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Zhu J, Liu G, Sayyad Z, Goins CM, Stauffer SR, Gack MU. ISGylation of the SARS-CoV-2 N protein by HERC5 impedes N oligomerization and thereby viral RNA synthesis. J Virol 2024:e0086924. [PMID: 39194248 DOI: 10.1128/jvi.00869-24] [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: 05/17/2024] [Accepted: 07/20/2024] [Indexed: 08/29/2024] Open
Abstract
Interferon (IFN)-stimulated gene 15 (ISG15), a ubiquitin-like protein, is covalently conjugated to host immune proteins such as MDA5 and IRF3 in a process called ISGylation, thereby promoting type I IFN induction to limit the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, whether SARS-CoV-2 proteins can be directly targeted for ISGylation remains elusive. In this study, we identified the nucleocapsid (N) protein of SARS-CoV-2 as a major substrate of ISGylation catalyzed by the host E3 ligase HERC5; however, N ISGylation is readily removed through deISGylation by the papain-like protease (PLpro) activity of NSP3. Mass spectrometry analysis identified that the N protein undergoes ISGylation at four lysine residues (K266, K355, K387, and K388), and mutational analysis of these sites in the context of a SARS-CoV-2 replicon (N-4KR) abolished N ISGylation and alleviated ISGylation-mediated inhibition of viral RNA synthesis. Furthermore, our results indicated that HERC5 targets preferentially phosphorylated N protein for ISGylation to regulate its oligomeric assembly. These findings reveal a novel mechanism by which the host ISGylation machinery directly targets SARS-CoV-2 proteins to restrict viral replication and illuminate how an intricate interplay of host (HERC5) and viral (PLpro) enzymes coordinates viral protein ISGylation and thereby regulates virus replication.IMPORTANCEThe role of protein ISGylation in regulating host cellular processes has been studied extensively; however, how ISG15 conjugation influences the activity of viral proteins, particularly coronaviral proteins, is largely unknown. Our study uncovered that the nucleocapsid (N) protein of SARS-CoV-2 is ISGylated by the HERC5 ISGylation machinery and that this modification impedes the functional assembly of N into oligomers ultimately inhibiting viral RNA synthesis. This antiviral restriction mechanism is antagonized by the PLpro deISGylation activity of SARS-CoV-2 NSP3. This study deepens our understanding of SARS-CoV-2 protein regulation by posttranslational modifications and may open new avenues for designing antiviral strategies for COVID-19.
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Affiliation(s)
- Junji Zhu
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, Florida, USA
| | - GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, Florida, USA
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, Canada
| | - Zuberwasim Sayyad
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, Florida, USA
| | - Christopher M Goins
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Shaun R Stauffer
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, Florida, USA
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2
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Miller LG, Chiok K, Mariasoosai C, Mohanty I, Pandit S, Deol P, Mehari L, Teng MN, Haas AL, Natesan S, Miura TA, Bose S. Extracellular ISG15 triggers ISGylation via a type-I interferon independent non-canonical mechanism to regulate host response during virus infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602290. [PMID: 39026703 PMCID: PMC11257485 DOI: 10.1101/2024.07.05.602290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Type-I interferons (IFN) induce cellular proteins with antiviral activity. One such protein is Interferon Stimulated Gene 15 (ISG15). ISG15 is conjugated to proteins during ISGylation to confer antiviral activity and regulate cellular activities associated with inflammatory and neurodegenerative diseases and cancer. Apart from ISGylation, unconjugated free ISG15 is also released from cells during various conditions, including virus infection. The role of extracellular ISG15 during virus infection was unknown. We show that extracellular ISG15 triggers ISGylation and acts as a soluble antiviral factor to restrict virus infection via an IFN-independent mechanism. Specifically, extracellular ISG15 acts post-translationally to markedly enhance the stability of basal intracellular ISG15 protein levels to support ISGylation. Furthermore, extracellular ISG15 interacts with cell surface integrin (α5β1 integrins) molecules via its RGD-like motif to activate the integrin-FAK (Focal Adhesion Kinase) pathway resulting in IFN-independent ISGylation. Thus, our studies have identified extracellular ISG15 protein as a new soluble antiviral factor that confers IFN-independent non-canonical ISGylation via the integrin-FAK pathway by post-translational stabilization of intracellular ISG15 protein.
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3
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Rhamadianti AF, Abe T, Tanaka T, Ono C, Katayama H, Makino Y, Deng L, Matsui C, Moriishi K, Shima F, Matsuura Y, Shoji I. SARS-CoV-2 papain-like protease inhibits ISGylation of the viral nucleocapsid protein to evade host anti-viral immunity. J Virol 2024:e0085524. [PMID: 39120134 DOI: 10.1128/jvi.00855-24] [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: 05/15/2024] [Accepted: 06/29/2024] [Indexed: 08/10/2024] Open
Abstract
A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes mild-to-severe respiratory symptoms, including acute respiratory distress. Despite remarkable efforts to investigate the virological and pathological impacts of SARS-CoV-2, many of the characteristics of SARS-CoV-2 infection still remain unknown. The interferon-inducible ubiquitin-like protein ISG15 is covalently conjugated to several viral proteins to suppress their functions. It was reported that SARS-CoV-2 utilizes its papain-like protease (PLpro) to impede ISG15 conjugation, ISGylation. However, the role of ISGylation in SARS-CoV-2 infection remains unclear. We aimed to elucidate the role of ISGylation in SARS-CoV-2 replication. We observed that the SARS-CoV-2 nucleocapsid protein is a target protein for the HERC5 E3 ligase-mediated ISGylation in cultured cells. Site-directed mutagenesis reveals that the residue K374 within the C-terminal spacer B-N3 (SB/N3) domain is required for nucleocapsid-ISGylation, alongside conserved lysine residue in MERS-CoV (K372) and SARS-CoV (K375). We also observed that the nucleocapsid-ISGylation results in the disruption of nucleocapsid oligomerization, thereby inhibiting viral replication. Knockdown of ISG15 mRNA enhanced SARS-CoV-2 replication in the SARS-CoV-2 reporter replicon cells, while exogenous expression of ISGylation components partially hampered SARS-CoV-2 replication. Taken together, these results suggest that SARS-CoV-2 PLpro inhibits ISGylation of the nucleocapsid protein to promote viral replication by evading ISGylation-mediated disruption of the nucleocapsid oligomerization.IMPORTANCEISG15 is an interferon-inducible ubiquitin-like protein that is covalently conjugated to the viral protein via specific Lys residues and suppresses viral functions and viral propagation in many viruses. However, the role of ISGylation in SARS-CoV-2 infection remains largely unclear. Here, we demonstrated that the SARS-CoV-2 nucleocapsid protein is a target protein for the HERC5 E3 ligase-mediated ISGylation. We also found that the residue K374 within the C-terminal spacer B-N3 (SB/N3) domain is required for nucleocapsid-ISGylation. We obtained evidence suggesting that nucleocapsid-ISGylation results in the disruption of nucleocapsid-oligomerization, thereby suppressing SARS-CoV-2 replication. We discovered that SARS-CoV-2 papain-like protease inhibits ISG15 conjugation of nucleocapsid protein via its de-conjugating enzyme activity. The present study may contribute to gaining new insight into the roles of ISGylation-mediated anti-viral function in SARS-CoV-2 infection and may lead to the development of more potent and selective inhibitors targeted to SARS-CoV-2 nucleocapsid protein.
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Affiliation(s)
- Aulia Fitri Rhamadianti
- Division of Infectious Disease Control, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
- Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Takayuki Abe
- Division of Infectious Disease Control, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
- Department of Virology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tomohisa Tanaka
- Department of Microbiology, Faculty of Medicine, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Yamanashi, Japan
- Division of Hepatitis Virology, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
| | - Chikako Ono
- Center for Infectious Diseases Education and Research (CiDER), Osaka University, Osaka, Japan
| | - Hisashi Katayama
- Division of Infectious Disease Control, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yoshiteru Makino
- Drug Discovery Science, Division of Advanced Medical Science, Department of Science, Technology and Innovation, Graduate School of Science, Kobe University, Kobe, Japan
- Center for Cell Signaling and Medical Innovation, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Lin Deng
- Division of Infectious Disease Control, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Chieko Matsui
- Division of Infectious Disease Control, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kohji Moriishi
- Department of Microbiology, Faculty of Medicine, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Yamanashi, Japan
- Division of Hepatitis Virology, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
| | - Fumi Shima
- Drug Discovery Science, Division of Advanced Medical Science, Department of Science, Technology and Innovation, Graduate School of Science, Kobe University, Kobe, Japan
| | - Yoshiharu Matsuura
- Center for Infectious Diseases Education and Research (CiDER), Osaka University, Osaka, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
| | - Ikuo Shoji
- Division of Infectious Disease Control, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
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Liu X, Zheng M, Zhang H, Feng B, Li J, Zhang Y, Zhang J, Zhao N, Li C, Song N, Song B, Yang D, Chen J, Qi A, Zhao L, Luo C, Zang Y, Liu H, Li J, Zhang B, Zhou Y, Zheng J. Characterization and noncovalent inhibition of the K63-deubiquitinase activity of SARS-cov-2 PLpro. Antiviral Res 2024; 228:105944. [PMID: 38914283 DOI: 10.1016/j.antiviral.2024.105944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 06/21/2024] [Accepted: 06/22/2024] [Indexed: 06/26/2024]
Abstract
SARS-CoV-2 papain-like protease (PLpro) could facilitate viral replication and host immune evasion by respectively hydrolyzing viral polyprotein and host ubiquitin conjugates, thereby rendering itself as an important antiviral target. Yet few noncovalent PLpro inhibitors of SARS-CoV-2 have been reported with improved directed towards pathogenic deubiquitinating activities inhibition. Herein, we report that coronavirus PLpro proteases have distinctive substrate bias and are conserved to deubiquitylate K63-linked polyubiquitination, thereby attenuating host type I interferon response. We identify a noncovalent compound specifically optimized towards halting the K63-deubiquitinase activity of SARS-CoV-2 PLpro, but not other coronavirus (CoV) counterparts or host deubiquitinase. Contrasting with GRL-0617, a SARS-CoV-1 PLpro inhibitor, SIMM-036 is 50-fold and 7-fold (half maximal inhibitory concentration (IC50)) more potent to inhibit viral replication during SARS-CoV-2 infection and restore the host interferon-β (IFN-β) response in human angiotensin-converting enzyme 2 (hACE2)-HeLa cells, respectively. Structure-activity relationship (SAR) analysis further reveals the importance of BL2 groove of PLpro, which could determine the selectivity of K63-deubiquitinase activity of the enzyme.
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Affiliation(s)
- Xin Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Miao Zheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Hongqing Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Bo Feng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jiaqi Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yanan Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Ji Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Na Zhao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Chaoqiang Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Ning Song
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Bin Song
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Dongyuan Yang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Jin Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ao Qi
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linxiang Zhao
- Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Cheng Luo
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yi Zang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Hong Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jia Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang, 110016, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yu Zhou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang, 110016, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China
| | - Jie Zheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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5
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Zhang W, Xiao L, Li D, Hu Y, Yu W. New Strategies for Responding to SARS-CoV-2: The Present and Future of Dual-Target Drugs. J Med Chem 2024; 67:11522-11542. [PMID: 38967785 DOI: 10.1021/acs.jmedchem.4c00384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
The 2019 coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of deaths, posing a serious threat to public health and safety. Rapid mutations of SARS-CoV-2 and complex interactions among multiple targets during infection pose a risk of expiry for small molecule inhibitors. This suggests that the traditional concept of "one bug, one drug" could be ineffective in dealing with the coronavirus. The dual-target drug strategy is expected to be the key to ending coronavirus infections. However, the lack of design method and improper combination of dual-targets poses obstacle to the discovery of new dual-target drugs. In this Perspective, we summarized the profiles concerning drug design methods, structure-activity relationships, and pharmacological parameters of dual-target drugs for the treatment of COVID-19. Importantly, we underscored how target combination and rational drug design illuminate the development of dual-target drugs for SARS-CoV-2.
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Affiliation(s)
- Wenyi Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Lecheng Xiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Dianyang Li
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Hu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Wenying Yu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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Jeremiah SS, Das P, Venkatesan M, Albinzayed R, Ahmed A, Stevenson NJ, Corbally M, Alqahtani M, Al-Wedaie F, Farid E, Hejres S. Humoral and Innate Immunological Profile of Paediatric Recipients of Pfizer-BioNTech BNT162b2 mRNA Vaccine. Microorganisms 2024; 12:1389. [PMID: 39065157 PMCID: PMC11278604 DOI: 10.3390/microorganisms12071389] [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: 06/02/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
The Pfizer-BioNTech vaccine was one of the essential tools in curtailing the COVID-19 pandemic. Unlike conventional vaccines, this newly approved mRNA vaccine is taken up by cells, which leads to the synthesis of the specific viral Spike antigen. The vaccine was initially introduced for adults, and the immunological profile of adult recipients is well-characterized. The vaccine was approved for paediatric use much later after its efficacy and safety had been confirmed in children. However, the complete picture of how the paediatric immune system in children reacts to the vaccine is not well documented. Therefore, in order to better understand the immune response in children, we analysed the humoral response, immune cell count, and interferon signalling in paediatric vaccine recipients ranging between 5 and 17 years of age. Our findings suggest that the paediatric recipients elicit a robust humoral response that is sustained for at least three months. We also found that the vaccine triggered a transient lymphocytopenia similar to that observed during viral infection. Interestingly, we also found that the vaccine may sensitise the interferon signalling pathway, priming the cells to mount a potent response when exposed to interferons during a subsequent infection. The study offers new insights into the workings of the paediatric immune system and innate immunity, thereby opening the doors for further research in this field.
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Affiliation(s)
- Sundararaj Stanleyraj Jeremiah
- School of Postgraduate Studies and Research, Royal College of Surgeons in Ireland—Medical University of Bahrain, Building 2441, Road 2835, Busaiteen 228, Bahrain; (P.D.)
| | - Priya Das
- School of Postgraduate Studies and Research, Royal College of Surgeons in Ireland—Medical University of Bahrain, Building 2441, Road 2835, Busaiteen 228, Bahrain; (P.D.)
| | - Manu Venkatesan
- Hematology and Hematopathology Laboratory, King Hamad University Hospital, Busaiteen 228, Bahrain; (M.V.); (S.H.)
| | - Reem Albinzayed
- Medical Internship, King Hamad University Hospital, Busaiteen 228, Bahrain; (R.A.); (A.A.)
| | - Aysha Ahmed
- Medical Internship, King Hamad University Hospital, Busaiteen 228, Bahrain; (R.A.); (A.A.)
| | - Nigel John Stevenson
- School of Postgraduate Studies and Research, Royal College of Surgeons in Ireland—Medical University of Bahrain, Building 2441, Road 2835, Busaiteen 228, Bahrain; (P.D.)
| | - Martin Corbally
- Department of Surgery, Royal College of Surgeons in Ireland—Medical University of Bahrain, Busaiteen 228, Bahrain;
| | - Manaf Alqahtani
- Department of Microbiology, Royal College of Surgeons in Ireland—Medical University of Bahrain, Busaiteen 228, Bahrain;
| | - Fatima Al-Wedaie
- Department of Pathology, Salmaniya Medical Complex, Government Hospital, Manama 329, Bahrain; (F.A.-W.); (E.F.)
| | - Eman Farid
- Department of Pathology, Salmaniya Medical Complex, Government Hospital, Manama 329, Bahrain; (F.A.-W.); (E.F.)
- Department of Microbiology, Immunology and Infectious Diseases, College of Medicine, Arabian Gulf University, Manama 329, Bahrain
| | - Suha Hejres
- Hematology and Hematopathology Laboratory, King Hamad University Hospital, Busaiteen 228, Bahrain; (M.V.); (S.H.)
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7
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Bhuiyan SA, Xu M, Yang L, Semizoglou E, Bhatia P, Pantaleo KI, Tochitsky I, Jain A, Erdogan B, Blair S, Cat V, Mwirigi JM, Sankaranarayanan I, Tavares-Ferreira D, Green U, McIlvried LA, Copits BA, Bertels Z, Del Rosario JS, Widman AJ, Slivicki RA, Yi J, Sharif-Naeini R, Woolf CJ, Lennerz JK, Whited JL, Price TJ, Robert W Gereau Iv, Renthal W. Harmonized cross-species cell atlases of trigeminal and dorsal root ganglia. SCIENCE ADVANCES 2024; 10:eadj9173. [PMID: 38905344 DOI: 10.1126/sciadv.adj9173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 05/16/2024] [Indexed: 06/23/2024]
Abstract
Sensory neurons in the dorsal root ganglion (DRG) and trigeminal ganglion (TG) are specialized to detect and transduce diverse environmental stimuli to the central nervous system. Single-cell RNA sequencing has provided insights into the diversity of sensory ganglia cell types in rodents, nonhuman primates, and humans, but it remains difficult to compare cell types across studies and species. We thus constructed harmonized atlases of the DRG and TG that describe and facilitate comparison of 18 neuronal and 11 non-neuronal cell types across six species and 31 datasets. We then performed single-cell/nucleus RNA sequencing of DRG from both human and the highly regenerative axolotl and found that the harmonized atlas also improves cell type annotation, particularly of sparse neuronal subtypes. We observed that the transcriptomes of sensory neuron subtypes are broadly similar across vertebrates, but the expression of functionally important neuropeptides and channels can vary notably. The resources presented here can guide future studies in comparative transcriptomics, simplify cell-type nomenclature differences across studies, and help prioritize targets for future analgesic development.
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Affiliation(s)
- Shamsuddin A Bhuiyan
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Mengyi Xu
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Alan Edwards Center for Research on Pain and Department of Physiology, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Lite Yang
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Evangelia Semizoglou
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Parth Bhatia
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Katerina I Pantaleo
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ivan Tochitsky
- F.M. Kirby Neurobiology Center and Department of Neurobiology, Boston Children's Hospital and Harvard Medical School, 3 Blackfan Cir., Boston, MA 02115, USA
| | - Aakanksha Jain
- F.M. Kirby Neurobiology Center and Department of Neurobiology, Boston Children's Hospital and Harvard Medical School, 3 Blackfan Cir., Boston, MA 02115, USA
| | - Burcu Erdogan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Steven Blair
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Victor Cat
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Juliet M Mwirigi
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080, USA
| | - Ishwarya Sankaranarayanan
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080, USA
| | - Diana Tavares-Ferreira
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080, USA
| | - Ursula Green
- Department of Pathology, Center for Integrated Diagnostics, Massachussetts General Hospital and Havard Medical School, Boston, MA 02114, USA
| | - Lisa A McIlvried
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Bryan A Copits
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Zachariah Bertels
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - John S Del Rosario
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Allie J Widman
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Richard A Slivicki
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Jiwon Yi
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Reza Sharif-Naeini
- Alan Edwards Center for Research on Pain and Department of Physiology, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Clifford J Woolf
- F.M. Kirby Neurobiology Center and Department of Neurobiology, Boston Children's Hospital and Harvard Medical School, 3 Blackfan Cir., Boston, MA 02115, USA
| | - Jochen K Lennerz
- Department of Pathology, Center for Integrated Diagnostics, Massachussetts General Hospital and Havard Medical School, Boston, MA 02114, USA
| | - Jessica L Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Theodore J Price
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080, USA
| | - Robert W Gereau Iv
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - William Renthal
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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8
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Malireddi RKS, Sharma BR, Kanneganti TD. Innate Immunity in Protection and Pathogenesis During Coronavirus Infections and COVID-19. Annu Rev Immunol 2024; 42:615-645. [PMID: 38941608 PMCID: PMC11373870 DOI: 10.1146/annurev-immunol-083122-043545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
The COVID-19 pandemic was caused by the recently emerged β-coronavirus SARS-CoV-2. SARS-CoV-2 has had a catastrophic impact, resulting in nearly 7 million fatalities worldwide to date. The innate immune system is the first line of defense against infections, including the detection and response to SARS-CoV-2. Here, we discuss the innate immune mechanisms that sense coronaviruses, with a focus on SARS-CoV-2 infection and how these protective responses can become detrimental in severe cases of COVID-19, contributing to cytokine storm, inflammation, long-COVID, and other complications. We also highlight the complex cross talk among cytokines and the cellular components of the innate immune system, which can aid in viral clearance but also contribute to inflammatory cell death, cytokine storm, and organ damage in severe COVID-19 pathogenesis. Furthermore, we discuss how SARS-CoV-2 evades key protective innate immune mechanisms to enhance its virulence and pathogenicity, as well as how innate immunity can be therapeutically targeted as part of the vaccination and treatment strategy. Overall, we highlight how a comprehensive understanding of innate immune mechanisms has been crucial in the fight against SARS-CoV-2 infections and the development of novel host-directed immunotherapeutic strategies for various diseases.
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Affiliation(s)
- R K Subbarao Malireddi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
| | - Bhesh Raj Sharma
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
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9
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Qin Y, Wang M, Meng X, Wang M, Jiang H, Gao Y, Li J, Zhao C, Han C, Zhao W, Zheng X. ISGylation by HERCs facilitates STING activation. Cell Rep 2024; 43:114135. [PMID: 38652662 DOI: 10.1016/j.celrep.2024.114135] [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: 11/06/2023] [Revised: 02/28/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Optimal activation of stimulator of interferon genes (STING) protein is crucial for host defenses against pathogens and avoiding detrimental effects. Various post-translational modifications control STING activity. However, the function of interferon (IFN)-stimulated gene (ISG) 15 modification (ISGylation) in controlling STING stability and activation is unclear. Here, we show that the E3 ISGylation ligases HECT domain- and RCC1-like domain-containing proteins (HERCs; HERC5 in humans and HERC6 in mice) facilitate STING activation by mediating ISGylation of STING at K150, preventing its K48-linked ubiquitination and degradation. Concordantly, Herc6 deficiency suppresses herpes simplex virus 1 infection-induced type I IFN responses and facilitates viral replication both in vitro and in vivo. Notably, severe acute respiratory syndrome coronavirus 2 protein papain-like protease cleaves HERC5-mediated ISGylation of STING, suppressing host antiviral responses. These data identify a mechanism by which HERCs-mediated ISGylation controls STING stability and activation and uncover the correlations and interactions of ISGylation and ubiquitination during STING activation.
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Affiliation(s)
- Ying Qin
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Min Wang
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xintong Meng
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Mengge Wang
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Haojia Jiang
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yanjie Gao
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Jingxin Li
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Chunyuan Zhao
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Chaofeng Han
- Department of Histology and Embryology and Shanghai Key Laboratory of Cell Engineering, Naval Medical University, Shanghai, China
| | - Wei Zhao
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education and Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China; Department of Histology and Embryology and Shanghai Key Laboratory of Cell Engineering, Naval Medical University, Shanghai, China.
| | - Xuexing Zheng
- Department of Virology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
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10
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Rosas-García J, Padilla-Zúñiga AJ, Ávila-Flores A, Gutiérrez-González LH, Mérida I, Santos-Mendoza T. Modeling of host PDZ-dependent interactions with SARS-CoV-2 Envelope protein and changes in PDZ proteins expression in macrophages and dendritic cells. J Leukoc Biol 2024:qiae118. [PMID: 38748862 DOI: 10.1093/jleuko/qiae118] [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: 11/13/2023] [Revised: 04/16/2024] [Accepted: 05/01/2024] [Indexed: 07/10/2024] Open
Abstract
PDZ (PSD-95/Dlg/ZO-1) domain-containing proteins constitute a large family of scaffolds involved in a wide range of cellular tasks, and mainly studied in polarity functions. Diverse host PDZ proteins can be targeted by viral pathogens which express proteins containing PDZ-binding motifs (PDZbm). Previously, we have identified host PDZ-based interactions with the SARS-CoV-2 E protein (2E) in human monocytes. Here, we deepen the study of these interactions by docking and molecular dynamics analyses to identify the most favorable PDZ-PDZbm interaction of seven host PDZ proteins with the PDZbm of 2E. In addition, we analyzed changes in the expression of three of the PDZ proteins identified as 2E interactors in monocytes (syntenin, ZO-2, and IL-16), in human monocyte-derived macrophages (MΦ) and in dendritic cells (DCs) upon stimulation. Our results suggest that these PDZ proteins may have important functions in professional antigen-presenting cells (APCs), and their targeting by the PDZbm of 2E, a central virulence determinant of SARS-CoV-2, support the hypothesis that such PDZ-dependent interaction in immune cells may constitute a viral evasion mechanism. Inhibitor design based on the PDZbm of 2E in the development of drugs against a variety of diseases is discussed.
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Affiliation(s)
- Jorge Rosas-García
- Laboratory of Transcriptomics and Molecular Immunology. Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | | | - Antonia Ávila-Flores
- Department of Immunology and Oncology, Spanish National Centre for Biotechnology. Madrid, Spain
| | - Luis Horacio Gutiérrez-González
- Laboratory of Transcriptomics and Molecular Immunology. Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Isabel Mérida
- Department of Immunology and Oncology, Spanish National Centre for Biotechnology. Madrid, Spain
| | - Teresa Santos-Mendoza
- Laboratory of Transcriptomics and Molecular Immunology. Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
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11
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Taefehshokr N, Lac A, Vrieze AM, Dickson BH, Guo PN, Jung C, Blythe EN, Fink C, Aktar A, Dikeakos JD, Dekaban GA, Heit B. SARS-CoV-2 NSP5 antagonizes MHC II expression by subverting histone deacetylase 2. J Cell Sci 2024; 137:jcs262172. [PMID: 38682259 PMCID: PMC11166459 DOI: 10.1242/jcs.262172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024] Open
Abstract
SARS-CoV-2 interferes with antigen presentation by downregulating major histocompatibility complex (MHC) II on antigen-presenting cells, but the mechanism mediating this process is unelucidated. Herein, analysis of protein and gene expression in human antigen-presenting cells reveals that MHC II is downregulated by the SARS-CoV-2 main protease, NSP5. This suppression of MHC II expression occurs via decreased expression of the MHC II regulatory protein CIITA. CIITA downregulation is independent of the proteolytic activity of NSP5, and rather, NSP5 delivers HDAC2 to the transcription factor IRF3 at an IRF-binding site within the CIITA promoter. Here, HDAC2 deacetylates and inactivates the CIITA promoter. This loss of CIITA expression prevents further expression of MHC II, with this suppression alleviated by ectopic expression of CIITA or knockdown of HDAC2. These results identify a mechanism by which SARS-CoV-2 limits MHC II expression, thereby delaying or weakening the subsequent adaptive immune response.
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Affiliation(s)
- Nima Taefehshokr
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Alex Lac
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Angela M. Vrieze
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Brandon H. Dickson
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Peter N. Guo
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Catherine Jung
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Eoin N. Blythe
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Corby Fink
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Amena Aktar
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
| | - Jimmy D. Dikeakos
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Gregory A. Dekaban
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
| | - Bryan Heit
- Department of Microbiology and Immunology, and the Western Infection, Immunity and Inflammation Centre, The University of Western Ontario, London, Ontario, CanadaN6A 5C1
- Robarts Research Institute, London, Ontario, CanadaN6A 3K7
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12
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Jové V, Wheeler H, Lee CW, Healy DR, Levine K, Ralph EC, Yamaguchi M, Jiang ZK, Cabral E, Xu Y, Stock J, Yang B, Giddabasappa A, Loria P, Casimiro-Garcia A, Kessler BM, Pinto-Fernández A, Frattini V, Wes PD, Wang F. Type I interferon regulation by USP18 is a key vulnerability in cancer. iScience 2024; 27:109593. [PMID: 38632987 PMCID: PMC11022047 DOI: 10.1016/j.isci.2024.109593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 01/12/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
Precise regulation of Type I interferon signaling is crucial for combating infection and cancer while avoiding autoimmunity. Type I interferon signaling is negatively regulated by USP18. USP18 cleaves ISG15, an interferon-induced ubiquitin-like modification, via its canonical catalytic function, and inhibits Type I interferon receptor activity through its scaffold role. USP18 loss-of-function dramatically impacts immune regulation, pathogen susceptibility, and tumor growth. However, prior studies have reached conflicting conclusions regarding the relative importance of catalytic versus scaffold function. Here, we develop biochemical and cellular methods to systematically define the physiological role of USP18. By comparing a patient-derived mutation impairing scaffold function (I60N) to a mutation disrupting catalytic activity (C64S), we demonstrate that scaffold function is critical for cancer cell vulnerability to Type I interferon. Surprisingly, we discovered that human USP18 exhibits minimal catalytic activity, in stark contrast to mouse USP18. These findings resolve human USP18's mechanism-of-action and enable USP18-targeted therapeutics.
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Affiliation(s)
- Veronica Jové
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Heather Wheeler
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | | | - David R. Healy
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Kymberly Levine
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Erik C. Ralph
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Masaya Yamaguchi
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | | | - Edward Cabral
- Comparative Medicine, Pfizer, La Jolla, CA 92121, USA
| | - Yingrong Xu
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Jeffrey Stock
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Bing Yang
- Comparative Medicine, Pfizer, La Jolla, CA 92121, USA
| | | | - Paula Loria
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | | | - Benedikt M. Kessler
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Adán Pinto-Fernández
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Véronique Frattini
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Paul D. Wes
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Feng Wang
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
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13
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O'Leary K, Zheng D. Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs. NPJ Syst Biol Appl 2024; 10:36. [PMID: 38580667 PMCID: PMC10997786 DOI: 10.1038/s41540-024-00364-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/27/2024] [Indexed: 04/07/2024] Open
Abstract
By profiling gene expression in individual cells, single-cell RNA-sequencing (scRNA-seq) can resolve cellular heterogeneity and cell-type gene expression dynamics. Its application to time-series samples can identify temporal gene programs active in different cell types, for example, immune cells' responses to viral infection. However, current scRNA-seq analysis has limitations. One is the low number of genes detected per cell. The second is insufficient replicates (often 1-2) due to high experimental cost. The third lies in the data analysis-treating individual cells as independent measurements leads to inflated statistics. To address these, we explore a new computational framework, specifically whether "metacells" constructed to maintain cellular heterogeneity within individual cell types (or clusters) can be used as "replicates" for increasing statistical rigor. Toward this, we applied SEACells to a time-series scRNA-seq dataset from peripheral blood mononuclear cells (PBMCs) after SARS-CoV-2 infection to construct metacells, and used them in maSigPro for quadratic regression to find significantly differentially expressed genes (DEGs) over time, followed by clustering expression velocity trends. We showed that such metacells retained greater expression variances and produced more biologically meaningful DEGs compared to either metacells generated randomly or from simple pseudobulk methods. More specifically, this approach correctly identified the known ISG15 interferon response program in almost all PBMC cell types and many DEGs enriched in the previously defined SARS-CoV-2 infection response pathway. It also uncovered additional and more cell type-specific temporal gene expression programs. Overall, our results demonstrate that the metacell-pseudoreplicate strategy could potentially overcome the limitation of 1-2 replicates.
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Affiliation(s)
- Kevin O'Leary
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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14
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Cao JB, Zhu ST, Huang XS, Wang XY, Wu ML, Li X, Liu FL, Chen L, Zheng YT, Wang JH. Mast cell degranulation-triggered by SARS-CoV-2 induces tracheal-bronchial epithelial inflammation and injury. Virol Sin 2024; 39:309-318. [PMID: 38458399 DOI: 10.1016/j.virs.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/27/2024] [Indexed: 03/10/2024] Open
Abstract
SARS-CoV-2 infection-induced hyper-inflammation is a key pathogenic factor of COVID-19. Our research, along with others', has demonstrated that mast cells (MCs) play a vital role in the initiation of hyper-inflammation caused by SARS-CoV-2. In previous study, we observed that SARS-CoV-2 infection induced the accumulation of MCs in the peri-bronchus and bronchioalveolar-duct junction in humanized mice. Additionally, we found that MC degranulation triggered by the spike protein resulted in inflammation in alveolar epithelial cells and capillary endothelial cells, leading to subsequent lung injury. The trachea and bronchus are the routes for SARS-CoV-2 transmission after virus inhalation, and inflammation in these regions could promote viral spread. MCs are widely distributed throughout the respiratory tract. Thus, in this study, we investigated the role of MCs and their degranulation in the development of inflammation in tracheal-bronchial epithelium. Histological analyses showed the accumulation and degranulation of MCs in the peri-trachea of humanized mice infected with SARS-CoV-2. MC degranulation caused lesions in trachea, and the formation of papillary hyperplasia was observed. Through transcriptome analysis in bronchial epithelial cells, we found that MC degranulation significantly altered multiple cellular signaling, particularly, leading to upregulated immune responses and inflammation. The administration of ebastine or loratadine effectively suppressed the induction of inflammatory factors in bronchial epithelial cells and alleviated tracheal injury in mice. Taken together, our findings confirm the essential role of MC degranulation in SARS-CoV-2-induced hyper-inflammation and the subsequent tissue lesions. Furthermore, our results support the use of ebastine or loratadine to inhibit SARS-CoV-2-triggered degranulation, thereby preventing tissue damage caused by hyper-inflammation.
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Affiliation(s)
- Jian-Bo Cao
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; School of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Shu-Tong Zhu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiao-Shan Huang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xing-Yuan Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Meng-Li Wu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xin Li
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Feng-Liang Liu
- Key Laboratory of Bioactive Peptides of Yunnan Province, Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ling Chen
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yong-Tang Zheng
- Key Laboratory of Bioactive Peptides of Yunnan Province, Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| | - Jian-Hua Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 101408, China.
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15
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Lin C, Kuffour EO, Li T, Gertzen CGW, Kaiser J, Luedde T, König R, Gohlke H, Münk C. The ISG15-Protease USP18 Is a Pleiotropic Enhancer of HIV-1 Replication. Viruses 2024; 16:485. [PMID: 38675828 PMCID: PMC11053637 DOI: 10.3390/v16040485] [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: 02/16/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
The innate immune response to viruses is formed in part by interferon (IFN)-induced restriction factors, including ISG15, p21, and SAMHD1. IFN production can be blocked by the ISG15-specific protease USP18. HIV-1 has evolved to circumvent host immune surveillance. This mechanism might involve USP18. In our recent studies, we demonstrate that HIV-1 infection induces USP18, which dramatically enhances HIV-1 replication by abrogating the antiviral function of p21. USP18 downregulates p21 by accumulating misfolded dominant negative p53, which inactivates wild-type p53 transactivation, leading to the upregulation of key enzymes involved in de novo dNTP biosynthesis pathways and inactivated SAMHD1. Despite the USP18-mediated increase in HIV-1 DNA in infected cells, it is intriguing to note that the cGAS-STING-mediated sensing of the viral DNA is abrogated. Indeed, the expression of USP18 or knockout of ISG15 inhibits the sensing of HIV-1. We demonstrate that STING is ISGylated at residues K224, K236, K289, K347, K338, and K370. The inhibition of STING K289-linked ISGylation suppresses its oligomerization and IFN induction. We propose that human USP18 is a novel factor that potentially contributes in multiple ways to HIV-1 replication.
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Affiliation(s)
- Chaohui Lin
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
| | - Edmund Osei Kuffour
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
| | - Taolan Li
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
| | - Christoph G. W. Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.G.W.G.); (J.K.); (H.G.)
| | - Jesko Kaiser
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.G.W.G.); (J.K.); (H.G.)
| | - Tom Luedde
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany;
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.G.W.G.); (J.K.); (H.G.)
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Carsten Münk
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
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16
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Kenney D, O’Connell AK, Tseng AE, Turcinovic J, Sheehan ML, Nitido AD, Montanaro P, Gertje HP, Ericsson M, Connor JH, Vrbanac V, Crossland NA, Harly C, Balazs AB, Douam F. Resolution of SARS-CoV-2 infection in human lung tissues is driven by extravascular CD163+ monocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.583965. [PMID: 38496468 PMCID: PMC10942442 DOI: 10.1101/2024.03.08.583965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The lung-resident immune mechanisms driving resolution of SARS-CoV-2 infection in humans remain elusive. Using mice co-engrafted with a genetically matched human immune system and fetal lung xenograft (fLX), we mapped the immunological events defining resolution of SARS-CoV-2 infection in human lung tissues. Viral infection is rapidly cleared from fLX following a peak of viral replication. Acute replication results in the emergence of cell subsets enriched in viral RNA, including extravascular inflammatory monocytes (iMO) and macrophage-like T-cells, which dissipate upon infection resolution. iMO display robust antiviral responses, are transcriptomically unique among myeloid lineages, and their emergence associates with the recruitment of circulating CD4+ monocytes. Consistently, mice depleted for human CD4+ cells but not CD3+ T-cells failed to robustly clear infectious viruses and displayed signatures of chronic infection. Our findings uncover the transient differentiation of extravascular iMO from CD4+ monocytes as a major hallmark of SARS-CoV-2 infection resolution and open avenues for unravelling viral and host adaptations defining persistently active SARS-CoV-2 infection.
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Affiliation(s)
- Devin Kenney
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Aoife K. O’Connell
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Anna E. Tseng
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Jacquelyn Turcinovic
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Meagan L. Sheehan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Adam D. Nitido
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Paige Montanaro
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Hans P. Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Maria Ericsson
- Electron Microscopy Core Facility, Harvard Medical School, Boston, MA, USA
| | - John H. Connor
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | | | - Nicholas A. Crossland
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Christelle Harly
- Université de Nantes, INSERM, CNRS, CRCINA, Nantes, France
- LabEx IGO ‘Immunotherapy, Graft, Oncology’, Nantes, France
- These authors contributed equally to the work
| | - Alejandro B. Balazs
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Florian Douam
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- These authors contributed equally to the work
- Lead contact
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17
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Zhou L, Liu R, Pathak H, Wang X, Jeong GH, Kumari P, Kumar M, Yin J. Ubiquitin Ligase Parkin Regulates the Stability of SARS-CoV-2 Main Protease and Suppresses Viral Replication. ACS Infect Dis 2024; 10:879-889. [PMID: 38386664 PMCID: PMC10928718 DOI: 10.1021/acsinfecdis.3c00418] [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: 08/17/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
The highly infectious coronavirus SARS-CoV-2 relies on the viral main protease (Mpro, also known as 3CLpro or Nsp5) to proteolytically process the polyproteins encoded by the viral genome for the release of functional units in the host cells to initiate viral replication. Mpro also interacts with host proteins of the innate immune pathways, such as IRF3 and STAT1, to suppress their activities and facilitate virus survival and proliferation. To identify the host mechanism for regulating Mpro, we screened various classes of E3 ubiquitin ligases and found that Parkin of the RING-between-RING family can induce the ubiquitination and degradation of Mpro in the cell. Furthermore, when the cells undergo mitophagy, the PINK1 kinase activates Parkin and enhances the ubiquitination of Mpro. We also found that elevated expression of Parkin in the cells significantly decreased the replication of SARS-CoV-2 virus. Interestingly, SARS-CoV-2 infection downregulates Parkin expression in the mouse lung tissues compared to healthy controls. These results suggest an antiviral role of Parkin as a ubiquitin ligase targeting Mpro and the potential for exploiting the virus-host interaction mediated by Parkin to treat SARS-CoV-2 infection.
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Affiliation(s)
- Li Zhou
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Ruochuan Liu
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Heather Pathak
- Department
of Biology and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Xiaoyu Wang
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Geon H. Jeong
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Pratima Kumari
- Department
of Biology and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Mukesh Kumar
- Department
of Biology and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Jun Yin
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
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18
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van Huizen M, Bloeme - ter Horst JR, de Gruyter HLM, Geurink PP, van der Heden van Noort GJ, Knaap RCM, Nelemans T, Ogando NS, Leijs AA, Urakova N, Mark BL, Snijder EJ, Myeni SK, Kikkert M. Deubiquitinating activity of SARS-CoV-2 papain-like protease does not influence virus replication or innate immune responses in vivo. PLoS Pathog 2024; 20:e1012100. [PMID: 38527094 PMCID: PMC10994560 DOI: 10.1371/journal.ppat.1012100] [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: 01/19/2024] [Revised: 04/04/2024] [Accepted: 03/04/2024] [Indexed: 03/27/2024] Open
Abstract
The coronavirus papain-like protease (PLpro) is crucial for viral replicase polyprotein processing. Additionally, PLpro can subvert host defense mechanisms by its deubiquitinating (DUB) and deISGylating activities. To elucidate the role of these activities during SARS-CoV-2 infection, we introduced mutations that disrupt binding of PLpro to ubiquitin or ISG15. We identified several mutations that strongly reduced DUB activity of PLpro, without affecting viral polyprotein processing. In contrast, mutations that abrogated deISGylating activity also hampered viral polyprotein processing and when introduced into the virus these mutants were not viable. SARS-CoV-2 mutants exhibiting reduced DUB activity elicited a stronger interferon response in human lung cells. In a mouse model of severe disease, disruption of PLpro DUB activity did not affect lethality, virus replication, or innate immune responses in the lungs. This suggests that the DUB activity of SARS-CoV-2 PLpro is dispensable for virus replication and does not affect innate immune responses in vivo. Interestingly, the DUB mutant of SARS-CoV replicated to slightly lower titers in mice and elicited a diminished immune response early in infection, although lethality was unaffected. We previously showed that a MERS-CoV mutant deficient in DUB and deISGylating activity was strongly attenuated in mice. Here, we demonstrate that the role of PLpro DUB activity during infection can vary considerably between highly pathogenic coronaviruses. Therefore, careful considerations should be taken when developing pan-coronavirus antiviral strategies targeting PLpro.
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Affiliation(s)
- Mariska van Huizen
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Jonna R. Bloeme - ter Horst
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Heidi L. M. de Gruyter
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Paul P. Geurink
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gerbrand J. van der Heden van Noort
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Centre, Leiden, The Netherlands
| | - Robert C. M. Knaap
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Tessa Nelemans
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Natacha S. Ogando
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Anouk A. Leijs
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Nadya Urakova
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Brian L. Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Eric J. Snijder
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Sebenzile K. Myeni
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
| | - Marjolein Kikkert
- Molecular Virology Laboratory, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, Netherlands
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19
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Zhao X, Perez JM, Faull PA, Chan C, Munting FW, Canadeo LA, Cenik C, Huibregtse JM. Cellular targets and lysine selectivity of the HERC5 ISG15 ligase. iScience 2024; 27:108820. [PMID: 38303729 PMCID: PMC10831901 DOI: 10.1016/j.isci.2024.108820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
ISG15 is a type I interferon-induced ubiquitin-like modifier that functions in innate immune responses. The major human ISG15 ligase is hHERC5, a ribosome-associated HECT E3 that broadly ISGylates proteins cotranslationally. Here, we characterized the hHERC5-dependent ISGylome and identified over 2,000 modified lysines in over 1,100 proteins in IFN-β-stimulated cells. In parallel, we compared the substrate selectivity hHERC5 to the major mouse ISG15 ligase, mHERC6, and analysis of sequences surrounding ISGylation sites revealed that hHERC5 and mHERC6 have distinct preferences for amino acid sequence context. Several features of the datasets were consistent with ISGylation of ribosome-tethered nascent chains, and mHERC6, like hHERC5, cotranslationally modified nascent polypeptides. The ISGylome datasets presented here represent the largest numbers of protein targets and modification sites attributable to a single Ub/Ubl ligase and the lysine selectivities of the hHERC5 and mHERC6 enzymes may have implications for the activities of HECT domain ligases, generally.
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Affiliation(s)
- Xu Zhao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jessica M. Perez
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Peter A. Faull
- Biological Mass Spectrometry Facility, Center for Biomedical Research Support, University of Texas at Austin, Austin, TX 78712, USA
| | - Catherine Chan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Femke W. Munting
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Larissa A. Canadeo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jon M. Huibregtse
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- John Ring LaMontagne Center for Infectious Disease, University of Texas at Austin, Austin, TX 78712, USA
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20
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Mazzarella L, Santoro F, Ravasio R, Fumagalli V, Massa PE, Rodighiero S, Gavilán E, Romanenghi M, Duso BA, Bonetti E, Manganaro L, Pallavi R, Trastulli D, Pallavicini I, Gentile C, Monzani S, Leonardi T, Pasqualato S, Buttinelli G, Di Martino A, Fedele G, Schiavoni I, Stefanelli P, Meroni G, de Francesco R, Steinkuhler C, Fossati G, Iannacone M, Minucci S, Pelicci PG. Inhibition of the lysine demethylase LSD1 modulates the balance between inflammatory and antiviral responses against coronaviruses. Sci Signal 2023; 16:eade0326. [PMID: 38113337 DOI: 10.1126/scisignal.ade0326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/01/2023] [Indexed: 12/21/2023]
Abstract
Innate immune responses to coronavirus infections are highly cell specific. Tissue-resident macrophages, which are infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients but are inconsistently infected in vitro, exert critical but conflicting effects by secreting both antiviral type I interferons (IFNs) and tissue-damaging inflammatory cytokines. Steroids, the only class of host-targeting drugs approved for the treatment of coronavirus disease 2019 (COVID-19), indiscriminately suppress both responses, possibly impairing viral clearance. Here, we established in vitro cell culture systems that enabled us to separately investigate the cell-intrinsic and cell-extrinsic proinflammatory and antiviral activities of mouse macrophages infected with the prototypical murine coronavirus MHV-A59. We showed that the nuclear factor κB-dependent inflammatory response to viral infection was selectively inhibited by loss of the lysine demethylase LSD1, which was previously implicated in innate immune responses to cancer, with negligible effects on the antiviral IFN response. LSD1 ablation also enhanced an IFN-independent antiviral response, blocking viral egress through the lysosomal pathway. The macrophage-intrinsic antiviral and anti-inflammatory activity of Lsd1 inhibition was confirmed in vitro and in a humanized mouse model of SARS-CoV-2 infection. These results suggest that LSD1 controls innate immune responses against coronaviruses at multiple levels and provide a mechanistic rationale for potentially repurposing LSD1 inhibitors for COVID-19 treatment.
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Affiliation(s)
- Luca Mazzarella
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Fabio Santoro
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Roberto Ravasio
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Valeria Fumagalli
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
- Vita-Salute San Raffaele University, Milan 20132, Italy
- Experimental Imaging Centre, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Paul E Massa
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Elena Gavilán
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Mauro Romanenghi
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Bruno A Duso
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Emanuele Bonetti
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Lara Manganaro
- Virology, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi," 20122 Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Rani Pallavi
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Deborah Trastulli
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Isabella Pallavicini
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Claudia Gentile
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Silvia Monzani
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Tommaso Leonardi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Sebastiano Pasqualato
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Gabriele Buttinelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Angela Di Martino
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Giorgio Fedele
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Ilaria Schiavoni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Giuseppe Meroni
- IFOM-FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Raffaele de Francesco
- Virology, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi," 20122 Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Christian Steinkuhler
- Preclinical R&D Italfarmaco SpA, Via dei Lavoratori 54, 20092 Cinisello Balsamo (Milan), Italy
| | - Gianluca Fossati
- Preclinical R&D Italfarmaco SpA, Via dei Lavoratori 54, 20092 Cinisello Balsamo (Milan), Italy
| | - Matteo Iannacone
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
- Vita-Salute San Raffaele University, Milan 20132, Italy
- Experimental Imaging Centre, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
- Department of Biosciences, University of Milan, Milan 20123, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hematology, University of Milan, Milan 20122, Italy
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21
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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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22
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Sarkar L, Liu G, Gack MU. ISG15: its roles in SARS-CoV-2 and other viral infections. Trends Microbiol 2023; 31:1262-1275. [PMID: 37573184 PMCID: PMC10840963 DOI: 10.1016/j.tim.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 08/14/2023]
Abstract
Interferon (IFN)-stimulated gene 15 (ISG15), a ubiquitin-like pleiotropic protein and one of the most abundant ISGs, has been studied extensively; however, its roles in SARS-CoV-2 and other viral infections have just begun to be elucidated. Emerging evidence suggests that ISG15 - either in its conjugated or unconjugated 'free' form - acts both intracellularly and extracellularly, and exerts anti- or pro-viral effects. To counteract ISG15's antiviral roles, viruses have evolved sophisticated tactics. Here, we discuss recent advances in ISG15's physiological functions as a post-translational modifier or 'cytokine-like' molecule during SARS-CoV-2 and other viral infections. Furthermore, we highlight the detailed mechanisms viruses use to block ISG15-dependent antiviral defenses. A comprehensive understanding of ISG15 biology in the context of virus infection may spur new therapeutic approaches for a range of viral infectious diseases.
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Affiliation(s)
- Lucky Sarkar
- Cleveland Clinic Florida Research and Innovation Center, Port St. Lucie, FL, USA
| | - GuanQun Liu
- Cleveland Clinic Florida Research and Innovation Center, Port St. Lucie, FL, USA
| | - Michaela U Gack
- Cleveland Clinic Florida Research and Innovation Center, Port St. Lucie, FL, USA.
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23
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Teo QW, Wong HH, Heunis T, Stancheva V, Hachim A, Lv H, Siu L, Ho J, Lan Y, Mok CKP, Ulferts R, Sanyal S. Usp25-Erlin1/2 activity limits cholesterol flux to restrict virus infection. Dev Cell 2023; 58:2495-2509.e6. [PMID: 37683630 PMCID: PMC10914638 DOI: 10.1016/j.devcel.2023.08.013] [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: 06/14/2022] [Revised: 05/20/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023]
Abstract
Reprogramming lipid metabolic pathways is a critical feature of activating immune responses to infection. However, how these reconfigurations occur is poorly understood. Our previous screen to identify cellular deubiquitylases (DUBs) activated during influenza virus infection revealed Usp25 as a prominent hit. Here, we show that Usp25-deleted human lung epithelial A549 cells display a >10-fold increase in pathogenic influenza virus production, which was rescued upon reconstitution with the wild type but not the catalytically deficient (C178S) variant. Proteomic analysis of Usp25 interactors revealed a strong association with Erlin1/2, which we confirmed as its substrate. Newly synthesized Erlin1/2 were degraded in Usp25-/- or Usp25C178S cells, activating Srebp2, with increased cholesterol flux and attenuated TLR3-dependent responses. Our study therefore defines the function of a deubiquitylase that serves to restrict a range of viruses by reprogramming lipid biosynthetic flux to install appropriate inflammatory responses.
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Affiliation(s)
- Qi Wen Teo
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ho Him Wong
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Tiaan Heunis
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK
| | - Viktoriya Stancheva
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK
| | - Asmaa Hachim
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK
| | - Huibin Lv
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lewis Siu
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Julian Ho
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yun Lan
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Chris Ka Pun Mok
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | | | - Sumana Sanyal
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford OX1 3RE, UK; HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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24
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Brewitz L, Henry Chan HT, Lukacik P, Strain-Damerell C, Walsh MA, Duarte F, Schofield CJ. Mass spectrometric assays monitoring the deubiquitinase activity of the SARS-CoV-2 papain-like protease inform on the basis of substrate selectivity and have utility for substrate identification. Bioorg Med Chem 2023; 95:117498. [PMID: 37857256 PMCID: PMC10933793 DOI: 10.1016/j.bmc.2023.117498] [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: 08/21/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
The SARS-CoV-2 papain-like protease (PLpro) and main protease (Mpro) are nucleophilic cysteine enzymes that catalyze hydrolysis of the viral polyproteins pp1a/1ab. By contrast with Mpro, PLpro is also a deubiquitinase (DUB) that accepts post-translationally modified human proteins as substrates. Here we report studies on the DUB activity of PLpro using synthetic Nε-lysine-branched oligopeptides as substrates that mimic post-translational protein modifications by ubiquitin (Ub) or Ub-like modifiers (UBLs), such as interferon stimulated gene 15 (ISG15). Mass spectrometry (MS)-based assays confirm the DUB activity of isolated recombinant PLpro. They reveal that the sequence of both the peptide fragment derived from the post-translationally modified protein and that derived from the UBL affects PLpro catalysis; the nature of substrate binding in the S sites appears to be more important for catalytic efficiency than binding in the S' sites. Importantly, the results reflect the reported cellular substrate selectivity of PLpro, i.e. human proteins conjugated to ISG15 are better substrates than those conjugated to Ub or other UBLs. The combined experimental and modelling results imply that PLpro catalysis is affected not only by the identity of the substrate residues binding in the S and S' sites, but also by the substrate fold and the conformational dynamics of the blocking loop 2 of the PLpro:substrate complex. Nε-Lysine-branched oligopeptides thus have potential to help the identification of PLpro substrates. More generally, the results imply that MS-based assays with Nε-lysine-branched oligopeptides have potential to monitor catalysis by human DUBs and hence to inform on their substrate preferences.
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Affiliation(s)
- Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom; The Ineos Oxford Institute for Antimicrobial Research, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom.
| | - H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, United Kingdom
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, United Kingdom
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, United Kingdom
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom; The Ineos Oxford Institute for Antimicrobial Research, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom.
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25
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Liu W, Wang J, Wang S, Yue K, Hu Y, Liu X, Wang L, Wan S, Xu X. Discovery of new non-covalent and covalent inhibitors targeting SARS-CoV-2 papain-like protease and main protease. Bioorg Chem 2023; 140:106830. [PMID: 37683544 DOI: 10.1016/j.bioorg.2023.106830] [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: 03/22/2023] [Revised: 06/04/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023]
Abstract
Global coronavirus disease 2019 (COVID-19) pandemic still threatens human health and public safety, and the development of effective antiviral agent is urgently needed. The SARS-CoV-2 main protease (Mpro) and papain-like protease (PLpro) are vital proteins in viral replication and promising therapeutic targets. Additionally, PLpro also modulates host immune response by cleaving ubiquitin and interferon-stimulated gene product 15 (ISG15) from ISGylated host proteins. In this report, we identified [1,2]selenazolo[5,4-c]pyridin-3(2H)-one and benzo[d]isothiazol-3(2H)-one as attractive scaffolds of PLpro and Mpro inhibitors. The representative compounds 6c and 7e exhibited excellent PLpro inhibition with percent inhibition of 42.9% and 44.9% at 50 nM, respectively. The preliminary enzyme kinetics experiment and fluorescent labelling experiment results determined that 6c was identified as a covalent PLpro inhibitor, while 7e was a non-covalent inhibitor. Molecular docking and dynamics simulations revealed that 6c and 7e bound to Zn-finger domain of PLpro. Compounds 6c and 7e were also identified to potent Mpro inhibitors, and they exhibited potent antiviral activities in SARS-CoV-2 infected Vero E6 cells, with EC50 value of 3.9 μM and 7.4 μM, respectively. In addition, the rat liver homogenate half-life of 6c and 7e exceeded 24 h. These findings suggest that 6c and 7e are promising led compounds for further development of PLpro/Mpro dual-target antiviral drugs.
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Affiliation(s)
- Wandong Liu
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | - Juan Wang
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | - Suyun Wang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, 430071 Wuhan, China
| | - Kairui Yue
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | - Yu Hu
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | - Xiaochun Liu
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | - Lihao Wang
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | - Shengbiao Wan
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China.
| | - Ximing Xu
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China.
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26
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Qin Y, Meng X, Wang M, Liang W, Xu R, Chen J, Song H, Fu Y, Li J, Gao C, Jia M, Zhao C, Zhao W. Posttranslational ISGylation of NLRP3 by HERC enzymes facilitates inflammasome activation in models of inflammation. J Clin Invest 2023; 133:e161935. [PMID: 37651190 PMCID: PMC10575725 DOI: 10.1172/jci161935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/24/2023] [Indexed: 09/02/2023] Open
Abstract
The NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) inflammasome is a crucial component of the innate immune system that initiates inflammatory responses. Posttranslational modifications (PTMs) of NLRP3, including ubiquitination and phosphorylation, control inflammasome activation and determine the intensity of inflammation. However, the role of other PTMs in controlling NLRP3 inflammasome activation remains unclear. This study found that TLR priming induced NLRP3 ISGylation (a type of PTM in which ISG15 covalently binds to the target protein) to stabilize the NLRP3 protein. Viral infection, represented by SARS-COV-2 infection, and type I IFNs induced expression of ISG15 and the predominant E3 ISGylation ligases HECT domain- and RCC1-like domain-containing proteins (HERCs; HERC5 in humans and HERC6 in mice). HERCs promoted NLRP3 ISGylation and inhibited K48-linked ubiquitination and proteasomal degradation, resulting in the enhancement of NLRP3 inflammasome activation. Concordantly, Herc6 deficiency ameliorated NLRP3-dependent inflammation as well as hyperinflammation caused by viral infection. The results illustrate the mechanism by which type I IFNs responses control inflammasome activation and viral infection-induced aberrant NLRP3 activation. This work identifies ISGylation as a PTM of NLRP3, revealing a priming target that modulates NLRP3-dependent immunopathology.
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Li Y, Dong X, He W, Quan H, Chen K, Cen C, Wei W. Ube2L6 Promotes M1 Macrophage Polarization in High-Fat Diet-Fed Obese Mice via ISGylation of STAT1 to Trigger STAT1 Activation. Obes Facts 2023; 17:24-36. [PMID: 37820603 PMCID: PMC10836867 DOI: 10.1159/000533966] [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: 03/13/2023] [Accepted: 08/31/2023] [Indexed: 10/13/2023] Open
Abstract
INTRODUCTION In obesity-related type 2 diabetes mellitus (T2DM), M1 macrophages aggravate chronic inflammation and insulin resistance. ISG15-conjugation enzyme E2L6 (Ube2L6) has been demonstrated as a promoter of obesity and insulin resistance. This study investigated the function and mechanism of Ube2L6 in M1 macrophage polarization in obesity. METHODS Obesity was induced in Ube2L6AKO mice and age-matched Ube2L6flox/flox control mice by high-fat diet (HFD). Stromal vascular cells were isolated from the epididymal white adipose tissue of mice. Polarization induction was performed in mouse bone marrow-derived macrophages (BMDMs) by exposure to IFN-γ, lipopolysaccharide, or IL-4. F4/80 expression was assessed by immunohistochemistry staining. Expressions of M1/M2 macrophage markers and target molecules were determined by flow cytometry, RT-qPCR, and Western blotting, respectively. Protein interaction was validated by co-immunoprecipitation (Co-IP) assay. The release of TNF-α and IL-10 was detected by ELISA. RESULTS The polarization of pro-inflammatory M1 macrophages together with an increase in macrophage infiltration was observed in HFD-fed mice, which could be restrained by Ube2L6 knockdown. Additionally, Ube2L6 deficiency triggered the repolarization of BMDMs from M1 to M2 phenotypes. Mechanistically, Ube2L6 promoted the expression and activation of signal transducer and activator of transcription 1 (STAT1) through interferon-stimulated gene 15 (ISG15)-mediated ISGlylation, resulting in M1 macrophage polarization. CONCLUSION Ube2L6 exerts as an activator of STAT1 via post-translational modification of STAT1 by ISG15, thereby triggering M1 macrophage polarization in HFD-fed obese mice. Overall, targeting Ube2L6 may represent an effective therapeutic strategy for ameliorating obesity-related T2DM.
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Affiliation(s)
- Yunqian Li
- Center of Gerontology and Geriatrics, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Xiao Dong
- Center of Gerontology and Geriatrics, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Wenqian He
- Department of Endocrinology, Hainan Medical College, Haikou, China
| | - Huibiao Quan
- Department of Endocrinology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Kaining Chen
- Department of Endocrinology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Chaoping Cen
- Department of Endocrinology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Weiping Wei
- Department of Endocrinology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
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28
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Eberhardt N, Noval MG, Kaur R, Amadori L, Gildea M, Sajja S, Das D, Cilhoroz B, Stewart O, Fernandez DM, Shamailova R, Guillen AV, Jangra S, Schotsaert M, Newman JD, Faries P, Maldonado T, Rockman C, Rapkiewicz A, Stapleford KA, Narula N, Moore KJ, Giannarelli C. SARS-CoV-2 infection triggers pro-atherogenic inflammatory responses in human coronary vessels. NATURE CARDIOVASCULAR RESEARCH 2023; 2:899-916. [PMID: 38076343 PMCID: PMC10702930 DOI: 10.1038/s44161-023-00336-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/23/2023] [Indexed: 12/19/2023]
Abstract
Patients with coronavirus disease 2019 (COVID-19) present increased risk for ischemic cardiovascular complications up to 1 year after infection. Although the systemic inflammatory response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection likely contributes to this increased cardiovascular risk, whether SARS-CoV-2 directly infects the coronary vasculature and attendant atherosclerotic plaques remains unknown. Here we report that SARS-CoV-2 viral RNA is detectable and replicates in coronary lesions taken at autopsy from severe COVID-19 cases. SARS-CoV-2 targeted plaque macrophages and exhibited a stronger tropism for arterial lesions than adjacent perivascular fat, correlating with macrophage infiltration levels. SARS-CoV-2 entry was increased in cholesterol-loaded primary macrophages and dependent, in part, on neuropilin-1. SARS-CoV-2 induced a robust inflammatory response in cultured macrophages and human atherosclerotic vascular explants with secretion of cytokines known to trigger cardiovascular events. Our data establish that SARS-CoV-2 infects coronary vessels, inducing plaque inflammation that could trigger acute cardiovascular complications and increase the long-term cardiovascular risk.
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Affiliation(s)
- Natalia Eberhardt
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Maria Gabriela Noval
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Ravneet Kaur
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Letizia Amadori
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Michael Gildea
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Swathy Sajja
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Dayasagar Das
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Burak Cilhoroz
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - O’Jay Stewart
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dawn M. Fernandez
- Department of Medicine, Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roza Shamailova
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Andrea Vasquez Guillen
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan D. Newman
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Peter Faries
- Department of Surgery, Vascular Division, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Maldonado
- Department of Surgery, Vascular Division, New York University Langone Health, New York, NY, USA
| | - Caron Rockman
- Department of Surgery, Vascular Division, New York University Langone Health, New York, NY, USA
| | - Amy Rapkiewicz
- Department of Pathology, NYU Winthrop Hospital, Long Island School of Medicine, New York, NY, USA
| | - Kenneth A. Stapleford
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Navneet Narula
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Kathryn J. Moore
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Chiara Giannarelli
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, New York University School of Medicine, New York, NY, USA
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Sanyal S. Crossroads in virology: current challenges and future perspectives in the age of emerging viruses. Dis Model Mech 2023; 16:dmm050476. [PMID: 37728628 PMCID: PMC10538290 DOI: 10.1242/dmm.050476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
Abstract
Ongoing global health challenges posed by emerging and re-emerging viruses have highlighted the critical importance of understanding virus-host interactions in countering these threats. Environmental changes, urbanisation and ecological disruption, coupled with the adaptable nature of viruses, facilitates the emergence and spread of new viruses. This Editorial emphasises the urgency of a concerted effort in understanding virus-host interactions to inform the development of therapeutics and vaccines, and help predict disease outcomes. Furthermore, efforts to monitor viral evolution, identify mutations of concern, and develop 'universal' vaccines and broad-spectrum antiviral drugs are needed to counter viral evolution and potentially prevent future viral emergences. Widespread public mistrust surrounding viruses and vaccines also calls for improvement in science communication. A 'One Health' approach that advocates the development of robust global health systems, interdisciplinary collaborations and equity in health access is therefore imperative for transforming the virology landscape.
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Affiliation(s)
- Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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30
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Bagdonas M, Čerepenkaitė K, Mickevičiūtė A, Kananavičiūtė R, Grybaitė B, Anusevičius K, Rukšėnaitė A, Kojis T, Gedgaudas M, Mickevičius V, Matulis D, Zubrienė A, Matulienė J. Screening, Synthesis and Biochemical Characterization of SARS-CoV-2 Protease Inhibitors. Int J Mol Sci 2023; 24:13491. [PMID: 37686295 PMCID: PMC10488051 DOI: 10.3390/ijms241713491] [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: 07/19/2023] [Revised: 08/18/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
The severe acute respiratory syndrome-causing coronavirus 2 (SARS-CoV-2) papain-like protease (PLpro) and main protease (Mpro) play an important role in viral replication events and are important targets for anti-coronavirus drug discovery. In search of these protease inhibitors, we screened a library of 1300 compounds using a fluorescence thermal shift assay (FTSA) and identified 53 hits that thermally stabilized or destabilized PLpro. The hit compounds structurally belonged to two classes of small molecules: thiazole derivatives and symmetrical disulfide compounds. Compound dissociation constants (Kd) were determined using an enzymatic inhibition method. Seven aromatic disulfide compounds were identified as efficient PLpro inhibitors with Kd values in the micromolar range. Two disulfides displayed six-fold higher potency for PLpro (Kd = 0.5 µM) than for Mpro. The disulfide derivatives bound covalently to both proteases, as confirmed through mass spectrometry. The identified compounds can serve as lead compounds for further chemical optimization toward anti-COVID-19 drugs.
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Affiliation(s)
- Martynas Bagdonas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
| | - Kamilė Čerepenkaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
| | - Aurelija Mickevičiūtė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
| | - Rūta Kananavičiūtė
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania;
| | - Birutė Grybaitė
- Department of Organic Chemistry, Kaunas University of Technology, Radvilenų pl. 19, LT-50254 Kaunas, Lithuania; (B.G.); (K.A.); (V.M.)
| | - Kazimieras Anusevičius
- Department of Organic Chemistry, Kaunas University of Technology, Radvilenų pl. 19, LT-50254 Kaunas, Lithuania; (B.G.); (K.A.); (V.M.)
| | - Audronė Rukšėnaitė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania;
| | - Tautvydas Kojis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
| | - Marius Gedgaudas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
| | - Vytautas Mickevičius
- Department of Organic Chemistry, Kaunas University of Technology, Radvilenų pl. 19, LT-50254 Kaunas, Lithuania; (B.G.); (K.A.); (V.M.)
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
| | - Jurgita Matulienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania; (M.B.); (K.Č.); (A.M.); (T.K.); (M.G.); (D.M.)
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Eberhardt N, Noval MG, Kaur R, Sajja S, Amadori L, Das D, Cilhoroz B, Stewart O, Fernandez DM, Shamailova R, Guillen AV, Jangra S, Schotsaert M, Gildea M, Newman JD, Faries P, Maldonado T, Rockman C, Rapkiewicz A, Stapleford KA, Narula N, Moore KJ, Giannarelli C. SARS-CoV-2 infection triggers pro-atherogenic inflammatory responses in human coronary vessels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553245. [PMID: 37645908 PMCID: PMC10461985 DOI: 10.1101/2023.08.14.553245] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
COVID-19 patients present higher risk for myocardial infarction (MI), acute coronary syndrome, and stroke for up to 1 year after SARS-CoV-2 infection. While the systemic inflammatory response to SARS-CoV-2 infection likely contributes to this increased cardiovascular risk, whether SARS-CoV-2 directly infects the coronary vasculature and attendant atherosclerotic plaques to locally promote inflammation remains unknown. Here, we report that SARS-CoV-2 viral RNA (vRNA) is detectable and replicates in coronary atherosclerotic lesions taken at autopsy from patients with severe COVID-19. SARS-CoV-2 localizes to plaque macrophages and shows a stronger tropism for arterial lesions compared to corresponding perivascular fat, correlating with the degree of macrophage infiltration. In vitro infection of human primary macrophages highlights that SARS-CoV-2 entry is increased in cholesterol-loaded macrophages (foam cells) and is dependent, in part, on neuropilin-1 (NRP-1). Furthermore, although viral replication is abortive, SARS-CoV-2 induces a robust inflammatory response that includes interleukins IL-6 and IL-1β, key cytokines known to trigger ischemic cardiovascular events. SARS-CoV-2 infection of human atherosclerotic vascular explants recapitulates the immune response seen in cultured macrophages, including pro-atherogenic cytokine secretion. Collectively, our data establish that SARS-CoV-2 infects macrophages in coronary atherosclerotic lesions, resulting in plaque inflammation that may promote acute CV complications and long-term risk for CV events.
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32
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Engel JJ, van der Made CI, Keur N, Setiabudiawan T, Röring RJ, Damoraki G, Dijkstra H, Lemmers H, Ioannou S, Poulakou G, van der Meer JWM, Giamarellos-Bourboulis EJ, Kumar V, van de Veerdonk FL, Netea MG, Ziogas A. Dexamethasone attenuates interferon-related cytokine hyperresponsiveness in COVID-19 patients. Front Immunol 2023; 14:1233318. [PMID: 37614228 PMCID: PMC10442808 DOI: 10.3389/fimmu.2023.1233318] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/18/2023] [Indexed: 08/25/2023] Open
Abstract
Background Dexamethasone improves the survival of COVID-19 patients in need of supplemental oxygen therapy. Although its broad immunosuppressive effects are well-described, the immunological mechanisms modulated by dexamethasone in patients hospitalized with COVID-19 remain to be elucidated. Objective We combined functional immunological assays and an omics-based approach to investigate the in vitro and in vivo effects of dexamethasone in the plasma and peripheral blood mononuclear cells (PBMCs) of COVID-19 patients. Methods Hospitalized COVID-19 patients eligible for dexamethasone therapy were recruited from the general care ward between February and July, 2021. Whole blood transcriptomic and targeted plasma proteomic analyses were performed before and after starting dexamethasone treatment. PBMCs were isolated from healthy individuals and COVID-19 patients and stimulated with inactivated SARS-CoV-2 ex vivo in the presence or absence of dexamethasone and transcriptome and cytokine responses were assessed. Results Dexamethasone efficiently inhibited SARS-CoV-2-induced in vitro expression of chemokines and cytokines in PBMCs at the transcriptional and protein level. Dexamethasone treatment in COVID-19 patients resulted in down-regulation of genes related to type I and II interferon (IFN) signaling in whole blood immune cells. In addition, dexamethasone attenuated circulating concentrations of secreted interferon-stimulating gene 15 (ISG15) and pro-inflammatory cytokines and chemokines correlating with disease severity and lethal outcomes, such as tumor necrosis factor (TNF), interleukin-6 (IL-6), chemokine ligand 2 (CCL2), C-X-C motif ligand 8 (CXCL8), and C-X-C motif chemokine ligand 10 (CXCL10). In PBMCs from COVID-19 patients that were stimulated ex vivo with multiple pathogens or Toll-like receptor (TLR) ligands, dexamethasone efficiently inhibited cytokine responses. Conclusion We describe the anti-inflammatory impact of dexamethasone on the pathways contributing to cytokine hyperresponsiveness observed in severe manifestations of COVID-19, including type I/II IFN signaling. Dexamethasone could have adverse effects in COVID-19 patients with mild symptoms by inhibiting IFN responses in early stages of the disease, whereas it exhibits beneficial effects in patients with severe clinical phenotypes by efficiently diminishing cytokine hyperresponsiveness.
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Affiliation(s)
- Job J. Engel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Caspar I. van der Made
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nick Keur
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Todia Setiabudiawan
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Rutger J. Röring
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Georgia Damoraki
- Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Helga Dijkstra
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Heidi Lemmers
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sofia Ioannou
- Department of Therapeutics, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Garyfallia Poulakou
- Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Jos W. M. van der Meer
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Vinod Kumar
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Genetics, University Medical Center Groningen, Groningen, Netherlands
| | - Frank L. van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Immunology and Metabolism, Life & Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Athanasios Ziogas
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
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Bhuiyan SA, Xu M, Yang L, Semizoglou E, Bhatia P, Pantaleo KI, Tochitsky I, Jain A, Erdogan B, Blair S, Cat V, Mwirigi JM, Sankaranarayanan I, Tavares-Ferreira D, Green U, McIlvried LA, Copits BA, Bertels Z, Del Rosario JS, Widman AJ, Slivicki RA, Yi J, Woolf CJ, Lennerz JK, Whited JL, Price TJ, Gereau RW, Renthal W. Harmonized cross-species cell atlases of trigeminal and dorsal root ganglia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.04.547740. [PMID: 37461736 PMCID: PMC10350076 DOI: 10.1101/2023.07.04.547740] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Peripheral sensory neurons in the dorsal root ganglion (DRG) and trigeminal ganglion (TG) are specialized to detect and transduce diverse environmental stimuli including touch, temperature, and pain to the central nervous system. Recent advances in single-cell RNA-sequencing (scRNA-seq) have provided new insights into the diversity of sensory ganglia cell types in rodents, non-human primates, and humans, but it remains difficult to compare transcriptomically defined cell types across studies and species. Here, we built cross-species harmonized atlases of DRG and TG cell types that describe 18 neuronal and 11 non-neuronal cell types across 6 species and 19 studies. We then demonstrate the utility of this harmonized reference atlas by using it to annotate newly profiled DRG nuclei/cells from both human and the highly regenerative axolotl. We observe that the transcriptomic profiles of sensory neuron subtypes are broadly similar across vertebrates, but the expression of functionally important neuropeptides and channels can vary notably. The new resources and data presented here can guide future studies in comparative transcriptomics, simplify cell type nomenclature differences across studies, and help prioritize targets for future pain therapy development.
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Affiliation(s)
- Shamsuddin A Bhuiyan
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Mengyi Xu
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Alan Edwards Center for Research on Pain and Department of Physiology, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Lite Yang
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Neurosciences, Division of Biology and Biomedical Sciences, Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Evangelia Semizoglou
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Parth Bhatia
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Katerina I Pantaleo
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ivan Tochitsky
- F.M. Kirby Neurobiology Center and Department of Neurobiology, Boston Children's Hospital and Harvard Medical School, 3 Blackfan Cir. Boston, MA 02115
| | - Aakanksha Jain
- F.M. Kirby Neurobiology Center and Department of Neurobiology, Boston Children's Hospital and Harvard Medical School, 3 Blackfan Cir. Boston, MA 02115
| | - Burcu Erdogan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, 02138
| | - Steven Blair
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, 02138
| | - Victor Cat
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, 02138
| | - Juliet M Mwirigi
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080
| | - Ishwarya Sankaranarayanan
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080
| | - Diana Tavares-Ferreira
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080
| | - Ursula Green
- Department of Pathology, Center for Integrated Diagnostics, Massachussetts General Hospital and Havard Medical School, Boston, MA 02114
| | - Lisa A McIlvried
- Program in Neurosciences, Division of Biology and Biomedical Sciences, Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Bryan A Copits
- Program in Neurosciences, Division of Biology and Biomedical Sciences, Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Zachariah Bertels
- Program in Neurosciences, Division of Biology and Biomedical Sciences, Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - John S Del Rosario
- Program in Neurosciences, Division of Biology and Biomedical Sciences, Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Allie J Widman
- Program in Neurosciences, Division of Biology and Biomedical Sciences, Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Richard A Slivicki
- Program in Neurosciences, Division of Biology and Biomedical Sciences, Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Jiwon Yi
- Program in Neurosciences, Division of Biology and Biomedical Sciences, Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Clifford J Woolf
- F.M. Kirby Neurobiology Center and Department of Neurobiology, Boston Children's Hospital and Harvard Medical School, 3 Blackfan Cir. Boston, MA 02115
| | - Jochen K Lennerz
- Department of Pathology, Center for Integrated Diagnostics, Massachussetts General Hospital and Havard Medical School, Boston, MA 02114
| | - Jessica L Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, 02138
| | - Theodore J Price
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080
| | - Robert W Gereau
- Program in Neurosciences, Division of Biology and Biomedical Sciences, Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - William Renthal
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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Lou S, Yang M, Li T, Zhao W, Cevasco H, Yang YT, Gerstein M. Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes. PLoS Comput Biol 2023; 19:e1011222. [PMID: 37410793 PMCID: PMC10325097 DOI: 10.1371/journal.pcbi.1011222] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/28/2023] [Indexed: 07/08/2023] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 virus has resulted in millions of deaths worldwide. The disease presents with various manifestations that can vary in severity and long-term outcomes. Previous efforts have contributed to the development of effective strategies for treatment and prevention by uncovering the mechanism of viral infection. We now know all the direct protein-protein interactions that occur during the lifecycle of SARS-CoV-2 infection, but it is critical to move beyond these known interactions to a comprehensive understanding of the "full interactome" of SARS-CoV-2 infection, which incorporates human microRNAs (miRNAs), additional human protein-coding genes, and exogenous microbes. Potentially, this will help in developing new drugs to treat COVID-19, differentiating the nuances of long COVID, and identifying histopathological signatures in SARS-CoV-2-infected organs. To construct the full interactome, we developed a statistical modeling approach called MLCrosstalk (multiple-layer crosstalk) based on latent Dirichlet allocation. MLCrosstalk integrates data from multiple sources, including microbes, human protein-coding genes, miRNAs, and human protein-protein interactions. It constructs "topics" that group SARS-CoV-2 with genes and microbes based on similar patterns of co-occurrence across patient samples. We use these topics to infer linkages between SARS-CoV-2 and protein-coding genes, miRNAs, and microbes. We then refine these initial linkages using network propagation to contextualize them within a larger framework of network and pathway structures. Using MLCrosstalk, we identified genes in the IL1-processing and VEGFA-VEGFR2 pathways that are linked to SARS-CoV-2. We also found that Rothia mucilaginosa and Prevotella melaninogenica are positively and negatively correlated with SARS-CoV-2 abundance, a finding corroborated by analysis of single-cell sequencing data.
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Affiliation(s)
- Shaoke Lou
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Mingjun Yang
- School of Electronic Engineering and Computer Science, Queen Mary University of London, Mile End Road, London, United Kingdom
| | - Tianxiao Li
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Weihao Zhao
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Hannah Cevasco
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Yucheng T. Yang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Shanghai, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Mark Gerstein
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
- Department of Statistics & Data Science Yale University, New Haven, Connecticut, United States of America
- Department of Biomedical Informatics & Data Science, Yale University, New Haven, Connecticut, United States of America
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Yang H, Sun H, Brackenridge S, Zhuang X, Wing PAC, Quastel M, Walters L, Garner L, Wang B, Yao X, Felce SL, Peng Y, Moore S, Peeters BWA, Rei M, Canto Gomes J, Tomas A, Davidson A, Semple MG, Turtle LCW, Openshaw PJM, Baillie JK, Mentzer AJ, Klenerman P, Borrow P, Dong T, McKeating JA, Gillespie GM, McMichael AJ. HLA-E-restricted SARS-CoV-2-specific T cells from convalescent COVID-19 patients suppress virus replication despite HLA class Ia down-regulation. Sci Immunol 2023; 8:eabl8881. [PMID: 37390223 DOI: 10.1126/sciimmunol.abl8881] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 06/07/2023] [Indexed: 07/02/2023]
Abstract
Pathogen-specific CD8+ T cell responses restricted by the nonpolymorphic nonclassical class Ib molecule human leukocyte antigen E (HLA-E) are rarely reported in viral infections. The natural HLA-E ligand is a signal peptide derived from classical class Ia HLA molecules that interact with the NKG2/CD94 receptors to regulate natural killer cell functions, but pathogen-derived peptides can also be presented by HLA-E. Here, we describe five peptides from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that elicited HLA-E-restricted CD8+ T cell responses in convalescent patients with coronavirus disease 2019. These T cell responses were identified in the blood at frequencies similar to those reported for classical HLA-Ia-restricted anti-SARS-CoV-2 CD8+ T cells. HLA-E peptide-specific CD8+ T cell clones, which expressed diverse T cell receptors, suppressed SARS-CoV-2 replication in Calu-3 human lung epithelial cells. SARS-CoV-2 infection markedly down-regulated classical HLA class I expression in Calu-3 cells and primary reconstituted human airway epithelial cells, whereas HLA-E expression was not affected, enabling T cell recognition. Thus, HLA-E-restricted T cells could contribute to the control of SARS-CoV-2 infection alongside classical T cells.
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Affiliation(s)
- Hongbing Yang
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
| | - Hong Sun
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Key Laboratory of AIDS Immunology, Department of Laboratory Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Simon Brackenridge
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Xiaodong Zhuang
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Peter A C Wing
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Max Quastel
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Lucy Walters
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Lee Garner
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Beibei Wang
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Xuan Yao
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
| | - Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Shona Moore
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Bas W A Peeters
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Margarida Rei
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus, Oxford, UK
| | - Joao Canto Gomes
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga, Portugal
| | - Ana Tomas
- Unidada de Investigacao em Patobiologia Molecular, Instituto Portugues de Oncologia de Lisboa Francisco Gentil, EPE Lisbon, Portugal
- Chronic Diseases Research Centre, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Andrew Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Malcolm G Semple
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Unit, Alder Hey Children's Hospital, Eaton Road, Liverpool L12 2AP, UK
| | - Lance C W Turtle
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust (member of Liverpool Health Partners), Liverpool, UK
| | | | | | - Alexander J Mentzer
- Welcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Persephone Borrow
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Tao Dong
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jane A McKeating
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Geraldine M Gillespie
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Andrew J McMichael
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
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36
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Velazquez-Salinas L, Medina GN, Valdez F, Zarate S, Collinson S, Zhu JJ, Rodriguez LL. Exploring the Molecular Basis of Vesicular Stomatitis Virus Pathogenesis in Swine: Insights from Expression Profiling of Primary Macrophages Infected with M51R Mutant Virus. Pathogens 2023; 12:896. [PMID: 37513744 PMCID: PMC10384765 DOI: 10.3390/pathogens12070896] [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: 05/04/2023] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
Vesicular stomatitis virus (VSV) is an emergent virus affecting livestock in the US. Previously, using a recombinant VSV carrying the M51R mutation in the matrix protein (rNJ0612NME6-M51R), we evaluated the pathogenesis of this virus in pigs. Our results indicated that rNJ0612NME6-M51R represented an attenuated phenotype in in-vivo and in ex-vivo in pig macrophages, resembling certain clinical features observed in field VSV isolates. In order to gain more insight into the molecular basis leading to the attenuation of rNJ0612NME6-M51R in pigs, we conducted a microarray analysis to assess the gene expression profiles of primary porcine macrophages infected with rNJ0612NME6-M51R compared to its parental virus (rNJ0612NME6). Our results showed an overall higher gene expression in macrophages infected with rNJ0612NME6-M51R. Specifically, we observed that the pathways related with immune cytokine signaling and interferon (IFN)-related responses (including activation, signaling, induction, and antiviral mechanisms) were the ones comprising most of the relevant genes identified during this study. Collectively, the results presented herein highlight the relevance of type I interferon during the pathogenesis of VSV in pigs. The information generated from this study may represent a framework for future studies intended to understand the molecular bases of the pathogenesis of field strains in livestock.
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Affiliation(s)
- Lauro Velazquez-Salinas
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, USDA, Greenport, NY 11944, USA
- National Bio and Agro-Defense Facility (NBAF), ARS, USDA, Manhattan, KS 66502, USA
| | - Gisselle N Medina
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, USDA, Greenport, NY 11944, USA
- National Bio and Agro-Defense Facility (NBAF), ARS, USDA, Manhattan, KS 66502, USA
| | - Federico Valdez
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, USDA, Greenport, NY 11944, USA
- Oak Ridge Institute for Science and Education (ORISE)-PIADC, Oak Ridge, TN 37831, USA
| | - Selene Zarate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de Mexico, Ciudad de Mexico 04510, Mexico
| | - Shannon Collinson
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, USDA, Greenport, NY 11944, USA
- Oak Ridge Institute for Science and Education (ORISE)-PIADC, Oak Ridge, TN 37831, USA
| | - James J Zhu
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, USDA, Greenport, NY 11944, USA
- National Bio and Agro-Defense Facility (NBAF), ARS, USDA, Manhattan, KS 66502, USA
| | - Luis L Rodriguez
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, USDA, Greenport, NY 11944, USA
- National Bio and Agro-Defense Facility (NBAF), ARS, USDA, Manhattan, KS 66502, USA
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37
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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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Falqui M, Perdiguero B, Coloma R, Albert M, Marcos-Villar L, McGrail JP, Sorzano CÓS, Esteban M, Gómez CE, Guerra S. An MVA-based vector expressing cell-free ISG15 increases IFN-I production and improves HIV-1-specific CD8 T cell immune responses. Front Cell Infect Microbiol 2023; 13:1187193. [PMID: 37313341 PMCID: PMC10258332 DOI: 10.3389/fcimb.2023.1187193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 06/15/2023] Open
Abstract
The human immunodeficiency virus (HIV), responsible of the Acquired Immune Deficiency Syndrome (AIDS), continues to be a major global public health issue with any cure or vaccine available. The Interferon-stimulated gene 15 (ISG15) encodes a ubiquitin-like protein that is induced by interferons and plays a critical role in the immune response. ISG15 is a modifier protein that covalently binds to its targets via a reversible bond, a process known as ISGylation, which is the best-characterized activity of this protein to date. However, ISG15 can also interact with intracellular proteins via non-covalent binding or act as a cytokine in the extracellular space after secretion. In previous studies we proved the adjuvant effect of ISG15 when delivered by a DNA-vector in heterologous prime-boost combination with a Modified Vaccinia virus Ankara (MVA)-based recombinant virus expressing HIV-1 antigens Env/Gag-Pol-Nef (MVA-B). Here we extended these results evaluating the adjuvant effect of ISG15 when expressed by an MVA vector. For this, we generated and characterized two novel MVA recombinants expressing different forms of ISG15, the wild-type ISG15GG (able to perform ISGylation) or the mutated ISG15AA (unable to perform ISGylation). In mice immunized with the heterologous DNA prime/MVA boost regimen, the expression of the mutant ISG15AA from MVA-Δ3-ISG15AA vector in combination with MVA-B induced an increase in the magnitude and quality of HIV-1-specific CD8 T cells as well as in the levels of IFN-I released, providing a better immunostimulatory activity than the wild-type ISG15GG. Our results confirm the importance of ISG15 as an immune adjuvant in the vaccine field and highlights its role as a potential relevant component in HIV-1 immunization protocols.
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Affiliation(s)
- Michela Falqui
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Beatriz Perdiguero
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Rocio Coloma
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Manuel Albert
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Laura Marcos-Villar
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Joseph Patrick McGrail
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Carlos Óscar S. Sorzano
- Biocomputing Unit and Computational Genomics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Carmen Elena Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Susana Guerra
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
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Lan Y, van Leur SW, Fernando JA, Wong HH, Kampmann M, Siu L, Zhang J, Li M, Nicholls JM, Sanyal S. Viral subversion of selective autophagy is critical for biogenesis of virus replication organelles. Nat Commun 2023; 14:2698. [PMID: 37164963 PMCID: PMC10171163 DOI: 10.1038/s41467-023-38377-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/25/2023] [Indexed: 05/12/2023] Open
Abstract
Infection by many (+)RNA viruses is accompanied by ER-expansion and membrane remodelling to form viral replication organelles, followed by assembly and secretion of viral progenies. We previously identified that virus-triggered lipophagy was critical for flaviviral assembly, and is driven by the lipid droplet associated protein Ancient ubiquitin protein 1 (Aup1). A ubiquitin conjugating protein Ube2g2 that functions as a co-factor for Aup1 was identified as a host dependency factor in our study. Here we characterized its function: Ube2g2-deficient cells displayed a dramatic reduction in virus production, which could be rescued by reconstituting the wild-type but not the catalytically deficient (C89K) mutant of Ube2g2, suggesting that its enzymatic activity is necessary. Ube2g2 deficiency did not affect entry of virus particles but resulted in a profound loss in formation of replication organelles, and production of infectious progenies. This phenomenon resulted from its dual activity in (i) triggering lipophagy in conjunction with Aup1, and (ii) degradation of ER chaperones such as Herpud1, SEL1L, Hrd1, along with Sec62 to restrict ER-phagy upon Xbp1-IRE1 triggered ER expansion. Our results therefore underscore an exquisite fine-tuning of selective autophagy by flaviviruses that drive host membrane reorganization during infection to enable biogenesis of viral replication organelles.
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Affiliation(s)
- Yun Lan
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | | | - Julia Ayano Fernando
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Ho Him Wong
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Martin Kampmann
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Lewis Siu
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Jingshu Zhang
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Mingyuan Li
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - John M Nicholls
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Sumana Sanyal
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China.
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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40
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Wydorski PM, Osipiuk J, Lanham BT, Tesar C, Endres M, Engle E, Jedrzejczak R, Mullapudi V, Michalska K, Fidelis K, Fushman D, Joachimiak A, Joachimiak LA. Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin. Nat Commun 2023; 14:2366. [PMID: 37185902 PMCID: PMC10126577 DOI: 10.1038/s41467-023-38031-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub2) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub2 combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub2 are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub2 modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.
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Affiliation(s)
- Pawel M Wydorski
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jerzy Osipiuk
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Benjamin T Lanham
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Christine Tesar
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Michael Endres
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Elizabeth Engle
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Robert Jedrzejczak
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Vishruth Mullapudi
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Karolina Michalska
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Krzysztof Fidelis
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, CA, 95616, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.
| | - Andrzej Joachimiak
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA.
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367, USA.
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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41
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Hersi F, Sebastian A, Tarazi H, Srinivasulu V, Mostafa A, Allayeh AK, Zeng C, Hachim IY, Liu SL, Abu-Yousef IA, Majdalawieh AF, Zaher DM, Omar HA, Al-Tel TH. Discovery of novel papain-like protease inhibitors for potential treatment of COVID-19. Eur J Med Chem 2023; 254:115380. [PMID: 37075625 PMCID: PMC10106510 DOI: 10.1016/j.ejmech.2023.115380] [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: 12/21/2022] [Revised: 03/09/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
The recent emergence of different SARS-CoV-2 variants creates an urgent need to develop more effective therapeutic agents to prevent COVID-19 outbreaks. Among SARS-CoV-2 essential proteases is papain-like protease (SARS-CoV-2 PLpro), which plays multiple roles in regulating SARS-CoV-2 viral spread and innate immunity such as deubiquitinating and deISG15ylating (interferon-induced gene 15) activities. Many studies are currently focused on targeting this protease to tackle SARS-CoV-2 infection. In this context, we performed a phenotypic screening using an in-house pilot compounds collection possessing a diverse skeleta against SARS-CoV-2 PLpro. This screen identified SIMR3030 as a potent inhibitor of SARS-CoV-2. SIMR3030 has been shown to exhibit deubiquitinating activity and inhibition of SARS-CoV-2 specific gene expression (ORF1b and Spike) in infected host cells and possessing virucidal activity. Moreover, SIMR3030 was demonstrated to inhibit the expression of inflammatory markers, including IFN-α, IL-6, and OAS1, which are reported to mediate the development of cytokine storms and aggressive immune responses. In vitro absorption, distribution, metabolism, and excretion (ADME) assessment of the drug-likeness properties of SIMR3030 demonstrated good microsomal stability in liver microsomes. Furthermore, SIMR3030 demonstrated very low potency as an inhibitor of CYP450, CYP3A4, CYP2D6 and CYP2C9 which rules out any potential drug-drug interactions. In addition, SIMR3030 showed moderate permeability in Caco2-cells. Critically, SIMR3030 has maintained a high in vivo safety profile at different concentrations. Molecular modeling studies of SIMR3030 in the active sites of SARS-CoV-2 and MERS-CoV PLpro were performed to shed light on the binding modes of this inhibitor. This study demonstrates that SIMR3030 is a potent inhibitor of SARS-CoV-2 PLpro that forms the foundation for developing new drugs to tackle the COVID-19 pandemic and may pave the way for the development of novel therapeutics for a possible future outbreak of new SARS-CoV-2 variants or other Coronavirus species.
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Affiliation(s)
- Fatema Hersi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Anusha Sebastian
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hamadeh Tarazi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Vunnam Srinivasulu
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, Environment and Climate Change Institute, National Research Centre, Giza, 12622, Egypt
| | - Abdou Kamal Allayeh
- Virology Lab 176, Water Pollution Research Department, Environment and Climate Change Institute, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Cong Zeng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Ibrahim Y Hachim
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Imad A Abu-Yousef
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, United Arab Emirates
| | - Amin F Majdalawieh
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, United Arab Emirates
| | - Dana M Zaher
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hany A Omar
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates; Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt.
| | - Taleb H Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates.
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42
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Gomez-Lopez N, Romero R, Escobar MF, Carvajal JA, Echavarria MP, Albornoz LL, Nasner D, Miller D, Gallo DM, Galaz J, Arenas-Hernandez M, Bhatti G, Done B, Zambrano MA, Ramos I, Fernandez PA, Posada L, Chaiworapongsa T, Jung E, Garcia-Flores V, Suksai M, Gotsch F, Bosco M, Than NG, Tarca AL. Pregnancy-specific responses to COVID-19 revealed by high-throughput proteomics of human plasma. COMMUNICATIONS MEDICINE 2023; 3:48. [PMID: 37016066 PMCID: PMC10071476 DOI: 10.1038/s43856-023-00268-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 03/03/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Pregnant women are at greater risk of adverse outcomes, including mortality, as well as obstetrical complications resulting from COVID-19. However, pregnancy-specific changes that underlie such worsened outcomes remain unclear. METHODS Plasma samples were collected from pregnant women and non-pregnant individuals (male and female) with (n = 72 pregnant, 52 non-pregnant) and without (n = 29 pregnant, 41 non-pregnant) COVID-19. COVID-19 patients were grouped as asymptomatic, mild, moderate, severe, or critically ill according to NIH classifications. Proteomic profiling of 7,288 analytes corresponding to 6,596 unique protein targets was performed using the SOMAmer platform. RESULTS Herein, we profile the plasma proteome of pregnant and non-pregnant COVID-19 patients and controls and show alterations that display a dose-response relationship with disease severity; yet, such proteomic perturbations are dampened during pregnancy. In both pregnant and non-pregnant state, the proteome response induced by COVID-19 shows enrichment of mediators implicated in cytokine storm, endothelial dysfunction, and angiogenesis. Shared and pregnancy-specific proteomic changes are identified: pregnant women display a tailored response that may protect the conceptus from heightened inflammation, while non-pregnant individuals display a stronger response to repel infection. Furthermore, the plasma proteome can accurately identify COVID-19 patients, even when asymptomatic or with mild symptoms. CONCLUSION This study represents the most comprehensive characterization of the plasma proteome of pregnant and non-pregnant COVID-19 patients. Our findings emphasize the distinct immune modulation between the non-pregnant and pregnant states, providing insight into the pathogenesis of COVID-19 as well as a potential explanation for the more severe outcomes observed in pregnant women.
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Affiliation(s)
- Nardhy Gomez-Lopez
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, USA.
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.
| | - Roberto Romero
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA.
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA.
- Detroit Medical Center, Detroit, MI, USA.
| | - María Fernanda Escobar
- Departamento de Ginecología y Obstetricia, Fundación Valle del Lili, Cali, Colombia
- Departamento de Ginecología y Obstetricia, Facultad de Ciencias de la Salud, Universidad Icesi, Cali, Colombia
| | - Javier Andres Carvajal
- Departamento de Ginecología y Obstetricia, Fundación Valle del Lili, Cali, Colombia
- Departamento de Ginecología y Obstetricia, Facultad de Ciencias de la Salud, Universidad Icesi, Cali, Colombia
| | - Maria Paula Echavarria
- Departamento de Ginecología y Obstetricia, Fundación Valle del Lili, Cali, Colombia
- Departamento de Ginecología y Obstetricia, Facultad de Ciencias de la Salud, Universidad Icesi, Cali, Colombia
| | - Ludwig L Albornoz
- Departamento de Laboratorio Clínico y Patología, Fundación Valle del Lili, Cali, Colombia
- Facultad de Ciencias de la Salud, Universidad Icesi, Cali, Colombia
| | - Daniela Nasner
- Centro de Investigaciones Clínicas, Fundación Valle del Lili, Cali, Colombia
| | - Derek Miller
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Dahiana M Gallo
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jose Galaz
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
- Division of Obstetrics and Gynecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcia Arenas-Hernandez
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Gaurav Bhatti
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Bogdan Done
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Maria Andrea Zambrano
- Departamento de Ginecología y Obstetricia, Facultad de Ciencias de la Salud, Universidad Icesi, Cali, Colombia
| | - Isabella Ramos
- Departamento de Ginecología y Obstetricia, Facultad de Ciencias de la Salud, Universidad Icesi, Cali, Colombia
| | - Paula Andrea Fernandez
- Departamento de Ginecología y Obstetricia, Facultad de Ciencias de la Salud, Universidad Icesi, Cali, Colombia
| | - Leandro Posada
- Departamento de Ginecología y Obstetricia, Facultad de Ciencias de la Salud, Universidad Icesi, Cali, Colombia
| | - Tinnakorn Chaiworapongsa
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Eunjung Jung
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Valeria Garcia-Flores
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Manaphat Suksai
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Francesca Gotsch
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Mariachiara Bosco
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Nandor Gabor Than
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA
- Systems Biology of Reproduction Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Maternity Private Clinic of Obstetrics and Gynecology, Budapest, Hungary
- Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
- Genesis Theranostix Group, Budapest, Hungary
| | - Adi L Tarca
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Detroit, MI, USA.
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.
- Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA.
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Abstract
Our understanding of the ubiquitin code has greatly evolved from conventional E1, E2 and E3 enzymes that modify Lys residues on specific substrates with a single type of ubiquitin chain to more complex processes that regulate and mediate ubiquitylation. In this Review, we discuss recently discovered endogenous mechanisms and unprecedented pathways by which pathogens rewrite the ubiquitin code to promote infection. These processes include unconventional ubiquitin modifications involving ester linkages with proteins, lipids and sugars, or ubiquitylation through a phosphoribosyl bridge involving Arg42 of ubiquitin. We also introduce the enzymatic pathways that write and reverse these modifications, such as the papain-like proteases of severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. Furthermore, structural studies have revealed that the ultimate functions of ubiquitin are mediated not simply by straightforward recognition by ubiquitin-binding domains. Instead, elaborate multivalent interactions between ubiquitylated targets or ubiquitin chains and their readers (for example, the proteasome, the MLL1 complex or DOT1L) can elicit conformational changes that regulate protein degradation or transcription. The newly discovered mechanisms provide opportunities for innovative therapeutic interventions for diseases such as cancer and infectious diseases.
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Affiliation(s)
- Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.
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44
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Olie CS, Pinto-Fernández A, Damianou A, Vendrell I, Mei H, den Hamer B, van der Wal E, de Greef JC, Raz V, Kessler BM. USP18 is an essential regulator of muscle cell differentiation and maturation. Cell Death Dis 2023; 14:231. [PMID: 37002195 PMCID: PMC10066380 DOI: 10.1038/s41419-023-05725-z] [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: 10/27/2022] [Revised: 02/14/2023] [Accepted: 03/07/2023] [Indexed: 04/03/2023]
Abstract
The ubiquitin proteasomal system is a critical regulator of muscle physiology, and impaired UPS is key in many muscle pathologies. Yet, little is known about the function of deubiquitinating enzymes (DUBs) in the muscle cell context. We performed a genetic screen to identify DUBs as potential regulators of muscle cell differentiation. Surprisingly, we observed that the depletion of ubiquitin-specific protease 18 (USP18) affected the differentiation of muscle cells. USP18 depletion first stimulated differentiation initiation. Later, during differentiation, the absence of USP18 expression abrogated myotube maintenance. USP18 enzymatic function typically attenuates the immune response by removing interferon-stimulated gene 15 (ISG15) from protein substrates. However, in muscle cells, we found that USP18, predominantly nuclear, regulates differentiation independent of ISG15 and the ISG response. Exploring the pattern of RNA expression profiles and protein networks whose levels depend on USP18 expression, we found that differentiation initiation was concomitant with reduced expression of the cell-cycle gene network and altered expression of myogenic transcription (co) factors. We show that USP18 depletion altered the calcium channel gene network, resulting in reduced calcium flux in myotubes. Additionally, we show that reduced expression of sarcomeric proteins in the USP18 proteome was consistent with reduced contractile force in an engineered muscle model. Our results revealed nuclear USP18 as a critical regulator of differentiation initiation and maintenance, independent of ISG15 and its role in the ISG response.
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Affiliation(s)
- Cyriel Sebastiaan Olie
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Adán Pinto-Fernández
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Andreas Damianou
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Iolanda Vendrell
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Bianca den Hamer
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Erik van der Wal
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Jessica C de Greef
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Vered Raz
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands.
| | - Benedikt M Kessler
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
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Zhao C, Bu E, Zhang C, Lai R, He J, Guo B, Guo W, Liu L, Pan H. Deciphering the molecular mechanisms of Maxing Huoqiao Decoction in treating pulmonary fibrosis via transcriptional profiling and circRNA-miRNA-mRNA network analysis. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 115:154754. [PMID: 37087790 DOI: 10.1016/j.phymed.2023.154754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 02/27/2023] [Accepted: 03/08/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, fibrotic interstitial lung condition with unknown etiology and high mortality. Chinese herbal medicine has been used for more than a thousand years to treat various lung diseases. PURPOSE The current study aimed to examine whether Chinese herbal Maxing Huoqiao Decoction (MXHQD) exerts therapeutic effects on IPF and to further uncover its underlying molecular mechanisms. METHODS Mouse model of acute lung injury (ALI) or IPF was induced by intratracheal instillation of LPS or bleomycin, respectively. ALI mice were treated with MXHQD for 7 days, and lung tissues were taken for test after modeling 24 h. IPF mice were gavaged for 21 days after modeling. Lung tissues were subjected to whole transcriptome detection, and the differential RNAs were experimentally verified. RESULTS The results showed that MXHQD alleviated the computed tomography (CT) and the pathological degree changes in mice with IPF, improved changes in the expression of fibrosis related genes and reduced the hydroxyproline expression in IPF mice. MXHQD also decreased the cell numbers in bronchoalveolar lavage fluids, and the expression levels of the inflammatory factors in the ALI mice lung tissues were significantly inhibited. By applying whole transcriptome analysis, results showed that MXHQD acted on 40 mRNAs, 15 miRNAs, 25 novel lncRNAs and 17 circRNAs to resist pulmonary fibrosis. The competing endogenous RNA (ceRNA) network diagram showed that the multiple components of MXHQD against fibrosis through a network of multiple targets. The differential mRNAs were mainly related to the innate immune response and the defense response to virus. Then the expression of mRNAs in the differential mRNA-miRNA-differential circRNA network in the lung tissue of IPF was verified. The expression of ZBP1 and ISG15 related to immune system and anti virus was verified at both gene and protein expressions. MXHQD could significantly inhibit the elevation of ZBP1 and ISG15 factors induced by the fibrosis model. CONCLUSION Overall, our findings provide compelling evidence that MXHQD can alleviate IPF by modulating innate immunity. This is the first study to reveal the molecular mechanism underlying the multi-components, multi-channels and multi-targets anti-IPF immune injury of MXHQD, and supports its potential clinical application for IPF.
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Affiliation(s)
- Caiping Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao, 999078, China
| | - Erfan Bu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao, 999078, China
| | - Chuanhai Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao, 999078, China
| | - Ruogu Lai
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao, 999078, China
| | - Jinlian He
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao, 999078, China
| | - Bin Guo
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao, 999078, China
| | - Wanyi Guo
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao, 999078, China
| | - Liang Liu
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510000, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, 510000, China; Guangzhou Laboratory, Guangzhou, China
| | - Hudan Pan
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510000, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, 510000, China.
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46
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Arya R, Prashar V, Kumar M. Identification and characterization of aurintricarboxylic acid as a potential inhibitor of SARS-CoV-2 PLpro. Int J Biol Macromol 2023; 230:123347. [PMID: 36682650 PMCID: PMC9851725 DOI: 10.1016/j.ijbiomac.2023.123347] [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: 07/22/2022] [Revised: 12/20/2022] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
As the global health crisis due to evolution of mutations in SARS-CoV-2 continues, it is important to develop several effective antivirals to control the disease. Targeting papain-like protease (PLpro) of SARS-CoV-2 for drug development is a promising strategy due to its dual role in promoting viral replication and dysregulating host immune responses. Here, we screened a library of compounds to find potential inhibitors of PLpro. We find aurintricarboxylic acid (ATA) inhibits PLpro with Ki and IC50 values of 16 μM and 30 μM, respectively. The binding of ATA to PLpro was further characterized using isothermal titration calorimetry, differential scanning fluorimetry, dynamic light scattering and circular dichroism spectrometry. In vitro assays showed the antiviral potential of ATA with IC50 of 50 μM. In vivo efficacy was studied in Syrian hamsters and the results are being discussed.
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Affiliation(s)
- Rimanshee Arya
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Vishal Prashar
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Mukesh Kumar
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India.
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47
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Yang T, Wang SC, Ye L, Maimaitiyiming Y, Naranmandura H. Targeting viral proteins for restraining SARS-CoV-2: focusing lens on viral proteins beyond spike for discovering new drug targets. Expert Opin Drug Discov 2023; 18:247-268. [PMID: 36723288 DOI: 10.1080/17460441.2023.2175812] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Emergence of highly infectious SARS-CoV-2 variants are reducing protection provided by current vaccines, requiring constant updates in antiviral approaches. The virus encodes four structural and sixteen nonstructural proteins which play important roles in viral genome replication and transcription, virion assembly, release , entry into cells, and compromising host cellular defenses. As alien proteins to host cells, many viral proteins represent potential targets for combating the SARS-CoV-2. AREAS COVERED Based on literature from PubMed and Web of Science databases, the authors summarize the typical characteristics of SARS-CoV-2 from the whole viral particle to the individual viral proteins and their corresponding functions in virus life cycle. The authors also discuss the potential and emerging targeted interventions to curb virus replication and spread in detail to provide unique insights into SARS-CoV-2 infection and countermeasures against it. EXPERT OPINION Our comprehensive analysis highlights the rationale to focus on non-spike viral proteins that are less mutated but have important functions. Examples of this include: structural proteins (e.g. nucleocapsid protein, envelope protein) and extensively-concerned nonstructural proteins (e.g. NSP3, NSP5, NSP12) along with the ones with relatively less attention (e.g. NSP1, NSP10, NSP14 and NSP16), for developing novel drugs to overcome resistance of SARS-CoV-2 variants to preexisting vaccines and antibody-based treatments.
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Affiliation(s)
- Tao Yang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Si Chun Wang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Linyan Ye
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yasen Maimaitiyiming
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, and MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hua Naranmandura
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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48
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Ramanathan R, Hatzios SK. Activity-based Tools for Interrogating Host Biology During Infection. Isr J Chem 2023; 63:e202200095. [PMID: 37744997 PMCID: PMC10512441 DOI: 10.1002/ijch.202200095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/18/2023]
Abstract
Host cells sense and respond to pathogens by dynamically regulating cell signaling. The rapid modulation of signaling pathways is achieved by post-translational modifications (PTMs) that can alter protein structure, function, and/or binding interactions. By using chemical probes to broadly profile changes in enzyme function or side-chain reactivity, activity-based protein profiling (ABPP) can reveal PTMs that regulate host-microbe interactions. While ABPP has been widely utilized to uncover microbial mechanisms of pathogenesis, in this review, we focus on more recent applications of this technique to the discovery of host PTMs and enzymes that modulate signaling within infected cells. Collectively, these advances underscore the importance of ABPP as a tool for interrogating the host response to infection and identifying potential targets for host-directed therapies.
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Affiliation(s)
- Renuka Ramanathan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516 USA
| | - Stavroula K. Hatzios
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516 USA
- Department of Chemistry, Yale University, New Haven, CT 06520 USA
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Engineering potent live attenuated coronavirus vaccines by targeted inactivation of the immune evasive viral deubiquitinase. Nat Commun 2023; 14:1141. [PMID: 36854765 PMCID: PMC9973250 DOI: 10.1038/s41467-023-36754-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/16/2023] [Indexed: 03/02/2023] Open
Abstract
Coronaviruses express a papain-like protease (PLpro) that is required for replicase polyprotein maturation and also serves as a deubiquitinating enzyme (DUB). In this study, using a Middle East respiratory syndrome virus (MERS-CoV) PLpro modified virus in which the DUB is selectively inactivated, we show that the PLpro DUB is an important MERS-CoV interferon antagonist and virulence factor. Although the DUB-negative rMERS-CoVMA replicates robustly in the lungs of human dipeptidyl peptidase 4 knock-in (hDPP4 KI) mice, it does not cause clinical symptoms. Interestingly, a single intranasal vaccination with DUB-negative rMERS-CoVMA induces strong and sustained neutralizing antibody responses and sterilizing immunity after a lethal wt virus challenge. The survival of naïve animals also significantly increases when sera from animals vaccinated with the DUB-negative rMERS-CoVMA are passively transferred, prior to receiving a lethal virus dose. These data demonstrate that DUB-negative coronaviruses could be the basis of effective modified live attenuated vaccines.
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Mucosal Gene Expression in Response to SARS-CoV-2 Is Associated with Viral Load. J Virol 2023; 97:e0147822. [PMID: 36656015 PMCID: PMC9973040 DOI: 10.1128/jvi.01478-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Little is known about the relationships between symptomatic early severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and upper airway mucosal gene expression and immune response. To examine the association of symptomatic SARS-CoV-2 early viral load with upper airway mucosal gene expression, we profiled the host mucosal transcriptome from nasopharyngeal swab samples from 68 adults with symptomatic, mild-to-moderate coronavirus disease 19 (COVID-19). We measured SARS-CoV-2 viral load using reverse transcription-quantitative PCR (RT-qPCR). We then examined the association of SARS-CoV-2 viral load with upper airway mucosal immune response. We detected SARS-CoV-2 in all samples and recovered >80% of the genome from 95% of the samples from symptomatic COVID-19 adults. The respiratory virome was dominated by SARS-CoV-2, with limited codetection of other respiratory viruses, with the human Rhinovirus C being identified in 4 (6%) samples. This limited codetection of other respiratory viral pathogens may be due to the implementation of public health measures, like social distancing and masking practices. We observed a significant positive correlation between SARS-CoV-2 viral load and interferon signaling (OAS2, OAS3, IFIT1, UPS18, ISG15, ISG20, IFITM1, and OASL), chemokine signaling (CXCL10 and CXCL11), and adaptive immune system (IFITM1, CD300E, and SIGLEC1) genes in symptomatic, mild-to-moderate COVID-19 adults, when adjusting for age, sex, and race. Interestingly, the expression levels of most of these genes plateaued at a cycle threshold (CT) value of ~25. Overall, our data show that the early nasal mucosal immune response to SARS-CoV-2 infection is viral load dependent, potentially modifying COVID-19 outcomes. IMPORTANCE Several prior studies have shown that SARS-CoV-2 viral load can predict the likelihood of disease spread and severity. A higher detectable SARS-CoV-2 plasma viral load was associated with worse respiratory disease severity. However, the relationship between SARS-CoV-2 viral load, airway mucosal gene expression, and immune response remains elusive. We profiled the nasal mucosal transcriptome from nasal samples collected from adults infected with SARS-CoV-2 during spring 2020 with mild-to-moderate symptoms using a comprehensive metatranscriptomics method. We observed a positive correlation between SARS-CoV-2 viral load, interferon signaling, chemokine signaling, and adaptive immune system in adults with COVID-19. Our data suggest that early nasal mucosal immune response to SARS-CoV-2 infection was viral load dependent and may modify COVID-19 outcomes.
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