrated that the IFN-λ1 and IFN-λ2/3 proteins effectively inhibit EV-D68 infection in respiratory epithelial cells. In summary, our study shows that EV-D68 induces type III IFN production via the activated MDA5-IRF3/IRF7 pathway and that type III IFNs inhibit EV-D68 replication in Calu-3 cells.
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Affiliation(s)
- Chi-Chong Chio
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan; Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Hio-Wai Chan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Shih-Hsiang Chen
- Division of Pediatric Hematology/Oncology, Linkou Chang Gung Memorial Hospital, Kwei-Shan, Tao-Yuan, Taiwan; College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Hsing-I Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan; Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan; Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Kwei-Shan, Tao-Yuan, Taiwan.
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29
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Jiang H, Nair V, Sun Y, Ding C. The diverse roles of peroxisomes in the interplay between viruses and mammalian cells. Antiviral Res 2024; 221:105780. [PMID: 38092324 DOI: 10.1016/j.antiviral.2023.105780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/26/2023]
Abstract
Peroxisomes are ubiquitous organelles found in eukaryotic cells that play a critical role in the oxidative metabolism of lipids and detoxification of reactive oxygen species (ROS). Recently, the role of peroxisomes in viral infections has been extensively studied. Although several studies have reported that peroxisomes exert antiviral activity, evidence indicates that viruses have also evolved diverse strategies to evade peroxisomal antiviral signals. In this review, we summarize the multiple roles of peroxisomes in the interplay between viruses and mammalian cells. Focus is given on the peroxisomal regulation of innate immune response, lipid metabolism, ROS production, and viral regulation of peroxisomal biosynthesis and degradation. Understanding the interactions between peroxisomes and viruses provides novel insights for the development of new antiviral strategies.
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Affiliation(s)
- Hui Jiang
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, China
| | - Venugopal Nair
- Avian Oncogenic Viruses Group, UK-China Centre of Excellence in Avian Disease Research, The Pirbright Institute, Pirbright, Guildford, Surrey, United Kingdom
| | - Yingjie Sun
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, China.
| | - Chan Ding
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu Province, China.
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Ji L, Li T, Chen H, Yang Y, Lu E, Liu J, Qiao W, Chen H. The crucial regulatory role of type I interferon in inflammatory diseases. Cell Biosci 2023; 13:230. [PMID: 38124132 PMCID: PMC10734085 DOI: 10.1186/s13578-023-01188-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023] Open
Abstract
Type I interferon (IFN-I) plays crucial roles in the regulation of inflammation and it is associated with various inflammatory diseases including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and periodontitis, impacting people's health and quality of life. It is well-established that IFN-Is affect immune responses and inflammatory factors by regulating some signaling. However, currently, there is no comprehensive overview of the crucial regulatory role of IFN-I in distinctive pathways as well as associated inflammatory diseases. This review aims to provide a narrative of the involvement of IFN-I in different signaling pathways, mainly mediating the related key factors with specific targets in the pathways and signaling cascades to influence the progression of inflammatory diseases. As such, we suggested that IFN-Is induce inflammatory regulation through the stimulation of certain factors in signaling pathways, which displays possible efficient treatment methods and provides a reference for the precise control of inflammatory diseases.
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Affiliation(s)
- Ling Ji
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
| | - Tianle Li
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
| | - Huimin Chen
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
| | - Yanqi Yang
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
- Division of Pediatric Dentistry and Orthodontics, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
| | - Eryi Lu
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 160 Pujian Road, Shanghai, China
| | - Jieying Liu
- Department of Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Qiao
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China.
- Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Level 3, 34 Hospital Road, Sai Ying Pun, Hong Kong, SAR, People's Republic of China.
| | - Hui Chen
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China.
- Division of Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Level 3, 34 Hospital Road, Sai Ying Pun, Hong Kong, SAR, People's Republic of China.
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Wang L, Zheng W, Lv X, Song Y, Xu T. circMORC3-encoded novel protein negatively regulates antiviral immunity through synergizing with host gene MORC3. PLoS Pathog 2023; 19:e1011894. [PMID: 38150467 PMCID: PMC10775979 DOI: 10.1371/journal.ppat.1011894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/09/2024] [Accepted: 12/12/2023] [Indexed: 12/29/2023] Open
Abstract
The protein-coding ability of circRNAs has recently been a hot topic, but the role of protein-coding circRNAs in antiviral innate immunity of teleost fish has rarely been reported. Here, we identified a novel circRNA, termed circMORC3, derived from Microrchidia 3 (MORC3) gene in Miichthys miiuy. circMORC3 can inhibit the expression of antiviral cytokines. In addition, circMORC3 encodes a novel peptide with a length of 84 amino acids termed MORC3-84aa. MORC3-84aa not only significantly inhibited TRIF-mediated activation of IRF3 and NF-κB signaling pathways, but also effectively suppressed the expression of antiviral cytokines triggered by RNA virus Siniperca chuatsi rhabdovirus (SCRV). We found that MORC3-84aa directly interacted with TRIF and negatively regulated TRIF protein expression. In addition, host gene MORC3 attenuates SCRV-induced IFN and ISG expression. Mechanistically, MORC3-84aa promotes autophagic degradation of TRIF by enhancing K6-linked ubiquitination and inhibits TRIF-mediated activation of the type I interferon signaling pathway. And the host gene MORC3 not only repressed IRF3 protein expression but also inhibited IRF3 phosphorylation levels. Our study shows that circMORC3 and host gene MORC3 played a synergistic role in viral immune escape.
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Affiliation(s)
- Linchao Wang
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xing Lv
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yanhong Song
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai, China
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Zheng Y, Yang H, Zhang X, Gao C. Regulation of SARS-CoV-2 infection and antiviral innate immunity by ubiquitination and ubiquitin-like conjugation. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194984. [PMID: 37717938 DOI: 10.1016/j.bbagrm.2023.194984] [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: 06/12/2023] [Revised: 08/30/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
A global pandemic COVID-19 resulting from SARS-CoV-2 has affected a significant portion of the human population. Antiviral innate immunity is critical for controlling and eliminating the viral infection. Ubiquitination is extensively involved in antiviral signaling, and recent studies suggest that ubiquitin-like proteins (Ubls) modifications also participate in innate antiviral pathways such as RLR and cGAS-STING pathways. Notably, virus infection harnesses ubiquitination and Ubls modifications to facilitate viral replication and counteract innate antiviral immunity. These observations indicate that ubiquitination and Ubls modifications are critical checkpoints for the tug-of-war between virus and host. This review discusses the current progress regarding the modulation of the SARS-CoV-2 life cycle and antiviral innate immune pathways by ubiquitination and Ubls modifications. This paper emphasizes the arising concept that ubiquitination and Ubls modifications are powerful modulators of virus and host interaction and potential drug targets for treating the infection of SARS-CoV-2.
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Affiliation(s)
- Yi Zheng
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China.
| | - Huiyu Yang
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Xuejing Zhang
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Chengjiang Gao
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China.
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Elahi R, Hozhabri S, Moradi A, Siahmansouri A, Jahani Maleki A, Esmaeilzadeh A. Targeting the cGAS-STING pathway as an inflammatory crossroad in coronavirus disease 2019 (COVID-19). Immunopharmacol Immunotoxicol 2023; 45:639-649. [PMID: 37335770 DOI: 10.1080/08923973.2023.2215405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/14/2023] [Indexed: 06/21/2023]
Abstract
CONTEXT AND OBJECTIVE The emerging pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has imposed significant mortality and morbidity on the world. An appropriate immune response is necessary to inhibit SARS-CoV-2 spread throughout the body. RESULTS During the early stages of infection, the pathway of stimulators of interferon genes (STING), known as the cGAS-STING pathway, has a significant role in the induction of the antiviral immune response by regulating nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and Interferon regulatory factor 3 (IRF3), two key pathways responsible for proinflammatory cytokines and type I IFN secretion, respectively. DISCUSSION During the late stages of COVID-19, the uncontrolled inflammatory responses, also known as cytokine storm, lead to the progression of the disease and poor prognosis. Hyperactivity of STING, leading to elevated titers of proinflammatory cytokines, including Interleukin-I (IL-1), IL-4, IL-6, IL-18, and tissue necrosis factor-α (TNF-α), is considered one of the primary mechanisms contributing to the cytokine storm in COVID-19. CONCLUSION Exploring the underlying molecular processes involved in dysregulated inflammation can bring up novel anti-COVID-19 therapeutic options. In this article, we aim to discuss the role and current studies targeting the cGAS/STING signaling pathway in both early and late stages of COVID-19 and COVID-19-related complications and the therapeutic potential of STING agonists/antagonists. Furthermore, STING agonists have been discussed as a vaccine adjuvant to induce a potent and persistent immune response.
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Affiliation(s)
- Reza Elahi
- School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Salar Hozhabri
- School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Amirhosein Moradi
- School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Amir Siahmansouri
- School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | | | - Abdolreza Esmaeilzadeh
- Department of Immunology, Zanjan University of Medical Sciences, Zanjan, Iran
- Cancer Gene Therapy Research Center (CGRC), Zanjan University of Medical Sciences, Zanjan, Iran
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Jiao P, Fan W, Ma X, Lin R, Zhao Y, Li Y, Zhang H, Jia X, Bi Y, Feng X, Li M, Liu W, Zhang K, Sun L. SARS-CoV-2 nonstructural protein 6 triggers endoplasmic reticulum stress-induced autophagy to degrade STING1. Autophagy 2023; 19:3113-3131. [PMID: 37482689 PMCID: PMC10621274 DOI: 10.1080/15548627.2023.2238579] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 07/14/2023] [Indexed: 07/25/2023] Open
Abstract
ABBREVIATIONS aa: amino acid; ATF6: activating transcription factor 6; ATG5: autophagy related 5; CCPG1: cell cycle progression 1; CFTR: CF transmembrane conductance regulator; cGAMP: cyclic GMP-AMP; CGAS: cyclic GMP-AMP synthase; CHX: cycloheximide; Co-IP: co-immunoprecipitation; CQ: chloroquine; EIF2A/eIF2α: eukaryotic translation initiation factor 2A; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; ER: endoplasmic reticulum; ERN1/IRE1: endoplasmic reticulum to nucleus signaling 1; GFP: green fluorescent protein; HSPA5/GRP78: heat shock protein family A (Hsp70) member 5; HSV-1: herpes simplex virus type 1; IFIT1: interferon induced protein with tetratricopeptide repeats 1; IFNB1/IFN-β: interferon beta 1; IRF3: interferon regulatory factor 3; ISG15: ISG15 ubiquitin like modifier; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MAP3K7/TAK1: mitogen-activated protein kinase kinase kinase 7; MAVS: mitochondrial antiviral signaling protein; MOI: multiplicity of infection; NFKB/NF-κB: nuclear factor kappa B; NSP6: non-structural protein 6; Δ106-108: deletion of amino acids 106-108 in NSP6 of SARS-CoV-2; Δ105-107: deletion of amino acids 105-107 in NSP6 of SARS-CoV-2; RETREG1/FAM134B: reticulophagy regulator 1; RIGI/DDX58: RNA sensor RIG-I; SQSTM1/p62: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TBK1: TANK binding kinase 1.
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Affiliation(s)
- Pengtao Jiao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenhui Fan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoya Ma
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Runshan Lin
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuna Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning, Guangxi, China
| | - Yabo Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning, Guangxi, China
| | - He Zhang
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Xiaojuan Jia
- The Biological Safety Level-3 (BSL-3) Laboratory of Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- The Biological Safety Level-3 (BSL-3) Laboratory of Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Feng
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Minghua Li
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning, Guangxi, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Ke Zhang
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Lei Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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Fricke C, Pfaff F, Ulrich L, Halwe NJ, Schön J, Timm L, Hoffmann W, Rauch S, Petsch B, Hoffmann D, Beer M, Corleis B, Dorhoi A. SARS-CoV-2 variants of concern elicit divergent early immune responses in hACE2 transgenic mice. Eur J Immunol 2023; 53:e2250332. [PMID: 37609807 DOI: 10.1002/eji.202250332] [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: 12/13/2022] [Revised: 07/20/2023] [Accepted: 08/21/2023] [Indexed: 08/24/2023]
Abstract
Knowledge about early immunity to SARS-CoV-2 variants of concern mainly comes from the analysis of human blood. Such data provide limited information about host responses at the site of infection and largely miss the initial events. To gain insights into compartmentalization and the early dynamics of host responses to different SARS-CoV-2 variants, we utilized human angiotensin converting enzyme 2 (hACE2) transgenic mice and tracked immune changes during the first days after infection by RNAseq, multiplex assays, and flow cytometry. Viral challenge infection led to divergent viral loads in the lungs, distinct inflammatory patterns, and innate immune cell accumulation in response to ancestral SARS-CoV-2, Beta (B.1.351) and Delta (B.1.617.2) variant of concern (VOC). Compared to other SARS-CoV-2 variants, infection with Beta (B.1.351) VOC spread promptly to the lungs, leading to increased inflammatory responses. SARS-CoV-2-specific antibodies and T cells developed within the first 7 days postinfection and were required to reduce viral spread and replication. Our studies show that VOCs differentially trigger transcriptional profiles and inflammation. This information contributes to the basic understanding of immune responses immediately postexposure to SARS-CoV-2 and is relevant for developing pan-VOC interventions including prophylactic vaccines.
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Affiliation(s)
- Charlie Fricke
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Lorenz Ulrich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Nico Joel Halwe
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jacob Schön
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Laura Timm
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Weda Hoffmann
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | | | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Björn Corleis
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Anca Dorhoi
- Institute of Immunology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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Pereira EPV, da Silva Felipe SM, de Freitas RM, da Cruz Freire JE, Oliveira AER, Canabrava N, Soares PM, van Tilburg MF, Guedes MIF, Grueter CE, Ceccatto VM. Transcriptional Profiling of SARS-CoV-2-Infected Calu-3 Cells Reveals Immune-Related Signaling Pathways. Pathogens 2023; 12:1373. [PMID: 38003837 PMCID: PMC10674242 DOI: 10.3390/pathogens12111373] [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: 09/15/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The COVID-19 disease, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), emerged in late 2019 and rapidly spread worldwide, becoming a pandemic that infected millions of people and caused significant deaths. COVID-19 continues to be a major threat, and there is a need to deepen our understanding of the virus and its mechanisms of infection. To study the cellular responses to SARS-CoV-2 infection, we performed an RNA sequencing of infected vs. uninfected Calu-3 cells. Total RNA was extracted from infected (0.5 MOI) and control Calu-3 cells and converted to cDNA. Sequencing was performed, and the obtained reads were quality-analyzed and pre-processed. Differential expression was assessed with the EdgeR package, and functional enrichment was performed in EnrichR for Gene Ontology, KEGG pathways, and WikiPathways. A total of 1040 differentially expressed genes were found in infected vs. uninfected Calu-3 cells, of which 695 were up-regulated and 345 were down-regulated. Functional enrichment analyses revealed the predominant up-regulation of genes related to innate immune response, response to virus, inflammation, cell proliferation, and apoptosis. These transcriptional changes following SARS-CoV-2 infection may reflect a cellular response to the infection and help to elucidate COVID-19 pathogenesis, in addition to revealing potential biomarkers and drug targets.
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Affiliation(s)
- Eric Petterson Viana Pereira
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | - Stela Mirla da Silva Felipe
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | - Raquel Martins de Freitas
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | - José Ednésio da Cruz Freire
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | | | - Natália Canabrava
- Biotechnology and Molecular Biology Laboratory, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (N.C.); (M.F.v.T.); (M.I.F.G.)
| | - Paula Matias Soares
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
| | - Mauricio Fraga van Tilburg
- Biotechnology and Molecular Biology Laboratory, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (N.C.); (M.F.v.T.); (M.I.F.G.)
| | - Maria Izabel Florindo Guedes
- Biotechnology and Molecular Biology Laboratory, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (N.C.); (M.F.v.T.); (M.I.F.G.)
| | - Chad Eric Grueter
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA;
| | - Vânia Marilande Ceccatto
- Superior Institute of Biomedical Sciences, State University of Ceará, Fortaleza 60714-903, CE, Brazil; (S.M.d.S.F.); (R.M.d.F.); (J.E.d.C.F.); (P.M.S.)
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Lee JS, Dittmar M, Miller J, Li M, Ayyanathan K, Ferretti M, Hulahan J, Whig K, Etwebi Z, Griesman T, Schultz DC, Cherry S. Evolutionary arms race between SARS-CoV-2 and interferon signaling via dynamic interaction with autophagy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566859. [PMID: 38014114 PMCID: PMC10680587 DOI: 10.1101/2023.11.13.566859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
SARS-CoV-2 emerged, and is evolving to efficiently infect humans worldwide. SARS-CoV-2 evades early innate recognition, interferon signaling activated only in bystander cells. This balance of innate activation and viral evasion has important consequences, but the pathways involved are incompletely understood. Here we find that autophagy genes regulate innate immune signaling, impacting the basal set point of interferons, and thus permissivity to infection. Mechanistically, autophagy genes negatively regulate MAVS, and this low basal level of MAVS is efficiently antagonized by SARS-CoV-2 ORF9b, blocking interferon activation in infected cells. However, upon loss of autophagy increased MAVS overcomes ORF9b-mediated antagonism suppressing infection. This has led to the evolution of SARS-CoV-2 variants to express higher levels of ORF9b, allowing SARS-CoV-2 to replicate under conditions of increased MAVS signaling. Altogether, we find a critical role of autophagy in the regulation of innate immunity and uncover an evolutionary trajectory of SARS-CoV-2 ORF9b to overcome host defenses.
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Iqbal K, Sinha S, David P, De Marco G, Taheri S, McLaren E, Maisuria S, Arumugakani G, Ash Z, Buckley C, Coles L, Hettiarachchi C, Smithson G, Slade M, Shah R, Marzo-Ortega H, Keen M, Lawson C, Mclorinan J, Nizam S, Reddy H, Sharif O, Sultan S, Tran G, Wood M, Wood S, Ghosh P, McGonagle D. MDA5-autoimmunity and Interstitial Pneumonitis Contemporaneous with the COVID-19 Pandemic (MIP-C). MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.03.23297727. [PMID: 37961408 PMCID: PMC10635254 DOI: 10.1101/2023.11.03.23297727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background Anti-MDA5 (Melanoma differentiation-associated protein-5) positive dermatomyositis (MDA5 + -DM) is characterised by rapidly progressive interstitial lung disease (ILD) and high mortality. MDA5 senses single-stranded RNA and is a key pattern recognition receptor for the SARS-CoV-2 virus. Methods This is a retrospective observational study of a surge in MDA5 autoimmunity, as determined using a 15 muscle-specific autoantibodies (MSAs) panel, between Janurary 2018-December 2022 in Yorkshire, UK. MDA5-positivity was correlated with clinical features and outcome, and regional SARS-CoV-2 positivity and vaccination rates. Gene expression patterns in COVID-19 were compared with autoimmune lung disease and idiopathic pulmonary fibrosis (IPF) to gain clues into the genesis of the observed MDA5 + -DM outbreak. Results Sixty new anti-MDA5+, but not other MSAs surged between 2020-2022, increasing from 0.4% in 2019 to 2.1% (2020), 4.8% (2021) and 1.7% (2022). Few (8/60) had a prior history of confirmed COVID-19, peak rates overlapped with regional SARS-COV-2 community positivity rates in 2021, and 58% (35/60) had received anti-SARS-CoV-2 RNA vaccines. Few (8/60) had a prior history of COVID-19, whereas 58% (35/60) had received anti-SARS-CoV-2 RNA vaccines. 25/60 cases developed ILD which rapidly progression with death in 8 cases. Among the 35/60 non-ILD cases, 14 had myositis, 17 Raynaud phenomena and 10 had dermatomyositis spectrum rashes. Transcriptomic studies showed strong IFIH1 (gene encoding for MDA5) induction in COVID-19 and autoimmune-ILD, but not IPF, and IFIH1 strongly correlated with an IL-15-centric type-1 interferon response and an activated CD8+ T cell signature that is an immunologic hallmark of progressive ILD in the setting of systemic autoimmune rheumatic diseases. The IFIH1 rs1990760TT variant blunted such response. Conclusions A distinct pattern of MDA5-autoimmunity cases surged contemporaneously with circulation of the SARS-COV-2 virus during COVID-19. Bioinformatic insights suggest a shared immunopathology with known autoimmune lung disease mechanisms.
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Grand RJ. SARS-CoV-2 and the DNA damage response. J Gen Virol 2023; 104:001918. [PMID: 37948194 PMCID: PMC10768691 DOI: 10.1099/jgv.0.001918] [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: 09/01/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
The recent coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is characterized by respiratory distress, multiorgan dysfunction and, in some cases, death. The virus is also responsible for post-COVID-19 condition (commonly referred to as 'long COVID'). SARS-CoV-2 is a single-stranded, positive-sense RNA virus with a genome of approximately 30 kb, which encodes 26 proteins. It has been reported to affect multiple pathways in infected cells, resulting, in many cases, in the induction of a 'cytokine storm' and cellular senescence. Perhaps because it is an RNA virus, replicating largely in the cytoplasm, the effect of SARS-Cov-2 on genome stability and DNA damage responses (DDRs) has received relatively little attention. However, it is now becoming clear that the virus causes damage to cellular DNA, as shown by the presence of micronuclei, DNA repair foci and increased comet tails in infected cells. This review considers recent evidence indicating how SARS-CoV-2 causes genome instability, deregulates the cell cycle and targets specific components of DDR pathways. The significance of the virus's ability to cause cellular senescence is also considered, as are the implications of genome instability for patients suffering from long COVID.
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Affiliation(s)
- Roger J. Grand
- Institute for Cancer and Genomic Science, The Medical School, University of Birmingham, Birmingham, UK
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Wong LYR, Odle A, Luhmann E, Wu DC, Wang Y, Teo QW, Ptak C, Sariol A, Lowery S, Mack M, Meyerholz DK, Wu NC, Radoshevich L, Perlman S. Contrasting roles of MERS-CoV and SARS-CoV-2 internal proteins in pathogenesis in mice. mBio 2023; 14:e0247623. [PMID: 37882568 PMCID: PMC10746224 DOI: 10.1128/mbio.02476-23] [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: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 10/27/2023] Open
Abstract
Betacoronaviruses encode an internal (I) gene via an alternative reading frame within the nucleocapsid gene, called ORF8b for Middle-East respiratory syndrome coronavirus (MERS-CoV) and ORF9b for severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. Previous reports suggested that proteins 8b and 9b are involved in evading multiple innate immune signaling pathways. However, their roles in mediating pathogenesis in infected animals have not been determined. In this study, we abrogated the expression of protein 8b in MERS-CoV and protein 9b in SARS-CoV-2. Using mouse models of MERS-CoV and SARS-CoV-2 infection, we found that MERS-CoV lacking protein 8b expression was more virulent, while SARS-CoV-2 lacking protein 9b expression was attenuated compared with the respective wild-type viruses. Upon further analysis, we detected increased levels of type I interferon and enhanced infiltration of immune cells to the lungs of mice infected with MERS-CoV lacking protein 8b expression. These data suggest that the I protein of MERS-CoV plays a role in limiting pathogenesis while that of SARS-CoV-2 enhances disease severity. IMPORTANCE The function of betacoronavirus internal protein has been relatively understudied. The earliest report on the internal protein of mouse hepatitis virus suggested that the internal protein is a structural protein without significant functions in virus replication and virulence. However, the internal proteins of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle-East respiratory syndrome coronavirus, and SARS-CoV-2 have been shown to evade immune responses. Despite the reported functions of the internal protein in these highly pathogenic human coronaviruses, its role in mediating pathogenesis in experimentally infected animals has not been characterized. Our data indicated that despite the similar genomic location and expression strategy of these internal proteins, their effects on virulence are vastly different and virus specific, highlighting the complexity between host-virus interaction and disease outcome.
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Affiliation(s)
- Lok-Yin Roy Wong
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Abby Odle
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Emma Luhmann
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Douglas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Qi Wen Teo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Celeste Ptak
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Alan Sariol
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Shea Lowery
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Matthias Mack
- Department of Internal Medicine, University Hospital Regensburg, Regensburg, Germany
| | | | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Lilliana Radoshevich
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Stanley Perlman
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
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Chilosi M, Doglioni C, Ravaglia C, Piciucchi S, Dubini A, Stefanizzi L, Poletti V. COVID-19. Biology, pathophysiology, and immunology: a pathologist view. Pathologica 2023; 115:248-256. [PMID: 38054899 DOI: 10.32074/1591-951x-954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 12/07/2023] Open
Abstract
Even if the SARS-CoV-2 pandemic has been declared over, several risks and clinical problems remain to be faced, including long-COVID sequelae and possible outbreaks of pathogenic variants. Intense research on COVID-19 has provided in these few years a striking amount of data covering different fields and disciplines, which can help to provide a knowledge shield against new potential infective spreads, and may also potentially be applied to other fields of medicine, including oncology and neurology. Nevertheless, areas of uncertainty still remain regarding the pathogenic mechanisms that subtend the multifaceted manifestations of the disease. To better clarify the pathogenesis of the disease, a systematic multidisciplinary evaluation of the many mechanisms involved in COVID-19 is mandatory, including clinical, physiological, radiological, immunological and pathological studies. In COVID-19 syndrome the pathological studies have been mainly performed on autopsy cases, and only a few studies are available on biopsies. Nevertheless, these studies have provided relevant information that can substantially contribute to decipher the complex scenario characterizing the different forms of COVID-19 and long-COVID-19. In this review the data provided by pathological investigations are recapitulated and discussed, in the light of different hypothesis and data provided by clinical, physiological and immunological data.
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Affiliation(s)
- Marco Chilosi
- Department of Pathology, Pederzoli Hospital, Peschiera del Garda, Italy
| | - Claudio Doglioni
- Department of Pathology, San Raffaele Scientific Institute. Milan, Italy
| | - Claudia Ravaglia
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
| | - Sara Piciucchi
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
| | | | | | - Venerino Poletti
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
- Department of Pathology, Ospedale GB Morgagni, Forlì, Italy
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Isazadeh A, Heris JA, Shahabi P, Mohammadinasab R, Shomali N, Nasiri H, Valedkarimi Z, Khosroshahi AJ, Hajazimian S, Akbari M, Sadeghvand S. Pattern-recognition receptors (PRRs) in SARS-CoV-2. Life Sci 2023; 329:121940. [PMID: 37451397 DOI: 10.1016/j.lfs.2023.121940] [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: 04/12/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Pattern recognition receptors (PRRs) are specific sensors that directly recognize various molecules derived from viral or bacterial pathogens, senescent cells, damaged cells, and apoptotic cells. These sensors act as a bridge between nonspecific and specific immunity in humans. PRRs in human innate immunity were classified into six types: toll-like receptors (TLR), C-type lectin receptors (CLRs), nucleotide-binding and oligomerization domain (NOD)-like receptors (NLRs), absent in melanoma 2 (AIM2)-like receptors (ALRs), retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), and cyclic GMP-AMP (cGAMP) synthase (cGAS). Numerous types of PRRs are responsible for recognizing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which is immensely effective in prompting interferon responses. Detection of SARS-CoV-2 infection by PRRs causes the initiation of an intracellular signaling cascade and subsequently the activation of various transcription factors that stimulate the production of cytokines, chemokines, and other immune-related factors. Therefore, it seems that PRRs are a promising potential therapeutic approach for combating SARS-CoV-2 infection and other microbial infections. In this review, we have introduced the current knowledge of various PRRs and related signaling pathways in response to SARS-CoV-2.
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Affiliation(s)
- Alireza Isazadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javad Ahmadian Heris
- Department of Allergy and Clinical Immunology, Pediatric Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parviz Shahabi
- Department of Physiology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Mohammadinasab
- Department of History of Medicine, School of Traditional Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Navid Shomali
- Department of Immunology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hadi Nasiri
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Valedkarimi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Saba Hajazimian
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Morteza Akbari
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Shahram Sadeghvand
- Department of Pediatrics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Wells EW, Parker MT. Regulating Select Agent Chimeras: Defining the Problem(s) Through the Lens of SARS-CoV-1/SARS-CoV-2 Chimeric Viruses. Health Secur 2023; 21:392-406. [PMID: 37703547 DOI: 10.1089/hs.2023.0008] [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] [Indexed: 09/15/2023] Open
Abstract
In late 2021, the US Centers for Disease Control and Prevention (CDC) posted an interim final rule (86 FR 64075) to the federal register regulating the possession, use, and transfer of SARS-CoV-1/SARS-CoV-2 chimeric viruses. In doing so, the CDC provided the reasoning that viral chimeras combining the transmissibility of SARS-CoV-2 with the pathogenicity and lethality of SARS-CoV-1 pose a significant risk to public health and should thus be placed on the select agents and toxins list. However, 86 FR 64075 lacked clarity in its definitions and scope, some of which the CDC addressed in response to public comments in the final rule, 88 FR 13322, in early 2023. To evaluate these regulatory actions, we reviewed the existing select agent regulations to understand the landscape of chimeric virus regulation. Based on our findings, we first present clear definitions for the terms "chimeric virus," "viral chimera," and "virulence factor" and provide a list of SARS-CoV-1 virulence factors in an effort to aid researchers and federal rulemaking for these agents moving forward. We then provide suggestions for a combination of similarity and functional characteristic cutoffs that the government could use to enable researchers to distinguish between regulated and nonregulated chimeras. Finally, we discuss current select agent regulations and their overlaps with 86 FR 64075 and 88 FR 13322 and make suggestions for how to address chimera concerns within and/or without these regulations. Collectively, we believe that our findings fill important gaps in current federal regulations and provide forward-looking philosophical and practical analysis that can guide future decisionmaking.
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Affiliation(s)
- Elizabeth W Wells
- Elizabeth W. Wells is a Student, Department of Biology, Georgetown College of Arts & Sciences, Georgetown University, Washington, DC
| | - Michael T Parker
- Michael T. Parker, PhD, is Assistant Dean, Georgetown College of Arts & Sciences, Georgetown University, Washington, DC
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Rubio-Casillas A, Redwan EM, Uversky VN. Does SARS-CoV-2 Induce IgG4 Synthesis to Evade the Immune System? Biomolecules 2023; 13:1338. [PMID: 37759738 PMCID: PMC10526126 DOI: 10.3390/biom13091338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
SARS-CoV-2, the virus that causes the COVID-19 disease, has been shown to cause immune suppression in certain individuals. This can manifest as a reduced ability of the host's immune system to effectively control the infection. Studies have reported that patients with COVID-19 can exhibit a decline in white blood cell counts, including natural killer cells and T cells, which are integral components of the immune system's response to viral pathogens. These cells play critical roles in the immune response to viral infections, and their depletion can make it harder for the body to mount an effective defense against the virus. Additionally, the virus can also directly infect immune cells, further compromising their ability to function. Some individuals with severe COVID-19 pneumonia may develop a "cytokine storm", an overactive immune response that may result in tissue damage and organ malfunction. The underlying mechanisms of immune suppression in SARS-CoV-2 are not entirely understood at this time, and research is being conducted to gain a more comprehensive understanding. Research has shown that severe SARS-CoV-2 infection promotes the synthesis of IgG4 antibodies. In this study, we propose the hypothesis that IgG4 antibodies produced by B cells in response to infection by SARS-CoV-2 generate immunological tolerance, which prevents its elimination and leads to persistent and chronic infection. In summary, we believe that this constitutes another immune evasion mechanism that bears striking similarities to that developed by cancer cells to evade immune surveillance.
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Affiliation(s)
- Alberto Rubio-Casillas
- Autlan Regional Hospital, Health Secretariat, Autlan 48900, Jalisco, Mexico
- Biology Laboratory, Autlan Regional Preparatory School, University of Guadalajara, Autlan 48900, Jalisco, Mexico
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia;
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg El-Arab 21934, Alexandria, Egypt
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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Shoraka S, Samarasinghe AE, Ghaemi A, Mohebbi SR. Host mitochondria: more than an organelle in SARS-CoV-2 infection. Front Cell Infect Microbiol 2023; 13:1228275. [PMID: 37692170 PMCID: PMC10485703 DOI: 10.3389/fcimb.2023.1228275] [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: 05/24/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
Since December 2019, the world has been facing viral pandemic called COVID-19 (Coronavirus disease 2019) caused by a new beta-coronavirus named severe acute respiratory syndrome coronavirus-2, or SARS-CoV-2. COVID-19 patients may present with a wide range of symptoms, from asymptomatic to requiring intensive care support. The severe form of COVID-19 is often marked by an altered immune response and cytokine storm. Advanced age, age-related and underlying diseases, including metabolic syndromes, appear to contribute to increased COVID-19 severity and mortality suggesting a role for mitochondria in disease pathogenesis. Furthermore, since the immune system is associated with mitochondria and its damage-related molecular patterns (mtDAMPs), the host mitochondrial system may play an important role during viral infections. Viruses have evolved to modulate the immune system and mitochondrial function for survival and proliferation, which in turn could lead to cellular stress and contribute to disease progression. Recent studies have focused on the possible roles of mitochondria in SARS-CoV-2 infection. It has been suggested that mitochondrial hijacking by SARS-CoV-2 could be a key factor in COVID-19 pathogenesis. In this review, we discuss the roles of mitochondria in viral infections including SARS-CoV-2 infection based on past and present knowledge. Paying attention to the role of mitochondria in SARS-CoV-2 infection will help to better understand the pathophysiology of COVID-19 and to achieve effective methods of prevention, diagnosis, and treatment.
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Affiliation(s)
- Shahrzad Shoraka
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Amali E. Samarasinghe
- Division of Pulmonology, Allergy and Immunology, Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Children’s Foundation Research Institute, Memphis, TN, United States
| | - Amir Ghaemi
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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López-Ayllón BD, de Lucas-Rius A, Mendoza-García L, García-García T, Fernández-Rodríguez R, Suárez-Cárdenas JM, Santos FM, Corrales F, Redondo N, Pedrucci F, Zaldívar-López S, Jiménez-Marín Á, Garrido JJ, Montoya M. SARS-CoV-2 accessory proteins involvement in inflammatory and profibrotic processes through IL11 signaling. Front Immunol 2023; 14:1220306. [PMID: 37545510 PMCID: PMC10399023 DOI: 10.3389/fimmu.2023.1220306] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/23/2023] [Indexed: 08/08/2023] Open
Abstract
SARS-CoV-2, the cause of the COVID-19 pandemic, possesses eleven accessory proteins encoded in its genome. Their roles during infection are still not completely understood. In this study, transcriptomics analysis revealed that both WNT5A and IL11 were significantly up-regulated in A549 cells expressing individual accessory proteins ORF6, ORF8, ORF9b or ORF9c from SARS-CoV-2 (Wuhan-Hu-1 isolate). IL11 is a member of the IL6 family of cytokines. IL11 signaling-related genes were also differentially expressed. Bioinformatics analysis disclosed that both WNT5A and IL11 were involved in pulmonary fibrosis idiopathic disease and functional assays confirmed their association with profibrotic cell responses. Subsequently, data comparison with lung cell lines infected with SARS-CoV-2 or lung biopsies from patients with COVID-19, evidenced altered profibrotic gene expression that matched those obtained in this study. Our results show ORF6, ORF8, ORF9b and ORF9c involvement in inflammatory and profibrotic responses. Thus, these accessory proteins could be targeted by new therapies against COVID-19 disease.
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Affiliation(s)
- Blanca D. López-Ayllón
- Molecular Biomedicine Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Ana de Lucas-Rius
- Molecular Biomedicine Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Laura Mendoza-García
- Molecular Biomedicine Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Tránsito García-García
- Department of Genetics, Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Raúl Fernández-Rodríguez
- Department of Genetics, Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - José M. Suárez-Cárdenas
- Department of Genetics, Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Fátima Milhano Santos
- Functional Proteomics Laboratory, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Natalia Redondo
- Molecular Biomedicine Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
- Unit of Infectious Diseases, University Hospital ‘12 de Octubre’, Institute for Health Research Hospital ‘12 de Octubre’ (imas12), Madrid, Spain
- Centre for Biomedical Research Network on Infectious Diseases (CIBERINFEC), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Federica Pedrucci
- Molecular Biomedicine Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Sara Zaldívar-López
- Department of Genetics, Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Ángeles Jiménez-Marín
- Department of Genetics, Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Juan J. Garrido
- Department of Genetics, Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - María Montoya
- Molecular Biomedicine Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
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Zhou T, Gilliam NJ, Li S, Spandau S, Osborn RM, Connor S, Anderson CS, Mariani TJ, Thakar J, Dewhurst S, Mathews DH, Huang L, Sun Y. Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection. mBio 2023; 14:e0025023. [PMID: 37074178 PMCID: PMC10294654 DOI: 10.1128/mbio.00250-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/28/2023] [Indexed: 04/20/2023] Open
Abstract
Defective viral genomes (DVGs) have been identified in many RNA viruses as a major factor influencing antiviral immune response and viral pathogenesis. However, the generation and function of DVGs in SARS-CoV-2 infection are less known. In this study, we elucidated DVG generation in SARS-CoV-2 and its relationship with host antiviral immune response. We observed DVGs ubiquitously from transcriptome sequencing (RNA-seq) data sets of in vitro infections and autopsy lung tissues of COVID-19 patients. Four genomic hot spots were identified for DVG recombination, and RNA secondary structures were suggested to mediate DVG formation. Functionally, bulk and single-cell RNA-seq analysis indicated the interferon (IFN) stimulation of SARS-CoV-2 DVGs. We further applied our criteria to the next-generation sequencing (NGS) data set from a published cohort study and observed a significantly higher amount and frequency of DVG in symptomatic patients than those in asymptomatic patients. Finally, we observed exceptionally diverse DVG populations in one immunosuppressive patient up to 140 days after the first positive test of COVID-19, suggesting for the first time an association between DVGs and persistent viral infections in SARS-CoV-2. Together, our findings strongly suggest a critical role of DVGs in modulating host IFN responses and symptom development, calling for further inquiry into the mechanisms of DVG generation and into how DVGs modulate host responses and infection outcome during SARS-CoV-2 infection. IMPORTANCE Defective viral genomes (DVGs) are generated ubiquitously in many RNA viruses, including SARS-CoV-2. Their interference activity to full-length viruses and IFN stimulation provide the potential for them to be used in novel antiviral therapies and vaccine development. SARS-CoV-2 DVGs are generated through the recombination of two discontinuous genomic fragments by viral polymerase complex, and this recombination is also one of the major mechanisms for the emergence of new coronaviruses. Focusing on the generation and function of SARS-CoV-2 DVGs, these studies identify new hot spots for nonhomologous recombination and strongly suggest that the secondary structures within viral genomes mediate the recombination. Furthermore, these studies provide the first evidence for IFN stimulation activity of de novo DVGs during natural SARS-CoV-2 infection. These findings set up the foundation for further mechanism studies of SARS-CoV-2 recombination and provide evidence to harness the immunostimulatory potential of DVGs in the development of a vaccine and antivirals for SARS-CoV-2.
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Affiliation(s)
- Terry Zhou
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Nora J. Gilliam
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Medical Scientist Training Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Translational Biomedical Sciences PhD Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Sizhen Li
- School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, Oregon, USA
| | - Simone Spandau
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Raven M. Osborn
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Translational Biomedical Sciences PhD Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Sarah Connor
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Christopher S. Anderson
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Thomas J. Mariani
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Juilee Thakar
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Stephen Dewhurst
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - David H. Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Liang Huang
- School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, Oregon, USA
| | - Yan Sun
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
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Mozzi A, Oldani M, Forcella ME, Vantaggiato C, Cappelletti G, Pontremoli C, Valenti F, Forni D, Saresella M, Biasin M, Sironi M, Fusi P, Cagliani R. SARS-CoV-2 ORF3c impairs mitochondrial respiratory metabolism, oxidative stress, and autophagic flux. iScience 2023; 26:107118. [PMID: 37361873 PMCID: PMC10265927 DOI: 10.1016/j.isci.2023.107118] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/08/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023] Open
Abstract
Coronaviruses encode a variable number of accessory proteins that are involved in host-virus interaction, suppression of immune responses, or immune evasion. SARS-CoV-2 encodes at least twelve accessory proteins, whose roles during infection have been studied. Nevertheless, the role of the ORF3c accessory protein, an alternative open reading frame of ORF3a, has remained elusive. Herein, we show that the ORF3c protein has a mitochondrial localization and alters mitochondrial metabolism, inducing a shift from glucose to fatty acids oxidation and enhanced oxidative phosphorylation. These effects result in increased ROS production and block of the autophagic flux. In particular, ORF3c affects lysosomal acidification, blocking the normal autophagic degradation process and leading to autolysosome accumulation. We also observed different effect on autophagy for SARS-CoV-2 and batCoV RaTG13 ORF3c proteins; the 36R and 40K sites are necessary and sufficient to determine these effects.
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Affiliation(s)
- Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, 23842, Italy
| | - Monica Oldani
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, 20126, Italy
| | - Matilde E Forcella
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, 20126, Italy
| | - Chiara Vantaggiato
- Scientific Institute IRCCS E. MEDEA, Laboratory of Molecular Biology, Bosisio Parini, 23842, Italy
| | - Gioia Cappelletti
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, 20157, Italy
| | - Chiara Pontremoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, 23842, Italy
| | - Francesca Valenti
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, 23842, Italy
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, 23842, Italy
| | - Marina Saresella
- Don C. Gnocchi Foundation ONLUS, IRCCS, Laboratory of Molecular Medicine and Biotechnology, Milan, 20148, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, 20157, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, 23842, Italy
| | - Paola Fusi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, 20126, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, 23842, Italy
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Zhao M, Zhang M, Yang Z, Zhou Z, Huang J, Zhao B. Role of E3 ubiquitin ligases and deubiquitinating enzymes in SARS-CoV-2 infection. Front Cell Infect Microbiol 2023; 13:1217383. [PMID: 37360529 PMCID: PMC10288995 DOI: 10.3389/fcimb.2023.1217383] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
Ever since its emergence in 2019, COVID-19 has rapidly disseminated worldwide, engendering a pervasive pandemic that has profoundly impacted healthcare systems and the socio-economic milieu. A plethora of studies has been conducted targeting its pathogenic virus, SARS-CoV-2, to find ways to combat COVID-19. The ubiquitin-proteasome system (UPS) is widely recognized as a crucial mechanism that regulates human biological activities by maintaining protein homeostasis. Within the UPS, the ubiquitination and deubiquitination, two reversible modifications, of substrate proteins have been extensively studied and implicated in the pathogenesis of SARS-CoV-2. The regulation of E3 ubiquitin ligases and DUBs(Deubiquitinating enzymes), which are key enzymes involved in the two modification processes, determines the fate of substrate proteins. Proteins associated with the pathogenesis of SARS-CoV-2 may be retained, degraded, or even activated, thus affecting the ultimate outcome of the confrontation between SARS-CoV-2 and the host. In other words, the clash between SARS-CoV-2 and the host can be viewed as a battle for dominance over E3 ubiquitin ligases and DUBs, from the standpoint of ubiquitin modification regulation. This review primarily aims to clarify the mechanisms by which the virus utilizes host E3 ubiquitin ligases and DUBs, along with its own viral proteins that have similar enzyme activities, to facilitate invasion, replication, escape, and inflammation. We believe that gaining a better understanding of the role of E3 ubiquitin ligases and DUBs in COVID-19 can offer novel and valuable insights for developing antiviral therapies.
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Affiliation(s)
- Mingjiu Zhao
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Mengdi Zhang
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhou Yang
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jiaqi Huang
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Xiangya School of Public Health, Central South University, Changsha, China
| | - Bin Zhao
- National Clinical Research Center for Metabolic Diseases, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Furong Laboratory, Central South University, Changsha, China
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50
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Bhowal C, Ghosh S, Ghatak D, De R. Pathophysiological involvement of host mitochondria in SARS-CoV-2 infection that causes COVID-19: a comprehensive evidential insight. Mol Cell Biochem 2023; 478:1325-1343. [PMID: 36308668 PMCID: PMC9617539 DOI: 10.1007/s11010-022-04593-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/13/2022] [Indexed: 10/31/2022]
Abstract
SARS-CoV-2 is a positive-strand RNA virus that infects humans through the nasopharyngeal and oral route causing COVID-19. Scientists left no stone unturned to explore a targetable key player in COVID-19 pathogenesis against which therapeutic interventions can be initiated. This article has attempted to review, coordinate and accumulate the most recent observations in support of the hypothesis predicting the altered state of mitochondria concerning mitochondrial redox homeostasis, inflammatory regulations, morphology, bioenergetics and antiviral signalling in SARS-CoV-2 infection. Mitochondria is extremely susceptible to physiological as well as pathological stimuli, including viral infections. Recent studies suggest that SARS-CoV-2 pathogeneses alter mitochondrial integrity, in turn mitochondria modulate cellular response against the infection. SARS-CoV-2 M protein inhibited mitochondrial antiviral signalling (MAVS) protein aggregation in turn hinders innate antiviral response. Viral open reading frames (ORFs) also play an instrumental role in altering mitochondrial regulation of immune response. Notably, ORF-9b and ORF-6 impair MAVS activation. In aged persons, the NLRP3 inflammasome is over-activated due to impaired mitochondrial function, increased mitochondrial reactive oxygen species (mtROS), and/or circulating free mitochondrial DNA, resulting in a hyper-response of classically activated macrophages. This article also tries to understand how mitochondrial fission-fusion dynamics is affected by the virus. This review comprehends the overall mitochondrial attribute in pathogenesis as well as prognosis in patients infected with COVID-19 taking into account pertinent in vitro, pre-clinical and clinical data encompassing subjects with a broad range of severity and morbidity. This endeavour may help in exploring novel non-canonical therapeutic strategies to COVID-19 disease and associated complications.
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Affiliation(s)
- Chandan Bhowal
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India
| | - Sayak Ghosh
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India
| | - Debapriya Ghatak
- Indian Association for the Cultivation of Science, Jadavpur, 700032, Kolkata, India
| | - Rudranil De
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India.
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