351
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Bussienne C, Marquet R, Paillart JC, Bernacchi S. Post-Translational Modifications of Retroviral HIV-1 Gag Precursors: An Overview of Their Biological Role. Int J Mol Sci 2021; 22:ijms22062871. [PMID: 33799890 PMCID: PMC8000049 DOI: 10.3390/ijms22062871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/06/2021] [Accepted: 03/09/2021] [Indexed: 11/24/2022] Open
Abstract
Protein post-translational modifications (PTMs) play key roles in eukaryotes since they finely regulate numerous mechanisms used to diversify the protein functions and to modulate their signaling networks. Besides, these chemical modifications also take part in the viral hijacking of the host, and also contribute to the cellular response to viral infections. All domains of the human immunodeficiency virus type 1 (HIV-1) Gag precursor of 55-kDa (Pr55Gag), which is the central actor for viral RNA specific recruitment and genome packaging, are post-translationally modified. In this review, we summarize the current knowledge about HIV-1 Pr55Gag PTMs such as myristoylation, phosphorylation, ubiquitination, sumoylation, methylation, and ISGylation in order to figure out how these modifications affect the precursor functions and viral replication. Indeed, in HIV-1, PTMs regulate the precursor trafficking between cell compartments and its anchoring at the plasma membrane, where viral assembly occurs. Interestingly, PTMs also allow Pr55Gag to hijack the cell machinery to achieve viral budding as they drive recognition between viral proteins or cellular components such as the ESCRT machinery. Finally, we will describe and compare PTMs of several other retroviral Gag proteins to give a global overview of their role in the retroviral life cycle.
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352
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Downregulated miR-451a as a feature of the plasma cfRNA landscape reveals regulatory networks of IL-6/IL-6R-associated cytokine storms in COVID-19 patients. Cell Mol Immunol 2021; 18:1064-1066. [PMID: 33637960 PMCID: PMC7907785 DOI: 10.1038/s41423-021-00652-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/03/2021] [Indexed: 02/07/2023] Open
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353
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EGCG, a Green Tea Catechin, as a Potential Therapeutic Agent for Symptomatic and Asymptomatic SARS-CoV-2 Infection. Molecules 2021; 26:molecules26051200. [PMID: 33668085 PMCID: PMC7956763 DOI: 10.3390/molecules26051200] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/20/2021] [Accepted: 02/20/2021] [Indexed: 12/26/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged to be the greatest threat to humanity in the modern world and has claimed nearly 2.2 million lives worldwide. The United States alone accounts for more than one fourth of 100 million COVID-19 cases across the globe. Although vaccination against SARS-CoV-2 has begun, its efficacy in preventing a new or repeat COVID-19 infection in immunized individuals is yet to be determined. Calls for repurposing of existing, approved, drugs that target the inflammatory condition in COVID-19 are growing. Our initial gene ontology analysis predicts a similarity between SARS-CoV-2 induced inflammatory and immune dysregulation and the pathophysiology of rheumatoid arthritis. Interestingly, many of the drugs related to rheumatoid arthritis have been found to be lifesaving and contribute to lower COVID-19 morbidity. We also performed in silico investigation of binding of epigallocatechin gallate (EGCG), a well-known catechin, and other catechins on viral proteins and identified papain-like protease protein (PLPro) as a binding partner. Catechins bind to the S1 ubiquitin-binding site of PLPro, which might inhibit its protease function and abrogate SARS-CoV-2 inhibitory function on ubiquitin proteasome system and interferon stimulated gene system. In the realms of addressing inflammation and how to effectively target SARS-CoV-2 mediated respiratory distress syndrome, we review in this article the available knowledge on the strategic placement of EGCG in curbing inflammatory signals and how it may serve as a broad spectrum therapeutic in asymptomatic and symptomatic COVID-19 patients.
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354
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Proteomic Analysis of ISGylation in Immortalized Porcine Alveolar Macrophage Cell Lines Induced by Type I Interferon. Vaccines (Basel) 2021; 9:vaccines9020164. [PMID: 33671165 PMCID: PMC7922875 DOI: 10.3390/vaccines9020164] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 12/21/2022] Open
Abstract
Interferon-stimulated gene product 15 (ISG15), a ubiquitin-like molecule, can be conjugated to protein substrates through a reversible process known as ISGylation. ISG15 and ISGylation are both strongly upregulated by type I interferons and play putative key roles in host innate immunity against viral infection. However, the function of ISGylation and identities of ISGylation substrates are largely unknown. Here, a novel monoclonal antibody (Mab) that specifically recognizes porcine ISG15 (pISG15) was employed to capture ISG15-conjugated proteins from IFNs-stimulated porcine cell lysates. Next, Mab-captured conjugates were analyzed using proteomics-based tools to identify potential ISGylation protein targets in order to elucidate the roles of ISG15 and ISGylation in porcine cells. Subsequently, 190 putative ISGylation sites were detected within 98 identified ISGylation candidates; several candidates contained more than one ISGylation-modifiable lysine residue, including pISG15 itself. Motif enrichment analysis of confirmed ISGylation sites demonstrated a moderate bias towards certain sites with specific upstream amino acid residues. Meanwhile, results of Gene Ontology (GO)-based annotation and functional enrichment and protein-protein interaction (PPI) network analyses of porcine ISG15-conjugated substrate proteins indicated that these substrates were mainly associated with the host metabolism, especially nucleotide metabolic pathways that ultimately may participate in cellular antiviral defenses. Notably, several ISGs (MX1, IFIT1, OAS1, ISG15 and putative ISG15 E3 ligase Herc6) were also identified as putative ISGylation substrates within a regulatory loop involving ISGylation of ISGs themselves. Taken together, proteomics analysis of porcine ISGylation substrates revealed putative functional roles of ISG15 and novel host ISGylation targets that may ultimately be involved in cellular antiviral responses.
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355
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Wang L, Sievert D, Gleeson J, Clark AE, Carlin AF, Federman H, Gastfriend BD, Shusta E, Palecek SP. A Human 3D neural assembloid model for SARS-CoV-2 infection. RESEARCH SQUARE 2021:rs.3.rs-214352. [PMID: 33594354 PMCID: PMC7885926 DOI: 10.21203/rs.3.rs-214352/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Clinical evidence suggests the central nervous system (CNS) is frequently impacted by SARS-CoV-2 infection, either directly or indirectly, although mechanisms remain unclear. Pericytes are perivascular cells within the brain that are proposed as SARS-CoV-2 infection points 1 . Here we show that pericyte-like cells (PLCs), when integrated into a cortical organoid, are capable of infection with authentic SARS-CoV-2. Prior to infection, PLCs elicited astrocytic maturation and production of basement membrane components, features attributed to pericyte functions in vivo. While traditional cortical organoids showed little evidence of infection, PLCs within cortical organoids served as viral 'replication hubs', with virus spreading to astrocytes and mediating inflammatory type I interferon transcriptional responses. Therefore, PLC-containing cortical organoids (PCCOs) represent a new 'assembloid' model 2 that supports SARS-CoV-2 entry and replication in neural tissue, and PCCOs serve as an experimental model for neural infection.
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Affiliation(s)
- Lu Wang
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA; Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, 92123, USA
| | - David Sievert
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA; Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Joseph Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA; Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, 92123, USA; Department for Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alex E Clark
- Department of Medicine; University of California San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Aaron F Carlin
- Department of Medicine; University of California San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Hannah Federman
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers-The State University, Newark, NJ, 07103, USA
| | - Benjamin D Gastfriend
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Eric Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
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356
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Wang L, Ning S. TRIMming Type I Interferon-Mediated Innate Immune Response in Antiviral and Antitumor Defense. Viruses 2021; 13:279. [PMID: 33670221 PMCID: PMC7916971 DOI: 10.3390/v13020279] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 12/17/2022] Open
Abstract
The tripartite motif (TRIM) family comprises at least 80 members in humans, with most having ubiquitin or SUMO E3 ligase activity conferred by their N-terminal RING domain. TRIMs regulate a wide range of processes in ubiquitination- or sumoylation-dependent manners in most cases, and fewer as adaptors. Their roles in the regulation of viral infections, autophagy, cell cycle progression, DNA damage and other stress responses, and carcinogenesis are being increasingly appreciated, and their E3 ligase activities are attractive targets for developing specific immunotherapeutic strategies for immune diseases and cancers. Given their importance in antiviral immune response, viruses have evolved sophisticated immune escape strategies to subvert TRIM-mediated mechanisms. In this review, we focus on their regulation of IFN-I-mediated innate immune response, which plays key roles in antiviral and antitumor defense.
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Affiliation(s)
- Ling Wang
- Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA;
- Center of Excellence for Inflammation, Infectious Diseases and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Shunbin Ning
- Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA;
- Center of Excellence for Inflammation, Infectious Diseases and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
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357
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Wang L, Sievert D, Clark AE, Federman H, Gastfriend BD, Shusta E, Palecek SP, Carlin AF, Gleeson J. A Human 3D neural assembloid model for SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33594369 DOI: 10.1101/2021.02.09.430349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Clinical evidence suggests the central nervous system (CNS) is frequently impacted by SARS-CoV-2 infection, either directly or indirectly, although mechanisms remain unclear. Pericytes are perivascular cells within the brain that are proposed as SARS-CoV-2 infection points 1 . Here we show that pericyte-like cells (PLCs), when integrated into a cortical organoid, are capable of infection with authentic SARS-CoV-2. Prior to infection, PLCs elicited astrocytic maturation and production of basement membrane components, features attributed to pericyte functions in vivo. While traditional cortical organoids showed little evidence of infection, PLCs within cortical organoids served as viral 'replication hubs', with virus spreading to astrocytes and mediating inflammatory type I interferon transcriptional responses. Therefore, PLC-containing cortical organoids (PCCOs) represent a new 'assembloid' model 2 that supports SARS-CoV-2 entry and replication in neural tissue, and PCCOs serve as an experimental model for neural infection.
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358
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Soday L, Potts M, Hunter LM, Ravenhill BJ, Houghton JW, Williamson JC, Antrobus R, Wills MR, Matheson NJ, Weekes MP. Comparative Cell Surface Proteomic Analysis of the Primary Human T Cell and Monocyte Responses to Type I Interferon. Front Immunol 2021; 12:600056. [PMID: 33628210 PMCID: PMC7897682 DOI: 10.3389/fimmu.2021.600056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/13/2021] [Indexed: 12/28/2022] Open
Abstract
The cellular response to interferon (IFN) is essential for antiviral immunity, IFN-based therapy and IFN-related disease. The plasma membrane (PM) provides a critical interface between the cell and its environment, and is the initial portal of entry for viruses. Nonetheless, the effect of IFN on PM proteins is surprisingly poorly understood, and has not been systematically investigated in primary immune cells. Here, we use multiplexed proteomics to quantify IFNα2a-stimulated PM protein changes in primary human CD14+ monocytes and CD4+ T cells from five donors, quantifying 606 and 482 PM proteins respectively. Comparison of cell surface proteomes revealed a remarkable invariance between donors in the overall composition of the cell surface from each cell type, but a marked donor-to-donor variability in the effects of IFNα2a. Furthermore, whereas only 2.7% of quantified proteins were consistently upregulated by IFNα2a at the surface of CD4+ T cells, 6.8% of proteins were consistently upregulated in primary monocytes, suggesting that the magnitude of the IFNα2a response varies according to cell type. Among these differentially regulated proteins, we found the viral target Endothelin-converting enzyme 1 (ECE1) to be an IFNα2a-stimulated protein exclusively upregulated at the surface of CD4+ T cells. We therefore provide a comprehensive map of the cell surface of IFNα2a-stimulated primary human immune cells, including previously uncharacterized interferon stimulated genes (ISGs) and candidate antiviral factors.
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Affiliation(s)
- Lior Soday
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Martin Potts
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Leah M. Hunter
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Benjamin J. Ravenhill
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Jack W. Houghton
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - James C. Williamson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Mark R. Wills
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Nicholas J. Matheson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Michael P. Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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359
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Shao DD, Meng FZ, Liu Y, Xu XQ, Wang X, Hu WH, Hou W, Ho WZ. Poly(dA:dT) Suppresses HSV-2 Infection of Human Cervical Epithelial Cells Through RIG-I Activation. Front Immunol 2021; 11:598884. [PMID: 33664729 PMCID: PMC7923882 DOI: 10.3389/fimmu.2020.598884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/16/2020] [Indexed: 12/25/2022] Open
Abstract
Epithelial cells of the female reproductive tract (FRT) participate in the initial innate immunity against viral infections. Poly(dA:dT) is a synthetic analog of B form double-stranded (ds) DNA which can activate the interferon (IFN) signaling pathway-mediated antiviral immunity through DNA-dependent RNA Polymerase III. Here we investigated whether poly(dA:dT) could inhibit herpes simplex virus type 2 (HSV-2) infection of human cervical epithelial cells (End1/E6E7). We demonstrated that poly(dA:dT) treatment of End1/E6E7 cells could significantly inhibit HSV-2 infection. Mechanistically, poly(dA:dT) treatment of the cells induced the expression of the intracellular IFNs and the multiple antiviral IFN-stimulated genes (ISGs), including IFN-stimulated gene 15 (ISG15), IFN-stimulated gene 56 (ISG56), 2'-5'-oligoadenylate synthetase 1 (OAS1), 2'-5'-oligoadenylate synthetase 2 (OAS2), myxovirus resistance protein A (MxA), myxovirus resistance protein B (MxB), virus inhibitory protein, endoplasmic reticulum-associated, IFN-inducible (Viperin), and guanylate binding protein 5 (GBP5). Further investigation showed that the activation of RIG-I was largely responsible for poly(dA:dT)-mediated HSV-2 inhibition and IFN/ISGs induction in the cervical epithelial cells, as RIG-I knockout abolished the poly(dA:dT) actions. These observations demonstrate the importance for design and development of AT-rich dsDNA-based intervention strategies to control HSV-2 mucosal transmission in FRT.
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Affiliation(s)
- Dan-Dan Shao
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Feng-Zhen Meng
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yu Liu
- Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Xi-Qiu Xu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xu Wang
- Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Wen-Hui Hu
- Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Wei Hou
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Wen-Zhe Ho
- Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
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360
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Sada M, Watanabe M, Inui T, Nakamoto K, Hirata A, Nakamura M, Honda K, Saraya T, Kurai D, Kimura H, Ishii H, Takizawa H. Ruxolitinib inhibits poly(I:C) and type 2 cytokines-induced CCL5 production in bronchial epithelial cells: A potential therapeutic agent for severe eosinophilic asthma. IMMUNITY INFLAMMATION AND DISEASE 2021; 9:363-373. [PMID: 33534941 PMCID: PMC8127547 DOI: 10.1002/iid3.397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 12/18/2022]
Abstract
Rationale Severe eosinophilic asthma is characterized by airway eosinophilia and corticosteroid‐resistance, commonly overlapping with type 2 inflammation. It has been reported that chemokine (C‐C motif) ligand 5 (CCL5) is involved in the exacerbation of asthma by RNA virus infections. Indeed, treatment with a virus‐associated ligand and a T helper type 2 cell (Th2) cytokine can synergistically stimulate CCL5 production in bronchial epithelial cells. We aimed to evaluate the mechanisms underlying CCL5 production in this in vitro model and to assess the potential of Janus kinase 1 (JAK1) as a novel therapeutic target via the use of ruxolitinib. Methods We stimulated primary normal human bronchial epithelial (NHBE) cells and BEAS‐2B cells with poly(I:C) along with interleukin‐13 (IL‐13) or IL‐4, and assessed CCL5 production. We also evaluated the signals involved in virus‐ and Th2‐cytokine‐induced CCL5 production and explored a therapeutic agent that attenuates the CCL5 production. Results Poly(I:C) stimulated NHBE and BEAS‐2B cells to produce CCL5. Poly(I:C) and IL‐13 increased CCL5 production. Poly(I:C)‐induced CCL5 production occurred via the TLR3–IRF3 and IFNAR/JAK1–phosphoinositide 3‐kinase (PI3K) pathways, but not the IFNAR/JAK1–STATs pathway. In addition, IL‐13 did not augment poly(I:C)‐induced CCL5 production via the canonical IL‐13R/IL‐4R/JAK1–STAT6 pathway but likely via subsequent TLR3‐IRF3‐IFNAR/JAK1‐PI3K pathways. JAK1 was identified to be a potential therapeutic target for severe eosinophilic asthma. The JAK1/2 inhibitor, ruxolitinib, was demonstrated to more effectively decrease CCL5 production in BEAS‐2B cells than fluticasone propionate. Conclusion We have demonstrated that JAK1 is a possible therapeutic target for severe corticosteroid‐resistant asthma with airway eosinophilia and persistent Th2‐type inflammation, and that ruxolitinib has potential as an alternative pharmacotherapy.
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Affiliation(s)
- Mitsuru Sada
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Masato Watanabe
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Toshiya Inui
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Keitaro Nakamoto
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Aya Hirata
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Masuo Nakamura
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Kojiro Honda
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Takeshi Saraya
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Daisuke Kurai
- Division of Infectious Diseases, Department of General Medicine, School of Medicine, Kyorin University, Tokyo, Japan
| | - Hirokazu Kimura
- Department of Health Science, Graduate School of Health Science, Gunma Paz University, Gunma, Japan
| | - Haruyuki Ishii
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Hajime Takizawa
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
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361
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Chiang C, Liu G, Gack MU. Viral Evasion of RIG-I-Like Receptor-Mediated Immunity through Dysregulation of Ubiquitination and ISGylation. Viruses 2021; 13:182. [PMID: 33530371 PMCID: PMC7910861 DOI: 10.3390/v13020182] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/15/2022] Open
Abstract
Viral dysregulation or suppression of innate immune responses is a key determinant of virus-induced pathogenesis. Important sensors for the detection of virus infection are the RIG-I-like receptors (RLRs), which, in turn, are antagonized by many RNA viruses and DNA viruses. Among the different escape strategies are viral mechanisms to dysregulate the post-translational modifications (PTMs) that play pivotal roles in RLR regulation. In this review, we present the current knowledge of immune evasion by viral pathogens that manipulate ubiquitin- or ISG15-dependent mechanisms of RLR activation. Key viral strategies to evade RLR signaling include direct targeting of ubiquitin E3 ligases, active deubiquitination using viral deubiquitinating enzymes (DUBs), and the upregulation of cellular DUBs that regulate RLR signaling. Additionally, we summarize emerging new evidence that shows that enzymes of certain coronaviruses such as SARS-CoV-2, the causative agent of the current COVID-19 pandemic, actively deISGylate key molecules in the RLR pathway to escape type I interferon (IFN)-mediated antiviral responses. Finally, we discuss the possibility of targeting virally-encoded proteins that manipulate ubiquitin- or ISG15-mediated innate immune responses for the development of new antivirals and vaccines.
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Affiliation(s)
| | | | - Michaela U. Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA; (C.C.); (G.L.)
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362
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Fu Z, Huang B, Tang J, Liu S, Liu M, Ye Y, Liu Z, Xiong Y, Zhu W, Cao D, Li J, Niu X, Zhou H, Zhao YJ, Zhang G, Huang H. The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery. Nat Commun 2021; 12:488. [PMID: 33473130 PMCID: PMC7817691 DOI: 10.1038/s41467-020-20718-8] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/16/2020] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 is the pathogen responsible for the COVID-19 pandemic. The SARS-CoV-2 papain-like cysteine protease (PLpro) has been implicated in playing important roles in virus maturation, dysregulation of host inflammation, and antiviral immune responses. The multiple functions of PLpro render it a promising drug target. Therefore, we screened a library of approved drugs and also examined available inhibitors against PLpro. Inhibitor GRL0617 showed a promising in vitro IC50 of 2.1 μM and an effective antiviral inhibition in cell-based assays. The co-crystal structure of SARS-CoV-2 PLproC111S in complex with GRL0617 indicates that GRL0617 is a non-covalent inhibitor and it resides in the ubiquitin-specific proteases (USP) domain of PLpro. NMR data indicate that GRL0617 blocks the binding of ISG15 C-terminus to PLpro. Using truncated ISG15 mutants, we show that the C-terminus of ISG15 plays a dominant role in binding PLpro. Structural analysis reveals that the ISG15 C-terminus binding pocket in PLpro contributes a disproportionately large portion of binding energy, thus this pocket is a hot spot for antiviral drug discovery targeting PLpro.
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Affiliation(s)
- Ziyang Fu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Bin Huang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Jinle Tang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Shuyan Liu
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Ming Liu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yuxin Ye
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Zhihong Liu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yuxian Xiong
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Wenning Zhu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Dan Cao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Jihui Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering, Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China
| | - Huan Zhou
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Yong Juan Zhao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China.
| | - Hao Huang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
- Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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363
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Spivack K, Muzzelo C, Hall M, Warga E, Neely C, Slepian H, Cunningham A, Tucker M, Elmer J. Enhancement of transgene expression by the β-catenin inhibitor iCRT14. Plasmid 2021; 114:102556. [PMID: 33472046 DOI: 10.1016/j.plasmid.2021.102556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/08/2020] [Accepted: 10/14/2020] [Indexed: 11/30/2022]
Abstract
The innate immune response is an essential defense mechanism that allows cells to detect pathogen-associated molecular patterns (PAMPs) like endotoxin or cytosolic DNA and then induce the expression of defensive genes that restrict the replication of viruses and other pathogens. However, the therapeutic DNA used in some gene therapy treatments can also trigger the innate immune response, which activates host cell genes that may inhibit transgene expression. The goal of this study was to enhance transgene expression by inhibiting key components of the innate immune response with small molecule inhibitors (iCRT14, curcumin, Amlexanox, H-151, SC-514, & VX-702). Most of the inhibitors significantly increased transgene (luciferase) expression at least 2-fold, but the β-catenin/TCF4 inhibitor iCRT14 showed the highest enhancement (16 to 35-fold) in multiple cell lines (PC-3, MCF7, & MB49) without significantly decreasing cellular proliferation. Alternatively, cloning a β-catenin/TCF4 binding motif (TCAAAG) into the EF1α promoter also enhanced transgene expression up to 8-fold. To further investigate the role of β-catenin/TCF4 in transgene expression, mRNA-sequencing experiments were conducted to identify host cell genes that were upregulated following transfection with PEI but down-regulated after the addition of iCRT14. As expected, transfection with plasmid DNA activated the innate immune response and upregulated hundreds (687) of defensive genes, but only 7 of those genes were down-regulated in the presence of iCRT14 (e.g., PTGS2 & PLA1A). Altogether, these results show that transgene expression can be enhanced by inhibiting the innate immune response with SMIs like iCRT14, which inhibits β-catenin/TCF4 to prevent the expression of specific host cell genes.
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Affiliation(s)
- Kyle Spivack
- Villanova University, Department of Chemical & Biological Engineering, United States
| | - Christine Muzzelo
- Villanova University, Department of Chemical & Biological Engineering, United States
| | - Matthew Hall
- Villanova University, Department of Chemical & Biological Engineering, United States
| | - Eric Warga
- Villanova University, Department of Chemical & Biological Engineering, United States
| | - Christopher Neely
- Villanova University, Department of Chemical & Biological Engineering, United States
| | - Holly Slepian
- Villanova University, Department of Chemical & Biological Engineering, United States
| | - Alyssa Cunningham
- Villanova University, Department of Chemical & Biological Engineering, United States
| | - Matthew Tucker
- Villanova University, Department of Chemical & Biological Engineering, United States
| | - Jacob Elmer
- Villanova University, Department of Chemical & Biological Engineering, United States.
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364
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Sauter D, Kirchhoff F. Evolutionary conflicts and adverse effects of antiviral factors. eLife 2021; 10:e65243. [PMID: 33450175 PMCID: PMC7811402 DOI: 10.7554/elife.65243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
Human cells are equipped with a plethora of antiviral proteins protecting them against invading viral pathogens. In contrast to apoptotic or pyroptotic cell death, which serves as ultima ratio to combat viral infections, these cell-intrinsic restriction factors may prevent or at least slow down viral spread while allowing the host cell to survive. Nevertheless, their antiviral activity may also have detrimental effects on the host. While the molecular mechanisms underlying the antiviral activity of restriction factors are frequently well investigated, potential undesired effects of their antiviral functions on the host cell are hardly explored. With a focus on antiretroviral proteins, we summarize in this review how individual restriction factors may exert adverse effects as trade-off for efficient defense against attacking pathogens.
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Affiliation(s)
- Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical CenterUlmGermany
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital TübingenTübingenGermany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical CenterUlmGermany
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365
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Zao X, Cheng J, Shen C, Guan G, Feng X, Zou J, Zhang J, Liu T, Zheng H, Zhang T, Wang J, Liu J, Li D, Lu F, You F, Chen X. NFATc3 inhibits hepatocarcinogenesis and HBV replication via positively regulating RIG-I-mediated interferon transcription. Oncoimmunology 2021; 10:1869388. [PMID: 33520407 PMCID: PMC7808430 DOI: 10.1080/2162402x.2020.1869388] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Nuclear factor of activated T cells 3 (NFATc3) has been reported to upregulate type I interferons (IFNs) expression, and the abnormal expression and activation of NFATc3 were closely related to tumorigenesis. However, the potential function of NFATc3 in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) remains to be elucidated. In this study, we found that NFATc3 gene was frequently deleted and downregulated in HCC tumor tissues, and that the downregulation of NFATc3 was associated with poor prognosis of HCC patients. The gain- and loss-of-function experiments demonstrated that NFATc3 inhibited HCC cell proliferation and invasion, as well as HBV replication. Mechanistically, NFATc3 could bind to the promoters of IFNL1 and IFNB1 genes and prompt the production of IFNs and interferon-stimulated genes. Furthermore, retinoic acid-inducible gene-I (RIG-I) pathway activation increased NFATc3 expression and nuclear localization, and activated NFATc3 further enhanced RIG-I-mediated IFN responses. Collectively, our findings reveal a novel regulatory signaling cascade, the RIG-I/NFATc3/IFNs axis, which inhibits hepatocarcinogenesis and HBV replication by enhancing the immune response in hepatocytes, and this functional axis might potentially be exploited for therapeutic benefits in the clinical treatment of HBV-related HCC.
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Affiliation(s)
- Xiaobin Zao
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Jin Cheng
- Department of Sports Medicine, Peking University Third Hospital, Institute of Sports Medicine of Peking University, Beijing Key Laboratory of Sports Injuries, Beijing, China
| | - Congle Shen
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Guiwen Guan
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Xiaoyu Feng
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Jun Zou
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Jing Zhang
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Tianxu Liu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Huiling Zheng
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Ting Zhang
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Jie Wang
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Jia Liu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Deyao Li
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
| | - Fengmin Lu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China.,Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Fuping You
- Institute of Systems Biomedicine, Department of Immunology, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Xiangmei Chen
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, China
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366
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Pacella I, Spinelli FR, Severa M, Timperi E, Tucci G, Zagaglioni M, Ceccarelli F, Rizzo F, Coccia EM, Patel RS, Martin-Fernandez M, Bogunovic D, Conti F, Barnaba V, Piconese S. ISG15 protects human Tregs from interferon alpha-induced contraction in a cell-intrinsic fashion. Clin Transl Immunology 2020; 9:e1221. [PMID: 33376595 PMCID: PMC7758615 DOI: 10.1002/cti2.1221] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/10/2020] [Accepted: 11/09/2020] [Indexed: 01/02/2023] Open
Abstract
Objectives Type I interferons (IFNs) inhibit regulatory T-cell (Treg) expansion and activation, making them beneficial in antiviral responses, but detrimental in autoimmune diseases. Herein, we investigate the role of ISG15 in human Tregs in the context of refractoriness to type I IFN stimulation. Methods ISG15 expression and Treg dynamics were analysed in vitro and ex vivo from patients with chronic hepatitis C, with lupus and ISG15 deficiency. Results ISG15 is expressed at high levels in human Tregs, renders them refractory to the IFN-STAT1 signal, and protects them from IFN-driven contraction. In vitro, Tregs from healthy controls upregulate ISG15 upon activation to higher levels than conventional CD4 T cells, and ISG15-silenced Tregs are more susceptible to IFNα-induced contraction. In human ISG15 deficiency, patient Tregs display an elevated IFN signature relative to Tregs from healthy control. In vivo, in patients with chronic hepatitis C, 2 days after starting pegIFN/ribavirin therapy, a stronger ISG15 inducibility correlates with a milder Treg depletion. Ex vivo, in systemic lupus erythematosus patients, higher levels of ISG15 are associated to reduced STAT1 phosphorylation in response to IFNα, and also to increased frequencies of Tregs, characterising active disease. Conclusion Our results reveal a Treg-intrinsic role of ISG15 in dictating their refractoriness to the IFN signal, thus preserving the Treg population under inflammatory conditions.
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Affiliation(s)
- Ilenia Pacella
- Dipartimento di Scienze Cliniche Internistiche, Anestesiologiche e Cardiovascolari Sapienza Università di Roma Rome Italy
| | - Francesca Romana Spinelli
- Dipartimento di Scienze Cliniche Internistiche, Anestesiologiche e Cardiovascolari Sapienza Università di Roma Rome Italy
| | - Martina Severa
- Department of Infectious Diseases Istituto Superiore di Sanità Rome Italy
| | - Eleonora Timperi
- Dipartimento di Scienze Cliniche Internistiche, Anestesiologiche e Cardiovascolari Sapienza Università di Roma Rome Italy.,Present address: Eleonora Timperi Institut Curie Paris France
| | - Gloria Tucci
- Dipartimento di Scienze Cliniche Internistiche, Anestesiologiche e Cardiovascolari Sapienza Università di Roma Rome Italy
| | - Marta Zagaglioni
- Dipartimento di Scienze Cliniche Internistiche, Anestesiologiche e Cardiovascolari Sapienza Università di Roma Rome Italy.,Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti Rome Italy
| | - Fulvia Ceccarelli
- Dipartimento di Scienze Cliniche Internistiche, Anestesiologiche e Cardiovascolari Sapienza Università di Roma Rome Italy
| | - Fabiana Rizzo
- Department of Infectious Diseases Istituto Superiore di Sanità Rome Italy
| | - Eliana M Coccia
- Department of Infectious Diseases Istituto Superiore di Sanità Rome Italy
| | - Roosheel S Patel
- Center for Inborn Errors of Immunity Icahn School of Medicine at Mount Sinai New York NY USA.,Precision Immunology Institute Icahn School of Medicine at Mount Sinai New York NY USA.,Mindich Child Health and Development Institute Icahn School of Medicine at Mount Sinai New York NY USA.,Department of Pediatrics Icahn School of Medicine at Mount Sinai New York NY USA.,Department of Microbiology Icahn School of Medicine at Mount Sinai New York NY USA
| | - Marta Martin-Fernandez
- Center for Inborn Errors of Immunity Icahn School of Medicine at Mount Sinai New York NY USA.,Precision Immunology Institute Icahn School of Medicine at Mount Sinai New York NY USA.,Mindich Child Health and Development Institute Icahn School of Medicine at Mount Sinai New York NY USA.,Department of Pediatrics Icahn School of Medicine at Mount Sinai New York NY USA.,Department of Microbiology Icahn School of Medicine at Mount Sinai New York NY USA
| | - Dusan Bogunovic
- Center for Inborn Errors of Immunity Icahn School of Medicine at Mount Sinai New York NY USA.,Precision Immunology Institute Icahn School of Medicine at Mount Sinai New York NY USA.,Mindich Child Health and Development Institute Icahn School of Medicine at Mount Sinai New York NY USA.,Department of Pediatrics Icahn School of Medicine at Mount Sinai New York NY USA.,Department of Microbiology Icahn School of Medicine at Mount Sinai New York NY USA
| | - Fabrizio Conti
- Dipartimento di Scienze Cliniche Internistiche, Anestesiologiche e Cardiovascolari Sapienza Università di Roma Rome Italy
| | - Vincenzo Barnaba
- Dipartimento di Scienze Cliniche Internistiche, Anestesiologiche e Cardiovascolari Sapienza Università di Roma Rome Italy.,Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti Rome Italy
| | - Silvia Piconese
- Dipartimento di Scienze Cliniche Internistiche, Anestesiologiche e Cardiovascolari Sapienza Università di Roma Rome Italy.,Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti Rome Italy
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367
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Enhancement of HIV-1 Env-Specific CD8 T Cell Responses Using Interferon-Stimulated Gene 15 as an Immune Adjuvant. J Virol 2020; 95:JVI.01155-20. [PMID: 33115866 DOI: 10.1128/jvi.01155-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/21/2020] [Indexed: 12/22/2022] Open
Abstract
Induction of the endogenous innate immune system by interferon (IFN) triggers the expression of many proteins that serve like alarm bells in the body, activating an immune response. After a viral infection, one of the genes activated by IFN induction is the IFN-stimulated gene 15 (ISG15), which encodes a ubiquitin-like protein that undergoes a reversible posttranslational modification (ISGylation). ISG15 protein can also act unconjugated, intracellularly and secreted, acting as a cytokine. Although ISG15 has an essential role in host defense responses to microbial infection, its role as an immunomodulator in the vaccine field remains to be defined. In this investigation, we showed that ISG15 exerts an immunomodulatory role in human immunodeficiency virus (HIV) vaccines. In mice, after priming with a DNA-ISG15 vector mixed with a DNA expressing HIV-1 gp120 (DNA-gp120), followed by a booster with a modified vaccinia virus Ankara (MVA) vector expressing HIV-1 antigens, both wild-type ISG15-conjugated (ISG15-wt) and mutant unconjugated (ISG15-mut) proteins act as immune adjuvants by increasing the magnitude and quality of HIV-1-specific CD8 T cells, with ISG15-wt providing better immunostimulatory activity than ISG15-mut. The HIV-1 Env-specific CD8 T cell responses showed a predominant T effector memory (TEM) phenotype in all groups. Moreover, the amount of DNA-gp120 used to immunize mice could be reduced 5-fold after mixing with DNA-ISG15 without affecting the potency and the quality of the HIV-1 Env-specific immune responses. Our study clearly highlights the potential use of the IFN-induced ISG15 protein as immune adjuvant to enhance immune responses to HIV antigens, suggesting that this molecule might be exploitable for prophylactic and therapeutic vaccine approaches against pathogens.IMPORTANCE Our study described the potential role of ISG15 as an immunomodulatory molecule in the optimization of HIV/AIDS vaccine candidates. Using a DNA prime-MVA boost immunization protocol, our results indicated an increase in the potency and the quality of the HIV-1 Env-specific CD8 T cell response. These results highlight the adjuvant potency of ISG15 to elicit improved viral antigen presentation to the immune system, resulting in an enhanced HIV-1 vaccine immune response. The DNA-ISG15 vector could find applicability in the vaccine field in combination with other nucleic acid-based vector vaccines.
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368
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Pitsillou E, Liang J, Ververis K, Lim KW, Hung A, Karagiannis TC. Identification of Small Molecule Inhibitors of the Deubiquitinating Activity of the SARS-CoV-2 Papain-Like Protease: in silico Molecular Docking Studies and in vitro Enzymatic Activity Assay. Front Chem 2020; 8:623971. [PMID: 33364229 PMCID: PMC7753156 DOI: 10.3389/fchem.2020.623971] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/16/2020] [Indexed: 12/14/2022] Open
Abstract
COVID-19 is an ongoing pandemic caused by the SARS-CoV-2 virus with important political, socio-economic, and public health consequences. Inhibiting replication represents an important antiviral approach, and in this context two viral proteases, the SARS-CoV-2 main and papain-like proteases (PLpro), which cleave pp1a and pp1ab polypeptides, are critical. Along with protease activity, the PLpro possesses deubiquitinating activity, which is important in immune regulation. Naphthalene-based inhibitors, such as the well-investigated GRL-0617 compound, have been shown to possess dual effects, inhibiting both protease and deubiquitinating activity of the PLpro. Rather than binding to the canonical catalytic triad, these type of non-covalent inhibitors target an adjacent pocket, the naphthalene-inhibitor binding site. Using a high-throughput screen, we have previously identified the dietary hypericin, rutin, and cyanidin-3-O-glucoside compounds as potential protease inhibitors targeting the naphthalene-inhibitor binding site. Here, our aim was to investigate the binding characteristics of these compounds to the PLpro, and to evaluate deubiquitinating activity, by analyzing seven different PLpro crystal structures. Molecular docking highlighted the relatively high affinity of GRL-0617 and dietary compounds. In contrast binding of the small molecules was abolished in the presence of ubiquitin in the palm subdomain of the PLpro. Further, docking the small molecules in the naphthalene-inhibitor binding site, followed by protein-protein docking revealed displacement of ubiquitin in a conformation inconsistent with functional activity. Finally, the deubiquitinating activity was validated in vitro using an enzymatic activity assay. The findings indicated that the dietary compounds inhibited deubiquitinase activity in the micromolar range with an order of activity of GRL-0167, hypericin >> rutin, cyanidin-3-O-glucoside > epigallocatechin gallate, epicatechin gallate, and cefotaxime. Our findings are in accordance with mechanisms and potential antiviral effects of the naphthalene-based, GRL-0617 inhibitor, which is currently progressing in preclinical trials. Further, our findings indicate that in particular hypericin, rutin, and cyanidin-3-O-glucoside, represent suitable candidates for subsequent evaluation as PLpro inhibitors.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
| | - Julia Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
| | - Katherine Ververis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Kah Wai Lim
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia
| | - Andrew Hung
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
| | - Tom C. Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
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369
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Narovlyansky AN, Poloskov VV, Ivanova AM, Kravchenko SK, Babayeva FE, Sychevskaya KA, Mezentseva MV, Suetina IA, Russu LI, Izmest'eva AV, Ospelnikova TP, Sarymsakov AA, Ershov FI. [Interferon-regulating activity of the celagrip antiviral drug and its influence on formation of reactive oxygen species and expression of innate immunity genes in the follicular lymphoma patients]. Vopr Virusol 2020; 65:284-293. [PMID: 33533212 DOI: 10.36233/0507-4088-2020-65-5-5] [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: 11/15/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
Abstract
INTRODUCTION Medicines from the group of interferon inducers (IFNs) "swith on" the synthesis of type 1 interferons (IFN-I) and induce the expression of IFN-stimulated genes (ISGs) that regulate innate immunity reactions and protect the host from infectious agents and the tumour pathology.The purpose of the study was to determine the role of the drug celagrip (CA) in the activation of innate immunity genes and the effect on the production of reactive oxygen species (ROS) in patients with follicular lymphoma (FL). OBJECTIVES to study the intensity of ROS production and the level of expression of the IFN-α2, IFN-λ1, ISG15, BCL2, P53(TP53) and USP18 genes in response to the treatment of blood cells of patients with FL with the preparation of CA. MATERIAL AND METHODS The study involved primary cancer patients diagnosed with follicular lymphoma (FL) and healthy volunteers. A kinetic analysis of the dynamics of production of reactive oxygen species (ROS) was performed in whose blood cells, and the expression of the group of genes was determined by real-time PCR in response to CA processing. RESULTS AND DISCUSSION ROS production by blood cells of patients with FL and volunteers in the presence of CA significantly decreased (P < 0.05). The level of gene expression of ISG15, P53(TR53) and USP 18 in the group of patients with FL was significantly higher than that in the group of volunteers. When treating blood cells with CA, it becomes possible to divide patients with FL into groups with a positive and negative response in accordance with the level of expression of the USP18 gene. We divided FL patients into groups with a positive and negative response in accordance with the level of USP18 gene expression after treatment of blood cells with CA. CONCLUSIONS The CA drug reduces the production of ROS and simultaneously stimulates the activity of the innate immunity genes ISG15, P53(TP53) and USP18 in the blood cells of patients with FL.
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Affiliation(s)
- A N Narovlyansky
- National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
| | - V V Poloskov
- National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
| | - A M Ivanova
- National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
| | | | | | | | - M V Mezentseva
- National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
| | - I A Suetina
- National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
| | - L I Russu
- National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
| | - A V Izmest'eva
- National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
| | - T P Ospelnikova
- National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
| | | | - F I Ershov
- National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
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370
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Sandy Z, da Costa IC, Schmidt CK. More than Meets the ISG15: Emerging Roles in the DNA Damage Response and Beyond. Biomolecules 2020; 10:E1557. [PMID: 33203188 PMCID: PMC7698331 DOI: 10.3390/biom10111557] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022] Open
Abstract
Maintenance of genome stability is a crucial priority for any organism. To meet this priority, robust signalling networks exist to facilitate error-free DNA replication and repair. These signalling cascades are subject to various regulatory post-translational modifications that range from simple additions of chemical moieties to the conjugation of ubiquitin-like proteins (UBLs). Interferon Stimulated Gene 15 (ISG15) is one such UBL. While classically thought of as a component of antiviral immunity, ISG15 has recently emerged as a regulator of genome stability, with key roles in the DNA damage response (DDR) to modulate p53 signalling and error-free DNA replication. Additional proteomic analyses and cancer-focused studies hint at wider-reaching, uncharacterised functions for ISG15 in genome stability. We review these recent discoveries and highlight future perspectives to increase our understanding of this multifaceted UBL in health and disease.
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Affiliation(s)
| | | | - Christine K. Schmidt
- Manchester Cancer Research Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M20 4GJ, UK; (Z.S.); (I.C.d.C.)
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371
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Zhou X, Zhou L, Ge X, Guo X, Han J, Zhang Y, Yang H. Quantitative Proteomic Analysis of Porcine Intestinal Epithelial Cells Infected with Porcine Deltacoronavirus Using iTRAQ-Coupled LC-MS/MS. J Proteome Res 2020; 19:4470-4485. [PMID: 33045833 PMCID: PMC7640975 DOI: 10.1021/acs.jproteome.0c00592] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Indexed: 12/14/2022]
Abstract
Porcine deltacoronavirus (PDCoV) is an emergent enteropathogenic coronavirus associated with swine diarrhea. Porcine small intestinal epithelial cells (IPEC) are the primary target cells of PDCoV infection in vivo. Here, isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled to liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to quantitatively identify differentially expressed proteins (DEPs) in PDCoV-infected IPEC-J2 cells. A total of 78 DEPs, including 23 upregulated and 55 downregulated proteins, were identified at 24 h postinfection. The data are available via ProteomeXchange with identifier PXD019975. To ensure reliability of the proteomics data, two randomly selected DEPs, the downregulated anaphase-promoting complex subunit 7 (ANAPC7) and upregulated interferon-induced protein with tetratricopeptide repeats 1 (IFIT1), were verified by real-time PCR and Western blot, and the results of which indicate that the proteomics data were reliable and valid. Bioinformatics analyses, including GO, COG, KEGG, and STRING, further demonstrated that a majority of the DEPs are involved in numerous crucial biological processes and signaling pathways, such as immune system, digestive system, signal transduction, RIG-I-like receptor, mTOR, PI3K-AKT, autophagy, and cell cycle signaling pathways. Altogether, this is the first study on proteomes of PDCoV-infected host cells, which shall provide valuable clues for further investigation of PDCoV pathogenesis.
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Affiliation(s)
- Xinrong Zhou
- Key
Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural
Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
| | - Lei Zhou
- Key
Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural
Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
| | - Xinna Ge
- Key
Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural
Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
| | - Xin Guo
- Key
Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural
Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
| | - Jun Han
- Key
Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural
Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
| | - Yongning Zhang
- Key
Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural
Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
| | - Hanchun Yang
- Key
Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural
Affairs, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
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372
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Cardon T, Ozcan B, Aboulouard S, Kobeissy F, Duhamel M, Rodet F, Fournier I, Salzet M. Epigenetic Studies Revealed a Ghost Proteome in PC1/3 KD Macrophages under Antitumoral Resistance Induced by IL-10. ACS OMEGA 2020; 5:27774-27782. [PMID: 33163760 PMCID: PMC7643081 DOI: 10.1021/acsomega.0c02530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Our previous investigation on macrophages has allowed us to show that the inhibition of the enzyme proprotein convertase (PC1/3) controls the activation of macrophages. We demonstrated that PC1/3 knockdown (KD) in macrophages exhibits an increased secretion of proinflammatory and antitumoral factors. In this biological context, we assessed the presence of histone modifications and the presence and contribution of a "ghost proteome" in these macrophages. We identified a set of alternative proteins (AltProts) that have a key role in the regulation of various signaling pathways. In this study, to further investigate the underlying mechanisms involved in the resistance of PC1/3-KD macrophages to anti-inflammatory stimuli, we have conducted a proteomic system biology study to assess the epigenome variation, focusing on histone modifications. Results from our study have indicated the presence of significant variations in histone modifications along with the identification of 28 AltProts, which can be correlated with antitumoral resistance under IL-10 stimulation. These findings highlight a key role of altered epigenome histone modifications in driving resistance and indicate that like the reference proteins, AltProts can have a major impact in the field of epigenetics and regulation of gene expression, as shown in our results.
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Affiliation(s)
- Tristan Cardon
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Bilgehan Ozcan
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Soulaimane Aboulouard
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Firas Kobeissy
- Department
of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Marie Duhamel
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Franck Rodet
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Isabelle Fournier
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
- Institut
Universitaire de France, Paris 75000, France
| | - Michel Salzet
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
- Institut
Universitaire de France, Paris 75000, France
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373
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Li M, Liu C, Xu X, Liu Y, Jiang Z, Li Y, Lv Y, Lu S, Hu C, Mao H. Grass carp (Ctenopharyngodon idella) GPATCH3 initiates IFN 1 expression via the activation of STING-IRF7 signal axis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 112:103781. [PMID: 32645337 DOI: 10.1016/j.dci.2020.103781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 06/11/2023]
Abstract
GPATCH3, a protein with G-patch domain, is known to participate in innate immune response and organ development in mammals. However, there are few reports on GPATCH3 in fish. Here the cDNA sequence of GPATCH3 was cloned from Ctenopharyngodon idella (CiGPATCH3, MN149902) and was determined its character. A cDNA sequence of CiGPATCH3 is 1646 bp and contains an ORF of 1221 bp translating a protein of 407 amino acids. Phylogenetic analysis uncovered that CiGPATCH3 possesses a relatively high degree of homology with Cyprinus carpio GPATCH3. The mRNA level of CiGPATCH3 was increased following the intracellular stimulation of poly (I:C) into CIK cells. In vivo, over-expression of CiGPATCH3 can significantly up-regulate IFN 1 and ISG15 expression at mRNA and protein levels. To investigate the molecular mechanism by which GPATCH3 initiates the innate immune response in fish, co-IP experiments were performed to analyze the substrates of CiGPATCH3. The results showed that CiGPATCH3 directly interacted with CiSTING, but not with CiIRF3, CiIRF7, CiTBK1 or CiIPS-1. As compared with the single transfection of CO cells with either CiGPATCH3 or CiSTING, the expression of IFN 1 was more significantly up-regulated in cells under treatment with dual transfection of CiGPATCH3 and CiSTING. Knockdown of CiGPATCH3 inhibited STING-mediated IFN 1 expression in fish cells. Over-expression of CiGPATCH3 and CiSTING facilitated the phosphorylation and cytoplasmic-to-nuclear translocation of CiIRF7. These results explicitly showed that CiGPATCH3 up-regulates IFN 1 and ISG15 expression via the activation of STING-IRF7 signal axis in vivo.
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Affiliation(s)
- Meifeng Li
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Changxin Liu
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Xiaowen Xu
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Yapeng Liu
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Zeying Jiang
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Yinping Li
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Yangfeng Lv
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Shina Lu
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Chengyu Hu
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China.
| | - Huiling Mao
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China.
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374
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Liu G, Lee JH, Parker ZM, Acharya D, Chiang JJ, van Gent M, Riedl W, Davis-Gardner ME, Wies E, Chiang C, Gack MU. ISG15-dependent Activation of the RNA Sensor MDA5 and its Antagonism by the SARS-CoV-2 papain-like protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33140045 PMCID: PMC7605552 DOI: 10.1101/2020.10.26.356048] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Activation of the RIG-I-like receptors, RIG-I and MDA5, establishes an antiviral state by upregulating interferon (IFN)-stimulated genes (ISGs). Among these is ISG15 whose mechanistic roles in innate immunity still remain enigmatic. Here we report that ISGylation is essential for antiviral IFN responses mediated by the viral RNA sensor MDA5. ISG15 conjugation to the caspase activation and recruitment domains of MDA5 promotes the formation of higher-order assemblies of MDA5 and thereby triggers activation of innate immunity against a range of viruses including coronaviruses, flaviviruses and picornaviruses. The ISG15-dependent activation of MDA5 is antagonized through direct de-ISGylation mediated by the papain-like protease (PLpro) of SARS-CoV-2, a recently emerged coronavirus that causes the COVID-19 pandemic. Our work demonstrates a crucial role for ISG15 in the MDA5-mediated antiviral response, and also identifies a novel immune evasion mechanism of SARS-CoV-2, which may be targeted for the development of new antivirals and vaccines to combat COVID-19.
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Affiliation(s)
- GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic, FL 34987, USA.,Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Jung-Hyun Lee
- Florida Research and Innovation Center, Cleveland Clinic, FL 34987, USA.,Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Zachary M Parker
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Dhiraj Acharya
- Florida Research and Innovation Center, Cleveland Clinic, FL 34987, USA.,Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Jessica J Chiang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Michiel van Gent
- Florida Research and Innovation Center, Cleveland Clinic, FL 34987, USA.,Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - William Riedl
- Florida Research and Innovation Center, Cleveland Clinic, FL 34987, USA.,Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | | | - Effi Wies
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Cindy Chiang
- Florida Research and Innovation Center, Cleveland Clinic, FL 34987, USA.,Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, FL 34987, USA.,Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
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375
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Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway. Cell Mol Life Sci 2020; 78:1423-1444. [PMID: 33084946 PMCID: PMC7576986 DOI: 10.1007/s00018-020-03671-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/14/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022]
Abstract
Antiviral responses of interferons (IFNs) are crucial in the host immune response, playing a relevant role in controlling viralw infections. Three types of IFNs, type I (IFN-α, IFN-β), II (IFN-γ) and III (IFN-λ), are classified according to their receptor usage, mode of induction, biological activity and amino acid sequence. Here, we provide a comprehensive review of type I IFN responses and different mechanisms that viruses employ to circumvent this response. In the first part, we will give an overview of the different induction and signaling cascades induced in the cell by IFN-I after virus encounter. Next, highlights of some of the mechanisms used by viruses to counteract the IFN induction will be described. And finally, we will address different mechanism used by viruses to interference with the IFN signaling cascade and the blockade of IFN induced antiviral activities.
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376
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Anderson SM, Thurman AR, Chandra N, Jackson SS, Asin S, Rollenhagen C, Ghosh M, Daniels J, Vann NC, Clark MR, Doncel GF. Vitamin D Status Impacts Genital Mucosal Immunity and Markers of HIV-1 Susceptibility in Women. Nutrients 2020; 12:nu12103176. [PMID: 33080839 PMCID: PMC7602985 DOI: 10.3390/nu12103176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 01/24/2023] Open
Abstract
While vitamin D insufficiency is known to impact a multitude of health outcomes, including HIV-1, little is known about the role of vitamin D-mediated immune regulation in the female reproductive tract (FRT). We performed a pilot clinical study of 20 women with circulating 25(OH)D levels <62.5 nmol/L. Participants were randomized into either weekly or daily high-dose oral vitamin D supplementation groups. In addition to serum vitamin D levels, genital mucosal endpoints, including soluble mediators, immune cell populations, gene expression, and ex vivo HIV-1 infection, were assessed. While systemic vitamin D levels showed a significant increase following supplementation, these changes translated into modest effects on the cervicovaginal factors studied. Paradoxically, post-supplementation vitamin D levels were decreased in cervicovaginal fluids. Given the strong correlation between vitamin D status and HIV-1 infection and the widespread nature of vitamin D deficiency, further understanding of the role of vitamin D immunoregulation in the female reproductive tract is important.
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Affiliation(s)
- Sharon M. Anderson
- CONRAD, Eastern Virginia Medical School, Norfolk, VA 23507, USA; (A.R.T.); (N.C.); (S.S.J.); (N.C.V.); (M.R.C.); (G.F.D.)
- CONRAD, Eastern Virginia Medical School, Arlington, VA 22209, USA
- Correspondence:
| | - Andrea R. Thurman
- CONRAD, Eastern Virginia Medical School, Norfolk, VA 23507, USA; (A.R.T.); (N.C.); (S.S.J.); (N.C.V.); (M.R.C.); (G.F.D.)
- CONRAD, Eastern Virginia Medical School, Arlington, VA 22209, USA
| | - Neelima Chandra
- CONRAD, Eastern Virginia Medical School, Norfolk, VA 23507, USA; (A.R.T.); (N.C.); (S.S.J.); (N.C.V.); (M.R.C.); (G.F.D.)
- CONRAD, Eastern Virginia Medical School, Arlington, VA 22209, USA
| | - Suzanne S. Jackson
- CONRAD, Eastern Virginia Medical School, Norfolk, VA 23507, USA; (A.R.T.); (N.C.); (S.S.J.); (N.C.V.); (M.R.C.); (G.F.D.)
- CONRAD, Eastern Virginia Medical School, Arlington, VA 22209, USA
| | - Susana Asin
- V.A. Medical Center, White River Junction, VT 05009, USA; (S.A.); (C.R.)
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Christiane Rollenhagen
- V.A. Medical Center, White River Junction, VT 05009, USA; (S.A.); (C.R.)
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Mimi Ghosh
- Milken Institute School of Public Health and Health Services, George Washington University, Washington, DC 20052, USA; (M.G.); (J.D.)
| | - Jason Daniels
- Milken Institute School of Public Health and Health Services, George Washington University, Washington, DC 20052, USA; (M.G.); (J.D.)
| | - Nikolas C. Vann
- CONRAD, Eastern Virginia Medical School, Norfolk, VA 23507, USA; (A.R.T.); (N.C.); (S.S.J.); (N.C.V.); (M.R.C.); (G.F.D.)
- CONRAD, Eastern Virginia Medical School, Arlington, VA 22209, USA
| | - Meredith R. Clark
- CONRAD, Eastern Virginia Medical School, Norfolk, VA 23507, USA; (A.R.T.); (N.C.); (S.S.J.); (N.C.V.); (M.R.C.); (G.F.D.)
- CONRAD, Eastern Virginia Medical School, Arlington, VA 22209, USA
| | - Gustavo F. Doncel
- CONRAD, Eastern Virginia Medical School, Norfolk, VA 23507, USA; (A.R.T.); (N.C.); (S.S.J.); (N.C.V.); (M.R.C.); (G.F.D.)
- CONRAD, Eastern Virginia Medical School, Arlington, VA 22209, USA
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377
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Genetic landscape and autoimmunity of monocytes in developing Vogt-Koyanagi-Harada disease. Proc Natl Acad Sci U S A 2020; 117:25712-25721. [PMID: 32989127 DOI: 10.1073/pnas.2002476117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Vogt-Koyanagi-Harada (VKH) disease is a systemic autoimmune disorder affecting multiple organs, including eyes, skin, and central nervous system. It is known that monocytes significantly contribute to the development of autoimmune disease. However, the subset heterogeneity with unique functions and signatures in human circulating monocytes and the identity of disease-specific monocytic populations remain largely unknown. Here, we employed an advanced single-cell RNA sequencing technology to systematically analyze 11,259 human circulating monocytes and genetically defined their subpopulations. We constructed a precise atlas of human blood monocytes, identified six subpopulations-including S100A12, HLA, CD16, proinflammatory, megakaryocyte-like, and NK-like monocyte subsets-and uncovered two previously unidentified subsets: HLA and megakaryocyte-like monocyte subsets. Relative to healthy individuals, cellular composition, gene expression signatures, and activation states were markedly alternated in VKH patients utilizing cell type-specific programs, especially the CD16 and proinflammatory monocyte subpopulations. Notably, we discovered a disease-relevant subgroup, proinflammatory monocytes, which showed a discriminative gene expression signature indicative of inflammation, antiviral activity, and pathologic activation, and converted into a pathologic activation state implicating the active inflammation during VKH disease. Additionally, we found the cell type-specific transcriptional signature of proinflammatory monocytes, ISG15, whose production might reflect the treatment response. Taken together, in this study, we present discoveries on accurate classification, molecular markers, and signaling pathways for VKH disease-associated monocytes. Therapeutically targeting this proinflammatory monocyte subpopulation would provide an attractive approach for treating VKH, as well as other autoimmune diseases.
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378
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Abstract
The intracellular protozoan parasite Toxoplasma gondii is capable of infecting most nucleated cells, where it survives in a specially modified compartment called the parasitophorous vacuole (PV). Interferon gamma (IFN-γ) is the major cytokine involved in activating cell-autonomous immune responses to inhibit parasite growth within this intracellular niche. In HeLa cells, IFN-γ treatment leads to ubiquitination of susceptible parasite strains, recruitment of the adaptors p62 and NDP52, and engulfment in microtubule-associated protein 1 light chain 3 (LC3)-positive membranes that restrict parasite growth. IFN-γ-mediated growth restriction depends on core members of the autophagy (ATG) pathway but not the initiation or degradative steps in the process. To explore the connection between these different pathways, we used permissive biotin ligation to identify proteins that interact with ATG5 in an IFN-γ-dependent fashion. Network analysis of the ATG5 interactome identified interferon-stimulated gene 15 (ISG15), which is highly upregulated by IFN treatment, as a hub connecting the ATG complex with other IFN-γ-induced genes, suggesting that it forms a functional link between the pathways. Deletion of ISG15 resulted in impaired recruitment of p62, NDP52, and LC3 to the PV and loss of IFN-γ-restricted parasite growth. The function of ISG15 required conjugation, and a number of ISGylated targets overlapped with the IFN-γ-dependent ATG5 interactome, including the adapter p62. Collectively, our findings establish a role for ISG15 in connecting the ATG pathway with IFN-γ-dependent restriction of T. gondii in human cells.IMPORTANCE Interferon(s) provide the primary defense against intracellular pathogens, a property ascribed to their ability to upregulate interferon-stimulated genes. Due to the sequestered niche occupied by Toxoplasma gondii, the host has elaborated intricate ways to target the parasite within its vacuole. One such mechanism is the recognition by a noncanonical autophagy pathway that envelops the parasite-containing vacuole and stunts growth in human cells. Remarkably, autophagy-dependent growth restriction requires interferon-γ, yet none of the classical components of autophagy are induced by interferon. Our studies draw a connection between these pathways by demonstrating that the antiviral protein ISG15, which is normally upregulated by interferons, links the autophagy-mediated control to ubiquitination of the vacuole. These findings suggest a similar link between interferon-γ signaling and autophagy that may underlie defense against other intracellular pathogens.
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379
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Jeong EH, Cho SY, Vaidya B, Ha SH, Jun S, Ro HJ, Lee Y, Lee J, Kwon J, Kim D. Human Norovirus Replication in Temperature-Optimized MDCK Cells by Forkhead Box O1 Inhibition. J Microbiol Biotechnol 2020; 30:1412-1419. [PMID: 32522961 PMCID: PMC9745657 DOI: 10.4014/jmb.2003.03071] [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: 03/31/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 12/15/2022]
Abstract
Human noroviruses (HuNoVs) are a leading cause of gastroenteritis outbreaks worldwide. However, the paucity of appropriate cell culture model for HuNoV replication has prevented developing effective anti-HuNoV therapy. In this study, first, the replication of the virus at various temperatures in different cells was compared, which showed that lowering the culture temperature from 37°C significantly increased virus replication in Madin-Darby canine kidney (MDCK) cells. Second, the expression levels of autophagy-, immune-, and apoptosis-related genes at 30°C and 37°C were compared to explore factors affecting HuNoV replication. HuNoV cultured at 37°C showed significantly increased autophagy- (ATG5 and ATG7) and immune- (IFNA, IFNB, ISG15, and NFKB) related genes compared to mock. However, the virus cultured at 30°C showed significantly decreased expression of autophagy- (ATG5 and ATG7) and not significantly different in major immune- (IFNA, ISG15, and NFKB) related genes compared to mock. Importantly, expression of the transcription factor FOXO1, which controls autophagy- and immune-related gene expression, was significantly lower at 30°C. Moreover, FOXO1 inhibition in temperature-optimized MDCK cells enhanced HuNoV replication, highlighting FOXO1 inhibition as an approach for successful virus replication. In the temperature-optimized cells, various HuNoV genotypes were successfully replicated, with GI.8 showing the highest replication levels followed by GII.1, GII.3, and GII.4. Furthermore, ultrastructural analysis of the infected cells revealed functional HuNoV replication at low temperature, with increased cellular apoptosis and decreased autophagic vacuoles. In conclusion, temperature-optimized MDCK cells can be used as a convenient culture model for HuNoV replication by inhibiting FOXO1, providing adaptability to different genotypes.
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Affiliation(s)
- Eun-Hye Jeong
- Department of Food Science and Technology and Foodborne Virus Research Center, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Se-Young Cho
- Department of Food Science and Technology and Foodborne Virus Research Center, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Bipin Vaidya
- Department of Food Science and Technology and Foodborne Virus Research Center, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sang Hoon Ha
- Division of Biotechnology, Chonbuk National University, Iksan 54596, Republic of Korea
| | - Sangmi Jun
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, Republic of Korea,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Hyun-Joo Ro
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, Republic of Korea,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Yujeong Lee
- Korea Basic Science Institute, Cheongju 28119, Republic of Korea,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Juhye Lee
- Department of Food Science and Technology and Foodborne Virus Research Center, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Joseph Kwon
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon 34133, Republic of Korea,J.K. Phone: +82-42-865-3446 Fax: +82-42-865-3419 E-mail:
| | - Duwoon Kim
- Department of Food Science and Technology and Foodborne Virus Research Center, Chonnam National University, Gwangju 61186, Republic of Korea,Corresponding authors D.K. Phone: +82-62-530-2144 Fax: +82-62-530-2149 E-mail:
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380
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Molina-Coto R, Moore SG, Mayo LM, Lamberson WR, Poock SE, Lucy MC. Ovarian function and the establishment and maintenance of pregnancy in dairy cows with and without evidence of postpartum uterine disease. J Dairy Sci 2020; 103:10715-10727. [PMID: 32896417 DOI: 10.3168/jds.2020-18694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/17/2020] [Indexed: 11/19/2022]
Abstract
Uterine disease early postpartum reduces fertility during the breeding period. One potential mechanism involves the reduced functional capacity of the uterus to support pregnancy. A second potential mechanism involves damage to ovarian follicles associated with systemic inflammation. We categorized lactating Holstein cows into healthy (n = 63) and diseased (n = 39) uterus groups based on the percentage of polymorphonuclear neutrophils in the uterine lumen during the second and third month postpartum and evaluated the functionality of their ovaries and their capacity to establish and maintain pregnancy. Cows were enrolled in a timed artificial insemination protocol (Presynch Ovsynch) so that the first artificial insemination was approximately 75 d postpartum. Ovarian follicles and corpora lutea were counted and measured using transrectal ultrasound, ovulatory responses were assessed, and luteal phase progesterone concentrations were measured. Pregnancy was detected on d 18, 20, 22, 25, 32, and 45 through chemical (d 18 to 25) or ultrasonographic methods (d 32 and 45). The percentage of cows ovulating during the Presynch period; the number, diameter, and ovulatory capacity of follicles during the Ovsynch period; and plasma progesterone concentrations following ovulation were similar for healthy and diseased cows. The initial period of pregnancy establishment (d 18 to 22) appeared to be unaffected by disease because a similar percentage of healthy and diseased cows were pregnant during this period. Embryonic loss occurred in both healthy and diseased cows after d 22. Based on a relatively small number of pregnancies (n = 30 healthy and n = 17 diseased), the cumulative embryonic loss after d 22 was greater in diseased compared with healthy cows. In short, uterine disease as defined in this study did not affect cyclicity, ovarian follicular growth, or plasma progesterone concentrations. Percentages of healthy and diseased cows that were pregnant were similar from d 18 to 22 after artificial insemination. Greater embryonic loss was observed after d 22 in diseased compared with healthy cows, but this observation was based on a small number of pregnancies and should be studied further in larger trials with greater statistical power.
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Affiliation(s)
- R Molina-Coto
- Division of Animal Sciences and College of Veterinary Medicine, University of Missouri, Columbia 65211
| | - S G Moore
- Division of Animal Sciences and College of Veterinary Medicine, University of Missouri, Columbia 65211
| | - L M Mayo
- Division of Animal Sciences and College of Veterinary Medicine, University of Missouri, Columbia 65211
| | - W R Lamberson
- Division of Animal Sciences and College of Veterinary Medicine, University of Missouri, Columbia 65211
| | - S E Poock
- Division of Animal Sciences and College of Veterinary Medicine, University of Missouri, Columbia 65211
| | - M C Lucy
- Division of Animal Sciences and College of Veterinary Medicine, University of Missouri, Columbia 65211.
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381
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Mao K, Geng W, Liao Y, Luo P, Zhong H, Ma P, Xu J, Zhang S, Tan Q, Jin Y. Identification of robust genetic signatures associated with lipopolysaccharide-induced acute lung injury onset and astaxanthin therapeutic effects by integrative analysis of RNA sequencing data and GEO datasets. Aging (Albany NY) 2020; 12:18716-18740. [PMID: 32969837 PMCID: PMC7585091 DOI: 10.18632/aging.104042] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/19/2020] [Indexed: 01/24/2023]
Abstract
Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) are life-threatening clinical conditions predominantly arising from uncontrolled inflammatory reactions. It has been found that the administration of astaxanthin (AST) can exert protective effects against lipopolysaccharide (LPS)-induced ALI; however, the robust genetic signatures underlying LPS induction and AST treatment remain obscure. Here we performed a statistical meta-analysis of five publicly available gene expression datasets from LPS-induced ALI mouse models, conducted RNA-sequencing (RNA-seq) to screen differentially expressed genes (DEGs) in response to LPS administration and AST treatment, and integrative analysis to determine robust genetic signatures associated with LPS-induced ALI onset and AST administration. Both the meta-analyses and our experimental data identified a total of 198 DEGs in response to LPS administration, and 11 core DEGs (Timp1, Ly6i, Cxcl13, Irf7, Cxcl5, Ccl7, Isg15, Saa3, Saa1, Tgtp1, and Gbp11) were identified to be associated with AST therapeutic effects. Further, the 11 core DEGs were verified by quantitative real-time PCR (qRT-PCR) and immunohistochemistry (IHC), and functional enrichment analysis revealed that these genes are primarily associated with neutrophils and chemokines. Collectively, these findings unearthed the robust genetic signatures underlying LPS administration and the molecular targets of AST for ameliorating ALI/ARDS which provide directions for further research.
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Affiliation(s)
- Kaimin Mao
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Wei Geng
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Yuhan Liao
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Ping Luo
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Hua Zhong
- College of Life Sciences, Wuhan University, Hubei Province, Wuhan, 430072, China
| | - Pei Ma
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Juanjuan Xu
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Shuai Zhang
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Qi Tan
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Yang Jin
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
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382
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Induction of the Antiviral Immune Response and Its Circumvention by Coronaviruses. Viruses 2020; 12:v12091039. [PMID: 32961897 PMCID: PMC7551260 DOI: 10.3390/v12091039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/12/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Some coronaviruses are zoonotic viruses of human and veterinary medical importance. The novel coronavirus, severe acute respiratory symptoms coronavirus 2 (SARS-CoV-2), associated with the current global pandemic, is characterized by pneumonia, lymphopenia, and a cytokine storm in humans that has caused catastrophic impacts on public health worldwide. Coronaviruses are known for their ability to evade innate immune surveillance exerted by the host during the early phase of infection. It is important to comprehensively investigate the interaction between highly pathogenic coronaviruses and their hosts. In this review, we summarize the existing knowledge about coronaviruses with a focus on antiviral immune responses in the respiratory and intestinal tracts to infection with severe coronaviruses that have caused epidemic diseases in humans and domestic animals. We emphasize, in particular, the strategies used by these coronaviruses to circumvent host immune surveillance, mainly including the hijack of antigen-presenting cells, shielding RNA intermediates in replication organelles, 2′-O-methylation modification for the evasion of RNA sensors, and blocking of interferon signaling cascades. We also provide information about the potential development of coronavirus vaccines and antiviral drugs.
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383
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Klemm T, Ebert G, Calleja DJ, Allison CC, Richardson LW, Bernardini JP, Lu BGC, Kuchel NW, Grohmann C, Shibata Y, Gan ZY, Cooney JP, Doerflinger M, Au AE, Blackmore TR, van der Heden van Noort GJ, Geurink PP, Ovaa H, Newman J, Riboldi‐Tunnicliffe A, Czabotar PE, Mitchell JP, Feltham R, Lechtenberg BC, Lowes KN, Dewson G, Pellegrini M, Lessene G, Komander D. Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2. EMBO J 2020; 39:e106275. [PMID: 32845033 PMCID: PMC7461020 DOI: 10.15252/embj.2020106275] [Citation(s) in RCA: 299] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/26/2022] Open
Abstract
The SARS-CoV-2 coronavirus encodes an essential papain-like protease domain as part of its non-structural protein (nsp)-3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin-like ISG15 protein modifications as well as, with lower activity, Lys48-linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin-binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clinical compounds against SARS2 PLpro identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non-covalent small molecule SARS PLpro inhibitors also target SARS2 PLpro, prevent self-processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS-CoV-2 infection model.
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Affiliation(s)
- Theresa Klemm
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Gregor Ebert
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Dale J Calleja
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Cody C Allison
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Lachlan W Richardson
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Jonathan P Bernardini
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
- Department of Biochemistry and Molecular BiologyMichael Smith Laboratories University of British ColumbiaVancouverBCCanada
| | - Bernadine GC Lu
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Nathan W Kuchel
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Christoph Grohmann
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Yuri Shibata
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Zhong Yan Gan
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - James P Cooney
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Marcel Doerflinger
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Amanda E Au
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Timothy R Blackmore
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | | | - Paul P Geurink
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CentreLeidenThe Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CentreLeidenThe Netherlands
| | - Janet Newman
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)Biomedical ProgramParkvilleVic.Australia
| | | | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Jeffrey P Mitchell
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Rebecca Feltham
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Bernhard C Lechtenberg
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Kym N Lowes
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Grant Dewson
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Marc Pellegrini
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Guillaume Lessene
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
- Pharmacology and Therapeutics DepartmentUniversity of MelbourneMelbourneVic.Australia
| | - David Komander
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
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384
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Zhu L, Yang P, Zhao Y, Zhuang Z, Wang Z, Song R, Zhang J, Liu C, Gao Q, Xu Q, Wei X, Sun HX, Ye B, Wu Y, Zhang N, Lei G, Yu L, Yan J, Diao G, Meng F, Bai C, Mao P, Yu Y, Wang M, Yuan Y, Deng Q, Li Z, Huang Y, Hu G, Liu Y, Wang X, Xu Z, Liu P, Bi Y, Shi Y, Zhang S, Chen Z, Wang J, Xu X, Wu G, Wang FS, Gao GF, Liu L, Liu WJ. Single-Cell Sequencing of Peripheral Mononuclear Cells Reveals Distinct Immune Response Landscapes of COVID-19 and Influenza Patients. Immunity 2020; 53:685-696.e3. [PMID: 32783921 PMCID: PMC7368915 DOI: 10.1016/j.immuni.2020.07.009] [Citation(s) in RCA: 242] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/07/2020] [Accepted: 07/14/2020] [Indexed: 12/14/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic poses a current world-wide public health threat. However, little is known about its hallmarks compared to other infectious diseases. Here, we report the single-cell transcriptional landscape of longitudinally collected peripheral blood mononuclear cells (PBMCs) in both COVID-19- and influenza A virus (IAV)-infected patients. We observed increase of plasma cells in both COVID-19 and IAV patients and XIAP associated factor 1 (XAF1)-, tumor necrosis factor (TNF)-, and FAS-induced T cell apoptosis in COVID-19 patients. Further analyses revealed distinct signaling pathways activated in COVID-19 (STAT1 and IRF3) versus IAV (STAT3 and NFκB) patients and substantial differences in the expression of key factors. These factors include relatively increase of interleukin (IL)6R and IL6ST expression in COVID-19 patients but similarly increased IL-6 concentrations compared to IAV patients, supporting the clinical observations of increased proinflammatory cytokines in COVID-19 patients. Thus, we provide the landscape of PBMCs and unveil distinct immune response pathways in COVID-19 and IAV patients.
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Affiliation(s)
- Linnan Zhu
- BGI-Shenzhen, 518103 Shenzhen, China; China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Penghui Yang
- Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, 100039 Beijing, China
| | - Yingze Zhao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China
| | - Zhenkun Zhuang
- BGI-Shenzhen, 518103 Shenzhen, China; China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China; School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | | | - Rui Song
- Center of Infectious Disease, Beijing Ditan Hospital, Capital Medical University, 100015 Beijing, China
| | - Jie Zhang
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China
| | | | | | - Qumiao Xu
- BGI-Shenzhen, 518103 Shenzhen, China
| | - Xiaoyu Wei
- BGI-Shenzhen, 518103 Shenzhen, China; BGI Education Center, University of Chinese Academy of Sciences, 518083 Shenzhen, China
| | - Hai-Xi Sun
- BGI-Shenzhen, 518103 Shenzhen, China; China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Beiwei Ye
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China
| | - Yanan Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China
| | - Ning Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Guanglin Lei
- Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, 100039 Beijing, China
| | - Lingxiang Yu
- Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, 100039 Beijing, China
| | - Jin Yan
- Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, 100039 Beijing, China
| | - Guanghao Diao
- Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, 100039 Beijing, China
| | - Fanping Meng
- Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, 100039 Beijing, China
| | - Changqing Bai
- Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, 100039 Beijing, China
| | - Panyong Mao
- Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, 100039 Beijing, China
| | - Yeya Yu
- BGI-Shenzhen, 518103 Shenzhen, China
| | | | - Yue Yuan
- BGI-Shenzhen, 518103 Shenzhen, China; BGI Education Center, University of Chinese Academy of Sciences, 518083 Shenzhen, China
| | - Qiuting Deng
- BGI-Shenzhen, 518103 Shenzhen, China; BGI Education Center, University of Chinese Academy of Sciences, 518083 Shenzhen, China
| | - Ziyi Li
- BGI-Shenzhen, 518103 Shenzhen, China; Northwest A&F University, Yangling, 712100 Shanxi, China
| | - Yunting Huang
- China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Guohai Hu
- China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Yang Liu
- BGI-Shenzhen, 518103 Shenzhen, China; BGI Education Center, University of Chinese Academy of Sciences, 518083 Shenzhen, China
| | - Xiaoqian Wang
- BGI-Shenzhen, 518103 Shenzhen, China; BGI-GenoImmune, BGI-Shenzhen, 4300794 Wuhan, China
| | - Ziqian Xu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China
| | - Peipei Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Shaogeng Zhang
- Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, 100039 Beijing, China
| | - Zhihai Chen
- Center of Infectious Disease, Beijing Ditan Hospital, Capital Medical University, 100015 Beijing, China
| | - Jian Wang
- BGI-Shenzhen, 518103 Shenzhen, China; China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Xun Xu
- BGI-Shenzhen, 518103 Shenzhen, China; China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Guizhen Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China
| | - Fu-Sheng Wang
- Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, 100039 Beijing, China.
| | - George F Gao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China.
| | - Longqi Liu
- BGI-Shenzhen, 518103 Shenzhen, China; China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China.
| | - William J Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China.
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385
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The Molecular Interactions of ZIKV and DENV with the Type-I IFN Response. Vaccines (Basel) 2020; 8:vaccines8030530. [PMID: 32937990 PMCID: PMC7565347 DOI: 10.3390/vaccines8030530] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/12/2022] Open
Abstract
Zika Virus (ZIKV) and Dengue Virus (DENV) are related viruses of the Flavivirus genus that cause significant disease in humans. Existing control measures have been ineffective at curbing the increasing global incidence of infection for both viruses and they are therefore prime targets for new vaccination strategies. Type-I interferon (IFN) responses are important in clearing viral infection and for generating efficient adaptive immune responses towards infection and vaccination. However, ZIKV and DENV have evolved multiple molecular mechanisms to evade type-I IFN production. This review covers the molecular interactions, from detection to evasion, of these viruses with the type-I IFN response. Additionally, we discuss how this knowledge can be exploited to improve the design of new vaccine strategies.
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386
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Suarez B, Prats-Mari L, Unfried JP, Fortes P. LncRNAs in the Type I Interferon Antiviral Response. Int J Mol Sci 2020; 21:E6447. [PMID: 32899429 PMCID: PMC7503479 DOI: 10.3390/ijms21176447] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022] Open
Abstract
The proper functioning of the immune system requires a robust control over a delicate equilibrium between an ineffective response and immune overactivation. Poor responses to viral insults may lead to chronic or overwhelming infection, whereas unrestrained activation can cause autoimmune diseases and cancer. Control over the magnitude and duration of the antiviral immune response is exerted by a finely tuned positive or negative regulation at the DNA, RNA, and protein level of members of the type I interferon (IFN) signaling pathways and on the expression and activity of antiviral and proinflammatory factors. As summarized in this review, committed research during the last decade has shown that several of these processes are exquisitely regulated by long non-coding RNAs (lncRNAs), transcripts with poor coding capacity, but highly versatile functions. After infection, viruses, and the antiviral response they trigger, deregulate the expression of a subset of specific lncRNAs that function to promote or repress viral replication by inactivating or potentiating the antiviral response, respectively. These IFN-related lncRNAs are also highly tissue- and cell-type-specific, rendering them as promising biomarkers or therapeutic candidates to modulate specific stages of the antiviral immune response with fewer adverse effects.
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Affiliation(s)
- Beatriz Suarez
- Program of Gene Therapy and Hepatology, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain; (B.S.); (L.P.-M.)
| | - Laura Prats-Mari
- Program of Gene Therapy and Hepatology, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain; (B.S.); (L.P.-M.)
| | - Juan P. Unfried
- Program of Gene Therapy and Hepatology, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain; (B.S.); (L.P.-M.)
| | - Puri Fortes
- Program of Gene Therapy and Hepatology, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain; (B.S.); (L.P.-M.)
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029 Madrid, Spain
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387
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Galimberti S, Petrini M, Baratè C, Ricci F, Balducci S, Grassi S, Guerrini F, Ciabatti E, Mechelli S, Di Paolo A, Baldini C, Baglietto L, Macera L, Spezia PG, Maggi F. Tyrosine Kinase Inhibitors Play an Antiviral Action in Patients Affected by Chronic Myeloid Leukemia: A Possible Model Supporting Their Use in the Fight Against SARS-CoV-2. Front Oncol 2020; 10:1428. [PMID: 33014780 PMCID: PMC7493657 DOI: 10.3389/fonc.2020.01428] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022] Open
Abstract
SARS-CoV-2 is the viral agent responsible for the pandemic that in the first months of 2020 caused about 400,000 deaths. Among compounds proposed to fight the SARS-CoV-2-related disease (COVID-19), tyrosine kinase inhibitors (TKIs), already effective in Philadelphia-positive acute lymphoblastic leukemia (Ph+ ALL) and chronic myeloid leukemia (CML), have been proposed on the basis of their antiviral action already demonstrated against SARS-CoV-1. Very few cases of COVID-19 have been reported in Ph+ ALL and in CML Italian cohorts; authors suggested that this low rate of infections might depend on the use of TKIs, but the biological causes of this phenomenon remain unknown. In this study, the CML model was used to test if TKIs would sustain or not the viral replication and if they could damage patient immunity. Firstly, the infection and replication rate of torquetenovirus (TTV), whose load is inversely proportional to the host immunological control, have been measured in CML patients receiving nilotinib. A very low percentage of subjects were infected at baseline, and TTV did not replicate or at least showed a low replication rate during the follow-up, with a mean load comparable to the measured one in healthy subjects. Then, after gene expression profiling experiments, we found that several “antiviral” genes, such as CD28 and IFN gamma, were upregulated, while genes with “proviral” action, such as ARG-1, CEACAM1, and FUT4, were less expressed during treatment with imatinib, thus demonstrating that TKIs are not detrimental from the immunological point of view. To sum up, our data could offer some biological explanations to the low COVID-19 occurrence in Ph+ ALL and CML patients and sustain the use of TKIs in COVID-19, as already proposed by several international ongoing studies.
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Affiliation(s)
- Sara Galimberti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Mario Petrini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | | | - Federica Ricci
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Serena Balducci
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Susanna Grassi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesca Guerrini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Elena Ciabatti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | | | - Antonello Di Paolo
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Chiara Baldini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Laura Baglietto
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Lisa Macera
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Pietro Giorgio Spezia
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Fabrizio Maggi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
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388
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Zhang X, Paget M, Wang C, Zhu Z, Zheng H. Innate immune evasion by picornaviruses. Eur J Immunol 2020; 50:1268-1282. [PMID: 32767562 DOI: 10.1002/eji.202048785] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 02/06/2023]
Abstract
The family Picornaviridae comprises a large number of viruses that cause disease in broad spectrum of hosts, which have posed serious public health concerns worldwide and led to significant economic burden. A comprehensive understanding of the virus-host interactions during picornavirus infections will help to prevent and cure these diseases. Upon picornavirus infection, host pathogen recognition receptors (PRRs) sense viral RNA to activate host innate immune responses. The activated PRRs initiate signal transduction through a series of adaptor proteins, which leads to activation of several kinases and transcription factors, and contributes to the consequent expression of interferons (IFNs), IFN-inducible antiviral genes, as well as various inflammatory cytokines and chemokines. In contrast, to maintain viral replication and spread, picornaviruses have evolved several elegant strategies to block innate immune signaling and hinder host antiviral response. In this review, we will summarize the recent progress of how the members of family Picornaviridae counteract host immune response through evasion of PRRs detection, blocking activation of adaptor molecules and kinases, disrupting transcription factors, as well as counteraction of antiviral restriction factors. Such knowledge of immune evasion will help us better understand the pathogenesis of picornaviruses, and provide insights into developing antiviral strategies and improvement of vaccines.
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Affiliation(s)
- Xiangle Zhang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Max Paget
- Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, U.S.A.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, U.S.A.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, MA, U.S.A
| | - Congcong Wang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Zixiang Zhu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
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389
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Arora S, Singh P, Dohare R, Jha R, Ali Syed M. Unravelling host-pathogen interactions: ceRNA network in SARS-CoV-2 infection (COVID-19). Gene 2020; 762:145057. [PMID: 32805314 PMCID: PMC7428439 DOI: 10.1016/j.gene.2020.145057] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/13/2020] [Accepted: 08/12/2020] [Indexed: 12/18/2022]
Abstract
Bioinformatics analysis of mouse mRNA expression dataset for presumptive SARS-CoV-2 targets. Induction of ISGs-Isg15, Oasl1, Usp18 and Ddx58 with no marked changes in the expression of IFNs. No induction of ACE2 and TMPRSS2, raising implications for host factor limitations. Identification of ceRNA network including miR-124-3p, Ddx58, lncRNA (Gm26917) and circRNAs (Ppp1r10, C330019G07RiK). Virus regulates the expression of lnc and circRNAs, acting as sponges for miR-124-3p targeting Ddx58.
COVID-19 is a lurking calamitous disease caused by an unusual virus, SARS-CoV-2, causing massive deaths worldwide. Nonetheless, explicit therapeutic drugs or clinically approved vaccines are not available for COVID-19. Thus, a comprehensive research is crucially needed to decode the pathogenic tools, plausible drug targets, committed to the development of efficient therapy. Host-pathogen interactions via host cellular components is an emerging field of research in this respect. miRNAs have been established as vital players in host-virus interactions. Moreover, viruses have the capability to manoeuvre the host miRNA networks according to their own obligations. Besides protein coding mRNAs, noncoding RNAs might also be targeted in infected cells and viruses can exploit the host miRNA network via ceRNA effect. We have predicted a ceRNA network involving one miRNA (miR-124-3p), one mRNA (Ddx58), one lncRNA (Gm26917) and two circRNAs (Ppp1r10, C330019G07RiK) in SARS-CoV infected cells. We have identified 4 DEGs-Isg15, Ddx58, Oasl1, Usp18 by analyzing a mRNA GEO dataset. There is no notable induction of IFNs and IFN-induced ACE2, significant receptor responsible for S-protein binding mediated viral entry. Pathway enrichment and GO analysis conceded the enrichment of pathways associated with interferon signalling and antiviral-mechanism by IFN-stimulated genes. Further, we have identified 3 noncoding RNAs, playing as potential ceRNAs to the genes associated with immune mechanisms. This integrative analysis has identified noncoding RNAs and their plausible targets, which could effectively enhance the understanding of molecular mechanisms associated with viral infection. However, validation of these targets is further corroborated to determine their therapeutic efficacy.
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Affiliation(s)
- Shweta Arora
- Translational Research Lab, Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Rishabh Jha
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Mansoor Ali Syed
- Translational Research Lab, Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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390
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Kumar V. Emerging Human Coronavirus Infections (SARS, MERS, and COVID-19): Where They Are Leading Us. Int Rev Immunol 2020; 40:5-53. [PMID: 32744465 DOI: 10.1080/08830185.2020.1800688] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Coronavirus infections are responsible for mild, moderate, and severe infections in birds and mammals. These were first isolated in humans as causal microorganisms responsible for common cold. The 2002-2003 SARS epidemic caused by SARS-CoV and 2012 MERS epidemic (64 countries affected) caused by MERS-CoV showed their acute and fatal side. These two CoV infections killed thousands of patients infected worldwide. However, WHO has still reported the MERS case in December 2019 in middle-eastern country (Saudi Arabia), indicating the MERS epidemic has not ended completely yet. Although we have not yet understood completely these two CoV epidemics, a third most dangerous and severe CoV infection has been originated in the Wuhan city, Hubei district of China in December 2019. This CoV infection called COVID-19 or SARS-CoV2 infection has now spread to 210 countries and territories around the world. COVID-19 has now been declared a pandemic by the World Health Organization (WHO). It has infected more than 16.69 million people with more than 663,540 deaths across the world. Thus the current manuscript aims to describe all three (SARS, MERS, and COVID-19) in terms of their causal organisms (SARS-CoV, MERS-CoV, and SARS-CoV2), similarities and differences in their clinical symptoms, outcomes, immunology, and immunopathogenesis, and possible future therapeutic approaches.
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Affiliation(s)
- Vijay Kumar
- Children's Health Queensland Clinical Unit, School of Clinical Medicine, Faculty of Medicine, Mater Research, University of Queensland, Brisbane, Queensland, Australia.,School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
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391
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Abstract
In this issue, Raso et al. (2020. J. Cell Biol.https://doi.org/10.1083/jcb.202002175) uncover a novel replication fork speed regulatory network controlled by the ubiquitin-like modifier interferon-stimulated gene 15 (ISG15), which plays a central role in the innate immune response and regulates tumorigenesis as well as chemotherapy response.
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Affiliation(s)
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
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392
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Masucci MG. Viral Ubiquitin and Ubiquitin-Like Deconjugases-Swiss Army Knives for Infection. Biomolecules 2020; 10:E1137. [PMID: 32752270 PMCID: PMC7464072 DOI: 10.3390/biom10081137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 12/16/2022] Open
Abstract
Posttranslational modifications of cellular proteins by covalent conjugation of ubiquitin and ubiquitin-like polypeptides regulate numerous cellular processes that are captured by viruses to promote infection, replication, and spreading. The importance of these protein modifications for the viral life cycle is underscored by the discovery that many viruses encode deconjugases that reverse their functions. The structural and functional characterization of these viral enzymes and the identification of their viral and cellular substrates is providing valuable insights into the biology of viral infections and the host's antiviral defense. Given the growing body of evidence demonstrating their key contribution to pathogenesis, the viral deconjugases are now recognized as attractive targets for the design of novel antiviral therapeutics.
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Affiliation(s)
- Maria Grazia Masucci
- Department of Cell and Molecular Biology, Karolinska Institutet, S-17177 Stockholm, Sweden
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393
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Rinchai D, Syed Ahamed Kabeer B, Toufiq M, Tatari-Calderone Z, Deola S, Brummaier T, Garand M, Branco R, Baldwin N, Alfaki M, Altman MC, Ballestrero A, Bassetti M, Zoppoli G, De Maria A, Tang B, Bedognetti D, Chaussabel D. A modular framework for the development of targeted Covid-19 blood transcript profiling panels. J Transl Med 2020; 18:291. [PMID: 32736569 PMCID: PMC7393249 DOI: 10.1186/s12967-020-02456-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Covid-19 morbidity and mortality are associated with a dysregulated immune response. Tools are needed to enhance existing immune profiling capabilities in affected patients. Here we aimed to develop an approach to support the design of targeted blood transcriptome panels for profiling the immune response to SARS-CoV-2 infection. METHODS We designed a pool of candidates based on a pre-existing and well-characterized repertoire of blood transcriptional modules. Available Covid-19 blood transcriptome data was also used to guide this process. Further selection steps relied on expert curation. Additionally, we developed several custom web applications to support the evaluation of candidates. RESULTS As a proof of principle, we designed three targeted blood transcript panels, each with a different translational connotation: immunological relevance, therapeutic development relevance and SARS biology relevance. CONCLUSION Altogether the work presented here may contribute to the future expansion of immune profiling capabilities via targeted profiling of blood transcript abundance in Covid-19 patients.
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Affiliation(s)
| | | | | | | | | | - Tobias Brummaier
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | - Nicole Baldwin
- Baylor Institute for Immunology Research and Baylor Research Institute, Dallas, TX, USA
| | | | - Matthew C Altman
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
- Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Alberto Ballestrero
- Department of Internal Medicine, Università degli Studi di Genova, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Matteo Bassetti
- Division of Infectious and Tropical Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine, Università degli Studi di Genova, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Andrea De Maria
- Division of Infectious and Tropical Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Benjamin Tang
- Nepean Clinical School, University of Sydney, Sydney, NSW, Australia
| | - Davide Bedognetti
- Sidra Medicine, Doha, Qatar
- Department of Internal Medicine, Università degli Studi di Genova, Genoa, Italy
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394
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Visser LJ, Aloise C, Swatek KN, Medina GN, Olek KM, Rabouw HH, de Groot RJ, Langereis MA, de los Santos T, Komander D, Skern T, van Kuppeveld FJM. Dissecting distinct proteolytic activities of FMDV Lpro implicates cleavage and degradation of RLR signaling proteins, not its deISGylase/DUB activity, in type I interferon suppression. PLoS Pathog 2020; 16:e1008702. [PMID: 32667958 PMCID: PMC7384677 DOI: 10.1371/journal.ppat.1008702] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 07/27/2020] [Accepted: 06/12/2020] [Indexed: 01/12/2023] Open
Abstract
The type I interferon response is an important innate antiviral pathway. Recognition of viral RNA by RIG-I-like receptors (RLRs) activates a signaling cascade that leads to type I interferon (IFN-α/β) gene transcription. Multiple proteins in this signaling pathway (e.g. RIG-I, MDA5, MAVS, TBK1, IRF3) are regulated by (de)ubiquitination events. Most viruses have evolved mechanisms to counter this antiviral response. The leader protease (Lpro) of foot-and-mouth-disease virus (FMDV) has been recognized to reduce IFN-α/β gene transcription; however, the exact mechanism is unknown. The proteolytic activity of Lpro is vital for releasing itself from the viral polyprotein and for cleaving and degrading specific host cell proteins, such as eIF4G and NF-κB. In addition, Lpro has been demonstrated to have deubiquitination/deISGylation activity. Lpro’s deubiquitination/deISGylation activity and the cleavage/degradation of signaling proteins have both been postulated to be important for reduced IFN-α/β gene transcription. Here, we demonstrate that TBK1, the kinase that phosphorylates and activates the transcription factor IRF3, is cleaved by Lpro in FMDV-infected cells as well as in cells infected with a recombinant EMCV expressing Lpro. In vitro cleavage experiments revealed that Lpro cleaves TBK1 at residues 692–694. We also observed cleavage of MAVS in HeLa cells infected with EMCV-Lpro, but only observed decreasing levels of MAVS in FMDV-infected porcine LFPK αVβ6 cells. We set out to dissect Lpro’s ability to cleave RLR signaling proteins from its deubiquitination/deISGylation activity to determine their relative contributions to the reduction of IFN-α/β gene transcription. The introduction of specific mutations, of which several were based on the recently published structure of Lpro in complex with ISG15, allowed us to identify specific amino acid substitutions that separate the different proteolytic activities of Lpro. Characterization of the effects of these mutations revealed that Lpro’s ability to cleave RLR signaling proteins but not its deubiquitination/deISGylation activity correlates with the reduced IFN-β gene transcription. Outbreaks of the picornavirus foot-and-mouth disease virus (FMDV) have significant consequences for animal health and product safety and place a major economic burden on the global livestock industry. Understanding how this notorious animal pathogen suppresses the antiviral type I interferon (IFN-α/β) response may help to develop countermeasures to control FMDV infections. FMDV suppresses the IFN-α/β response through the activity of its Leader protein (Lpro), a protease that can cleave host cell proteins. Lpro was also shown to have deubiquitinase and deISGylase activity, raising the possibility that Lpro suppresses IFN-α/β by removing ubiquitin and/or ISG15, two posttranslational modifications that can regulate the activation, interactions and localization of (signaling) proteins. Here, we show that TBK1 and MAVS, two signaling proteins that are important for activation of IFN-α/β gene transcription, are cleaved by Lpro. By generating Lpro mutants lacking either of these two activities, we demonstrate that Lpro’s ability to cleave signaling proteins, but not its deubiquitination/deISGylase activity, correlates with suppression of IFN-β gene transcription.
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Affiliation(s)
- Linda J. Visser
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
| | - Chiara Aloise
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
| | - Kirby N. Swatek
- Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Gisselle N. Medina
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, New York, United States of America
| | - Karin M. Olek
- Department of Medical Biochemistry, Max Perutz Labs, Vienna Biocenter, Medical University of Vienna, Vienna, Austria
| | - Huib H. Rabouw
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
| | - Raoul J. de Groot
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
| | - Martijn A. Langereis
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
| | - Teresa de los Santos
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, New York, United States of America
| | - David Komander
- Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
- Ubiquitin Signaling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Tim Skern
- Department of Medical Biochemistry, Max Perutz Labs, Vienna Biocenter, Medical University of Vienna, Vienna, Austria
| | - Frank J. M. van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
- * E-mail:
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395
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Chandler LC, Yusuf IH, McClements ME, Barnard AR, MacLaren RE, Xue K. Immunomodulatory Effects of Hydroxychloroquine and Chloroquine in Viral Infections and Their Potential Application in Retinal Gene Therapy. Int J Mol Sci 2020; 21:E4972. [PMID: 32674481 PMCID: PMC7404262 DOI: 10.3390/ijms21144972] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/02/2020] [Accepted: 07/09/2020] [Indexed: 12/25/2022] Open
Abstract
Effective treatment of retinal diseases with adeno-associated virus (AAV)-mediated gene therapy is highly dependent on the proportion of successfully transduced cells. However, due to inflammatory reactions at high vector doses, adjunctive treatment may be necessary to enhance the therapeutic outcome. Hydroxychloroquine and chloroquine are anti-malarial drugs that have been successfully used in the treatment of autoimmune diseases. Evidence suggests that at high concentrations, hydroxychloroquine and chloroquine can impact viral infection and replication by increasing endosomal and lysosomal pH. This effect has led to investigations into the potential benefits of these drugs in the treatment of viral infections, including human immunodeficiency virus and severe acute respiratory syndrome coronavirus-2. However, at lower concentrations, hydroxychloroquine and chloroquine appear to exert immunomodulatory effects by inhibiting nucleic acid sensors, including toll-like receptor 9 and cyclic GMP-AMP synthase. This dose-dependent effect on their mechanism of action supports observations of increased viral infections associated with lower drug doses. In this review, we explore the immunomodulatory activity of hydroxychloroquine and chloroquine, their impact on viral infections, and their potential to improve the efficacy and safety of retinal gene therapy by reducing AAV-induced immune responses. The safety and practicalities of delivering hydroxychloroquine into the retina will also be discussed.
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Affiliation(s)
- Laurel C. Chandler
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences & NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK; (I.H.Y.); (M.E.M.); (A.R.B.); (R.E.M.)
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Imran H. Yusuf
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences & NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK; (I.H.Y.); (M.E.M.); (A.R.B.); (R.E.M.)
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Michelle E. McClements
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences & NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK; (I.H.Y.); (M.E.M.); (A.R.B.); (R.E.M.)
| | - Alun R. Barnard
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences & NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK; (I.H.Y.); (M.E.M.); (A.R.B.); (R.E.M.)
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences & NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK; (I.H.Y.); (M.E.M.); (A.R.B.); (R.E.M.)
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Kanmin Xue
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences & NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK; (I.H.Y.); (M.E.M.); (A.R.B.); (R.E.M.)
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
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396
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Duque-Correa MA, Schreiber F, Rodgers FH, Goulding D, Forrest S, White R, Buck A, Grencis RK, Berriman M. Development of caecaloids to study host-pathogen interactions: new insights into immunoregulatory functions of Trichuris muris extracellular vesicles in the caecum. Int J Parasitol 2020; 50:707-718. [PMID: 32659277 PMCID: PMC7435689 DOI: 10.1016/j.ijpara.2020.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 12/14/2022]
Abstract
Development of new methods to generate, culture and characterise mouse caecaloids is described. Caecaloids recapitulate the caecal epithelium composition and spatial organisation. Caecaloids can be used to study host–caecal pathogen interactions in vitro. Trichuris muris EVs exert novel immunoregulatory effects on intestinal epithelial cells.
The caecum, an intestinal appendage in the junction of the small and large intestines, displays a unique epithelium that serves as an exclusive niche for a range of pathogens including whipworms (Trichuris spp.). While protocols to grow organoids from small intestine (enteroids) and colon (colonoids) exist, the conditions to culture organoids from the caecum have yet to be described. Here, we report methods to grow, differentiate and characterise mouse adult stem cell-derived caecal organoids, termed caecaloids. We compare the cellular composition of caecaloids with that of enteroids, identifying differences in intestinal epithelial cell populations that mimic those found in the caecum and small intestine. The remarkable similarity in the intestinal epithelial cell composition and spatial conformation of caecaloids and their tissue of origin enables their use as an in vitro model to study host interactions with important caecal pathogens. Thus, exploiting this system, we investigated the responses of caecal intestinal epithelial cells to extracellular vesicles secreted/excreted by the intracellular helminth Trichuris muris. Our findings reveal novel immunoregulatory effects of whipworm extracellular vesicles on the caecal epithelium, including the downregulation of responses to nucleic acid recognition and type-I interferon signalling.
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Affiliation(s)
| | | | - Faye H Rodgers
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - David Goulding
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Sally Forrest
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Ruby White
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Amy Buck
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Richard K Grencis
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research and Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
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397
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Østvik AE, Svendsen TD, Granlund AVB, Doseth B, Skovdahl HK, Bakke I, Thorsvik S, Afroz W, Walaas GA, Mollnes TE, Gustafsson BI, Sandvik AK, Bruland T. Intestinal Epithelial Cells Express Immunomodulatory ISG15 During Active Ulcerative Colitis and Crohn's Disease. J Crohns Colitis 2020; 14:920-934. [PMID: 32020185 PMCID: PMC7392169 DOI: 10.1093/ecco-jcc/jjaa022] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND AIMS Intestinal epithelial cells [IECs] secrete cytokines that recruit immune cells to the mucosa and regulate immune responses that drive inflammation in inflammatory bowel disease [IBD]. However, experiments in patient-derived IEC models are still scarce. Here, we aimed to investigate how innate immunity and IEC-specific pattern recognition receptor [PRR] signalling can be involved in an enhanced type I interferon [IFN] gene signature observed in colon epithelium of patients with active IBD, with a special focus on secreted ubiquitin-like protein ISG15. METHODS Gene and protein expression in whole mucosa biopsies and in microdissected human colonic epithelial lining, in HT29 human intestinal epithelial cells and primary 3D colonoids treated with PRR-ligands and cytokines, were detected by transcriptomics, in situ hybridisation, immunohistochemistry, western blots, and enzyme-linked immunosorbent assay [ELISA]. Effects of IEC-secreted cytokines were examined in human peripheral blood mononuclear cells [PBMCs] by multiplex chemokine profiling and ELISA. RESULTS The type I IFN gene signature in human mucosal biopsies was mimicked in Toll-like receptor TLR3 and to some extent tumour necrosis factor [TNF]-treated human IECs. In intestinal biopsies, ISG15 expression correlated with expression of the newly identified receptor for extracellular ISG15, LFA-1 integrin. ISG15 was expressed and secreted from HT29 cells and primary 3D colonoids through both JAK1-pSTAT-IRF9-dependent and independent pathways. In experiments using PBMCs, we show that ISG15 releases IBD-relevant proinflammatory cytokines such as CXCL1, CXCL5, CXCL8, CCL20, IL1, IL6, TNF, and IFNγ. CONCLUSIONS ISG15 is secreted from primary IECs upon extracellular stimulation, and mucosal ISG15 emerges as an intriguing candidate for immunotherapy in IBD.
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Affiliation(s)
- Ann Elisabet Østvik
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Trondheim, Norway,Department of G2astroenterology and Hepatology, Clinic of Medicine, St. Olav’s University Hospital, Trondheim, Norway
| | - Tarjei Dahl Svendsen
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
| | - Atle van Beelen Granlund
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Trondheim, Norway,Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
| | - Berit Doseth
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
| | - Helene Kolstad Skovdahl
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingunn Bakke
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Trondheim, Norway,Clinic of Medicine, St Olav’s University Hospital, Trondheim, Norway,Clinic of Laboratory Medicine, St. Olav’s University Hospital, Trondheim, Norway
| | - Silje Thorsvik
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Trondheim, Norway,Department of G2astroenterology and Hepatology, Clinic of Medicine, St. Olav’s University Hospital, Trondheim, Norway,Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
| | - Wahida Afroz
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
| | - Gunnar Andreas Walaas
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
| | - Tom Eirik Mollnes
- Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway,Research Laboratory, Nordland Hospital, Bodo, Norway,K.G. Jebsen Thrombosis Research and Expertise Center, Institute of Clinical Medicine, University of Tromsø, Tromsø, Norway,Department of Immunology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Björn Inge Gustafsson
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Trondheim, Norway,Department of G2astroenterology and Hepatology, Clinic of Medicine, St. Olav’s University Hospital, Trondheim, Norway
| | - Arne Kristian Sandvik
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Trondheim, Norway,Department of G2astroenterology and Hepatology, Clinic of Medicine, St. Olav’s University Hospital, Trondheim, Norway,Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
| | - Torunn Bruland
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Trondheim, Norway,Clinic of Medicine, St Olav’s University Hospital, Trondheim, Norway,Corresponding author: Torunn Bruland, PhD, Department of Clinical and Molecular Medicine [IKOM], Faculty of Medicine and Health Sciences [MH], NTNU-Norwegian University of Science and Technology, Prinsesse Kristinas gate 1, NO-7489 Trondheim, Norway. Tel.: +47 72825324; E-mail
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Nicolaou O, Sokratous K, Makowska Z, Morell M, De Groof A, Montigny P, Hadjisavvas A, Michailidou K, Oulas A, Spyrou GM, Demetriou C, Alarcón-Riquelme ME, Psarellis S, Kousios A, Lauwerys B, Kyriacou K. Proteomic analysis in lupus mice identifies Coronin-1A as a potential biomarker for lupus nephritis. Arthritis Res Ther 2020; 22:147. [PMID: 32552896 PMCID: PMC7301983 DOI: 10.1186/s13075-020-02236-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Approximately 50% of systemic lupus erythematosus (SLE) patients develop nephritis, which is among the most severe and frequent complications of the disease and a leading cause of morbidity and mortality. Despite intensive research, there are still no reliable lupus nephritis (LN) markers in clinical use that can assess renal damage and activity with a high sensitivity and specificity. To this end, the aim of this study was to identify new clinically relevant tissue-specific protein biomarkers and possible underlying molecular mechanisms associated with renal involvement in SLE, using mass spectrometry (MS)-based proteomics. METHODS Kidneys were harvested from female triple congenic B6.NZMsle1/sle2/sle3 lupus mice model, and the respective sex- and age-matched C57BL/6 control mice at 12, 24 and 36 weeks of age, representing pre-symptomatic, established and end-stage LN, respectively. Proteins were extracted from kidneys, purified, reduced, alkylated and digested by trypsin. Purified peptides were separated by liquid chromatography and analysed by high-resolution MS. Data were processed by the Progenesis QIp software, and functional annotation analysis was performed using DAVID bioinformatics resources. Immunofluorescence and multiple reaction monitoring (MRM) MS methods were used to confirm prospective biomarkers in SLE mouse strains as well as human serum samples. RESULTS Proteomic profiling of kidney tissues from SLE and control mice resulted in the identification of more than 3800 unique proteins. Pathway analysis revealed a number of dysregulated molecular pathways that may be mechanistically involved in renal pathology, including phagosome and proximal tubule bicarbonate reclamation pathways. Proteomic analysis supported by human transcriptomic data and pathway analysis revealed Coronin-1A, Ubiquitin-like protein ISG15, and Rho GDP-dissociation inhibitor 2, as potential LN biomarkers. These results were further validated in other SLE mouse strains using MRM-MS. Most importantly, experiments in humans showed that measurement of Coronin-1A in human sera using MRM-MS can segregate LN patients from SLE patients without nephritis with a high sensitivity (100%) and specificity (100%). CONCLUSIONS These preliminary findings suggest that serum Coronin-1A may serve as a promising non-invasive biomarker for LN and, upon validation in larger cohorts, may be employed in the future as a screening test for renal disease in SLE patients.
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Affiliation(s)
- Orthodoxia Nicolaou
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
| | - Kleitos Sokratous
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Present Address: OMass Therapeutics, The Schrödinger Building, Heatley Road, The Oxford Science Park, Oxford, OX4 4GE, UK
| | | | - María Morell
- Genomic Medicine Department, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
| | - Aurélie De Groof
- Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
| | - Pauline Montigny
- Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
- CHU UCL Namur, Yvoir, Belgium
| | - Andreas Hadjisavvas
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
| | - Kyriaki Michailidou
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Anastasis Oulas
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George M Spyrou
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Christiana Demetriou
- Department of Primary Care and Population Health, University of Nicosia Medical School, Nicosia, Cyprus
| | - Marta E Alarcón-Riquelme
- Genomic Medicine Department, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
- Unit of Immunology and Chronic Disease, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Savvas Psarellis
- Department of Rheumatology, Nicosia General Hospital, Nicosia, Cyprus
| | - Andreas Kousios
- Renal and Transplant Centre Hammersmith Hospital Imperial College Healthcare NHS Trust, London, UK
| | - Bernard Lauwerys
- Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
- Department of Rheumatology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Kyriacos Kyriacou
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus.
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus.
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399
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Impairment of the DeISGylation Activity of Foot-and-Mouth Disease Virus Lpro Causes Attenuation In Vitro and In Vivo. J Virol 2020; 94:JVI.00341-20. [PMID: 32295921 PMCID: PMC7307143 DOI: 10.1128/jvi.00341-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/08/2020] [Indexed: 01/25/2023] Open
Abstract
Foot-and-mouth disease virus (FMDV) leader proteinase (Lpro) affects several pathways of the host innate immune response. Previous studies in bovine cells demonstrated that deletions (leaderless [LLV]) or point mutations in Lpro result in increased expression of interferon (IFN) and IFN-stimulated genes (ISGs), including, among others, the ubiquitin-like protein modifier ISG15 and the ubiquitin specific peptidase USP18. In addition to its conventional papain-like protease activity, Lpro acts as a deubiquitinase (DUB) and deISGylase. In this study, we identified a conserved residue in Lpro that is involved in its interaction with ISG15. Mutation W105A rendered Escherichia coli-expressed Lpro unable to cleave the synthetic substrate pro-ISG15 while preserving cellular eIF4G cleavage. Interestingly, mutant FMDV W105A was viable. Overexpression of ISG15 and the ISGylation machinery in porcine cells resulted in moderate inhibition of FMDV replication, along with a decrease of the overall state of ISGylation in wild-type (WT)-infected cells. In contrast, reduced deISGylation was observed upon infection with W105A and leaderless virus. Reduction in the levels of deubiquitination was also observed in cells infected with the FMDV LproW105A mutant. Surprisingly, similarly to WT, infection with W105A inhibited IFN/ISG expression despite displaying an attenuated phenotype in vivo in mice. Altogether, our studies indicate that abolishing/reducing the deISGylase/DUB activity of Lpro causes viral attenuation independently of its ability to block the expression of IFN and ISG mRNA. Furthermore, our studies highlight the potential of ISG15 to be developed as a novel biotherapeutic molecule against FMD.IMPORTANCE In this study, we identified an aromatic hydrophobic residue in foot-and-mouth disease virus (FMDV) leader proteinase (Lpro) (W105) that is involved in the interaction with ISG15. Mutation in Lpro W105 (A12-LproW105A) resulted in reduced deISGylation in vitro and in porcine-infected cells. Impaired deISGylase activity correlated with viral attenuation in vitro and in vivo and did not affect the ability of Lpro to block expression of type I interferon (IFN) and other IFN-stimulated genes. Moreover, overexpression of ISG15 resulted in the reduction of FMDV viral titers. Thus, our study highlights the potential use of Lpro mutants with modified deISGylase activity for development of live attenuated vaccine candidates, and ISG15 as a novel biotherapeutic against FMD.
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400
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Zhou Z, Ren L, Zhang L, Zhong J, Xiao Y, Jia Z, Guo L, Yang J, Wang C, Jiang S, Yang D, Zhang G, Li H, Chen F, Xu Y, Chen M, Gao Z, Yang J, Dong J, Liu B, Zhang X, Wang W, He K, Jin Q, Li M, Wang J. Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients. Cell Host Microbe 2020. [PMID: 32407669 DOI: 10.1016/jxhom.2020.04.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
The outbreaks of 2019 novel coronavirus disease (COVID-19) caused by SARS-CoV-2 infection have posed a severe threat to global public health. It is unclear how the human immune system responds to this infection. Here, we used metatranscriptomic sequencing to profile immune signatures in the bronchoalveolar lavage fluid of eight COVID-19 cases. The expression of proinflammatory genes, especially chemokines, was markedly elevated in COVID-19 cases compared to community-acquired pneumonia patients and healthy controls, suggesting that SARS-CoV-2 infection causes hypercytokinemia. Compared to SARS-CoV, which is thought to induce inadequate interferon (IFN) responses, SARS-CoV-2 robustly triggered expression of numerous IFN-stimulated genes (ISGs). These ISGs exhibit immunopathogenic potential, with overrepresentation of genes involved in inflammation. The transcriptome data was also used to estimate immune cell populations, revealing increases in activated dendritic cells and neutrophils. Collectively, these host responses to SARS-CoV-2 infection could further our understanding of disease pathogenesis and point toward antiviral strategies.
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Affiliation(s)
- Zhuo Zhou
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking University Genome Editing Research Center, School of Life Sciences, Peking University, Beijing 100871, China; National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Lili Ren
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Li Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
| | - Jiaxin Zhong
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Xiao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Zhilong Jia
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing 100853, China
| | - Li Guo
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Jing Yang
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chun Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Jiang
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
| | - Donghong Yang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory for Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Hongru Li
- Fujian Provincial Hospital, Fujian 350000, China
| | - Fuhui Chen
- Department of respiratory, the Second Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Yu Xu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Mingwei Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi Province 710061, China
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Jian Yang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Jie Dong
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Bo Liu
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Xiannian Zhang
- School of Basic Medical Sciences, Beijing Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Weidong Wang
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing 100853, China
| | - Kunlun He
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing 100853, China
| | - Qi Jin
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Mingkun Li
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China; Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| | - Jianwei Wang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China.
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