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Le Pen J, Paniccia G, Kinast V, Moncada-Velez M, Ashbrook AW, Bauer M, Hoffmann HH, Pinharanda A, Ricardo-Lax I, Stenzel AF, Rosado-Olivieri EA, Dinnon KH, Doyle WC, Freije CA, Hong SH, Lee D, Lewy T, Luna JM, Peace A, Schmidt C, Schneider WM, Winkler R, Yip EZ, Larson C, McGinn T, Menezes MR, Ramos-Espiritu L, Banerjee P, Poirier JT, Sànchez-Rivera FJ, Cobat A, Zhang Q, Casanova JL, Carroll TS, Glickman JF, Michailidis E, Razooky B, MacDonald MR, Rice CM. A genome-wide arrayed CRISPR screen identifies PLSCR1 as an intrinsic barrier to SARS-CoV-2 entry that recent virus variants have evolved to resist. PLoS Biol 2024; 22:e3002767. [PMID: 39316623 DOI: 10.1371/journal.pbio.3002767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 07/25/2024] [Indexed: 09/26/2024] Open
Abstract
Interferons (IFNs) play a crucial role in the regulation and evolution of host-virus interactions. Here, we conducted a genome-wide arrayed CRISPR knockout screen in the presence and absence of IFN to identify human genes that influence Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. We then performed an integrated analysis of genes interacting with SARS-CoV-2, drawing from a selection of 67 large-scale studies, including our own. We identified 28 genes of high relevance in both human genetic studies of Coronavirus Disease 2019 (COVID-19) patients and functional genetic screens in cell culture, with many related to the IFN pathway. Among these was the IFN-stimulated gene PLSCR1. PLSCR1 did not require IFN induction to restrict SARS-CoV-2 and did not contribute to IFN signaling. Instead, PLSCR1 specifically restricted spike-mediated SARS-CoV-2 entry. The PLSCR1-mediated restriction was alleviated by TMPRSS2 overexpression, suggesting that PLSCR1 primarily restricts the endocytic entry route. In addition, recent SARS-CoV-2 variants have adapted to circumvent the PLSCR1 barrier via currently undetermined mechanisms. Finally, we investigate the functional effects of PLSCR1 variants present in humans and discuss an association between PLSCR1 and severe COVID-19 reported recently.
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Affiliation(s)
- Jérémie Le Pen
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Gabrielle Paniccia
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Volker Kinast
- Department of Medical Microbiology and Virology, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
- Department for Molecular and Medical Virology, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Marcela Moncada-Velez
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
| | - Alison W Ashbrook
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Michael Bauer
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - H-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Ana Pinharanda
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Inna Ricardo-Lax
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Ansgar F Stenzel
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Edwin A Rosado-Olivieri
- Laboratory of Synthetic Embryology, The Rockefeller University, New York, New York, United States of America
| | - Kenneth H Dinnon
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - William C Doyle
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Catherine A Freije
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Seon-Hui Hong
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Danyel Lee
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Tyler Lewy
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Joseph M Luna
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Avery Peace
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Carltin Schmidt
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
| | - William M Schneider
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Roni Winkler
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Elaine Z Yip
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Chloe Larson
- Fisher Drug Discovery Resource Center, The Rockefeller University, New York, New York, United States of America
| | - Timothy McGinn
- Fisher Drug Discovery Resource Center, The Rockefeller University, New York, New York, United States of America
| | - Miriam-Rose Menezes
- Fisher Drug Discovery Resource Center, The Rockefeller University, New York, New York, United States of America
| | - Lavoisier Ramos-Espiritu
- Fisher Drug Discovery Resource Center, The Rockefeller University, New York, New York, United States of America
| | - Priyam Banerjee
- Bio-Imaging Resource Center, The Rockefeller University, New York, New York, United States of America
| | - John T Poirier
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, New York, United States of America
| | - Francisco J Sànchez-Rivera
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Aurélie Cobat
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Qian Zhang
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, New York, United States of America
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, New York, United States of America
| | - J Fraser Glickman
- Fisher Drug Discovery Resource Center, The Rockefeller University, New York, New York, United States of America
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Brandon Razooky
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Margaret R MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
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Ip JD, Chu WM, Chan WM, Chu AWH, Leung RCY, Peng Q, Tam AR, Chan BPC, Cai JP, Yuen KY, Kok KH, Shi Y, Hung IFN, To KKW. The significance of recurrent de novo amino acid substitutions that emerged during chronic SARS-CoV-2 infection: an observational study. EBioMedicine 2024; 107:105273. [PMID: 39146693 PMCID: PMC11379563 DOI: 10.1016/j.ebiom.2024.105273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 07/24/2024] [Accepted: 07/27/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND De novo amino acid substitutions (DNS) frequently emerge among immunocompromised patients with chronic SARS-CoV-2 infection. While previous studies have reported these DNS, their significance has not been systematically studied. METHODS We performed a review of DNS that emerged during chronic SARS-CoV-2 infection. We searched PubMed until June 2023 using the keywords "(SARS-CoV-2 or COVID-19) and (mutation or sequencing) and ((prolonged infection) or (chronic infection) or (long term))". We included patients with chronic SARS-CoV-2 infection who had SARS-CoV-2 sequencing performed for at least 3 time points over at least 60 days. We also included 4 additional SARS-CoV-2 patients with chronic infection of our hospital not reported previously. We determined recurrent DNS that has appeared in multiple patients and determined the significance of these mutations among epidemiologically-significant variants. FINDINGS A total of 34 cases were analyzed, including 30 that were published previously and 4 from our hospital. Twenty two DNS appeared in ≥3 patients, with 14 (64%) belonging to lineage-defining mutations (LDMs) of epidemiologically-significant variants and 10 (45%) emerging among chronically-infected patients before the appearance of the corresponding variant. Notably, nsp9-T35I substitution (Orf1a T4175I) emerged in all three patients with BA.2.2 infection in 2022 before the appearance of Variants of Interest that carry nsp9-T35I as LDM (EG.5 and BA.2.86/JN.1). Structural analysis suggests that nsp9-T35I substitution may affect nsp9-nsp12 interaction, which could be critical for the function of the replication and transcription complex. INTERPRETATION DNS that emerges recurrently in different chronically-infected patients may be used as a marker for potential epidemiologically-significant variants. FUNDING Theme-Based Research Scheme [T11/709/21-N] of the Research Grants Council (See acknowledgements for full list).
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Affiliation(s)
- Jonathan Daniel Ip
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Wing-Ming Chu
- Division of Infectious Diseases, Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Rhoda Cheuk-Ying Leung
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Qi Peng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Anthony Raymond Tam
- Division of Infectious Diseases, Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Brian Pui-Chun Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jian-Piao Cai
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Kin-Hang Kok
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Yi Shi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ivan Fan-Ngai Hung
- Division of Infectious Diseases, Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Infectious Diseases Division, Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
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3
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Pan R, Li P, Meyerholz DK, Perlman S. Mutations in nonstructural proteins essential for pathogenicity in SARS-CoV-2-infected mice. J Virol 2024; 98:e0058424. [PMID: 38888344 PMCID: PMC11265370 DOI: 10.1128/jvi.00584-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has resulted in substantial morbidity and mortality. The basis of severe disease in humans is difficult to determine without the use of experimental animal models. Mice are resistant to infection with ancestral strains of SARS-CoV-2, although many variants that arose later in the pandemic were able to directly infect mice. In almost all cases, viruses that naturally infected mice or were engineered to enable mouse infection required mouse passage to become virulent. In most cases, changes in structural and nonstructural changes occurred during mouse adaptation. However, the mechanism of increased virulence in mice is not understood. Here, using a recently described strain of mouse-adapted SARS-CoV-2 (rSARS2-MA30N501Y), we engineered a series of recombinant viruses that expressed a subset of the mutations present in rSARS2-MA30N501Y. Mutations were detected in the spike protein and in three nonstructural proteins (nsp4, nsp8, and nsp9). We found that infection of mice with recombinant SARS-CoV-2 expressing only the S protein mutations caused very mild infection. Addition of the mutations in nsp4 and nsp8 was required for complete virulence. Of note, all these recombinant viruses replicated equivalently in cultured cells. The innate immune response was delayed after infection with virulent compared to attenuated viruses. Further, using a lineage tracking system, we found that attenuated virus was highly inhibited in the ability to infect the parenchyma, but not the airway after infection. Together, these results indicate that mutations in both the S protein and nonstructural proteins are required for maximal virulence during mouse adaptation.IMPORTANCEUnderstanding the pathogenesis of coronavirus disease 2019 (COVID-19) requires the study of experimental animals after infection with severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). For this purpose, several mouse-adapted SARS-CoV-2 strains have been developed. Here, using a strain of mouse-adapted virus that causes a range of diseases ranging from mild to severe, we show that mutations in both a structural protein [spike (S) protein] and nonstructural proteins are required for maximal virulence. Thus, changes in the S protein, the most widely studied viral protein, while required for mouse adaptation, are not sufficient to result in a virulent virus.
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Affiliation(s)
- Ruangang Pan
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Pengfei Li
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | | | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
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4
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Baker DL, Wang B, Wilkinson-White LE, El-Kamand S, Allport TA, Ataide SF, Kwan AH, Artsimovitch I, Cubeddu L, Gamsjaeger R. A Biochemical and Biophysical Analysis of the Interaction of nsp9 with nsp12 from SARS-CoV-2-Implications for Future Drug Discovery Efforts. Proteins 2024. [PMID: 38958516 DOI: 10.1002/prot.26725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/27/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024]
Abstract
The ongoing global pandemic of the coronavirus 2019 (COVID-19) disease is caused by the virus SARS-CoV-2, with very few highly effective antiviral treatments currently available. The machinery responsible for the replication and transcription of viral RNA during infection is made up of several important proteins. Two of these are nsp12, the catalytic subunit of the viral polymerase, and nsp9, a cofactor of nsp12 involved in the capping and priming of viral RNA. While several recent studies have determined the structural details of the interaction of nsp9 with nsp12 in the context of RNA capping, very few biochemical or biophysical details are currently available. In this study, we have used a combination of surface plasmon resonance (SPR) experiments, size exclusion chromatography (SEC) experiments, and biochemical assays to identify specific nsp9 residues that are critical for nsp12 binding as well as RNAylation, both of which are essential for the RNA capping process. Our data indicate that nsp9 dimerization is unlikely to play a significant functional role in the virus. We confirm that a set of recently discovered antiviral peptides inhibit nsp9-nsp12 interaction by specifically binding to nsp9; however, we find that these peptides do not impact RNAylation. In summary, our results have important implications for future drug discovery efforts to combat SARS-CoV-2 and any newly emerging coronaviruses.
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Affiliation(s)
- David L Baker
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Bing Wang
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Lorna E Wilkinson-White
- Sydney Analytical, Core Research Facilities, University of Sydney, Camperdown, New South Wales, Australia
| | - Serene El-Kamand
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Thomas A Allport
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Sandro F Ataide
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Ann H Kwan
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Liza Cubeddu
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Roland Gamsjaeger
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
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5
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Lundrigan E, Toudic C, Pennock E, Pezacki JP. SARS-CoV-2 Protein Nsp9 Is Involved in Viral Evasion through Interactions with Innate Immune Pathways. ACS OMEGA 2024; 9:26428-26438. [PMID: 38911767 PMCID: PMC11191075 DOI: 10.1021/acsomega.4c02631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/13/2024] [Accepted: 04/23/2024] [Indexed: 06/25/2024]
Abstract
The suppression of the host's innate antiviral immune response by SARS-CoV-2, a contributing factor to the severity of disease, has been considerably studied in recent years. Many of these studies have focused on the actions of the structural proteins of the virus because of their accessibility to host immunological components. However, less is known about SARS-CoV-2 nonstructural and accessory proteins in relation to viral evasion. Herein, we study SARS-CoV-2 nonstructural proteins Orf3a, Orf6, and Nsp9 in a mimicked virus-infected state using poly(I:C), a synthetic analog of viral dsRNA, that elicits the antiviral immune response. Through genome-wide expression profiling, we determined that Orf3a, Orf6, and Nsp9 all modulate the host antiviral signaling transcriptome to varying extents, uniquely suppressing aspects of innate immune signaling. Our data suggest that SARS-CoV-2 Nsp9 hinders viral detection through suppression of RIG-I expression and antagonizes the interferon antiviral cascade by downregulating NF-kB and TBK1. Our data point to unique molecular mechanisms through which the different SARS-CoV-2 proteins suppress immune signaling and promote viral evasion. Nsp9 in particular acts on major elements of the host antiviral pathways to impair the antiviral immune response.
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Affiliation(s)
- Eryn Lundrigan
- Department of Chemistry and
Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Caroline Toudic
- Department of Chemistry and
Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Emily Pennock
- Department of Chemistry and
Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and
Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
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6
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Su HH, Lin ES, Huang YH, Lien Y, Huang CY. Inhibition of SARS-CoV-2 Nsp9 ssDNA-Binding Activity and Cytotoxic Effects on H838, H1975, and A549 Human Non-Small Cell Lung Cancer Cells: Exploring the Potential of Nepenthes miranda Leaf Extract for Pulmonary Disease Treatment. Int J Mol Sci 2024; 25:6120. [PMID: 38892307 PMCID: PMC11173125 DOI: 10.3390/ijms25116120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
Carnivorous pitcher plants from the genus Nepenthes are renowned for their ethnobotanical uses. This research explores the therapeutic potential of Nepenthes miranda leaf extract against nonstructural protein 9 (Nsp9) of SARS-CoV-2 and in treating human non-small cell lung carcinoma (NSCLC) cell lines. Nsp9, essential for SARS-CoV-2 RNA replication, was expressed and purified, and its interaction with ssDNA was assessed. Initial tests with myricetin and oridonin, known for targeting ssDNA-binding proteins and Nsp9, respectively, did not inhibit the ssDNA-binding activity of Nsp9. Subsequent screenings of various N. miranda extracts identified those using acetone, methanol, and ethanol as particularly effective in disrupting Nsp9's ssDNA-binding activity, as evidenced by electrophoretic mobility shift assays. Molecular docking studies highlighted stigmast-5-en-3-ol and lupenone, major components in the leaf extract of N. miranda, as potential inhibitors. The cytotoxic properties of N. miranda leaf extract were examined across NSCLC lines H1975, A549, and H838, focusing on cell survival, apoptosis, and migration. Results showed a dose-dependent cytotoxic effect in the following order: H1975 > A549 > H838 cells, indicating specificity. Enhanced anticancer effects were observed when the extract was combined with afatinib, suggesting synergistic interactions. Flow cytometry indicated that N. miranda leaf extract could induce G2 cell cycle arrest in H1975 cells, potentially inhibiting cancer cell proliferation. Gas chromatography-mass spectrometry (GC-MS) enabled the tentative identification of the 19 most abundant compounds in the leaf extract of N. miranda. These outcomes underscore the dual utility of N. miranda leaf extract in potentially managing SARS-CoV-2 infection through Nsp9 inhibition and offering anticancer benefits against lung carcinoma. These results significantly broaden the potential medical applications of N. miranda leaf extract, suggesting its use not only in traditional remedies but also as a prospective treatment for pulmonary diseases. Overall, our findings position the leaf extract of N. miranda as a promising source of natural compounds for anticancer therapeutics and antiviral therapies, warranting further investigation into its molecular mechanisms and potential clinical applications.
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Affiliation(s)
- Hsin-Hui Su
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan City 717, Taiwan
| | - En-Shyh Lin
- Department of Beauty Science, National Taichung University of Science and Technology, Taichung City 403, Taiwan
| | - Yen-Hua Huang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
| | - Yi Lien
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Cheng-Yang Huang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung City 402, Taiwan
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7
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Gribling-Burrer AS, Bohn P, Smyth RP. Isoform-specific RNA structure determination using Nano-DMS-MaP. Nat Protoc 2024; 19:1835-1865. [PMID: 38347203 DOI: 10.1038/s41596-024-00959-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/12/2023] [Indexed: 06/12/2024]
Abstract
RNA structure determination is essential to understand how RNA carries out its diverse biological functions. In cells, RNA isoforms are readily expressed with partial variations within their sequences due, for example, to alternative splicing, heterogeneity in the transcription start site, RNA processing or differential termination/polyadenylation. Nanopore dimethyl sulfate mutational profiling (Nano-DMS-MaP) is a method for in situ isoform-specific RNA structure determination. Unlike similar methods that rely on short sequencing reads, Nano-DMS-MaP employs nanopore sequencing to resolve the structures of long and highly similar RNA molecules to reveal their previously hidden structural differences. This Protocol describes the development and applications of Nano-DMS-MaP and outlines the main considerations for designing and implementing a successful experiment: from bench to data analysis. In cell probing experiments can be carried out by an experienced molecular biologist in 3-4 d. Data analysis requires good knowledge of command line tools and Python scripts and requires a further 3-5 d.
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Affiliation(s)
- Anne-Sophie Gribling-Burrer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
| | - Patrick Bohn
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
- Faculty of Medicine, University of Würzburg, Würzburg, Germany.
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8
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Aydin J, Gabel A, Zielinski S, Ganskih S, Schmidt N, Hartigan C, Schenone M, Carr S, Munschauer M. SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in live cells. Nucleic Acids Res 2024; 52:e26. [PMID: 38281241 PMCID: PMC10954451 DOI: 10.1093/nar/gkae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/29/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024] Open
Abstract
RNA-protein interactions determine the cellular fate of RNA and are central to regulating gene expression outcomes in health and disease. To date, no method exists that is able to identify proteins that interact with specific regions within endogenous RNAs in live cells. Here, we develop SHIFTR (Selective RNase H-mediated interactome framing for target RNA regions), an efficient and scalable approach to identify proteins bound to selected regions within endogenous RNAs using mass spectrometry. Compared to state-of-the-art techniques, SHIFTR is superior in accuracy, captures minimal background interactions and requires orders of magnitude lower input material. We establish SHIFTR workflows for targeting RNA classes of different length and abundance, including short and long non-coding RNAs, as well as mRNAs and demonstrate that SHIFTR is compatible with sequentially mapping interactomes for multiple target RNAs in a single experiment. Using SHIFTR, we comprehensively identify interactions of cis-regulatory elements located at the 5' and 3'-terminal regions of authentic SARS-CoV-2 RNAs in infected cells and accurately recover known and novel interactions linked to the function of these viral RNA elements. SHIFTR enables the systematic mapping of region-resolved RNA interactomes for any RNA in any cell type and has the potential to revolutionize our understanding of transcriptomes and their regulation.
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Affiliation(s)
- Jens Aydin
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Alexander Gabel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Sebastian Zielinski
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Sabina Ganskih
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Nora Schmidt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | | | - Monica Schenone
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mathias Munschauer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
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9
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Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait BT, Darst SA, Campbell EA. Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain. Mol Cell 2023; 83:3921-3930.e7. [PMID: 37890482 PMCID: PMC10843261 DOI: 10.1016/j.molcel.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/28/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023]
Abstract
The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5' cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here, we determine high-resolution cryoelectron microscopy (cryo-EM) structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.
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Affiliation(s)
- Gabriel I Small
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Olga Fedorova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Joshua Chandanani
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Anoosha Banerjee
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Tri-Institutional Program in Chemical Biology, The Rockefeller University, New York, New York, USA
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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