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Song G, Lee EM, Pan J, Xu M, Rho HS, Cheng Y, Whitt N, Yang S, Kouznetsova J, Klumpp-Thomas C, Michael SG, Moore C, Yoon KJ, Christian KM, Simeonov A, Huang W, Xia M, Huang R, Lal-Nag M, Tang H, Zheng W, Qian J, Song H, Ming GL, Zhu H. Corrigendum to "An Integrated Systems Biology Approach Identifies the Proteasome as A Critical Host Machinery for ZIKV and DENV Replication" [Genomics Proteomics Bioinformatics19 (1) (2021) 108-122]. Genomics Proteomics Bioinformatics 2022; 20:808-809. [PMID: 36669818 PMCID: PMC9880883 DOI: 10.1016/j.gpb.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Guang Song
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Emily M. Lee
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jianbo Pan
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Hee-Sool Rho
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Yichen Cheng
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Nadia Whitt
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shu Yang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Kouznetsova
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel G. Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cedric Moore
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ki-Jun Yoon
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kimberly M. Christian
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wenwei Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Madhu Lal-Nag
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding authors.
| | - Hengli Tang
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA,Corresponding authors.
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding authors.
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA,Corresponding authors.
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,The Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Corresponding authors.
| | - Guo-li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Corresponding authors.
| | - Heng Zhu
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA,Corresponding authors.
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Song G, Lee EM, Pan J, Xu M, Rho HS, Cheng Y, Whitt N, Yang S, Kouznetsova J, Klumpp-Thomas C, Michael SG, Moore C, Yoon KJ, Christian KM, Simeonov A, Huang W, Xia M, Huang R, Lal-Nag M, Tang H, Zheng W, Qian J, Song H, Ming GL, Zhu H. An Integrated Systems Biology Approach Identifies the Proteasome as A Critical Host Machinery for ZIKV and DENV Replication. Genomics Proteomics Bioinformatics 2021; 19:108-122. [PMID: 33610792 PMCID: PMC8498969 DOI: 10.1016/j.gpb.2020.06.016] [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] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/04/2020] [Accepted: 08/06/2020] [Indexed: 01/22/2023]
Abstract
The Zika virus (ZIKV) and dengue virus (DENV) flaviviruses exhibit similar replicative processes but have distinct clinical outcomes. A systematic understanding of virus-host protein-protein interaction networks can reveal cellular pathways critical to viral replication and disease pathogenesis. Here we employed three independent systems biology approaches toward this goal. First, protein array analysis of direct interactions between individual ZIKV/DENV viral proteins and 20,240 human proteins revealed multiple conserved cellular pathways and protein complexes, including proteasome complexes. Second, an RNAi screen of 10,415 druggable genes identified the host proteins required for ZIKV infection and uncovered that proteasome proteins were crucial in this process. Third, high-throughput screening of 6016 bioactive compounds for ZIKV inhibition yielded 134 effective compounds, including six proteasome inhibitors that suppress both ZIKV and DENV replication. Integrative analyses of these orthogonal datasets pinpoint proteasomes as critical host machinery for ZIKV/DENV replication. Our study provides multi-omics datasets for further studies of flavivirus-host interactions, disease pathogenesis, and new drug targets.
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Affiliation(s)
- Guang Song
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Emily M. Lee
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jianbo Pan
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Hee-Sool Rho
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Yichen Cheng
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Nadia Whitt
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shu Yang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Kouznetsova
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel G. Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cedric Moore
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ki-Jun Yoon
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kimberly M. Christian
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wenwei Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Madhu Lal-Nag
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding authors.
| | - Hengli Tang
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA,Corresponding authors.
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding authors.
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA,Corresponding authors.
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,The Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Corresponding authors.
| | - Guo-li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Corresponding authors.
| | - Heng Zhu
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA,Corresponding authors.
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Martin S, Chiramel AI, Schmidt ML, Chen YC, Whitt N, Watt A, Dunham EC, Shifflett K, Traeger S, Leske A, Buehler E, Martellaro C, Brandt J, Wendt L, Müller A, Peitsch S, Best SM, Stech J, Finke S, Römer-Oberdörfer A, Groseth A, Feldmann H, Hoenen T. A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle. Genome Med 2018; 10:58. [PMID: 30081931 PMCID: PMC6090742 DOI: 10.1186/s13073-018-0570-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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: 02/12/2018] [Accepted: 07/13/2018] [Indexed: 01/01/2023] Open
Abstract
Background The 2014–2016 Ebola virus (EBOV) outbreak in West Africa highlighted the need for improved therapeutic options against this virus. Approaches targeting host factors/pathways essential for the virus are advantageous because they can potentially target a wide range of viruses, including newly emerging ones and because the development of resistance is less likely than when targeting the virus directly. However, systematic approaches for screening host factors important for EBOV have been hampered by the necessity to work with this virus at biosafety level 4 (BSL4). Methods In order to identify host factors involved in the EBOV life cycle, we performed a genome-wide siRNA screen comprising 64,755 individual siRNAs against 21,566 human genes to assess their activity in EBOV genome replication and transcription. As a screening platform, we used reverse genetics-based life cycle modelling systems that recapitulate these processes without the need for a BSL4 laboratory. Results Among others, we identified the de novo pyrimidine synthesis pathway as an essential host pathway for EBOV genome replication and transcription, and confirmed this using infectious EBOV under BSL4 conditions. An FDA-approved drug targeting this pathway showed antiviral activity against infectious EBOV, as well as other non-segmented negative-sense RNA viruses. Conclusions This study provides a minable data set for every human gene regarding its role in EBOV genome replication and transcription, shows that an FDA-approved drug targeting one of the identified pathways is highly efficacious in vitro, and demonstrates the power of life cycle modelling systems for conducting genome-wide host factor screens for BSL4 viruses. Electronic supplementary material The online version of this article (10.1186/s13073-018-0570-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Scott Martin
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA.,Present address: Department of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Abhilash I Chiramel
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Marie Luisa Schmidt
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Yu-Chi Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA
| | - Nadia Whitt
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA
| | - Ari Watt
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Eric C Dunham
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Kyle Shifflett
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Shelby Traeger
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Anne Leske
- Junior Research Group Arenavirus Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Eugen Buehler
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA
| | - Cynthia Martellaro
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Janine Brandt
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Lisa Wendt
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Andreas Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Stephanie Peitsch
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Sonja M Best
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Jürgen Stech
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Stefan Finke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Angela Römer-Oberdörfer
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Allison Groseth
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA.,Junior Research Group Arenavirus Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Thomas Hoenen
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA. .,Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany.
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Song G, Lee E, Pan J, Xu M, Rho H, Cheng Y, Whitt N, Yang S, Kouznetsova J, Klumpp‐Thomas C, Michael SG, Simeonov A, Huang W, Xia M, Huang R, Lal‐Nag M, Zhu H, Tang H, Zheng W, Qian J, Song H. An Integrated System Approach Identified the Human Proteasome as a Conserved Critical Machinery for ZIKV and DENV Replication. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.669.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Guang Song
- Johns Hopkins School of MedicineBaltimoreMD
| | - Emily Lee
- Department of Biological ScienceFlorida State UniversityFlorida State UniversityTallahasseeFL
| | - Jianbo Pan
- Department of OphthalmologyJohns Hopkins School of MedicineBaltimoreMD
| | - Miao Xu
- National Institutes of HealthBethesdaMD
| | | | - Yichen Cheng
- Department of Biological ScienceFlorida State UniversityFlorida State UniversityTallahasseeFL
| | | | - Shu Yang
- National Institutes of HealthBethesdaMD
| | | | | | | | | | | | | | | | | | - Heng Zhu
- Johns Hopkins School of MedicineBaltimoreMD
| | - Hengli Tang
- Department of Biological ScienceFlorida State UniversityFlorida State UniversityTallahasseeFL
| | - Wei Zheng
- National Institutes of HealthBethesdaMD
| | - Jiang Qian
- Department of OphthalmologyJohns Hopkins School of MedicineBaltimoreMD
| | - Hongjun Song
- Institute for Cell EngineeringJohns Hopkins School of MedicineBaltimoreMD
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