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McMillan RE, Lo MK, Zhang XQ, Beadle JR, Valiaeva N, Garretson AF, Clark AE, Freshman JE, Murphy J, Montgomery JM, Spiropoulou CF, Schooley RT, Hostetler KY, Carlin AF. Enhanced broad spectrum in vitro antiviral efficacy of 3-F-4-MeO-Bn, 3-CN, and 4-CN derivatives of lipid remdesivir nucleoside monophosphate prodrugs. Antiviral Res 2023; 219:105718. [PMID: 37758067 PMCID: PMC10790242 DOI: 10.1016/j.antiviral.2023.105718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/02/2023] [Accepted: 09/06/2023] [Indexed: 10/02/2023]
Abstract
Broad spectrum oral antivirals are urgently needed for the early treatment of many RNA viruses of clinical concern. We previously described the synthesis of 1-O-octadecyl-2-O-benzyl-glycero-3-phospho-RVn (V2043), an orally bioavailable lipid prodrug of remdesivir nucleoside (RVn, GS-441524) with broad spectrum antiviral activity against viruses with pandemic potential. Here we compared the relative activity of V2043 with new RVn lipid prodrugs containing sn-1 alkyl ether or sn-2 glycerol modifications. We found that 3-F-4-MeO-Bn, 3-CN-Bn, and 4-CN-Bn sn-2 glycerol modifications improved antiviral activity compared to V2043 when tested in vitro against clinically important RNA viruses from 5 virus families. These results support the continued development of V2043 and sn-2 glycerol modified RVn lipid prodrugs for the treatment of a broad range of RNA viruses for which there are limited therapies.
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Affiliation(s)
- Rachel E McMillan
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA; Department of Pathology, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Michael K Lo
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Department of Health and Human Services, Atlanta, CA, USA
| | - Xing-Quan Zhang
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - James R Beadle
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Nadejda Valiaeva
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Aaron F Garretson
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA; Department of Pathology, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Alex E Clark
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA; Department of Pathology, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Jon E Freshman
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA; Department of Pathology, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Joyce Murphy
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Joel M Montgomery
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Department of Health and Human Services, Atlanta, CA, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Department of Health and Human Services, Atlanta, CA, USA
| | - Robert T Schooley
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Karl Y Hostetler
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Aaron F Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA; Department of Pathology, University of California San Diego, School of Medicine, La Jolla, CA, USA.
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2
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Abstract
Objectives: Breastfeeding and human milk (HM) improve maternal and infant morbidities and mortality. Therefore, monitoring the safety of breastfeeding and access to HM is of critical importance. In this study, we assessed tools to monitor the presence of monkeypox virus (MPXV) in HM and whether standard Holder pasteurization inactivates MPXV. Materials and Methods: Heat-inactivated MPXV was added to HM or viral transport media (VTM) and analyzed using both research and clinical MPXV quantitative polymerase chain reaction (qPCR) tests. Infectious MPXV was added to HM and was exposed to 1 cycle of freeze-thaw, incubation for 1 hour at room temperature, or conditions of Holder pasteurization (62.5°C for 30 minutes) followed by infectious unit quantification by plaque assay. Results: Research and clinical nucleic acid tests detect MPXV that was added to HM but with reduced sensitivity compared with equivalent samples in VTM at low virus inoculum. MPXV added to HM to achieve a starting concentration of 225,000 plaque forming units (pfu)/mL remains infectious after freeze-thaw or 1 hour storage at room temperature. However, Holder pasteurization reduced infectious virus below the limit of detection, >2,000-fold reduction in viral titer. Conclusion: MPXV can be detected when added to HM using a clinical laboratory-developed qPCR test without modification, but the detection limit is reduced compared with equivalent samples in VTM. MPXV remains viable in HM should the virus ever gain access to HM, but Holder pasteurization reduces infectious MPXV to below detection limits and can be used to reduce the risk of MPXV transmission to infants who receive pasteurized (donor) HM.
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Affiliation(s)
- Alex E. Clark
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Annalee Furst
- Department of Pediatrics, and University of California, San Diego, La Jolla, California, USA
| | - Kristija Sejane
- Department of Pediatrics, and University of California, San Diego, La Jolla, California, USA
| | - Lisa Stellwagen
- UC Health Milk Bank, University of California, San Diego, La Jolla, California, USA
- Human Milk Institute (HMI), University of California, San Diego, La Jolla, California, USA
| | - Marissa Proost
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Davey M. Smith
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
- VA San Diego Healthcare System, San Diego, California, USA
| | - Aaron F. Carlin
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Lars Bode
- Department of Pediatrics, and University of California, San Diego, La Jolla, California, USA
- Human Milk Institute (HMI), University of California, San Diego, La Jolla, California, USA
- Larsson-Rosenquist Foundation Mother-Milk-Infant Center of research Excellence (MOMI CORE), University of California, San Diego, La Jolla, California, USA
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3
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McMillan RE, Wang E, Carlin AF, Coufal NG. Human microglial models to study host-virus interactions. Exp Neurol 2023; 363:114375. [PMID: 36907350 PMCID: PMC10521930 DOI: 10.1016/j.expneurol.2023.114375] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/13/2023] [Accepted: 03/02/2023] [Indexed: 03/14/2023]
Abstract
Microglia, the resident macrophage of the central nervous system, are increasingly recognized as contributing to diverse aspects of human development, health, and disease. In recent years, numerous studies in both mouse and human models have identified microglia as a "double edged sword" in the progression of neurotropic viral infections: protecting against viral replication and cell death in some contexts, while acting as viral reservoirs and promoting excess cellular stress and cytotoxicity in others. It is imperative to understand the diversity of human microglial responses in order to therapeutically modulate them; however, modeling human microglia has been historically challenging due to significant interspecies differences in innate immunity and rapid transformation upon in vitro culture. In this review, we discuss the contribution of microglia to the neuropathogenesis of key neurotropic viral infections: human immunodeficiency virus 1 (HIV-1), Zika virus (ZIKV), Japanese encephalitis virus (JEV), West Nile virus (WNV), Herpes simplex virus (HSV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We pay special attention to recent work with human stem cell-derived microglia and propose strategies to leverage these powerful models to further uncover species- and disease-specific microglial responses and novel therapeutic interventions for neurotropic viral infections.
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Affiliation(s)
- Rachel E McMillan
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, United States of America; Department of Pathology and Medicine, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States of America
| | - Ellen Wang
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States of America; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92093, United States of America
| | - Aaron F Carlin
- Department of Pathology and Medicine, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States of America.
| | - Nicole G Coufal
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States of America; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92093, United States of America.
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4
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Carlin AF, Clark AE, Garretson AF, Bray W, Porrachia M, Santos AT, Rana TM, Chaillon A, Smith DM. Neutralizing Antibody Responses After Severe Acute Respiratory Syndrome Coronavirus 2 BA.2 and BA.2.12.1 Infection Do Not Neutralize BA.4 and BA.5 and Can Be Blunted by Nirmatrelvir/Ritonavir Treatment. Open Forum Infect Dis 2023; 10:ofad154. [PMID: 37096144 PMCID: PMC10122487 DOI: 10.1093/ofid/ofad154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/17/2023] [Indexed: 04/26/2023] Open
Abstract
The factors contributing to the rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) BA.4 and BA.5 subvariants in populations that experienced recent surges of BA.2 and BA.2.12.1 infections are not understood. Neutralizing antibodies (NAbs) are likely to protect against severe disease if present in sufficient quantity. We found that after BA.2 or BA.2.12.1 infection, NAb responses were largely cross-neutralizing but were much less effective against BA.5. In addition, individuals who were infected and treated early with nirmatrelvir/ritonavir (Paxlovid) had lower NAb levels than untreated individuals.
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Affiliation(s)
- Aaron F Carlin
- Correspondence: Aaron F. Carlin, MD, PhD, Department of Pathology and Medicine University of California San Diego, 9500 Gilman Drive, GPL 118, La Jolla, CA 92093-0640 (). Davey M. Smith, MD, Department of Medicine University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0507 ()
| | | | - Aaron F Garretson
- School of Medicine, University of California San Diego, La Jolla, California, USA
| | - William Bray
- School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Magali Porrachia
- School of Medicine, University of California San Diego, La Jolla, California, USA
| | - AsherLev T Santos
- Department of Public Health, College of Education, Health and Human Services, California State University San Marcos, San Marcos, California, USA
| | - Tariq M Rana
- School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Antoine Chaillon
- School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Davey M Smith
- Correspondence: Aaron F. Carlin, MD, PhD, Department of Pathology and Medicine University of California San Diego, 9500 Gilman Drive, GPL 118, La Jolla, CA 92093-0640 (). Davey M. Smith, MD, Department of Medicine University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0507 ()
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5
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Cheng Y, Clark AE, Yim W, Borum RM, Chang YC, Jin Z, He T, Carlin AF, Jokerst JV. Protease-Responsive Potential-Tunable AIEgens for Cell Selective Imaging of TMPRSS2 and Accurate Inhibitor Screening. Anal Chem 2023; 95:3789-3798. [PMID: 36753444 PMCID: PMC10614162 DOI: 10.1021/acs.analchem.2c04988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Transmembrane protease serine 2 (TMPRSS2) is a plasma membrane protease that activates both spike protein of coronaviruses for cell entry and oncogenic signaling pathways for tumor progression. TMPRSS2 inhibition can reduce cancer invasion and metastasis and partially prevent the entry of SARS-CoV-2 into host cells. Thus, there is an urgent need for both TMPRSS2-selective imaging and precise screening of TMPRSS2 inhibitors. Here, we report a TMPRSS2-responsive surface-potential-tunable peptide-conjugated probe (EGTP) with aggregation-induced emission (AIE) features for TMPRSS2 selective imaging and accurate inhibitor screening. The amphiphilic EGTP was constructed with tunable surface potential and responsive efficiency with TMPRSS2 and its inhibitor. The rational construction of AIE luminogens (AIEgens) with modular peptides indicated that the cleavage of EGTP led to a gradual aggregation with bright fluorescence in high TMPRSS2-expressing cells. This strategy may have value for selective detection of cancer cells, SARS-CoV-2-target cells, and screening of protease inhibitors.
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Affiliation(s)
- Yong Cheng
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Alex E Clark
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Wonjun Yim
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, California 92093, United States
| | - Raina M Borum
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Yu-Ci Chang
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, California 92093, United States
| | - Zhicheng Jin
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Tengyu He
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, California 92093, United States
| | - Aaron F Carlin
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, United States
- Department of Pathology, University of California, San Diego, La Jolla, California 92093, United States
| | - Jesse V Jokerst
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, California 92093, United States
- Department of Radiology, University of California, San Diego, La Jolla, California 92093, United States
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6
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Sørensen DM, Büll C, Madsen TD, Lira-Navarrete E, Clausen TM, Clark AE, Garretson AF, Karlsson R, Pijnenborg JFA, Yin X, Miller RL, Chanda SK, Boltje TJ, Schjoldager KT, Vakhrushev SY, Halim A, Esko JD, Carlin AF, Hurtado-Guerrero R, Weigert R, Clausen H, Narimatsu Y. Identification of global inhibitors of cellular glycosylation. Nat Commun 2023; 14:948. [PMID: 36804936 PMCID: PMC9941569 DOI: 10.1038/s41467-023-36598-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
Small molecule inhibitors of glycosylation enzymes are valuable tools for dissecting glycan functions and potential drug candidates. Screening for inhibitors of glycosyltransferases are mainly performed by in vitro enzyme assays with difficulties moving candidates to cells and animals. Here, we circumvent this by employing a cell-based screening assay using glycoengineered cells expressing tailored reporter glycoproteins. We focused on GalNAc-type O-glycosylation and selected the GalNAc-T11 isoenzyme that selectively glycosylates endocytic low-density lipoprotein receptor (LDLR)-related proteins as targets. Our screen of a limited small molecule compound library did not identify selective inhibitors of GalNAc-T11, however, we identify two compounds that broadly inhibited Golgi-localized glycosylation processes. These compounds mediate the reversible fragmentation of the Golgi system without affecting secretion. We demonstrate how these inhibitors can be used to manipulate glycosylation in cells to induce expression of truncated O-glycans and augment binding of cancer-specific Tn-glycoprotein antibodies and to inhibit expression of heparan sulfate and binding and infection of SARS-CoV-2.
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Affiliation(s)
- Daniel Madriz Sørensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Christian Büll
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Thomas D Madsen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erandi Lira-Navarrete
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- The Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, 50018, Zaragoza, Spain
- Fundación ARAID, 50018, Zaragoza, Spain
| | - Thomas Mandel Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alex E Clark
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Aaron F Garretson
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Richard Karlsson
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Johan F A Pijnenborg
- Institute for Molecules and Materials, Department of Synthetic Organic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Xin Yin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Rebecca L Miller
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Thomas J Boltje
- Institute for Molecules and Materials, Department of Synthetic Organic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Aaron F Carlin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ramon Hurtado-Guerrero
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- The Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, 50018, Zaragoza, Spain
- Fundación ARAID, 50018, Zaragoza, Spain
| | - Roberto Weigert
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark.
- GlycoDisplay ApS, Copenhagen, Denmark.
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7
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Wang L, Wang S, Wu L, Li W, Bray W, Clark AE, Gonzalez GM, Wang Y, Carlin AF, Rana TM. PCIF1-mediated deposition of 5'-cap N6,2'- O-dimethyladenosine in ACE2 and TMPRSS2 mRNA regulates susceptibility to SARS-CoV-2 infection. Proc Natl Acad Sci U S A 2023; 120:e2210361120. [PMID: 36689652 PMCID: PMC9945940 DOI: 10.1073/pnas.2210361120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/14/2022] [Indexed: 01/25/2023] Open
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be a major health problem worldwide. Due to the fast emergence of SARS-CoV-2 variants, understanding the molecular mechanisms of viral pathogenesis and developing novel inhibitors are essential and urgent. Here, we investigated the potential roles of N6,2'-O-dimethyladenosine (m6Am), one of the most abundant modifications of eukaryotic messenger ribonucleic acid (mRNAs), in SARS-CoV-2 infection of human cells. Using genome-wide m6Am-exo-seq, RNA sequencing analysis, and Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 genome editing, we demonstrate that phosphorylated C-terminal domain (CTD)-interacting factor 1 (PCIF1), a cap-specific adenine N6-methyltransferase, plays a major role in facilitating infection of primary human lung epithelial cells and cell lines by SARS-CoV-2, variants of concern, and other coronaviruses. We show that PCIF1 promotes infection by sustaining expression of the coronavirus receptors angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) via m6Am-dependent mRNA stabilization. In PCIF1-depleted cells, both ACE2/TMPRSS2 expression and viral infection are rescued by re-expression of wild-type, but not catalytically inactive, PCIF1. These findings suggest a role for PCIF1 and cap m6Am in regulating SARS-CoV-2 susceptibility and identify a potential therapeutic target for prevention of infection.
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Affiliation(s)
- Lingling Wang
- Division of Genetics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Shaobo Wang
- Division of Genetics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Lujing Wu
- Division of Genetics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Wanyu Li
- Division of Genetics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - William Bray
- Division of Genetics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Alex E. Clark
- Division of Infectious Diseases and Global Public Health, Department of Medicine, Department of Pathology, University of California San Diego, La Jolla, CA92093
| | - Gwendolyn Michelle Gonzalez
- Environmental Toxicology Graduate Program, University of California, Riverside, CA92521
- Department of Chemistry University of California, Riverside, CA92521
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA92521
- Department of Chemistry University of California, Riverside, CA92521
| | - Aaron F. Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, Department of Pathology, University of California San Diego, La Jolla, CA92093
| | - Tariq M. Rana
- Division of Genetics, Program in Immunology, Bioinformatics and Systems Biology Program, Institute for Genomic Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
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8
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Leibel SL, McVicar RN, Murad R, Kwong EM, Clark AE, Alvarado A, Grimmig BA, Nuryyev R, Young RE, Lee JC, Peng W, Zhu YP, Griffis E, Nowell CJ, Liu K, James B, Alarcon S, Malhotra A, Gearing LJ, Hertzog PJ, Galapate CM, Galenkamp KM, Commisso C, Smith DM, Sun X, Carlin AF, Croker BA, Snyder EY. The lung employs an intrinsic surfactant-mediated inflammatory response for viral defense. bioRxiv 2023:2023.01.26.525578. [PMID: 36747824 PMCID: PMC9900938 DOI: 10.1101/2023.01.26.525578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes an acute respiratory distress syndrome (ARDS) that resembles surfactant deficient RDS. Using a novel multi-cell type, human induced pluripotent stem cell (hiPSC)-derived lung organoid (LO) system, validated against primary lung cells, we found that inflammatory cytokine/chemokine production and interferon (IFN) responses are dynamically regulated autonomously within the lung following SARS-CoV-2 infection, an intrinsic defense mechanism mediated by surfactant proteins (SP). Single cell RNA sequencing revealed broad infectability of most lung cell types through canonical (ACE2) and non-canonical (endocytotic) viral entry routes. SARS-CoV-2 triggers rapid apoptosis, impairing viral dissemination. In the absence of surfactant protein B (SP-B), resistance to infection was impaired and cytokine/chemokine production and IFN responses were modulated. Exogenous surfactant, recombinant SP-B, or genomic correction of the SP-B deletion restored resistance to SARS-CoV-2 and improved viability.
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9
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Pereira de Jesus BA, Gomes AA, Clark AE, Rodrigues TA, Ledgerwood-Lee M, Van Zant W, Brickner H, Wang M, Blum DL, Cassera MB, Carlin AF, Aronoff-Spencer ES, da Silva GF, Magalhães MDLB, Ray P. In Vitro Diagnostic Assay to Detect SARS-CoV-2-Neutralizing Antibody in Patient Sera Using Engineered ACE-2 Mini-Protein. Viruses 2022; 14:2823. [PMID: 36560827 PMCID: PMC9780992 DOI: 10.3390/v14122823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
The recent development and mass administration of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) vaccines allowed for disease control, reducing hospitalizations and mortality. Most of these vaccines target the SARS-CoV-2 Spike (S) protein antigens, culminating with the production of neutralizing antibodies (NAbs) that disrupt the attachment of the virus to ACE2 receptors on the host cells. However, several studies demonstrated that the NAbs typically rise within a few weeks after vaccination but quickly reduce months later. Thus, multiple booster administration is recommended, leading to vaccination hesitancy in many populations. Detecting serum anti-SARS-CoV-2 NAbs can instruct patients and healthcare providers on correct booster strategies. Several in vitro diagnostics kits are available; however, their high cost impairs the mass NAbs diagnostic testing. Recently, we engineered an ACE2 mimetic that interacts with the Receptor Binding Domain (RBD) of the SARS-2 S protein. Here we present the use of this engineered mini-protein (p-deface2 mut) to develop a detection assay to measure NAbs in patient sera using a competitive ELISA assay. Serum samples from twenty-one patients were tested. Nine samples (42.8%) tested positive, and twelve (57.1%) tested negative for neutralizing sera. The data correlated with the result from the standard commercial assay that uses human ACE2 protein. This confirmed that p-deface2 mut could replace human ACE2 in ELISA assays. Using bacterially expressed p-deface2 mut protein is cost-effective and may allow mass SARS-CoV-2 NAbs detection, especially in low-income countries where economical diagnostic testing is crucial. Such information will help providers decide when a booster is required, reducing risks of reinfection and preventing the administration before it is medically necessary.
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Affiliation(s)
| | - Anderson Albino Gomes
- Biochemistry Laboratory, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages 88520-000, Brazil
| | - Alex E. Clark
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA
| | | | - Melissa Ledgerwood-Lee
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA
| | - Westley Van Zant
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA
| | - Howard Brickner
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA
| | - Meiqiao Wang
- Bioexpression and Fermentation Facility, University of Georgia, Athens, GA 30602, USA
| | - David L. Blum
- Bioexpression and Fermentation Facility, University of Georgia, Athens, GA 30602, USA
| | - Maria B. Cassera
- Department of Biochemistry and Molecular Biology and Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Athens, GA 30602, USA
| | - Aaron F. Carlin
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA
- Department of Pathology, University of California, San Diego, CA 92093, USA
| | - Eliah S. Aronoff-Spencer
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA
| | - Gustavo Felippe da Silva
- Biochemistry Laboratory, Center of Agroveterinary Sciences, State University of Santa Catarina, Lages 88520-000, Brazil
| | | | - Partha Ray
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA
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10
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Branche E, Wang YT, Viramontes KM, Valls Cuevas JM, Xie J, Ana-Sosa-Batiz F, Shafee N, Duttke SH, McMillan RE, Clark AE, Nguyen MN, Garretson AF, Crames JJ, Spann NJ, Zhu Z, Rich JN, Spector DH, Benner C, Shresta S, Carlin AF. SREBP2-dependent lipid gene transcription enhances the infection of human dendritic cells by Zika virus. Nat Commun 2022; 13:5341. [PMID: 36097162 PMCID: PMC9465152 DOI: 10.1038/s41467-022-33041-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 08/29/2022] [Indexed: 02/07/2023] Open
Abstract
The emergence of Zika virus (ZIKV) as a global health threat has highlighted the unmet need for ZIKV-specific vaccines and antiviral treatments. ZIKV infects dendritic cells (DC), which have pivotal functions in activating innate and adaptive antiviral responses; however, the mechanisms by which DC function is subverted to establish ZIKV infection are unclear. Here we develop a genomics profiling method that enables discrete analysis of ZIKV-infected versus neighboring, uninfected primary human DCs to increase the sensitivity and specificity with which ZIKV-modulated pathways can be identified. The results show that ZIKV infection specifically increases the expression of genes enriched for lipid metabolism-related functions. ZIKV infection also increases the recruitment of sterol regulatory element-binding protein (SREBP) transcription factors to lipid gene promoters, while pharmacologic inhibition or genetic silencing of SREBP2 suppresses ZIKV infection of DCs. Our data thus identify SREBP2-activated transcription as a mechanism for promoting ZIKV infection amenable to therapeutic targeting.
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Affiliation(s)
- Emilie Branche
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Ying-Ting Wang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Karla M Viramontes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Joan M Valls Cuevas
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Jialei Xie
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Fernanda Ana-Sosa-Batiz
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Norazizah Shafee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Sascha H Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, 99163, USA
| | - Rachel E McMillan
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Graduate Program, University of California, La Jolla, CA, 92093, USA
| | - Alex E Clark
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michael N Nguyen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Aaron F Garretson
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jan J Crames
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Nathan J Spann
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Zhe Zhu
- Department of Medicine, Division of Regenerative Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA
| | - Jeremy N Rich
- Department of Medicine, Division of Regenerative Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Neurology, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania; Department of Neurology, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Deborah H Spector
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Christopher Benner
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.
| | - Aaron F Carlin
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
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11
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Xu M, Zhou J, Cheng Y, Jin Z, Clark AE, He T, Yim W, Li Y, Chang YC, Wu Z, Fajtová P, O’Donoghue AJ, Carlin AF, Todd MD, Jokerst JV. A Self-Immolative Fluorescent Probe for Selective Detection of SARS-CoV-2 Main Protease. Anal Chem 2022; 94:11728-11733. [PMID: 35973073 PMCID: PMC9396966 DOI: 10.1021/acs.analchem.2c02381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/10/2022] [Indexed: 02/06/2023]
Abstract
Existing tools to detect and visualize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) suffer from low selectivity, poor cell permeability, and high cytotoxicity. Here we report a novel self-immolative fluorescent probe (MP590) for the highly selective and sensitive detection of the SARS-CoV-2 main protease (Mpro). This fluorescent probe was prepared by connecting a Mpro-cleavable peptide (N-acetyl-Abu-Tle-Leu-Gln) with a fluorophore (i.e., resorufin) via a self-immolative aromatic linker. Fluorescent titration results show that MP590 can detect Mpro with a limit of detection (LoD) of 35 nM and is selective over interferents such as hemoglobin, bovine serum albumin (BSA), thrombin, amylase, SARS-CoV-2 papain-like protease (PLpro), and trypsin. The cell imaging data indicate that this probe can report Mpro in HEK 293T cells transfected with a Mpro expression plasmid as well as in TMPRSS2-VeroE6 cells infected with SARS-CoV-2. Our results suggest that MP590 can both measure and monitor Mpro activity and quantitatively evaluate Mpro inhibition in infected cells, making it an important tool for diagnostic and therapeutic research on SARS-CoV-2.
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Affiliation(s)
- Ming Xu
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jiajing Zhou
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yong Cheng
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Zhicheng Jin
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Alex E. Clark
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Tengyu He
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Wonjun Yim
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yi Li
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yu-Ci Chang
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Zhuohong Wu
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Aaron F. Carlin
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael D. Todd
- Department of Structural Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jesse V. Jokerst
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department of Radiology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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12
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Cantú VJ, Belda-Ferre P, Salido RA, Tsai R, Austin B, Jordan W, Asudani M, Walster A, Magallanes CG, Valentine H, Manjoonian A, Wijaya C, Omaleki V, Sanders K, Aigner S, Baer NA, Betty M, Castro-Martínez A, Cheung W, Crescini ES, De Hoff P, Eisner E, Hakim A, Kapadia B, Lastrella AL, Lawrence ES, Ngo TT, Ostrander T, Sathe S, Seaver P, Smoot EW, Carlin AF, Yeo GW, Laurent LC, Manlutac AL, Fielding-Miller R, Knight R. Implementation of Practical Surface SARS-CoV-2 Surveillance in School Settings. mSystems 2022; 7:e0010322. [PMID: 35703437 PMCID: PMC9426517 DOI: 10.1128/msystems.00103-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/02/2022] [Indexed: 11/20/2022] Open
Abstract
Surface sampling for SARS-CoV-2 RNA detection has shown considerable promise to detect exposure of built environments to infected individuals shedding virus who would not otherwise be detected. Here, we compare two popular sampling media (VTM and SDS) and two popular workflows (Thermo and PerkinElmer) for implementation of a surface sampling program suitable for environmental monitoring in public schools. We find that the SDS/Thermo pipeline shows superior sensitivity and specificity, but that the VTM/PerkinElmer pipeline is still sufficient to support surface surveillance in any indoor setting with stable cohorts of occupants (e.g., schools, prisons, group homes, etc.) and may be used to leverage existing investments in infrastructure. IMPORTANCE The ongoing COVID-19 pandemic has claimed the lives of over 5 million people worldwide. Due to high density occupancy of indoor spaces for prolonged periods of time, schools are often of concern for transmission, leading to widespread school closings to combat pandemic spread when cases rise. Since pediatric clinical testing is expensive and difficult from a consent perspective, we have deployed surface sampling in SASEA (Safer at School Early Alert), which allows for detection of SARS-CoV-2 from surfaces within a classroom. In this previous work, we developed a high-throughput method which requires robotic automation and specific reagents that are often not available for public health laboratories such as the San Diego County Public Health Laboratory (SDPHL). Therefore, we benchmarked our method (Thermo pipeline) against SDPHL's (PerkinElmer) more widely used method for the detection and prediction of SARS-CoV-2 exposure. While our method shows superior sensitivity (false-negative rate of 9% versus 27% for SDPHL), the SDPHL pipeline is sufficient to support surface surveillance in indoor settings. These findings are important since they show that existing investments in infrastructure can be leveraged to slow the spread of SARS-CoV-2 not in just the classroom but also in prisons, nursing homes, and other high-risk, indoor settings.
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Affiliation(s)
- Victor J. Cantú
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Rodolfo A. Salido
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Brett Austin
- San Diego County Public Health Lab, San Diego, California, USA
| | - William Jordan
- San Diego County Public Health Lab, San Diego, California, USA
| | - Menka Asudani
- San Diego County Public Health Lab, San Diego, California, USA
| | - Amanda Walster
- San Diego County Public Health Lab, San Diego, California, USA
| | - Celestine G. Magallanes
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | - Holly Valentine
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | - Araz Manjoonian
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
- San Diego State University, San Diego, California, USA
| | - Carrissa Wijaya
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
| | - Vinton Omaleki
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Nathan A. Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Maryann Betty
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Rady Children's Hospital, San Diego, California, USA
| | - Anelizze Castro-Martínez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- San Diego State University, San Diego, California, USA
| | - Evelyn S. Crescini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | - Emily Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Bhavika Kapadia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Alma L. Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Elijah S. Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Toan T. Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Elizabeth W. Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Aaron F. Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Gene W. Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | | | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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13
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Cantú VJ, Sanders K, Belda-Ferre P, Salido RA, Tsai R, Austin B, Jordan W, Asudani M, Walster A, Magallanes CG, Valentine H, Manjoonian A, Wijaya C, Omaleki V, Aigner S, Baer NA, Betty M, Castro-Martínez A, Cheung W, De Hoff P, Eisner E, Hakim A, Lastrella AL, Lawrence ES, Ngo TT, Ostrander T, Plascencia A, Sathe S, Smoot EW, Carlin AF, Yeo GW, Laurent LC, Manlutac AL, Fielding-Miller R, Knight R. Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School Settings. mSystems 2022; 7:e0010922. [PMID: 35703436 PMCID: PMC9426498 DOI: 10.1128/msystems.00109-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/20/2022] [Indexed: 11/28/2022] Open
Abstract
A promising approach to help students safely return to in person learning is through the application of sentinel cards for accurate high resolution environmental monitoring of SARS-CoV-2 traces indoors. Because SARS-CoV-2 RNA can persist for up to a week on several indoor surface materials, there is a need for increased temporal resolution to determine whether consecutive surface positives arise from new infection events or continue to report past events. Cleaning sentinel cards after sampling would provide the needed resolution but might interfere with assay performance. We tested the effect of three cleaning solutions (BZK wipes, Wet Wipes, RNase Away) at three different viral loads: "high" (4 × 104 GE/mL), "medium" (1 × 104 GE/mL), and "low" (2.5 × 103 GE/mL). RNase Away, chosen as a positive control, was the most effective cleaning solution on all three viral loads. Wet Wipes were found to be more effective than BZK wipes in the medium viral load condition. The low viral load condition was easily reset with all three cleaning solutions. These findings will enable temporal SARS-CoV-2 monitoring in indoor environments where transmission risk of the virus is high and the need to avoid individual-level sampling for privacy or compliance reasons exists. IMPORTANCE Because SARS-CoV-2, the virus that causes COVID-19, persists on surfaces, testing swabs taken from surfaces is useful as a monitoring tool. This approach is especially valuable in school settings, where there are cost and privacy concerns that are eliminated by taking a single sample from a classroom. However, the virus persists for days to weeks on surface samples, so it is impossible to tell whether positive detection events on consecutive days are a persistent signal or new infectious cases and therefore whether the positive individuals have been successfully removed from the classroom. We compare several methods for cleaning "sentinel cards" to show that this approach can be used to identify new SARS-CoV-2 signals day to day. The results are important for determining how to monitor classrooms and other indoor environments for SARS-CoV-2 virus.
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Affiliation(s)
- Victor J. Cantú
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Rodolfo A. Salido
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Brett Austin
- San Diego County Public Health Lab, San Diego, California, USA
| | - William Jordan
- San Diego County Public Health Lab, San Diego, California, USA
| | - Menka Asudani
- San Diego County Public Health Lab, San Diego, California, USA
| | - Amanda Walster
- San Diego County Public Health Lab, San Diego, California, USA
| | - Celestine G. Magallanes
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | - Holly Valentine
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | - Araz Manjoonian
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
- San Diego State University, San Diego, California, USA
| | - Carrissa Wijaya
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
| | - Vinton Omaleki
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Nathan A. Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Maryann Betty
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Rady Children's Hospital, San Diego, California, USA
| | - Anelizze Castro-Martínez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- San Diego State University, San Diego, California, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | - Emily Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Alma L. Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Elijah S. Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Toan T. Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Elizabeth W. Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Aaron F. Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, USA
| | - Gene W. Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | | | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
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14
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Cheng Y, Clark AE, Zhou J, He T, Li Y, Borum RM, Creyer MN, Xu M, Jin Z, Zhou J, Yim W, Wu Z, Fajtová P, O’Donoghue AJ, Carlin AF, Jokerst JV. Protease-Responsive Peptide-Conjugated Mitochondrial-Targeting AIEgens for Selective Imaging and Inhibition of SARS-CoV-2-Infected Cells. ACS Nano 2022; 16:12305-12317. [PMID: 35878004 PMCID: PMC9344892 DOI: 10.1021/acsnano.2c03219] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/11/2022] [Indexed: 05/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious threat to human health and lacks an effective treatment. There is an urgent need for both real-time tracking and precise treatment of the SARS-CoV-2-infected cells to mitigate and ultimately prevent viral transmission. However, selective triggering and tracking of the therapeutic process in the infected cells remains challenging. Here, we report a main protease (Mpro)-responsive, mitochondrial-targeting, and modular-peptide-conjugated probe (PSGMR) for selective imaging and inhibition of SARS-CoV-2-infected cells via enzyme-instructed self-assembly and aggregation-induced emission (AIE) effect. The amphiphilic PSGMR was constructed with tunable structure and responsive efficiency and validated with recombinant proteins, cells transfected with Mpro plasmid or infected by SARS-CoV-2, and a Mpro inhibitor. By rational construction of AIE luminogen (AIEgen) with modular peptides and Mpro, we verified that the cleavage of PSGMR yielded gradual aggregation with bright fluorescence and enhanced cytotoxicity to induce mitochondrial interference of the infected cells. This strategy may have value for selective detection and treatment of SARS-CoV-2-infected cells.
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Affiliation(s)
- Yong Cheng
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alex E. Clark
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jiajing Zhou
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tengyu He
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yi Li
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Raina M. Borum
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew N. Creyer
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ming Xu
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhicheng Jin
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jingcheng Zhou
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wonjun Yim
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhuohong Wu
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Aaron F. Carlin
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jesse V. Jokerst
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Radiology, University of California, San Diego, La Jolla, CA 92093, USA
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15
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Li R, Mor M, Ma B, Clark AE, Alter J, Werbner M, Lee JC, Leibel SL, Carlin AF, Dessau M, Gal-Tanamy M, Croker BA, Xiang Y, Freund NT. Conformational flexibility in neutralization of SARS-CoV-2 by naturally elicited anti-SARS-CoV-2 antibodies. Commun Biol 2022; 5:789. [PMID: 35931732 PMCID: PMC9355996 DOI: 10.1038/s42003-022-03739-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/18/2022] [Indexed: 11/15/2022] Open
Abstract
As new variants of SARS-CoV-2 continue to emerge, it is important to assess the cross-neutralizing capabilities of antibodies naturally elicited during wild type SARS-CoV-2 infection. In the present study, we evaluate the activity of nine anti-SARS-CoV-2 monoclonal antibodies (mAbs), previously isolated from convalescent donors infected with the Wuhan-Hu-1 strain, against the SARS-CoV-2 variants of concern (VOC) Alpha, Beta, Gamma, Delta and Omicron. By testing an array of mutated spike receptor binding domain (RBD) proteins, cell-expressed spike proteins from VOCs, and neutralization of SARS-CoV-2 VOCs as pseudoviruses, or as the authentic viruses in culture, we show that mAbs directed against the ACE2 binding site (ACE2bs) are more sensitive to viral evolution compared to anti-RBD non-ACE2bs mAbs, two of which retain their potency against all VOCs tested. At the second part of our study, we reveal the neutralization mechanisms at high molecular resolution of two anti-SARS-CoV-2 neutralizing mAbs by structural characterization. We solve the structures of the Delta-neutralizing ACE2bs mAb TAU-2303 with the SARS-CoV-2 spike trimer and RBD at 4.5 Å and 2.42 Å resolutions, respectively, revealing a similar mode of binding to that between the RBD and ACE2. Furthermore, we provide five additional structures (at resolutions of 4.7 Å, 7.3 Å, 6.4 Å, 3.3 Å, and 6.1 Å) of a second antibody, TAU-2212, complexed with the SARS-CoV-2 spike trimer. TAU-2212 binds an exclusively quaternary epitope, and exhibits a unique, flexible mode of neutralization that involves transitioning between five different conformations, with both arms of the antibody recruited for cross linking intra- and inter-spike RBD subunits. Our study provides additional mechanistic understanding about how antibodies neutralize SARS-CoV-2 and its emerging variants and provides insights on the likelihood of reinfections. The neutralization of SARS-CoV-2 and variants of concern by nine monoclonal antibodies (mAb) isolated from convalescent donors infected with the Wuhan-Hu-1 strain alongside structural characterization of two of the mAbs in complex with the RBD and spike are presented.
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Affiliation(s)
- Ruofan Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Michael Mor
- Department for Microbiology and Clinical Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Bingting Ma
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Alex E Clark
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joel Alter
- The Laboratory of Structural Biology of Infectious Diseases, Azrieli Faculty of Medicine, Bar Ilan University, Tsafed, Israel
| | - Michal Werbner
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar Ilan University, Tsafed, Israel
| | - Jamie Casey Lee
- Department of Pediatrics, School of Medicine, UC San Diego, La Jolla, CA, USA
| | - Sandra L Leibel
- Department of Pediatrics, School of Medicine, UC San Diego, La Jolla, CA, USA.,Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Aaron F Carlin
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Moshe Dessau
- The Laboratory of Structural Biology of Infectious Diseases, Azrieli Faculty of Medicine, Bar Ilan University, Tsafed, Israel
| | - Meital Gal-Tanamy
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar Ilan University, Tsafed, Israel
| | - Ben A Croker
- Department of Pediatrics, School of Medicine, UC San Diego, La Jolla, CA, USA.
| | - Ye Xiang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.
| | - Natalia T Freund
- Department for Microbiology and Clinical Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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16
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Carlin AF, Clark AE, Chaillon A, Garretson AF, Bray W, Porrachia M, Santos AT, Rana TM, Smith DM. Virologic and Immunologic Characterization of Coronavirus Disease 2019 Recrudescence After Nirmatrelvir/Ritonavir Treatment. Clin Infect Dis 2022; 76:e530-e532. [PMID: 35723411 PMCID: PMC9278181 DOI: 10.1093/cid/ciac496] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/03/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
We isolated a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) BA.2 variant from a person with coronavirus disease 2019 recrudescence after nirmatrelvir/ritonavir treatment. Antiviral sensitivity and neutralizing antibody testing were performed with both parental SARS-CoV-2 and multiple variants of concern. We found that neither nirmatrelvir resistance nor absence of neutralizing immunity was a likely cause of the recrudescence.
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Affiliation(s)
- Aaron F Carlin
- Department of Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Alex E Clark
- Department of Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Antoine Chaillon
- Department of Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Aaron F Garretson
- Department of Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - William Bray
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Magali Porrachia
- Department of Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - AsherLev T Santos
- Department of Public Health, College of Education, Health and Human Services, California State University San Marcos, San Marcos, California, USA
| | - Tariq M Rana
- Division of Genetics, Department of Pediatrics, Program in Immunology, Institute for Genomic Medicine, UCSD Center for AIDS Research, University of California, San Diego, La Jolla, California, USA
| | - Davey M Smith
- Correspondence: D. M. Smith, Department of Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0676 ()
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17
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Carlin AF, Clark AE, Chaillon A, Garretson AF, Bray W, Porrachi M, Santos AT, Smith DM. Virologic and Immunologic Characterization of COVID-19 Recrudescence after Nirmatrelvir/Ritonavir Treatment. Res Sq 2022:rs.3.rs-1662783. [PMID: 35611335 PMCID: PMC9128786 DOI: 10.21203/rs.3.rs-1662783/v1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We isolated a SARS-CoV-2 BA.2 variant from a person with COVID-19 recrudescence after nirmatrelvir/ritonavir treatment. Antiviral sensitivity and neutralizing antibody testing was performed and compared with parental SARS-CoV-2 and multiple variants of concern. We found that neither NM resistance nor absence of neutralizing immunity were likely causes of the recrudescence.
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18
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Xiang JS, Mueller JR, Luo EC, Yee BA, Schafer D, Schmok JC, Tan FE, Rothamel K, McVicar RN, Kwong EM, Croker BA, Jones KL, Her HL, Chen CY, Vu AQ, Jin W, Park SS, Le P, Brannan KW, Kofman ER, Li Y, Tankka AT, Dong KD, Song Y, Clark AE, Carlin AF, Van Nostrand EL, Leibel SL, Yeo GW. Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions. Res Sq 2022:rs.3.rs-1394331. [PMID: 35313591 PMCID: PMC8936114 DOI: 10.21203/rs.3.rs-1394331/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs in authentic virus-infected cells. SARS-CoV-2 proteins, NSP8, NSP12, and nucleocapsid display distinct preferences to specific regions in the RNA viral genome, providing evidence for their shared and separate roles in replication, transcription, and viral packaging. SARS-CoV-2 proteins expressed in human lung epithelial cells bind to 4773 unique host coding RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 and ORF9c, whose RNA substrates are associated with pathways in protein N-linked glycosylation ER processing and mitochondrial processes. Furthermore, siRNA knockdown of host genes targeted by viral proteins in human lung organoid cells identify potential antiviral host targets across different SARS-CoV-2 variants. Conversely, NSP9 inhibits host gene expression by blocking mRNA export and dampens cytokine productions, including interleukin-1α/β. Our viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.
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Affiliation(s)
- Joy S. Xiang
- Institute of Molecular and Cellular Biology, A*STAR, Singapore
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jasmine R. Mueller
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - En-Ching Luo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Danielle Schafer
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jonathan C. Schmok
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Frederick E. Tan
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Katherine Rothamel
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Rachael N. McVicar
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Elizabeth M. Kwong
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Ben A. Croker
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92037, USA
| | - Krysten L. Jones
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Hsuan-Lin Her
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Chun-Yuan Chen
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Anthony Q. Vu
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Samuel S. Park
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Phuong Le
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kristopher W. Brannan
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eric R. Kofman
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Yanhua Li
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alexandra T. Tankka
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kevin D. Dong
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Yan Song
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Alex E. Clark
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Aaron F. Carlin
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eric L. Van Nostrand
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sandra L. Leibel
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92037, USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
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19
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Xiang JS, Mueller JR, Luo EC, Yee BA, Schafer D, Schmok JC, Tan FE, Rothamel K, McVicar RN, Kwong EM, Jones KL, Her HL, Chen CY, Vu AQ, Jin W, Park SS, Le P, Brannan KW, Kofman ER, Li Y, Tankka AT, Dong KD, Song Y, Carlin AF, Van Nostrand EL, Leibel SL, Yeo GW. Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions. bioRxiv 2022:2022.02.21.481223. [PMID: 35233578 PMCID: PMC8887137 DOI: 10.1101/2022.02.21.481223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs in authentic virus-infected cells. SARS-CoV-2 proteins, NSP8, NSP12, and nucleocapsid display distinct preferences to specific regions in the RNA viral genome, providing evidence for their shared and separate roles in replication, transcription, and viral packaging. SARS-CoV-2 proteins expressed in human lung epithelial cells bind to 4773 unique host coding RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 and ORF9c, whose RNA substrates are associated with pathways in protein N-linked glycosylation ER processing and mitochondrial processes. Furthermore, siRNA knockdown of host genes targeted by viral proteins in human lung organoid cells identify potential antiviral host targets across different SARS-CoV-2 variants. Conversely, NSP9 inhibits host gene expression by blocking mRNA export and dampens cytokine productions, including interleukin-1α/β. Our viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.
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Affiliation(s)
- Joy S. Xiang
- Institute of Molecular and Cellular Biology, A*STAR, Singapore
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jasmine R. Mueller
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - En-Ching Luo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Danielle Schafer
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jonathan C. Schmok
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Frederick E. Tan
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Katherine Rothamel
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Rachael N. McVicar
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Elizabeth M. Kwong
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Krysten L. Jones
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Hsuan-Lin Her
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Chun-Yuan Chen
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Anthony Q. Vu
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Samuel S. Park
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Phuong Le
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kristopher W. Brannan
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eric R. Kofman
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Yanhua Li
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alexandra T. Tankka
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kevin D. Dong
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Yan Song
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Aaron F. Carlin
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eric L. Van Nostrand
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sandra L. Leibel
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92037, USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
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20
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Duttke SH, Beyhan S, Singh R, Neal S, Viriyakosol S, Fierer J, Kirkland TN, Stajich JE, Benner C, Carlin AF. Decoding Transcription Regulatory Mechanisms Associated with Coccidioides immitis Phase Transition Using Total RNA. mSystems 2022; 7:e0140421. [PMID: 35076277 PMCID: PMC8788335 DOI: 10.1128/msystems.01404-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/04/2022] [Indexed: 01/07/2023] Open
Abstract
New or emerging infectious diseases are commonly caused by pathogens that cannot be readily manipulated or studied under common laboratory conditions. These limitations hinder standard experimental approaches and our abilities to define the fundamental molecular mechanisms underlying pathogenesis. The advance of capped small RNA sequencing (csRNA-seq) now enables genome-wide mapping of actively initiated transcripts from genes and other regulatory transcribed start regions (TSRs) such as enhancers at a precise moment from total RNA. As RNA is nonpathogenic and can be readily isolated from inactivated infectious samples, csRNA-seq can detect acute changes in gene regulation within or in response to a pathogen with remarkable sensitivity under common laboratory conditions. Studying valley fever (coccidioidomycosis), an emerging endemic fungal infection that increasingly impacts livestock, pet, and human health, we show how csRNA-seq can unravel transcriptional programs driving pathogenesis. Performing csRNA-seq on RNA isolated from different stages of the valley fever pathogen Coccidioides immitis revealed alternative promoter usage, connected cis-regulatory domains, and a WOPR family transcription factor, which are known regulators of virulence in other fungi, as being critical for pathogenic growth. We further demonstrate that a C. immitis WOPR homologue, CIMG_02671, activates transcription in a WOPR motif-dependent manner. Collectively, these findings provide novel insights into valley fever pathogenesis and provide a proof of principle for csRNA-seq as a powerful means to determine the genes, regulatory mechanisms, and transcription factors that control the pathogenesis of highly infectious agents. IMPORTANCE Infectious pathogens like airborne viruses or fungal spores are difficult to study; they require high-containment facilities, special equipment, and expertise. As such, establishing approaches such as genome editing or other means to identify the factors and mechanisms underlying caused diseases, and, thus, promising drug targets, is costly and time-intensive. These obstacles particularly hinder the analysis of new, emerging, or rare infectious diseases. We recently developed a method termed capped small RNA sequencing (csRNA-seq) that enables capturing acute changes in active gene expression from total RNA. Prior to csRNA-seq, such an analysis was possible only by using living cells or nuclei, in which pathogens are highly infectious. The process of RNA purification, however, inactivates pathogens and thus enables the analysis of gene expression during disease progression under standard laboratory conditions. As a proof of principle, here, we use csRNA-seq to unravel the gene regulatory programs and factors likely critical for the pathogenesis of valley fever, an emerging endemic fungal infection that increasingly impacts livestock, pet, and human health.
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Affiliation(s)
- Sascha H. Duttke
- Department of Medicine, Division of Endocrinology, UC San Diego School of Medicine, La Jolla, California, USA
| | - Sinem Beyhan
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
- J. Craig Venter Institute, Department of Infectious Diseases, La Jolla, California, USA
| | - Rajendra Singh
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
| | - Sonya Neal
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Suganya Viriyakosol
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
| | - Joshua Fierer
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
- Infectious Diseases Section, VA Healthcare San Diego, San Diego, California, USA
- Department of Pathology, UC San Diego School of Medicine, La Jolla, California, USA
| | - Theo N. Kirkland
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
- Department of Pathology, UC San Diego School of Medicine, La Jolla, California, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, California, USA
| | - Christopher Benner
- Department of Medicine, Division of Endocrinology, UC San Diego School of Medicine, La Jolla, California, USA
| | - Aaron F. Carlin
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
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21
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Cheng Y, Borum RM, Clark AE, Jin Z, Moore C, Fajtová P, O'Donoghue AJ, Carlin AF, Jokerst JV. A Dual-Color Fluorescent Probe Allows Simultaneous Imaging of Main and Papain-like Proteases of SARS-CoV-2-Infected Cells for Accurate Detection and Rapid Inhibitor Screening. Angew Chem Int Ed Engl 2022; 61:e202113617. [PMID: 34889013 PMCID: PMC8854376 DOI: 10.1002/anie.202113617] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 11/15/2022]
Abstract
The main protease (Mpro ) and papain-like protease (PLpro ) play critical roles in SARS-CoV-2 replication and are promising targets for antiviral inhibitors. The simultaneous visualization of Mpro and PLpro is extremely valuable for SARS-CoV-2 detection and rapid inhibitor screening. However, such a crucial investigation has remained challenging because of the lack of suitable probes. We have now developed a dual-color probe (3MBP5) for the simultaneous detection of Mpro and PLpro by fluorescence (or Förster) resonance energy transfer (FRET). This probe produces fluorescence from both the Cy3 and Cy5 fluorophores that are cleaved by Mpro and PLpro . 3MBP5-activatable specificity was demonstrated with recombinant proteins, inhibitors, plasmid-transfected HEK 293T cells, and SARS-CoV-2-infected TMPRSS2-Vero cells. Results from the dual-color probe first verified the simultaneous detection and intracellular distribution of SARS-CoV-2 Mpro and PLpro . This is a powerful tool for the simultaneous detection of different proteases with value for the rapid screening of inhibitors.
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Affiliation(s)
- Yong Cheng
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Raina M. Borum
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Alex E. Clark
- Department of MedicineUniversity of California, San DiegoLa JollaCA 92093USA
| | - Zhicheng Jin
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Colman Moore
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCA 92093USA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCA 92093USA
| | - Aaron F. Carlin
- Department of MedicineUniversity of California, San DiegoLa JollaCA 92093USA
| | - Jesse V. Jokerst
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
- Materials Science and Engineering ProgramUniversity of California, San DiegoLa JollaCA 92093USA
- Department of RadiologyUniversity of California, San DiegoLa JollaCA 92093USA
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22
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Cheng Y, Borum RM, Clark AE, Jin Z, Moore C, Fajtová P, O'Donoghue AJ, Carlin AF, Jokerst JV. A Dual‐Color Fluorescent Probe Allows Simultaneous Imaging of Main and Papain‐like Proteases of SARS‐CoV‐2‐Infected Cells for Accurate Detection and Rapid Inhibitor Screening. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yong Cheng
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Raina M. Borum
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Alex E. Clark
- Department of Medicine University of California, San Diego La Jolla CA 92093 USA
| | - Zhicheng Jin
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Colman Moore
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Aaron F. Carlin
- Department of Medicine University of California, San Diego La Jolla CA 92093 USA
| | - Jesse V. Jokerst
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
- Materials Science and Engineering Program University of California, San Diego La Jolla CA 92093 USA
- Department of Radiology University of California, San Diego La Jolla CA 92093 USA
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23
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Ortega-Rivera OA, Shukla S, Shin MD, Chen A, Beiss V, Moreno-Gonzalez MA, Zheng Y, Clark AE, Carlin AF, Pokorski JK, Steinmetz NF. Cowpea Mosaic Virus Nanoparticle Vaccine Candidates Displaying Peptide Epitopes Can Neutralize the Severe Acute Respiratory Syndrome Coronavirus. ACS Infect Dis 2021; 7:3096-3110. [PMID: 34672530 PMCID: PMC8547496 DOI: 10.1021/acsinfecdis.1c00410] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Indexed: 12/28/2022]
Abstract
The development of vaccines against coronaviruses has focused on the spike (S) protein, which is required for the recognition of host-cell receptors and thus elicits neutralizing antibodies. Targeting conserved epitopes on the S protein offers the potential for pan-beta-coronavirus vaccines that could prevent future pandemics. We displayed five B-cell epitopes, originally identified in the convalescent sera from recovered severe acute respiratory syndrome (SARS) patients, on the surface of the cowpea mosaic virus (CPMV) and evaluated these formulations as vaccines. Prime-boost immunization of mice with three of these candidate vaccines, CPMV-988, CPMV-1173, and CPMV-1209, elicited high antibody titers that neutralized the severe acute respiratory syndrome coronavirus (SARS-CoV) in vitro and showed an early Th1-biased profile (2-4 weeks) transitioning to a slightly Th2-biased profile just after the second boost (6 weeks). A pentavalent slow-release implant comprising all five peptides displayed on the CPMV elicited anti-S protein and epitope-specific antibody titers, albeit at a lower magnitude compared to the soluble formulations. While the CPMV remained intact when released from the PLGA implants, processing results in loss of RNA, which acts as an adjuvant. Loss of RNA may be a reason for the lower efficacy of the implants. Finally, although the three epitopes (988, 1173, and 1209) that were found to be neutralizing the SARS-CoV were 100% identical to the SARS-CoV-2, none of the vaccine candidates neutralized the SARS-CoV-2 in vitro suggesting differences in the natural epitope perhaps caused by conformational changes or the presence of N-linked glycans. While a cross-protective vaccine candidate was not developed, a multivalent SARS vaccine was developed. The technology discussed here is a versatile vaccination platform that can be pivoted toward other diseases and applications that are not limited to infectious diseases.
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Affiliation(s)
- Oscar A. Ortega-Rivera
- Department of NanoEngineering, University
of California-San Diego, La Jolla, California 92039, United
States
- Center for Nano-ImmunoEngineering,
University of California-San Diego, La Jolla, California
92039, United States
| | - Sourabh Shukla
- Department of NanoEngineering, University
of California-San Diego, La Jolla, California 92039, United
States
- Center for Nano-ImmunoEngineering,
University of California-San Diego, La Jolla, California
92039, United States
| | - Matthew D. Shin
- Department of NanoEngineering, University
of California-San Diego, La Jolla, California 92039, United
States
- Center for Nano-ImmunoEngineering,
University of California-San Diego, La Jolla, California
92039, United States
| | - Angela Chen
- Department of NanoEngineering, University
of California-San Diego, La Jolla, California 92039, United
States
- Center for Nano-ImmunoEngineering,
University of California-San Diego, La Jolla, California
92039, United States
| | - Veronique Beiss
- Department of NanoEngineering, University
of California-San Diego, La Jolla, California 92039, United
States
- Center for Nano-ImmunoEngineering,
University of California-San Diego, La Jolla, California
92039, United States
| | - Miguel A. Moreno-Gonzalez
- Department of NanoEngineering, University
of California-San Diego, La Jolla, California 92039, United
States
- Center for Nano-ImmunoEngineering,
University of California-San Diego, La Jolla, California
92039, United States
| | - Yi Zheng
- Department of NanoEngineering, University
of California-San Diego, La Jolla, California 92039, United
States
- Center for Nano-ImmunoEngineering,
University of California-San Diego, La Jolla, California
92039, United States
| | - Alex E. Clark
- Department of Medicine, University of
California-San Diego, La Jolla, California 92039, United
States
| | - Aaron F. Carlin
- Department of Medicine, University of
California-San Diego, La Jolla, California 92039, United
States
| | - Jonathan K. Pokorski
- Department of NanoEngineering, University
of California-San Diego, La Jolla, California 92039, United
States
- Center for Nano-ImmunoEngineering,
University of California-San Diego, La Jolla, California
92039, United States
- Institute for Materials Discovery and Design,
University of California-San Diego, La Jolla, California
92039, United States
| | - Nicole F. Steinmetz
- Department of NanoEngineering, University
of California-San Diego, La Jolla, California 92039, United
States
- Center for Nano-ImmunoEngineering,
University of California-San Diego, La Jolla, California
92039, United States
- Institute for Materials Discovery and Design,
University of California-San Diego, La Jolla, California
92039, United States
- Department of Bioengineering, University
of California-San Diego, La Jolla, California 92039, United
States
- Department of Radiology, University of
California-San Diego, La Jolla, California 92039, United
States
- Moores Cancer Center, University of
California-San Diego, La Jolla, California 92039, United
States
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24
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Huff S, Kummetha IR, Tiwari SK, Huante MB, Clark AE, Wang S, Bray W, Smith D, Carlin AF, Endsley M, Rana TM. Discovery and Mechanism of SARS-CoV-2 Main Protease Inhibitors. J Med Chem 2021; 65:2866-2879. [PMID: 34570513 PMCID: PMC8491550 DOI: 10.1021/acs.jmedchem.1c00566] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The emergence of a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents an urgent public health crisis. Without available targeted therapies, treatment options remain limited for COVID-19 patients. Using medicinal chemistry and rational drug design strategies, we identify a 2-phenyl-1,2-benzoselenazol-3-one class of compounds targeting the SARS-CoV-2 main protease (Mpro). FRET-based screening against recombinant SARS-CoV-2 Mpro identified six compounds that inhibit proteolysis with nanomolar IC50 values. Preincubation dilution experiments and molecular docking determined that the inhibition of SARS-CoV-2 Mpro can occur by either covalent or noncovalent mechanisms, and lead E04 was determined to inhibit Mpro competitively. Lead E24 inhibited viral replication with a nanomolar EC50 value (844 nM) in SARS-CoV-2-infected Vero E6 cells and was further confirmed to impair SARS-CoV-2 replication in human lung epithelial cells and human-induced pluripotent stem cell-derived 3D lung organoids. Altogether, these studies provide a structural framework and mechanism of Mpro inhibition that should facilitate the design of future COVID-19 treatments.
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Affiliation(s)
- Sarah Huff
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Indrasena Reddy Kummetha
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Shashi Kant Tiwari
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Matthew B Huante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Alex E Clark
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Shaobo Wang
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - William Bray
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Davey Smith
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Aaron F Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Mark Endsley
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Tariq M Rana
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States.,Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
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25
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Schooley RT, Carlin AF, Beadle JR, Valiaeva N, Zhang XQ, Clark AE, McMillan RE, Leibel SL, McVicar RN, Xie J, Garretson AF, Smith VI, Murphy J, Hostetler KY. Rethinking Remdesivir: Synthesis, Antiviral Activity, and Pharmacokinetics of Oral Lipid Prodrugs. Antimicrob Agents Chemother 2021; 65:e0115521. [PMID: 34310217 PMCID: PMC8448143 DOI: 10.1128/aac.01155-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/20/2021] [Indexed: 12/19/2022] Open
Abstract
Remdesivir (RDV; GS-5734) is currently the only FDA-approved antiviral drug for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The drug is approved for use in adults or children 12 years or older who are hospitalized for the treatment of COVID-19 on the basis of an acceleration of clinical recovery for inpatients with this disease. Unfortunately, the drug must be administered intravenously, restricting its use to those requiring hospitalization for relatively advanced disease. RDV is also unstable in plasma and has a complex activation pathway which may contribute to its highly variable antiviral efficacy in SARS-CoV-2-infected cells. Potent orally bioavailable antiviral drugs for early treatment of SARS-CoV-2 infection are urgently needed, and several, including molnupiravir and PF-07321332, are currently in clinical development. We focused on making simple, orally bioavailable lipid analogs of remdesivir nucleoside (RVn; GS-441524) that are processed to RVn monophosphate, the precursor of the active RVn triphosphate, by a single-step intracellular cleavage. In addition to high oral bioavailability, stability in plasma, and simpler metabolic activation, new oral lipid prodrugs of RVn had submicromolar anti-SARS-CoV-2 activity in a variety of cell types, including Vero E6, Calu-3, Caco-2, human pluripotent stem cell (PSC)-derived lung cells, and Huh7.5 cells. In Syrian hamsters, oral treatment with 1-O-octadecyl-2-O-benzyl-glycero-3-phosphate RVn (ODBG-P-RVn) was well tolerated and achieved therapeutic levels in plasma above the 90% effective concentration (EC90) for SARS-CoV-2. The results suggest further evaluation as an early oral treatment for SARS-CoV-2 infection to minimize severe disease and reduce hospitalizations.
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Affiliation(s)
- Robert T. Schooley
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, California, USA
| | - Aaron F. Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, California, USA
| | - James R. Beadle
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, California, USA
| | - Nadejda Valiaeva
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, California, USA
| | - Xing-Quan Zhang
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, California, USA
| | - Alex E. Clark
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, California, USA
| | - Rachel E. McMillan
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, California, USA
| | - Sandra L. Leibel
- Department of Pediatrics, University of California San Diego, School of Medicine, La Jolla, California, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, California, USA
| | - Rachael N. McVicar
- Sanford Consortium for Regenerative Medicine, La Jolla, California, USA
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Jialei Xie
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, California, USA
| | - Aaron F. Garretson
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, California, USA
| | - Victoria I. Smith
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, California, USA
| | - Joyce Murphy
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, California, USA
| | - Karl Y. Hostetler
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, School of Medicine, La Jolla, California, USA
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26
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Wang L, Sievert D, Clark AE, Lee S, Federman H, Gastfriend BD, Shusta EV, Palecek SP, Carlin AF, Gleeson JG. A human three-dimensional neural-perivascular 'assembloid' promotes astrocytic development and enables modeling of SARS-CoV-2 neuropathology. Nat Med 2021; 27:1600-1606. [PMID: 34244682 PMCID: PMC8601037 DOI: 10.1038/s41591-021-01443-1] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 06/15/2021] [Indexed: 11/09/2022]
Abstract
Clinical evidence suggests the central nervous system is frequently impacted by SARS-CoV-2 infection, either directly or indirectly, although the mechanisms are unclear. Pericytes are perivascular cells within the brain that are proposed as SARS-CoV-2 infection points. Here we show that pericyte-like cells (PLCs), when integrated into a cortical organoid, are capable of infection with authentic SARS-CoV-2. Before 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 that supports astrocytic maturation as well as SARS-CoV-2 entry and replication in neural tissue; thus, 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, USA.,Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - David Sievert
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.,Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Alex E Clark
- Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Sangmoon Lee
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.,Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Hannah Federman
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.,Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.,Center for Immunity and Inflammation, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Benjamin D Gastfriend
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Eric V Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.,Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Aaron F Carlin
- Department of Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA.
| | - Joseph G Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA. .,Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA. .,Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
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27
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Singh NK, Ray P, Carlin AF, Morgan SC, Magallanes C, Laurent LC, Aronoff-Spencer ES, Hall DA. Dataset on optimization and development of a point-of-care glucometer-based SARS-CoV-2 detection assay using aptamers. Data Brief 2021; 38:107278. [PMID: 34401413 PMCID: PMC8359508 DOI: 10.1016/j.dib.2021.107278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/25/2021] [Accepted: 08/09/2021] [Indexed: 11/17/2022] Open
Abstract
We present supplementary data for the published article, “Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer” [1]. The assay described is designed to be performed at home or in a clinic without expensive instrumentation or professional training. SARS-CoV-2 is detected by an aptamer-based assay that targets the Nucleocapsid (N) or Spike (S) antigens. Binding of the N or S protein to their respective aptamer results in the competitive release of a complementary antisense-invertase enzyme complex. The released enzyme then catalyzes the conversion of sucrose to glucose that is measured by an off-the-shelf glucometer. The data presented here describe the optimization of the assay parameters and their contribution to developing this aptamer-based assay to detect SARS-CoV-2. The assay performance was checked in a standard buffer, contrived samples, and patient samples validated with well-established scientific methods. The resulting dataset can be used to further develop glucometer-based assays for diagnosing other communicable and non-communicable diseases.
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Affiliation(s)
- Naveen K Singh
- Department of Electrical and Computer Engineering, University of California - San Diego, La Jolla, CA 92093, USA
| | - Partha Ray
- Division of Surgical Oncology, Department of Surgery, Moores Cancer Center, University of California - San Diego Health, La Jolla, CA 92093, USA
| | - Aaron F Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California - San Diego, La Jolla, CA 92093, USA
| | - Sydney C Morgan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California - San Diego, La Jolla, CA 92093, USA
| | - Celestine Magallanes
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California - San Diego, La Jolla, CA 92093, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California - San Diego, La Jolla, CA 92093, USA
| | - Eliah S Aronoff-Spencer
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California - San Diego, La Jolla, CA 92093, USA
| | - Drew A Hall
- Department of Electrical and Computer Engineering, University of California - San Diego, La Jolla, CA 92093, USA.,Department of Bioengineering, University of California - San Diego, La Jolla, CA 92093, USA
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28
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Inde Z, Croker BA, Yapp C, Joshi GN, Spetz J, Fraser C, Qin X, Xu L, Deskin B, Ghelfi E, Webb G, Carlin AF, Zhu YP, Leibel SL, Garretson AF, Clark AE, Duran JM, Pretorius V, Crotty-Alexander LE, Li C, Lee JC, Sodhi C, Hackam DJ, Sun X, Hata AN, Kobzik L, Miller J, Park JA, Brownfield D, Jia H, Sarosiek KA. Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 severity. Sci Adv 2021; 7:eabf8609. [PMID: 34407940 PMCID: PMC8373124 DOI: 10.1126/sciadv.abf8609] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/25/2021] [Indexed: 05/02/2023]
Abstract
Novel coronavirus disease 2019 (COVID-19) severity is highly variable, with pediatric patients typically experiencing less severe infection than adults and especially the elderly. The basis for this difference is unclear. We find that mRNA and protein expression of angiotensin-converting enzyme 2 (ACE2), the cell entry receptor for the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19, increases with advancing age in distal lung epithelial cells. However, in humans, ACE2 expression exhibits high levels of intra- and interindividual heterogeneity. Further, cells infected with SARS-CoV-2 experience endoplasmic reticulum stress, triggering an unfolded protein response and caspase-mediated apoptosis, a natural host defense system that halts virion production. Apoptosis of infected cells can be selectively induced by treatment with apoptosis-modulating BH3 mimetic drugs. Notably, epithelial cells within young lungs and airways are more primed to undergo apoptosis than those in adults, which may naturally hinder virion production and support milder COVID-19 severity.
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Affiliation(s)
- Zintis Inde
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Ben A Croker
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarence Yapp
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
- Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA
| | - Gaurav N Joshi
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
- Integrated Cellular Imaging Core, Emory University, Atlanta, GA, USA
| | - Johan Spetz
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Cameron Fraser
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Xingping Qin
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Le Xu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brian Deskin
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Elisa Ghelfi
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Gabrielle Webb
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Aaron F Carlin
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yanfang Peipei Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Sandra L Leibel
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Aaron F Garretson
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Alex E Clark
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jason M Duran
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Victor Pretorius
- Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | | | - Chendi Li
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jamie Casey Lee
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Chhinder Sodhi
- Department of Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - David J Hackam
- Department of Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - Xin Sun
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Aaron N Hata
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Lester Kobzik
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jeffrey Miller
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jin-Ah Park
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Douglas Brownfield
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hongpeng Jia
- Department of Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - Kristopher A Sarosiek
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
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29
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Salido RA, Cantú VJ, Clark AE, Leibel SL, Foroughishafiei A, Saha A, Hakim A, Nouri A, Lastrella AL, Castro-Martínez A, Plascencia A, Kapadia B, Xia B, Ruiz C, Marotz CA, Maunder D, Lawrence ES, Smoot EW, Eisner E, Crescini ES, Kohn L, Vargas LF, Chacón M, Betty M, Machnicki M, Wu MY, Baer NA, Belda-Ferre P, Hoff PD, Seaver P, Ostrander RT, Tsai R, Sathe S, Aigner S, Morgan SC, Ngo TT, Barber T, Cheung W, Carlin AF, Yeo GW, Laurent LC, Fielding-Miller R, Knight R. Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence. bioRxiv 2021:2021.07.16.452756. [PMID: 34312621 PMCID: PMC8312891 DOI: 10.1101/2021.07.16.452756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with COVID-19 and inform appropriate infection mitigation responses. Research groups have reported detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on surfaces days or weeks after the virus has been deposited, making it difficult to estimate when an infected individual may have shed virus onto a SARS-CoV-2 positive surface, which in turn complicates the process of establishing effective quarantine measures. In this study, we determined that reverse transcription-quantitative polymerase chain reaction (RT-qPCR) detection of viral RNA from heat-inactivated particles experiences minimal decay over seven days of monitoring on eight out of nine surfaces tested. The properties of the studied surfaces result in RT-qPCR signatures that can be segregated into two material categories, rough and smooth, where smooth surfaces have a lower limit of detection. RT-qPCR signal intensity (average quantification cycle (Cq)) can be correlated to surface viral load using only one linear regression model per material category. The same experiment was performed with infectious viral particles on one surface from each category, with essentially identical results. The stability of RT-qPCR viral signal demonstrates the need to clean monitored surfaces after sampling to establish temporal resolution. Additionally, these findings can be used to minimize the number of materials and time points tested and allow for the use of heat-inactivated viral particles when optimizing environmental monitoring methods.
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Affiliation(s)
- Rodolfo A Salido
- These authors contributed equally
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Victor J Cantú
- These authors contributed equally
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alex E Clark
- Division of Infectious Diseases and Global Public Health, Department of Medicine; University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Sandra L Leibel
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Anahid Foroughishafiei
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anushka Saha
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Alhakam Nouri
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Anelizze Castro-Martínez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Bhavika Kapadia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Bing Xia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Christopher Ruiz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Clarisse A Marotz
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Daniel Maunder
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Emily Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Evelyn S Crescini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Laura Kohn
- Herbert Wertheim School of Public Health, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093
| | - Lizbeth Franco Vargas
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Maryann Betty
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Rady Children's Hospital, San Diego, CA
| | - Michal Machnicki
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Min Yi Wu
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Peter De Hoff
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - R Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Shashank Sathe
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Stefan Aigner
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Sydney C Morgan
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Willi Cheung
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- San Diego State University, San Diego, CA
| | - Aaron F Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine; University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Gene W Yeo
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Louise C Laurent
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093
- Co-corresponding authors
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Co-corresponding authors
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30
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Schooley RT, Carlin AF, Beadle JR, Valiaeva N, Zhang XQ, Clark AE, McMillan RE, Leibel SL, McVicar RN, Xie J, Garretson AF, Smith VI, Murphy J, Hostetler KY. Rethinking Remdesivir: Synthesis, Antiviral Activity and Pharmacokinetics of Oral Lipid Prodrugs. bioRxiv 2021. [PMID: 32869033 PMCID: PMC7457622 DOI: 10.1101/2020.08.26.269159] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Remdesivir (RDV, GS-5734) is currently the only FDA-approved antiviral drug for the treatment of SARS CoV-2 infection. The drug is approved for use in adults or children 12-years or older who are hospitalized for the treatment of COVID-19 on the basis of an acceleration of clinical recovery for inpatients with this disease. Unfortunately, the drug must be administered intravenously, restricting its use to those requiring hospitalization for relatively advanced disease. RDV is also unstable in plasma and has a complex activation pathway which may contribute to its highly variable antiviral efficacy in SARS-CoV-2 infected cells. Potent orally bioavailable antiviral drugs for early treatment of SARS-CoV-2 infection are urgently needed and several including molnupiravir and PF-07321332 are currently in clinical development. We focused on making simple, orally bioavailable lipid analogs of Remdesivir nucleoside (RVn, GS-441524) that are processed to RVn-monophosphate, the precursor of the active RVn-triphosphate, by a single-step intracellular cleavage. In addition to high oral bioavailability, stability in plasma and simpler metabolic activation, new oral lipid prodrugs of RVn had submicromolar anti-SARS-CoV-2 activity in a variety of cell types including Vero E6, Calu-3, Caco-2, human pluripotent stem cell (PSC)-derived lung cells and Huh7.5 cells. In Syrian hamsters oral treatment with ODBG-P-RVn was well tolerated and achieved therapeutic levels in plasma above the EC90 for SARS-CoV-2. The results suggest further evaluation as an early oral treatment for SARS-CoV-2 infection to minimize severe disease and reduce hospitalizations.
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Affiliation(s)
- Robert T Schooley
- Division of Infectious Diseases and Global Public Health, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0676, USA
| | - Aaron F Carlin
- Division of Infectious Diseases and Global Public Health, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0676, USA
| | - James R Beadle
- Division of Infectious Diseases and Global Public Health, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0676, USA
| | - Nadejda Valiaeva
- Division of Infectious Diseases and Global Public Health, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0676, USA
| | - Xing-Quan Zhang
- Division of Infectious Diseases and Global Public Health, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0676, USA
| | - Alex E Clark
- Division of Infectious Diseases and Global Public Health, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0676, USA
| | - Rachel E McMillan
- Division of Infectious Diseases and Global Public Health, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0676, USA
| | - Sandra L Leibel
- Department of Pediatrics, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0676, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Rachael N McVicar
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA.,Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jialei Xie
- Division of Infectious Diseases and Global Public Health, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0676, USA
| | - Aaron F Garretson
- Division of Infectious Diseases and Global Public Health, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0676, USA
| | - Victoria I Smith
- Division of Infectious Diseases and Global Public Health, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0676, USA
| | - Joyce Murphy
- Division of Infectious Diseases and Global Public Health, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0676, USA
| | - Karl Y Hostetler
- Division of Infectious Diseases and Global Public Health, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0676, USA
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31
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Park SH, Siddiqi H, Castro DV, De Angelis AA, Oom AL, Stoneham CA, Lewinski MK, Clark AE, Croker BA, Carlin AF, Guatelli J, Opella SJ. Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. PLoS Pathog 2021; 17:e1009519. [PMID: 34003853 PMCID: PMC8184013 DOI: 10.1371/journal.ppat.1009519] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/07/2021] [Accepted: 04/29/2021] [Indexed: 11/24/2022] Open
Abstract
SARS-CoV-2 is the novel coronavirus that is the causative agent of COVID-19, a sometimes-lethal respiratory infection responsible for a world-wide pandemic. The envelope (E) protein, one of four structural proteins encoded in the viral genome, is a 75-residue integral membrane protein whose transmembrane domain exhibits ion channel activity and whose cytoplasmic domain participates in protein-protein interactions. These activities contribute to several aspects of the viral replication-cycle, including virion assembly, budding, release, and pathogenesis. Here, we describe the structure and dynamics of full-length SARS-CoV-2 E protein in hexadecylphosphocholine micelles by NMR spectroscopy. We also characterized its interactions with four putative ion channel inhibitors. The chemical shift index and dipolar wave plots establish that E protein consists of a long transmembrane helix (residues 8–43) and a short cytoplasmic helix (residues 53–60) connected by a complex linker that exhibits some internal mobility. The conformations of the N-terminal transmembrane domain and the C-terminal cytoplasmic domain are unaffected by truncation from the intact protein. The chemical shift perturbations of E protein spectra induced by the addition of the inhibitors demonstrate that the N-terminal region (residues 6–18) is the principal binding site. The binding affinity of the inhibitors to E protein in micelles correlates with their antiviral potency in Vero E6 cells: HMA ≈ EIPA > DMA >> Amiloride, suggesting that bulky hydrophobic groups in the 5’ position of the amiloride pyrazine ring play essential roles in binding to E protein and in antiviral activity. An N15A mutation increased the production of virus-like particles, induced significant chemical shift changes from residues in the inhibitor binding site, and abolished HMA binding, suggesting that Asn15 plays a key role in maintaining the protein conformation near the binding site. These studies provide the foundation for complete structure determination of E protein and for structure-based drug discovery targeting this protein. The novel coronavirus SARS-CoV-2, the causative agent of the world-wide pandemic of COVID-19, has become one of the greatest threats to human health. While rapid progress has been made in the development of vaccines, drug discovery has lagged, partly due to the lack of atomic-resolution structures of the free and drug-bound forms of the viral proteins. The SARS-CoV-2 envelope (E) protein, with its multiple activities that contribute to viral replication, is widely regarded as a potential target for COVID-19 treatment. As structural information is essential for drug discovery, we established an efficient sample preparation system for biochemical and structural studies of intact full-length SARS-CoV-2 E protein and characterized its structure and dynamics. We also characterized the interactions of amilorides with specific E protein residues and correlated this with their antiviral activity during viral replication. The binding affinity of the amilorides to E protein correlated with their antiviral potency, suggesting that E protein is indeed the likely target of their antiviral activity. We found that residue asparagine15 plays an important role in maintaining the conformation of the amiloride binding site, providing molecular guidance for the design of inhibitors targeting E protein.
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Affiliation(s)
- Sang Ho Park
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Haley Siddiqi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Daniela V. Castro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Anna A. De Angelis
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Aaron L. Oom
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Charlotte A. Stoneham
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Mary K. Lewinski
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Alex E. Clark
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Ben A. Croker
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Aaron F. Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - John Guatelli
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Stanley J. Opella
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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32
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Singh NK, Ray P, Carlin AF, Magallanes C, Morgan SC, Laurent LC, Aronoff-Spencer ES, Hall DA. Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer. Biosens Bioelectron 2021; 180:113111. [PMID: 33743492 PMCID: PMC7908832 DOI: 10.1016/j.bios.2021.113111] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/15/2021] [Accepted: 02/22/2021] [Indexed: 12/19/2022]
Abstract
Significant barriers to the diagnosis of latent and acute SARS-CoV-2 infection continue to hamper population-based screening efforts required to contain the COVID-19 pandemic in the absence of widely available antiviral therapeutics or vaccines. We report an aptamer-based SARS-CoV-2 salivary antigen assay employing only low-cost reagents ($3.20/test) and an off-the-shelf glucometer. The test was engineered around a glucometer as it is quantitative, easy to use, and the most prevalent piece of diagnostic equipment globally, making the test highly scalable with an infrastructure that is already in place. Furthermore, many glucometers connect to smartphones, providing an opportunity to integrate with contact tracing apps, medical providers, and electronic health records. In clinical testing, the developed assay detected SARS-CoV-2 infection in patient saliva across a range of viral loads - as benchmarked by RT-qPCR - within 1 h, with 100% sensitivity (positive percent agreement) and distinguished infected specimens from off-target antigens in uninfected controls with 100% specificity (negative percent agreement). We propose that this approach provides an inexpensive, rapid, and accurate diagnostic for distributed screening of SARS-CoV-2 infection at scale.
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Affiliation(s)
- Naveen K. Singh
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Partha Ray
- Division of Surgical Oncology, Department of Surgery, Moores Cancer Center, University of California San Diego Health, La Jolla, CA, 92093, USA
| | - Aaron F. Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Celestine Magallanes
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sydney C. Morgan
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Louise C. Laurent
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Eliah S. Aronoff-Spencer
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA,Corresponding author
| | - Drew A. Hall
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, 92093, USA,Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA,Corresponding author
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33
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Li N, Hui H, Bray B, Gonzalez GM, Zeller M, Anderson KG, Knight R, Smith D, Wang Y, Carlin AF, Rana TM. METTL3 regulates viral m6A RNA modification and host cell innate immune responses during SARS-CoV-2 infection. Cell Rep 2021; 35:109091. [PMID: 33961823 PMCID: PMC8090989 DOI: 10.1016/j.celrep.2021.109091] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 02/18/2021] [Accepted: 04/16/2021] [Indexed: 01/05/2023] Open
Abstract
It is urgent and important to understand the relationship of the widespread severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) with host immune response and study the underlining molecular mechanism. N6-methylation of adenosine (m6A) in RNA regulates many physiological and disease processes. Here, we investigate m6A modification of the SARS-CoV-2 gene in regulating the host cell innate immune response. Our data show that the SARS-CoV-2 virus has m6A modifications that are enriched in the 3' end of the viral genome. We find that depletion of the host cell m6A methyltransferase METTL3 decreases m6A levels in SARS-CoV-2 and host genes, and m6A reduction in viral RNA increases RIG-I binding and subsequently enhances the downstream innate immune signaling pathway and inflammatory gene expression. METTL3 expression is reduced and inflammatory genes are induced in patients with severe coronavirus disease 2019 (COVID-19). These findings will aid in the understanding of COVID-19 pathogenesis and the design of future studies regulating innate immunity for COVID-19 treatment.
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Affiliation(s)
- Na Li
- Division of Genetics, Program in Immunology, Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Hui Hui
- Division of Genetics, Program in Immunology, Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Bill Bray
- Division of Genetics, Program in Immunology, Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Gwendolyn Michelle Gonzalez
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kristian G Anderson
- Department of Immunology and Microbiology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovations, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Davey Smith
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Aaron F Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Tariq M Rana
- Division of Genetics, Program in Immunology, Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA.
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Carlin AF, Beyhan S, Peña JF, Stajich JE, Viriyakosol S, Fierer J, Kirkland TN. Transcriptional Analysis of Coccidioides immitis Mycelia and Spherules by RNA Sequencing. J Fungi (Basel) 2021; 7:jof7050366. [PMID: 34067070 PMCID: PMC8150946 DOI: 10.3390/jof7050366] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/13/2021] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
Coccidioides immitis and C. posadasii are dimorphic fungi that transform from mycelia with internal arthroconidia in the soil to a tissue form known as a spherule in mammals. This process can be recapitulated in vitro by increasing the temperature, CO2 and changing other culture conditions. In this study, we have analyzed changes in gene expression in mycelia and young and mature spherules. Genes that were highly upregulated in young spherules include a spherule surface protein and iron and copper membrane transporters. Genes that are unique to Coccidioides spp. are also overrepresented in this group, suggesting that they may be important for spherule differentiation. Enriched GO terms in young spherule upregulated genes include oxidation-reduction, response to stress and membrane proteins. Downregulated genes are enriched for transcription factors, especially helix–loop–helix and C2H2 type zinc finger domain-containing proteins, which is consistent with the dramatic change in transcriptional profile. Almost all genes that are upregulated in young spherules remain upregulated in mature spherules, but a small number of genes are differentially expressed in those two stages of spherule development. Mature spherules express more Hsp31 and amylase and less tyrosinase than young spherules. Some expression of transposons was detected and most of the differentially expressed transposons were upregulated in spherules.
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Affiliation(s)
- Aaron F. Carlin
- Department of Medicine, Division of Infectious Disease, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA; (A.F.C.); (S.V.); (J.F.)
| | - Sinem Beyhan
- J. Craig Venter Institute, La Jolla, CA 92037, USA;
| | - Jesús F. Peña
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, USA; (J.F.P.); (J.E.S.)
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, USA; (J.F.P.); (J.E.S.)
| | - Suganya Viriyakosol
- Department of Medicine, Division of Infectious Disease, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA; (A.F.C.); (S.V.); (J.F.)
| | - Joshua Fierer
- Department of Medicine, Division of Infectious Disease, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA; (A.F.C.); (S.V.); (J.F.)
- Infectious Diseases Section, VA Healthcare San Diego, San Diego, CA 92161, USA
- Department of Pathology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Theo N. Kirkland
- Department of Medicine, Division of Infectious Disease, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA; (A.F.C.); (S.V.); (J.F.)
- Department of Pathology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA
- Correspondence:
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35
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Mellott DM, Tseng CT, Drelich A, Fajtová P, Chenna BC, Kostomiris DH, Hsu J, Zhu J, Taylor ZW, Kocurek KI, Tat V, Katzfuss A, Li L, Giardini MA, Skinner D, Hirata K, Yoon MC, Beck S, Carlin AF, Clark AE, Beretta L, Maneval D, Hook V, Frueh F, Hurst BL, Wang H, Raushel FM, O’Donoghue AJ, de Siqueira-Neto JL, Meek TD, McKerrow JH. A Clinical-Stage Cysteine Protease Inhibitor blocks SARS-CoV-2 Infection of Human and Monkey Cells. ACS Chem Biol 2021; 16:642-650. [PMID: 33787221 PMCID: PMC8029441 DOI: 10.1021/acschembio.0c00875] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/18/2021] [Indexed: 12/11/2022]
Abstract
Host-cell cysteine proteases play an essential role in the processing of the viral spike protein of SARS coronaviruses. K777, an irreversible, covalent inactivator of cysteine proteases that has recently completed phase 1 clinical trials, reduced SARS-CoV-2 viral infectivity in several host cells: Vero E6 (EC50< 74 nM), HeLa/ACE2 (4 nM), Caco-2 (EC90 = 4.3 μM), and A549/ACE2 (<80 nM). Infectivity of Calu-3 cells depended on the cell line assayed. If Calu-3/2B4 was used, EC50 was 7 nM, but in the ATCC Calu-3 cell line without ACE2 enrichment, EC50 was >10 μM. There was no toxicity to any of the host cell lines at 10-100 μM K777 concentration. Kinetic analysis confirmed that K777 was a potent inhibitor of human cathepsin L, whereas no inhibition of the SARS-CoV-2 cysteine proteases (papain-like and 3CL-like protease) was observed. Treatment of Vero E6 cells with a propargyl derivative of K777 as an activity-based probe identified human cathepsin B and cathepsin L as the intracellular targets of this molecule in both infected and uninfected Vero E6 cells. However, cleavage of the SARS-CoV-2 spike protein was only carried out by cathepsin L. This cleavage was blocked by K777 and occurred in the S1 domain of the SARS-CoV-2 spike protein, a different site from that previously observed for the SARS-CoV-1 spike protein. These data support the hypothesis that the antiviral activity of K777 is mediated through inhibition of the activity of host cathepsin L and subsequent loss of cathepsin L-mediated viral spike protein processing.
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Affiliation(s)
- Drake M. Mellott
- Department of Biochemistry and Biophysics and
Department of Chemistry, Texas A&M
University, 301 Old Main Drive, College Station, Texas 77843,
United States
| | - Chien-Te Tseng
- Department of Microbiology and Immunology,
University of Texas, Medical Branch, 3000 University
Boulevard, Galveston, Texas 77755-1001, United States
| | - Aleksandra Drelich
- Department of Microbiology and Immunology,
University of Texas, Medical Branch, 3000 University
Boulevard, Galveston, Texas 77755-1001, United States
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
- Institute of Organic Chemistry and Biochemistry,
Academy of Sciences of the Czech Republic, 16610 Prague,
Czech Republic
| | - Bala C. Chenna
- Department of Biochemistry and Biophysics and
Department of Chemistry, Texas A&M
University, 301 Old Main Drive, College Station, Texas 77843,
United States
| | - Demetrios H. Kostomiris
- Department of Biochemistry and Biophysics and
Department of Chemistry, Texas A&M
University, 301 Old Main Drive, College Station, Texas 77843,
United States
| | - Jason Hsu
- Department of Microbiology and Immunology,
University of Texas, Medical Branch, 3000 University
Boulevard, Galveston, Texas 77755-1001, United States
| | - Jiyun Zhu
- Department of Biochemistry and Biophysics and
Department of Chemistry, Texas A&M
University, 301 Old Main Drive, College Station, Texas 77843,
United States
| | - Zane W. Taylor
- Department of Biochemistry and Biophysics and
Department of Chemistry, Texas A&M
University, 301 Old Main Drive, College Station, Texas 77843,
United States
| | - Klaudia I. Kocurek
- Department of Biochemistry and Biophysics and
Department of Chemistry, Texas A&M
University, 301 Old Main Drive, College Station, Texas 77843,
United States
| | - Vivian Tat
- Department of Microbiology and Immunology,
University of Texas, Medical Branch, 3000 University
Boulevard, Galveston, Texas 77755-1001, United States
| | - Ardala Katzfuss
- Department of Biochemistry and Biophysics and
Department of Chemistry, Texas A&M
University, 301 Old Main Drive, College Station, Texas 77843,
United States
| | - Linfeng Li
- Department of Biochemistry and Biophysics and
Department of Chemistry, Texas A&M
University, 301 Old Main Drive, College Station, Texas 77843,
United States
| | - Miriam A. Giardini
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Danielle Skinner
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Ken Hirata
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Michael C. Yoon
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Sungjun Beck
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Aaron F. Carlin
- Department of Medicine, Division of Infectious
Diseases and Global Public Health, University of California San
Diego, La Jolla, California 92037, United States
| | - Alex E. Clark
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Laura Beretta
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Daniel Maneval
- Selva Therapeutics and Institute for Antiviral
Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State
University, 5600 Old Main Hill, Logan, Utah 84322, United
States
| | - Vivian Hook
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Felix Frueh
- Selva Therapeutics and Institute for Antiviral
Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State
University, 5600 Old Main Hill, Logan, Utah 84322, United
States
| | - Brett L. Hurst
- Selva Therapeutics and Institute for Antiviral
Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State
University, 5600 Old Main Hill, Logan, Utah 84322, United
States
| | - Hong Wang
- Selva Therapeutics and Institute for Antiviral
Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State
University, 5600 Old Main Hill, Logan, Utah 84322, United
States
| | - Frank M. Raushel
- Department of Biochemistry and Biophysics and
Department of Chemistry, Texas A&M
University, 301 Old Main Drive, College Station, Texas 77843,
United States
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Jair Lage de Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Thomas D. Meek
- Department of Biochemistry and Biophysics and
Department of Chemistry, Texas A&M
University, 301 Old Main Drive, College Station, Texas 77843,
United States
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
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36
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Frankel AE, Reddy R, DeSuza KR, Deeb K, Carlin AF, Smith D, Xie Y, Naik E, Silver RT, Hasselbalch HC. Response to pegylated interferon in a COVID-19-positive elderly woman with primary myelofibrosis treated with ruxolitinib. Clin Case Rep 2021; 9:2228-2235. [PMID: 33936671 PMCID: PMC8077319 DOI: 10.1002/ccr3.3997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 01/28/2021] [Accepted: 02/07/2021] [Indexed: 01/08/2023] Open
Abstract
An 83-year-old female had asymptomatic SARS-CoV-2 infection while taking ruxolitinib. She remained RT-PCR positive for viral RNA for >120 days, and Pegylated interferon for 4 weeks led to viral RNA clearance. The observations support combination therapy of ruxolitinib + interferon for COVID-19.
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Affiliation(s)
- Arthur E. Frankel
- Department of MedicineWest Palm Beach VA Medical CenterWest Palm BeachFLUSA
| | - Renuka Reddy
- Department of MedicineWest Palm Beach VA Medical CenterWest Palm BeachFLUSA
| | - Kayla R. DeSuza
- Department of MedicineWest Palm Beach VA Medical CenterWest Palm BeachFLUSA
| | - Khaled Deeb
- Department of MedicineWest Palm Beach VA Medical CenterWest Palm BeachFLUSA
| | - Aaron F. Carlin
- Division of Infectious DiseaseUCSD Medical SchoolSan DiegoCAUSA
| | - Davey Smith
- Division of Infectious DiseaseUCSD Medical SchoolSan DiegoCAUSA
| | - Yushuang Xie
- Department of MedicineWest Palm Beach VA Medical CenterWest Palm BeachFLUSA
| | - Eknath Naik
- Department of MedicineWest Palm Beach VA Medical CenterWest Palm BeachFLUSA
| | - Richard T. Silver
- Division of Hematology and Medical OncologyWeill Cornell MedicineNew YorkNYUSA
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37
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Sandoval DR, Clausen TM, Nora C, Cribbs AP, Denardo A, Clark AE, Garretson AF, Coker JKC, Narayanan A, Majowicz SA, Philpott M, Johansson C, Dunford JE, Spliid CB, Golden GJ, Payne NC, Tye MA, Nowell CJ, Griffis ER, Piermatteo A, Grunddal KV, Alle T, Magida JA, Hauser BM, Feldman J, Caradonna TM, Pu Y, Yin X, McVicar RN, Kwong EM, Weiss RJ, Downes M, Tsimikas S, Smidt AG, Ballatore C, Zengler K, Evans RM, Chanda SK, Croker BA, Leibel SL, Jose J, Mazitschek R, Oppermann U, Esko JD, Carlin AF, Gordts PLSM. The Prolyl-tRNA Synthetase Inhibitor Halofuginone Inhibits SARS-CoV-2 Infection. bioRxiv 2021. [PMID: 33791697 PMCID: PMC8010724 DOI: 10.1101/2021.03.22.436522] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We identify the prolyl-tRNA synthetase (PRS) inhibitor halofuginone 1 , a compound in clinical trials for anti-fibrotic and anti-inflammatory applications 2 , as a potent inhibitor of SARS-CoV-2 infection and replication. The interaction of SARS-CoV-2 spike protein with cell surface heparan sulfate (HS) promotes viral entry 3 . We find that halofuginone reduces HS biosynthesis, thereby reducing spike protein binding, SARS-CoV-2 pseudotyped virus, and authentic SARS-CoV-2 infection. Halofuginone also potently suppresses SARS-CoV-2 replication post-entry and is 1,000-fold more potent than Remdesivir 4 . Inhibition of HS biosynthesis and SARS-CoV-2 infection depends on specific inhibition of PRS, possibly due to translational suppression of proline-rich proteins. We find that pp1a and pp1ab polyproteins of SARS-CoV-2, as well as several HS proteoglycans, are proline-rich, which may make them particularly vulnerable to halofuginone's translational suppression. Halofuginone is orally bioavailable, has been evaluated in a phase I clinical trial in humans and distributes to SARS-CoV-2 target organs, including the lung, making it a near-term clinical trial candidate for the treatment of COVID-19.
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38
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Tiwari SK, Wang S, Smith D, Carlin AF, Rana TM. Revealing Tissue-Specific SARS-CoV-2 Infection and Host Responses using Human Stem Cell-Derived Lung and Cerebral Organoids. Stem Cell Reports 2021; 16:437-445. [PMID: 33631122 PMCID: PMC7879814 DOI: 10.1016/j.stemcr.2021.02.005] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/07/2021] [Accepted: 02/07/2021] [Indexed: 12/19/2022] Open
Abstract
COVID-19 is a transmissible respiratory disease caused by a novel coronavirus, SARS-CoV-2, and has become a global health emergency. There is an urgent need for robust and practical in vitro model systems to investigate viral pathogenesis. Here, we generated human induced pluripotent stem cell (iPSC)-derived lung organoids (LORGs), cerebral organoids (CORGs), neural progenitor cells (NPCs), neurons, and astrocytes. LORGs containing epithelial cells, alveolar types 1 and 2, highly express ACE2 and TMPRSS2 and are permissive to SARS-CoV-2 infection. SARS-CoV-2 infection induces interferons, cytokines, and chemokines and activates critical inflammasome pathway genes. Spike protein inhibitor, EK1 peptide, and TMPRSS2 inhibitors (camostat/nafamostat) block viral entry in LORGs. Conversely, CORGs, NPCs, astrocytes, and neurons express low levels of ACE2 and TMPRSS2 and correspondingly are not highly permissive to SARS-CoV-2 infection. Infection in neuronal cells activates TLR3/7, OAS2, complement system, and apoptotic genes. These findings will aid in understanding COVID-19 pathogenesis and facilitate drug discovery.
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Affiliation(s)
- Shashi Kant Tiwari
- Division of Genetics, Department of Pediatrics, Program in Immunology, Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Shaobo Wang
- Division of Genetics, Department of Pediatrics, Program in Immunology, Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Davey Smith
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Aaron F Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Tariq M Rana
- Division of Genetics, Department of Pediatrics, Program in Immunology, Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA.
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39
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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. Res Sq 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] [What about the content of this article? (0)] [Affiliation(s)] [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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40
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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 2021. [PMID: 33594369 DOI: 10.1101/2021.02.09.430349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Mor M, Werbner M, Alter J, Safra M, Chomsky E, Lee JC, Hada-Neeman S, Polonsky K, Nowell CJ, Clark AE, Roitburd-Berman A, Ben-Shalom N, Navon M, Rafael D, Sharim H, Kiner E, Griffis ER, Gershoni JM, Kobiler O, Leibel SL, Zimhony O, Carlin AF, Yaari G, Dessau M, Gal-Tanamy M, Hagin D, Croker BA, Freund NT. Multi-clonal SARS-CoV-2 neutralization by antibodies isolated from severe COVID-19 convalescent donors. PLoS Pathog 2021; 17:e1009165. [PMID: 33571304 PMCID: PMC7877634 DOI: 10.1371/journal.ppat.1009165] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/25/2020] [Indexed: 11/19/2022] Open
Abstract
The interactions between antibodies, SARS-CoV-2 and immune cells contribute to the pathogenesis of COVID-19 and protective immunity. To understand the differences between antibody responses in mild versus severe cases of COVID-19, we analyzed the B cell responses in patients 1.5 months post SARS-CoV-2 infection. Severe, and not mild, infection correlated with high titers of IgG against Spike receptor binding domain (RBD) that were capable of ACE2:RBD inhibition. B cell receptor (BCR) sequencing revealed that VH3-53 was enriched during severe infection. Of the 22 antibodies cloned from two severe donors, six exhibited potent neutralization against authentic SARS-CoV-2, and inhibited syncytia formation. Using peptide libraries, competition ELISA and mutagenesis of RBD, we mapped the epitopes of the neutralizing antibodies (nAbs) to three different sites on the Spike. Finally, we used combinations of nAbs targeting different immune-sites to efficiently block SARS-CoV-2 infection. Analysis of 49 healthy BCR repertoires revealed that the nAbs germline VHJH precursors comprise up to 2.7% of all VHJHs. We demonstrate that severe COVID-19 is associated with unique BCR signatures and multi-clonal neutralizing responses that are relatively frequent in the population. Moreover, our data support the use of combination antibody therapy to prevent and treat COVID-19.
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Affiliation(s)
- Michael Mor
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Michal Werbner
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Joel Alter
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Modi Safra
- Alexander Kofkin Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Elad Chomsky
- ImmunAi, New York, New York, United States of America
| | - Jamie C. Lee
- School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Smadar Hada-Neeman
- George S. Wise Life sciences Faculty, Tel Aviv University, Tel-Aviv, Israel
| | - Ksenia Polonsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Cameron J. Nowell
- Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia
| | - Alex E. Clark
- School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | | | - Noam Ben-Shalom
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Michal Navon
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Dor Rafael
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Hila Sharim
- ImmunAi, New York, New York, United States of America
| | - Evgeny Kiner
- ImmunAi, New York, New York, United States of America
| | - Eric R. Griffis
- Nikon Imaging Center, University of California San Diego, California, United States of America
| | | | - Oren Kobiler
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Sandra Lawrynowicz Leibel
- School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | | | - Aaron F. Carlin
- School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Gur Yaari
- Alexander Kofkin Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Moshe Dessau
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | | | | | - Ben A. Croker
- School of Medicine, University of California San Diego, La Jolla, California, United States of America
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Wang S, Li W, Hui H, Tiwari SK, Zhang Q, Croker BA, Rawlings S, Smith D, Carlin AF, Rana TM. Cholesterol 25-Hydroxylase inhibits SARS-CoV-2 and other coronaviruses by depleting membrane cholesterol. EMBO J 2020; 39:e106057. [PMID: 32944968 PMCID: PMC7537045 DOI: 10.15252/embj.2020106057] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/09/2020] [Accepted: 09/14/2020] [Indexed: 12/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2 and has spread across the globe. SARS-CoV-2 is a highly infectious virus with no vaccine or antiviral therapy available to control the pandemic; therefore, it is crucial to understand the mechanisms of viral pathogenesis and the host immune responses to SARS-CoV-2. SARS-CoV-2 is a new member of the betacoronavirus genus like other closely related viruses including SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Both SARS-CoV and MERS-CoV have caused serious outbreaks and epidemics in the past eighteen years. Here, we report that one of the interferon-stimulated genes (ISGs), cholesterol 25-hydroxylase (CH25H), is induced by SARS-CoV-2 infection in vitro and in COVID-19-infected patients. CH25H converts cholesterol to 25-hydrocholesterol (25HC) and 25HC shows broad anti-coronavirus activity by blocking membrane fusion. Furthermore, 25HC inhibits USA-WA1/2020 SARS-CoV-2 infection in lung epithelial cells and viral entry in human lung organoids. Mechanistically, 25HC inhibits viral membrane fusion by activating the ER-localized acyl-CoA:cholesterol acyltransferase (ACAT) which leads to the depletion of accessible cholesterol from the plasma membrane. Altogether, our results shed light on a potentially broad antiviral mechanism by 25HC through depleting accessible cholesterol on the plasma membrane to suppress virus-cell fusion. Since 25HC is a natural product with no known toxicity at effective concentrations, it provides a potential therapeutic candidate for COVID-19 and emerging viral diseases in the future.
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Affiliation(s)
- Shaobo Wang
- Division of GeneticsDepartment of PediatricsInstitute for Genomic MedicineProgram in ImmunologyUniversity of California San DiegoLa JollaCAUSA
| | - Wanyu Li
- Division of GeneticsDepartment of PediatricsInstitute for Genomic MedicineProgram in ImmunologyUniversity of California San DiegoLa JollaCAUSA
- Department of BiologyUniversity of California San DiegoLa JollaCAUSA
| | - Hui Hui
- Division of GeneticsDepartment of PediatricsInstitute for Genomic MedicineProgram in ImmunologyUniversity of California San DiegoLa JollaCAUSA
- Department of BiologyUniversity of California San DiegoLa JollaCAUSA
- Bioinformatics ProgramUniversity of California San DiegoLa JollaCAUSA
| | - Shashi Kant Tiwari
- Division of GeneticsDepartment of PediatricsInstitute for Genomic MedicineProgram in ImmunologyUniversity of California San DiegoLa JollaCAUSA
| | - Qiong Zhang
- Division of GeneticsDepartment of PediatricsInstitute for Genomic MedicineProgram in ImmunologyUniversity of California San DiegoLa JollaCAUSA
| | - Ben A Croker
- Division of Allergy, Immunology, and RheumatologyDepartment of PediatricsUniversity of California San DiegoLa JollaCAUSA
| | - Stephen Rawlings
- Division of Infectious Diseases and Global Public HealthDepartment of MedicineUniversity of California San DiegoLa JollaCAUSA
| | - Davey Smith
- Division of Infectious Diseases and Global Public HealthDepartment of MedicineUniversity of California San DiegoLa JollaCAUSA
| | - Aaron F Carlin
- Division of Infectious Diseases and Global Public HealthDepartment of MedicineUniversity of California San DiegoLa JollaCAUSA
| | - Tariq M Rana
- Division of GeneticsDepartment of PediatricsInstitute for Genomic MedicineProgram in ImmunologyUniversity of California San DiegoLa JollaCAUSA
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Mellott DM, Tseng CT, Drelich A, Fajtová P, Chenna BC, Kostomiris DH, Hsu J, Zhu J, Taylor ZW, Tat V, Katzfuss A, Li L, Giardini MA, Skinner D, Hirata K, Beck S, Carlin AF, Clark AE, Beretta L, Maneval D, Frueh F, Hurst BL, Wang H, Kocurek KI, Raushel FM, O’Donoghue AJ, de Siqueira-Neto JL, Meek TD, McKerrow JH. A cysteine protease inhibitor blocks SARS-CoV-2 infection of human and monkey cells. bioRxiv 2020:2020.10.23.347534. [PMID: 33140046 PMCID: PMC7605553 DOI: 10.1101/2020.10.23.347534] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
K777 is a di-peptide analog that contains an electrophilic vinyl-sulfone moiety and is a potent, covalent inactivator of cathepsins. Vero E6, HeLa/ACE2, Caco-2, A549/ACE2, and Calu-3, cells were exposed to SARS-CoV-2, and then treated with K777. K777 reduced viral infectivity with EC50 values of inhibition of viral infection of: 74 nM for Vero E6, <80 nM for A549/ACE2, and 4 nM for HeLa/ACE2 cells. In contrast, Calu-3 and Caco-2 cells had EC50 values in the low micromolar range. No toxicity of K777 was observed for any of the host cells at 10-100 μM inhibitor. K777 did not inhibit activity of the papain-like cysteine protease and 3CL cysteine protease, encoded by SARS-CoV-2 at concentrations of ≤ 100 μM. These results suggested that K777 exerts its potent anti-viral activity by inactivation of mammalian cysteine proteases which are essential to viral infectivity. Using a propargyl derivative of K777 as an activity-based probe, K777 selectively targeted cathepsin B and cathepsin L in Vero E6 cells. However only cathepsin L cleaved the SARS-CoV-2 spike protein and K777 blocked this proteolysis. The site of spike protein cleavage by cathepsin L was in the S1 domain of SARS-CoV-2 , differing from the cleavage site observed in the SARS CoV-1 spike protein. These data support the hypothesis that the antiviral activity of K777 is mediated through inhibition of the activity of host cathepsin L and subsequent loss of viral spike protein processing.
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Affiliation(s)
- Drake M. Mellott
- Department of Biochemistry and Biophysics, Texas A&M University, 301 Old Main Drive, College Station, Texas 77843
| | - Chien-Te Tseng
- Department of Microbiology and Immunology, University of Texas, Medical Branch, 3000 University Boulevard, Galveston, Texas, 77755-1001
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, University of Texas, Medical Branch, 3000 University Boulevard, Galveston, Texas, 77755-1001
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague, Czech Republic
| | - Bala C. Chenna
- Department of Biochemistry and Biophysics, Texas A&M University, 301 Old Main Drive, College Station, Texas 77843
| | - Demetrios H. Kostomiris
- Department of Biochemistry and Biophysics, Texas A&M University, 301 Old Main Drive, College Station, Texas 77843
| | - Jason Hsu
- Department of Microbiology and Immunology, University of Texas, Medical Branch, 3000 University Boulevard, Galveston, Texas, 77755-1001
| | - Jiyun Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, 301 Old Main Drive, College Station, Texas 77843
| | - Zane W. Taylor
- Department of Chemistry, Texas A&M University, 301 Old Main Drive, College Station, Texas 77843
- Current address: Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99353
| | - Vivian Tat
- Department of Microbiology and Immunology, University of Texas, Medical Branch, 3000 University Boulevard, Galveston, Texas, 77755-1001
| | - Ardala Katzfuss
- Department of Biochemistry and Biophysics, Texas A&M University, 301 Old Main Drive, College Station, Texas 77843
| | - Linfeng Li
- Department of Biochemistry and Biophysics, Texas A&M University, 301 Old Main Drive, College Station, Texas 77843
| | - Miriam A. Giardini
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Danielle Skinner
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Ken Hirata
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Sungjun Beck
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Aaron F. Carlin
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Alex E. Clark
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Laura Beretta
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Daniel Maneval
- Selva Therapeutics, Department of Animal, Dairy, and Veterinary Sciences, 5600 Old Main Hill, Utah State University, Logan, Utah, 84322
| | - Felix Frueh
- Selva Therapeutics, Department of Animal, Dairy, and Veterinary Sciences, 5600 Old Main Hill, Utah State University, Logan, Utah, 84322
| | - Brett L. Hurst
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, 5600 Old Main Hill, Utah State University, Logan, Utah, 84322
| | - Hong Wang
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, 5600 Old Main Hill, Utah State University, Logan, Utah, 84322
| | - Klaudia I. Kocurek
- Department of Chemistry, Texas A&M University, 301 Old Main Drive, College Station, Texas 77843
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, 301 Old Main Drive, College Station, Texas 77843
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | | | - Thomas D. Meek
- Department of Biochemistry and Biophysics, Texas A&M University, 301 Old Main Drive, College Station, Texas 77843
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
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44
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Mor M, Werbner M, Alter J, Safra M, Chomsky E, Hada-Neeman S, Polonsky K, Nowell CJ, Clark AE, Roitburd-Berman A, Shalom NB, Navon M, Rafael D, Sharim H, Kiner E, Griffis E, Gershoni JM, Kobiler O, Leibel SL, Zimhony O, Carlin AF, Yaari G, Dassau M, Gal-Tanamy M, Hagin D, Croker BA, Freund NT. Multi-Clonal Live SARS-CoV-2 In Vitro Neutralization by Antibodies Isolated from Severe COVID-19 Convalescent Donors. bioRxiv 2020:2020.10.06.323634. [PMID: 33052341 PMCID: PMC7553166 DOI: 10.1101/2020.10.06.323634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The interactions between antibodies, SARS-CoV-2 and immune cells contribute to the pathogenesis of COVID-19 and protective immunity. To understand the differences between antibody responses in mild versus severe cases of COVID-19, we analyzed the B cell responses in patients 1.5 months post SARS-CoV-2 infection. Severe and not mild infection correlated with high titers of IgG against Spike receptor binding domain (RBD) that were capable of viral inhibition. B cell receptor (BCR) sequencing revealed two VH genes, VH3-38 and VH3-53, that were enriched during severe infection. Of the 22 antibodies cloned from two severe donors, six exhibited potent neutralization against live SARS-CoV-2, and inhibited syncytia formation. Using peptide libraries, competition ELISA and RBD mutagenesis, we mapped the epitopes of the neutralizing antibodies (nAbs) to three different sites on the Spike. Finally, we used combinations of nAbs targeting different immune-sites to efficiently block SARS-CoV-2 infection. Analysis of 49 healthy BCR repertoires revealed that the nAbs germline VHJH precursors comprise up to 2.7% of all VHJHs. We demonstrate that severe COVID-19 is associated with unique BCR signatures and multi-clonal neutralizing responses that are relatively frequent in the population. Moreover, our data support the use of combination antibody therapy to prevent and treat COVID-19.
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Affiliation(s)
- Michael Mor
- Department for Microbiology and Clinical Immunology, Faculty of Medicine, Tel Aviv University, Israel
| | - Michal Werbner
- Azrieli Faculty of Medicine, Bar Ilan University, 2800123, Israel
| | - Joel Alter
- Azrieli Faculty of Medicine, Bar Ilan University, 2800123, Israel
| | - Modi Safra
- Faculty of Engineering, Bar Ilan University, 5290002, Israel
| | | | - Smadar Hada-Neeman
- George S Weiss, Life sciences Faculty, Tel Aviv University, 699780, Israel
| | - Ksenia Polonsky
- Department for Microbiology and Clinical Immunology, Faculty of Medicine, Tel Aviv University, Israel
| | - Cameron J Nowell
- Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia
| | - Alex E Clark
- Department of Cellular and Molecular Medicine, School of Medicine, UC San Diego, La Jolla, CA 92093 USA
| | | | - Noam Ben Shalom
- Department for Microbiology and Clinical Immunology, Faculty of Medicine, Tel Aviv University, Israel
| | - Michal Navon
- Department for Microbiology and Clinical Immunology, Faculty of Medicine, Tel Aviv University, Israel
| | - Dor Rafael
- Department for Microbiology and Clinical Immunology, Faculty of Medicine, Tel Aviv University, Israel
| | | | | | - Eric Griffis
- Nikon Imaging Center, UC San Diego, CA, 92093 USA
| | | | - Oren Kobiler
- Department for Microbiology and Clinical Immunology, Faculty of Medicine, Tel Aviv University, Israel
| | | | - Oren Zimhony
- Infectious Diseases unit, Kaplan Medical Center, Rehovot, 7610001, affiliated to the School of Medicine Hebrew University and Hadassah, Israel
| | - Aaron F Carlin
- Department of Cellular and Molecular Medicine, School of Medicine, UC San Diego, La Jolla, CA 92093 USA
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, 5290002, Israel
| | - Moshe Dassau
- Azrieli Faculty of Medicine, Bar Ilan University, 2800123, Israel
| | | | - David Hagin
- Department of Immunology Ichilov Hospital, 623906, Israel
| | - Ben A Croker
- Department of Pediatrics, School of Medicine, UC San Diego, La Jolla, CA 92093 USA
| | - Natalia T Freund
- Department for Microbiology and Clinical Immunology, Faculty of Medicine, Tel Aviv University, Israel
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45
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Chao DL, Sridhar J, Kuriyan AE, Leng T, Barnett BP, Carlin AF, Wykoff CC, Gayer S, Mruthyunjaya P, Yonekawa Y, Fawzi AA, Berrocal AM, Yeh S, Ting D, Modi Y, Zacks DN, Yannuzzi N, Afshari NA, Murray T. Rationale for American Society of Retina Specialists Best Practice Recommendations for Conducting Vitreoretinal Surgery during the COVID-19 Era. J Vitreoretin Dis 2020; 4:420-429. [PMID: 34222758 PMCID: PMC8247449 DOI: 10.1177/2474126420941707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
PURPOSE To detail the rationale behind recommendations recently published by the American Society of Retina Specialists (ASRS) outlining best practices for safety of vitreoretinal surgeons and staff while performing vitreoretinal surgery during the coronavirus disease (COVID)-19 pandemic. METHODS The committee for ASRS Best Practices for Retinal Surgery during the COVID-19 Pandemic reviewed existing evidence and information on SARS-CoV-2 transmission, and risk factors during vitreoretinal surgery. Recommendations were based on best available published data, cumulative clinical experiences, and recommendations and policies from other organizations. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used to assess the strength of recommendations and confidence in the evidence. These serve as interim recommendations which are routinely updated given gaps of knowledge and lack of high-quality data on this evolving subject. RESULTS Relevant existing literature related to methods of transmission, and ocular manifestations of SARS-CoV-2 are summarized. The data and clinical experiences driving recommendations for pre-operative, intraoperative and post-operative surgical considerations, anesthesia choice, as well as considerations for intravitreal injections are provided. CONCLUSION Recommendations are provided with the goal of protecting vitreoretinal surgeons and associated personnel from exposure to SARS-CoV-2 during interventional vitreoretinal procedures. This is a rapidly evolving topic with numerous remaining gaps in our current knowledge. As such, recommendations will evolve and the current manuscript is intended to serve as a foundation for continued dialogue on best practices.
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Affiliation(s)
- Daniel L. Chao
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute,
University of California San Diego, La Jolla, CA, USA
| | - Jayanth Sridhar
- Bascom Palmer Eye Institute, University of Miami, Miami, FL,
USA
| | - Ajay E. Kuriyan
- Wills Eye Hospital, Mid Atlantic Retina, Thomas Jefferson
University, Philadelphia, PA, USA
| | - Theodore Leng
- Department of Ophthalmology, Byers Eye Institute at Stanford,
Stanford University, Palo Alto, CA, USA
| | - Brad P. Barnett
- Department of Ophthalmology, Duke Eye Center, Duke University,
Durham, NC, USA
| | - Aaron F. Carlin
- Department of Medicine, Division of Infectious Diseases and Global
Public Health, University, of California, San Diego, La Jolla, CA, USA
| | - Charles C. Wykoff
- Retina Consultants of Houston, Retina Consultants of America;
Blanton Eye Institute, Houston Methodist Hospital & Weill Cornell Medical
College, Houston, TX, USA
| | - Stephen Gayer
- Department of Anesthesia, University of Miami, Miami, FL, USA
| | - Prithvi Mruthyunjaya
- Department of Ophthalmology, Byers Eye Institute at Stanford,
Stanford University, Palo Alto, CA, USA
| | - Yoshihiro Yonekawa
- Wills Eye Hospital, Mid Atlantic Retina, Thomas Jefferson
University, Philadelphia, PA, USA
| | - Amani A. Fawzi
- Department of Ophthalmology, Northwestern University, Chicago, IL,
USA
| | | | - Steven Yeh
- Department of Ophthalmology, Emory Eye Center, Emory University,
Atlanta, GA, USA
| | - Daniel Ting
- Singapore National Eye Center, Singapore, Singapore
| | - Yasha Modi
- Department of Ophthalmology, New York University, New York, NY,
USA
| | - David N. Zacks
- Department of Ophthalmology, Kellogg Eye Center, University of
Michigan, Ann Arbor, MI, USA
| | | | - Natalie A. Afshari
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute,
University of California San Diego, La Jolla, CA, USA
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46
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Clausen TM, Sandoval DR, Spliid CB, Pihl J, Perrett HR, Painter CD, Narayanan A, Majowicz SA, Kwong EM, McVicar RN, Thacker BE, Glass CA, Yang Z, Torres JL, Golden GJ, Bartels PL, Porell RN, Garretson AF, Laubach L, Feldman J, Yin X, Pu Y, Hauser BM, Caradonna TM, Kellman BP, Martino C, Gordts PLSM, Chanda SK, Schmidt AG, Godula K, Leibel SL, Jose J, Corbett KD, Ward AB, Carlin AF, Esko JD. SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2. Cell 2020; 183:1043-1057.e15. [PMID: 32970989 PMCID: PMC7489987 DOI: 10.1016/j.cell.2020.09.033] [Citation(s) in RCA: 740] [Impact Index Per Article: 185.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/16/2020] [Accepted: 09/10/2020] [Indexed: 12/28/2022]
Abstract
We show that SARS-CoV-2 spike protein interacts with both cellular heparan sulfate and angiotensin-converting enzyme 2 (ACE2) through its receptor-binding domain (RBD). Docking studies suggest a heparin/heparan sulfate-binding site adjacent to the ACE2-binding site. Both ACE2 and heparin can bind independently to spike protein in vitro, and a ternary complex can be generated using heparin as a scaffold. Electron micrographs of spike protein suggests that heparin enhances the open conformation of the RBD that binds ACE2. On cells, spike protein binding depends on both heparan sulfate and ACE2. Unfractionated heparin, non-anticoagulant heparin, heparin lyases, and lung heparan sulfate potently block spike protein binding and/or infection by pseudotyped virus and authentic SARS-CoV-2 virus. We suggest a model in which viral attachment and infection involves heparan sulfate-dependent enhancement of binding to ACE2. Manipulation of heparan sulfate or inhibition of viral adhesion by exogenous heparin presents new therapeutic opportunities. SARS-CoV-2 spike protein interacts with heparan sulfate and ACE2 through the RBD Heparan sulfate promotes Spike-ACE2 interaction SARS-CoV-2 infection is co-dependent on heparan sulfate and ACE2 Heparin and non-anticoagulant derivatives block SARS-CoV-2 binding and infection
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Affiliation(s)
- Thomas Mandel Clausen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Department of Infectious Disease, Copenhagen University Hospital, 2200 Copenhagen, Denmark.
| | - Daniel R Sandoval
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Charlotte B Spliid
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Department of Infectious Disease, Copenhagen University Hospital, 2200 Copenhagen, Denmark
| | - Jessica Pihl
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Department of Infectious Disease, Copenhagen University Hospital, 2200 Copenhagen, Denmark
| | - Hailee R Perrett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chelsea D Painter
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - Anoop Narayanan
- Department of Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Sydney A Majowicz
- Department of Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Elizabeth M Kwong
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Rachael N McVicar
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Bryan E Thacker
- TEGA Therapeutics, Inc., 3550 General Atomics Court, G02-102, San Diego, CA 92121, USA
| | - Charles A Glass
- TEGA Therapeutics, Inc., 3550 General Atomics Court, G02-102, San Diego, CA 92121, USA
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Molecular and Cellular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gregory J Golden
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - Phillip L Bartels
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ryan N Porell
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Aaron F Garretson
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Logan Laubach
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Xin Yin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yuan Pu
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Blake M Hauser
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Benjamin P Kellman
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cameron Martino
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Philip L S M Gordts
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Kamil Godula
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sandra L Leibel
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Joyce Jose
- Department of Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aaron F Carlin
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA.
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47
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Clausen TM, Sandoval DR, Spliid CB, Pihl J, Painter CD, Thacker BE, Glass CA, Narayanan A, Majowicz SA, Zhang Y, Torres JL, Golden GJ, Porell R, Garretson AF, Laubach L, Feldman J, Yin X, Pu Y, Hauser B, Caradonna TM, Kellman BP, Martino C, Gordts PLSM, Leibel SL, Chanda SK, Schmidt AG, Godula K, Jose J, Corbett KD, Ward AB, Carlin AF, Esko JD. SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2. bioRxiv 2020. [PMID: 32699853 PMCID: PMC7373134 DOI: 10.1101/2020.07.14.201616] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We show that SARS-CoV-2 spike protein interacts with cell surface heparan sulfate and angiotensin converting enzyme 2 (ACE2) through its Receptor Binding Domain. Docking studies suggest a putative heparin/heparan sulfate-binding site adjacent to the domain that binds to ACE2. In vitro, binding of ACE2 and heparin to spike protein ectodomains occurs independently and a ternary complex can be generated using heparin as a template. Contrary to studies with purified components, spike protein binding to heparan sulfate and ACE2 on cells occurs codependently. Unfractionated heparin, non-anticoagulant heparin, treatment with heparin lyases, and purified lung heparan sulfate potently block spike protein binding and infection by spike protein-pseudotyped virus and SARS-CoV-2 virus. These findings support a model for SARS-CoV-2 infection in which viral attachment and infection involves formation of a complex between heparan sulfate and ACE2. Manipulation of heparan sulfate or inhibition of viral adhesion by exogenous heparin may represent new therapeutic opportunities.
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48
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Grifoni A, Weiskopf D, Ramirez SI, Mateus J, Dan JM, Moderbacher CR, Rawlings SA, Sutherland A, Premkumar L, Jadi RS, Marrama D, de Silva AM, Frazier A, Carlin AF, Greenbaum JA, Peters B, Krammer F, Smith DM, Crotty S, Sette A. Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell 2020; 181:1489-1501.e15. [PMID: 32473127 PMCID: PMC7237901 DOI: 10.1016/j.cell.2020.05.015] [Citation(s) in RCA: 2528] [Impact Index Per Article: 632.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 02/07/2023]
Abstract
Understanding adaptive immunity to SARS-CoV-2 is important for vaccine development, interpreting coronavirus disease 2019 (COVID-19) pathogenesis, and calibration of pandemic control measures. Using HLA class I and II predicted peptide "megapools," circulating SARS-CoV-2-specific CD8+ and CD4+ T cells were identified in ∼70% and 100% of COVID-19 convalescent patients, respectively. CD4+ T cell responses to spike, the main target of most vaccine efforts, were robust and correlated with the magnitude of the anti-SARS-CoV-2 IgG and IgA titers. The M, spike, and N proteins each accounted for 11%-27% of the total CD4+ response, with additional responses commonly targeting nsp3, nsp4, ORF3a, and ORF8, among others. For CD8+ T cells, spike and M were recognized, with at least eight SARS-CoV-2 ORFs targeted. Importantly, we detected SARS-CoV-2-reactive CD4+ T cells in ∼40%-60% of unexposed individuals, suggesting cross-reactive T cell recognition between circulating "common cold" coronaviruses and SARS-CoV-2.
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Affiliation(s)
- Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Sydney I Ramirez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jose Mateus
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Jennifer M Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | | | - Stephen A Rawlings
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Aaron Sutherland
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Ramesh S Jadi
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Daniel Marrama
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Aravinda M de Silva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Aaron F Carlin
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jason A Greenbaum
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Davey M Smith
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA.
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA.
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49
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Wang YT, Branche E, Viramontes KM, Cuevas JV, Carlin AF, Shresta S. Zika virus suppresses maturation of human dendritic cells. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.248.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Zika virus (ZIKV) belongs to the genus Flavivirus, which includes several medically relevant viruses, including dengue, yellow fever and Japanese encephalitis viruses. ZIKV causes congenital Zika syndrome in neonates and Guillain-Barré syndrome in adults, and has emerged as a major public health problem worldwide. Dendritic cells (DCs) serve as the major cellular hosts of ZIKV, and T cell responses to flaviviruses may play a dual role in protection and pathogenesis. To decipher the precise interactions between DCs and ZIKV, we profiled the transcriptomic features of ZIKV-infected DCs versus uninfected bystander DCs in primary human blood monocyte-derived DC cultures. RNA sequencing data revealed that the expression of genes related to antigen processing/presentation pathways was reduced in ZIKV-infected DCs relative to uninfected bystander DCs that were exposed to the same environmental stimuli as ZIKV-infected DCs. Flow cytometric analysis of ZIKV-infected DCs for the expression of key DC maturation markers confirmed the RNA sequencing data. Thus, ZIKV hinders DC maturation, suggesting that ZIKV may modulate T cell responses by directly manipulating DC functions. Studies are in progress to determine how ZIKV inhibits DC maturation and influences T cell responses. Results of these studies will provide key insights towards the development of safe and effective vaccines against ZIKV and related flaviviruses.
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Affiliation(s)
| | | | | | | | - Aaron F. Carlin
- 2Department of Medicine, University of California San Diego (UCSD)
| | - Sujan Shresta
- 1La Jolla Institute for Immunology
- 2Department of Medicine, University of California San Diego (UCSD)
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50
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Fowler AM, Tang WW, Young MP, Mamidi A, Viramontes KM, McCauley MD, Carlin AF, Schooley RT, Swanstrom J, Baric RS, Govero J, Diamond MS, Shresta S. Maternally Acquired Zika Antibodies Enhance Dengue Disease Severity in Mice. Cell Host Microbe 2019; 24:743-750.e5. [PMID: 30439343 DOI: 10.1016/j.chom.2018.09.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/21/2018] [Accepted: 09/20/2018] [Indexed: 01/08/2023]
Abstract
Antibody (Ab)-dependent enhancement can exacerbate dengue virus (DENV) infection due to cross-reactive Abs from an initial DENV infection, facilitating replication of a second DENV. Zika virus (ZIKV) emerged in DENV-endemic areas, raising questions about whether existing immunity could affect these related flaviviruses. We show that mice born with circulating maternal Abs against ZIKV develop severe disease upon DENV infection. Compared with pups of naive mothers, those born to ZIKV-immune mice lacking type I interferon receptor in myeloid cells (LysMCre+Ifnar1fl/fl) exhibit heightened disease and viremia upon DENV infection. Passive transfer of IgG isolated from mice born to ZIKV-immune mothers resulted in increased viremia in naive recipient mice. Treatment with Abs blocking inflammatory cytokine tumor necrosis factor linked to DENV disease or Abs blocking DENV entry improved survival of DENV-infected mice born to ZIKV-immune mothers. Thus, the maternal Ab response to ZIKV infection or vaccination might predispose to severe dengue disease in infants.
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Affiliation(s)
- Angela M Fowler
- Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - William W Tang
- Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Matthew P Young
- Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Anila Mamidi
- Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Karla M Viramontes
- Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Melanie D McCauley
- Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Aaron F Carlin
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Robert T Schooley
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jesica Swanstrom
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jennifer Govero
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sujan Shresta
- Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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